|
| Status |
Public on Oct 01, 2012 |
| Title |
M1_2 |
| Sample type |
SRA |
| |
|
| Source name |
human monocyte derived macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 2
cell type: M1 macrophages (classically activated)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Macrophages were harvested and directly lyzed using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
instrument name: Illumina HiScanSQ
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
M1
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then mapped to hg19 whole genome using Casava1.8.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Casava1.8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
All analysis concerning differential expression of total transcripts were calculated using the values from Casava 1.8.
We only used TopHat/Cufflinks for analyzing the transcript variants, etc. and these tables/results are part of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM.txt file includes RPKM values for each Sample.
|
| |
|
| Submission date |
Mar 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrea Nino Castro |
| E-mail(s) |
anino@uni-bonn.de
|
| Organization name |
Life and Medical Sciences institute
|
| Lab |
Genomics and Immunoregulation
|
| Street address |
Carl Troll str. 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE36952 |
Transcriptome wide analysis of classically and alternatively activated macrophages |
|
| Relations |
| SRA |
SRX134853 |
| BioSample |
SAMN00848521 |
