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Series GSE96106 Query DataSets for GSE96106
Status Public on May 02, 2017
Title Single cell RNA-sequencing of day 15 cells derived from the directed differentiation of human iPSCs towards lung epithelium
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary It has been postulated that during human fetal development all cells of the lung epithelium derive from an embryonic endodermal NKX2-1+ precursor, however, this hypothesis has not been formally tested due to an inability to purify or track this theorized cell for detailed characterization. Progress has been made in deriving lung epithelial cells from human induced pluripotent stem cells (iPSCs). However, little is known about the heterogeneity or genetic programs of the cells generated using these lung differentiation protocols. We engineered and differentiated NKX2-1GFP reporter iPSCs in vitro, recapitulating the major developmental milestones of lung development, to generate and isolate human primordial lung progenitors (day 15 of differentiation) that expresses NKX2-1 but are initially devoid of markers of differentiated lung lineages. To further characterize the cells generated in the lung directed differentiation protocol we performed single cell RNA-seq analysis of cells on day 15 of lung directed differentiation. We analyzed sorted NKX2-1GFP+ cells for the iPSC line C17 and cells from the iPSC line BU3.
 
Overall design We sorted C17NKX2-1GFP+ and BU3 cells on day 15 of the lung directed differentiation and loaded into separate Fluidigm C1 integrated fluidics circuits (IFCs). Lysis, conversion polyA+RNA into full length cDNA and amplification of cDNA was performed using the Fluidigm C1 according to the manufacturer’s protocol. After sequencing on an Illumina Hiseq2500 80 single cell transcriptional profiles from BU3 and 65 from ips17 cell line were compared after filtering and normalization.
Web link https://www.jci.org/articles/view/89950
 
Contributor(s) Hawkins F, Kotton D, Driver I
Citation(s) 28463226
Submission date Mar 11, 2017
Last update date May 15, 2019
Contact name Ian Driver
E-mail(s) driver.ian@gmail.com
Phone 4155020840
Organization name UCSF
Department Anatomy
Street address 513 Parnassus Avenue, Medical Sciences S1364
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (145)
GSM2533673 BU3_C10_B9
GSM2533674 BU3_C11_B8
GSM2533675 BU3_C12_B7
Relations
BioProject PRJNA378848
SRA SRP101750

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Supplementary file Size Download File type/resource
GSE96106_ips17_BU3_normalized_edgeR_counts_TMM_all.txt.gz 12.8 Mb (ftp)(http) TXT
GSE96106_rsem_results_h38_ips17_BU3.gene.count.matrix.txt.gz 4.4 Mb (ftp)(http) TXT
GSE96106_rsem_results_h38_ips17_BU3_gene_fpkm_matrix.txt.gz 4.5 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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