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Series GSE136591 Query DataSets for GSE136591
Status Public on Aug 30, 2019
Title Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: This is a post-GWAS functional study that aims to determine the effect of Akap11 knockout in mouse preosteoblastic cell line MC3T3-E1 during osteogenesis.
Methods: mRNA profile of WT (treated with CRISPR and remains unedited) and Akap11 knockout MC3T3-E1 cells were generated by RNAseq from pooled RNA (from 3 biological triplicate at equal quantity) of various timepoint during osteogenesis (Day 0, 7,16, 25).100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche). Pair-End 101bp sequencing was performed in the Illumin HiSq1500 sequencer using the HiSeq SBS Kit v4 (Illumina). Data was collected with SCS version 1.4.8. Base calling was performed using Illumina’s RTA (Version 7 samples were sequenced per lane and achieved a sequencing depth of ~65 million read per sample.
Results: Expression of osteogentic markers in Akap11 knockout MC3T3-E1 cells were suppressed. Genes invovled in IGF-I signaling pathway were signficantly altered.
Overall design mRNA profile of Day0, 7, 16, 25 WT (treated with CRISPR and remains unedited) and Akap11 knockout MC3T3-E1 cells were generated by pooled PolyA mRNA Sequencing .
Contributor(s) Li GH, Cheng VK, Cheung CL
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Submission date Aug 29, 2019
Last update date Aug 31, 2019
Contact name Vincent Ka Fai Cheng
Phone 67383950
Organization name The University of Hong Kong
Department Pharmacology and Pharmacy
Street address L202 lab block 21 Sassoon road Pokfulam Hong Kong
City Hong Kong
State/province -- select --
ZIP/Postal code 000
Country Hong Kong
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (8)
GSM4052376 WT_Day0
GSM4052377 WT_Day7
GSM4052378 WT_Day16
BioProject PRJNA562822
SRA SRP219825

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Supplementary file Size Download File type/resource
GSE136591_D00_KOvsWT_gene_exp.diff.gz 1.4 Mb (ftp)(http) DIFF
GSE136591_D07_KOvsWT_gene_exp.diff.gz 1.4 Mb (ftp)(http) DIFF
GSE136591_D16_KOvsWT_gene_exp.diff.gz 1.4 Mb (ftp)(http) DIFF
GSE136591_D25_KOvsWT_gene_exp.diff.gz 1.4 Mb (ftp)(http) DIFF
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