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Encyclopedia of C. elegans 3'UTRs and their regulatory elements

experiment: Encyclopedia of C. elegans 3'UTRs and their regulatory elements project: The 3' UTRome PI: Fabio Piano Labs: Fabio Piano, John Kim
The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues.

All features generated by this experiment:
Feature Export
Exon ? 21355
This represents 21353 unique Exons
TAB CSV GFF3 (for UCSC) SEQ
Gene ? 20220
This represents 19958 unique Genes
TAB CSV GFF3 (for UCSC) SEQ
MRNA ? 3720 TAB CSV GFF3 SEQ
PolyASignalSequence ? 27135
This represents 21718 unique PolyASignalSequences
TAB CSV GFF3 (for UCSC) SEQ
Transcript ? 27417 TAB CSV GFF3 SEQ
ThreePrimeRACEClone ? 2700 TAB CSV GFF3 SEQ
PolyASite ? 35382
This represents 27773 unique PolyASites
TAB CSV GFF3 (for UCSC) SEQ
EST ? 2694 TAB CSV GFF3 SEQ
ThreePrimeRST ? 2700 TAB CSV GFF3 SEQ
ThreePrimeUST ? 2700 TAB CSV GFF3 SEQ
ThreePrimeUTR ? 24055
This represents 22993 unique ThreePrimeUTRs
TAB CSV GFF3 (for UCSC) SEQ
NO GBROWSE TRACKS FOR THIS EXPERIMENT
GFF3 for the experiment (with Genes, UTRs, Transcripts, mRNA) (for UCSC) All entries in public repositories generated by this experiment
There are 41 Sample creation, RNA-seq and RACE submissions for this experiment:
DCC id Name developmental stage strain temperature tissue Embargoed until Features, GBrowse and Data Files
modENCODE_2332


Related to: modENCODE_2460

3' UTR Staged 454 Sequencing - hermaphrodite adult - alignments Adult 20dC 70hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2465


Related to: modENCODE_2331

3' UTR Staged 454 Sequencing - embryo - sequences Mixed Embryos 20dC [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446651
Download data files
modENCODE_2333


Related to: modENCODE_2459

3' UTR Staged 454 Sequencing - male adult - alignments Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2460


Related to: modENCODE_2332

3' UTR Staged 454 Sequencing - hermaphrodite adult - sequences Adult 20dC 70hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446656
Download data files
modENCODE_2330


Related to: modENCODE_2458

3' UTR Staged 454 Sequencing - L4 - alignments L4 20dC 45hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2457


Related to: modENCODE_2329

3' UTR Staged 454 Sequencing - L3 - sequences L3 20dC 30hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446654
Download data files
modENCODE_2331


Related to: modENCODE_2465

3' UTR Staged 454 Sequencing - embryo - alignments Mixed Embryos 20dC [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2458


Related to: modENCODE_2330

3' UTR Staged 454 Sequencing - L4 - sequences L4 20dC 45hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446655
Download data files
modENCODE_2831

small RNA 454 sequencing of N2 young adults young Adult 25dC [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

3 files Download data files
modENCODE_2328


Related to: modENCODE_2456

3' UTR Staged 454 Sequencing - L2 - alignments L2 20dC 20hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2832

small RNA 454 sequencing of fer-1 unfertilized oocytes Adult male 20dC 70hr post-L1 stage larvae [ALL]
BA1 [ALL]
25 degree celsius [ALL]
unfertilized oocytes [ALL]
embargo expired

1 files Download data files
modENCODE_2484


Related to: modENCODE_2501

3' UTRome Solexa sequencing & alignment Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired GEO: GSM469439


6 files Download data files
modENCODE_2455


Related to: modENCODE_2327

3' UTR Staged 454 Sequencing - L1 - sequences L1 20dC 8hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446652
Download data files
modENCODE_2329


Related to: modENCODE_2457

3' UTR Staged 454 Sequencing - L3 - alignments L3 20dC 30hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_3404

utrome 454 minipools Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

2 files Download data files
modENCODE_2456


Related to: modENCODE_2328

3' UTR Staged 454 Sequencing - L2 - sequences L2 20dC 20hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446653
Download data files
modENCODE_2829

small RNA 454 sequencing of him-8 sperm Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
25 degree celsius [ALL]
spermatids [ALL]
embargo expired

3 files Download data files
modENCODE_2828

small RNA 454 sequencing of glp-4(bn2) young Adult 25dC [ALL]
SS104 [ALL]
25 degree celsius [ALL]
embargo expired

3 files Download data files
modENCODE_2327


Related to: modENCODE_2455

3' UTR Staged 454 Sequencing - L1 - alignments L1 20dC 8hr post-L1 stage larvae [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2501


Related to: modENCODE_2482
modENCODE_2484

3' UTRome sample pools Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2830

small RNA Illumina sequencing of fer-1 unfertilized oocytes Adult male 20dC 70hr post-L1 stage larvae [ALL]
BA1 [ALL]
25 degree celsius [ALL]
unfertilized oocytes [ALL]
embargo expired

2 files Download data files
modENCODE_2826

small RNA Illumina sequencing of N2 embryos Mixed Embryos 20dC [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

4 files Download data files
modENCODE_2825

small RNA Illumina sequencing of N2 whole worms Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired

2 files Download data files
modENCODE_2827

small RNA 454 sequencing of eri-1(mg366) young Adult 25dC [ALL]
GR1373 [ALL]
25 degree celsius [ALL]
embargo expired GEO: ???


1 files Download data files
modENCODE_2482


Related to: modENCODE_2501

3' UTRome 454 sequencing & alignment Mixed Worm Stages [ALL]
N2 [ALL]
25 degree celsius [ALL]
embargo expired GEO: GSM469976


17 files Download data files
modENCODE_2337


Related to: modENCODE_2463

3' UTR Staged 454 Sequencing - daf-9 - alignments Dauer Larvae [ALL]
DR2281 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2822

small RNA Illumina sequencing of glp-4(bn2) young Adult 25dC [ALL]
SS104 [ALL]
25 degree celsius [ALL]
embargo expired

2 files Download data files
modENCODE_2462


Related to: modENCODE_2336

3' UTR Staged 454 Sequencing - daf-7 - sequences Dauer Larvae [ALL]
CB1372 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446659
Download data files
modENCODE_2823

small RNA Illumina sequencing of him-8 sperm Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
25 degree celsius [ALL]
spermatids [ALL]
embargo expired

2 files Download data files
modENCODE_2463


Related to: modENCODE_2337

3' UTR Staged 454 Sequencing - daf-9 - sequences Dauer Larvae [ALL]
DR2281 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446660
Download data files
modENCODE_515


Related to: modENCODE_2934

3'UTRome CEUP1 sequences, alignments, annotation Mixed Worm Stages [ALL]
N2 [ALL]
20 degree celsius [ALL]
embargo expired
? Gene: 2630   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? MRNA: 3720   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeRACEClone: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? PolyASite: 2700   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 2694   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeRST: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeUST: 2700   export: TAB   CSV GFF3 SEQ    create LIST
? ThreePrimeUTR: 2700   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]
Trace Archive: 2216286010
Trace Archive: 2216286011
Trace Archive: 2216286013
Trace Archive: 2216286014
Trace Archive: 2216286015
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_2464


Related to: modENCODE_2334

3' UTR Staged 454 Sequencing - daf-11 - sequences Dauer Larvae [ALL]
DR47 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446661
Download data files
modENCODE_2335


Related to: modENCODE_2461

3' UTR Staged 454 Sequencing - daf-2 - alignments Dauer Larvae [ALL]
CB1370 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_2461


Related to: modENCODE_2335

3' UTR Staged 454 Sequencing - daf-2 - sequences Dauer Larvae [ALL]
CB1370 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446658
Download data files
modENCODE_896


Related to: modENCODE_992

3'UTR 454 sequencing pilot - Level 1 L1 20dC 8hr post-L1 stage larvae [ALL]
L2 20dC 20hr post-L1 stage larvae [ALL]
L3 20dC 30hr post-L1 stage larvae [ALL]
L4 20dC 45hr post-L1 stage larvae [ALL]
Mixed Embryos 20dC [ALL]
...
all 6 developmental stages
N2 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM443959
GEO: GSM443960
GEO: GSM443961
GEO: GSM443962
GEO: GSM443963
...All entries in public repositories generated by this submission

Download data files
modENCODE_2745

UTRome V2 3UTRs multiple evidences embargo expired
? Gene: 20214   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Exon: 21355   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? PolyASignalSequence: 27135   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? Transcript: 27417   export: TAB   CSV GFF3 SEQ    create LIST
? PolyASite: 32682   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? ThreePrimeUTR: 21355   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
[full gff3]   [find nearby features]


1 files Download data files
modENCODE_2336


Related to: modENCODE_2462

3' UTR Staged 454 Sequencing - daf-7 - alignments Dauer Larvae [ALL]
CB1372 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files
modENCODE_992


Related to: modENCODE_896

3' UTR 454 sequencing pilot - alignments L1 20dC 8hr post-L1 stage larvae [ALL]
L2 20dC 20hr post-L1 stage larvae [ALL]
L3 20dC 30hr post-L1 stage larvae [ALL]
L4 20dC 45hr post-L1 stage larvae [ALL]
Mixed Embryos 20dC [ALL]
...
all 6 developmental stages
N2 [ALL]
20 degree celsius [ALL]
embargo expired

6 files Download data files
modENCODE_2821

small RNA Illumina sequencing of eri-1(mg366) young Adult 25dC [ALL]
GR1373 [ALL]
25 degree celsius [ALL]
embargo expired

2 files Download data files
modENCODE_2459


Related to: modENCODE_2333

3' UTR Staged 454 Sequencing - male adult - sequences Adult male 20dC 70hr post-L1 stage larvae [ALL]
CB1489 [ALL]
20 degree celsius [ALL]
embargo expired GEO: GSM446657
Download data files
modENCODE_2334


Related to: modENCODE_2464

3' UTR Staged 454 Sequencing - daf-11 - alignments Dauer Larvae [ALL]
DR47 [ALL]
20 degree celsius [ALL]
embargo expired

1 files Download data files