|
| Status |
Public on Apr 01, 2012 |
| Title |
CD11c+TAMs_001 |
| Sample type |
SRA |
| |
|
| Source name |
F4/80+CD11c+ tumor-associated macrophages (TAMs) isolated from Lewis Lung Carcinoma
|
| Organism |
Mus musculus |
| Characteristics |
cell type: F4/80+CD11c+ tumor-associated macrophages
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to Illumina TruSeq RNA sample preparation guide Part# 15008136 Rev.A. RNA fragmentation with “Elute, Prime, Fragment Mix” was performed for 4 minutes at 94 oC.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
TAM1.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; www.ensembl.org) using Bowtie (doi:10.1186/gb-2009-10-3-r25) and TopHat (doi:10.1093/bioinformatics/btp120). Reads were mapped to known genes and splice junctions by providing TopHat (1.2.0) with an annotation file (Mus_musculus.NCBIM37.62.gtf; www.ensembl.org). Samtools (doi: 10.1093/bioinformatics/btp352; samtools-0.1.12a) was then used to remove PCR-generated duplicate reads. Count data for each exon was generated using htseq-count from the HTseq package (http://www-huber.embl.de/users/anders/HTSeq/; 0.5.1p2).
|
| |
|
| Submission date |
Jan 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Camilla Stormo |
| E-mail(s) |
[email protected]
|
| Organization name |
Oslo University Hospital
|
| Department |
Department of Medical Genetics
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0407 |
| Country |
Norway |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE34903 |
Gene expression profiles of tumor-associated macrophages (TAMs) overexpressing miR-511-3p |
|
| Relations |
| SRA |
SRX115013 |
| BioSample |
SAMN00771325 |
