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Status |
Public on Jun 12, 2019 |
Title |
The hypoxic landscape of melanoma |
Organism |
Homo sapiens |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing
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Summary |
Micro-environment played an important role in the disease progression and overall survival. More recently, hypoxic signature were identified as one of the key signatures of innate anti-PD1 resistance, however, relatively little had been done to identify the key molecular signature of hypoxic response in melanoma and how these may correlated with other know signatures which correlate with poor prognosis. In this study we performed large scale study which integrate ChIP-seq of HIF (in one cell line) and RNA-seq (in three commonly used melanoma cell lines) to identify a common melanoma hypoxic signature. The finding were used to further integrated with our other genome wide which focus on MITF (the master regulator of the melanocyte lineage and a melanoma lineage oncogene, GSE77609) to elucidate the intricate interplay between MITF and HIF and how this interplay define a melanoma specific response to hypoxia.
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Overall design |
Three melanoma cell lines were subjected to time course hypoxic induction. Triplicate samples were collected in three consecutive weeks.
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Contributor(s) |
Goding CR, Louphrasitthiphol P, Ledaki I |
Citation(s) |
31207090 |
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Submission date |
Feb 23, 2017 |
Last update date |
Sep 11, 2019 |
Contact name |
Pakavarin Louphrasitthiphol |
E-mail(s) |
pakavarin.louphrasitthiphol@ludwig.ox.ac.uk
|
Phone |
01865 617543
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Organization name |
Ludwig Institute for Cancer Research
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Department |
Nuffield Department of Clinical Medicine
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Lab |
Prof. CRGoding
|
Street address |
Old Road Campus Research Building (off Roosevelt Drive)
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City |
Oxford |
ZIP/Postal code |
OX3 7DQ |
Country |
United Kingdom |
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Platforms (2) |
GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (42)
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Relations |
BioProject |
PRJNA376554 |
SRA |
SRP100624 |
Supplementary file |
Size |
Download |
File type/resource |
GSE95280_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
GSE95280_edgeR_501_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
425.9 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_501_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
416.4 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_501_hypoxia_t48h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
418.6 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_IGR37_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
420.8 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_IGR39_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
419.9 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_IGR39_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
421.5 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_shHIF1a_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
395.3 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_shHIF1a_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
406.2 Kb |
(ftp)(http) |
TXT |
GSE95280_edgeR_shHIF1a_hypoxia_t48h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt.gz |
418.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
Processed data provided as supplementary file |