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Series GSE186599 Query DataSets for GSE186599
Status Public on Jul 05, 2024
Title TULIPs decorate the three-dimensional genome of PFA ependymoma
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Hi-C and RNA-seq for a large cohort of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more.
 
Overall design Assessing 3D genome conformation by Hi-C for many types of pediatric brain tumors.

>>>Submitter states that raw data have been deposited at EGA under accession EGAS00001005476<<<
Web link https://doi.org/10.1016/j.cell.2024.06.023
 
Contributor(s) Gallo M, Taylor MD, Jabado N
Citation(s) 38986619
Submission date Oct 26, 2021
Last update date Sep 30, 2024
Contact name Marco Gallo
E-mail(s) marco.gallo@bcm.edu
Organization name Baylor College of Medicine
Department Pediatrics
Street address 1102 Bates Avenue
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (160)
GSM5657317 3004
GSM5657318 170922
GSM5657319 180509
Relations
BioProject PRJNA774780

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE186599_PFA_recurrent.tulips.bed.gz 1.2 Kb (ftp)(http) BED
GSE186599_PFA_specific.tulips.bed.gz 1.1 Kb (ftp)(http) BED
GSE186599_RAW.tar 717.4 Gb (http)(custom) TAR (of BED, BEDGRAPH, BEDPE, BROADPEAK, BW, HIC, MCOOL, TDF, TSV, WIG)
GSE186599_all_recurrent.tulips.bed.gz 1.2 Kb (ftp)(http) BED
GSE186599_chromosight_scores.tsv.gz 13.7 Mb (ftp)(http) TSV
GSE186599_diff_loops.chromosight.chromosight.tsv.gz 246.4 Kb (ftp)(http) TSV
GSE186599_diff_loops.hiccups.chromosight.tsv.gz 109.1 Kb (ftp)(http) TSV
GSE186599_diff_loops.mustache.chromosight.tsv.gz 241.7 Kb (ftp)(http) TSV
GSE186599_hicrep.scc.tsv.gz 27.6 Kb (ftp)(http) TSV
GSE186599_insulationScores.cooltools.tsv.gz 171.4 Mb (ftp)(http) TSV
GSE186599_merged.TADBoundaryCalls_chrAll_50kb.tsv.gz 10.4 Mb (ftp)(http) TSV
GSE186599_mustache_loops.count_table.tsv.gz 20.4 Mb (ftp)(http) TSV
GSE186599_nonTumor_recurrent.tulips.bed.gz 288 b (ftp)(http) BED
GSE186599_rna.htseq_count_table.tsv.gz 3.0 Mb (ftp)(http) TSV
GSE186599_rna.limma.PFA.wrt.nonPFA.tsv.gz 1.9 Mb (ftp)(http) TSV
GSE186599_stringTie.pedBrainTx.annotated.sorted.gtf.gz 23.9 Mb (ftp)(http) GTF
GSE186599_tumor_specific.tulips.bed.gz 1.1 Kb (ftp)(http) BED
GSE186599_union.kallistoAbundance.gene.Rdata.gz 15.1 Mb (ftp)(http) RDATA
GSE186599_union.kallistoAbundance.gene.tsv.gz 9.7 Mb (ftp)(http) TSV
GSE186599_union.kallistoAbundance.tx.Rdata.gz 69.3 Mb (ftp)(http) RDATA
GSE186599_union.kallistoAbundance.tx.tsv.gz 38.7 Mb (ftp)(http) TSV
GSE186599_union_arrowhead_scores.tsv.gz 64.2 Mb (ftp)(http) TSV
GSE186599_union_eigenvalues.tsv.gz 17.3 Mb (ftp)(http) TSV
GSE186599_union_hiccups_scores.tsv.gz 8.5 Mb (ftp)(http) TSV
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record
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