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Sample GSM4005281 Query DataSets for GSM4005281
Status Public on Apr 06, 2020
Title 31CBS-WT-inv-H3K4me3-CHIP-seq
Sample type SRA
 
Source name Jurkat
Organism Homo sapiens
Characteristics cell line: Jurkat
cell type: T cell leukemia
tissue: peripheral blood
genotype: 31CBS-WT
chip antibody: anti-H3K4me3
Treatment protocol Immediately extract RNA from Jurkat T-ALL and K562 cells without any treatment
Growth protocol Human Jurkat leukemia cells and K562 cells were culture at RMPI1640 and 10% FBS media.
Extracted molecule genomic DNA
Extraction protocol RNA samples extracted with Trizon and treated with Dnase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K4me2, H3K9/14ac and H3K27ac antibody (H3K4me3 (Millipore, #04-745), H3K4me2 (Millipore, 07-030), H3K27Ac (Abcam, #ab4729), and H3K9/14ac (Diagenode, #C15410005)). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq and ChIP-seq.
 
Submission date Aug 02, 2019
Last update date Apr 06, 2020
Contact name Huacheng Luo
E-mail(s) luohuacheng@him.cas.cn
Organization name Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences
Street address No. 150, Fucheng Road, Qiantang District
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310018
Country China
 
Platform ID GPL16791
Series (1)
GSE135320 Alteration of CTCF associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis
Relations
BioSample SAMN12476065
SRA SRX6647338

Supplementary file Size Download File type/resource
GSM4005281_31CBS-inv-Jurkat-H3K4me3-CHIP-seq_peaks.bed.gz 232.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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