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Sample GSM7461665 Query DataSets for GSM7461665
Status Public on Mar 11, 2024
Title SMF_ESC_BPTFko_rep3
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
BioSample SAMN35652668
SRA SRX20607934

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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