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Sample GSM1537998 Query DataSets for GSM1537998
Status Public on Apr 15, 2015
Title Day 14 Control Neural Progenitior Cells, Replicate 3
Sample type SRA
 
Source name Neural progenitor cells
Organism Homo sapiens
Characteristics cell type: ES-derived neural progenitor cells
passage number: 48
treatment: control
Growth protocol hESCs were differentiated in three-dimenstional condition with SFEBq culture.
Extracted molecule total RNA
Extraction protocol hESC-derived neural progenitors were collected, and RNA was extracted with buffer RLT in Rneasy kit (Quiagen cat#74104).
Libraries were prepared using 1μg of total RNA, according to the protocol of TruSeq Stranded mRNA Sample Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description none
Data processing Basecalls were performed using illumina RTA software (version 1.17.21.3) and reads were de-multiplexed using bcl2fastq ( version 1.8.4).
Quality check of the reads was performes using FastQC(version 0.11.2). High quality reads were mapped to hg19 human genome assembly using Tophat (version 2.0.8b) with default parameter settings.
Number of reads originating from genes were quantified by cuffdiff program in Cufflinks package (version 2.1.1). These count values were subsequently used to test for differential expression using edgeR(version 3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized expression values for each sample
 
Submission date Nov 05, 2014
Last update date May 15, 2019
Contact name Keiko Muguruma
E-mail(s) muguruma@cdb.riken.jp
Organization name RIKEN:Center for Developmental Biology
Lab Organogenesis and Neurogenesis Group
Street address 2-2-3 Minatojima-minamimachi
City Chuo-ku
State/province Kobe
ZIP/Postal code 650-0047
Country Japan
 
Platform ID GPL18460
Series (1)
GSE63015 Self-organization of polarized cerebellar plate neuroepithelium in three-dimensional culture of human pluripotent stem cells
Relations
BioSample SAMN03164185
SRA SRX751563

Supplementary file Size Download File type/resource
GSM1537998_d14_cont_rep3_cpm.txt.gz 408.6 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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