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Sample GSM4052383 Query DataSets for GSM4052383
Status Public on Aug 30, 2019
Title Akap11-KO_Day25
Sample type SRA
 
Source name MC3T3-E1
Organism Mus musculus
Characteristics genotype: Akap11 -/-
cell line: MC3T3-E1
Treatment protocol 50 µg/ml ascorbic acid and 5 mM β-glycerophosphate were added to the medium for osteogenic differentiation. Medium was changed every 3 days and cells were incubated at 37 °C in a 5% CO2 atmosphere.
Growth protocol Cell were maintained in proliferation medium, α‐MEM (Gibco, Thermo Fisher Scientific, Waltham, MA, USA; catalog # 12571) containing 10% v/v fetal bovine serum (FBS), 100 units/mL penicillin and 100 μg/mL streptomycin.
Extracted molecule total RNA
Extraction protocol Cell were washed with PBS and RNA was harvested using Trizol reagent.
100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description D25_KOvsWT_gene_exp.diff
Data processing Base calling was performed using Illumina’s RTA (Version 1.12.4.2).
Adapters of RNA-seq reads were trimmed.
The BAM files with coordinate-sorted alignments were imported to Cufflinks 2.2.1 to assemble and quantify the transcripts as fragments per kilobase per million aligned reads (FPKM).
Cuffdiff 2 was employed to perform differential expression analysis.
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: tab-delimited text files include log2 foldchange value
 
Submission date Aug 29, 2019
Last update date Aug 31, 2019
Contact name Vincent Ka Fai Cheng
E-mail(s) u3003930@connect.hku.hk
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
 
Platform ID GPL18480
Series (1)
GSE136591 Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1
Relations
BioSample SAMN12651291
SRA SRX6777947

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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