|
| 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.
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| |
|
| 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).
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| |
|
| 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 |
| |
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| Platforms (4)
|
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (94)
|
|
| Relations |
| BioProject |
PRJNA555083 |
| SRA |
SRP215051 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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