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Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions

experiment: Definition of comprehensive set of C. elegans transcripts and expression for various stages and conditions project: The C. elegans Transcriptome PI: Robert Waterston Labs: Robert Waterston
Using massively parallel sequencing by synthesis methods, we are surveying transcripts from various stages, tissues and conditions of the nematode C. elegans. We use novel statistical approaches to evaluate coverage of annotated features of the genome and of candidate processed transcripts. We then provide lists of evidence of level of expression per transcript and catalogs of confirmed splice junctions, trans-spliced leader sequences, start sites, end sites, and poly-adenylation tracts for each stage/tissue/condition.

All features generated by this experiment:
Feature Export
TSS ? 124709
This represents 38624 unique TSSs 		TAB CSV GFF3 (for UCSC) SEQ
Exon ? 1936598 Expression Levels 1890438
This represents 484418 unique Exons 		TAB CSV GFF3 (for UCSC) SEQ
OverlappingESTSet ? 414417 TAB CSV GFF3 SEQ
SL1AcceptorSite ? 116460
This represents 24656 unique SL1AcceptorSites 		TAB CSV GFF3 (for UCSC) SEQ
Transcript ? 697746 Expression Levels 697746 TAB CSV GFF3 SEQ
Chromosome 6 TAB CSV GFF3 SEQ
MatureTranscript 12316
This represents 10354 unique MatureTranscripts 		TAB CSV GFF3 (for UCSC) SEQ
PolyASite ? 209185
This represents 46754 unique PolyASites 		TAB CSV GFF3 (for UCSC) SEQ
Intron ? 1201171
This represents 117811 unique Introns 		TAB CSV GFF3 (for UCSC) SEQ
TranscriptionEndSite ? 109712
This represents 48789 unique TranscriptionEndSites 		TAB CSV GFF3 (for UCSC) SEQ
SL2AcceptorSite ? 33248
This represents 8195 unique SL2AcceptorSites 		TAB CSV GFF3 (for UCSC) SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All 330 tracks I II III IV V X
GFF3 for the experiment (with Transcripts, introns, exons, polyA sites, TSS, TES, acceptor sites) (for UCSC) All entries in public repositories generated by this experiment
There are 113 RNA-seq submissions for this experiment:
DCC id Name developmental stage strain temperature Embargoed until Features, GBrowse and Data Files
modENCODE_2861

 L2 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L2 stage larvae [ALL]
mid-L4 stage larvae [ALL]
N2 [ALL]
embargo expired
? TSS: 12264   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 129605   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  129605   export: TAB   CSV
? OverlappingESTSet: 25556   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 46261   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  46261   export: TAB   CSV
? SL1AcceptorSite: 9795   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 98616   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
MatureTranscript: 2701   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 2283   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 13284   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 21   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L2
rainbow_itransRNA_L2
itranscript_confirmed_introns_L2
itranscript_confirmed_polyA_L2
itranscript_confirmed_SL_L2


13 files Download data files
modENCODE_2862

 L3 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
mid-L3 stage larvae [ALL]
N2 [ALL]
embargo expired
? TSS: 12450   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 128379   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  128379   export: TAB   CSV
? OverlappingESTSet: 24222   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 44713   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  44713   export: TAB   CSV
? SL1AcceptorSite: 9373   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 97394   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 17196   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 11761   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 2326   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L3
rainbow_itransRNA_L3
itranscript_confirmed_introns_L3
itranscript_confirmed_polyA_L3
itranscript_confirmed_SL_L3


13 files Download data files
modENCODE_2863

 L4 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
N2 [ALL]
embargo expired
? TSS: 11679   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 126137   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  126137   export: TAB   CSV
? OverlappingESTSet: 23616   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 41031   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  41031   export: TAB   CSV
? SL1AcceptorSite: 8342   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 96295   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 16826   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 11937   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 2289   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L4
rainbow_itransRNA_L4
itranscript_confirmed_introns_L4
itranscript_confirmed_polyA_L4
itranscript_confirmed_SL_L4


13 files Download data files
modENCODE_3526

 RNAseq - N2 EE-2cap5 alignments early Embryo capture EE-2cap5 [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired SRA: SRR089795
SRA: SRR089796


3 files Download data files
modENCODE_2851

 Young Adult N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
Young Adult [ALL]
N2 [ALL]
embargo expired
? TSS: 12084   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 127667   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  127667   export: TAB   CSV
? OverlappingESTSet: 24867   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 43882   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  43882   export: TAB   CSV
? SL1AcceptorSite: 9293   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 17145   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 96849   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 12783   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 2739   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_YA
rainbow_itransRNA_YA
itranscript_confirmed_introns_YA
itranscript_confirmed_polyA_YA
itranscript_confirmed_SL_YA


13 files Download data files
modENCODE_2855

 early embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
early Embryo [ALL]
N2 [ALL]
embargo expired
? TSS: 2301   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 132010   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  132010   export: TAB   CSV
? OverlappingESTSet: 2972   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 49005   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  49005   export: TAB   CSV
? SL1AcceptorSite: 8919   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 100334   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 17005   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 671   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 1969   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_EE
rainbow_itransRNA_EE
itranscript_confirmed_introns_EE
itranscript_confirmed_polyA_EE
itranscript_confirmed_SL_EE


13 files Download data files
modENCODE_2856

 embryo him-8 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
Embryo him-8(e1480) 20dC [ALL]
CB1489 [ALL]
embargo expired
? TSS: 9130   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 125068   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  125068   export: TAB   CSV
? OverlappingESTSet: 17241   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 41720   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  41720   export: TAB   CSV
? SL1AcceptorSite: 8661   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 95376   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 16083   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 8111   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 2137   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_EHIM8
rainbow_itransRNA_EHIM8
itranscript_confirmed_introns_EHIM8
itranscript_confirmed_polyA_EHIM8
itranscript_confirmed_SL_EHIM8


13 files Download data files
modENCODE_2857

 late embryo N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
late Embryo 20dC 4.5 hours post-early embryo [ALL]
N2 [ALL]
embargo expired
? TSS: 4858   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 133710   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  133710   export: TAB   CSV
? OverlappingESTSet: 6184   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 51360   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  51360   export: TAB   CSV
? SL1AcceptorSite: 9035   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 101617   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 17078   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 1326   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 1984   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_LE
rainbow_itransRNA_LE
itranscript_confirmed_introns_LE
itranscript_confirmed_polyA_LE
itranscript_confirmed_SL_LE


13 files Download data files
modENCODE_2858

 L1 lin-35(n745) integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, and wormbase splice junctions larva mid-L1 25dC 4.0 hrs post-L1 stage larvae [ALL]
lin-35(n745) larva mid-L1 25dC 4.0 hrs post-L1 stage larvae [ALL]
MT10430 [ALL]
embargo expired
? TSS: 9476   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 128644   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  128644   export: TAB   CSV
? OverlappingESTSet: 10921   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 44022   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  44022   export: TAB   CSV
? SL1AcceptorSite: 8956   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 16761   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 97913   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 2155   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 1445   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L1LIN35
rainbow_itransRNA_L1LIN35
itranscript_confirmed_introns_L1LIN35
itranscript_confirmed_polyA_L1LIN35
itranscript_confirmed_SL_L1LIN35


13 files Download data files
modENCODE_2859

 L4 male integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs Male larva mid-L4 25dC 30 hrs post-L1 stage larvae [ALL]
CB4689 [ALL]
embargo expired
? TSS: 6329   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 130932   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  130932   export: TAB   CSV
? OverlappingESTSet: 9911   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 43767   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  43767   export: TAB   CSV
? SL1AcceptorSite: 8978   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 16823   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 100515   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 3582   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 1936   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L4MALE
rainbow_itransRNA_L4MALE
itranscript_confirmed_introns_L4MALE
itranscript_confirmed_polyA_L4MALE
itranscript_confirmed_SL_L4MALE


13 files Download data files
modENCODE_2860

 L1 N2 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs mid-L4 stage larvae [ALL]
larva mid-L1 25dC 4.0 hrs post-L1 stage larvae [ALL]
N2 [ALL]
embargo expired
? TSS: 13434   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 134292   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  134292   export: TAB   CSV
? OverlappingESTSet: 23266   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 52633   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  52633   export: TAB   CSV
? SL1AcceptorSite: 53   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 17388   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Intron: 101406   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
MatureTranscript: 9615   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 9820   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 3721   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_L1
rainbow_itransRNA_L1
itranscript_confirmed_introns_L1
itranscript_confirmed_polyA_L1
itranscript_confirmed_SL_L1


13 files Download data files
modENCODE_2850

 Adult spe-9 integrated transcripts from RNA-seq, mRNA/EST, RTPCR, mass-spec, polyA sites, and SLs Adult spe-9(hc88) 23dC 8 days post-L4 molt [ALL]
BA671 [ALL]
embargo expired
? TSS: 12201   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 127283   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  127283   export: TAB   CSV
? OverlappingESTSet: 22880   export: TAB   CSV GFF3 SEQ    create LIST
? SL1AcceptorSite: 11371   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Transcript: 46116   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  46116   export: TAB   CSV
? Intron: 97177   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 16329   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 4192   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 10679   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
GBrowse tracks: rainbow_itrans_SPE9A
rainbow_itransRNA_SPE9A
itranscript_confirmed_introns_SPE9A
itranscript_confirmed_polyA_SPE9A
itranscript_confirmed_SL_SPE9A


13 files Download data files
modENCODE_4543


Related to: modENCODE_3909

 C. elegans him-8(e1489) L4 Male combined replicates confirmed sites Male larva mid-L4 25dC 30 hrs post-L1 stage larvae [ALL]
Male larva mid-L4 L4MALE5 [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4543
POLYA_4543
SLSITES_4543


3 files Download data files
modENCODE_4520


Related to: modENCODE_4152

 C. elegans him-8(e1489) Embryo Male replicate 1 confirmed sites Embryo [ALL]
CB4689 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4520
POLYA_4520
SLSITES_4520


3 files Download data files
modENCODE_4152


Related to: modENCODE_4520

 RNA-seq C. elegans him-8 Embryo Males replicate 1 sequence & alignments Embryo [ALL]
CB4689 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: 4152_EmMalesHIM8.sam.gz.bam.sorted
SRA: SRR027904
SRA: SRR027905


4 files Download data files
modENCODE_3908


Related to: modENCODE_4538

 RNA-seq C. elegans JK1107 Soma L4 sequence & alignments L4 soma JK1107 no DNaseI [ALL]
L4 soma JK1107 no DNaseI L4JK1107soma-2 [ALL]
JK1107 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: L4_soma_JK1107_no_DNaseI.alignments.ws220.bam.sorted
L4_soma_JK1107_no_DNaseI.alignments.ws220.bam.sorted
SRA: SRR031122
SRA: SRR031123
SRA: SRR089799


8 files Download data files
modENCODE_4538


Related to: modENCODE_3908

 C. elegans JK1107(glp-1(q224)) L4 combined replicates confirmed sites L4 soma JK1107 no DNaseI [ALL]
L4 soma JK1107 no DNaseI L4JK1107soma-2 [ALL]
JK1107 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4538
POLYA_4538
SLSITES_4538


3 files Download data files
modENCODE_3909


Related to: modENCODE_4543

 RNA-seq C. elegans N2 L4 Male sequence & alignments Male larva mid-L4 25dC 30 hrs post-L1 stage larvae [ALL]
Male larva mid-L4 L4MALE5 [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: yM_male_mid-L4_25dC_30hrs_post-L1.alignments.ws220.bam.sorted
yM_male_mid-L4_25dC_30hrs_post-L1.alignments.ws220.bam.sorted
SRA: SRR016684
SRA: SRR016685
SRA: SRR016686
SRA: SRR124273
SRA: SRR124274


8 files Download data files
modENCODE_3883

 RNA-seq C. elegans N2 Late Embryo sequence & alignments early Embryo EE-2 [ALL]
late Embryo LE-1 [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: embryo_20dC_4.5hrs_post-early_embryo.alignments.ws220.bam.sorted
embryo_20dC_4.5hrs_post-early_embryo.alignments.ws220.bam.sorted
SRA: SRR016676
SRA: SRR016677
SRA: SRR016678
SRA: SRR016687
SRA: SRR124255
...All entries in public repositories generated by this submission



8 files Download data files
modENCODE_3877

 C. elegans N2 Early Embryo (50hrs post L1, 120 minutes) N2 EE 50-120 [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: N2_EE_50-120.sam.gz.bam.sorted
SRA: SRR317082


3 files Download data files
modENCODE_2934


Related to: modENCODE_515
modENCODE_445
modENCODE_446
modENCODE_447
modENCODE_448
modENCODE_2304
modENCODE_2935

 Aggregate C. elegans transcript creation from 19 stages Mixed Larval Stages Grown for 4-5 Days [ALL]
N2 [ALL]
embargo expired
? TSS: 18503   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 187991   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Expression Levels:  466711   export: TAB   CSV
? OverlappingESTSet: 222781   export: TAB   CSV GFF3 SEQ    create LIST
? Transcript: 193236   export: TAB   CSV GFF3 SEQ    create LIST
Expression Levels:  193236   export: TAB   CSV
? SL1AcceptorSite: 23684   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
Chromosome: 6   export: TAB   CSV GFF3 SEQ    create LIST
? Intron: 117679   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASite: 38268   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? TranscriptionEndSite: 24313   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? SL2AcceptorSite: 7779   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]


33 files Download data files
modENCODE_3531

 RNAseq - N2 LE-2cap6 alignments N2 LE-2cap6 [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired SRA: SRR136599


3 files Download data files
modENCODE_3733

 RNAseq - C. elegans N2 hand picked 4 cell embryosDSN-Negative-Positive N2 EE 50-120 [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: submission_3733.sorted
SRA: SRR317082


3 files Download data files
modENCODE_2647

 RNAseq - 0911 aggregate fourteen stages - non-redundant exons embargo expired
? Exon: 167248   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: EXONS_W2647


16 files Download data files
modENCODE_4566

 C. elegans N2 Early Embryo (50hrs post L1, +570 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4566
POLYA_4566
SLSITES_4566


3 files Download data files
modENCODE_4565

 C. elegans N2 Early Embryo (50hrs post L1, +540 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4565
POLYA_4565
SLSITES_4565


3 files Download data files
modENCODE_4568

 C. elegans N2 Early Embryo (50hrs post L1, +60 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4568
POLYA_4568
SLSITES_4568


3 files Download data files
modENCODE_4567

 C. elegans N2 Early Embryo (50hrs post L1, +600 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4567
POLYA_4567
SLSITES_4567


3 files Download data files
modENCODE_4570

 C. elegans N2 Early Embryo (50hrs post L1, +660 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4570
POLYA_4570
SLSITES_4570


3 files Download data files
modENCODE_4569

 C. elegans N2 Early Embryo (50hrs post L1, +630 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4569
POLYA_4569
SLSITES_4569


3 files Download data files
modENCODE_4572

 C. elegans N2 Early Embryo (50hrs post L1, +720 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4572
POLYA_4572
SLSITES_4572


3 files Download data files
modENCODE_4571

 C. elegans N2 Early Embryo (50hrs post L1, +690 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4571
POLYA_4571
SLSITES_4571


3 files Download data files
modENCODE_4574

 C. elegans N2 L1 replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4574
POLYA_4574
SLSITES_4574


3 files Download data files
modENCODE_4573

 C. elegans N2 Early Embryo (50hrs post L1, +90 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4573
POLYA_4573
SLSITES_4573


3 files Download data files
modENCODE_4576

 C. elegans N2 L3 replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4576
POLYA_4576
SLSITES_4576


3 files Download data files
modENCODE_4575

 C. elegans N2 L2 replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4575
POLYA_4575
SLSITES_4575


3 files Download data files
modENCODE_4578

 C. elegans N2 L4 rRNA removed array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4578
POLYA_4578
SLSITES_4578


3 files Download data files
modENCODE_4577

 C. elegans N2 L4 array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4577
POLYA_4577
SLSITES_4577


3 files Download data files
modENCODE_4580

 C. elegans N2 Late Embryo array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4580
POLYA_4580
SLSITES_4580


3 files Download data files
modENCODE_4579

 C. elegans N2 Late Embryo replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4579
POLYA_4579
SLSITES_4579


3 files Download data files
modENCODE_4548

 C. elegans N2 Early Embryo array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4548
POLYA_4548
SLSITES_4548


3 files Download data files
modENCODE_4549

 C. elegans N2 Early Embryo (50hrs post L1, +0 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4549
POLYA_4549
SLSITES_4549


3 files Download data files
modENCODE_4550

 C. elegans N2 Early Embryo (50hrs post L1, +120 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4550
POLYA_4550
SLSITES_4550


3 files Download data files
modENCODE_4551

 C. elegans N2 Early Embryo (50hrs post L1, +150 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4551
POLYA_4551
SLSITES_4551


3 files Download data files
modENCODE_4552

 C. elegans N2 Early Embryo (50hrs post L1, +180 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4552
POLYA_4552
SLSITES_4552


3 files Download data files
modENCODE_4553

 C. elegans N2 Early Embryo (50hrs post L1, +210 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4553
POLYA_4553
SLSITES_4553


3 files Download data files
modENCODE_4554

 C. elegans N2 Early Embryo (50hrs post L1, +240 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4554
POLYA_4554
SLSITES_4554


3 files Download data files
modENCODE_4555

 C. elegans N2 Early Embryo (50hrs post L1, +270 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4555
POLYA_4555
SLSITES_4555


3 files Download data files
modENCODE_4556

 C. elegans N2 Early Embryo (50hrs post L1, +30 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4556
POLYA_4556
SLSITES_4556


3 files Download data files
modENCODE_2935


Related to: modENCODE_2934

 RNAseq - 1003 aggregate 19 stages - non-redundant exons embargo expired
? Exon: 157632   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
  [find nearby features]
GBrowse tracks: EXONS_W2935


2 files Download data files
modENCODE_4557

 C. elegans N2 Early Embryo (50hrs post L1, +300 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4557
POLYA_4557
SLSITES_4557


3 files Download data files
modENCODE_4558

 C. elegans N2 Early Embryo (50hrs post L1, +330 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4558
POLYA_4558
SLSITES_4558


3 files Download data files
modENCODE_4559

 C. elegans N2 Early Embryo (50hrs post L1, +360 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4559
POLYA_4559
SLSITES_4559


3 files Download data files
modENCODE_4561

 C. elegans N2 Early Embryo (50hrs post L1, +420 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4561
POLYA_4561
SLSITES_4561


3 files Download data files
modENCODE_4562

 C. elegans N2 Early Embryo (50hrs post L1, +450 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4562
POLYA_4562
SLSITES_4562


3 files Download data files
modENCODE_4563

 C. elegans N2 Early Embryo (50hrs post L1, +480 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4563
POLYA_4563
SLSITES_4563


3 files Download data files
modENCODE_4564

 C. elegans N2 Early Embryo (50hrs post L1, +510 min) confirmed sites embargo expired
GBrowse tracks: INTRONS_4564
POLYA_4564
SLSITES_4564


3 files Download data files
modENCODE_4719

 RNA-seq C. elegans daf-2 Dauer Entry combined replicates sequence & alignments dauer entry daf-2(el370) 25dC 48 hrs post-L1 stage larvae [ALL]
CB1370 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: 4719_DauerEntryDAF2.sam.gz.bam.sorted
SRA: SRR027189
SRA: SRR027190
SRA: SRR124275
SRA: SRR124276
SRA: SRR358688
...All entries in public repositories generated by this submission



19 files Download data files
modENCODE_4583

 C. elegans N2 Young Adult rRNA removed replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4583
POLYA_4583
SLSITES_4583


3 files Download data files
modENCODE_4585

 C. elegans Pharyngeal Muscle (OK0640) confirmed sites embargo expired
GBrowse tracks: INTRONS_4585
POLYA_4585
SLSITES_4585


3 files Download data files
modENCODE_4581

 C. elegans N2 Young Adult replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4581
POLYA_4581
SLSITES_4581


3 files Download data files
modENCODE_4582

 C. elegans N2 Young Adult rRNA removed replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4582
POLYA_4582
SLSITES_4582


3 files Download data files
modENCODE_4592

 C. elegans N2 Adults Serratia macescens Db10 E. coli control confirmed sites embargo expired
GBrowse tracks: INTRONS_4592
POLYA_4592
SLSITES_4592


3 files Download data files
modENCODE_4593

 C. elegans N2 Young Adult replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4593
POLYA_4593
SLSITES_4593


3 files Download data files
modENCODE_4586

 C. elegans N2 Adults Photorhabdus luminescens 24 hour exposure confirmed sites embargo expired
GBrowse tracks: INTRONS_4586
POLYA_4586
SLSITES_4586


3 files Download data files
modENCODE_4591

 C. elegans N2 Adults Serratia macescens Db10 confirmed sites embargo expired
GBrowse tracks: INTRONS_4591
POLYA_4591
SLSITES_4591


3 files Download data files
modENCODE_4594

 C. elegans N2 Young Adult combined replicates confirmed sites embargo expired
GBrowse tracks: INTRONS_4594
POLYA_4594
SLSITES_4594


3 files Download data files
modENCODE_4503

 C. elegans daf-2(e1370) Dauer replicate 4 confirmed sites embargo expired
GBrowse tracks: INTRONS_4503
POLYA_4503
SLSITES_4503


3 files Download data files
modENCODE_4502

 C. elegans daf-2(e1370) Dauer replicate 3 confirmed sites embargo expired
GBrowse tracks: INTRONS_4502
POLYA_4502
SLSITES_4502


3 files Download data files
modENCODE_4504


Related to: modENCODE_4692

 C. elegans daf-2(e1370) Dauer combined replicates confirmed sites dauer daf-2(el370) 25dC 91hrs post-L1 stage larvae [ALL]
CB1370 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4504
POLYA_4504
SLSITES_4504


3 files Download data files
modENCODE_4501

 C. elegans daf-2(e1370) Dauer replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4501
POLYA_4501
SLSITES_4501


3 files Download data files
modENCODE_4500

 C. elegans daf-2(e1370) Dauer replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4500
POLYA_4500
SLSITES_4500


3 files Download data files
modENCODE_4507

 C. elegans daf-2(e1370) Dauer Entry replicate 3 confirmed sites embargo expired
GBrowse tracks: INTRONS_4507
POLYA_4507
SLSITES_4507


3 files Download data files
modENCODE_4506

 C. elegans daf-2(e1370) Dauer Entry replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4506
POLYA_4506
SLSITES_4506


3 files Download data files
modENCODE_4510

 C. elegans daf-2(e1370) Dauer Exit replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4510
POLYA_4510
SLSITES_4510


3 files Download data files
modENCODE_4508

 C. elegans daf-2(e1370) Dauer Entry replicate 4 confirmed sites embargo expired
GBrowse tracks: INTRONS_4508
POLYA_4508
SLSITES_4508


3 files Download data files
modENCODE_4505

 C. elegans daf-2(e1370) Dauer Entry replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4505
POLYA_4505
SLSITES_4505


3 files Download data files
modENCODE_4692


Related to: modENCODE_4504

 RNA-seq C. elegans daf-2(e1370) Dauer combined replicates sequences and alignments dauer daf-2(el370) 25dC 91hrs post-L1 stage larvae [ALL]
CB1370 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: submission_4692.sorted
SRA: SRR027187
SRA: SRR027188
SRA: SRR360120
SRA: SRR360121
SRA: SRR360122
...All entries in public repositories generated by this submission



15 files Download data files
modENCODE_4584


Related to: modENCODE_4168

 C. elegans fer-15(b26) Adult Drechmeria coniospora E. coli control confirmed sites Young Adult [ALL]
DH26 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4584
POLYA_4584
SLSITES_4584


3 files Download data files
modENCODE_4153


Related to: modENCODE_4521

 RNA-seq C. elegans him-8 Embryo Males replicate 2 sequence & alignments Embryo [ALL]
CB4689 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: 4153_EmMalesHIM8-2.sam.gz.bam.sorted
SRA: SRR089797
SRA: SRR125491


4 files Download data files
modENCODE_4521


Related to: modENCODE_4153

 C. elegans him-8(e1489) Embryo Male replicate 2 confirmed sites Embryo [ALL]
CB4689 [ALL]
20 degree celsius [ALL]
embargo expired
GBrowse tracks: INTRONS_4521
POLYA_4521
SLSITES_4521


3 files Download data files
modENCODE_4168


Related to: modENCODE_4584

 RNA-seq C. elegans Drechmeria coniospora E. coli control sequence & alignments Young Adult [ALL]
DH26 [ALL]
25 degree celsius [ALL]
embargo expired
GBrowse tracks: OPDC-2-12.sam.gz.bam.sorted
SRA: SRR089352
SRA: SRR089353
SRA: SRR089354


4 files Download data files
modENCODE_4494

 C. elegans spe-9(hc88) Young Adult confirmed Sites embargo expired
GBrowse tracks: INTRONS_4494
POLYA_4494
SLSITES_4494


3 files Download data files
modENCODE_4493

 C. elegans N2 Early Embryo confirmed sites embargo expired
GBrowse tracks: INTRONS_4493
POLYA_4493
SLSITES_4493


3 files Download data files
modENCODE_4537

 C. elegans JK1107(glp-1(q224)) L4 replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4537
POLYA_4537
SLSITES_4537


3 files Download data files
modENCODE_4536

 C. elegans JK1107(glp-1(q224)) L4 replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4536
POLYA_4536
SLSITES_4536


3 files Download data files
modENCODE_4535

 C. elegans N2 L4 replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4535
POLYA_4535
SLSITES_4535


3 files Download data files
modENCODE_4534

 C. elegans N2 L4 replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4534
POLYA_4534
SLSITES_4534


3 files Download data files
modENCODE_4533

 C. elegans N2 L3 combined replicates confirmed sites embargo expired
GBrowse tracks: INTRONS_4533
POLYA_4533
SLSITES_4533


3 files Download data files
modENCODE_4532

 C. elegans N2 L3 replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4532
POLYA_4532
SLSITES_4532


3 files Download data files
modENCODE_4531

 C. elegans N2 L2 combined replicates confirmed sites embargo expired
GBrowse tracks: INTRONS_4531
POLYA_4531
SLSITES_4531


3 files Download data files
modENCODE_4547

 C. elegans N2 Early Embryo replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4547
POLYA_4547
SLSITES_4547


3 files Download data files
modENCODE_4546

 C. elegans lin-35(n745) L1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4546
POLYA_4546
SLSITES_4546


3 files Download data files
modENCODE_4544

 C. elegans N2 Late Embryo replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4544
POLYA_4544
SLSITES_4544


3 files Download data files
modENCODE_4542

 C. elegans him-8(e1489) L4 Male replicate array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4542
POLYA_4542
SLSITES_4542


3 files Download data files
modENCODE_4541

 C. elegans him-8(e1489) L4 Male replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4541
POLYA_4541
SLSITES_4541


3 files Download data files
modENCODE_4540

 C. elegans him-8(e1489) L4 Male replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4540
POLYA_4540
SLSITES_4540


3 files Download data files
modENCODE_4519

 C. elegans N2 Enterococcus faecalis 24 hour exposure confirmed sites embargo expired
GBrowse tracks: INTRONS_4519
POLYA_4519
SLSITES_4519


3 files Download data files
modENCODE_4522

 C. elegans him-8(e1489) Embryo Male combined replicates confirmed sites embargo expired
GBrowse tracks: INTRONS_4522
POLYA_4522
SLSITES_4522


3 files Download data files
modENCODE_4516

 C. elegans fer-15(b26) Adult Drechmeria coniospora 12 hour exposure confirmed sites embargo expired
GBrowse tracks: INTRONS_4516
POLYA_4516
SLSITES_4516


3 files Download data files
modENCODE_4517

 C. elegans N2 4 cell embryos DSN-Negative-Positive confirmed sites embargo expired
GBrowse tracks: INTRONS_4517
POLYA_4517
SLSITES_4517


3 files Download data files
modENCODE_4513

 C. elegans daf-2(e1370) Dauer Exit replicate 4 confirmed sites embargo expired
GBrowse tracks: INTRONS_4513
POLYA_4513
SLSITES_4513


3 files Download data files
modENCODE_4515

 C. elegans fer-15(b26) Adult Drechmeria coniospora 5 hour exposure confirmed sites embargo expired
GBrowse tracks: INTRONS_4515
POLYA_4515
SLSITES_4515


3 files Download data files
modENCODE_4511

 C. elegans daf-2(e1370) Dauer Exit replicate 2 confirmed sites embargo expired
GBrowse tracks: INTRONS_4511
POLYA_4511
SLSITES_4511


3 files Download data files
modENCODE_4512

 C. elegans daf-2(e1370) Dauer Exit replicate 3 confirmed sites embargo expired
GBrowse tracks: INTRONS_4512
POLYA_4512
SLSITES_4512


3 files Download data files
modENCODE_4529

 C. elegans N2 L1 combined replicates confirmed sites embargo expired
GBrowse tracks: INTRONS_4529
POLYA_4529
SLSITES_4529


3 files Download data files
modENCODE_4530

 C. elegans N2 L2 replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4530
POLYA_4530
SLSITES_4530


3 files Download data files
modENCODE_4527

 C. elegans N2 L1 replicate 1 confirmed sites embargo expired
GBrowse tracks: INTRONS_4527
POLYA_4527
SLSITES_4527


3 files Download data files
modENCODE_4528

 C. elegans lin-35(n745) L1 array captured confirmed sites embargo expired
GBrowse tracks: INTRONS_4528
SLSITES_4528


3 files Download data files
modENCODE_4525

 C. elegans fer-15(b26) L4 Haptocillium sphaerosporum confirmed sites embargo expired
GBrowse tracks: INTRONS_4525
POLYA_4525
SLSITES_4525


3 files Download data files
modENCODE_4526

 C. elegans fer-15(b26) L4 Haptocillium sphaerosporum E. coli control confirmed sites embargo expired
GBrowse tracks: INTRONS_4526
POLYA_4526
SLSITES_4526


3 files Download data files
modENCODE_4523

 C. elegans fer-15(b26) Adult Harposporium exposure confirmed sites embargo expired
GBrowse tracks: INTRONS_4523
POLYA_4523
SLSITES_4523


3 files Download data files
modENCODE_4524

 C. elegans fer-15(b26) Adult Harposporium E. coli control confirmed sites embargo expired
GBrowse tracks: INTRONS_4524
POLYA_4524
SLSITES_4524


3 files Download data files




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Cambridge CB2 3EH, United Kingdom