Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 28 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 28 samples: 11 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
- Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48Genome 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 GSE228608_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA950436 and SRA study SRP430194. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 11 replicated groups read from 28 sample titles; they account for 24 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.
- GSM7133913 ChIP-seq of ZBTB48 in HEK293 cells, replicate 1 ChIP-seq of ZBTB48 in H…
- GSM7133914 ChIP-seq of ZBTB48 in HEK293 cells, replicate 2 ChIP-seq of ZBTB48 in H…
- GSM7133915 Input of ChIP, replicate 1 Input of ChIP,
- GSM7133916 Input of ChIP, replicate 2 Input of ChIP,
- GSM7133917 RNA-seq of HEK293 cells upon knockdown of ZBTB48, replicate 1 RNA-seq of HEK293 cells…
- GSM7133918 RNA-seq of HEK293 cells upon knockdown of ZBTB48, replicate 2 RNA-seq of HEK293 cells…
- GSM7133919 RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 1 RNA-seq of HEK293 cells…
- GSM7133920 RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 2 RNA-seq of HEK293 cells…
- GSM7133921 iCLIP-seq of ZBTB48, replicate 1 iCLIP-seq of ZBTB48,
- GSM7133922 iCLIP-seq of ZBTB48, replicate 2 iCLIP-seq of ZBTB48,
- GSM7133923 Size-matched input for ZBTB48 iCLIP
- GSM7133924 iCLIP-seq of FTO, replicate 1 iCLIP-seq of FTO,
- GSM7133925 iCLIP-seq of FTO, replicate 2 iCLIP-seq of FTO,
- GSM7133926 iCLIP-seq of FTO, replicate 3 iCLIP-seq of FTO,
- GSM7133927 iCLIP-seq of FTO, replicate 4 iCLIP-seq of FTO,
- GSM7133928 Size-matched input for FTO iCLIP
- GSM7133929 m6A iCLIP-seq upon FTO overexpression, replicate 1 m6A iCLIP-seq upon FTO …
- GSM7133930 m6A iCLIP-seq upon FTO overexpression, replicate 2 m6A iCLIP-seq upon FTO …
- GSM7133931 m6A iCLIP-seq upon GFP control overexpression, replicate 1 m6A iCLIP-seq upon GFP …
- GSM7133932 m6A iCLIP-seq upon GFP control overexpression, replicate 2 m6A iCLIP-seq upon GFP …
- GSM7133933 m6A iCLIP-seq upon ZBTB48 overexpression, replicate 1 m6A iCLIP-seq upon ZBTB…
- GSM7133934 m6A iCLIP-seq upon ZBTB48 overexpression, replicate 2 m6A iCLIP-seq upon ZBTB…
- GSM7133935 FTO iCLIP-seq upon ZBTB48 knockdown, replicate 1 FTO iCLIP-seq upon ZBTB…
- GSM7133936 FTO iCLIP-seq upon ZBTB48 knockdown, replicate 2 FTO iCLIP-seq upon ZBTB…
- GSM7133937 FTO iCLIP-seq upon control non-targeting knockdown, replicate 1 FTO iCLIP-seq upon cont…
- GSM7133938 FTO iCLIP-seq upon control non-targeting knockdown, replicate 2 FTO iCLIP-seq upon cont…
- GSM7133939 Size-matched input for FTO CLIP upon ZBTB48 knockdown
- GSM7133940 Size-matched input for FTO CLIP upon control non-targeting knockdown
- GSE228606 Recruitment of the m6A/Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48 [RNA-seq] 4 samples shares zbtb48, fto, recruitment, demethylase, telomeric, protein, target, finger
- GSE240411 Identification of potential targets of FTO in GIST via transcriptome-wide RNA-seq 24 samples shares fto, target
- GSE236272 Nitric oxide inhibits FTO demethylase activity to regulate N6-methyladenosine mRNA methylation 20 samples shares fto, demethylase
- GSE79577 High throughput characterization of the m6A demethylase FTO by CLIP and RNAseq 12 samples shares fto, demethylase
- GSE211743 KDM6A and B-mediated transcriptional activation of EWSR1-FLI1 targets coordinates demethylase dependent and independent mechanisms in Ewing sarcoma 99 samples shares demethylase, target
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples shares demethylase, protein
- GSE300308 Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering 51 samples shares recruitment, finger
- GSE278498 Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B 36 samples shares demethylase, target
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.