|
| Status |
Public on Jul 02, 2024 |
| Title |
Tumor-897 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
cell line: MDA-MB-231
cell type: breast cancer
treatment: NA
|
| Treatment protocol |
No treatment was performed.
|
| Growth protocol |
Hypoxia fate-mapping MDA-MB-231 tumors (Godet et. al, 2019) were harvested 18 days post-implantation and immediately frozen in clear OCT. 10 μm tumor slices were placed within the fiducial frame of the Visium slide. The tissue was pre-fixed in cold methanol and imaged at 10X magnification using a Cytation5 in the RFP and GFP channels to acquire native fluorescence. The slide was immediately transferred to cold methanol with DAPI. DAPI staining was imaged at 10X using Cytation5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Visium spatial gene expression protocol was followed according to the manufacturer’s instructions (#PN-1000187, 10X Genomics). Briefly, tissue permeabilization was followed by cDNA synthesis, second strand synthesis and cDNA denaturation. The ideal cycle number was determined by qPCR and cDNA was amplified and cleaned using SPRIselect. The amount of cDNA was measured to determine the cDNA input for library construction.
Library construction was performed following the Visium protocol. Briefly, cDNA was fragmented and submitted to end repair and A-tailing. Adaptor sequences were ligated, and the post-ligation product was cleaned and subjected to Index PCR.
Overall, the P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen spatial transcriptomics sequencing
|
| Data processing |
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generte fastq files.
Sequences were aligned to hg38 genome using Space Ranger's default settings.
Gene expression of reference coding genes was quantifies uisng Space Ranger's deault settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of genes ID
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
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 with spots
Supplementary files format and content: scalefactors_json.json.gz: 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 list of spatial barcodes and the coordinates of corresponding spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Ines Godet |
| Organization name |
Johns Hopkins University
|
| Department |
Oncology
|
| Lab |
Gilkes
|
| Street address |
1650 Orleans Street, CRB1, room 128
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE240212 |
Spatial Transcriptomics reveals that cells that experience intratumoral hypoxia retain hypoxia-associated transcriptional programs after invading into oxygenated tumor regions. |
|
| Relations |
| BioSample |
SAMN36871511 |
| SRA |
SRX21278142 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7688224_Tumor-897_aligned_fiducials.jpg.gz |
1.0 Mb |
(ftp)(http) |
JPG |
| GSM7688224_Tumor-897_barcodes.tsv.gz |
14.3 Kb |
(ftp)(http) |
TSV |
| GSM7688224_Tumor-897_detected_tissue_image.jpg.gz |
1.1 Mb |
(ftp)(http) |
JPG |
| GSM7688224_Tumor-897_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM7688224_Tumor-897_matrix.mtx.gz |
45.6 Mb |
(ftp)(http) |
MTX |
| GSM7688224_Tumor-897_scalefactors_json.json.gz |
164 b |
(ftp)(http) |
JSON |
| GSM7688224_Tumor-897_tissue_hires_image.png.gz |
7.5 Mb |
(ftp)(http) |
PNG |
| GSM7688224_Tumor-897_tissue_lowres_image.png.gz |
788.6 Kb |
(ftp)(http) |
PNG |
| GSM7688224_Tumor-897_tissue_positions_list.csv.gz |
56.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
