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Sample GSM3878681 Query DataSets for GSM3878681
Status Public on Aug 26, 2020
Title 180605_CEMBA_mm_P56_P63_4C_CEMBA180417_4C_5_CEMBA180417_4C_6_A4_AD012_indexed
Sample type SRA
 
Source name C57BL/6J Male P56 Mouse Brain
Organism Mus musculus
Characteristics brain region: SSp
Sex: male
age: P56
strain: C57BL/6J
cemba_id: 4C
Growth protocol All mice are C57BL/6J Male, brain dissected in P56
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.
 
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 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
Genome_build: 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
 
Submission date Jun 12, 2019
Last update date Aug 26, 2020
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
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 GPL24247
Series (1)
GSE132601 Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180417_4C]
Relations
BioSample SAMN12037537
SRA SRX6050445

Supplementary file Size Download File type/resource
GSM3878681_allc_180605_CEMBA_mm_P56_P63_4C_CEMBA180417_4C_5_CEMBA180417_4C_6_A4_AD012_indexed.tsv.gz 130.8 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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