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| Status |
Public on Jul 05, 2024 |
| Title |
LP, B16, scRNAseq |
| 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
condition: low pigment
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| Growth protocol |
B16 F10 cells were cultured at a very low density of 100 cells/cm2 for 7 days in DMEM high glucose supplemented with 10% fetal bovin serum at 37 °C, 5% CO2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
B16 F10 cells were trypsinized at day 7, spun down at 400g, then washed and resuspended in 1x DPBS. Low and high pigmented cells were sorted using the side scatter intensity of a flow cytometer and taken for library preparation
Libraries was prepared according to the manufacter’s instructions (single cell 3’ v3.1 (single index) protocol, 10x Genomics). Briefly, B16 cells 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 |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| 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 software v6.1.2 (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 and matrix 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) |
| GSE233136 |
Gene expression profile at single cell level of low and high pigmented B16 cells [B16_D7_LP_HP_scRNA] |
| GSE233198 |
Differential programs of melanocyte cell states |
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| Relations |
| BioSample |
SAMN35306297 |
| SRA |
SRX20464969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7401925_LP_barcodes_filtered.tsv.gz |
16.0 Kb |
(ftp)(http) |
TSV |
| GSM7401925_LP_features_filtered.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7401925_LP_matrix_filtered.mtx.gz |
35.9 Mb |
(ftp)(http) |
MTX |
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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