|
| Status |
Public on Jun 09, 2021 |
| Title |
wild type untagged t4 WCE |
| Sample type |
SRA |
| |
|
| Source name |
meiotic yeast cells
|
| Organisms |
Saccharomyces cerevisiae; Nakaseomyces glabratus |
| Characteristics |
strain: SK1 + CBS138
antibody: none
index 1: AGCGATAG
index 2: CCTATCCT
|
| Treatment protocol |
All cells were crosslinked for 15 min in 1 % formaldehyde at room temperature. The formaldehyde was stopped by addition of glycine to 131 mM. For each ChIP, 2x109 S. cerevisiae cells were mixed with 2x108 C. glabrata cells which where crosslinked separately. ChIP from meiotic cultures was performed as described in Mendoza et al., Methods Mol Biol. 2009;557:267-83.
|
| Growth protocol |
S. cer. cells (experimental strain) were sporulated in 2% potassium acetate supplemented with 0.1% (w/v) polypropylene glycol (PPG) to undergo synchronous meiosis at 30°C by the SPS pre-growth method described in Mendoza et al., Methods Mol Biol. 2009;557:267-83. C. gla. cells (calibrating strain) were grown in YPD to reach a density of 0.6 at OD660 (Hu et al., Nucleic Acids Res. 2015).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were opened by FastPrep-24™ 5G Instrument (MP Biomedicals) followed by sonication with Bioruptor® Pico instrument. After removing the cell debris, the supernatant was used for the chromatin immuno-precipitation with anti-myc 9E11 antibody. To reverse crosslink, all the samples were incubated in 65°C overnight. DNA purification was conducted by regular phenol/chloroform/isoamyl alcohol extraction.
Library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit according to the manufacturer´s protocol. Amplified library DNA was purified and subjected to ~140 bp - 800 bp size selection using Agencourt AMPure XP beads (Beckman Coulter) and quantified by NanoDrop™ 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Unaligned bam files were converted to fastq files with the help of SamToFastq.jar (picard-tools v1.119). After removal of adapter sequences with cutadapt (-O 3 -e 0.15 -m 15 –max-n 3), read pairs were aligned to both the ASMv1 and the calibration genome CBS138 with NextGenMap (“local”, allowing up to 10% soft clipping and 4% error), in order to get specific alignments from either species.
Aligned read pairs were "filled up" to cover the whole insert length before calculation of the depths per position ("filled dpp") with a custom Java script. Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.cbs138 / IP.cbs138 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M), 10M/IP.asmv1.
Wiggle files were created with the help of IGVTools v. 2.3.72.
Genome_build: ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer.; CBS138 genome version s02-m07-r01 for C. gla.
Supplementary_files_format_and_content: For each IP sample, filled dpp (chrom, position, depth) and corresponding wiggle files (numbers preceding the .wig file extension correspond to the RGB color code) are provided
|
| |
|
| Submission date |
Mar 26, 2021 |
| Last update date |
Jun 09, 2021 |
| Contact name |
Franz Klein |
| E-mail(s) |
franz.klein@univie.ac.at
|
| Organization name |
Max Perutz Labs, University of Vienna
|
| Department |
Chromosome Biology
|
| Street address |
Dr. Bohr-Gasse 9
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL29937 |
| Series (2) |
| GSE169760 |
Spo11 generates gaps through concerted cuts at sites of topological stress [Top2] |
| GSE171046 |
Spo11 generates gaps through concerted cuts at sites of topological stress |
|
| Relations |
| BioSample |
SAMN18514579 |
| SRA |
SRX10459803 |
