modENCODE |  Help
Hide

The table data can be sorted according to the content of a given column, just click on the column header.

5' RACE

experiment: 5' RACE project: The Drosophila Transcriptome PI: Sue Celniker Labs: Sue Celniker
To map transcription start sites (TSSs) of capped transcripts, 5' RLM (RNA Ligase Mediated)-RACE (Rapid Amplification of cDNA Ends) is performed. The 5' ends of uncapped RNAs are dephosphorylated; 5' ends of capped RNAs are protected. The 5' cap structure is then removed from capped RNAs, leaving a 5' phosphate group. An RNA oligonucleotide adapter is ligated to the 5' ends of the decapped transcripts. First-strand cDNA is synthesized using a random dodecamer primer, and the products are aliquoted into transcript-specific reactions. Two rounds of nested PCR are performed using transcript-specific primers; the number of cycles of amplification is limited in an effort to preserve the diversity of TSSs of each transcript. The products are sequenced by one of two methods. In the first method, the products are cloned in the vector pCR2.1, and the sequences of individual clones are determined using conventional capillary sequencing. In the second method, RACE products are analyzed on agarose gels to estimate product sizes and concentrations, and normalized equimolar pools of 1,000 to 5,000 products are sequenced on the Roche 454 Life Sciences platform. The sequence data then undergo base calling, vector or linker trimming, RLM adapter identification, and quality trimming. Sequences for which the RLM adapter can be identified are aligned to the genome and, in cases where the aligned location is near a transcript targeted in the pool, transcription start sites are identified. The 5' RLM-RACE sequence reads are submitted to dbEST (capillary sequencing) or the Short Read Archive (454 sequencing) at Genbank.

All features generated by this experiment:
Feature Export
Pseudogene 2 TAB CSV GFF3 SEQ
MRNA ? 5604
This represents 4805 unique MRNAs
TAB CSV GFF3 (for UCSC) SEQ
NcRNA 2 TAB CSV GFF3 (for UCSC) SEQ
EST ? 1730720 TAB CSV GFF3 SEQ
All GBrowse tracks generated for this experiment:
GBrowse tracks: by chromosome
All entries in public repositories generated by this experiment
There are 8 RACE submissions for this experiment:
DCC id Name developmental stage strain Embargoed until Features, GBrowse and Data Files
modENCODE_1041


Related to: modENCODE_574
modENCODE_2929

5'RACE 454 sequencing - pool 2 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? EST: 249671   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR013488
SRA: SRR013489
SRA: SRR013490
SRA: SRR013491
SRA: SRR013492


1819 files Download data files
modENCODE_1043


Related to: modENCODE_574
modENCODE_2929

5'RACE 454 sequencing - pool 4 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? EST: 289993   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR013488
SRA: SRR013489
SRA: SRR013490
SRA: SRR013491
SRA: SRR013492


1658 files Download data files
modENCODE_1042


Related to: modENCODE_574
modENCODE_2929

5'RACE 454 sequencing - pool 3 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? EST: 251368   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR013488
SRA: SRR013489
SRA: SRR013490
SRA: SRR013491
SRA: SRR013492


1649 files Download data files
modENCODE_1044


Related to: modENCODE_574
modENCODE_2929

5'RACE 454 sequencing - pool 5 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? EST: 148486   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR023779
SRA: SRR023780


2128 files Download data files
modENCODE_34


Related to: modENCODE_574

5' RACE (mixed-stage embryos) Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? MRNA: 686   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 3562   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: RACE_mi_match_664_34
dbEST: FD585471
dbEST: FD585472
dbEST: FD585473
dbEST: FD585474
dbEST: FD585475
...All entries in public repositories generated by this submission



1 files Download data files
modENCODE_3723


Related to: modENCODE_574

Dm Embryonic 5'RACE 454 sequencing - pool 7 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
Pseudogene: 2   export: TAB   CSV GFF3 SEQ    create LIST
? MRNA: 3224   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 275107   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR069030


3082 files Download data files
modENCODE_1040


Related to: modENCODE_574
modENCODE_2929

5'RACE 454 sequencing - pool 1 Mixed Embryo 0-24 h [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? EST: 249998   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
GBrowse tracks: RACE_454_match_ALL
SRA: SRR013488
SRA: SRR013489
SRA: SRR013490
SRA: SRR013491
SRA: SRR013492


1434 files Download data files
modENCODE_3721


Related to: modENCODE_574

Dm Adult 5'RACE 454 sequencing - pool 6 Mixed Adult 7-11 day [ALL]
yellow cinnabar brown speck [ALL]
embargo expired
? MRNA: 1697   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
NcRNA: 2   export: TAB   CSV  GFF3  (for UCSC)  SEQ    create LIST
? EST: 262535   export: TAB   CSV GFF3 SEQ    create LIST
  [find nearby features]
SRA: SRR068619


1581 files Download data files