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| Status |
Public on Mar 06, 2015 |
| Title |
Raji H3K27ac rep1 |
| Sample type |
SRA |
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| Source name |
Raji cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Raji cells
chip antibody: H3K27ac (Millipore, 07-360)
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| Growth protocol |
Raji and RJ2.2.5 cells were cultured in RPMI supplemented with 5% FCS, 5% FBS, and 100 U/ml Penecillin/Streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1-0.1 ng of IP'ed DNA was processed into a sequencing library using the Kapa Hyper Prep kit (Cat# KK8500) according to the manufacturers instructions.
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-600 bp. 30 mg chromatin was immunoprecipitated with 5 μg anti-CIITA, anti-H3K27ac or anti-H3K4me3 antibody over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified. Input fraction was isolated after sonication and prior to the IP.
See each sample for speicific extract protocols
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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 |
Raw sequencing reads were mapped to the hg19 version of the mouse genome with Bowtie using the default options
For CIITA ChIPseq peak calling HOMER software (Heinz et al. Mol Cell, 2010. 38:576-589) was used with the options "-style factor"
For ATACseq paired-end and single end fastq files from the same cell type were merged into one bigWig file
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are normalized to reads per million (rpm) using R/Bioconductor. Bed files contain the genomic locations of significantly enriched peaks as determined by HOMER
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| Submission date |
Feb 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Scharer |
| E-mail(s) |
cdschar@emory.edu
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| Organization name |
Emory University
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| Department |
Microbiology and Immunology
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| Lab |
Chris Scharer
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| Street address |
1510 Clifton Rd, Suite 3086A
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE52941 |
CIITA regulated genes in human B cells |
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| Relations |
| BioSample |
SAMN03329462 |
| SRA |
SRX865415 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1602237_Raji.H3K27ac.rep1.bigWig |
238.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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