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| Status |
Public on May 21, 2019 |
| Title |
4-F-R1 |
| Sample type |
SRA |
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| Source name |
Yeast colony
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
biomass: 4 mg
condition: FAIRE
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| Growth protocol |
Yeast giant colonies (6 per plate) were grown at 28 °C on GMA (1 % yeast extract, 3 % glycerol, 2 % agar, 1 % ethanol, 10 mM CaCl2, 0.05 % glucose, and 0.002 % uracil) with pH dye indicator bromocresol purple.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell subpopulations removed using a spatula at 3 days, FAIRE samples (but not input samples) cross-linked with formaldehyde, DNA sheared by sonication, phenol-chloroform extraction carried out to purify DNA fragments
FAIRE and input DNA samples were prepared for sequencing using ThruPLEX reagents (Rubicon Genomics, Ann Arbor, MI). 2-5 ng FAIRE or input control DNA was used as starting material for library preparation. Sequencing was performed on a NextSeq 500 instrument (Illumina, San Diego, CA) with 75 bp single-end reads.
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| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped using Bowtie2 version 2.2.8 and quality checking was done using Samtools version 1.4, Sambamba v. 0.6.6, Bedtools v. 2.26.0 and FastQC v. 0.11.5
Mapped reads were downsampled to 10 million reads per sample and metrics were collected for unmapped, multi-mapping, single-mapping and optical duplicate reads
Unique reads that map to a single location were retained and further downsampled to 3 million reads per sample
Peak calling was performed with MACS2 v. 2.1.1.20160309 using the following settings: -q 0.1, -m 2 50, --bw 186, -g 12000000
Overlapping peaks were counted using Bedtools' intersect and the three most similar replicates per group were retained for IDR analysis.
Genome_build: SacCer3 R64
Supplementary_files_format_and_content: Narrowpeak files containing peaks called for each corresponding pair of FAIRE and input samples
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| Submission date |
Sep 22, 2017 |
| Last update date |
May 21, 2019 |
| Contact name |
Alexandru Mizeranschi |
| Organization name |
BIOCEV
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| Street address |
Průmyslová 595
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| City |
Vestec |
| ZIP/Postal code |
252 50 |
| Country |
Czech Republic |
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| Platform ID |
GPL19756 |
| Series (1) |
| GSE104124 |
An optimized FAIRE procedure for low cell numbers in yeast. |
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| Relations |
| BioSample |
SAMN07687683 |
| SRA |
SRX3205119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2790315_BY-0-4-72-1_1-faire_peaks.narrowPeak.gz |
128.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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