|
Status |
Public on Nov 03, 2015 |
Title |
Het (Q111) 2 month Female Hippocampus mRNA rep2 |
Sample type |
SRA |
|
|
Source name |
Het (Q111) 2 month_Female_Hippocampus
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: Het (Q111) Knock-In age: 2 months Sex: Female tissue: Brain - Hippocampus tissue: Brain - Hippocampus housing condition: housed with Het (Q111) mice
|
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 |
372442_2749_1_L4.D709
|
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 for Omnisoft: 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: Excel files include FPKM and Count values for each Sample
|
|
|
Submission date |
Sep 28, 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) |
GSE73503 |
Transcriptome profiling in knock-in mouse models of Huntington's disease [Hippocampus_mRNA] |
GSE73508 |
Transcriptome profiling in knock-in mouse models of Huntington's disease [cerebellum; hippocampus] |
|
Relations |
SRA |
SRX1292525 |
BioSample |
SAMN04116295 |