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Sample GSM1098606 Query DataSets for GSM1098606
Status Public on Dec 31, 2013
Title TLR9KO Rep4
Sample type SRA
Source name TLR9KO_myeloid cells
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: TLR9-/- (TLR9KO)
cell type: CD11b-positive tumor-infiltrating myeloid cells
Treatment protocol Subcutaneously implanted tumors were locally irradiated at 15 Gy and harvested four days later.
Growth protocol Freshly isolated primary myeloid cells without in vitro culture.
Extracted molecule total RNA
Extraction protocol CD11b-positive tumor-infiltrating myeloid cells were enriched using specific antibodies and magnetic bead isolation (StemCell Technologies). The total RNA was isolated by using miRVana™ kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Sample 8
Data processing Basecalls and barcode analysis were performed using CASAVA version 1.7
Sequenced reads were mapped to mm9 whole genome using rnaseq alignment tool tophat 1.3.1 (bowtie ver 0.12.7) with parameters --max-insertion-length 10 --max-deletion-length 10 --segment-length 20. Other configuarions were kept default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genome Suite ver 6.12.0713. An expectation/maximization algorithm was used to determine relative isoform abundance levels, and the isoform abundance counts were summarized to the gene level for normalized gene expression abundance counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (normalized gene expression abundance counts)
Submission date Mar 14, 2013
Last update date May 15, 2019
Contact name Haiqing Li
Phone 626-256-4673
Organization name Beckman Research Institute of City of Hope, Center for Informatics
Department Department of Computational & Quantitative Medicine
Lab Research Informatics
Street address 1500 East Duarte Road
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platform ID GPL13112
Series (1)
GSE45180 Gene expression data from CD11b-positive myeloid cells infiltrating tumors after local irradiation
SRA SRX249608
BioSample SAMN01978626

Supplementary file Size Download File type/resource
GSM1098606_TLR9KO_rep4.txt.gz 100.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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