|
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.
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|
|
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 |