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| Status |
Public on Apr 26, 2019 |
| Title |
ChIP.rep3 |
| Sample type |
SRA |
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| Source name |
DAC4-FLAG strain ChIP-seq sample, replicate 3
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| Organism |
Cryptococcus neoformans H99 |
| Characteristics |
genotype: DAC4-FLAG
growth phase: logarithmic phase, OD600=1.0
antibody: Anti-Flag ChIP grade (AB1162, Abcam, USA)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assay: The ChIP assay was performed using the ChIP-IT High Sensitivity Kit (Active Motif, Carlsbad). The DAC4-FLAG strain cells were diluted in fresh YPD medium. Cells were fixed with 1% formaldehyde (Sigma, USA) for 15 mins and quenched by 125 mM glycine. Cells were washed three times with ice-cold PBS buffer supplemented with 125 mM glycine. Cells were then lysed with the lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL). Cell pellets were suspended in sonication buffer (20 mM Tris-HCL (PH 8.0), 2 mM EDTA, 1% Triton-X100, 150 mM NaCl, 1% SDS, 100 µM PMSF and 1x proteinase inhibitor). The samples were sheared with a Diagenode Pico device using 30 s on and off for 30 cycles. After centrifugation, the supernatant was collected and diluted in IP dilution buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, 100 μM PMSF and 1x proteinase inhibitor). The immunoprecipitation was performed with 5 μg of anti-Flag ChIP grade antibody and Protein G Beads at 4°C overnight. The beads were then washed 4 times in IP dilution buffer. The sample was then eluted with elution buffer and treated with Proteinase K overnight at 65°C. DNA samples were purified with DNA purification columns. The ChIP-seq library was constructed with the MicroPlex Library Preparation Kit v2 (Diagenode, Liège, Belgium) according to the manufacturer’s instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ChIP-DNA
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2
Software used for RPKM calculation: HTSeq 0.6.1p2
Software used for creation of the wig files: MACS
Genome_build: Cryptococcus neoformans var. grubii H99 .
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample (RNA-seq), wig files for ChIP-seq
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| Submission date |
Jun 20, 2018 |
| Last update date |
Apr 28, 2019 |
| Contact name |
Li Hailong |
| E-mail(s) |
lihailong1166@gmail.com
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| Organization name |
Northeastern University
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| Street address |
NO. 3-11, Wenhua Road, Heping District
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| City |
ShenYang |
| State/province |
Liaoning |
| ZIP/Postal code |
110001 |
| Country |
China |
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| Platform ID |
GPL23176 |
| Series (1) |
| GSE116040 |
Fungal acetylome comparative analysis identifies an essential role of acetylation in human fungal pathogen virulence |
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| Relations |
| BioSample |
SAMN09461762 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3207839_ChIP.rep3.wig.gz |
10.0 Mb |
(ftp)(http) |
WIG |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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