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| Status |
Public on Oct 06, 2021 |
| Title |
MM_M1_1_sample 342 |
| Sample type |
SRA |
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| Source name |
Marmoset-1
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| Organism |
Callithrix jacchus |
| Characteristics |
tissue: brain
brain region: M1
gender: M
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
M1 regions of human/marmoset brains were dissected.
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 |
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted 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
Genome_build: ASM275486v1
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
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| Submission date |
Mar 08, 2020 |
| Last update date |
Oct 06, 2021 |
| 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 |
GPL28240 |
| Series (1) |
| GSE146608 |
Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1] |
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| Relations |
| BioSample |
SAMN14333781 |
| SRA |
SRX7875869 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4396784_allc_MM-M1-1-190110-P1-P2-D5_ad001.tsv.gz |
83.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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