GEO series

Effect of MITF depletion on gene expression in U2OS cells

GSE264653 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/04/23 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 6 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.

Summary (written by the submitters)

Summary (abstract): The transcriptional factor MITF is a central regulator of melanocytes and plays an important role in melanoma. In melanocytes MITF regulates the transcription of large number of genes with approximately 500 genes as validated targets. Functionally, MITF target genes are quite diverse including genes involved in pigmentation, DNA damage response, mitotic regulation, and DNA replication.

Read the full summary ↓

Considering the transcriptional regulation of genes involved in non-melanocyte specific processes and the fact that MITF is expressed across tissue types, raises the question of whether the role of MITF outside the melanocyte lineage might be underestimated. Our data shows that in the osteosarcoma cell line, significant number of genes involved in DNA replication, DNA repair and mitotic regulation are downregulated upon MITF depletion, suggesting that the protein might be vital to maintain genome stability in the cell line.

This dataset

Open GSE264653 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 GSE264653_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: 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 PRJNA1103746 and SRA study SRP503565. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

U2OS, siControl, 1h, ×3 U2OS, siControl, 4h, ×3 U2OS, si Control, UT, ×3 U2OS, siMITF, 1h, ×3 U2OS, siMITF, 4h, ×3 U2OS, siMITF, UT, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8224566 U2OS, siControl, 1h, rep1 U2OS, siControl, 1h,
GSM8224567 U2OS, siControl, 4h, rep1 U2OS, siControl, 4h,
GSM8224568 U2OS, si Control, UT, rep1 U2OS, si Control, UT,
GSM8224569 U2OS, siMITF, 1h, rep1 U2OS, siMITF, 1h,
GSM8224570 U2OS, siMITF, 4h, rep1 U2OS, siMITF, 4h,
GSM8224571 U2OS, siMITF, UT, rep1 U2OS, siMITF, UT,
GSM8224572 U2OS, siControl, 1h, rep2 U2OS, siControl, 1h,
GSM8224573 U2OS, siControl, 4h, rep2 U2OS, siControl, 4h,
GSM8224574 U2OS, si Control, UT, rep2 U2OS, si Control, UT,
GSM8224575 U2OS, siMITF, 1h, rep2 U2OS, siMITF, 1h,
GSM8224576 U2OS, siMITF, 4h, rep2 U2OS, siMITF, 4h,
GSM8224577 U2OS, siMITF, UT, rep2 U2OS, siMITF, UT,
GSM8224578 U2OS, siControl, 1h, rep3 U2OS, siControl, 1h,
GSM8224579 U2OS, siControl, 4h, rep3 U2OS, siControl, 4h,
GSM8224580 U2OS, si Control, UT, rep3 U2OS, si Control, UT,
GSM8224581 U2OS, siMITF, 1h, rep3 U2OS, siMITF, 1h,
GSM8224582 U2OS, siMITF, 4h, rep3 U2OS, siMITF, 4h,
GSM8224583 U2OS, siMITF, UT, rep3 U2OS, siMITF, UT,

Datasets on a similar topic

GSE250492 Effect of over expression of MED13 IDR in human osteosarcoma U2OS cell line 6 samples shares u2os
GSE283855 Direct Targeting of the Oncogene Microphthalmia-Associated Transcription Factor (MITF) by Fragment-Based Discovery [RNA-seq] 42 samples shares mitf
GSE280432 RNA sequencing of non-targetting ASOs on HEK293 and U2OS cells 36 samples shares u2os
GSE223513 QuantSeq from Nutlin-3a-treated MCF-7, U2OS, and RPE-1 cells 20 samples shares u2os
GSE223512 CAGE-seq from Nutlin-3a-treated MCF-7, U2OS, and RPE-1 cells 20 samples shares u2os
GSE224502 RNA-Seq profiles of pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells with Pin1 knocking down 18 samples shares u2os
GSE342354 Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout 12 samples shares u2os
GSE255256 Transcriptomics profiling of the effect of inducible knock-down of the melanocyte inducing transcription factor (MITF) in melanoma cell lines 12 samples shares mitf

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