|
Status |
Public on Jun 28, 2021 |
Title |
LH M2-rep3 |
Sample type |
SRA |
|
|
Source name |
in vitro induced cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: THP-1 derived macrophage treatment: Maintained in growth medium with extra lipid mixture (0.25%)and treated with IL-4 20ng/ml+IL-13 20ng/ml
|
Treatment protocol |
For M1 activation, add LPS(100ng/ml) and IFNγ(25ng/ml) to M0 cells.For M2 activation, add IL-4(20ng/ml)and IL-13(20ng/ml)to M0 cells.For extra lipid, add lipid mixture (Sigma Aldrich,0.25%) to growth medium during LPS+IFNγ or IL-4+IL-13 treating.
|
Growth protocol |
THP-1 derived macrophage were routinely generated by incubating THP-1(at 2*10e6/well) with PMA (in growth medium) for 48h.Then remove PMA and repace with growth medium without PMA and rest for 24h, collect cells for M0.
|
Extracted molecule |
total RNA |
Extraction protocol |
After treatment, cells were collected and flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
|
|
Description |
gene_fpkm.txt
|
Data processing |
Illumina HiSeq sequencer and software used for sequencing and basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of hg19 using HISTA2. Transcript assembly were performed using Cufflink. DEG analyses were performed using DESeq2. Genome_build: UCSC_hg19 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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|
|
Submission date |
Oct 06, 2020 |
Last update date |
Jun 28, 2021 |
Contact name |
Miao Xu |
Organization name |
West China hospital of Sichuan university
|
Department |
Clinical Nutrition
|
Street address |
37#,Guoxue alley, Wuhou district
|
City |
Chengdu |
ZIP/Postal code |
610041 |
Country |
China |
|
|
Platform ID |
GPL20795 |
Series (1) |
GSE159112 |
RNA Sequencing of human THP-1 derived macrophages transcriptomes |
|
Relations |
BioSample |
SAMN16380635 |
SRA |
SRX9250922 |