|
| Status |
Public on Sep 07, 2023 |
| Title |
Mouse timecourse KPC day30 Tumor spatial transcriptomics section A1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
strain: C57BL/6N
genotype: WT
Sex: F
time: Day 30
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumor biopsies of day-30 orthotopic mouse PDAC were gently washed in PBS, snap frozen via bathing in liquid nitrogen-chilled isopentane and embedded with Optimal Cutting Temperature (OCT) compound. From five to ten sections were collected to evaluate RNA quality at TapeStation system (Agilent). The tissue blocks were then processed to retrieve two non-sequential 10µm sections (100 µm apart), which were placed within the capture areas of a Visium slide equilibrated at cryostat temperature (-20°C). Sections were immediately fixed in chilled methanol at -20°C for 30 min and stained via immunofluorescence as stated above preserving RNA degradation using buffers supplemented with Recombinant RNase inhibitor (Takara 2313A, 2 U/µl). Whole-slide images were acquired using the MAVIG RS-G4 (Caliber I.D.) confocal microscope at 20x magnification. Barcoded libraries were generated by permeabilizing tissue at 37°C for 15 min and performing in situ reverse transcription at 53°C for 45 min, followed by second-strand synthesis at 65°C for 15 min. cDNA was denatured and transferred to tubes for PCR amplification and library construction, including fragmentation, adaptor ligation and sample indexing.
Spatial transcriptomics data were generated using the Visium Spatial Gene Expression Reagent Kits (10X Genomics) according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
Fastq files were processed with Space Ranger (v.1.2.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)
Supplementary files format and content: Image outputs from Space Ranger (jpg and png format), scale factors (json) and tissue coordinates (csv format)
|
| |
|
| Submission date |
Nov 12, 2022 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Renato Ostuni |
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina 58
|
| City |
Milano |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE217843 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Spatial transcriptomics of mouse PDAC samples |
| GSE217847 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN31700904 |
| SRA |
SRX18243100 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6727528_Tumor_DAY_30_ST_A1_aligned_fiducials.jpg.gz |
1.2 Mb |
(ftp)(http) |
JPG |
| GSM6727528_Tumor_DAY_30_ST_A1_barcodes.tsv.gz |
19.3 Kb |
(ftp)(http) |
TSV |
| GSM6727528_Tumor_DAY_30_ST_A1_detected_tissue_image.jpg.gz |
1.2 Mb |
(ftp)(http) |
JPG |
| GSM6727528_Tumor_DAY_30_ST_A1_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM6727528_Tumor_DAY_30_ST_A1_matrix.mtx.gz |
36.7 Mb |
(ftp)(http) |
MTX |
| GSM6727528_Tumor_DAY_30_ST_A1_scalefactors_json.json.gz |
150 b |
(ftp)(http) |
JSON |
| GSM6727528_Tumor_DAY_30_ST_A1_tissue_hires_image.png.gz |
3.5 Mb |
(ftp)(http) |
PNG |
| GSM6727528_Tumor_DAY_30_ST_A1_tissue_lowres_image.png.gz |
323.4 Kb |
(ftp)(http) |
PNG |
| GSM6727528_Tumor_DAY_30_ST_A1_tissue_positions_list.csv.gz |
65.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
