|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|