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Sample GSM3121903 Query DataSets for GSM3121903
Status Public on May 01, 2018
Title Mb1.Cre.2
Sample type SRA
Source name Thymus
Organism Mus musculus
Characteristics strain: C57BL/6;CBA
tissue: Thymus
age: 20 months-old
genotype: Rosa26-Lmo2+Mb1-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
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]
BioSample SAMN09002808
SRA SRX4014189

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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