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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 06, 2023 |
| Title |
18A_M_339 |
| Sample type |
SRA |
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| Source name |
C57BL/6J Male P56 Mouse Brain
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| Organism |
Mus musculus |
| Characteristics |
brain region: CB-5
age: P56
strain: C57BL/6J
cemba_id: 18A
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| Growth protocol |
All mice are C57BL/6J Male, brain dissected in P56
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3
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| Submission date |
Jul 03, 2023 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
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| Phone |
8584534100
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| Organization name |
HHMI-Salk-Institute
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| Department |
Genomic Analysis Laboratory
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| Lab |
Ecker lab
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| Street address |
10010 North Torrey Pines Road
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE236451 |
DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [18A, 18B, 6E, 6F] |
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| Relations |
| BioSample |
SAMN36293369 |
| SRA |
SRX20888371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7536447_CEMBA210107_18A_1-3-L20-E6.allc.tsv.gz |
43.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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