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Sample GSM6928821 Query DataSets for GSM6928821
Status Public on May 01, 2024
Title PATJJX-D ATAC
Sample type SRA
 
Source name primary bone marrow
Organism Homo sapiens
Characteristics disease state: B-ALL
cell type: primary bone marrow
genotype: Diagnosis
Growth protocol Cryopreserved paired diagnosis/relapse primary patient bone marrow samples from individual patients were obtained from the Children’s Oncology group (COG) ALL biorepository or St. Jude Children’s Research Hospital.
Extracted molecule genomic DNA
Extraction protocol Following FACS, 50,000 leukemic cells were immediately processed for ATACseq by the NYU Genome Technology Center.
ATAC libraries were generated based on the protocol by Buenrostro et al. Briefly, cells are resuspended in cold lysis buffer (10 mM Tris Cl, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630, pH 7.4) and centrifuged for 1 minuted at 500xg. with one modification. Nuclei were tagmented using Nextera (Illumina) Tagmentation DNA buffer and enzyme.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Slide-n-Seq (sns) pipeline: https://igordot.github.io/sns/
Aigned to reference genome (hg19) using Bowtie2
Filtering of duplicate reads by Sambamba
Peak-calling conducted with MACS2
Assembly: hg19
Supplementary files format and content: bigwigs and bedfiles with MACS2 peak calls for each sample
 
Submission date Jan 11, 2023
Last update date May 01, 2024
Contact name Sonali Narang
E-mail(s) sonali.narang@nyulangone.org
Phone 5169652665
Organization name NYU Langone
Street address 435 east 30th street
City New York
State/province NY
ZIP/Postal code 10016
Country USA
 
Platform ID GPL24676
Series (2)
GSE222675 Clonal evolution of the 3D chromatin landscape of relapsed ALL [ATAC-seq]
GSE222687 Clonal evolution of the 3D chromatin landscape of relapsed ALL
Relations
BioSample SAMN32680674
SRA SRX19006421

Supplementary file Size Download File type/resource
GSM6928821_PATJJX-D.bin1.rpkm.bw 276.8 Mb (ftp)(http) BW
GSM6928821_PATJJX-D.peaks.bed.gz 521.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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