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Sample GSM282598 Query DataSets for GSM282598
Status Public on May 05, 2008
Title RNA-seq analysis of oligo(dT)- and random-hexamer-primed yeast polyA RNA
Sample type RNA
 
Source name yeast BY4741, mid-exponential phase
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741(leu2D0 ura3D0 met15D0 his3D1)
Growth protocol Yeast strain BY4741(leu2D0 ura3D0 met15D0 his3D1) was grown at 30C to mid exponential phase (OD 600=1.0) in YPAD rich medium.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from Ribopure Yeast kit (Ambion) and treated for 30 min at 37C with RNAse free DNase I (Ambion). Poly(A) RNA was purified with Micro Poly(A) Purist Kit according to the manufacturer's instructions (Ambion), and used to generate double stranded cDNA by reverse transcription with either random hexamers or oligo(dT) primers. The double stranded cDNA was fragmented and subjected to high throughput Illumina sequencing in which 35 bp of sequence was determined from the fragment ends.
 
Description Transcriptome analysis
Data processing The processed data on this record (linked in the 'Supplementary file' section below) are derived from raw samples of oligo(dT)-primed and RandomHexamer-primed polyA cDNA, as well as original, biological and technical replicates. Consequently, fastq raw data files are composed of 6 batches of sequences:
RH_bio:SRX000564
RH_ori:SRX000562
RH_tech:SRX000563
dT_bio:SRX000561
dT_ori:SRX000559
dT_tech:SRX000560

After removing adapter and low quality sequences (N-runs, N>=12), short sequence reads were mapped to a recent reference yeast genome assembly (January, 2008) with software SOAP and BLAT. Reads aligning to two different locations in the genome represent splicing junctions and reads have leading Ts and trailing As (hereafter referred as End Tags) represent the 3'ends of mRNA. These reads were also recovered in order to define intron and mRNA ends.
 
Submission date Apr 17, 2008
Last update date May 15, 2019
Contact name Zhong Wang
Organization name Yale University
Department MCDB
Lab Michael Snyder
Street address 266 Whitney Avn, KBT716
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL6750
Series (1)
GSE11209 The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Relations
SRA SRX000560
SRA SRX000563
SRA SRX000561
SRA SRX000559
SRA SRX000562
SRA SRX000564

Supplementary file Size Download File type/resource
GSM282598_README.txt.txt.gz 544 b (ftp)(http) TXT
GSM282598_all.unique.end3.txt.gz 1.2 Mb (ftp)(http) TXT
GSM282598_all.unique.exons.txt.gz 192.5 Mb (ftp)(http) TXT
GSM282598_all.unique.junctions.txt.gz 4.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file

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