|
| Status |
Public on Dec 26, 2014 |
| Title |
4i WIS2 hESC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cell cultured in 4i condition
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human embryonic stem cell cultured in 4i condition
facs: TNAP+
gender: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the PicoPure RNA Isolation Kit. Total RNA (0.5-2 ng) was reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen) according to manufacturer’s instructions.
Amplified cDNA was sonicated into 250 bp by Covaris S220 Focused-ultrasonicators. Subsequently, RNASeq library was generated with 500 ng of fragmented cDNA using Ovation Ultralow DR Multiplex System (Nugen). Library was quantified by KAPA Library Quantification Kit (Kapa Biosystems) using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Cultured cells
|
| Data processing |
Low quality bases (q < 20) from the 3' end and adapter sequences were removed with the TrimGalore wrapper scripts (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Reads were mapped to the human (GRCh37/hg19) reference genome with Tophat 2.0.12 (http://ccb.jhu.edu/software/tophat)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain read counts per RefSeq transcripts generated by using the HTSeq 0.6.1 python package (http://www-huber.embl.de/users/anders/HTSeq)
|
| |
|
| Submission date |
Aug 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Dietmann |
| Organization name |
Washington University School of Medicine
|
| Street address |
4565 McKinley Avenue
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE60138 |
SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate |
|
| Relations |
| BioSample |
SAMN02953226 |
| SRA |
SRX670406 |
