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| Status |
Public on Jan 13, 2020 |
| Title |
STRIPEseq_K562_100ng_untreated_3 |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
treatment: untreated
input to technology: 100 ng
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| Growth protocol |
DMEM + 10% FBS & 1x penicillin/streptomycin at 37°C with 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Invitrogen TRIzol
STRIPE-seq
stripe-seq-library-construction-2ivgce6.pdf
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| 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).
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| Submission date |
Dec 23, 2019 |
| Last update date |
Jan 13, 2020 |
| Contact name |
Gabriel E Zentner |
| E-mail(s) |
gzentner@indiana.edu
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| Phone |
812-856-7377
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| Organization name |
Indiana University
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| Department |
Biology
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| Street address |
915 E 3rd St
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| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE142524 |
Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq |
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| Relations |
| BioSample |
SAMN13672587 |
| SRA |
SRX7433665 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4231306_STRIPEseq_K562_100ng_untreated_3_TSRs.bed.gz |
118.9 Kb |
(ftp)(http) |
BED |
| GSM4231306_STRIPEseq_K562_100ng_untreated_3_minus.bedgraph.gz |
180.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM4231306_STRIPEseq_K562_100ng_untreated_3_plus.bedgraph.gz |
193.2 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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