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Sample GSM4761250 Query DataSets for GSM4761250
Status Public on Feb 04, 2021
Title 1440313_H3K9ac_H2-D3
Sample type SRA
 
Source name 1440313_H3K9ac_H2-D3
Organism Homo sapiens
Characteristics cell line: Hudep2
antibody: H3K9ac
Treatment protocol NA
Growth protocol Approximately 2.5 × 107 cells were used for each immunoprecipitation. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with rotation, and the reaction was quenched with glycine at a final concentration of 125 mM. Cross-linked cells were then lysed and resuspended in 2 mL of RIPA buffer and sonicated for 12 cycles with a Branson 250 sonifier (10 s on/90 s off for a total of 2 min of pulses with 20% output from the micro-tip) to obtain fragments of chromatin approximately 200–300 bp in size. Supernatants were precleared by incubation with 200 µL of protein A/G agarose bead slurry (Thermo Fisher Scientific, cat. #15918014) overnight at 4°C with rotation. Meanwhile, 12.5 µg of IP antibody was incubated with 50 µL of protein A/G agarose bead slurry in 1 mL of PBS overnight at 4°C with rotation. Saved precleared chromatin (20 µL) was used as the input sample. Precleared chromatin was incubated with the antibody–bead complex for 7 h at 4°C with rotation. Cross-linking of DNA was reversed by incubation with RNase A (1 µg/µL), proteinase K (0.2 mg/mL), and 0.25 M NaCl overnight at 65°C.
Extracted molecule genomic DNA
Extraction protocol Immunoprecipitated DNA was purified using the Qiagen PCR Extraction Kit and eluted with 20 µL of EB elution buffer. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, cat. #E7645) with homemade TruSeq adaptors. Libraries were sequenced using an Illumina HiSeq 4000 system.
NA
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description ChIP-seq
Data processing FASTQ files were mapped to hg19 by using BWA mem (v0.7.16a).
ChIP-seq peaks were called by using MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle
 
Submission date Sep 01, 2020
Last update date Feb 04, 2021
Contact name Yong Cheng
E-mail(s) Yong.Cheng@stjude.org
Organization name St. Jude Children’s Research Hospital
Department Department of Hematology
Lab Yong Cheng Lab
Street address 262 Danny Thomas Place
City Memphis
State/province Tennessee
ZIP/Postal code 38018
Country USA
 
Platform ID GPL20301
Series (2)
GSE157308 Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression (histone ChIP-Seq)
GSE157311 Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression
Relations
BioSample SAMN15961536
SRA SRX9055427

Supplementary file Size Download File type/resource
GSM4761250_1440313_H3K9ac_H2_D3.all.bw 224.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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