|
| Status |
Public on Jan 01, 2020 |
| Title |
PTC_2_p29 |
| Sample type |
SRA |
| |
|
| Source name |
Primary trachea cells
|
| Organism |
Pteropus vampyrus |
| Characteristics |
cell type: Primary trachea cells
media: Seric medium
|
| Treatment protocol |
Cells were dissociated, washed in PBS and immediately frozen at -80° before RNAs were extracted.
|
| Growth protocol |
Cells were maintained in culture at 37°C in 7.5% CO2 in different media in the presence of Doxycycline for the reprogrammed cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were obtained following Trizol extraction of frozen cell pellets.
Libraries were synthesized according to the Illumina procedure by Eurofins genomics from total RNAs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PTC_2_p29
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx
|
| Data processing |
The raw files were converted into Fastq files and demultiplexed using bcl2fastq-1.8.4 software (Illumina).
Quality control was performed on Fastq files using the MultiQC 1.7 software aggregating data from fastp 0.19.6, FastQ Screen v0.13.0, kallisto v0.8.1.
fastq.gz files were pseudo-aligned using kallisto v0.8.1.
Normalized counts and DE genes were calculated using DESeq2 v1.24.0.
Genome_build: n/a
Supplementary_files_format_and_content: Table1.xlsx: kallisto
Supplementary_files_format_and_content: Table2.xlsx: ISG_PTC_vs_ES2_results
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Bertrand Pierre-Yves PAIN |
| E-mail(s) |
bertrand.pain@inserm.fr
|
| Phone |
33632513528
|
| Organization name |
U1208, INSERM
|
| Street address |
18, Avenue du Doyen Lépine
|
| City |
Bron |
| ZIP/Postal code |
69675 |
| Country |
France |
| |
|
| Platform ID |
GPL26939 |
| Series (1) |
| GSE134585 |
Somatic reprogramming of pteropus bat cells provides new insights in bat antiviral response |
|
| Relations |
| BioSample |
SAMN12325127 |
| SRA |
SRX6477596 |
