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Series GSE134432 Query DataSets for GSE134432
Status Public on Jul 10, 2020
Title Single-cell analysis of gene expression variation and phenotype switching in melanoma
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We combine extensive profiling of single-cell gene expression (scRNA-seq of 39,263 cells) and chromatin accessibility applied to ten genetically-homogeneous, patient-derived melanoma cultures, to examine intra- and intertumoral phenotypic heterogeneity, to identify new cell states, and to track dynamic transitions at single-cell resolution.
Overall design scRNA-seq (10x Genomics Chromium Single Cell 3’ Solution V2 Chemistry and Drop-seq) of human melanoma cell lines with and without perturbations (SOX10-KD)
Bulk RNA-seq of human melanoma cell lines with and without perturbations (baselines, SOX10/EGR3/NFATC2 knockdown and THZ2 treatment)
ATAC-seq of human melanoma cell lines (untreated).
Contributor(s) Wouters J, Kalender-Atak Z, Christiaens V, Spanier KI, Aerts S
Citation(s) 32753671
Submission date Jul 17, 2019
Last update date Sep 14, 2020
Contact name k spanier
Organization name KU Leuven
Street address Herestraat 49
City Leuven
ZIP/Postal code 3000
Country Belgium
Platforms (4)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (94)
GSM3946506 10x 10 cell lines Baselines
GSM3946507 10x MM074 and MM057 NTC
GSM3946508 10x MM074, MM057 and MM087 SOX10-KD 24h
BioProject PRJNA555083
SRA SRP215051

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
GSE134432_RAW.tar 1.1 Gb (http)(custom) TAR (of BW, TSV)
GSE134432_bulkRNASeq_33MelanomaBaselines_normalized_counts.tsv.gz 4.4 Mb (ftp)(http) TSV
GSE134432_bulkRNASeq_33MelanomaBaselines_raw_counts.tsv.gz 1.2 Mb (ftp)(http) TSV
GSE134432_bulkRNASeq_EGR3_KD_normalized_counts.tsv.gz 464.6 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_EGR3_KD_raw_counts.tsv.gz 318.2 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_NFATC2_KD_normalized_counts.tsv.gz 426.6 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_NFATC2_KD_raw_counts.tsv.gz 330.8 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_SOX10KD_normalized_counts.tsv.gz 1.4 Mb (ftp)(http) TSV
GSE134432_bulkRNASeq_SOX10KD_raw_counts.tsv.gz 511.9 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_TGFb_TNFa_72h_normalized_counts.tsv.gz 915.6 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_TGFb_TNFa_72h_raw_counts.tsv.gz 392.9 Kb (ftp)(http) TSV
GSE134432_bulkRNASeq_THZ2_normalized_counts.tsv.gz 1.8 Mb (ftp)(http) TSV
GSE134432_bulkRNASeq_THZ2_raw_counts.tsv.gz 637.2 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data provided as supplementary file

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