|
Status |
Public on Apr 15, 2015 |
Title |
Day 14 Control Neural Progenitior Cells, Replicate 1 |
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
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|
|
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
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|
|
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 |
SAMN03164183 |
SRA |
SRX751561 |