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| Status |
Public on Mar 05, 2019 |
| Title |
chr III tDNA-D Total Input DNA Seq |
| Sample type |
SRA |
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| Source name |
chr III tDNA-D Total Input_chr III tDNA-D
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ROY5151 W-303
genotype: MATa SCC2-13xMyc::KanMX ade2-1 trp1-1 ura3-1 chrIII (t0D, t1D, t3D, t4D, t5D, t6D, t7D, t8D+t9D::LEU2), T1+T7::HIS3
chip antibody: none (input)
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| Growth protocol |
Cells were grown to early log phase in 300ml YPD
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde, quenched, lysed and sonicated to generate small DNA fragments. ChIPs were performed with 5ug of 9E10 from Covance (now Biolegend).
Libraries were prepared at the Functional Genomics Laboratory, UC Berkeley and sequenced at the Vincent J Coates Sequencing Laboratory at UC Berkeley.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Total Input DNA
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| Data processing |
Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, Nature Methods, 2012) with the default settings.
The typical DNA fragment length was estimated based on strand cross-correlation maxima using the SPP package (Kharchenko et al., Nat Biotechnol., 2008) (available at https://github.com/hms-dbmi/spp/).
The reads were extended to the estimated typical fragment size of 170 bp and genome-wide coverage profiles were computed in MATLAB. The coverage profiles were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser
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| Submission date |
Oct 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
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| Phone |
301-435-8670
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| Organization name |
National Institutes of Health
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| Department |
NICHD
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| Lab |
David J. Clark Lab
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| Street address |
6 Center Drive, Room 2A14
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21656 |
| Series (2) |
| GSE106249 |
Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq] |
| GSE106250 |
Transfer RNA Genes Affect Chromosome Architecture and Function |
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| Relations |
| BioSample |
SAMN07839682 |
| SRA |
SRX3334035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2832775_ROY5151_Scc2_Input.tdf |
47.2 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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