|
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.
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|
|
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
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|
|
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 |