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| Status |
Public on Nov 03, 2021 |
| Title |
cdp_4 |
| Sample type |
SRA |
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| Source name |
CDPs
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| Organism |
Mus musculus |
| Characteristics |
cell type: CDPs
cell marker: Lin- cKit Flt3+ CD115+
strain: C57BL/6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
All populations were isolated from 8- to 12-week-old C57BL/6J mice by fluorescence activated cell sorting. The following hematopoietic cell populations were isolated from bone marrow cells: MDPs, CDPs, cMoPs and monocytes. Monocytes were sorted from total bone morrow. MDPs, CDPs and cMoPs were sorted from lineage negative cells. Lineage depletion of mature hematopoietic cell lineages was performed using Sheep anti-Rat IgG magnetic beads and rat IgG isotype lineage antibodies. The following hematopoietic cell populations were isolated from splenic cell suspensions: pDC, cDC CD8a+, cDC CD11b+. DNA was isolated from snap-frozen cell pellets (10.000 - 25.000 sorted cells) using the QIAamp DNA Micro Kit (Qiagen) according to the manufacturer’s instructions.
Tagmentation-based whole-genome bisulfite sequencing (TWGBS) libraries were prepared as described previously (Wang et al., Nat. Prot., 2013). We used 10-30 ng genomic DNA as input.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
bisulfite converted genomic DNA
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| Data processing |
Sequence alignment was performed using an updated version of the workflow published in (Wang et al., Nat. Prot., 2013). The workflow was implemented as a Roddy Workflow (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows). Alignment was performed against the mm10 reference genome extended with the PhiX and lambda phage sequences. Briefly, before alignment, trimmomatic was used for adapter trimming and reads were in silico converted (C>T for the first read in the pair, G>A for the second). Alignments of the individual libraries were performed against the concatenated C>T and G>A in silico converted reference genomes using bwa mem with default parameters. After alignment, reads were converted back to their original state.
PCR duplicate removal was performed per library using Picard MarkDuplicates before merging reads from all libraries.
At each cytosine position, reads that maintain the cytosine status were considered methylated, and the reads that have cytosine converted to thymine were considered unmethylated.
Only reads with a mapping quality >= 25 and bases with Phred-scaled quality score ≥25 were considered for methylation calling.
At least the first 9 bp of the second read and last 9 bp before the adapter in the first read were excluded from methylation calling. The in silico conversion and methylation calling steps were performed using bistro (https://github.com/stephenkraemer/bistro).
Genome_build: mm10
Supplementary_files_format_and_content: QC-filtered methylation calls for all autosomal CpGs in BED6+3 format, with the following columns: chrom, start, end, motif, score, strand, beta_value, n_meth, n_total. The two cytosines in a CpG motif were merged, and the CpG position is given on the plus strand. The score column holds no information (always '.').
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| Submission date |
Dec 31, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Stephen J Kraemer |
| E-mail(s) |
s.kraemer@dkfz.de
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| Organization name |
German Cancer Research Center
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| Lab |
Bioinformatics and Omics Data Analytics
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE164124 |
Methylomes of macrophage-DC progenitors (MDPs), monocytes, common monocyte progenitors (cMoPs), common dendritic cell progenitors (CDPs), plasmacytoid dendritic cells (pDCs), and cDC CD8a+ as well as cDC CD11b+ dendritic cells |
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| Relations |
| BioSample |
SAMN17191974 |
| SRA |
SRX9765305 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4997073_mcalls_cdp_4_CG_chrom-merged_strands-merged.bed.gz |
159.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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