RNA sequencing data of intestinal tissue from wild-type C57BL/6 mice and ITGB6-overexpressing transgenic mice
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 10 samples: 3 × WT_WT vs 3 × TG_WT vs 2 × WT_DSS vs 2 × TG_DSSGroups 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.
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 GSE188361_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 PRJNA778535 and SRA study SRP344940. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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.
- GSM5678234 WT_WTR1 WT_WT
- GSM5678235 WT_WTR2 WT_WT
- GSM5678236 WT_WTR3 WT_WT
- GSM5678237 TG_WTR1 TG_WT
- GSM5678238 TG_WTR2 TG_WT
- GSM5678239 TG_WTR3 TG_WT
- GSM5678240 WT_DSS1 WT_DSS
- GSM5678241 WT_DSS2 WT_DSS
- GSM5678242 TG_DSS1 TG_DSS
- GSM5678243 TG_DSS2 TG_DSS
- GSE302019 Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS. 24 samples shares c57bl, wild-type
- GSE276797 Gene expression profile at single cell level of immune cells from the deep cervical lymph nodes (dCLNs), superficial cervical lymph nodes (sCLNs), and inguinal lymph nodes (iLNs) of wild-type (WT) and Alzheimer's disease (AD) transgenic animals (5xFAD) 34 samples shares transgenic, wild-type
- GSE228455 Gene expression profile at single cell level of monocytes sorted from C57BL/6J mouse ear tissue at 3 weeks post Leishmania major infection [scRNA-seq] 218 samples shares c57bl
- GSE226609 Mouse lung tissue RNA-Seq from C57Bl6 wild type and ALOX15 KO mice with and without house dust mite (HDM) exposure. 20 samples shares c57bl
- GSE246154 Single-nucleus RNA-sequencing (snRNA-Seq) of brain cells from tumor-bearing C57BL/6 mice 19 samples shares c57bl
- GSE228456 Cell-intrinsic effect of IL-7R signaling of monocytes within C57BL/6J mouse ears infected with Leishmania major [bulk RNA-seq] 87 samples shares c57bl
- GSE263132 Naïve CD8 T cell RNA sequencing in C57BL/6 and MD4 mice 10 samples shares c57bl
- GSE274825 RNA sequencing of MC38 tumor cells from control-diet- and high-fat-diet-fed C57BL/6J mice 10 samples shares c57bl
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.