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| Status |
Public on May 19, 2022 |
| Title |
IgG ChIP-Seq |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: erythroleukemia cells
chip antibody: IgG (sc-2027, Santa Cruz)
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| Growth protocol |
K562 cells were cultured in RPMI1640, 10% FBS, and 1% penicillin/streptomycin (Invitrogen).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
30 million K562 cells per sample were cross-linked for 10 minutes at room temperature with 1% formaldehyde. Nuclei were isolated and sonicated in lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) on a Diagenode Standard Bioruptor for 18 cycles at 20 seconds each with 60 seconds rest between cycles. Sonicated lysates were then immunoprecipitated by overnight incubation at 4°C with Dynabeads magnetic protein G beads (Thermofisher) bound with antibody against protein of choice.
ChIP samples were converted into libraries by the Yale Center for Genome Analysis facility using the Illumina ChIP sequencing library preparation kit and sequenced using the high-throughput Illumina platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The reads were trimmed for length and quality using custom scripts.
bwa mem was used to align the trimmed reads to the hg19 (UCSC reference) version of the reference genome.
The MACS2 algorithm was used on the aligned files to generate peaks.
For both GATA, and GK1 the same IgG was used as control.
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak file generated by MACS2
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| Submission date |
May 20, 2019 |
| Last update date |
May 19, 2022 |
| Contact name |
Gary Kupfer |
| E-mail(s) |
gary.kupfer@yale.edu
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| Organization name |
Yale
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| Street address |
333 Cedar St
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| City |
New Haven |
| ZIP/Postal code |
06460 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE131510 |
Genome-wide identification of codanin-1 binding sites in human K562 erythroleukemia cells with chromatin immunoprecipitation coupled with next-generation sequencing |
| GSE131515 |
Codanin-1 binding sites in human K562 erythroleukemia cells; Global Gene expression changes in response codanin-1 knockdown in erythroid-committed cells |
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| Relations |
| BioSample |
SAMN11786198 |
| SRA |
SRX5869440 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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