NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6755917 Query DataSets for GSM6755917
Status Public on Nov 29, 2022
Title 140421_PY02_Somatic_WGBS
Sample type SRA
 
Source name Somatic
Organism Trichosurus vulpecula
Characteristics Sex: Male
cell type: Somatic
developmental stage: 16 days postpartum
treatment: GFP (SSEA1) negative
number of_cells: 150
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)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model NextSeq 2000
 
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
 
Submission date Nov 25, 2022
Last update date Nov 29, 2022
Contact name Donna Bond
Organization name University of Otago
Department Department of Anatomy
Street address 270 Great King Street
City Dunedin
ZIP/Postal code 9016
Country New Zealand
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.