GEO series

Temporal regulation of gene expression through integration of dynamics and modifications

GSE256300 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2024/10/05 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 40 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: 40 samples: 40 samples, each with a distinct title — no replicated groupsGroups 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: Temporal regulation of gene expression through integration of p53 dynamics and modificationsScience advances · 2024

Summary (written by the submitters)

The master regulator of the DNA damage response, the transcription factor p53, orchestrates multiple downstream responses and coordinates repair processes. In response to double-strand DNA breaks, p53 exhibits pulses of expression, but how it achieves temporal coordination of downstream responses remains unclear. Here, we show that p53's post-translational modification state is altered between its first and second pulses of expression.

Read the full summary ↓

We show that acetylations at two sites, K373 and K382, reduced in the second pulse and these acetylations differentially affected p53 target genes, resulting in changes in gene expression programs over time. This interplay between dynamics and modification may offer a strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells.

Published in

Temporal regulation of gene expression through integration of p53 dynamics and modifications

Lu D, Faizi M, Drown B et al. · Science advances 2024 · PMID 39454005 · doi:10.1126/sciadv.adp2229

This dataset

Open GSE256300 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 GSE256300_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 PRJNA1078898 and SRA study SRP490882. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39454005) ↗

Study design

40 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 40 sample titles: 40 distinct titles with little repetition. 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

GSM8093293 MCF7, WT, 0h, Rep 1 [WT0A_S1]
GSM8093294 MCF7, WT, 1h, Rep 1 [WT1A_S2]
GSM8093295 MCF7, WT, 2h, Rep 1 [WT2A_S3]
GSM8093296 MCF7, WT, 3h, Rep 1 [WT3A_S4]
GSM8093297 MCF7, WT, 4h, Rep 1 [WT4A_S5]
GSM8093298 MCF7, WT, 5h, Rep 1 [WT5A_S6]
GSM8093299 MCF7, WT, 6h, Rep 1 [WT6A_S7]
GSM8093300 MCF7, WT, 7h, Rep 1 [WT7A_S8]
GSM8093301 MCF7, WT, 8h, Rep 1 [WT8A_S9]
GSM8093302 MCF7, WT, 9h, Rep 1 [WT9A_S10]
GSM8093303 MCF7, 2KR, 0h, Rep 1 [2R0A_S31]
GSM8093304 MCF7, 2KR, 1h, Rep 1 [2R1A_S32]
GSM8093305 MCF7, 2KR, 2h, Rep 1 [2R2A_S33]
GSM8093306 MCF7, 2KR, 3h, Rep 1 [2R3A_S34]
GSM8093307 MCF7, 2KR, 4h, Rep 1 [2R4A_S35]
GSM8093308 MCF7, 2KR, 5h, Rep 1 [2R5A_S36]
GSM8093309 MCF7, 2KR, 6h, Rep 1 [2R6A_S37]
GSM8093310 MCF7, 2KR, 7h, Rep 1 [2R7A_S38]
GSM8093311 MCF7, 2KR, 8h, Rep 1 [2R8A_S39]
GSM8093312 MCF7, 2KR, 9h, Rep 1 [2R9A_S40]
GSM8093313 MCF7, WT, 0h, Rep 2 [WT0B_S16]
GSM8093314 MCF7, WT, 1h, Rep 2 [WT1B_S17]
GSM8093315 MCF7, WT, 2h, Rep 2 [WT2B_S18]
GSM8093316 MCF7, WT, 3h, Rep 2 [WT3B_S19]
GSM8093317 MCF7, WT, 4h, Rep 2 [WT4B_S20]
GSM8093318 MCF7, WT, 5h, Rep 2 [WT5B_S21]
GSM8093319 MCF7, WT, 6h, Rep 2 [WT6B_S22]
GSM8093320 MCF7, WT, 7h, Rep 2 [WT7B_S23]
GSM8093321 MCF7, WT, 8h, Rep 2 [WT8B_S24]
GSM8093322 MCF7, WT, 9h, Rep 2 [WT9B_S25]
GSM8093323 MCF7, 2KR, 0h, Rep 2 [2R0B_S46]
GSM8093324 MCF7, 2KR, 1h, Rep 2 [2R1B_S47]
GSM8093325 MCF7, 2KR, 2h, Rep 2 [2R2B_S48]
GSM8093326 MCF7, 2KR, 3h, Rep 2 [2R3B_S49]
GSM8093327 MCF7, 2KR, 4h, Rep 2 [2R4B_S50]
GSM8093328 MCF7, 2KR, 5h, Rep 2 [2R5B_S51]
GSM8093329 MCF7, 2KR, 6h, Rep 2 [2R6B_S52]
GSM8093330 MCF7, 2KR, 7h, Rep 2 [2R7B_S53]
GSM8093331 MCF7, 2KR, 8h, Rep 2 [2R8B_S54]
GSM8093332 MCF7, 2KR, 9h, Rep 2 [2R9B_S55]

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