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Sample GSM4282225 Query DataSets for GSM4282225
Status Public on Apr 15, 2020
Title P2.FGF1
Sample type SRA
 
Source name human embryonic stem cell H9 (WA09)
Organism Homo sapiens
Characteristics passage: 2
fgf: 1
Treatment protocol On final passage, hNSCs were exposed to different FGF2 concentrations.
Growth protocol H9 hESCs were dissociated to single cells and maintained in feeder-free conditions. Neural differentiation from hESCs was induced using dual SMAD inhibition. hNSCs were expanded and serially passaged every 6 days in 20 ng/ml FGF2.
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 P2_1
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: hg19
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 GPL21290
Series (2)
GSE144156 Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [human RNAseq #1]
GSE144159 Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates
Relations
BioSample SAMN13910417
SRA SRX7624820

Supplementary file Size Download File type/resource
GSM4282225_P2_1_H5NNKBBXX.count.txt.gz 96.2 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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