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Status |
Public on Oct 08, 2022 |
Title |
BMDM_DKO-1 |
Sample type |
SRA |
|
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Source name |
macrophages, Double KO (ALDH2/LDL)
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: bone marrow derived macrophages age: 8w genotype/variation: Low Density Lipoprotein (LDL) receptor knockout genotype/variation: Acetaldehyde dehydrogenase 2 (ALDH2) knockout
|
Growth protocol |
mice bone marrow derived macrophages are seperated from mice bone marrow and then culture 7days finally treat macrophages with oxLDL
|
Extracted molecule |
total RNA |
Extraction protocol |
cell total RNA was extracted by using Trizol RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: mm8 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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Submission date |
Oct 16, 2018 |
Last update date |
Oct 09, 2022 |
Contact name |
shanshan zhong |
E-mail(s) |
sszhong@sibs.ac.cn
|
Organization name |
Chinese Academy of Sciences (CAS)
|
Street address |
320 Yueyang Rd
|
City |
shanghai |
ZIP/Postal code |
200031 |
Country |
China |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE121310 |
RNAseq of Bone Marrow-Derived Macrophages (BMDMs) |
|
Relations |
BioSample |
SAMN10246458 |
SRA |
SRX4892083 |