CRISPR screens unveil nutrient-dependent lysosomal and mitochondrial nodes impacting intestinal tissue-resident memory CD8+ T cell formation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 108 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 108 samples: 26 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
- Paper
- CRISPR screens unveil nutrient-dependent lysosomal and mitochondrial nodes impacting intestinal tissue-resident memory CD8(+) T cell formationImmunity · 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 GSE231502_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA966158 and SRA study SRP435584. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 100 samples.
How we read this: 26 replicated groups read from 108 sample titles; they account for 100 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.
- GSM7265386 Arg_cntl1 Arg_cntl
- GSM7265387 Arg_cntl2 Arg_cntl
- GSM7265388 Arg_cntl3 Arg_cntl
- GSM7265389 Arg_cntl_plus_TGFb1 Arg_cntl_plus_TGFb
- GSM7265390 Arg_cntl_plus_TGFb2 Arg_cntl_plus_TGFb
- GSM7265391 Arg_cntl_plus_TGFb3 Arg_cntl_plus_TGFb
- GSM7265392 Arg_free1 Arg_free
- GSM7265393 Arg_free2 Arg_free
- GSM7265394 Arg_free3 Arg_free
- GSM7265395 Arg_free4 Arg_free
- GSM7265396 Arg_free_plus_TGFb1 Arg_free_plus_TGFb
- GSM7265397 Arg_free_plus_TGFb2 Arg_free_plus_TGFb
- GSM7265398 Arg_free_plus_TGFb3 Arg_free_plus_TGFb
- GSM7265399 Arg_free_plus_TGFb4 Arg_free_plus_TGFb
- GSM7286745 RNA-Seq S1_sgNTC_day4.5
- GSM7286746 RNA-Seq S2_sgFlcn_day4.5
- GSM7286747 RNA-Seq S3_sgNTC_day4.5
- GSM7286748 RNA-Seq S4_sgFlcn_day4.5
- GSM7286749 RNA-Seq S5_sgNTC_day7.5
- GSM7286750 RNA-Seq S6_sgFlcn_day7.5
- GSM7286751 RNA-Seq S7_sgNTC_day7.5
- GSM7286752 RNA-Seq S8_sgFlcn_day7.5
- GSM7286754 ATAC-Seq siIEL_Control1 ATAC-Seq siIEL_Control
- GSM7286755 ATAC-Seq siIEL_FlcnKO1 ATAC-Seq siIEL_FlcnKO
- GSM7286756 ATAC-Seq siIEL_Control2 ATAC-Seq siIEL_Control
- GSM7286757 ATAC-Seq siIEL_FlcnKO2 ATAC-Seq siIEL_FlcnKO
- GSM7286758 ATAC-Seq siIEL_Control3 ATAC-Seq siIEL_Control
- GSM7286759 ATAC-Seq siIEL_FlcnKO3 ATAC-Seq siIEL_FlcnKO
- GSM7286760 ATAC-Seq siIEL_Control4 ATAC-Seq siIEL_Control
- GSM7286761 ATAC-Seq siIEL_FlcnKO4 ATAC-Seq siIEL_FlcnKO
- GSM7286762 ATAC-Seq siIEL_Control5 ATAC-Seq siIEL_Control
- GSM7286763 ATAC-Seq siIEL_FlcnKO5 ATAC-Seq siIEL_FlcnKO
- GSM7286764 ATAC-Seq spleen_Control1 ATAC-Seq spleen_Control
- GSM7286765 ATAC-Seq spleen_FlcnKO1 ATAC-Seq spleen_FlcnKO
- GSM7286766 ATAC-Seq spleen_Control2 ATAC-Seq spleen_Control
- GSM7286767 ATAC-Seq spleen_FlcnKO2 ATAC-Seq spleen_FlcnKO
- GSM7286768 ATAC-Seq spleen_Control3 ATAC-Seq spleen_Control
- GSM7286769 ATAC-Seq spleen_FlcnKO3 ATAC-Seq spleen_FlcnKO
- GSM7286770 ATAC-Seq spleen_Control4 ATAC-Seq spleen_Control
- GSM7286771 ATAC-Seq spleen_FlcnKO4 ATAC-Seq spleen_FlcnKO
+ 68 more — browse all 108 samples with per-sample file links →
- GSE334845 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors [RNA-Seq] 86 samples shares crispr, cd8
- GSE334890 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors 48 samples shares crispr, cd8
- GSE306058 scCRISPR screens of CD8⁺ T cells in young vs. aged tumors and tdLNs 11 samples shares crispr, cd8
- GSE296763 Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate 99 samples shares cd8, mitochondrial
- GSE272357 Transcriptional response of BMDMs to CRISPR KO of key lysosomal genes [HEX000527] 69 samples shares crispr, lysosomal
- GSE341988 Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis 8 samples shares cd8, tissue-resident
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares tissue-resident, mitochondrial
- GSE263763 Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation 175 samples shares crispr
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.