|
| Status |
Public on Mar 11, 2024 |
| Title |
SMF_ESC_BPTFko_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cells
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
genotype: BPTF knock-out
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using phenol:chloroform and further extracted with chloroform.
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) .
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were trimmed using Trimmomatic v0.32 (24695404) in paired-end mode using the ILLUMINACLIP option. Trimmed reads were mapped to the mm10 mouse genome using the qAlign function from the QuasR package v_1.36.0 with parameters for bisulfite data.
Supplementary files format and content: DNA methylation was quantified for all Cs using qMeth and then separated into Cs in the CpG or GpC context, removing GCG and CCG sequence contexts as these cannot be distinguished between endogenous methylation and SMF methylation. Plots of SMF data are of 1 − GpC methylation to visualize the footprint.
Library strategy: Single-molecule footprinting
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE234293 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [SMF] |
| GSE234295 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF |
|
| Relations |
| BioSample |
SAMN35652670 |
| SRA |
SRX20607938 |
