|
| Status |
Public on Aug 25, 2018 |
| Title |
end stage PFN1 G118V 3 |
| Sample type |
SRA |
| |
|
| Source name |
end stage PFN1 G118V
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N-Tg(Prnp-PFN1*G118V)838Kiaei/J
age: 245
batch: 1
mouse id tag: A411
data analysis id: MO3
tissue: spinal cord
|
| Growth protocol |
Male mice were housed under 12-hour light/dark conditions and fed 4-5 gram chow diet (Harlan/Teklad #7001) per day per mouse with free access to water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cords were removed and RNA was harvested using Trizol reagent (Invitrogen).
Illumina TruSeq Stranded mRNA Sample Preparation Kit (Cat# RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries according to manufacturer's protocols. Sequencing was performed on the Illumina NextSeq 500 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A411:MO3
|
| Data processing |
Illumina RTA v2, FASTQ, software was used for base-calling
Trimmomatic was used to filter out low quality reads and possible Illumina Adaptor or PCR primer contaminations
Reads were aligned to the mm10 UCSC mouse reference genome using TopHat.
Gene expression was normalized in fragments per kilo base of transcript per million mapped reads (FPKM) with Cufflinks
FPKM values were log2-transformed after adding 1
Genes with 0 expression in at least 8 samples were removed to filter out unexpressed genes
The 'Combat' function from Bioconductor package sva was used to removed batch effects between samples from batches 1 and 2
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated values file include log2(1+FPKM) values for each sample
|
| |
|
| Submission date |
May 01, 2018 |
| Last update date |
Aug 25, 2018 |
| Contact name |
Kiaei Mahmoud |
| E-mail(s) |
mkiaei@uams.edu
|
| Organization name |
University of Arkansas for Medical Sciences
|
| Street address |
4301 W. Markham St., Slot 611 (BioMed 1, Rm B-306A)
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72205 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE113924 |
RNA-Seq Analysis of Spinal Cord Tissues from hPFN1G118V Transgenic Mouse Model of ALS at Presymptomatic and End Stages of Disease |
|
| Relations |
| BioSample |
SAMN09007191 |
| SRA |
SRX4018328 |
