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| Status |
Public on Nov 15, 2023 |
| Title |
CEMBA3C_MarmosetM1_R1_P1-1-C23-A13 |
| Sample type |
SRA |
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| Source name |
Marmoset_M1C
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| Organism |
Callithrix jacchus |
| Characteristics |
brain region: Motor cortex
gender: M
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| Treatment protocol |
For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Motor cortex of 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 |
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
Assembly: cj1700_1.1 (calJac4), annotation: GCA_009663435.2
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 |
Aug 21, 2023 |
| Last update date |
Nov 15, 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 |
GPL28240 |
| Series (1) |
| GSE241339 |
Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex [marmoset] |
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| Relations |
| BioSample |
SAMN37097975 |
| SRA |
SRX21439775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7721189_CEMBA3C_MarmosetM1_R1_P1-1-C23-A13.allc.tsv.gz |
133.0 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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