|
| Status |
Public on Apr 01, 2016 |
| Title |
893 untreated |
| Sample type |
SRA |
| |
|
| Source name |
ESdM
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESdM
stimulation: unstimulated
|
| Treatment protocol |
ESdM were either left untreated or stimulated with a combination of LPS+IFNg (500+20 ng/ml), IL4 (100U/ml), or TGFb (50ng/ml) for 24h to polarize ESdM into different activation states
|
| Growth protocol |
ESdM, generated from C57BL/6-ATCC ES cells, were grown in sterile-filtered N2-medium (DMEM/F12, supplemented with 5 ml N2 supplement, 0.48 mM L-glutamine, and 100 μg/ml penicillin/streptomycin) at 37°C and 5 % CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured ESdM 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 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against themm10 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 genome
|
| |
|
| Submission date |
Jun 29, 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 |
GPL16173 |
| Series (2) |
| GSE70383 |
Characterization of pro- and anti-inflammatory activation states in embryonic stem cell derived microglia |
| GSE77065 |
Genoma-wide analysis of pro- and anti-inflammatory activation states in embryonic stem cell-derived microglia |
|
| Relations |
| BioSample |
SAMN03801253 |
| SRA |
SRX1076939 |
