High throughput characterization of the m6A demethylase FTO by CLIP and RNAseq
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 3 × FTO_CLIP vs 3 × FTO_Input vs 3 × FTO_KO vs 3 × TREX_WTGroups 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 GSE79577_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 PRJNA316214 and SRA study SRP072286. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 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.
- GSM2098533 FTO_CLIP1 FTO_CLIP
- GSM2098534 FTO_CLIP2 FTO_CLIP
- GSM2098535 FTO_CLIP3 FTO_CLIP
- GSM2098536 FTO_Input1 FTO_Input
- GSM2098537 FTO_Input2 FTO_Input
- GSM2098538 FTO_Input3 FTO_Input
- GSM2098539 FTO_KO_1 FTO_KO
- GSM2098540 FTO_KO_2 FTO_KO
- GSM2098541 FTO_KO_3 FTO_KO
- GSM2098542 TREX_WT_1 TREX_WT
- GSM2098543 TREX_WT_2 TREX_WT
- GSM2098544 TREX_WT_3 TREX_WT
- GSE236272 Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation 20 samples shares fto, demethylase
- GSE228608 Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 28 samples shares fto, demethylase
- GSE228606 Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 [RNA-seq] 4 samples shares fto, demethylase
- GSE189878 M6A Demethylase FTO-mediated downregulation of DACT1 mRNA stability promotes Wnt signaling to facilitate osteosarcoma progression [RNA-seq] 4 samples shares fto, demethylase
- GSE242124 CLIP (NOVA1 & AGO) and RNAseq (control & NOVA1KD) in human GBM cells 36 samples shares clip
- GSE213807 RNA-seq and iCLIP-seq of cells that harbor retinitis pigmentosa mutations 31 samples shares clip
- GSE213806 Transcriptome-wide mapping of RNA:protein interactions of PRPF8 and SNRNP200 (BRR2) with retinitis pigmentosa (RP) mutations by iCLIP 27 samples shares clip
- GSE285088 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [eCLIP-seq] 24 samples shares clip
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.