|
Status |
Public on Dec 22, 2011 |
Title |
3P-Seq Adult |
Sample type |
SRA |
|
|
Source name |
mixed gender adults
|
Organism |
Danio rerio |
Characteristics |
tissue: whole adult developmental stage: mixed gender adults genotype: wt
|
Treatment protocol |
For adult fish, anesthetized fish were homogenized in the TissueRuptor (Qiagen). Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed, and pellets were rinsed twice with PBS, flash frozen in liquid nitrogen and stored at –80C.
|
Growth protocol |
Zebrafish embryos or adults grown under standard condition
|
Extracted molecule |
polyA RNA |
Extraction protocol |
3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html
|
Data processing |
Reads were reverse complemented and aligned to the D. rerio genome (Zv9/danRer7) using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. (GSE24924)
|
|
|
Submission date |
Oct 11, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Igor Ulitsky |
Organization name |
Whitehead Institute for Biomedical Research
|
Street address |
9 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02472 |
Country |
USA |
|
|
Platform ID |
GPL9319 |
Series (1) |
GSE32880 |
Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution |
|
Relations |
SRA |
SRX100938 |
BioSample |
SAMN00739149 |