Transcriptomic profiling of A375 and PC9 cells following knockdown of the VCX gene family
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × PC9-NC vs 3 × PC9-KD vs 3 × A375-NC vs 3 × A375-KDGroups 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.
Read the full summary ↓
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 GSE293413_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 PRJNA1244386 and SRA study SRP575472. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8881807 PC9-NC-1 PC9-NC
- GSM8881808 PC9-NC-2 PC9-NC
- GSM8881809 PC9-NC-3 PC9-NC
- GSM8881810 PC9-KD-1 PC9-KD
- GSM8881811 PC9-KD-2 PC9-KD
- GSM8881812 PC9-KD-3 PC9-KD
- GSM8881813 A375-NC-1 A375-NC
- GSM8881814 A375-NC-2 A375-NC
- GSM8881815 A375-NC-3 A375-NC
- GSM8881816 A375-KD-1 A375-KD
- GSM8881817 A375-KD-2 A375-KD
- GSM8881818 A375-KD-3 A375-KD
- GSE247684 Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: A375_PC9] 6 samples shares a375, pc9
- GSE328454 Gene expression profiling of A498 clear cell renal cell carcinoma cells following HIF1A and HIF2A knockdown 12 samples shares following, knockdown
- GSE324459 RNA sequencing analysis of A498 renal cancer cells following knockdown of ELOVL2 and ELOVL5 12 samples shares following, knockdown
- GSE336727 RB and KDM5A CUT&RUN profiling in MCF7 cells following KDM5A knockdown and abemaciclib treatment 12 samples shares following, knockdown
- GSE285131 Comparative gene expression profiling of parental A375 melanoma cells and a panel of spontaneously vemurafenib-resistant derivative cell lines 33 samples shares a375
- GSE319449 RNA-seq profiling of SOX10 overexpression in TADA2B KO A375 melanoma cells 18 samples shares a375
- GSE285537 The response of Melanoma cell line A375 to cytotoxic T lyphocyte killing after serum starvation and MKL1 overexpression 15 samples shares a375
- GSE255437 Analysis of A375 and SKMEL-103 cells after treatment with with DMSO as control or BAY-850 12 samples shares a375
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.