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Sample GSM813764 Query DataSets for GSM813764
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

Supplementary file Size Download File type/resource
GSM813764_3P_Seq_Adult.bed.gz 4.2 Mb (ftp)(http) BED
GSM813764_3P_Seq_Adult.bw 17.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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