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| Status |
Public on Nov 10, 2014 |
| Title |
ccc1-w52a replicate 1 |
| Sample type |
SRA |
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| Source name |
Yeast
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| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: ccc1-w52a mutant
media: YPAD media
cell density: OD=1.0
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| Growth protocol |
100ml cultures of cells in YPAD were grown at 30˚C to an OD600 of 1.0
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| Extracted molecule |
total RNA |
| 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 by SDS/proteinase K followed by purification using MN Nucleospin Gel Cleanup column
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 amplifying for 15 cycles, size selection betwen 200-350bp
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
paired with WT replicates 1 and 2
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| Data processing |
ChIP-seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence and, if a read could align equally well to multiple loci, a locus was chosen at random
Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDtools
A sliding window of 1000-bp size was used to smooth the bedgraphs for each ChIP-Seq dataset and then subtelomere regions were called using those smoothed bedgraphs.
RNA-seq data were aligned using Tophat, allowing reads to align to up to 50 loci in the genome. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wildtype samples and knockout mutant samples.
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: Bedgraph files with 1000-bp sliding window called on them for ChIP-Seq samples and RPKM tables for RNA-seq table.
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| Submission date |
Sep 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Phillip Anthony Dumesic |
| Organization name |
Dana-Farber Cancer Institute
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| Street address |
360 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL19081 |
| Series (1) |
| GSE61550 |
Product binding enforces the genomic specificity of a yeast Polycomb repressive complex |
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| Relations |
| BioSample |
SAMN03074142 |
| SRA |
SRX706399 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1508070_RNA_ccc1-W52A-1.txt.gz |
120.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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