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Series GSE76983 Query DataSets for GSE76983
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
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.
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.

Contributor(s) Boisset J, Grün D, van Oudenaarden A
Citation(s) 27345837
Submission date Jan 19, 2016
Last update date May 15, 2019
Contact name Jean-Charles Boisset
Organization name Hubrecht Institute
Lab A. van Oudenaarden
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (23)
GSM2041916 micro-dissected cells [JC20]
GSM2041917 micro-dissected cells [JC21]
GSM2041918 micro-dissected cells [JC26]
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
BioProject PRJNA309169
SRA SRP068586

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE76983_RAW.tar 3.2 Mb (http)(custom) TAR (of CSV)
GSE76983_cel-seq_barcodes.csv.gz 424 b (ftp)(http) CSV
GSE76983_expdata_BMJhscC.csv.gz 2.6 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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