TULIPs decorate the three-dimensional genome of PFA ependymoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 160 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
- 160 samples: 9 conditions, mostly with about 29 replicates eachGroups 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
- TULIPs decorate the three-dimensional genome of PFA ependymomaCell · 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 GSE186599_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 PRJNA774780. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 89 samples.
How we read this: 9 replicated groups read from 160 sample titles; they account for 89 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.
- GSM5657317 3004
- GSM5657318 170922
- GSM5657319 180509
- GSM5657320 180618
- GSM5657321 190109
- GSM5657322 BT2018011 BT
- GSM5657323 BT2018078 BT
- GSM5657324 BT2018110 BT
- GSM5657325 BT245_parental_K27M
- GSM5657326 DIPG13_C8_K27M
- GSM5657327 DIPG13_parental_K27M
- GSM5657328 DIPG6
- GSM5657329 E1697 E
- GSM5657330 E1816 E
- GSM5657331 E1858 E
- GSM5657332 E1859 E
- GSM5657333 E1864 E
- GSM5657334 E2051 E
- GSM5657335 E2053 E
- GSM5657336 E2061 E
- GSM5657337 E2074 E
- GSM5657338 E2105 E
- GSM5657339 E2112 E
- GSM5657340 E2113 E
- GSM5657341 E2115 E
- GSM5657342 E2181 E
- GSM5657343 E2223 E
- GSM5657344 E519 E
- GSM5657345 E562 E
- GSM5657346 E767 E
- GSM5657347 E782 E
- GSM5657348 E783 E
- GSM5657349 E805 E
- GSM5657350 E809 E
- GSM5657351 E820 E
- GSM5657352 E823 E
- GSM5657353 E833 E
- GSM5657354 E835 E
- GSM5657355 E838 E
- GSM5657356 E840 E
+ 120 more — browse all 160 samples with per-sample file links →
- GSE275007 Loss of LDOC1 by chromatin compaction in mesenchymal tumor cells is required for PFA1 ependymoma growth 30 samples shares pfa, ependymoma
- GSE274877 Loss of LDOC1 by chromatin compaction in mesenchymal tumor cells is required for PFA1 ependymoma growth [CUT&RUN] 16 samples shares pfa, ependymoma
- GSE274879 Loss of LDOC1 by chromatin compaction in mesenchymal tumor cells is required for PFA1 ependymoma growth [RNA-seq] 14 samples shares pfa, ependymoma
- GSE313992 Comparative Immunotoxicity and Transcriptomic Profiling of Seven PFAS in THP-1 Macrophages 252 samples shares pfa
- GSE311566 Mechanistic insights into PFAS-induced effects on B lymphocyte activation and antibody secretion [PBMCs] 41 samples shares pfa
- GSE311234 Mechanistic insights into PFAS-induced effects on B lymphocyte activation and antibody secretion 36 samples shares pfa
- GSE254408 Investigating the Mechanism of Neurotoxic Effects of PFAS in Differentiated Neuronal Cells through Transcriptomics and Lipidomics Analysis 21 samples shares pfa
- GSE279836 Environmentally relevant concentrations of individual per- and polyfluoroalkyl substances (PFAS) and a PFAS mixture impact proliferation and gene transcription in a human myometrial cell line. 18 samples shares pfa
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.