GEO series

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (RNA-Seq)

GSE256466 Homo sapiens (human) Single-cell RNA-seq 69 samples Submitted 2024/04/24 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 69 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 69 samples: 21 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: DrugMap: A quantitative pan-cancer analysis of cysteine ligandabilityCell · 2024

Summary (written by the submitters)

SOX10 is a lineage-restricted transcription factor important for melanoma proliferation and survival. Our data demonstrate that SOX10 genetic depletion by CRISPR/Cas9 significantly impaired melanoma proliferation. We chose 7 different melanoma, all of which exhibited growth dependency on SOX10 with different levels. To define the SOX10 transcriptional signature shared with different SOX10-dependent melanoma, we performed bulk RNA-seq on 7 melanoma transfected with siSOX10 or siControl.

Read the full summary ↓

Each melanoma cell line was plated and transfected with each siRNA to deplete SOX10 protein expression. After 72 hrs, cells were lysed with Buffer TCL(QIAGEN) supplemented with 2-ME and stored at -80C until use. Libraries from each cell line were made with the modified Smart-seq2 protocol. Each replicate was uniquely barcoded and all the samples were pooled for sequencing. (2) We developed a chemical probe (SH-0029) that covalently engages SOX10. To examine the effect of SH-0029 on SOX10 target genes, SOX10-dependent SKMEL5 melanoma were plated and treated with SH-0029, SH-0105 (a control probe), or DMSO(vehicle) for 48h. Total RNA was extracted with NucleoSpin RNA extraction kit (MACHEREY-NAGEL) and mRNA was subsequently purified with poly dT-attached magnetic beads. We found that downregulated genes induced by SH-0029 treatment strongly overlapped with those by SOX10 genetic depletion, suggesting that SOX10 covalent ligand controls SOX10 transcriptional network.

Published in

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

Takahashi M, Chong HB, Zhang S et al. · Cell 2024 · PMID 38653237 · doi:10.1016/j.cell.2024.03.027

This dataset

Open GSE256466 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE256466_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1079745 and SRA study SRP491378. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38653237) ↗

Study design

21 conditions, mostly in triplicate

C_13_F10 ×6 C_16_H03 ×6 SK_MEL2_siSOX10_B ×3 SK_MEL28_siSOX10_C ×3 U257_siSOX10_E ×3 I_DMSO ×3 I_13_F10 ×3 I_16_H03 ×3 +22 more

Supports a between-group comparison across 60 samples.

How we read this: 21 replicated groups read from 69 sample titles; they account for 60 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.

Samples in this study

GSM8098898 HMCB_siControl_F10
GSM8098899 HMCB_siControl_G10
GSM8098900 HMCB_siControl_H10
GSM8098901 HMCB_siSOX10_C10
GSM8098902 HMCB_siSOX10_D10
GSM8098903 HMCB_siSOX10_E10
GSM8098904 Mewo_siControl_A01 Mewo_siControl_A
GSM8098905 Mewo_siControl_A03 Mewo_siControl_A
GSM8098906 Mewo_siSOX10_A05 Mewo_siSOX10_A
GSM8098907 Mewo_siSOX10_A06 Mewo_siSOX10_A
GSM8098908 SK_MEL2_siControl_B01 SK_MEL2_siControl_B
GSM8098909 SK_MEL2_siControl_B03 SK_MEL2_siControl_B
GSM8098910 SK_MEL2_siSOX10_B04 SK_MEL2_siSOX10_B
GSM8098911 SK_MEL2_siSOX10_B05 SK_MEL2_siSOX10_B
GSM8098912 SK_MEL2_siSOX10_B06 SK_MEL2_siSOX10_B
GSM8098913 SK_MEL5_siControl_D01 SK_MEL5_siControl_D
GSM8098914 SK_MEL5_siControl_D03 SK_MEL5_siControl_D
GSM8098915 SK_MEL5_siSOX10_D04 SK_MEL5_siSOX10_D
GSM8098916 SK_MEL5_siSOX10_D05 SK_MEL5_siSOX10_D
GSM8098917 SK_MEL28_siControl_C01 SK_MEL28_siControl_C
GSM8098918 SK_MEL28_siControl_C03 SK_MEL28_siControl_C
GSM8098919 SK_MEL28_siSOX10_C04 SK_MEL28_siSOX10_C
GSM8098920 SK_MEL28_siSOX10_C05 SK_MEL28_siSOX10_C
GSM8098921 SK_MEL28_siSOX10_C06 SK_MEL28_siSOX10_C
GSM8098922 U62_siControl_H01 U62_siControl_H
GSM8098923 U62_siControl_H03 U62_siControl_H
GSM8098924 U62_siSOX10_H04 U62_siSOX10_H
GSM8098925 U62_siSOX10_H06 U62_siSOX10_H
GSM8098926 U257_siControl_E01 U257_siControl_E
GSM8098927 U257_siControl_E03 U257_siControl_E
GSM8098928 U257_siSOX10_E04 U257_siSOX10_E
GSM8098929 U257_siSOX10_E05 U257_siSOX10_E
GSM8098930 U257_siSOX10_E06 U257_siSOX10_E
GSM8098931 C_DMSO_10_1
GSM8098932 C_DMSO_11_1
GSM8098933 C_DMSO_12_1
GSM8098934 C_13_F10_16 C_13_F10
GSM8098935 C_13_F10_17 C_13_F10
GSM8098936 C_13_F10_18 C_13_F10
GSM8098937 C_16_H03_13 C_16_H03

+ 29 more — browse all 69 samples with per-sample file links →

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