Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [bulk RNA-seq]
Single-cell RNA-seq · human · 3 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 3 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
- GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral densitybioRxiv : 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 GSE261282_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 PRJNA1086389 and SRA study SRP494456. 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.
+ 3 more — browse all 3 samples with per-sample file links →
- GSE261284 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD 53 samples shares bmd, bioinformatics, crispri-based, multi-tissue, single-cell, implicates, effector, etiology
- GSE261280 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [ATAC-seq] 31 samples shares bmd, bioinformatics, crispri-based, multi-tissue, single-cell, implicates, effector, etiology
- GSE261283 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [scCRISPR screen] 16 samples shares bmd, bioinformatics, crispri-based, multi-tissue, single-cell, implicates, effector, etiology
- GSE261281 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [Capture-C] 3 samples shares bmd, bioinformatics, crispri-based, multi-tissue, single-cell, implicates, effector, etiology
- GSE293846 Identification of known and novel long non-coding RNAs potentially responsible for the effects of BMD GWAS loci [hFOB RNA-seq] 18 samples shares bmd
- GSE201774 LINE-1 retrotransposons are reduced in bone of osteoporotic patients, correlate positively to BMD, and stimulate bone anabolism in transfected mesenchymal stem cells 16 samples shares bmd
- GSE340442 total RNA-seq from CD4-positive, alpha-beta T cell (ENCSR547BMD) 1 samples shares bmd
- GSE319266 Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition [hFOB BMD STING-seq] 24 samples shares bmd
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.