NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2640683 Query DataSets for GSM2640683
Status Public on Jul 31, 2017
Title Ptpn2sg3_IFNbTNFa_rep1
Sample type SRA
 
Source name Ptpn2sg3_IFNbTNFa
Organism Mus musculus
Characteristics cell line: B16
cell type: melanoma
genotype/variation: Ptpn2ko
infected with lentivirus containing sgrna against: Ptpn2sg3
treated with: IFNbTNFa
Treatment protocol Cells were treated with either 1000 U/mL IFNb, 100ng/mL IFNg, 10ng/mL TNFa, alone or in combination, or an equivalent volume of vehicle control (PBS + 0.1% BSA) for 48 hours.
Growth protocol Cells were grown in DMEM supplemented with 10% heat-inactivated FBS and 2.5% Pen-Strep
Extracted molecule total RNA
Extraction protocol Cells were trypsinized and lysed in QIAGEN RLT buffer and frozen at -80C. RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions.
Libraries were constructed using the NEB Ultra-Directional RNA kit using the mRNA capture module, according to manufacturer's instructions.
Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Data processing NextSeq raw data demultiplexed and converted to fastq files using the Illumina software Bcl2fastq v2.17.1.14.
Fastq files were quality-trimmed and illumina adaptors removed using Trimmomatic v0.33
Fastq files were aligned to the relevant genome assembly (mm10 for mouse, hg19 for human) using Bowtie2 v2.2.4.
Feature counts were aggregated into a single data matrix using HTSeq v0.6.1p1.
DESeq2 library size normalization by scale factor of normcounts. Differential expression performed using DESeq2.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Aggregated raw count matrix (output from HTSeq) in tab-delimited .txt file
 
Submission date May 25, 2017
Last update date May 15, 2019
Contact name Kathleen B Yates
Organization name Broad Institute
Department Cancer Program
Lab Manguso
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL21626
Series (1)
GSE99299 Cytokine Stimulation of PTPN2-deleted cancer cells
Relations
BioSample SAMN07168057
SRA SRX2857398

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap