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Sample GSM1673365 Query DataSets for GSM1673365
Status Public on Jun 11, 2015
Title XBP1-KO rep3
Sample type SRA
Source name ovarian cancer ascites_XBP1-KO
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: conditional knockout selectively deleting XBP1 in CD11c positive cells
tissue: ID8-based tumors (day 23)
cell type: sorted tumor-associated DCs
Growth protocol in vivo tumor and ascites
Extracted molecule total RNA
Extraction protocol Total RNA from sorted tumor-associated DCs (N=3/genotype) was independently isolated using the miRVANA kit Life Technologies and further purified and concentrated using minElute columns (Qiagen). RNA integrity was confirmed using an Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Sample_tDC6-KO
Data processing Align to contamination (mm9 related) (chrM and Ribosomal RNA) and get rid of chrM and ribo mapped reads
None aligned reads from step 2 are the possible reads coming from mRNAs. Use these reads to estimate isoform/gene level raw read counts using RSEM package (1).
Normalize read raw counts from rsem using edgeR bioconductor R package (2).Filter low count genes from complete data set.Normalize using Upper quartile normalization
Use edgeR to find differentially expressed genes.
Result will be sorted based on adjusted p-value and genes has small adjusted p-value are considered as differentially expressed based on comparison.
Genome_build: MM9
Supplementary_files_format_and_content: text, csv - Estimated counts, Normalized estimated counts
Submission date May 01, 2015
Last update date May 15, 2019
Contact name Juan R Cubillos-Ruiz
Organization name Weill Cornell Medicine
Department Medicine
Street address 1300 York Ave, E-907
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL17021
Series (1)
GSE68472 Transcriptional profile of XBP1-deficient ovarian cancer-associated dendritic cells (DCs)
BioSample SAMN03579587
SRA SRX1015895

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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