|
Status |
Public on Jan 01, 2020 |
Title |
ECM_E2_p18 |
Sample type |
SRA |
|
|
Source name |
Reprogrammed cells derived from the somatic PTC cells
|
Organism |
Pteropus vampyrus |
Characteristics |
cell type: Reprogrammed cells derived from the somatic PTC cells media: Non-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 |
ECM_E2_p18 Reprogrammed with ECM gene cocktail. 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 |
SAMN12325130 |
SRA |
SRX6477600 |