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Sample GSM857328 Query DataSets for GSM857328
Status Public on Apr 01, 2012
Title CD11c+TAMs_002
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 TAM2.count; genome build: mm9
count. Paired-end sequence reads were aligned to the mouse genome (mm9; 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; 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 (; 0.5.1p2).
Submission date Jan 06, 2012
Last update date May 15, 2019
Contact name Camilla Stormo
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
SRA SRX115014
BioSample SAMN00771326

Supplementary file Size Download File type/resource
GSM857328_TAM2.count.txt.gz 140.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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