NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3908373 Query DataSets for GSM3908373
Status Public on Jul 16, 2019
Title KO_3
Sample type SRA
 
Source name primary neurosphere derived from dorsal cortex
Organism Mus musculus
Characteristics tissue: primary neurosphere derived from dorsal cortex
strain: C57BL/6
age: E14.5
genotype: Ash2l cKO
Growth protocol NPCs were isolated from E14.5 mice by dissection of the lateral walls of the lateral ventricles and digested into single cell suspension with Accutase (Sigma). Cells were cultured in DMEM/F12 proliferation medium supplemented with 2% B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 0.2% BSA for proliferation.
Extracted molecule total RNA
Extraction protocol Neurosphere RNA isolated from the 6th day culturing NPCs dissected from E14.5 mice.
A total amount of 3 µg RNAper sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential gene expression analysis was performed through DESeq2 (v1.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
 
Submission date Jun 27, 2019
Last update date Jul 16, 2019
Contact name Xiaozhong Peng
E-mail(s) pengxiaozhong@pumc.edu.cn
Phone 86 69156434
Organization name Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College
Department Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences
Lab Lab of Xiaozhong Peng
Street address No.5, Dongdan Santiao, Dongcheng District
City Beijing
ZIP/Postal code 100005
Country China
 
Platform ID GPL21273
Series (2)
GSE120988 COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling
GSE133413 COMPASS Family Histone Methyltransferase ASH2L Mediates Corticogenesis via Transcriptional Regulation of Wnt Signaling [RNA-Seq 2]
Relations
BioSample SAMN12147672
SRA SRX6370218

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