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| Status |
Public on Dec 04, 2023 |
| Title |
snmC-seq2 of mus musculus: adult male ventral hippocampus AJ [AJ_vhipp_2_methyl] |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: AJ
tissue: Brain
age: adult
Sex: male
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2023
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2023
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
AJ_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar
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| Data processing |
snmC2-seq
Reads were mapped using Bismark V0.22.3, followed by cell filtering based on mCCC levels, global mCG levels, global mCH levels, total mapped reads, Bismark mapping rate, and percent genome covered
Methylation features were calculated as fractions of methylcytosine over total cytosine across gene bodies ± 2kb flanking regions and 100kb bins spanning the entire genome. Methylation features were further split into CG and CH methylation types. Principal component analysis was run using Scanpy followed by knn using only the top 16 principal components by amount of variance explained and k=15. Harmony was used to correct batch between strains and unbias clusters arising from strain differences. After Harmony was applied, iterative clustering was performed with a combination of leiden unsupervised clustering and UMAP dimensionality reduction, identifying clusters as cell types by marker gene hypomethylation
Assembly: mm10
Supplementary files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
Supplementary files format and content: tab-separated file including number of cells for each sample and cell type
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| Submission date |
Oct 13, 2023 |
| Last update date |
Dec 04, 2023 |
| Contact name |
Patrick Chen |
| E-mail(s) |
pbc9@ucla.edu
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| Organization name |
UCLA
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| Department |
Psychiatry
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| Street address |
635 Charles E Young Dr S
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90024 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE245367 |
Single cell methylation, RNA, and ATAC sequencing of ventral hippocampal brain tissue from inbred mouse strains |
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| Relations |
| BioSample |
SAMN36274590 |
| SRA |
SRX20869093 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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