|
| Status |
Public on Oct 14, 2017 |
| Title |
undifferentiated hESC line H9 cells, biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
time point: 0 hour (undifferentiated)
|
| Treatment protocol |
For trophoblast differentiation, cells were seeded at 100% confluency on Matrigel-coated plates containing KSR-based differentiation medium and 50 ng/ml BMP4. During the time course, medium was changed every 24 hours.
|
| Growth protocol |
H9 cell line was grown on Geltrex-coated plates in mTESR1 medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer's instructions
Total RNA libraries were prepared from 1 µg of total RNA using Illumina TruSeq Stranded Total RNA LT kit according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ generation was done automatically in Illumina BaseSpace application
Reads were aligned to human genome h38 using STAR aligner 2.4.2a with default parameters
Gene count table was generated using featureCounts software from Rsubread package 1.20.0
Normalized gene count table was generated using DEseq2 1.15.3
Genome_build: h38
Supplementary_files_format_and_content: csv file containing normalized gene counts for all samples
|
| |
|
| Submission date |
Oct 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dmitry Shaposhnikov |
| E-mail(s) |
dmitry.shaposhnikov@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Center Munich
|
| Street address |
Ingolstädter Landstraße 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE104969 |
Time series total RNA sequencing of a differentiation of human embryonic stem cells towards trophoblast lineage |
|
| Relations |
| BioSample |
SAMN07782539 |
| SRA |
SRX3282174 |
