|
| Status |
Public on Oct 18, 2024 |
| Title |
HY2Y2CCXY_7_rna |
| Sample type |
SRA |
| |
|
| Source name |
2 Colorectal pre-malignant and 4 malignant lesions
|
| Organism |
Mus musculus |
| Characteristics |
tissue: 2 Colorectal pre-malignant and 4 malignant lesions
cell line: N/A
cell type: Unsorted cells
genotype: Apcfl/flVillincreERT2 mice and Apcfl/fl; LSL-KrasG12D; Trp53fl/fl;Rosa26LSL-tdTomato/+; VillinCreERT2 mice
treatment: Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM (for the mice that were kept for 3 weeks after injection) or 30 mM (for the mice that were kept for 9 weeks after injection). Tumors were resected at either 3 or 9 weeks after 4-hydroxytamoxifen injection
library type: mRNA
|
| Treatment protocol |
Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM. Tumors and matching colon tisuuea were resected at 3 weeks after 4-hydroxytamoxifen injection.
|
| Growth protocol |
N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell suspensions from healthy colon or dysplastic lesions were processed using a modified version of a previously published protocol40. Tissue samples were rinsed in 30ml of ice-cold PBS (ThermoFisher 10010-049), chopped to small pieces and washed twice in 25 ml PBS, 5mM EDTA (ThermoFisher AM9261), 1%FBS (ThermoFisher 10082-147). To prime tissue for enzymatic digestion, samples were incubated for 10 minutes at 37°C, placed on ice for 10 minutes before shaking vigorously 15 times followed by supernatant removal. Tissues were placed into a large volume of ice-cold PBS to rinse prior to transferring to 5ml of enzymatic digestion mix (Base: RPMI1640, 10 mM HEPES (ThermoFisher 15630-080), 2% FBS), freshly supplemented immediately before use with 100 mg/mL of Liberase TM (Roche 5401127001) and 50 mg/mL of DNase I (Roche 10104159001), and incubated at 37°C with 120 rpm rotation for 30 minutes. After 30 minutes, enzymatic dissociation was quenched by addition of 1ml of 100% FBS and 10mM EDTA. Samples were then filtered through a 40 mM cell strainer into a new 50 mL conical tube and rinsed with PBS to 30 mL total volume. Tubes were spun down at 400 g for 7 minutes, at 4°C. Resulting cell pellets were resuspended in 1ml PBS, placed on ice and counted.
10XV2, following the manufacturer protocol for the v2 kit (10X Genomics, Pleasanton, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
GEX (3' mRNA) library: R1 file contains cell barcode and UMI; R2 file contains transcript
|
| Data processing |
The demultiplexing, barcoded processing and gene counting were made using the 10x Genomics Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) within the Cumulus feature barcoding workflow v0.2.0
Assembly: mm10-3.0.0
Supplementary files format and content: XXX_matrix.mtx.gz is the raw gene count matrix
Supplementary files format and content: XXX_barcodes.tsv.gz is the list of barcodes associated with XXX_matrix.mtx.gz
Supplementary files format and content: XXX_features.tsv.gz is the list of genes associated with XXX_matrix.mtx.gz
Supplementary files format and content: XXX_adt.csv give the HTO counts per sample
|
| |
|
| Submission date |
Mar 04, 2024 |
| Last update date |
Oct 18, 2024 |
| Contact name |
Simon Mages |
| Organization name |
Broad Institute
|
| Lab |
Regev Lab
|
| Street address |
415 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE260801 |
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics |
|
| Relations |
| BioSample |
SAMN40251716 |
| SRA |
SRX23827601 |
