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| Status |
Public on Feb 28, 2018 |
| Title |
heart.hFc.24hr |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
treatment: hFc.24hr
tissue: normal heart
strain: CB.17/SCID (Taconic)
tissue: heart
age: adult
genotype: WT
gender: male
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| 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.
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| Growth protocol |
2x10^6 COLO205 human colon carcinoma cells were grown s.c. in male CB.17/SCID mice (Taconic).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Feb 12, 2018 |
| Last update date |
Mar 02, 2018 |
| Contact name |
Qi Zhao |
| E-mail(s) |
qi.zhao@regeneron.com
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| Organization name |
Regeneron Pharmaceuticals Inc
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| Street address |
777 Old Saw Mill River Road
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| City |
Tarrytown |
| ZIP/Postal code |
10591 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE110501 |
Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following anti-angiogenic treatment |
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| Relations |
| BioSample |
SAMN08519532 |
| SRA |
SRX3684085 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2994876_898100.heart.hFc.24hr.UMI.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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