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Series GSE146972 Query DataSets for GSE146972
Status Public on Mar 17, 2020
Title An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.
Overall design Analysis of CARLIN arrays sequenced from mouse embryonic stem cells and different mouse tissues in presence/absence of Doxycycline. Single-cell transcriptomic sequencing during developmental and adult hematopoiesis.
Contributor(s) Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan W, Fujiwara Y, Li BE, Orkin SH, Hormoz S, Camargo FD
Citation(s) 32413320
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HL128850 Clonal analysis of hematopoietic stem and progenitor biology in situ CHILDREN'S HOSPITAL Fernando Camargo
Submission date Mar 13, 2020
Last update date May 21, 2020
Contact name Duluxan Sritharan
Organization name Harvard University
Street address 240 Longwood Avenue, Bldg. C
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (201)
GSM4413139 ChronicInduction_PosDox_0h
GSM4413140 ChronicInduction_PosDox_High_12h
GSM4413141 ChronicInduction_PosDox_High_24h
BioProject PRJNA612835
SRA SRP252955

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Supplementary file Size Download File type/resource
GSE146972_RAW.tar 223.3 Mb (http)(custom) TAR (of H5)
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