|
| Status |
Public on Sep 16, 2016 |
| Title |
mRNA-seq_48hr_ActivinA_rep2_haib3866_1 |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESC treated with a 50 ng/mL final concentration of Activin A for 6 hours
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: N/A
passage: 58-60
treatment: 50 ng/mL Activin A for 48 hours
|
| Growth protocol |
For Activin A treatment cells were grown to about 75 – 80% confluency. The cells were washed with PBS and 10 ml of RPMI 1640 (GE Healthcare # SH30027.01) was added with 1X B-27 supplement (life technologies # 17504-044) along with Activin A (sigma # SRP3003) to a final concentration of 50 ng/ml for 48 hours. Old media was removed and replaced with fresh media/Activin A at 24 hours.
|
| 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 |
SAMN05163673 |
| SRA |
SRX1793171 |
