Role of ATF4 in regulation of kidney gene expressions, signaling pathways and functions
RNA-seq (gene expression) · human · 23 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
- 23 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.
- Paper
- Deletion of the transcription factor ATF4 in a model of clear cell renal cell carcinomaNeoplasia (New York, N.Y.) · 2025
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 GSE291049_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 PRJNA1231456 and SRA study SRP567824. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 23 samples.
How we read this: 6 replicated groups read from 23 sample titles; they account for 23 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.
- GSM8828019 WT_1 WT
- GSM8828020 WT_2 WT
- GSM8828021 WT_3 WT
- GSM8828022 WT_4 WT
- GSM8828023 WT_5 WT
- GSM8828024 GCERAd_1 GCERAd
- GSM8828025 GCERAd_2 GCERAd
- GSM8828026 GCERAd_3 GCERAd
- GSM8828027 GCERAd_4 GCERAd
- GSM8828028 GCERAd_5 GCERAd
- GSM8828029 TRACK_1 TRACK
- GSM8828030 TRACK_2 TRACK
- GSM8828031 TRACK_3 TRACK
- GSM8828032 GCERAdT_1 GCERAdT
- GSM8828033 GCERAdT_2 GCERAdT
- GSM8828034 GCERAdT_3 GCERAdT
- GSM8828035 GCERAdT_4 GCERAdT
- GSM8828036 RCC4P_1 RCC4P
- GSM8828037 RCC4P_2 RCC4P
- GSM8828038 RCC4P_3 RCC4P
- GSM8828039 RCC4A_1 RCC4A
- GSM8828040 RCC4A_2 RCC4A
- GSM8828041 RCC4A_3 RCC4A
- GSE241047 PRDM16 deficiency triggered by TGF-β1 signaling promotes aberrant mitochondrial homeostasis and kidney fibrosis 11 samples shares kidney
- GSE25965 Transduction signaling signature of Wilms tumor revealed by parallel analysis of kidney differentiation 78 samples shares kidney
- GSE324329 A kidney-protective mechanism via cellular oxidative stress reduction induced by CD5L protein 38 samples shares kidney
- GSE315101 Soluble DLK1 secreted by telomere-shortening-induced senescent microglia impairs oligodendrocyte functions and alters neuronal activity [DLK1_snRNA-seq] 27 samples shares functions
- GSE284715 Injured epithelial cell states impact kidney allograft survival after T-cell-mediated rejection 14 samples shares kidney
- GSE291551 Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas 11 samples shares kidney
- GSE51334 DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions 993 samples shares functions
- GSE290623 Opposing functions of distinct regulatory T cell subsets in colorectal cancer 142 samples shares functions
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.