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Sample GSM7152469 Query DataSets for GSM7152469
Status Public on Apr 10, 2023
Title 1098561_Hudep2_CTCF
Sample type SRA
 
Source name umbilical cord blood
Organism Homo sapiens
Characteristics tissue: umbilical cord blood
cell type: Human Umbilical Cord Blood-Derived Erythroid Progenitor cell line 2, abbreviated HUDEP2, expresses beta-globin upon induced differentiation
target: CTCF
Extracted molecule genomic DNA
Extraction protocol Approximately 2.5 × 10^7 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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description HUDEP2 CTCF
Data processing Reads were mapped to hg38 using BWA mem (v0.7.16a).
Duplicated and multi-mapped reads were removed using samtools (v0.17)
Genome signal tracks (.bw files) were generated using DeepTools bamCoverage (v3.2.0)
Assembly: hg38
Supplementary files format and content: bigWig
 
Submission date Apr 06, 2023
Last update date Apr 11, 2023
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL20301
Series (2)
GSE229099 Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [human ChIP]
GSE229101 Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
Relations
BioSample SAMN34091151
SRA SRX19892757

Supplementary file Size Download File type/resource
GSM7152469_1098561_Hudep2_CTCF.markdup.uq.bw 205.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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