RNAseq and Small-RNAseq dataset to comprehensively study the miRNA expression profiling of drug-resistant melanoma patients and cell lines
Non-coding RNA profiling · human · 29 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Topic
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 29 samples: 5 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- 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 GSE165338_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.
Also filed as BioProject PRJNA694121 and SRA study SRP302890. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 29 samples.
How we read this: 5 replicated groups read from 29 sample titles; they account for 29 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM5031698 A375-BIR_DMSO #Crt_1 A375-BIR_DMSO #Crt
- GSM5031699 A375-BIR_DMSO #Crt_2 A375-BIR_DMSO #Crt
- GSM5031700 A375-BIR_DMSO #Crt_3 A375-BIR_DMSO #Crt
- GSM5031701 A375_BIR_DAB200 #1 A375_BIR_DAB200 #
- GSM5031702 A375_BIR_DAB200 #2 A375_BIR_DAB200 #
- GSM5031703 A375_BIR_DAB200 #3 A375_BIR_DAB200 #
- GSM5031704 A375_DMSO #_Crt_1 A375_DMSO #_Crt
- GSM5031705 A375_DMSO #_Crt_2 A375_DMSO #_Crt
- GSM5031706 A375_DMSO #_Crt_3 A375_DMSO #_Crt
- GSM5031707 A375_DAB200 #1 A375_DAB200 #
- GSM5031708 A375_DAB200 #2 A375_DAB200 #
- GSM5031709 A375_DAB200 #3 A375_DAB200 #
- GSM5031711 PC_SR_1 PC_S
- GSM5031712 PC_SR_3 PC_S
- GSM5031713 PC_SR_4 PC_S
- GSM5031714 PC_SR_6 PC_S
- GSM5031715 PC_SR_5 PC_S
- GSM5031716 PC_SR_9 PC_S
- GSM5031717 PC_SR_11 PC_S
- GSM5031718 PC_SR_12 PC_S
- GSM5031719 PC_SR_14 PC_S
- GSM5031720 PC_SR_13 PC_S
- GSM5031721 PC_SR_17 PC_S
- GSM5031722 PC_SR_18 PC_S
- GSM5031723 PC_SR_19 PC_S
- GSM5031724 PC_SR_20 PC_S
- GSM5031725 PC_SR_21 PC_S
- GSM5031726 PC_SR_22 PC_S
- GSM5031727 PC_SR_23 PC_S
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma, lines
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma, lines
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing · shares lines
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares melanoma
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
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.