NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4120839 Query DataSets for GSM4120839
Status Public on Feb 19, 2020
Title ShhN IUE rep 2
Sample type SRA
 
Source name Shh-P0-2
Organism Mus musculus
Characteristics strain: a mixed genetic background of C57BL/6J, 129S6 and CD1
tissue: Cortex
developmental stage: Postnatal day 0
genotype: ShhN IUE brain
Treatment protocol Cortex from P0 WT mice, ShhN IUE mice and hGFAP-Cre,SmoM2f/+ mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome(version:GRCm38.p4)using Hisat2(version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
 
Submission date Oct 15, 2019
Last update date Feb 19, 2020
Contact name Guoping Liu
E-mail(s) gpliu@fudan.edu.cn
Phone 18521006300
Organization name Fudan University
Street address 138 Yi Xue Yuan Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL17021
Series (2)
GSE138878 Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [bulk RNA-seq]
GSE140817 Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog
Relations
BioSample SAMN13031895
SRA SRX6993229

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