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| Status |
Public on Aug 12, 2022 |
| Title |
Acinar4 (NOMe-seq) |
| Sample type |
SRA |
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| Source name |
exocrine pancreas
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| Organism |
Mus musculus |
| Characteristics |
tissue: exocrine pancreas
cell type: acinar cell
genotype: wild type
strain: C57BL6
culture condition: 9 days as 3D organoids
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary pancreatic acinar cells were isolated by digestive dissociation of pancreatic tissue and subsequent density gradient centrifugation. After cultivation as 3D matrigel embedded organoids for 9 days, the cells were harvested and subjected to the scNMT-seq protocol. For more information on the generation of pancreatic organoids, see the following papers (Wollny et al., 2016; Krieger et al., 2021).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.
Single-cell NOMe-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
single-cell NOMe-seq
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| Data processing |
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: NOMe-seq
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| Submission date |
Aug 09, 2022 |
| Last update date |
Aug 12, 2022 |
| Contact name |
Ana Martin-Villalba |
| Organization name |
German Cancer Research Center
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| Department |
Molecular Neurobiology
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69121 |
| Country |
Germany |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE210804 |
scNMT-seq of pancreatic organoids - DNA methylation and chromatin accessibility |
| GSE210806 |
Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain |
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| Relations |
| BioSample |
SAMN30215466 |
| SRA |
SRX17002103 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6438122_AS-630734-LR-56692_R1R2_dedup.NOMe.CpG.cov.gz |
206 b |
(ftp)(http) |
COV |
| GSM6438122_AS-630734-LR-56692_R1R2_dedup.NOMe.GpC.cov.gz |
993 b |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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