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Sample GSM2197877 Query DataSets for GSM2197877
Status Public on Jan 18, 2017
Title KO-0h
Sample type SRA
 
Source name Macrophages
Organism Mus musculus
Characteristics cell type: Bone marrow-derived macrophages
strain: C57BL/6
genotype/variation: JNK1 knockout
treatment: Untreated
Treatment protocol C. albicans were heat-inactivaed and add to BMDMs for 24 hours for stimulation at MOI=10
Growth protocol Bone marrows cells were cultured for 6 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate
Extracted molecule total RNA
Extraction protocol Cell supernatant were remove, wasded with PBS twice and TRIZOl were added to extract the total cell mRNA
Sequencing libraries were generated using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description q4 in gene_exp. Diff
Data processing The filtered reads were aligned to the mouse most recent genome reference mm10 by using TopHat (version 2.1.0)
the BAM files of each individual alignment were used to analyze genes differential expression by using Cufflinks (version 2.2.1)
Supplementary_files_format_and_content: diff files
 
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Xin Lin
Organization name Tsinghua University
Street address Haidian Qu Tsinghua yuan
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21103
Series (1)
GSE83265 RNA-seq data for bone-marrow-derived macrophages from wildtype and JNK1 knockout mice stimulated with yeast form Candida albicans
Relations
BioSample SAMN05232075
SRA SRX1838223

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

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