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Sample GSM857335 Query DataSets for GSM857335
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.
 
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).
 
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

Supplementary file Size Download File type/resource
GSM857335_308R5.count.txt.gz 138.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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