|
| Status |
Public on Jul 04, 2020 |
| Title |
DM504_MNase_rep2_0_min |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303 (MATa, leu2-3,112, trp1-1, can1-100, ura3-1, ade2-1, his3-11,15)
treatment: 0 mM Cd
time: 0 min
|
| Treatment protocol |
Samples were removed for both MNase treatment and RNA-seq as a 0 time point before addition of Cadmium Chloride to a final concentration of 1mM for 120 min.
|
| Growth protocol |
Cells were grown in rich medium at 30C to an OD600 0.8.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin were prepared as in Belsky et. al. Genes and Development, 2015
See Belsky et al.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MNase chromatin at T=0 prior to Cd addition
|
| Data processing |
Reads were aligned using Bowtie 0.12.7 with parameters "-n 2 -l 20 -m 1 -k 1 -X 1000" to release 64 (sacCer3) of the S.cerevisiae genomic sequence obtained from downloads.yeastgenome.org.
Data processing code from github.com/HarteminkLab/cadmium-paper was run against aligned reads. The following steps from this code were performed:
Chromatin replicates were merged and randomly sampled to equivalent proportions for each time point.
For each base pair at each ORF of the genome, chromatin characterization of transcription factors and nucleosomes were computed relative to TSSs obtained from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973313/bin/supp_42_6_3736__index.html
Transcription factor occupancy was characterized using MNase reads shorter than 100 base pairs and within 200 base pairs upstream of TSSs, defined as the "small fragment promoter occupancy" for each ORF.
Nucleosomes were characterized through cross correlating a bivariate Gaussian distribution against MNase reads at high scoring nucleosomes obtained from GEO/GSE36063. An information entropy score was computed using this per base pair cross correlation for first three nucleosomes downstream of each ORF’s TSS, defined as a gene's "gene body nucleosome disorganization".
RNA reads were counted at non-intronic regions inside ORF boundaries. TPM was computed by scaling read counts by ORF length and normalizing to an equivalent sum for each time point.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3)
|
| |
|
| Submission date |
Jul 01, 2020 |
| Last update date |
May 25, 2021 |
| Contact name |
David M MacAlpine |
| Organization name |
Duke University Medical Center
|
| Department |
Department of Pharmacology and Cancer Biology
|
| Lab |
MacAlpine Laboratory
|
| Street address |
Duke University
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE153609 |
Time series data of chromatin occupancy and transcription under cadmium stress |
|
| Relations |
| BioSample |
SAMN15413893 |
| SRA |
SRX8646174 |
