|
| Status |
Public on Apr 06, 2021 |
| Title |
Total RNA Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells expressing P301S-tau RD -YFP and P301S-tau RD-CFP
|
| Organism |
Homo sapiens |
| Characteristics |
transfection_status: Transfected with clarified brain homogenate from P301S mice
genotype: HEK293 Tau-RD-P301S-CFP/YFP
cell line: HEK293
sample: total RNA
|
| Treatment protocol |
200 ug of WT or P301S tau clarified mouse brain homogenate was transfected per dish using lipofectamine 2000 and incubated at 37C for 24 hours. Tau aggregation was monitored using the Evos M500 Imaging System with a GFP filter. Cells were harvested by scraping, centrifuged at 1500g, snap frozen in liquid nitrogen, and stored at -80C.
|
| Growth protocol |
HEK293 biosensor cells were grown to 70-80% confluency in 245 mm square tissue culture treated dishes (Corning 07-200-599) in 50mL of DMEM (one plate per biologic replicate).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
large tau aggregates were enriched for by differential centrifugation and then further purified using fluroescence automated particle sorting. Tau aggregates were denatured and RNA was isolated from all samples using proteinase K, Guanadinium HCL, and Trizol LS reagent.
KAPA RNA HyperPrep Kit with RiboErase
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Random hexamer primed RNA
|
| 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 (UCSC hg38 humRibosomal.fa) and keeping the unmapped reads.
Reads were then mapped to GRCh38 using STAR v2.6.0c in two pass alignment mode with --outFilterMultimapNmax 20)
FPKM was calculated using the longest transcript lengths taken from from ensembl biomart GRCh38.p13
Genome_build: Genome Reference Consortium Human Build 38
|
| |
|
| Submission date |
Apr 15, 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 |
GPL18573 |
| Series (1) |
| GSE148716 |
Tau aggregates are RNA-protein assemblies that mis-localize multiple nuclear speckle components |
|
| Relations |
| BioSample |
SAMN14601127 |
| SRA |
SRX8119071 |
