|
| Status |
Public on Apr 27, 2015 |
| Title |
TOX knockout mouse RNA 3 |
| Sample type |
SRA |
| |
|
| Source name |
sorted isolated bone marrow cell populations
|
| Organism |
Mus musculus |
| Characteristics |
genotype: TOX knockout
cell type: sorted isolated bone marrow cell populations
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA sequencing libraries were made from total RNA using ClonTech SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Torrent Ion Xpress Plus Fragment Library Kit per manufacturers' instructions. RNAseq libraries were assessed for concentration and length using Invitrogen's Qubit® dsDNA HS Assay Kit (Carlsbad, CA) and Agilent High Sensitivity DNA Kit respectively (Santa Clara, CA). The samples were amplified onto Ion Sphere Particles using the Ion PI™ Template OT2 200 Kit v3 (Ion Torrent) per manufacturer’s instructions. The libraries were sequenced on the Ion Proton™ System using the Ion PI™ Sequencing 200 Kit v3 (Ion Torrent). Samples were multiplexed to obtain at least 10 million reads each for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
base-calling was performed on Ion Torrent suite software
Raw sequencing reads in FASTQ format were aligned to the UCSC mouse reference genome (mm10) using TOPHAT21.
Gene expression for each sample was calculated using reference-guided transcript assembly using a gene transfer file (GTF) from UCSC genes (http://genome.ucsc.edu/) and normalized quantification of reads as FPKM (fragments per kilo bases of exons for per million mapped reads) calculated with Cufflinks and finally compiled into a gene counts table for all samples in preparation for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample
|
| |
|
| Submission date |
Feb 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wolf Wiedemeyer |
| Organization name |
Cedars-Sinai
|
| Department |
BMS
|
| Street address |
8700 Beverly Blvd.
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE65850 |
Innate lymphoid cell development requires TOX-dependent generation of a common ILC progenitor |
|
| Relations |
| BioSample |
SAMN03340013 |
| SRA |
SRX873877 |
