|
| Status |
Public on Sep 16, 2016 |
| Title |
mRNA-seq_hESC_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESC
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: N/A
passage: 58-60
treatment: none
|
| Growth protocol |
H9 ESCs were obtained from WiCell as per agreement 15-W0341. H9 ESCs were cultured on matrigel coated plates (corning #354277) in mTeSR 1 media (stemcell technologies # 05857), washed with DMEM/F12 (GE healthcare # SH3002302) and passaged with accutase (MP Biomedicals # 091000449) and ROCK Inhibitor Y-27632 (BD # 562822).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Trizol followed by 2 rounds of poly A selection.
Libraries were prepared by Illumina's Tru-seq Library Preparation Kit v2. Paired-end sequencing was carried out on Hi-Seq_v4 (PE50 runs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq datsets were aligned to hg19 using Tophat2 using default conditions.
Differential gene expression for mRNA-seq datasets was determined by running DEseq2 in R Statistical Environment.
Data file which was used for DESeq2 analysis is included as processed data file "S1SupportingInfo".
Sample named 'mRNA-seq_48hr_ActivinA_rep2' in count table tab of "S1SupportingInfo" represents a concatenation of raw files: mRNA-seq_48hr_ActivinA_rep2_heflin, mRNA-seq_48hr_ActivinA_rep2_haib3866_1, and mRNA-seq_48hr_ActivinA_rep2_haib3866_2
Sample named 'mRNA-seq_48hr_CX-5461_rep2' in count table tab of "S1SupportingInfo" represents a concatenation of raw files: mRNA-seq_48hr_CX5461_rep2_heflin, mRNA-seq_48hr_CX-5461_rep2_haib3866_1, and mRNA-seq_48hr_CX-5461_rep2_haib3866_2
Genome_build: hg19
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica L Woolnough |
| E-mail(s) |
jlmakofske@gmail.com
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Genetics
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE76586 |
The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation. |
|
| Relations |
| BioSample |
SAMN05163667 |
| SRA |
SRX1793165 |
