|
| Status |
Public on Aug 13, 2024 |
| Title |
non_nuc_pool1_R3 |
| Sample type |
SRA |
| |
|
| Source name |
129S6/SvEvTac
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with Phenol/Chlroform, bisulfite converted and then PCR was performed. PCR was purified with SPRI beads and submitted to library preparation.
Libraries were prepared using the NEBNext ChIP-Seq Library Prep Master Mix Set following manufacturer instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
non_nuc_pool1.fasta
|
| Data processing |
Reads were trimmed to remove adapters using Trimmomatic version 0.32.
Reads were mapped using the Bioconductor package QuasR with default settings for bisulfite-converted templates.
Methylation of Cs in the GpC contexts was quantified using qMeth, excluding GCG and GCCG contexts and Cs with coverage <10. Such GpCs were defined as GCH.
Supplementary files format and content: Average methylation data are tab separated tables with three columns: position of the Cs in the GCH context, average methylation values, inserted constructs.
Supplementary files format and content: Single molecule data are tar.gz archives containing tab separated tables for each inserted construct. Each table is a matrix where each column is the position of the Cs in the GCH context, and each row is the binary methylation data for a single read.
|
| |
|
| Submission date |
Aug 31, 2023 |
| Last update date |
Aug 13, 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) |
| GSE242066 |
Genome access is transcription factor specific and defined by nucleosome position [NOMe-seq] |
| GSE242067 |
Genome access is transcription factor specific and defined by nucleosome position |
|
| Relations |
| BioSample |
SAMN37215742 |
| SRA |
SRX21559103 |
