|
Status |
Public on Oct 31, 2018 |
Title |
Chow_24h_LPS_rep1 |
Sample type |
SRA |
|
|
Source name |
Peritoneal macrophages
|
Organism |
Mus musculus |
Characteristics |
tissue: Peritoneal macrophages diet: chow lps_treatment: 24h Sex: Female
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted uisng the Qiagen RNAeasy mini kit Libraries were constructed using the NuGen Ovation Universal RNA-seq kit
|
|
|
Library strategy |
ssRNA-seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
FC_24h_1_S16_L008_R1_001
|
Data processing |
Bases were called using Illumina CASAVA 1.8.2 Reads were aligned to the mouse genome mm10 by STAR 2.5.2b BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1 Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script Genome_build: mm10 Supplementary_files_format_and_content: matrix of read counts per gene
|
|
|
Submission date |
Nov 28, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Menno de Winther |
E-mail(s) |
m.dewinther@amc.uva.nl
|
Phone |
+31205666762
|
Organization name |
Academic Medical Center University of Amsterdam
|
Department |
Medical Biochemistry
|
Lab |
Experimental Vascular Biology
|
Street address |
Meibergdreef 9
|
City |
Amsterdam |
ZIP/Postal code |
1105AZ |
Country |
Netherlands |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE107412 |
A defective pentose phosphate pathway reduces inflammatory macrophage responses during hypercholesterolemia |
|
Relations |
BioSample |
SAMN08103887 |
SRA |
SRX3425813 |