NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6612390 Query DataSets for GSM6612390
Status Public on May 08, 2024
Title CD38KO MSU treated 3
Sample type SRA
 
Source name Bone marrow derived macrophages
Organism Mus musculus
Characteristics cell type: Bone marrow derived macrophages
genotype: CD38KO
treatment: MSU
Treatment protocol WT BMDMs in the presence or absence of apigenin (25 uM) and CD38KO BMDMs were stimulated with MSU crystals (0.2 mg/ml) for 6 hours.
Growth protocol Isolated mouse bone marrows were cultured in RPMI containing 10% FBS, penicillin (100 U/ml), streptomycin (100 μg/ml) and 20% L929 conditioned media for 7 days. After priming with GM-CSF (20 ng/ml) for 24 hours, cells were washed with PBS and subjected to experiments in RPMI containing 1% FBS.
Extracted molecule polyA RNA
Extraction protocol RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA samples were sent to LC sciences for RNA-seq
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library was then constructed.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie
Assembly: All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Supplementary files format and content: Excel file include FPKM values for each sample
 
Submission date Oct 01, 2022
Last update date May 08, 2024
Contact name Paulo VG Alabarse
E-mail(s) pvgalabarse@gmail.com
Organization name University of California, San Diego
Department Rheumatology
Lab Bryan
Street address 9500 Gilman Drive
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL24247
Series (1)
GSE214587 The NADase CD38 is a central regulator in gouty inflammation and a novel druggable therapeutic target
Relations
BioSample SAMN31117471
SRA SRX17771213

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap