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| Status |
Public on Feb 08, 2024 |
| Title |
PC2, 210927, Pc_H4 |
| Sample type |
SRA |
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| Source name |
lungs
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| Organism |
Pneumocystis carinii |
| Characteristics |
tissue: lungs
cell line: infected rat 2
cell type: infection level 5+
genotype: collect date: 11/07/00
chip antibody: H4 (Abcam # ab10158)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formaldehyde for 10 minutes using the active motif Low cell ChIP-seq (cat # 53084). After quenching and cell lysis, chromatin was sonicated using a Q800R3 Sonicator (Qsonica) with recirculating chiller.
ChIP-seq libraries were prepared using the active motif Low cell ChIP-seq (cat # 53084) that include the Next Gen DNA library kit and Next Gen Indexing kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Hiseq X output.
To remove rat DNA, ChIP-seq reads were aligned to the rat genome ( GCF_000001895.5) using Bowtie2 version 2.2.5. Only unmapped reads were retained.
ChIP-seq reads were aligned to the Pneumocystis carinii genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_001477545.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
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| Submission date |
May 11, 2023 |
| Last update date |
Feb 08, 2024 |
| Contact name |
Ousmane Hamadoun Cisse |
| E-mail(s) |
ousmane.cisse@nih.gov
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| Phone |
301-594-2123
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| Organization name |
National Institutes of Health
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| Street address |
10 Center Dr,
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL33206 |
| Series (2) |
| GSE232355 |
Characterizing Pneumocystis carinii centromeres with ChIP-seq (pc_210927) |
| GSE255275 |
Regional Centromere Configuration in the Fungal Pathogens of Pneumocystis Genus |
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| Relations |
| BioSample |
SAMN35052111 |
| SRA |
SRX20302015 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7329360_Pc_H4.bw |
939.3 Kb |
(ftp)(http) |
BW |
| GSM7329360_Pc_H4_peaks.narrowPeak.gz |
11.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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