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Status |
Public on Oct 06, 2021 |
Title |
MM_M1_1_sample 125 |
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 |
SAMN14333753 |
SRA |
SRX7877509 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4396567_allc_MM-M1-1-190110-P1-P2-B2_ad012.tsv.gz |
115.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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