Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions
Non-coding RNA profiling · human · 18 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Samples
- 18 samples: 9 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.
Read the full summary ↓
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 GSE56010_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.
Also filed as BioProject PRJNA242201 and SRA study SRP040278. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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.
- GSM1350192 PARCLIP-MeRIP-Input-rep1 PARCLIP-MeRIP-Input
- GSM1350193 PARCLIP-MeRIP-Input-rep2 PARCLIP-MeRIP-Input
- GSM1350194 PARCLIP-MeRIP-IP-rep1 PARCLIP-MeRIP-IP
- GSM1350195 PARCLIP-MeRIP-IP-rep2 PARCLIP-MeRIP-IP
- GSM1350196 hnRNPC-PAR-CLIP-Control-rep1 hnRNPC-PAR-CLIP-Control
- GSM1350197 hnRNPC-PAR-CLIP-Control-rep2 hnRNPC-PAR-CLIP-Control
- GSM1350198 hnRNPC-PAR-CLIP-METTL3KD-rep1 hnRNPC-PAR-CLIP-METTL3KD
- GSM1350199 hnRNPC-PAR-CLIP-METTL3KD-rep2 hnRNPC-PAR-CLIP-METTL3KD
- GSM1350200 hnRNPC-PAR-CLIP-METTL14KD-rep1 hnRNPC-PAR-CLIP-METTL14…
- GSM1350201 hnRNPC-PAR-CLIP-METTL14KD-rep2 hnRNPC-PAR-CLIP-METTL14…
- GSM1502498 RNA-seq-control-rep1 RNA-seq-control
- GSM1502499 RNA-seq-control-rep2 RNA-seq-control
- GSM1502500 RNA-seq-HNRNPCKD-rep1 RNA-seq-HNRNPCKD
- GSM1502501 RNA-seq-HNRNPCKD-rep2 RNA-seq-HNRNPCKD
- GSM1502502 RNA-seq-METTL3KD-rep1 RNA-seq-METTL3KD
- GSM1502503 RNA-seq-METTL3KD-rep2 RNA-seq-METTL3KD
- GSM1502504 RNA-seq-METTL14KD-rep1 RNA-seq-METTL14KD
- GSM1502505 RNA-seq-METTL14KD-rep2 RNA-seq-METTL14KD
- GSE310006 The NuRD chromatin remodeling complex regulates tRNA genes through direct interactions with RNA polymerase III 54 samples shares interactions, regulate
- GSE281237 Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients 29 samples shares interactions, widespread
- GSE274484 The Long Non-coding RNA Lnc-RAINY Regulates Genes Involved in Radiation Susceptibility Through DNA:DNA:RNA triplex-forming Interactions and has Tumor Therapeutic Potential in Non-small Cell Lung Cancers [ATAC-seq] 16 samples shares interactions, regulate
- GSE311392 The NuRD chromatin remodeling complex regulates tRNA genes through direct interactions with RNA polymerase III [Nuclei run-on (nascent RNA) profiling] 6 samples shares interactions, regulate
- GSE276935 The activity of tertiary lymphoid structures in high grade serous ovarian cancer is governed by site, stroma, and cellular interactions 417 samples shares interactions
- GSE277500 Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (pA-DamID) 226 samples shares interactions
- GSE276856 Selective interactions at pre-replication complexes categorize baseline and dormant origins 211 samples shares interactions
- GSE271752 Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq] 194 samples shares interactions
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.