|
| Status |
Public on Jan 17, 2018 |
| Title |
Sample_3502, CD_LPS |
| Sample type |
SRA |
| |
|
| Source name |
granulocyte-monocyte progenitor (GMP) cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: granulocyte-monocyte progenitor (GMP) cells
genotype: Ldlr-/- NLRP3-/-
stimulation: LPS
diet: chow-diet
batch: batch2
|
| Treatment protocol |
Mice were intravenously injected with PBS (vehicle control) or E.coli derived ultrapure LPS (0111:B4; 10ug/ mouse) six hours prior to sacrifice
|
| Growth protocol |
-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-sequencing 10.000-50.000 sorted GMPs were collected immediately in Trizol containing b-mercaptoethanol. RNA was extracted using the RNeasy Micro RNA Isolation kit (Quiagen)
Library preparation for subsequent RNA-sequencing analysis was performed using the TruSeq. RNA Library Prep Kitv2 (Illumina) following manufacturer’s protocol instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Sample_3502
|
| Data processing |
Illumina Casava1.81 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with Hisat2 (v2.0.6) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome
|
| |
|
| Submission date |
Nov 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE97926 |
Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells |
| GSE106789 |
Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells II [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN08013575 |
| SRA |
SRX3384010 |
