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| Status |
Public on Jul 05, 2024 |
| Title |
D3, B16, scATACseq |
| Sample type |
SRA |
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| Source name |
B16 F10
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| Organism |
Mus musculus |
| Characteristics |
cell type: Melanocytes
cell line: B16 F10
time: Day 3
molecule subtype: nuclear chromatin
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| Growth protocol |
B16 F10 cells were cultured at a very low density of 100 cells/cm2 in DMEM high glucose supplemented with 10% fetal bovine serum at 37 °C, 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Day 0, 3 and 5 B16 F10 cells were trypsinized on the same day, spun down at 400g, then washed and resuspended in 1x DPBS. All the three samples were then taken for library preparation
scMultiome (ATAC+Gene Expression):
Libraries were prepared according to the manufacter’s instructions (single cell multiome ATAC + Gene Expression protocol, 10x Genomics). Briefly, samples were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index were added.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger Arc software v2.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, peak files and fragments files
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| Submission date |
May 22, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Vivek T Natarajan |
| E-mail(s) |
tnvivek@igib.in
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| Organization name |
CSIR-IGIB
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| Lab |
Pigment Cell Biology Lab
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| Street address |
Mathura Road
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| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110025 |
| Country |
India |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE233134 |
Gene expression and chromatin accessibility profile at single cell level of B16 cells [B16_D0_3_5_scMulti] |
| GSE233198 |
Differential programs of melanocyte cell states |
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| Relations |
| BioSample |
SAMN35305536 |
| SRA |
SRX20464943 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7401914_D3_atac_fragments.tsv.gz |
809.1 Mb |
(ftp)(http) |
TSV |
| GSM7401914_D3_atac_fragments.tsv.gz.tbi.gz |
652.7 Kb |
(ftp)(http) |
TBI |
| GSM7401914_D3_atac_peaks.bed.gz |
922.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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