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| Status |
Public on Jan 02, 2023 |
| Title |
WGBS_TSC4_WT |
| Sample type |
SRA |
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| Source name |
Trophoblast stem cells
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| Organism |
Mus musculus |
| Characteristics |
condition: WT
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| Treatment protocol |
no treatment
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| Growth protocol |
TSCs (TSC line 4) were cultured in TSC medium (RPMI+GlutaMAX (Thermo, #61870044), 20 % fetal bovine serum (PAN, #P30-2602), 1 mM sodium pyruvate (Thermo, #11360070), 100 µM 2-mercaptoethanol (Thermo, #21985023) and 1X Penicillin/Streptomycin (Thermo, #15140122); 25 ng/ml FGF4 (R&D systems, #235-F4-025) and 1 µg/ml Heparin (Sigma, #H3149).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermo, #K182002) according to manufacturer’s instructions.
Concentration of genomic DNA (gDNA) was quantified using a Qubit 3.0 Fluorometer. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Bisulfite-converted DNA
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| Data processing |
Raw reads were subjected to adapter and quality trimming using cutadapt (version 2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
The trimmed reads were aligned to the mouse genome (mm10) using BSMAP (version 2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R).
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
All analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file containing methylation rates for CpGs covered by at least 10 and at most 150 reads: <chr> <start> <end> <methylation rate>
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| Submission date |
Feb 17, 2022 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Sara Hetzel |
| E-mail(s) |
hetzel@molgen.mpg.de
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| Organization name |
Max Planck Institute for Molecular Genetics
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| Department |
Genome Regulation
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| Lab |
Meissner Lab
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| Street address |
Ihnestraße 63
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| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE166362 |
Dynamic antagonism between key repressive pathways maintains the placental epigenome |
| GSE196977 |
Dynamic antagonism between key repressive pathways maintains the placental epigenome (WGBS) |
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| Relations |
| BioSample |
SAMN26027656 |
| SRA |
SRX14214736 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5906226_WGBS_TSC4_WT_mm10.bw |
211.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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