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| Status |
Public on Jun 20, 2013 |
| Title |
EFG1_ip3 |
| Sample type |
SRA |
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| Source name |
EFG1_IP
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| Organism |
Candida parapsilosis |
| Characteristics |
strain: LCP3M
growth phase: log phase
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| Treatment protocol |
1% formaldehyde was added to cultures and samples were incubated at room temperature for 30 min, shaking at 50 rpm. 125mM glycine was added to each sample and left incubate for 5 min at room temperature, shaking at 50 rpm. Cells were centrifuges and collected. Samples were sonicated using a Biorupter™ (Diagenode) for 15 min at 30 s intervals at high power setting in an ice bath. The ice was then changed and the sonication was repeated. Input samples before the addition of antibody were used as control. Regions bound to Efg1 were immunoprecipitated using a mouse monoclonal antibody (Myc-tag 9B11, Cell Signaling).
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| Growth protocol |
Cells were grown from single colonies overnight in 5 ml YPD (1% Yeast Extract, 2% Peptone, 2% Glucose; FormediumTM) at 30°C . They were diluted in 50 ml fresh YPD to an A600 of 0.2, and grown to an A600 of 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were generated according to the protocol Preparing Samples for ChIP Sequencing of DNA (Illumina Guide Part # 11257047 Rev. A). The library preparation methodology of end repair to create blunt ended fragments, addition of 3’- A overhang for efficient adapter ligation, ligation of the SR adapters (Illumina Single Read Adapters (FC-102-1003) - aliquots kindly provided by A. Lohan), size selection of adapter ligated material was carried out utilizing enzymes indicated in the protocol. All enzymes for library generation were purchased from New England Biolabs (Ipswitch, MA, USA). A limited 18 cycle amplification of size selected libraries was carried out. To eliminate adapter -dimers libraries were further sized selected a 2.5% TAE agarose gels. Purified libraries were quantified using a Qubit™ fluorometer (Invitrogen, Carlsbad, CA, USA) and a Quant-iT™ double-stranded DNA High-Sensitivity Assay Kit (Invitrogen, Carlsbad, CA, USA). Clustering and sequencing of the material was carried out as per manufacturers instructions on the Illumina GAIIx platform in the UCD Conway Institute (UCD, Dublin Ireland).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 6
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| Data processing |
basecalling with CASAVA v1.8
fastq reads mapped to C. parapsilosis genome with BWA
BAM files used for peak calling with MACS 1.4, genome size = 12600000, keep duplicate reads = auto
MACS peaks filtered (max False Discovery Rate: 5%)
filtered peaks and WIG files from MACS processed with Peak Splitter to get subpeaks, valley cutoff = 0.1
subpeaks' low coverage extremities shortened with a custom Java script,coverage threshold = 0.5 of coverage at subpeak summit
shortened subpeaks assigned to C. parapsilosis coding genes using a custom Python pipeline. Peaks were not assigned were covering an entire coding sequence or when located 3' to two genes, on the sense and antisense strands.
summit fold change was calculated for each shortened subpeak as ratio of read coverage in the sample at summit position from Peak Splitter and coverage in the control in the corresponding position
summit fold change values lower than 2.0 were ignored
gene assignments supported by only 1 on 3 samples were discarded
results were ranked in decreasing order by Summit Fold Change for sample 1, then sample 2, then sample 3
in case of divergent promoters only one of the two corresponding genes has values in the final table
Genome_build: parapsilosis_genome.fasta (available on a Series records)
Supplementary_files_format_and_content: The 'EFG1chipseq_assignments.txt' file includes information on our ChIP-seq analysis. The first lines include a legend. Promoter region type (column 3) has been determined with a script: divergent promoters are regions in 5 prime to both a sense and an antisense coding gene. A distinction was made between genes predicted to be regulated by EFG1 and promoters: genes were sorted by decreasing order of summit fold change for sample 1, then for sample 2 then for sample 3, then for gene identifier; in case of divergent promoters, values were kept for only one of the two genes.
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| Submission date |
Sep 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Geraldine Butler |
| E-mail(s) |
[email protected]
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| Organization name |
University Colege Dublin Conway Institute
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| Department |
School of Biomolecular and Biomedical Science
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| Lab |
Butler lab
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| Street address |
Belfield
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| City |
Dublin |
| ZIP/Postal code |
D4 |
| Country |
Ireland |
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| Platform ID |
GPL16091 |
| Series (2) |
| GSE41063 |
The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis [ChIP-seq]. |
| GSE41065 |
The APSES Transcription factor Efg1 regulates a novel phenotype switch in Candida parapsilosis. |
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| Relations |
| SRA |
SRX189106 |
| BioSample |
SAMN01180777 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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