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Series GSE76342 Query DataSets for GSE76342
Status Public on Dec 25, 2015
Title RNAseq profiling of multiciliated cells
Organism Xenopus laevis
Experiment type Expression profiling by high throughput sequencing
Summary To determine what genes are upregulated in multiciliated cells, we manipulated Xenopus laevis ectoderm to either make more or fewer of this cell type with multiple approaches across multiple timepoints. By finding differentially expressed genes in common across all comparisons in which multiciliated cell number changed, we obtained a robust, but conservative, core group of multiciliated cell genes.
Overall design We suppressed multiciliated cell development by activating the notch pathway with an injected mRNA encoding the intracellular domain of notch (icd) or by injecting an mRNA encoding a dominant-negative form of multicilin (dnmcidas). Conversely, we promoted multiciliated cell differentiation by blocking notch signaling with a DNA-binding mutant of Suppressor of Hairless (dbm), or by overexpressing an inducible form of multicilin (mcidas). We also coinjected these constructs in a way aimed at causing the greatest change in multiciliated cells and reducing background transcriptional programs not associated with these cells: for example, we coinjected icd with mcidas, in order to reduce other cell types specified by notch. After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested RNA at 3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18 and performed poly-a+ RNAseq (Illumina Truseq v2). We then aligned reads to X. laevis gene models (Mayball version, Chung and Kwon et al. 2014) and took the intersection of genes differentially expressed between all comparisons in which the multiciliated cell number dramatically changed (icd vs. icd + mcidas, icd vs. dbm, dbm vs. dbm + dnmcidas) to obtain a core list of multiciliated cell genes.
Contributor(s) Quigley IK, Kintner C
Citation(s) 28103240
Submission date Dec 24, 2015
Last update date May 15, 2019
Contact name Ian K Quigley
Phone 858-453-4100
Organization name Salk Institute
Department Molecular Neurobiology Lab
Lab Kintner
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL18936 Illumina HiSeq 2500 (Xenopus laevis)
Samples (36)
GSM1981745 notch-icd_RNAseq_3h_rep_1
GSM1981746 notch-icd_RNAseq_3h_rep_2
GSM1981747 notch-icd_RNAseq_6h_rep_1
BioProject PRJNA306946
SRA SRP067781

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Supplementary file Size Download File type/resource
GSE76342_RAW.tar 66.4 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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