Transcriptional remodeling of human hematopoeitic stem cells in vitro by Interleukin-1β
RNA-seq (gene expression) · human · 12 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
- 12 samples: 12 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
- Interleukin-1β induces trained innate immunity in human hematopoietic progenitor cells in vitroStem cell reports · 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 GSE253764_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 PRJNA1066945 and SRA study SRP484834. 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 12 sample titles: 12 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.
- GSM8027625 Donor_1_uns_IMDM
- GSM8027626 Donor_1_uns_IL1
- GSM8027627 Donor_1_LPS_IMDM
- GSM8027628 Donor_1_LPS_IL1
- GSM8027629 Donor_2_uns_IMDM
- GSM8027630 Donor_2_uns_IL1
- GSM8027631 Donor_2_LPS_IMDM
- GSM8027632 Donor_2_LPS_IL1
- GSM8027633 Donor_3_uns_IMDM
- GSM8027634 Donor_3_uns_IL1
- GSM8027635 Donor_3_LPS_IMDM
- GSM8027636 Donor_3_LPS_IL1
- GSE261731 Gene expression profile of in-vitro differentiated Dendritic Cells (DCs) from induced pluripotent stem cell (iPSC) and cord blood sources 19 samples shares vitro, stem
- GSE313528 Development of a human induced pluripotent stem cell-derived ovarian support cell clinical grade product for in vitro fertilization 13 samples shares vitro, stem
- GSE241130 In Vitro Mesenchymal Stem Cell Differentiation Landscape 27 samples shares vitro, stem
- GSE262097 Remodeling of Histone 3 Lysine 18 lactylation (H3K18lac) in monocytes-to-macrophage differentiation and induction of Trained Immunity by BCG in vitro 37 samples shares remodeling, vitro
- GSE305135 Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Cells in vitro Basic Characterisation Bulk RNA-seq Dataset 45 samples shares vitro
- GSE288064 RNA sequencing of HUVEC, HCMEC and human primary skeletal muscle cells in response to in vitro mechanical loading 36 samples shares vitro
- GSE287078 Time- and Dose-Dependent Effects of Irradiation on Endothelial and Tumor Endothelial Cells: Transcriptional, Molecular, and Functional Changes Driving Activation In Vitro and In Vivo 30 samples shares vitro
- GSE327707 Sorted bulk RNA-seq profiling of human peripheral blood mononuclear cell populations across diverse in vitro immune stimuli 150 samples shares vitro
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.