|
| Status |
Public on Apr 06, 2021 |
| Title |
P301S Tau-12 IP RNA Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Tau-IP IP RNA from P301L mouse (Tg4510)
|
| Organism |
Mus musculus |
| Characteristics |
strain: FvBB6F1-Tg(Camk2a-tTA)1Mmay, (tet)-tdTomato-Syp/EGFP)1.1Luo/J,(tetO-MAPT*P301L)4510 (referred to as rTg4510 or P301L mice)
tissue: brain
molecule type: RNA that is associated with sarkosyl (1%) insoluble tau
molecule type: Random hexamer primed RNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Animals were maintained in a facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care in accord with the Guide for the Care and Use of Laboratory Animals. All procedures were approved by the University of California, San Francisco, Institutional Animal Care and Use Committee. Animals were maintained under standard environmental conditions, with a cycle of 12 hours light and 12 hours dark and free access to food and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, tau aggregates were isolated by 1% sarkosyl extraction (to enrich for insoluble proteins) followed by immunoprecipitation of tau using the tau-12 antibody (see Methods section of associated paper for further details).
NuGen Ovation SoLo RNA-seq
Random hexamer primed RNA seq. Ribodepletion following amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
This dataset is the RNA that is associated with sarkosyl (1%) insoluble tau from the brains of mice expressiong P301L tau (tau aggregates)
Mouse_brain_tau_S12
|
| Data processing |
Timmomatic 0.36 to trim Illumina TruSeq3 adapters and low quality reads (options: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Ribosomal reads were filtered out by mapping to a ribosome reference genome (Ensembl GRCm38 musRibosomal.fa) and keeping the unmapped reads.
Reads were then mapped to GRCm38.p6 using STAR 2.6.0c in two pass alignment mode with --outFilterMultimapNmax 20)
FPKM was calculated using the longest transcript lengths taken from from ensembl biomart GRCm38.p6
Genome_build: Genome Reference Consortium Mouse Build 38 p6
Supplementary_files_format_and_content: csv file containing gene names and FPKM
|
| |
|
| Submission date |
Apr 17, 2020 |
| Last update date |
Apr 06, 2021 |
| Contact name |
Evan Lester |
| Organization name |
University of Colorado
|
| Department |
Biochemistry
|
| Lab |
Roy Parker
|
| Street address |
JSC Biotech bldg
|
| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE148716 |
Tau aggregates are RNA-protein assemblies that mis-localize multiple nuclear speckle components |
|
| Relations |
| BioSample |
SAMN14613951 |
| SRA |
SRX8132661 |
