|
| Status |
Public on Aug 27, 2024 |
| Title |
Breast_adjacent_tissue_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer adjacent tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer adjacent tissue
cell type: Breast tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Breast tissue was acquired from three Tru-Cut biopsies. The tissue was sectioned into small fragments and cryopreserved in FBS (Gibco) supplemented with 10% dimethyl sulfoxide (DMSO, Sigma). Upon thawing, the tissue was enzymatically dissociated using Accumax solution (Sigma) and incubated for 30 minutes. The resulting cell suspension was filtered through a 40 µm filter, followed by processing using the Dead Cell Removal Kit (Miltenyi Biotec #130090101) through two rounds to ensure sufficient viability.
The scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3´Reagent Kits v3.1 (Dual Index) following the manufacturer's instructions (10X Genomics). Briefly, the cell suspension was minimally manipulated as described above and loaded onto the Chromium Next GEM Chip G, avoiding bubble formation. Then the chip was inserted into the Chromium Single Cell Controller. Subsequently, the cDNA library was produced, cleaned, and amplified using 11 cycles of the specified PCR program. Libraries were constructed by adding the appropriate adapters and indices (Dual Index TT Set A) provided by the manufacturer. The final amplification was carried out with 12 cycles of the specified PCR program.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The barcode processing and gene counting were made using Cell Ranger software v 6.0.1. The feature-barcode matrices are contained intheTSVfiles.
Assembly: GRCh38
Supplementary files format and content: The feature files contain the gene ID, the barcode file contains the identification of the cell, the matrix file containsthecounts.
|
| |
|
| Submission date |
Jun 20, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
mfurlan@ifc.unam.mx
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE270362 |
Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis [scRNA-seq 2] |
| GSE270363 |
Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single cell transcriptome analysis |
|
| Relations |
| SRA |
SRX24993349 |
| BioSample |
SAMN41941329 |
