|
| Status |
Public on Oct 14, 2022 |
| Title |
LacQ140I 12 months Striatum male mRNA rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Striatum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Corpus Striatum
genotype: Hdh(LacO-140Q/+):beta-actin-LacIR tg
strain/background: C57BL/6
age: 12 months
Sex: Male
treatment: None
treatment initiation: N/A
treatment withdrawal: N/A
batch: batch2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Q140_12M_ALW_STR_301_M_R2
Hdh(LacO-140Q/+):β-actin-LacIR tg
mRNA
processed data file: laco12m_counts_unswapped.txt
|
| Data processing |
Libraries for RNA-seq were sequenced using an Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to mouse genome Mouse.B38 (GeneModel Ensembl.R94).
a) Trimmed low-quality bases from the reads, aligned reads to the mouse genome GRCm38 with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Mouse.B38 (GeneModel Ensembl.R94)
Supplementary_files_format_and_content: Tab-delimited text files include Count values for each Sample.
|
| |
|
| Submission date |
Aug 13, 2020 |
| Last update date |
Oct 14, 2022 |
| 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 |
GPL24247 |
| Series (1) |
| GSE156236 |
Transcriptional profiling of striatum and cortex from a LacO-Q140 inducible mouse model of Huntington’s disease with early and late mutant HTT lowering |
|
| Relations |
| BioSample |
SAMN15815587 |
| SRA |
SRX8945594 |
