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Sample GSM4052378 Query DataSets for GSM4052378
Status Public on Aug 30, 2019
Title WT_Day16
Sample type SRA
Source name MC3T3-E1
Organism Mus musculus
Characteristics genotype: WT
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 D16_KOvsWT_gene_exp.diff
Data processing Base calling was performed using Illumina’s RTA (Version
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
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
BioSample SAMN12651296
SRA SRX6777942

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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