|
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 |