|
Status |
Public on May 01, 2018 |
Title |
Sca1.Lmo2.2 |
Sample type |
SRA |
|
|
Source name |
Thymus
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6;CBA tissue: Thymus age: 7 months-old genotype: Sca1-Lmo2
|
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 referbamence 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 |
SAMN09002803 |
SRA |
SRX4014194 |