GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM6921813

Query DataSets for GSM6921813

Status

Public on Jan 12, 2023

Title

H2810_R_2

Sample type

SRA

Source name

pleura

Organism

Homo sapiens

Characteristics

tissue: pleura
cell line: H2810
genotype: Random shRNA

Extracted molecule

total RNA

Extraction protocol

for RNA seq: RNA was isolated from tumor cell lines and mouse tumors with the Qiagen All Prep DNA/RNA kit. Quantification and quality assessment for RNA were performed with a Bioanalyzer (RIN >6.5) (Agilent, Santa Clara, CA, USA).
for RNAseq: Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

shBAP1_genecounts.txt

Data processing

Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10) or hg 38, using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2
Assembly: mm10, Grcm38
Supplementary files format and content: read counts table
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

Submission date

Jan 08, 2023

Last update date

Jan 12, 2023

Contact name

Jitendra Badhai

E-mail(s)

j.badhai@nki.nl

Organization name

Netherlands Cancer Institute

Department

Division Molecular Genetics