|
| Status |
Public on Jul 07, 2020 |
| Title |
Zebrafish WT1 (TruSeq) reanalysis |
| Sample type |
SRA |
| |
|
| Source name |
control rep1
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
genotype: wt
strain: mixed background
surface phenotype: n/a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 3 dnmt1+/+ and 3 dnmt1-/- zebrafish at 18 dpf using the DNeasy blood and tissue kit (Qiagen).
1mg and 0.5mg of DNA was used for bisulfite reactions and library construction using the TruSeq DNA PCR-free library preparation kit (Illumina) and the EpiGnome Methyl-Seq kit (Epicentre), respectively. The fragments were sequenced in paired-end 100bp mode on 1 lane of Illumina HiSeq 2500 instrument.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Zebrafish WT1 (TruSeq)
GSM2607706
|
| Data processing |
Basecalling was performed with Illumina HiSeq Control Software/RTA version 1.18.64.
Raw sequencing reads were trimmed with cutadapt version 1.9.1 (Martin, 2011) as follows: first 2 (TruSeq) or 6 (Epignome) 5'-most nucleotides were hard-trimmed and Illumina adapter sequences removed.
Bisulfite-specific operations on reads and reference genome were performed with methylCtools version 0.9.4 (Hovestadt et al., 2014). Bisulfite-converted reads were mapped to bisulfite-converted GRCz10 zebrafish genome with bwa-mem version 0.7.12 separately for the two library types.
Back-converted bam files were sorted with samtools version 1.3.1, PCR duplicates removed and read group information added with Picard tools v1.136. The two resulting bam files per sample were merged with samtools and methylation bias profiled with MethylDackel v0.1.7. Methylated and unmethylated read counts per CpG position were extracted with methylCtools v0.9.4 with mapping quality threshold of 10, SNP detection, counting only one of two overlapping paired end reads, skipping 5 nucleotides from each read length and zero-padding of uncovered positions.
Data postprocessing was performed in R version 3.2.3. Raw methylation values were set to NA for CpG positions with at least 0.25 SNP allelic frequency as well as for positions with aggregate coverage of less than 10 reads. Single CpG methylation values were aggregated per target genomic interval as mean values.
Genome_build: GRCz10
Supplementary_files_format_and_content: Whole genome single CpG as well as mean methylation values in target genomic intervals are summarized in corresponding tab-separated tables for all samples.
|
| |
|
| Submission date |
Nov 27, 2019 |
| 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 |
GPL18413 |
| Series (2) |
| GSE98648 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 |
| GSE141114 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 (Zebrafish) |
|
| Relations |
| Reanalysis of |
GSM2607706 |
| BioSample |
SAMN13412412 |
| SRA |
SRX7228452 |
