Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq
RNA-seq (gene expression) · human · 26 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
- Homo sapiens (human)
- Samples
- 26 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.
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 GSE172281_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 PRJNA722745 and SRA study SRP315224. 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.
+ 26 more — browse all 26 samples with per-sample file links →
- GSE229451 BAP-seq proximity labeling of subcellular compartments 16 samples shares subcellular, proximity, labeling
- GSE295471 in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes 8 samples shares transcriptomes, subcellular, proximity
- GSE319782 in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes 4 samples shares transcriptomes, subcellular, proximity
- GSE262170 Directed evolution improves the catalytic efficiency of APEX2-mediated proximity-dependent RNA labeling 54 samples shares proximity, labeling
- GSE311747 RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution [CLIP] 27 samples shares subcellular, proximity
- GSE316735 Directed Evolution of Enzymes for Bioorthogonal Chemistry Using Acid Chloride Proximity Labeling 16 samples shares proximity, labeling
- GSE307813 Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator [total RNA-seq] 15 samples shares proximity, labeling
- GSE260463 Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosis 14 samples shares proximity, labeling
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.