|
| Status |
Public on Aug 27, 2015 |
| Title |
untreated KhES-1, replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
dox-untreated tet-shLbc hESCs
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
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 |
SAMN03436245 |
| SRA |
SRX963268 |
