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Sample GSM1597982 Query DataSets for GSM1597982
Status Public on Aug 24, 2015
Title iNkx6.1-P2A-Olig2_rep2
Sample type SRA
Source name Neural progenitor cells
Organism Mus musculus
Characteristics cell type: ES-derived neural progenitor cells
strain: 129/Ola
transgene: TRE_Nkx6.1-P2A-Olig2
Treatment protocol To activate transgene, neural progenitors were induced for 12hr with 1ug/ml doxycycline
Growth protocol mESCs were maintained in a serum free condition with CHIR99021, PD184352, and LIF on sparse feeder cells. Neural progenitors were derived by depleting feeder cells and culturing cells in suspension in neural differentiation basal medium (DFNB) for 2 days followed by 500nM all-trans retinoic acid treatment in DFNB.
Extracted molecule total RNA
Extraction protocol NucleoSpin RNA column (Clontech)
Library was constructed with TruSeq kit (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Nkx6.1-P2A-Olig2 overexpression rep2
Data processing Basecall was performed with the default pipeline for Illumina NextSeq
Sequence tags were aligned with the mm10 genome with STAR aligner
Differentially expressed genes were identified with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for all replicates and all analyzed genes (tab1) and fold repression values for genes repressed by at least one transgene by 2 fold
Submission date Jan 30, 2015
Last update date May 15, 2019
Contact name Yuichi Nishi
Phone 323-442-8077
Organization name University of Southern California
Department Eli and Edythe Broad-CIRM Center for Regenerative Medicine
Lab Andrew McMahon
Street address 1425 San Pablo St.
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platform ID GPL19057
Series (2)
GSE65457 mRNAseq analysis of Nkx2.2, Nkx6.1, and Olig2 overexpression in neural progenitors
GSE65462 Nkx2.2, Nkx6.1, Olig2, and Gli3 genomic binding regions and overexpression in neural progenitors
BioSample SAMN03322528
SRA SRX860872

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

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