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Series GSE95280 Query DataSets for GSE95280
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
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.
 
Overall design Three melanoma cell lines were subjected to time course hypoxic induction. Triplicate samples were collected in three consecutive weeks.
 
Contributor(s) Goding CR, Louphrasitthiphol P, Ledaki I
Citation(s) 31207090
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
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
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (42)
GSM2501225 HIF1a
GSM2501226 HIF1b
GSM2501227 HIF2a
Relations
BioProject PRJNA376554
SRA SRP100624

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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