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Sample GSM4349554

Query DataSets for GSM4349554

Status

Public on Sep 13, 2021

Title

PDX23_AA_SJBALL020589_Input_ChIP-seq

Sample type

SRA

Source name

Tissue

Organism

Homo sapiens

Characteristics

tissue: patient-derived xenografts
chip-seq antibody: Input

Growth protocol

ALL patient cells were intravenously injected into 8- to 10-week-old female NSG-SGM362 mice that were sublethally irradiated (250 RAD) 6–24 h before transplantation. Human leukaemia engraftment was monitored in peripheral blood by performing serial retro-orbital bleeds monthly after injections. Peripheral blood samples were analysed by flow cytometry for human CD45+ cells and when CD45+ cells were >5%, mice were euthanized, and blood, bone marrow, and spleen samples were used to sort human leukemia cells, which were fixed with FA for following Hi-C or ChIP-seq experiments.

Extracted molecule

genomic DNA

Extraction protocol

10 M cells are fixed with 1% FA for 15 mins in room temperature, then stoped with Glycine. Chromatin was extracted with cell lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA). 100 ug chromatin was sonicated to 100-300 bp by Covaris E220, and 5 ug chromatin was used as input. Bead-antibody complex was prepared by incubating 11 ul of sheep anti-mouse IgG dynabeads (ThermoFisher, 11201D) with anti-GATA3 (Santa Cruz, sc268) at 4°C for 4 hours with shaking. Then fragmented chromatin was incubated with bead-antibody complex overnight with shaking followed by stringent wash and elution.
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq platform.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina Genome Analyzer

Data processing

ChIP-seq reads mad ATAC-seq were aliged to female_hg19 genome using Bowtie2, the peaks were called using MACS2.
RNA-seq reads were aligned to female_hg19_genome assembly using STAR
HiC reads were aligned to zv10 genome assembly using BWA
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using paritools
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The cool file were the matrix of Hi-C for each Sample.
Genome_build: female_hg19

Submission date

Feb 26, 2020

Last update date

Sep 13, 2021

Contact name

Yu Luan

E-mail(s)

[email protected]

Organization name

Northwestern University Feinberg School of Medicine

Department

Department of Biochemistry and Molecular Genetics