Landscape of TFs binding in mouse early embryos [RNA-seq]
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: 5 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.
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 GSE212567_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 PRJNA875960 and SRA study SRP395281. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 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.
- GSM6537765 8Cell_Arpc1bE_CdxE1_KO_rep1 8Cell_Arpc1bE_CdxE1_KO
- GSM6537766 8Cell_Arpc1bE_CdxE1_KO_rep2 8Cell_Arpc1bE_CdxE1_KO
- GSM6537767 8Cell_CdxE2_KO_rep1 8Cell_CdxE2_KO
- GSM6537768 8Cell_CdxE2_KO_rep2 8Cell_CdxE2_KO
- GSM6537769 8Cell_Ctrl_rep1 8Cell_Ctrl
- GSM6537770 8Cell_Ctrl_rep2 8Cell_Ctrl
- GSM6537771 8Cell_siKlf5_rep1 8Cell_siKlf5
- GSM6537772 8Cell_siKlf5_rep2 8Cell_siKlf5
- GSM6537773 8Cell_siTfap2c_rep1 8Cell_siTfap2c
- GSM6537774 8Cell_siTfap2c_rep2 8Cell_siTfap2c
- GSE330728 Single-nucleus RNA-seq atlas of 17 ASD-risk mouse lines under early-postnatal fluoxetine or lithium exposure (4-plex On-Chip Multiplexed) 53 samples shares rna-seq, early
- GSE297298 Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer 18 samples shares rna-seq, early
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares rna-seq, early
- GSE314859 The degradation of maternal RNA-binding protein 4E-T regulates translational activation to ensure maternal-to-zygotic transition in mouse embryos 67 samples shares binding, embryos
- GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares embryos, early
- GSE222656 RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited 40 samples shares embryos, rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares 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.