 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 14, 2022 |
| Title |
ATAC-Seq of wide type cell: budding yeast by4741 repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: yeast cells
genotype: wild type
growth phase: mid-log phase yeast cells, cultured at 30°C
|
| Growth protocol |
Cells were cultured at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5×10^4 mid-log phase yeast cells (OD600 ~1.0) were collected and digested for 50 min at 30°C by using 1 μg/μL zymolyase in sorbitol buffer (1.1 M sorbitol, 0.1 M K2HPO4, pH 7.5). Then, the spheroplast was centrifuged for 5 min at 2000g (room temperature). Wash the spheroplast once with sorbitol buffer. The cell pellet was re-suspended in 50μL Tn5 digestion mix by using TruePrepTMDNA Library Prep Kit V2 for IIIumina（Vazyme#TD501-01）: 5*TTBL, 10ul; TTE MIX V50, 5ul; ddH2O, 35ul, and incubated at 37°C for 30 min. VAHTS DNA Clean Beads (Vazyme#N411) were used to purify the Tn5 digested product.
Sequencing library was amplificated by PCR with TruePrepTM Index Kit V2 for IIIumina (Vazyme#TD202). PCR product was purified by using VAHTS DNA Clean Beads (Vazyme#N411) and eluted in 20 μL ddH2O.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw read files were first processed by Trim Galore version 0.5.0 (Babraham Institute) to trim low-quality reads and remove adapters.
Bowtie2 version 2.3.1 was used for mapping reads to S. cerevisiae using the ‘-t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant’ parameter, where ‘-X 2000’ allows the maximum fragment length to be 2000bp, ‘--no-mixed’ suppresses unpaired alignments for paired reads and ‘--no-discordant’ suppress discordant alignments for paired reads.
To minimize PCR and sequencing optical bias, Picard version 2.18.7 subcommand MarkDuplicates was used to remove duplicates (defined as the same start and end positions) and CollectInsertSizeMetrics was used to estimate fragment size distribution. Samtools version 1.4 was used for SAM file manipulation. Specifically, subcommand view with ‘-q 10 -b’ parameter was used to remove low-quality, unmapped, unpaired and duplicated reads, as well as convert to BAM format.
Subcommands sort and index with default parameters were used to sort and index BAM files. BigWig format files were generated via bamCoverage version 1.5.11 with the ‘--bs 10 --normalizeUsingRPKM’ parameter.
HMMRATAC version 1.2.10 was used to call peaks using the sorted BAM file.
Assembly: S.cerevisiae (sacCer3)
Supplementary files format and content: bigWig, narrowPeak, gappedPeak
Supplementary files format and content: bigWig and gappedPeak files on the series record represent the integrated data for repeat 1 and 2 for each genotype.
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
May 17, 2022 |
| Contact name |
Yue Pan |
| E-mail(s) |
panyue@shanghaitech.edu.cn
|
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Department |
Center for Excellence in Molecular Cell Science, CAS
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL27812 |
| Series (2) |
| GSE202946 |
Swc4 protects nucleosome free chromatin of telomeres, tRNA genes and rDNA loci to inhibit genome instability [ATAC-seq] |
| GSE215375 |
Swc4 protects nucleosome free chromatin of telomeres, tRNA genes and rDNA loci to inhibit genome instability |
|
| Relations |
| BioSample |
SAMN24492649 |
| SRA |
SRX13554641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6139041_WT_2.bw |
5.4 Mb |
(ftp)(http) |
BW |
| GSM6139041_WT_2_peakcall_peaks.narrowPeak.gz |
34.1 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
