|
| Status |
Public on Dec 12, 2023 |
| Title |
Breast tissue from BRCA2 mutation carrier 0259 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Mammary gland
genotype: BRCA2
patient: 0259
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
OCT-embedded frozen tissues were sectioned, placed on Visium slides and imaged
Libraries were prepared according to the 10x Visium Spatial Transcritpomics protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Fresh frozen Spatial transcriptome sequencing
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq 500/2000.
Read alignment and count summarization were performed using spaceranger v1.3.0 using the Illumina BCL files as input.
Assembly: GRCh38
Supplementary files format and content: h5 files contain genewise read counts for all spots. Row names are Ensembl IDs and column names are 10x spatial barcodes used to identify spots.
Supplementary files format and content: csv files contain the spatial coordinates of the visium spots
Supplementary files format and content: png files contain the tissue H&E images
Library strategy: Visium Spatial Transcritpomics
|
| |
|
| Submission date |
Oct 30, 2023 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Yunshun Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
ACRF Cancer Biology and Stem Cells
|
| Lab |
Chen
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE246518 |
Spatial transcriptomics sequencing profiles of human breast tissue |
|
