|
| Status |
Public on Jul 07, 2020 |
| Title |
bone marrow progenitors, control rep1 (EMSeq) |
| Sample type |
SRA |
| |
|
| Source name |
lin- bone marrow progenitors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wt
strain: BALB/c
cell type: lin- bone marrow progenitors
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NEBNext Enzymatic Methyl-Seq
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
0.5mg and 0.1mg of DNA was used for library construction using the TruSeq DNA Methylation kit (Illumina) and the NEBNext Enzymatic Methyl-Seq (NEB), respectively. The fragments were sequenced in paired-end 100bp mode .
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
WT1
HSC_metileneDMR_aggregate_methylation_values.tsv
HSC_hypomethylated_metileneDMRs.tsv
HSC_hypermethylated_metileneDMRs.tsv
|
| Data processing |
Library strategy: non-bisulfite EM-seq
Basecalling was performed with Illumina HiSeq Control Software/RTA version 2.7.6.
Raw sequencing reads were processed with the snakePipes version 1.2.0 WGBS workflow to produce bam files filtered for PCR duplicates, separately for reads obtained with each library preparation kit. The resulting bam files were merged per sample.
Merged bams from the previous step were processed with the snakePipes version 1.2.0 WGBS workflow using the –fromBam argument and providing a sample sheet. This produced a.o. a list of differentially methylated regions between the mutant and the wildtype sample groups filtered for FDR<2% and absolute methylation difference between groups of at least 20%.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated tables with methylation values aggregated over DMR intervals per sample are available, as well as tables with filtered hyper- and hypo-methylated DMRs annotated with statistical metrics and distance to nearest gene.
|
| |
|
| Submission date |
Jan 02, 2020 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Thomas Boehm |
| E-mail(s) |
boehm@ie-freiburg.mpg.de
|
| Organization name |
MPI-IE Freiburg
|
| Department |
Immunology
|
| Street address |
Stübeweg 51
|
| City |
Freiburg im Breisgau |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE98648 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 |
| GSE142834 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 [Mouse WGBS] |
|
| Relations |
| BioSample |
SAMN13708315 |
| SRA |
SRX7488530 |
