|
Status |
Public on Feb 15, 2016 |
Title |
HET (Q111) 2 month Female striatum mRNA rep1 |
Sample type |
SRA |
|
|
Source name |
striatum
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: striatum genotype: Het (Q111) Knock-In age: 2 month Sex: Female housing condition: housed with Het (Q111) mice
|
Extracted molecule |
polyA 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 1.25 ug of total RNA were used to collect polyA-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 |
299956_Q111B0021_02_L15 Sequencing may have been performed on either of the following Illumina instruments: HiSeq 2500 or HiSeq 2000
|
Data processing |
Illumina CASAVA 1.8.2 software used for basecalling Genome mapped via Omnisoft OSA 2.0 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: 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 B.38, gene models version Ensembl R.75 Supplementary_files_format_and_content: Text file containing abundance measurements in FPKM Supplementary_files_format_and_content: Text file containing abundance measurements in counts
|
|
|
Submission date |
Feb 09, 2015 |
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 (2) |
GSE65774 |
Transcriptome profiling in knock-in mouse models of Huntington's disease [Striatum_mRNA] |
GSE65776 |
Transcriptome profiling in knock-in mouse models of Huntington's disease [striatum; cortex; liver; tissue survey] |
|
Relations |
BioSample |
SAMN03334121 |
SRA |
SRX870391 |