|
Status |
Public on Jul 06, 2018 |
Title |
CA23_3MC_1 (rna-seq) |
Sample type |
SRA |
|
|
Source name |
lymphoblastoid cell line
|
Organism |
Homo sapiens |
Characteristics |
treatment: 3-MC cell line: GM17223
|
Biomaterial provider |
Coriell lymphoblastoid cell line GM17223 https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM17223
|
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 |
SAMN09604074 |
SRA |
SRX4342309 |