|
| Status |
Public on Jun 13, 2019 |
| Title |
IGR39_t12_R1 (3 phenotypically distinct states dataset) |
| Sample type |
SRA |
| |
|
| Source name |
IGR39
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: melanoma
treatment: 12h Hypoxia
|
| Treatment protocol |
Cells were treated at 1% O2 level in hypoxia chamber for the indicated time
|
| Growth protocol |
All cell lines were grown at 37°C with 10% CO2 in DMEM (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
12h_Hypoxia
edgeR_IGR39_DMEM_1%O2_12h_relative_to_0h_QLF-test_filtered_1cpm_3rep.csv
|
| Data processing |
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Raw fastq files were then trimmed of poly-A using cutadapt {Martin, 2011 }
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is count-per-million prior to glmQLFTest.
Genome_build: hg38
Supplementary_files_format_and_content: csv table of differential gene expression of treated vs control and the associated statistically analysis
|
| |
|
| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 13, 2019 |
| Contact name |
Pakavarin Louphrasitthiphol |
| E-mail(s) |
pakavarin.louphrasitthiphol@ludwig.ox.ac.uk
|
| Phone |
01865 617543
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Nuffield Department of Clinical Medicine
|
| Lab |
Prof. CRGoding
|
| Street address |
Old Road Campus Research Building (off Roosevelt Drive)
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7DQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE132624 |
MITF controls the TCA cycle to modulate the melanoma hypoxia response |
|
| Relations |
| BioSample |
SAMN12039974 |
| SRA |
SRX6052971 |
