Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data
RNA-seq (gene expression) · human · 15 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
- 15 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 GSE21918_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 PRJNA129395 and SRA study SRP002487. 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.
+ 15 more — browse all 15 samples with per-sample file links →
- GSE178943 Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins 12 samples shares microrna, protein, target
- GSE240411 Identification of potential targets of FTO in GIST via transcriptome-wide RNA-seq 24 samples shares transcriptome-wide, target
- GSE254194 Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing 20 samples shares transcriptome-wide, protein
- GSE248461 An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II] 14 samples shares transcriptome-wide, protein
- GSE290248 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection 97 samples shares rna-binding, protein
- GSE290282 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq] 92 samples shares rna-binding, protein
- GSE301521 FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer [FOCAS_4cellline_RNAseq] 72 samples shares transcriptome-wide, sites
- GSE268946 RNA-binding proteins DND1 and NANOS3 coordinately suppress SOX4 in processing bodies for restricting the entry of germ cell lineage 36 samples shares rna-binding, protein
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.