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| Status |
Public on Jan 03, 2023 |
| Title |
spt650-1alpha-MCM-IP |
| Sample type |
SRA |
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| Source name |
his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: S. cerevisiae (S. pombe spike-in)
treatment: alpha arrested
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| Treatment protocol |
Yeast strains were grown to an OD~0.2 and then synchronized by treatment with alpha factor for 2 hours. Visual inspection confirmed >90% of cells had shmoo-like morphology.
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| Growth protocol |
All S. cerevisiae strains used in this study are in the S288C background. All S. cerevisiae liquid cultures were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30°C . For spike-in normalization, S. pombe liquid cultures were grown in YES (0.5% yeast extract, 3% glucose, 225 mg/l each of adenine, histidine, leucine, uracil, and lysine) at 32°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared with Qiagen GeneRead Kit according to manufacturers instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
his3D200 lys2-128d ura3-52 leu2D0 bar1D::URA3 spt6-50
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| Data processing |
Briefly, data was aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2 (Langmead and Salzberg, 2012). Sequences were trimmed with cutadapt and processed using samtools (Li et al., 2009), bedtools, and deeptools (Ramírez et al., 2016) to generate genome coverage tracks. Samples are spike-in normalized.
Assembly: S. cerevisiae R64-2-1, S. pombe ASM294v2
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| Submission date |
Dec 29, 2022 |
| Last update date |
Jan 03, 2023 |
| Contact name |
Catherine LW Miller |
| Organization name |
Harvard Medical School
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| Street address |
77 Ave Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19756 |
| Series (2) |
| GSE201634 |
The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome instability |
| GSE221913 |
The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome stability [MCM ChIPseq] |
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| Relations |
| BioSample |
SAMN32492290 |
| SRA |
SRX18884234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6909601_s50-alpha1-IP_spikein.bw |
3.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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