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| Status |
Public on Aug 05, 2018 |
| Title |
3bp_substitution_genomic_1 |
| Sample type |
SRA |
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| Source name |
Cells
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| Organism |
Saccharomyces cerevisiae x Saccharomyces uvarum |
| Characteristics |
growth conditions: saturated in YPD
restriction enzyme: DpnII
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| Treatment protocol |
Cells were crosslinked by addition of 37% formaldehyde to a 1% final concentration, for 20 minutes at room temperature, and then quenched by addition of 2.5M glycine, incubation for 5 minutes, and a TBS (Tris-buffered saline) wash.
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| Growth protocol |
Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
3bp_substitution.fa
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| Data processing |
Library strategy: 3 bp substitution cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the mutagenized subset of the S. cerevisiae HAS1pr-TDA1pr region using Bowtie2. The read alignments were scored for the number of substitutions, insertions, and deletions, and the frequency of each substitution and the total number of reads were calculated.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "mutcounts.txt" include the 1) set of mutations, 2) the total number of mutations, 3) the number of substitutions, 4) the number of deletions, 5) the number of insertions, 6) the number of reads with this set of mutations. tab-delimited text files ending in "subcounts.txt" include the number of reads with each substitution and the total number of reads. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.
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| Submission date |
Aug 03, 2018 |
| Last update date |
Feb 15, 2019 |
| Contact name |
Seungsoo Kim |
| Organization name |
Stanford University
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| Department |
Chemical and Systems Biology
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| Lab |
Joanna Wysocka
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| Street address |
265 Campus Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL25423 |
| Series (1) |
| GSE118118 |
A combination of transcription factors mediates inducible interchromosomal contacts |
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| Relations |
| BioSample |
SAMN09765430 |
| SRA |
SRX4507101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3318835_3bp_substitution_genomic_1.mutcounts.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSM3318835_3bp_substitution_genomic_1.subcounts.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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