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Sample GSM4231304 Query DataSets for GSM4231304
Status Public on Jan 13, 2020
Title STRIPEseq_K562_100ng_untreated_1
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
treatment: untreated
input to technology: 100 ng
Growth protocol DMEM + 10% FBS & 1x penicillin/streptomycin at 37°C with 5% CO2
Extracted molecule total RNA
Extraction protocol Invitrogen TRIzol
STRIPE-seq
stripe-seq-library-construction-2ivgce6.pdf
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: STRIPE-seq
Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (https://github.com/BrendelGroup/GoSTRIPES)
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
E-mail(s) gzentner@indiana.edu
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 GPL18573
Series (1)
GSE142524 Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
Relations
BioSample SAMN13672556
SRA SRX7433663

Supplementary file Size Download File type/resource
GSM4231304_STRIPEseq_K562_100ng_untreated_1_TSRs.bed.gz 110.6 Kb (ftp)(http) BED
GSM4231304_STRIPEseq_K562_100ng_untreated_1_minus.bedgraph.gz 160.0 Kb (ftp)(http) BEDGRAPH
GSM4231304_STRIPEseq_K562_100ng_untreated_1_plus.bedgraph.gz 169.5 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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