Transcriptomic profile of melanoma clinical samples treated with BRAF and MEK- inhibitors
RNA-seq (gene expression) · human · 17 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 17 samples
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Integrated Genomics Identifies miR-181/TFAM Pathway as a Critical Driver of Drug Resistance in MelanomaInternational journal of molecular sciences · 2021
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE165337_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA694125 and SRA study SRP302890. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run PC_SR_1 … PC_SR_23 and carry no group information.
- GSM5031711 PC_SR_1
- GSM5031712 PC_SR_3
- GSM5031713 PC_SR_4
- GSM5031714 PC_SR_6
- GSM5031715 PC_SR_5
- GSM5031716 PC_SR_9
- GSM5031717 PC_SR_11
- GSM5031718 PC_SR_12
- GSM5031719 PC_SR_14
- GSM5031720 PC_SR_13
- GSM5031721 PC_SR_17
- GSM5031722 PC_SR_18
- GSM5031723 PC_SR_19
- GSM5031724 PC_SR_20
- GSM5031725 PC_SR_21
- GSM5031726 PC_SR_22
- GSM5031727 PC_SR_23
- GSE275078 In vitro drug screening of RAF/MEK/ERK Inhibitors in combination with Autophagy inhibition in the context of two PDA Cell Lines 136 samples shares mek, inhibitors
- GSE277629 RNA-seq of AsPC-1 cell line-derived xenograft mouse tumors treated with a MEK-RAF molecular glue, IK-595 24 samples shares mek, treated
- GSE268982 Synthetic RIG-I agonist-mediated cancer immunotherapy synergizes with MAP-Kinase inhibition against BRAF mutated melanoma 15 samples shares braf, melanoma
- GSE252781 Temporal dynamics of signaling and transcription underlying early adaptation to oncogenic BRAF inhibition in melanoma 13 samples shares braf, melanoma
- GSE329903 RNA-seq studies in dabrafenib treated endothelial cells 12 samples shares braf, treated
- GSE272460 Transcriptome analysis of pancreatic progenitor organoids (POs) carrying PDAC related mutations, treated with ERK inhibitors and depleted of AP-1 factors 40 samples shares inhibitors, treated
- GSE319664 RNA-seq analysis of tumors derived from a xenograft model treated with the KDM5B inhibitors JB-157 or JB-161. 29 samples shares inhibitors, treated
- GSE217707 Single-cell sequencing analysis reveals the tissue architecture and empowers clinical trial in advanced conjunctival melanoma 10 samples shares melanoma, clinical
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.