|
| Status |
Public on Dec 27, 2018 |
| Title |
Kupffer cell-LPS-4hr-1 |
| Sample type |
SRA |
| |
|
| Source name |
Kupffer cell-LPS-4hr-1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
agent: LPS
time point: 4hr
marker: CD45+F4/80+CD64+
|
| Treatment protocol |
mice of 7~12 wks of age were injected intraperitoneally (i.p) with LPS (20 mg/kg) for 1hr or 4hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Dec 27, 2017 |
| Last update date |
Dec 27, 2018 |
| Contact name |
Daun Jung |
| E-mail(s) |
jhd2800@gmail.com
|
| Phone |
+82)10-9498-2801
|
| Organization name |
CHA Bundang Medical Center
|
| Department |
Department of Pathology
|
| Street address |
Bundang-gu, 삼평동 689
|
| City |
Seongnam-si |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
13488 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE108553 |
Genome-wide transcriptional profiles of Kupffer cells and alveolar macrophages from naïve and LPS-injected mice |
|
| Relations |
| BioSample |
SAMN08245412 |
| SRA |
SRX3516412 |
