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Sample GSM6042445 Query DataSets for GSM6042445
Status Public on Oct 28, 2022
Title siINTS11 RNA-seq Rep 3
Sample type SRA
 
Source name Embryonic stem cell
Organism Mus musculus
Characteristics tissue: Embryonic stem cell
cell line: F121-9
cell type: Embryonic stem cell
genotype: WT
treatment: siINTS11
Treatment protocol Cells were either not treated or treated with siRNA (siNT or siINTS11) for 48 hours.
Growth protocol INTS11Halo cells were maintained in SFES+2i/LIF.
Extracted molecule total RNA
Extraction protocol RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Untreated RNA-seq samples were mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
siNT and siINTS11 were first mapped to an ERCC spike genome, and reads not mappping to spike were subsequently mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
bigWigs output from STAR were used for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: bigWigs representing coverage (no normalization for untreated; DEseq-normalized for siNT and siINTS11)
 
Submission date Apr 12, 2022
Last update date Oct 28, 2022
Contact name Karen Adelman
E-mail(s) karen_adelman@hms.harvard.edu
Organization name Harvard Medical School
Department Biological Chemistry and Molecular Pharmacology
Street address 45 Shattuck St. LHRRB-201a
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24247
Series (2)
GSE200699 Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci (RNA-Seq)
GSE200702 Integrator endonuclease drives promoter-proximal termination at all RNAPII transcribed loci
Relations
BioSample SAMN27549619
SRA SRX14835839

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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