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Sample GSM4396587 Query DataSets for GSM4396587
Status Public on Oct 06, 2021
Title MM_M1_1_sample 145
Sample type SRA
Source name Marmoset-1
Organism Callithrix jacchus
Characteristics tissue: brain
brain region: M1
gender: M
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.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
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
Submission date Mar 08, 2020
Last update date Oct 06, 2021
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL28240
Series (1)
GSE146608 Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1]
BioSample SAMN14333599
SRA SRX7876234

Supplementary file Size Download File type/resource
GSM4396587_allc_MM-M1-1-190110-P1-P2-B4_ad006.tsv.gz 5.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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