PGE2 alters chromatin through H2A.Zvariant enhancer nucleosome modification to promote hematopoietic stem cell fate (RNA-Seq)
RNA-seq (gene expression) · human · 10 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
- 10 samples: 3 × CD34plusDMSO_2h_No vs 3 × CD34plusPGE2_2h_No vs 2 × ASGroups 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
- PGE(2) alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fateProceedings of the National Academy of Sciences of the United States of America · 2023
Read the full summary ↓
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 GSE229398_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 PRJNA954362 and SRA study SRP432051. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 8 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.
- GSM7162827 AS1 AS
- GSM7162828 AS2 AS
- GSM7162829 CD34plus-DMSO_2h
- GSM7162830 CD34plus-PGE2_2h
- GSM7162831 CD34plusDMSO_2h_No20170829 CD34plusDMSO_2h_No
- GSM7162832 CD34plusDMSO_2h_No72 CD34plusDMSO_2h_No
- GSM7162833 CD34plusDMSO_2h_No99 CD34plusDMSO_2h_No
- GSM7162834 CD34plusPGE2_2h_No20170829 CD34plusPGE2_2h_No
- GSM7162835 CD34plusPGE2_2h_No72 CD34plusPGE2_2h_No
- GSM7162836 CD34plusPGE2_2h_No99 CD34plusPGE2_2h_No
- GSE310173 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer 300 samples shares h2a, chromatin
- GSE310165 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ChIPRx-seq) 73 samples shares h2a, chromatin
- GSE310167 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ChIP-seq) 54 samples shares h2a, chromatin
- GSE310144 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ATAC-seq) 16 samples shares h2a, chromatin
- GSE249136 Transcriptional memory is conferred by combined heritable maintenance and local removal of selective chromatin modifications 102 samples shares modification, chromatin
- GSE287825 The METTL3-YTHDC1 axis mediates architectural RNA m6A modification to modulate the integrity of chromatin TADs in MLLr+ AML genome 36 samples shares modification, chromatin
- GSE210848 Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer 32 samples shares modification, chromatin
- GSE193713 Genome-wide maps of chromatin state for histone modifications and chromatin remodeling factors in WT and PHF6-KO conditions in Jurkat T-ALL cells. 20 samples shares modification, chromatin
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.