|
| Status |
Public on Oct 08, 2022 |
| Title |
BMDM_DKO-2 |
| Sample type |
SRA |
| |
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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 ...
|
| |
|
| 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 |
SAMN10246469 |
| SRA |
SRX4892084 |
