|
| Status |
Public on May 01, 2018 |
| Title |
WT.3 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6;CBA
tissue: Thymus
age: 4 months-old
genotype: Wild type control
|
| 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) |
[email protected]
|
| 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 |
SAMN09002799 |
| SRA |
SRX4014199 |
