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Sample GSM5862289 Query DataSets for GSM5862289
Status Public on Apr 26, 2024
Title ctl rep2
Sample type SRA
 
Source name RAW macrophages
Organism Mus musculus
Characteristics tissue: tissue culture
cell type: RAW macrophages
treatment: none
Treatment protocol RAW 267.4 macrophage cells were maintained in DMEM supplemented with 10% FCS at 37 °C in a 5% CO2 incubator. Cells were treated with MCD (5 mM) in 1 mg/ml BSA for 1 hour or statin (7 υM) plus lipoprotein deficient serum (LPDS). For LPS, cells were stimulated with 100 ng/ml LPS in DMEM supplemented with 1 mg/ml BSA for 3 h.
Growth protocol RAW 267.4 macrophage cells were maintained in DMEM supplemented with 10% FCS at 37 °C in a 5% CO2 incubator.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020)
Total RNA (approx. 350 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Read alignment to mm10 was performed with STAR v2.5.3;
HTSeq v0.9.1 was used for transcript quantification;
DESeq2 v1.18.1 was used for differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts + tabluar format with DESeq2 output
 
Submission date Feb 05, 2022
Last update date Apr 26, 2024
Contact name Jeffrey Dilworth
E-mail(s) fdilworth@wisc.edu
Phone 6082653758
Organization name University of Wisconsin
Street address 1111 Highland Ave
City Madison
State/province Wisconsin
ZIP/Postal code 53705
Country USA
 
Platform ID GPL24247
Series (1)
GSE196187 Cholesterol in macrophage regulate gene expersion with or without LPS [MCD and LPS RNA-seq]
Relations
BioSample SAMN25686806
SRA SRX14052339

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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