|
| Status |
Public on May 08, 2015 |
| Title |
PBS+DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Female ES cells_DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell line: LF2
strain: 129/J
gender: female
cell type: embryonic stem cells
|
| Treatment protocol |
LF2 ESCs were cultured with DMSO or GSK-J4 (10 µM) in the absence or presence of 50 µg/ml of L-ascorbic acid (AA) for 24 hr.
|
| Growth protocol |
LF2 female ESCs were cultured on the feeder cells and passed twice without feeder before treatments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent and RNeasy column (Qiagen) was used for purification.
The Illumina TrueSeq DNA Sample Prep Kit was used for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
total RNA
|
| Data processing |
TopHat2 was used with default setting to map the sequence tags after removal of duplicates.
Fragments Per Kilobase of exon per Million base reads (FPKM) was calculated as described in the manuscript
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and statistics for differential gene expression
|
| |
|
| Submission date |
Apr 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary E Donohoe |
| E-mail(s) |
med2008@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Burme Medical Research Institute
|
| Lab |
Mary Donohoe lab
|
| Street address |
785 Mamaroneck
|
| City |
White Plains |
| State/province |
NY |
| ZIP/Postal code |
10605 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE67674 |
Transcriptome analysis of the effects of GSK-J4 and L-ascorbic acid in female embryonic stem cells |
|
| Relations |
| BioSample |
SAMN03465498 |
| SRA |
SRX982781 |
