|
| Status |
Public on Apr 08, 2018 |
| Title |
3E |
| Sample type |
SRA |
| |
|
| Source name |
in vitro reprogrammed cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: somatically reprogrammed stem cell
|
| Growth protocol |
Cells were isolated and maintained as described in Fuet et al., (2017). Submitted and in Vautherot et al., (2017). PLoS ONE 12(4): e0175259. https://doi.org/10.1371/journal. pone.0175259
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared by Trizol extraction using standard protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The raw files were convereted into Fastq files (fastq.gz) and demultiplexed using Bcl2fastq 2.0 software (Illumina)
Quality control was performed on Fastq files using the FastQC v0.11.5 software
Sequenced reads were pseudoaligned against ref_mRNA of galGal5 using kallisto v0.43.0 with parameters -t 4 -b 100 –rf-stranded
Normalized counts and DE genes were calculated using DESeq2
Genome_build: ref_mRNA of galGal5
Supplementary_files_format_and_content: Normalized counts and DE genes were calculated using DESeq2
|
| |
|
| Submission date |
Aug 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bertrand Pierre-Yves PAIN |
| E-mail(s) |
[email protected]
|
| Phone |
33632513528
|
| Organization name |
U1208, INSERM
|
| Street address |
18, Avenue du Doyen Lépine
|
| City |
Bron |
| ZIP/Postal code |
69675 |
| Country |
France |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE102353 |
NANOG is required for the long-term establishment of avian somatic reprogrammed cells [chicken] |
| GSE109970 |
NANOG is required for the long-term establishment of avian somatic reprogrammed cells |
|
| Relations |
| BioSample |
SAMN07460470 |
| SRA |
SRX3070413 |
