|
| Status |
Public on May 16, 2020 |
| Title |
Dendritic cells from IRE1 wild type mice treated with LPS, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
ire1: WT
treatment: LPS
replicate: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy MinElute kit (Qiagen) from LPS- or zymosan-stimulated murine bone marrow-derived DC.
All samples passed RNA quality control examined by Agilent Bioanalyzer 2100, and mRNA libraries were generated and sequenced at the Weill Cornell Epigenomics Core Facility
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GEO_Cubillos_DC_IRE1_data.txt
|
| Data processing |
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
May 16, 2020 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE131404 |
IRE1α-XBP1 signaling in leukocytes controls prostaglandin biosynthesis and pain |
|
| Relations |
| BioSample |
SAMN11669344 |
| SRA |
SRX5855617 |
