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Sample GSM4282313 Query DataSets for GSM4282313
Status Public on Apr 15, 2020
Title hr144.FGF100
Sample type SRA
 
Source name primary mouse neural stem cell
Organism Mus musculus
Characteristics hours: 144
fgf: 100
Treatment protocol Thawed NSCs were expanded for 4 days in 10 ng/ml and passaged into varying concentration of FGF2 without astrocytes. Differentiation of mouse NSCs was induced 2 days after plating, by FGF2 withdrawal. At DIV 4, N2 was replaced with NeuroBasal medium and neurotrophins.
Growth protocol Embryonic day (E)11.5 embryos were isolated from pregnant C57BL/6 mice (Charles River) and dorsal telencephalic cortex was collected. 1 x 106 cells were plated and expanded in 10 ng/ml FGF2. NSCs were lifted and frozen.
Extracted molecule total RNA
Extraction protocol RNeasy Mini Kit (Qiagen, Ct# 74106)
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description NM40
Data processing After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample
 
Submission date Jan 23, 2020
Last update date Apr 16, 2020
Contact name Carlo Colantuoni
E-mail(s) ccolantu@jhmi.edu
Phone 4104931439
Organization name Johns Hopkins Univ. School of Medicine
Department Neurology
Street address 733 N Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL21493
Series (2)
GSE144158 Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [mouse RNAseq]
GSE144159 Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates
Relations
BioSample SAMN13910531
SRA SRX7624808

Supplementary file Size Download File type/resource
GSM4282313_NM40_H5WTMBBXX.count.txt.gz 100.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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