|
| Status |
Public on Dec 28, 2024 |
| Title |
distal paracancerous region |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreas
cell line: CAFs
cell type: MFAP5+ fibroblasts
treatment: untreated
|
| Treatment protocol |
WT or KO mice were injected with 3 × 106 MFC cells/per mouse to induce tumor formation for 3d or 10d.
|
| Growth protocol |
Tissues were processed with DPBS on ice, minced, and digested with trypsin and DNase I in PBS containing 5% FBS for 40 minutes at 37°C. Cells were extracted and filtered every twenty minutes, and red blood cells were lysed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The study was approved by the Ethics Committee of USTC (Ethics Approval No.: 2024-RE-359). All pancreatic cancer patients who participated in this study at the No. 1 Affliated Hospital of USTC provided consent forms. None of the patients received any neoadjuvant therapy before tissue collection. Fresh tumor specimens and adjacent mucosal specimens were resected intraoperatively and there were no cancer cells remaining at the end of the resected samples as confirmed by the histopathologist. Representative hemoglobin/eosin (H&E)-stained sections of the excised specimens used for scRNA-seq were delineated with the help of a pathologist to delineate the three adjacent subregions (tumor core, tumor margin, and distal paracancerous region), after which each of the three regions was digested into single-cell suspensions and analyzed using droplet-based scRNA-seq.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: sameple 3
|
| Data processing |
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0) in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Assembly: mm10;hsa
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
|
| |
|
| Submission date |
Dec 23, 2024 |
| Last update date |
Dec 28, 2024 |
| Contact name |
午洋 张 |
| E-mail(s) |
zhangwuyang10@gmail.com
|
| Phone |
18155660907
|
| Organization name |
The First Affiliated Hospital of USTC
|
| Street address |
No.17 Lujiang Road, Hefei City, Anhui Province, China
|
| City |
Anhui |
| State/province |
State |
| ZIP/Postal code |
230001 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE285264 |
Single-cell RNA sequencing combined with multiplex immunofluorescence probes the role of MFAP5+ fibroblasts in the microenvironment of pancreatic ductal adenocarcinoma |
|
| Relations |
| BioSample |
SAMN45953895 |
| SRA |
SRX27174918 |
