Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]
Single-cell RNA-seq · mouse · 2 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 2 samples
- 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
- Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endodermbioRxiv : the preprint server for biology · 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 GSE254428_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1070557 and SRA study SRP486460. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 2 more — browse all 2 samples with per-sample file links →
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares otx2, specification, remodeling, patterning, definitive, mammalian, endoderm
- GSE269347 Daunorubicin-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ prolifeating T cells [scRNA-Seq] 16 samples shares remodeling, scrna-seq
- GSE229129 Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion 13 samples shares specification, mammalian
- GSE267192 PPARγ-dependent Remodeling of Translational Machinery in Adipose Progenitors is Impaired in Obesity [scRNA-seq] 12 samples shares remodeling, scrna-seq
- GSE272849 EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling 119 samples shares remodeling, endoderm
- GSE306026 Dosage-dependent role of Gata3 in primitive endoderm and trophectoderm specification in embryonic stem cells 22 samples shares specification, endoderm
- GSE288730 Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging 21 samples shares remodeling, mammalian
- GSE289298 OTX2 controls chromatin accessibility to direct somatic versus germline differentiation [ATAC-Seq] 32 samples shares otx2
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.