|
| Status |
Public on Jun 12, 2017 |
| Title |
799: Macrophages_RPMI_None_4 |
| Sample type |
SRA |
| |
|
| Source name |
macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 799
treatment: RPMI
time: 4
donor: F
|
| Treatment protocol |
24h co-incubation between TPC1 cell line and human primary macrophage
|
| Growth protocol |
RPMI with gentamycin 5 mg/ml, pyruvate 100 mM, glutamax 200 mM and 10% Fetal Calf Serum
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy kits (Qiagen)
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 HiSeq 1500 |
| |
|
| 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
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: hg19
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the hg19 reference genome
|
| |
|
| Submission date |
Dec 31, 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 |
GPL18460 |
| Series (1) |
| GSE76445 |
Trascriptome of thyroid cancer-induced macrophages |
|
| Relations |
| BioSample |
SAMN04378244 |
| SRA |
SRX1509586 |
