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Sample GSM1639787 Query DataSets for GSM1639787
Status Public on Aug 27, 2015
Title AKAP-Lbc-depleted KhES-1, replicate1
Sample type SRA
 
Source name dox-treated tet-shLbc hESCs
Organism Homo sapiens
Characteristics treatment: dox-treated
strain: tet-shLbc:Bcl-XL KhES-1
Treatment protocol Dox solution was added to the culture at a final concentration of 1 μg/ml, and cultured for 72 hr with daily medium changes.
Growth protocol hESC colonies were cultured on matrigel-coated 6-well plate using MEF-conditioned standard 10%KSR medium and maintained at 37C and 2% CO2.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy kit (Qiagen) using the company-provided protocol. On the culture plate, cells were lysed in 700uL buffer RLT and spun through QIAshredder (Qiagen) prior to RNA extraction.
Libraries were prepared using 1μg of total RNA, according to the protocol of TruSeq RNA Sample Prep Kit v2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls were performed using illumina RTA software (version 1.17.21.3) and reads were de-multiplexed using bcl2fastq ( version 1.8.3).
Quality check of the reads was performes using FastQC(version 0.10.1). Ascertaining the high quality of sequencing, reads were mappedto 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 Mar 20, 2015
Last update date May 15, 2019
Contact name Masatoshi Ohgushi
E-mail(s) mohgushi@cdb.riken.jp
Organization name RIKEN Center for Developmental Biology
Lab Laboratory for Organogenesis and Neurogenesis
Street address 2-2-3 Minatojima-minamimachi,
City Chuou-ku
State/province Kobe
ZIP/Postal code 6500047
Country Japan
 
Platform ID GPL18460
Series (1)
GSE67128 Comparative whole-transcriptomic analysis between normal and AKAP-Lbc-depleted human embryonic stem cells
Relations
BioSample SAMN03436247
SRA SRX963269

Supplementary file Size Download File type/resource
GSM1639787_AKAP-Lbc-depleted_KhES-1_CPM_rep1.txt.gz 446.1 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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