RNA-seq of human THP-1 macrophages infected with adherent-invasive E. coli (AIEC) strains
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: 6 conditions, mostly in duplicateGroups 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
- Persistence mechanisms of Crohn's disease-associated adherent invasive Escherichia coli within macrophagesGut microbes · 2025
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 GSE307944_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 PRJNA1327855 and SRA study SRP619761. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9234432 LF82_rep_1 LF82
- GSM9234433 LF82_rep_2 LF82
- GSM9234434 CEA224S_rep_1 CEA224S
- GSM9234435 CEA224S_rep_2 CEA224S
- GSM9234436 CEA601S_rep_1 CEA601S
- GSM9234437 CEA601S_rep_2 CEA601S
- GSM9234438 CEA212U_rep_1 CEA212U
- GSM9234439 CEA212U_rep_2 CEA212U
- GSM9234440 CEA106S_rep_1 CEA106S
- GSM9234441 CEA106S_rep_2 CEA106S
- GSM9234442 Non-infected_rep_1 Non-infected
- GSM9234443 Non-infected_rep_2 Non-infected
- GSE328953 Transcriptomics of THP-1-derived macrophages infected with mycobacteria 15 samples shares thp-1, macrophages, infected
- GSE305300 Human memory CD4+ T cells recognize Mycobacterium tuberculosis-infected macrophages amid broader pathogen-specific responses [scRNA-seq] 36 samples shares macrophages, infected, rna-seq
- GSE313992 Comparative Immunotoxicity and Transcriptomic Profiling of Seven PFAS in THP-1 Macrophages 252 samples shares thp-1, macrophages
- GSE327840 RNA-seq profiling of LPS tolerance in monocytes, THP-1, fibroblasts, smooth muscle cells, and endothelial cells 58 samples shares thp-1, rna-seq
- GSE315572 RXR binding pattern in human PMA-differentiated THP-1 cells upon ligand stimulation [RNA-seq] 9 samples shares thp-1, rna-seq
- GSE281471 Targeting CD206+ macrophages disrupts the establishment of a key anti-tumor immune axis [Bulk RNA-seq] 243 samples shares macrophages, rna-seq
- GSE269009 RNA-seq of monocyte derived macrophages and dendritic cells in a Peruvian Tuberculosis cohort 227 samples shares macrophages, rna-seq
- GSE272019 Opposing Regulation of TNF Responses and IL-1b+ Macrophages by PGE2-cAMP Signaling and IFN-g [RNA-seq] 48 samples shares macrophages, rna-seq
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.