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Sample GSM1958553 Query DataSets for GSM1958553
Status Public on Dec 01, 2019
Title DNP-IgE (0.5 ug/ml) treated BMMC [IgE2]
Sample type SRA
 
Source name BMMCs_DNP-IgE
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: wild type
cell type: Bone marrow derived mast cells (BMMCs)
passages: >95% FcER1+ CD117+
treatment group: sensitized overnight with DNP-IgE (0.5 ug/ml)
molecule subtype: mRNA and lncRNA
Treatment protocol IgE (0.5 ug/ml) treatment for 18 h, Ag (50 ng/ml) treatment for 2h after IgE treatment
Growth protocol 10 ng/ml IL-3 and 10 ng/ml SCF for 4-6 weeks after bone marrow isolation
Extracted molecule total RNA
Extraction protocol RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The sequenced reads were mapped tomm9 build of the human genome using TopHat version 2.0.12 with the aligner Bowtie 0.12.7 with their default parameters except –m 1 and –segment-mismatches 2.
FPKMs were calculated by Cufflink (2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
 
Submission date Nov 30, 2015
Last update date Dec 01, 2019
Contact name Jingxian Zhang
E-mail(s) zhangjingxian.nus@gmail.com
Organization name Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
Department IMCB
Street address 61 Biopolis Drive Proteos
City Singapore
State/province Singpaore
ZIP/Postal code 138673
Country Singapore
 
Platform ID GPL19057
Series (2)
GSE75526 Transcriptomic profiling of bone marrow derived mast cells (BMMCs) [RNA-seq]
GSE111547 Landscape of mouse mast cell chromatin: a rich resource for identification of novel mediators and genetic drivers of allergic and inflammatory diseases
Relations
BioSample SAMN04302838
SRA SRX1456406

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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