|
| Status |
Public on Oct 07, 2019 |
| Title |
20ng-72h-3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hCMEC/D3
treatment: 20 ng/mL interleukin-6 for 72h
|
| Treatment protocol |
Cells were exposed or not to 20 ng/mL interleukin-6 for 72h. Medium with or without IL-6 was renewed every 24h.
|
| Growth protocol |
4-5 10^5 cells/cm2 were coated in a 6-well plate on EBM-2 medium supplemented with 5% FBS, penicillin-streptomycin 100 µg/mL, 1.4 µM hydrocortisone, 5 µg/mL acid ascorbic, 10 mM HEPES, 1% chemically defined lipid concentrate and 1 ng/mL bFGF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was performed using the Maxwell 16 LEV Simply RNA cells kit
RNA libraries were prepared for sequencing using 1 µg of total mRNA with NEB library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
The sequencing reads were obtained after demultiplexing the raw sequencing data using bcl2fastq v2.19.1.403 Version v2.15.0 for NextSeq™ 500 (Illumina)
We validated the quality controls of each sample using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then generated alignment files using STAR v2.5.2b in the “2-pass” mode, on the hg19 human genome.
Upon obtaining the final sorted alignment file, the count of reads was performed using GFOLD V1.1.4 (option: count; https://bitbucket.org/feeldead/gfold/)
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM for each samples
|
| |
|
| Submission date |
Oct 02, 2019 |
| Last update date |
Oct 07, 2019 |
| Contact name |
Florian SIMON |
| E-mail(s) |
florian.simon@univ-lyon1.fr
|
| Organization name |
University Lyon 1
|
| Street address |
165 Chemin du Grand Revoyet
|
| City |
Oullins |
| ZIP/Postal code |
69921 |
| Country |
France |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE138309 |
RNA sequencing of blood-brain barrier cells exposed to interleukin-6 |
|
| Relations |
| BioSample |
SAMN12896835 |
| SRA |
SRX6937076 |
