|
| Status |
Public on Aug 30, 2023 |
| Title |
Homo sapiens MNase digestion products |
| Sample type |
SRA |
| |
|
| Source name |
synthetic construct (Widom 601 145 bp DNA) amplified in Escherichia coli cells
|
| Organism |
synthetic construct |
| Characteristics |
cell line: synthetic construct (Widom 601 145 bp DNA) amplified in Escherichia coli cells
cell type: not applicable
genotype: not applicable
treatment: not applicable
|
| Treatment protocol |
3 μg of NCPs (A260 DNA-based quantification) and 18 U of MNase were incubated in 150 μl reactions for 30 min at 37°C (50 mM Tris pH 8.0, 2.5% glycerol, 25 mM NaCl, 5 mM CaCl2, 1.5 mM DTT). Reactions were quenched with 75 μl of stop solution (20 mM Tris pH 8.0, 80 mM EDTA, 80 mM EGTA, 0.25% SDS, 0.5 mg/ml Proteinase K).
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Around 1μg of DNA was isolated from each MNase reaction using a Monarch PCR & DNA Cleanup Kit (elution volume of 15 μl, NEB). The DNA was treated with 5 U of Antarctic Phosphatase (NEB #M0289S) for 1h at 37°C in 20 μl reactions. The phosphatase was heat-inactivated for 2 min at 37°C.
Libraries were constructred using the Azenta Amplicon-EZ service
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
MNase_Sequencing_Processed.xlsx
|
| Data processing |
Adapter trimming with Cutadapt
Alignment to the reference Widom 601 145 bp DNA sequence using the Burrows-Wheeler Aligner
Filtering reads for length <= 145 bp
Assembly: reference sequence: ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACgTGTCAGATATATACATCGAT
Supplementary files format and content: "MNase_Sequencing_Processed.xlsx" - excel format; contains sequencing details and unfiltered/filtered read start and end positions
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Shaun Michael Webb |
| E-mail(s) |
shaun.webb@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
2.21 Swann Building, Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17769 |
| Series (1) |
| GSE226029 |
Histone divergence in Trypanosoma brucei results in unique alterations in nucleosome structure |
|
| Relations |
| BioSample |
SAMN33434653 |
| SRA |
SRX19494933 |
