|
| Status |
Public on Jul 13, 2023 |
| Title |
MCF7 Y537S cells, no treatment, sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver metastatic breast tumor
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Liver metastatic breast tumor
cell line: MCF7 Y537S
cell type: metastatic tumor cells
genotype: NOD scid gamma
treatment: None
slide serial_and_position: V11F09-092 A1
|
| Treatment protocol |
Fulvestrant (Sigma) was dissolved in 10% DMSO and 90% corn oil
|
| Growth protocol |
1x106 MCF7 Y537S cells resuspended in 1% PBS were injected to ovariectomized, NOD SCID gamma (NSG) immunodeficient female mice via tail vein
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen Spatial transcriptome sequencing
|
| Data processing |
Raw sequencing data were processed using the 10x Genomics Space Ranger (v1.3) pipeline to generate FASTQ files
Sequences were aligned to a custom combined reference of hg38 and mm10 genomes (Ensembl 104) and gene expressison quantified using Space Ranger's default settings
Assembly: hg38 and mm10
Supplementary files format and content: 08.12.2021.ZME.GE.*.Li.tif: brightfield image of tissue and spots
Supplementary files format and content: *_aligned_fiducials.jpg - aligned fiducials of the tissue image
Supplementary files format and content: *_detected_tissue_image.jpg - image of tissue and spots
Supplementary files format and content: *_scalefactors_json.json - scale factors in json format
Supplementary files format and content: *_tissue_hires_image.png - hi-res image of tissue
Supplementary files format and content: *_tissue_lowres_image.png - low res image of tissue
Supplementary files format and content: *_tissue_positions_list.csv
Supplementary files format and content: *_barcodes.tsv.gz - list of spatial barcodes
Supplementary files format and content: *_features.tsv.gz - list of gene IDs
Supplementary files format and content: *_matrix.mtx.gz UMI count data in Matrix Market Exchange format
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jul 06, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Zeynep Madak Erdogan |
| Organization name |
UIUC
|
| Department |
FSHN
|
| Lab |
Zeynep Madak Erdogan
|
| Street address |
1201 S Goodwin Ave
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE236681 |
Targeting Metabolic Adaptations in the Breast Cancer–Liver Metastatic Niche Using Dietary Approaches to Improve Endocrine Therapy Efficacy |
|
| Relations |
| BioSample |
SAMN36345319 |
| SRA |
SRX20928470 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7567492_08.12.2021.ZME.GE.V1.3.Li.tif.gz |
6.1 Mb |
(ftp)(http) |
TIFF |
| GSM7567492_V1_3_aligned_fiducials.jpg.gz |
1.6 Mb |
(ftp)(http) |
JPG |
| GSM7567492_V1_3_barcodes.tsv.gz |
11.0 Kb |
(ftp)(http) |
TSV |
| GSM7567492_V1_3_detected_tissue_image.jpg.gz |
1.9 Mb |
(ftp)(http) |
JPG |
| GSM7567492_V1_3_features.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
| GSM7567492_V1_3_matrix.mtx.gz |
53.0 Mb |
(ftp)(http) |
MTX |
| GSM7567492_V1_3_scalefactors_json.json.gz |
171 b |
(ftp)(http) |
JSON |
| GSM7567492_V1_3_tissue_hires_image.png.gz |
3.7 Mb |
(ftp)(http) |
PNG |
| GSM7567492_V1_3_tissue_lowres_image.png.gz |
395.6 Kb |
(ftp)(http) |
PNG |
| GSM7567492_V1_3_tissue_positions_list.csv.gz |
58.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
