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Sample GSM7164134 Query DataSets for GSM7164134
Status Public on Jan 18, 2024
Title U2932_shZNF587-417v1_D6_RNA_Rep1_2
Sample type SRA
 
Source name U2932
Organism Homo sapiens
Characteristics cell line: U2932
cell type: Diffuse large B cell lymphoma
genotype: ZNF587,ZNF417 knockdown
treatment: Lentiviral transduction
time: Day 6
Treatment protocol Lentiviral transduction
Growth protocol U2932 = RPMI 1640 + 10% FCS + 1% Pen-Strep / OCI-Ly7 = IMDM + 20% FCS + 1% Pen-Strep
Extracted molecule polyA RNA
Extraction protocol Total RNA extraction was performed using the NucleoSpin RNA plus kit (Machery-Nagel) according to the manufacturer’s recommendations. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description OCI_Ly7_U2932_D6_RNA.tab
OCI_Ly7_U2932_D6_RNA_TEs.tab
Data processing RNA-seq reads were mapped to the hg19 using hisat v2.1.0
Mapped reads were filtered for uniquely mapping reads (MAPQ > 10)
Read counts on genes and repetitive sequence integrants was performed with featureCounts v2
Assembly: hg19
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA.tab: coma-separated table containing raw read counts on genes
Supplementary files format and content: OCI_Ly7_U2932_D6_RNA_TEs.tab: coma-separated table containing raw read counts on TEs
 
Submission date Apr 12, 2023
Last update date Jan 18, 2024
Contact name Filipe Martins
E-mail(s) [email protected]
Organization name Epfl
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL20301
Series (2)
GSE229468 KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation [RNA_D6]
GSE229471 KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation.
Relations
SRA SRX19940413
BioSample SAMN34154169

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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