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Status |
Public on Nov 29, 2022 |
Title |
140421_PY02_Somatic_WGBS |
Sample type |
SRA |
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Source name |
Somatic
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Organism |
Trichosurus vulpecula |
Characteristics |
Sex: Male cell type: Somatic developmental stage: 16 days postpartum treatment: GFP (SSEA1) negative number of_cells: 150
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Extracted molecule |
genomic DNA |
Extraction protocol |
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. GFP-negative cells (somatic cells) were sorted as negative controls into 0.2 % Triton-X and stored at -80 °C. Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
NextSeq 2000 |
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Data processing |
Raw reads were trimmed using Trim Galore! (v0.4.2) by removing 10 bp from the 5’ end of all reads and removing low-quality base calls (Phred score < 20). Bismark (v0.19.0), with the -pbat option, was used to map the trimmed reads to the possum genome reference (GCA_011100635), deduplicate and extract methylation calls in the CG dinucleotide context. Assembly: Trichosurus vulpecula (GCA_011100635.1) Supplementary files format and content: tab-delimited text file that includes Bismark mapping report for each sample
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Submission date |
Nov 25, 2022 |
Last update date |
Nov 29, 2022 |
Contact name |
Donna Bond |
Organization name |
University of Otago
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Department |
Department of Anatomy
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Street address |
270 Great King Street
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City |
Dunedin |
ZIP/Postal code |
9016 |
Country |
New Zealand |
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Platform ID |
GPL32879 |
Series (2) |
GSE218734 |
The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genesed genes [WGBS] |
GSE218811 |
The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes |
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Relations |
BioSample |
SAMN31871608 |
SRA |
SRX18377697 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6755917_CpG_context_140421_PY02_Somatic_WGBS_trimmed_bismark_bt2.deduplicated.txt.gz |
81.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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