|
| Status |
Public on Jun 12, 2017 |
| Title |
TSC_Ctrl_2 |
| Sample type |
SRA |
| |
|
| Source name |
TSC_control
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E 3.5 isolated trophoblast stem cells
passage: 15-20
genotype/variation: +/+; TSC wild type
treated with: DMSO
|
| Treatment protocol |
24 hrs with DMSO or Inhibitor changing media every 12 hrs; 8 days with DMSO or 4OHT
|
| Growth protocol |
TSCs medium suplemented with Fgf4 and Heparin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiagen kit. Strand-Specific RNA Seq with Agilent kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TSC treated with DMSO
processed data file: diff_edgeR_D0_Lsd1i.txt
|
| Data processing |
Raw sequence files (.fastq files) were aligned to mouse genome (mm10) using TopHat
Counting of the aligned reads was performed using homer software (analyze RNA). Differentially expressed genes were identified with EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include processed raw counts, pvalues and fold changes
|
| |
|
| Submission date |
Mar 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Josefina Castex |
| Organization name |
Freiburg Uniklinik
|
| Street address |
BreisacherStrasse 66
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE78781 |
Trophoblast stem cells (TSC) global transcriptome in stemness conditions after treatment with Lsd1 inhibitor or induction of Lsd1 depletion [RNA-seq] |
| GSE78782 |
Deletion of Lsd1 triggers Senescence in Trophoblast Stem Cells by Induction of Sirt4 |
|
| Relations |
| BioSample |
SAMN04525180 |
| SRA |
SRX1606652 |
