|
| Status |
Public on Feb 28, 2016 |
| Title |
M-baseline-3 |
| Sample type |
SRA |
| |
|
| Source name |
unstimulated primary human macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 3
cell type: human monocyte derived macrophages
stimulated with: none (unstimulated)
|
| Treatment protocol |
Fractions of baseline macrophages were further stimulated for 72h in culture medium with the addition of a combination of TNF-α (800U/ml), PGE2 (1µg/ml) and Pam3CSK4 (1µg/ml) (=TPP) to differentiate macrophages into subtypes
|
| Growth protocol |
MACS beads isolated CD14 primary human monocytes were cultured for 72 h with granulocyte/macrophage colony stimulating factor (GM-CSF; 500U/ml) in RPMI1640 medium containing 10 % fetal calf serum (FCS) and 1% Penicillin/Streptomycin to generate unstimulated baseline macrophages
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cultured macrophages were lysed in TRIZOL (Invitrogen) and total RNA was extracted according to the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Mb-1
Normalized-RNA-seq-tag-counts-annotated.txt
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome (RefSeq database release 64).
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. Sequencing datasets for M-IFNy and M-IL4 are available on Gene expression omnibus (GEO) platform with reference number GSE36952 labeled as M1 and M2 macrophages.
Genome_build: hg 19
Supplementary_files_format_and_content: Normalized RNA-seq tag counts annotated to the hg19 reference genome for three independent biological replicates
|
| |
|
| Submission date |
Mar 05, 2015 |
| 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 |
GPL15456 |
| Series (2) |
| GSE66593 |
Epigenomic landscapes of human inflammation associated macrophages [RNA-seq] |
| GSE66595 |
Epigenomic landscapes of human inflammation associated macrophages |
|
| Relations |
| BioSample |
SAMN03389879 |
| SRA |
SRX903241 |
