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| Status |
Public on Sep 13, 2021 |
| Title |
PDX29_AA_SJBALL020579_HiC |
| Sample type |
SRA |
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| Source name |
Tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: patient-derived xenografts
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C in GM12878 cells and PDX samples were performed using the Arima-HiC kit as per the manufacturer’s instructions. Briefly, 1 million GM12878 WT, A/A cells and PDX sample were fixed with 1% formaldehyde, digested with restriction enzyme, end-labeled with Biotin-14-dATP, and then followed by ligation. The ligated chromatin was reverse-crosslinked and sonicated by Covaris E220 to produce 300–500 bp fragments . Biotin labeled DNA fragments were isolated using dynabeads Streptavidin C1 beads.
To prepare the library, eluted DNA was processed by end repair, adenylation, adaptor ligation, PCR amplification with KAPA DNA library prepare kit. The libraries were sequenced on Illumina HiSeq platform.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
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| 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
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| Submission date |
Feb 26, 2020 |
| Last update date |
Sep 13, 2021 |
| Contact name |
Yu Luan |
| E-mail(s) |
[email protected]
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| Organization name |
Northwestern University Feinberg School of Medicine
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| Department |
Department of Biochemistry and Molecular Genetics
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| Lab |
Feng Yue
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| Street address |
303 E. Superior Simpson Querrey 7-518
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| City |
CHICAGO |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE145997 |
Non-coding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation |
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| Relations |
| BioSample |
SAMN14214488 |
| SRA |
SRX7807613 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4349544_PDX29_A-A_SJBALL020579_Arima_HiC.mcool.multires.cool.gz |
1.1 Gb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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