A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development
RNA-seq (gene expression) · mouse · 20 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
- Mus musculus (mouse)
- Samples
- 20 samples: 20 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
- IκBα controls dormancy in hematopoietic stem cells via retinoic acid during embryonic developmentNature communications · 2024
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 GSE188525_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 PRJNA779261 and SRA study SRP345391. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 20 sample titles: 20 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.
- GSM5684837 LT-HSCs_Ikba_WT_3 [RNA-seq]
- GSM5684838 LT-HSCs_Ikba_Het_2 [RNA-seq]
- GSM5684839 LT-HSCs_Ikba_Het_3 [RNA-seq]
- GSM5684840 LT-HSCs_Ikba_KO_1 [RNA-seq]
- GSM5684841 LT-HSCs_Ikba_KO_2 [RNA-seq]
- GSM5684844 E11.5_Ikba_CD31_1 [Cut&Tag]
- GSM6614373 E14.5_Ikba_LT-HSC_1 [Cut&Tag]
- GSM6614374 Ikba_WT_LT-HSC_H3K27me3_2 [Cut&Tag]
- GSM6614375 Ikba_KO_LT-HSC_H3K27me3_2 [Cut&Tag]
- GSM6614376 Ikba_KO_LT-HSC_H3K27me3_1 [Cut&Tag]
- GSM6614377 Ikba_WT_LT-HSC_H3K27me3_1 [Cut&Tag]
- GSM6614378 Ikba_WT_LT-HSC_H3K27me3_3 [Cut&Tag]
- GSM6614379 Ikba_KO_LT-HSC_H3K27me3_3 [Cut&Tag]
- GSM6614472 IκBα WT, E14.5 LT-HSC Fetal liver, replicate 1, 10x scRNAseq
- GSM6614473 IκBα KO, E14.5 LT-HSC Fetal liver, replicate 1, 10x scRNAseq
- GSM7951673 LT-HSCs_Ikba_Het_1 [RNA-seq]
- GSM7951674 LT-HSCs_Ikba_WT_1 [RNA-seq]
- GSM7951675 LT-HSCs_Ikba_WT_2 [RNA-seq]
- GSM8120337 E11.5_Ikba_CD31_2 [Cut&Tag]
- GSM8120338 E14.5_Ikba_LT-HSC_2 [Cut&Tag]
- GSE278947 An unbiased genomewide screen uncovers 7 genes that drive hematopoietic stem cell fate from mouse embryonic stem cells 16 samples shares hematopoietic, embryonic, stem
- GSE272452 Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition 202 samples shares embryonic, stem
- GSE271800 Diploid embryo complementation of embryonic stem cells efficiently generates a homozygous Gjb2 mutant deaf mouse model 131 samples shares embryonic, stem
- GSE229137 Autophagy engaging and non-engaging hematopoietic stem cells 607 samples shares hematopoietic, stem
- GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic, stem
- GSE202079 Short term perturbation of mouse embryonic stem cells with morphogens and small molecule compounds 208 samples shares embryonic, stem
- GSE285231 Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells 186 samples shares embryonic, stem
- GSE252199 Quantification of subcellular mRNA kinetics in mouse embryonic stem cells 100 samples shares embryonic, stem
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.