Xist RNA targets selective autosomal genes to modulate expression in a Repeat B-dependent manner [RNA-seq]
RNA-seq (gene expression) · mouse · 30 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
- 30 samples: 15 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.
- Paper
- Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expressionbioRxiv : the preprint server for biology · 2024
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 GSE271097_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 PRJNA1129839 and SRA study SRP517001. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 15 replicated groups read from 30 sample titles; they account for 30 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.
- GSM8368737 MALE, ES, d0, rep1 MALE, ES, d0,
- GSM8368738 MALE, ES, d0, rep2 MALE, ES, d0,
- GSM8368739 RepB, ES, d0, rep1 RepB, ES, d0,
- GSM8368740 RepB, ES, d0, rep2 RepB, ES, d0,
- GSM8368741 WT, ES, d0, rep1 WT, ES, d0,
- GSM8368742 WT, ES, d0, rep2 WT, ES, d0,
- GSM8368743 MALE, ES, d4, rep1 MALE, ES, d4,
- GSM8368744 MALE, ES, d4, rep2 MALE, ES, d4,
- GSM8368745 RepB, ES, d4, rep1 RepB, ES, d4,
- GSM8368746 RepB, ES, d4, rep2 RepB, ES, d4,
- GSM8368747 WT, ES, d4, rep1 WT, ES, d4,
- GSM8368748 WT, ES, d4, rep2 WT, ES, d4,
- GSM8368749 MALE, ES, d7, rep1 MALE, ES, d7,
- GSM8368750 MALE, ES, d7, rep2 MALE, ES, d7,
- GSM8368751 RepB, ES, d7, rep1 RepB, ES, d7,
- GSM8368752 RepB, ES, d7, rep2 RepB, ES, d7,
- GSM8368753 WT, ES, d7, rep1 WT, ES, d7,
- GSM8368754 WT, ES, d7, rep2 WT, ES, d7,
- GSM8368755 MALE, ES, d14, rep1 MALE, ES, d14,
- GSM8368756 MALE, ES, d14, rep2 MALE, ES, d14,
- GSM8368757 RepB, ES, d14, rep1 RepB, ES, d14,
- GSM8368758 RepB, ES, d14, rep2 RepB, ES, d14,
- GSM8368759 WT, ES, d14, rep1 WT, ES, d14,
- GSM8368760 WT, ES, d14, rep2 WT, ES, d14,
- GSM8368761 RepB, MEF, rep1 RepB, MEF,
- GSM8368762 RepB, MEF, rep2 RepB, MEF,
- GSM8368763 RepE, MEF, rep1 RepE, MEF,
- GSM8368764 RepE, MEF, rep2 RepE, MEF,
- GSM8368765 WT, MEF, rep1 WT, MEF,
- GSM8368766 WT, MEF, rep2 WT, MEF,
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- GSE276731 Fibroblast growth factor receptor signaling modulates cholesterol storage in a SOAT1-dependent manner to promote mammary tumor cell invasion 18 samples shares modulate, manner
- GSE252928 Berberine directly targets AKR1B10 protein to modulate lipid and glucose metabolism disorders in NAFLD 16 samples shares modulate, targets
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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.