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Sample GSM3121904 Query DataSets for GSM3121904
Status Public on May 01, 2018
Title Rosa26.Lmo2.1
Sample type SRA
 
Source name Thymus
Organism Mus musculus
Characteristics strain: C57BL/6;CBA
tissue: Thymus
age: 9 months-old
genotype: Rosa26-Lmo2+Sca1-Cre
Extracted molecule total RNA
Extraction protocol Thymus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; Non-stranded-RNA Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description rawCounts.xls
Data processing Illumina RTA and bcl2fastq software
The RNA-seq data was aligned against the mouse reference genome (mm10/GRCm38.83) with TopHat 2.1.0, and FPKM values per gene were calculated with the R/Bioconductor package bamsignals.
Genes with FPKM values > 1 in less than three samples were excluded from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file, including raw counts (produced by bamsignals) of sequencing reads for each gene
 
Submission date Apr 30, 2018
Last update date May 02, 2018
Contact name Isidro Sánchez García
E-mail(s) isg@usal.es
Organization name Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).
Department Centro de inv. del Cáncer (CIC).
Street address Campus Miguel de Unamuno
City Salamanca
ZIP/Postal code E37007
Country Spain
 
Platform ID GPL24247
Series (2)
GSE83572 LMO2 expression in HSCs causes T-ALL in the presence of an intact thymic niche
GSE113864 Impact of Lmo2 expression on cell lineage decision during T-cell leukemogenesis [RNA-seq]
Relations
BioSample SAMN09002807
SRA SRX4014190

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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