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| Status |
Public on Jun 08, 2016 |
| Title |
Input ChIP-Seq Replicate 3 |
| Sample type |
SRA |
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| Source name |
Yeast
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| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: N/A
cell density: OD=2.5
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| Growth protocol |
50 ODs of cells from overnight YPAD cultures were washed once in water and resuspended in 20 mLs DMEM, transferred to 150mm tissue culture dishes, and incubated for 24 hours at 37ºC, 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
mRNA was isolated using trizol to isolate total RNA and oligotex mRNA mini kit to isolate mRNA. ChIP DNA was isolated from antibody incubation by SDS/proteinase K followed by purification using MN Nucleospin Gel Cleanup columns
cDNA libraries were prepared from DNase-treated mRNA using NEBNext Ultra Directional RNA Library Prep Kit. ChIP DNA libraries were prepared using End-It DNA End Repair Kit followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp
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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 |
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.
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| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christina M. Homer |
| E-mail(s) |
[email protected]
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| Organization name |
UCSF
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| Department |
Biochemistry & Biophysics
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| Lab |
Madhani Lab
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| Street address |
600 16th St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL19081 |
| Series (1) |
| GSE73203 |
Convergent evolution of peptide-based quorum sensing required for virulence in a eukaryotic pathogen |
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| Relations |
| BioSample |
SAMN04096352 |
| SRA |
SRX1261434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1888507_input_rep3_peaks.txt.gz |
60 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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