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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 12, 2019 |
| Title |
H3K27me3_scRNAseq_HBCx-95 |
| Sample type |
SRA |
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| Source name |
HBCx-95
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: mouse PDX human tumor
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| Growth protocol |
Female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific pathogen-free conditions. Their care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). A PDX model of luminal breast cancer (HBCx-22) was previously established at Institut Curie from untreated early-stage luminal breast cancer with informed consent from the patient (Cottu et al, Breast Cancer Research Treatment, 2012). Acquisition of a resistant phenotype for a derivative of HBCx-22, HBCx-22-TamR, was previously established and maintained as previously described in Cottu et al, Clinical Cancer Research 2014. A PDX from a residual triple negative breast cancer post neo-adjuvant chemotherapy (HBCx-95) was previously established at Institut Curie with informed consent from the patient (Marangoni et al, Clinical Cancer Research, 2018). HBCx-95 xenografts were treated with Capecitabine (Xeloda, Roche Laboratories) orally at a dose of 540 mg/kg/day, 5 days a week for 6 weeks. Relative tumor volumes (RTV, mm^3) were calculated as previously described (Marangoni et al, Clinical Cancer Research, 2007). Mice with recurrent tumors were treated for a second round of Capecitabine when PDX reached a volume of over 200 mm^3. Mouse which did not respond to Capecitabine and PDX specimen was extracted at 1100mm^3 and tagged as HBCx-95-CapaR.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Prior scChIP-seq and scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).
scRNA-seq libraries were prepared with Chromium Single cell 3' reagent v2 kit according to manufacturer's recommendations (10X Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
scRNA-seq libraries were prepared with Chromium Single cell 3' reagent v2 kit according to manufacturer's recommendations (10X Genomics).
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| Data processing |
scRNA-seq: Single-cell sequencing files were processed using the Cell Ranger Single Cell Software Suite (v1.3.1) to perform quality control, sample de-multiplexing, barcode processing, and single-cell 3′ gene counting. Samples were first demultiplexed and then aligned to the UCSC mouse (mm10) and human (hg19) transcriptome and genome using "cellranger mkfastq" with default parameters. UMI were counted using "cellrangercount".
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell in genes (scRNA-seq, TAR of MTX and TSV) or genomic bins (scChIP-seq)
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| Submission date |
Jul 18, 2018 |
| Last update date |
Apr 12, 2019 |
| Contact name |
Kevin Grosselin |
| E-mail(s) |
kevin.grosselin@espci.fr
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| Organization name |
ESPCI Paris
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| Department |
CBI
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| Lab |
Andrew Griffiths
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| Street address |
10 rue Vauquelin
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL22245 |
| Series (1) |
| GSE117309 |
High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer |
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| Relations |
| BioSample |
SAMN09689461 |
| SRA |
SRX4404429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3290893_CountTable_HBCx-95_scRNA.tar.gz |
12.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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