|
| Status |
Public on Feb 10, 2016 |
| Title |
2-6323-NTg-2 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: cortex
genotype: nontransgenic (NTg)
|
| Growth protocol |
Mouse brains and spinal cords were collected at 6 month
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Brain and spinal cords were flash frozen on dry ice, and RNA was harvested using Trizol. Total RNA isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Iontorrent (brain) or Illumina (spinal cord) protocols. RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits v2 from Illumina. 12 RNA samples were indexed with different adapters and pooled for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
NTG-6323
|
| Data processing |
fastq reads were alignd to the mouse genome (mm9) with tophat v2.0.8b with parameters -G --no-novel-juncs
bam files were annotated in using Partek software to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm10 (brain) and mm9 (spinal cord)
|
| |
|
| Submission date |
Feb 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacqueline Gire O'Rourke |
| E-mail(s) |
jacqueline.orourke@cshs.org
|
| Phone |
310-248-8550
|
| Organization name |
Cedars Sinai Medical Center
|
| Street address |
8700 Beverly Blvd
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE77720 |
C9orf72 BAC Transgenic Mice Display Typical Pathologic Features of ALS/FTD |
|
| Relations |
| BioSample |
SAMN04481474 |
| SRA |
SRX1567886 |
