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Sample GSM4231285 Query DataSets for GSM4231285
Status Public on Jan 13, 2020
Title RNAseq_S288C_10ug_untreated_3
Sample type SRA
Source name S288C
Organism Saccharomyces cerevisiae
Characteristics strain: S288C
treatment: untreated
input to technology: 10 ug
Growth protocol YPD to mid-log phase at 30°C
Extracted molecule polyA RNA
Extraction protocol Lucigen MasterPure Yeast RNA Purification Kit
RNA-seq (Illumina TruSeq Stranded mRNA Library Prep Kit)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
TSS bedgraphs and TSR beds derived from TSRchitect were CPM normalized via edgeR (v3.28.0) and exported with rtracklayer (v1.42.1)
For human and yeast RNA-seq samples, rRNA reads were first removed using tagdust (v2.33.0) with additional settings -fe 3 -dust 97
STAR (v2.7.0e) was used to generate genome indices (with the additional setting --genomeSAindexNbases 10 for yeast) and align reads to coordinate sorted bam files.
Rsubread (v1.6.4) featureCounts was utilized to count fragments overlapping annotated exons.
RNA-seq bigwigs were generated with deepTools (3.3.0) bamCoverage using the settings -bs 1 --normalizeUsing CPM --smoothLength 25. RNA-seq libraries were constructed using the dUTP method, so coverage of positively-stranded transcripts was obtained with --filterRNAstrand forward, which excludes positively-stranded reads, as negatively-stranded reads correspond to positively-stranded transcripts in the dUTP protocol. Similarly, coverage of negatively-stranded transcripts was obtained with --filterRNAstrand reverse.
Genome_build: human (GRCh38.p13), yeast (R64-1-1)
Supplementary_files_format_and_content: CPM-normalized RNA-seq signal (.bw), CPM-normalized TSS signal (.bedgraph), CPM-normalized TSR signal (.bed).
Submission date Dec 23, 2019
Last update date Jan 13, 2020
Contact name Gabriel E Zentner
Phone 812-856-7377
Organization name Indiana University
Department Biology
Street address 915 E 3rd St
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platform ID GPL19756
Series (1)
GSE142524 Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
BioSample SAMN13672578
SRA SRX7433644

Supplementary file Size Download File type/resource
GSM4231285_RNAseq_S288C_10ug_untreated_3_minus.bigwig 47.8 Mb (ftp)(http) BIGWIG
GSM4231285_RNAseq_S288C_10ug_untreated_3_plus.bigwig 48.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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