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Status |
Public on Apr 01, 2012 |
Title |
SFFV.miR-511-3p-mut_TAMs_003 |
Sample type |
SRA |
|
|
Source name |
F4/80+ tumor-associated macrophages (TAMs) overexpressing mutated miR-511-3p (miR-511-3p-mut), isolated from Lewis Lung Carcinoma
|
Organism |
Mus musculus |
Characteristics |
cell type: F4/80+ tumor-associated macrophages (TAMs) overexpressing mutated miR-511-3p (miR-511-3p-mut) 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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
308R5.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).
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|
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Submission date |
Jan 06, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Camilla Stormo |
E-mail(s) |
Camilla.Stormo@medisin.uio.no
|
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 |
SRX115021 |
BioSample |
SAMN00771333 |