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| Status |
Public on Jun 24, 2016 |
| Title |
Single-cell RNA-seq of sorted and micro-dissected mouse bone marrow cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We here systematically studied the interaction network of bone marrow cells. To this end, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs, to infer cell identity. After grouping the cells into cell types (based on the single-cell transcriptomes), we identified actual physical interactions that occurred more, or less, than what would be expected by chance. We compared the micro-dissected data to sorted hematopoietic stem cells.
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| Overall design |
After mild dissociation of the bone marrow, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs. In addition, single hematopoietic stem cells were sorted (Lineage- Kit+ Sca1+ CD150+ CD48-) to sequence their transcriptome.
In detail, the bone marrow was mildly flushed. Structures composed of about 10 to 20 cells were set apart. With needles and a micro-dissection microscope, we trimmed of smaller structures from these big structure. These smaller structures are mainly two to four cells attached together. These small structures were then further micro-dissected to single cells. The goal of doing these sequential dissections was to keep track of which cells were interacting with which.
Each micro-dissected cell sample contains RNA-seq data for 96 single cells. Each single cells received a different barcode that allow us to entangle them, and to produce the processed .coutt.csv file. Each sorted hematopoietic stem cell sample represents a single cell. The processed data file expdata_BMJhscC.csv contains transcript counts for all analyzed cells.
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| Contributor(s) |
Boisset J, Grün D, van Oudenaarden A |
| Citation(s) |
27345837 |
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| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Charles Boisset |
| E-mail(s) |
[email protected]
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| Organization name |
Hubrecht Institute
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| Lab |
A. van Oudenaarden
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (23)
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| This SubSeries is part of SuperSeries: |
| GSE89379 |
Transcriptomics of single-cell and bulk sorted and micro-dissected mouse bone marrow, fetal liver and small intestine crypt cells |
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| Relations |
| BioProject |
PRJNA309169 |
| SRA |
SRP068586 |
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