|
| Status |
Public on Aug 31, 2017 |
| Title |
PolyA RNA-seq BmalKO KLA6h |
| Sample type |
SRA |
| |
|
| Source name |
mouse BMDM
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: bone marrow-derived macrophage
treatment: KLA 6h
|
| Treatment protocol |
Mouse macrophages are treated with bacterial lipopolysaccharide (LPS) or Kdo2-Lipid A,chemically defined substructure of LPS specifically recognized by Toll-like receptor 4 for indicated time.
|
| Growth protocol |
Mouse thioglycollate-elicited macrophages and bone marrow-derived macrophages were isolated from male 6- to 9-weeks old C57BL/6J (Charles River laboratories) and Arntl-/- mice. Cells are cultured in RPMI-1640 medium containing 10% FCS. M-CSF (20ug/ml) was added for BMDM culture medium for 6 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles.
RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA. RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA). Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA)
Reads were aligned to mm9 genome using default parameter for RNA-star. Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: mm9
|
| |
|
| Submission date |
Mar 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yumiko Oishi |
| E-mail(s) |
yuooishi-circ@umin.ac.jp
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Department of Cellular and Molecular Medicine
|
| Street address |
1-5-45, Yushima
|
| City |
Bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE95712 |
Bmal1 regulates inflammatory response in macrophage |
|
| Relations |
| BioSample |
SAMN06480877 |
| SRA |
SRX2613933 |
