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Sample GSM6222386 Query DataSets for GSM6222386
Status Public on Jun 09, 2023
Title BMAd cells, GC3 [G3]
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics tissue: Bone marrow
cell line: BMAd
cell type: Adipocyte
genotype: WT
treatment: adipogenic differentiation, GC
Treatment protocol Adipogenic differentiation was induced by StemPro Adipogenesis Differentiation kit (Gibco) for 14 days
Cells were treated with 10−6M DEX or 10−6M DEX plus GW9662 for 24 hours.
Growth protocol Bone marrow stem cells were maintained in αMEM supplemented with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy mini kit (Qiagen). At least 100 ug of total RNA was sent for further process.
Libraries were prepared using the Smart-Seq 2 protocol with a template switching oligonucleotide, followed by PCR amplification and purification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description G3
Data processing Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality
Total reads were aligned to the reference genome using HISAT2 v2.1.0
Featurecount was used to count the reads numbers mapped to each gene. And then TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
 
Submission date Jun 08, 2022
Last update date Jun 09, 2023
Contact name Mei Wan
E-mail(s) mwan4@jhmi.edu
Phone 2054470577
Organization name Johns Hopkins Hospital
Department Department of Orthopedics
Lab Mei Wan
Street address 720 Rutland Ave,Ross research buil
City baltimore
State/province Maryland
ZIP/Postal code 21205
Country USA
 
Platform ID GPL13112
Series (1)
GSE205732 Glucocorticoid-stimulated senescence phenotype in differentiated bone marrow adipocytes treated with PPARgamma inhibitor
Relations
BioSample SAMN28925645
SRA SRX15640754

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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