|
| Status |
Public on Nov 18, 2016 |
| Title |
BG_4h_6714 |
| Sample type |
SRA |
| |
|
| Source name |
Adult Human Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocyte
treatment protocol: BG exposed, collected at 4 hours post exposure.
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 |
SAMN05513913 |
| SRA |
SRX2004110 |
