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| Status |
Public on Mar 20, 2017 |
| Title |
K562 ChIP input exp. 2 |
| Sample type |
SRA |
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| Source name |
K562 strain
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| Organism |
Homo sapiens |
| Characteristics |
sample id: K562 1
gender: female
chip antibody: H3K9me2 (ab1220 Abcam)
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| Treatment protocol |
Some K562 samples (K562-UNC0638) were grown for 5 days with 0.5 micromole UNC0638, a specific inhibitor of histone methyltransferase G9a, before isolation.
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| Growth protocol |
Normal polymorphonuclear granulocytes (predominantly neutrophils) were isolated from discarded fresh white blood cells (buffy coats) from unidentified healthy donors using standard OptiPrep density centrifugation, resuspended in PBS buffer and fixed with 1% formaldehyde. Cryopreserved CD34+ bone marrow hematopoietic progenitors were obtained from Allcells, Emeryville, Ca. Cryopreserved AML cellswere isolated from bone-marrow samples by Ficoll-Pacque density gradient centrifugation. The cryopreserved samples were thawed, resuspended in PBS, and fixed with 1% formaldehyde immediately after thawing. The human samples were collected and analyzed under Penn State Hershey IRB protocols 2000-186, HY03-136EP-A, and STUDY00002518. Cultured cells K562 (ATCC CCL-243) were grown in suspension as recommended by ATCC, washed with PBS and fixed with 1% formaldehyde.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were fixed with 1% formaldehyde for 10 min. After fixation, nuclei were isolated, the nuclear DNA was digested by micrococcal nuclease to 150-200 bp DNA fragments, the DNA fragments with attached proteins were resuspended in SDS-containing lysis buffer, and immunoprecipitated by antibodies against various histone modifications.
For Illumina Hi-Seq 2500 sequencing we used New England BioLabs NEBNext ChIP-Seq library preparation reagent set for Illumina and and constructed library as described in the E6240 instruction manual. For SOLiD sequencing we used Applied Biosystems SOLiD 4 System and constructed library as described in the SOLiD 4 System Library Preparation Guide.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0.
Domains were called using the RSEG software version 0.4.8 RC with the provided deadzone file “deadzones-k41-hg19.bed” and the following parameters: -s 10000 -i 20 -duplicates. The chrX and chrY mapped sequences of the male samples were duplicated prior to calling RSEG.
To comply with Penn State's IRB, sequence reads had individual SNPs eliminated based on hg19.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain domains output by RSEG
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| Submission date |
May 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Salzberg |
| Organization name |
Rubius Therapeutics
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| Street address |
399 Binney St UNIT 300
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE71809 |
Genome-wide mapping of histone H3 lysine 9 dimethylation in normal myeloid cells and acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN04999907 |
| SRA |
SRX1761304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2152610_2_F3.rsegout.bed.gz |
322.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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