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Sample GSM1130106 Query DataSets for GSM1130106
Status Public on May 01, 2016
Title APL 2
Sample type SRA
Source name leukemia progenitor
Organism Mus musculus
Characteristics sample type: GFP-labeled c-Kit+ mouse APL cells
strain: FVB N/J
Growth protocol GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description BM-E-2
Data processing Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000 --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
Submission date Apr 26, 2013
Last update date May 15, 2019
Contact name Jiang Zhu
Organization name Shanghai institute of hematology
Street address 197, rui-jin 2nd Road
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL13112
Series (1)
GSE46434 Expression data from GFP-labeled c-Kit+ mouse APL cells and normal Lin-Sca-1-c-Kit+ mouse bone marrow cells
BioSample SAMN02058601
SRA SRX272202

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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