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GSE245585 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/09/01 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 8 conditions, mostly in duplicateGroups 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
Monoallelic loss of RB1 enhances osteogenic differentiation and delays DNA repair without inducing tumorigenicityDifferentiation; research in biological diversity · 2024
Summary (written by the submitters)
The RB1 gene plays a pivotal role in the process of osteogenic differentiation.To gain insights into this role, we conducted high-throughput RNA sequencing during the invitro osteogenesis of patient-derived heterozygous RB mutant and wildtype. Our analysis involved stage-specific differential gene expression analysis and a comprehensive time series analysis of both wild-type and RB mutant cells during the osteogenic differentiation process.
Read the full summary ↓
The findings from our study indicate that the deficiency in RB1 results in significant disruptions in cellular functions, primarily mediated by E2F1. Our results suggest compelling role for RB1 in osteogenic differentiation with its loss leading to an immature phenotype, potentially compromising the osteogenic differentiation process which might subsequently contribute to tumorigenesis.
Published in
Monoallelic loss of RB1 enhances osteogenic differentiation and delays DNA repair without inducing tumorigenicity
Vincent A, Krishnakumar S, Parameswaran S · Differentiation; research in biological diversity 2024 · PMID 39342657 · doi:10.1016/j.diff.2024.100815
This dataset
Open GSE245585 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 GSE245585_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 PRJNA1029027 and SRA study SRP466821. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39342657) ↗
Study design
8 conditions, mostly in duplicate
WT1_D0 ×2 WT1_D7 ×2 WT1_D14 ×2 WT1_D21 ×2 MT1_D0 ×2 MT1_D7 ×2 MT1_D14 ×2 MT1_D21 ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
Datasets on a similar topic

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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.