RNase H1-dependent R-loop Clearance is a Prerequisite for Genome Silencing in Mouse Oogenesis [RNA-Seq]
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- 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.
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 GSE288679_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 PRJNA1219053 and SRA study SRP561431. 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.
- GSM8772967 WT-NGO-1 WT-NGO
- GSM8772968 WT-NGO-2 WT-NGO
- GSM8772969 WT-GO-1 WT-GO
- GSM8772970 WT-GO-2 WT-GO
- GSM8772971 WT-FGO-1 WT-FGO
- GSM8772972 WT-FGO-2 WT-FGO
- GSM8772973 KO-NGO-1 KO-NGO
- GSM8772974 KO-NGO-2 KO-NGO
- GSM8772975 KO-GO-1 KO-GO
- GSM8772976 KO-GO-2 KO-GO
- GSM8772977 KO-FGO-1 KO-FGO
- GSM8772978 KO-FGO-2 KO-FGO
- GSE271100 Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq] 1037 samples shares clearance, rna-seq
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares silencing, rna-seq
- GSE299303 mRNA-Engineered CRISPR-Cas Epigenetic Editors Enable Durable and Efficient Gene Silencing in Vivo [RNA-seq] 66 samples shares silencing, rna-seq
- GSE271029 Mex3a-dependent post-transcriptional silencing assures olfactory receptor diversity and axon guidance specificity [RNA-Seq] 46 samples shares silencing, rna-seq
- GSE276607 The retrotransposable element-silencing factor Daxx controls microglia identity and function in the adult brain [RNA-seq] 30 samples shares silencing, rna-seq
- GSE247082 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [RNA-seq] 30 samples shares silencing, rna-seq
- GSE295125 Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle [ACO2_citrate_kidney_RNAseq] 25 samples shares clearance, rnase
- GSE304692 Hepatocyte Circadian Clocks Control Cholesterol Metabolism and Protect From Metabolic Dysfunction-Associated Steatohepatitis (MASH) [RNAseq_palmitate_silencing] 24 samples shares silencing, rnase
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.