|
| Status |
Public on Oct 01, 2019 |
| Title |
Monocyte_3 |
| Sample type |
SRA |
| |
|
| Source name |
monocyte
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: healthy
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy kits (Qiagen)
100 ng 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 |
| |
|
| Description |
658
|
| 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 |
Oct 25, 2016 |
| Last update date |
Oct 01, 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) |
| GSE89187 |
Transcriptome analysis of peripheral blood monocytes |
|
| Relations |
| BioSample |
SAMN05941964 |
| SRA |
SRX2268500 |
