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| Status |
Public on Aug 02, 2022 |
| Title |
NCCBC6vs |
| Sample type |
SRA |
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| Source name |
Human Breast Cancer
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| Organism |
Homo sapiens |
| Characteristics |
cell type: DCIS
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| Extracted molecule |
total RNA |
| Extraction protocol |
A fresh tissue sample was embedded in OCT and stored at -80 °C. Tissue block was cut into 10-μm sections, which were analyzed with a Visium Spatial Gene Expression Kit 3' v1 (10x Genomics) according to the manufacturer’s instructions in the Visium Spatial Gene Expression Reagent Kit User Guide(10X Genomics). The optimal permeabilization time was 24 min. Sliced tissue pieces were stained with H&E, imaged using a BZ-X710 microscope (Keyence, Osaka, Japan) under a 20 x objective, and processed for spatial transcriptomics.
After permeablization, mRNA released from the overlying cells is captured by the primers on the spots. Then spatially barcoded cDNA is synthesied from mRNA. Library preparation was performed included cDNA amplification, fragmentation, hearing and 5′ adaptor and sample index attachment. Sequencing was performed on a DNBSEQ (MGI Tech, Shenzhen, China).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
Library strategy: Spatial Transcriptomics
Raw sequencing data were processed with the SpaceRanger pipeline (version 1.2.2, 10X Genomics) and mapped to the human genome (GRCh38) to generate matrices of gene counts by spatially barcodes.
Genome_build: GRCh38
Supplementary_files_format_and_content: H5
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| Submission date |
Feb 06, 2022 |
| Last update date |
Aug 02, 2022 |
| Contact name |
Jun Nakayama |
| E-mail(s) |
jnakayama.re@gmail.com
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| Organization name |
National Cancer Center
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| Street address |
Tsukiji 5-1-1
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| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
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| Platform ID |
GPL28038 |
| Series (1) |
| GSE196208 |
Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Ductal Carcinoma In Situ of the Breast |
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| Relations |
| BioSample |
SAMN25689698 |
| SRA |
SRX14059569 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5862787_NCCBC6vs.ktf.tar.gz |
14.0 Mb |
(ftp)(http) |
TAR |
| GSM5862787_NCCBC6vs.tif.gz |
129.1 Mb |
(ftp)(http) |
TIFF |
| GSM5862787_NCCBC6vs_filtered_feature_bc_matrix.h5 |
2.5 Mb |
(ftp)(http) |
H5 |
| GSM5862787_NCCBC6vs_scalefactors_json.json.gz |
173 b |
(ftp)(http) |
JSON |
| GSM5862787_NCCBC6vs_tissue_hires_image.png.gz |
4.2 Mb |
(ftp)(http) |
PNG |
| GSM5862787_NCCBC6vs_tissue_positions_list.csv.gz |
60.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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