|
| Status |
Public on Oct 30, 2017 |
| Title |
R6/2_HD_Cortex_Male_Vehicle_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
R6/2, Cortex, Vehicle
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL6/J
genotype: Tg(HDexon1)62Gpb
tissue: Cortex
Sex: Male
age: 12 weeks
treatment: Vehicle
treatment administration route: Oral
treatment frequency: Twice-Daily (b.i.d)
treatment duration: from 4 to 12 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
409965_R62J3184_02_Right_Cortex_L8.D704
|
| Data processing |
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming /Mode=TrimByQuality /ReadTrimQuality=2; Options /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.mm10, gene models version Ensembl.R78
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample
|
| |
|
| Submission date |
Oct 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeff Aaronson |
| E-mail(s) |
jeff.aaronson@chdifoundation.org
|
| Phone |
(609) 945-9616
|
| Organization name |
CHDI
|
| Department |
Discovery & Systems Biology
|
| Street address |
155 Village Boulevard, Suite 200
|
| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE105158 |
RNA-Seq data on KMO inhibitor (CHDI-00340246) subchronic treated R6/2 mice. |
|
| Relations |
| BioSample |
SAMN07814783 |
| SRA |
SRX3300002 |
