|
Status |
Public on Nov 18, 2016 |
Title |
IBET_d6_BG_0uM_9882 |
Sample type |
SRA |
|
|
Source name |
Adult Human Peripheral Blood
|
Organism |
Homo sapiens |
Characteristics |
cell type: Monocyte treatment protocol: BG exposed 24 hours, culture for 5 days to macrophage. library strategy: RNA-Seq chip antibody: none
|
Growth protocol |
Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Tolerization was induced by treatment of monocytes with 10-100ng/mL LPS for 24 hours, followed by washout and five days culture in RPMI + 10% human serum, while trained innate immunity was induced by treatment with 5 ng/mL BG for 24 hours, followed by washout and 5 days in culture. Establishment of tolerance or training in the resulting macrophages at day 6 was determined by TNF and IL6 release at 24 hours following LPS stimulation using ELISA. For ChIP-seq, 10x106 monocytes were seeded in 10cm dishes, for RNAseq and ATAC-seq 1.5 x 106 monocytes were seeded in 6 well plates.
|
Extracted molecule |
total RNA |
Extraction protocol |
Libraries were prepared according to Illumina's instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina Casava software 1.8.2 used for basecalling of Hiseq2000 data. Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation (Ensemble release 68). Genome_build: hg19
|
|
|
Submission date |
Aug 05, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Hendrik G Stunnenberg |
E-mail(s) |
H.Stunnenberg@ncmls.ru.nl
|
Phone |
+31 (0)24 3610524
|
Organization name |
Radboud University
|
Department |
Molecular Biology
|
Street address |
Geert Grooteplein 28
|
City |
Nijmegen |
ZIP/Postal code |
6525 GA |
Country |
Netherlands |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE85243 |
Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory (RNA-Seq) |
GSE85246 |
Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory |
|
Relations |
BioSample |
SAMN05513978 |
SRA |
SRX2004123 |