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Series GSE127232 Query DataSets for GSE127232
Status Public on Nov 26, 2019
Title In vitro and in vivo epigenome-wide CRISPR screens in mouse KrasG12D/P53-/- (KP) lung adenocarcinoma model
Organisms Mus musculus; synthetic construct
Experiment type Other
Summary To systematically study the functions of epigenetic genes in controlling tumor progression and regulating anti-tumor immunity, we performed a series of in vitro and in vivo epigenome-wide CRISPR screens in mouse KP lung adenocarcinoma model. We constructed an epigenetic-focused sgRNA library, established KP-Cas9-library pools, and then performed in vitro and in vivo CRISPR screens. For in vitro screens, we compared the cell pools harvested at week 4 with the cells pools harvested at week 2 to check the functions of epigenetic genes in tumor cell proliferation. For in vivo screens, we compared the IgG treated tumors in Rag1-/- mice or WT mice with the input cell pool to check the functions of epigenetic genes in tumor growth; we compared the IgG treated tumors in WT mice with the IgG treated tumors in Rag1-/- mice to check the functions of epigenetic genes in regulating anti-tumor immunity; we compared the anti-PD-1 treated tumors in WT mice with IgG treated tumors in WT mice to check the functions of epigenetic genes in modulating sensitivity to anti-PD-1 treatment.

 
Overall design Examination of sgRNA abundance in library, cultured cell pools, input cell pool and tumors with different treatments.
 
Contributor(s) Li F, Khodadadi-Jamayran A, Wong KK
Citation(s) 31744829
Submission date Feb 26, 2019
Last update date Jun 26, 2020
Contact name Alireza Khodadadi-Jamayran
Organization name New York University, NYU Langone Medical Center
Department Division of Advanced Research Technologies (DART)
Lab Applied Bioinformatics Laboratories (ABL)
Street address 550 1st Ave, MSB 304
City New York City
State/province NY
ZIP/Postal code 10016
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (54)
GSM3631295 Library
GSM3631296 Input
GSM3631297 ID-IgG-1
Relations
BioProject PRJNA524379
SRA SRP186949

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
GSE127232_RAW.tar 5.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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