5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [RNA-seq]
RNA-seq (gene expression) · human · 14 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
- 14 samples: 7 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 GSE294308_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 PRJNA1248975 and SRA study SRP577998. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 14 sample titles; they account for 14 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.
- GSM8902185 BE2 cells, H2O, rep1 BE2 cells, H2O,
- GSM8902186 BE2 cells, H2O, rep2 BE2 cells, H2O,
- GSM8902187 BE2 cells, CoCl2 10uM, rep1 BE2 cells, CoCl2 10uM,
- GSM8902188 BE2 cells, CoCl2 10uM, rep2 BE2 cells, CoCl2 10uM,
- GSM8902189 BE2 cells, CoCl2 50uM, rep1 BE2 cells, CoCl2 50uM,
- GSM8902190 BE2 cells, CoCl2 50uM, rep2 BE2 cells, CoCl2 50uM,
- GSM8902191 BE2 cells, WT, rep1 BE2 cells, WT,
- GSM8902192 BE2 cells, WT, rep2 BE2 cells, WT,
- GSM8902193 BE2 cells, TET2KO #1, rep1 BE2 cells, TET2KO #1,
- GSM8902194 BE2 cells, TET2KO #1, rep2 BE2 cells, TET2KO #1,
- GSM8902195 BE2 cells, TET2KO #2, rep1 BE2 cells, TET2KO #2,
- GSM8902196 BE2 cells, TET2KO #2, rep2 BE2 cells, TET2KO #2,
- GSM8902197 BE2 cells, TET2KO #3, rep1 BE2 cells, TET2KO #3,
- GSM8902198 BE2 cells, TET2KO #3, rep2 BE2 cells, TET2KO #3,
- GSE294307 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [CUT&Run] 18 samples shares 5-hydroxymethylcytosine, mycn-amplified, neuroblastoma, deposition, repressive, mediates, polycomb, complex
- GSE294304 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [nano-seal, 5hmC] 18 samples shares 5-hydroxymethylcytosine, mycn-amplified, neuroblastoma, deposition, repressive, mediates, polycomb, complex
- GSE211354 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [RNA-Seq] 54 samples shares mycn-amplified, neuroblastoma, complex
- GSE211953 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ChIP-Seq] 35 samples shares mycn-amplified, neuroblastoma, complex
- GSE49711 RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] 498 samples shares neuroblastoma, complex
- GSE294526 The USP11/TCEAL1 complex promotes transcription elongation to sustain oncogenic gene expression in neuroblastoma [RNA-seq II] 21 samples shares neuroblastoma, complex
- GSE307922 Destabilization of the noncanonical PRC1.1 complex via USP7 inhibition induces neuronal differentiation in neuroblastoma [RNA-Seq] 18 samples shares neuroblastoma, complex
- GSE49710 RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray] 498 samples shares neuroblastoma, complex
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.