|
| Status |
Public on Jan 05, 2023 |
| Title |
MNase-Seq Control 1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741+ChrXVII: pCC1BAC-LCyeast-20-kb-random-DNA
fraction: naked DNA (control)
|
| Treatment protocol |
Nucleosomal DNA was obtained following the protocol described by Rando, 2010 with the modifications: crosslinked spheroplasts stemming from 100 ml culture were treated with 1600 U MNase (Worthington Biochemical Corporation) for 1-1.5 h at 37 ˚C. A control DNA was obtained by MNase-treatment of genomic DNA from the same experiment (genomic DNA isolated from formaldehyde-crosslinked spheroplasts).
|
| Growth protocol |
Yeast were grown in SD his- medium at 30˚C to OD(595)=~0.55.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mononucleosomes and genomic DNA digestion product corresponding to mononucleosomal-sized DNA were excised from the agarose gel.
Library preparation was performed as described in Wong et al., 2013 with the following exception: 1 μg gel-excised mononucleosomal DNA/control DNA was used as the starting material.
TrueSeq combinatorial dual sequencing primers (Illumina) were used for library ligation and amplification; the library was amplified for 12 cycles.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Random DNA is at ChrXVII from 3911 to 21878 bp.
MNase_control_fragment_location.bed
|
| Data processing |
bowtie2 --no-mixed --no-discordant --no-dovetail --no-contain --no-overlap
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Assembly: sacCer3
Supplementary files format and content: After checking the replicates, all fastq files were unified (into one R1 and one R2 file). Paired-end read derived MNase-Seq fragments (MNase_fragment_location.bed for chromatin, and MNase_control_fragment_location.bed for naked DNA) have 3 columns: chromosome name, start location and end location. Midpoints derived for the chromatin fragments (MNase_midpoint_list.bed) have 3 columns: chromosome name, nt location, and number of midpoints per nt location. MNase midpoints per 10 bp sliding window (MNase_midpoint_10bp_sliding_window_chrXVIInorm_copy_number.bed) have 4 columns: chromosome name, start, end, and the count of midpoints per sliding window. In the later one, ChrXVII copy number were adjusted to allow comparison with genomic data.
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Jan 05, 2023 |
| Contact name |
Zlata Gvozdenov |
| E-mail(s) |
zlata_gvozdenov@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
BCMP
|
| Lab |
Kevin Struhl
|
| Street address |
240 Longwood Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL31112 |
| Series (2) |
| GSE216309 |
High level and nature of transcriptional noise in yeast cells [MNase-Seq] |
| GSE216450 |
High level and nature of transcriptional noise in yeast cells |
|
| Relations |
| BioSample |
SAMN31429355 |
| SRA |
SRX18012522 |
