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Series GSE99299 Query DataSets for GSE99299
Status Public on Jul 31, 2017
Title Cytokine Stimulation of PTPN2-deleted cancer cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary PTPN2 was deleted from a selection of murine and human cancer cells using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control.
 
Overall design In order to determine the effect of PTPN2-inhibition of interferon signalling, Cas9-expressing murine (B16 melanoma) and human (A375, A549, HT29, MelJuSo) cancer cells were infected with lentivirus containing guide RNA (sgRNA) against Ptpn2 or a non-targeting sequence. After Ptpn2 deletion was verified, the cell lines were treated with vehicle control (PBS with 0.1% BSA), interferon-beta (IFNb), interferon-gamma (IFNg), or tumor necrosis factor (TNFa), alone or in combination, and transcriptionally profiled by directional, paired-end RNAseq after a 48 hour stimulation.!Series_overall_design = Please note that 'Bro3' and 'Bro4' refer to non-targeting guides provided by the Broad Institute.

Please note that 'Bro3' and 'Bro4' refer to non-targeting guides provided by the Broad Institute.
 
Contributor(s) Manguso R, Yates K
Citation(s) 28723893
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
 
Platforms (2)
GPL21626 NextSeq 550 (Mus musculus)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (81)
GSM2640644 Bro3_IFNbTNFa_rep1
GSM2640645 Bro3_IFNbTNFa_rep2
GSM2640646 Bro3_IFNbTNFa_rep3
Relations
BioProject PRJNA388068
SRA SRP108032

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99299_a375.rawCount.txt.gz 339.6 Kb (ftp)(http) TXT
GSE99299_a549.rawCount.txt.gz 268.6 Kb (ftp)(http) TXT
GSE99299_b16.rawCount.txt.gz 914.1 Kb (ftp)(http) TXT
GSE99299_ht29.rawCount.txt.gz 265.6 Kb (ftp)(http) TXT
GSE99299_meljuso.rawCount.txt.gz 353.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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