|
| Status |
Public on Jul 06, 2018 |
| Title |
CA81_DMSO_1 (rna-seq) |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DMSO
cell line: GM17281
|
| Biomaterial provider |
Coriell lymphoblastoid cell line GM17281
https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM17281
|
| Treatment protocol |
Cells treated with 1uM 3-MC, 1uM GNF-351 or 0.1% DMSO in fresh media for 24 hours
|
| Growth protocol |
Gown in RPMI 1640 + 15% FBS +1% P/S; passaged by spinning down at 120g for 5 minutes and resuspended in growth media; cultured in 37C with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted at 300g for 5 minutes at 4C, resuspended in ice cold phosphate buffered saline and pelleted again. RNA was extracted using the miRNeasy RNA extraction kit.
TruSeq RNA Library Prep Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
counts.txt
|
| Data processing |
Sequences were aligned to hg38 genome with Tophat (2.0.14)
Raw counts were calculated with subread (1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: tab separated file with raw counts for each sample in the columns
|
| |
|
| Submission date |
Jul 05, 2018 |
| Last update date |
Jul 06, 2018 |
| Contact name |
Drew Neavin |
| E-mail(s) |
d.neavin@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Cellular Science
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
New South Wales |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE116637 |
RNA-seq of eight lymphoblastoid cell lines after AHR ligand treatments |
| GSE116638 |
Role of AHR in lymphoblastoid cell lines |
|
| Relations |
| BioSample |
SAMN09604090 |
| SRA |
SRX4342341 |
