|
| Status |
Public on Feb 28, 2018 |
| Title |
COLO205.xenograft.hFc.24hr.mm10 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
treatment: hFc.24hr
tissue: COLO205 tumor
strain: CB.17/SCID (Taconic)
tissue: tumor
age: adult
genotype: WT
gender: male
|
| Treatment protocol |
When tumors reached 100-150 mm3, mice remained untreated or were treated by s.c. injection with hFc (control protein, 25 mg/kg), aflibercept (VEGF Trap, ziv-aflibercept, 25 mg/kg), a DLL4 blocker (REGN 1035, 10 mg/kg) or a combination (combo) of aflibercept plus anti-Dll4 antibody. 24hr and 72hr post treatment heart and tumor tissues were harvested.
|
| Growth protocol |
2x10^6 COLO205 human colon carcinoma cells were grown s.c. in male CB.17/SCID mice (Taconic).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were minced, enzymatically digested for 10 minutes using 2.5 mg/ml collagenase Type II, 2.5 mg/ml collagenase Type IV (Gibco), and 0.5 mg/ml DNase (Sigma) in PBS / 1% BSA at 37°C, treated with DMEM containing 10% FBS and filtered (70-µm nylon filter; Falcon). Single cell suspensions were subjected to 1X PharMLyse for 4 (tumor) or 10 (heart) minutes, washed and subjected to dead cell removal kit (130-090-101, Miltenyi). The remaining cells were used for single cell sequencing.
Tumor single cell suspensions underwent a depletion step using the following FITC conjugated Abs: COLO205 cells were incubated with anti-CD24 (11-0247-42, eBioscience) and anti-E-Cadherin (324104, Biolegend) using 10 µl anti-FITC-beads for 1x10^6 total cells. The remaining cells were used for single cell sequencing.
Cellular suspensions (~6000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell GEMs. Single-cell RNAseq libraries were prepared using version 1 Chromium Single cell 3’ Library, Gel beads & Mutiplex kit (10X Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The Cell Ranger Suite version 1.1.0 was used to perform sample de-multiplexing, barcode processing and single cell gene UMI (unique molecular index)
Genome_build: mm10 for mouse cells and B37 for human cells
Supplementary_files_format_and_content: tab-delimited text files include UMI values for samples/cells
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Mar 02, 2018 |
| Contact name |
Qi Zhao |
| E-mail(s) |
qi.zhao@regeneron.com
|
| Organization name |
Regeneron Pharmaceuticals Inc
|
| Street address |
777 Old Saw Mill River Road
|
| City |
Tarrytown |
| ZIP/Postal code |
10591 |
| Country |
USA |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE110501 |
Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following anti-angiogenic treatment |
|
| Relations |
| BioSample |
SAMN08519621 |
| SRA |
SRX3684081 |
