|
| Status |
Public on Apr 06, 2021 |
| Title |
Tau aggregates 1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells expressing P301S-tau RD -YFP and P301S-tau RD-CFP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
transfection_status: Transfected with clarified brain homogenate from P301S mice
genotype: HEK293 Tau-RD-P301S-CFP/YFP
sample type: with tau aggregates
|
| 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 96 hours. Tau aggregation was monitored using the Evos M500 Imaging System with a GFP filter
|
| 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 |
RNA was extracted from cells using Trizol LS reagent
NovoGene Random Hexamer Primed RNA library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 4
MAJIQ_delta_psi.tsv
iREADs_analysis.csv
|
| 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)
MAJIQ v2.1 and iRead v0.8.5 were used to examine splicing changes in cells with and without tau aggregates
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: MAJIQ_delta_psi.tsv (.tsv showingMAJIQ splicing analysis output)
iREADs_analysis.csv (.csv file showing intron retetion analysis using iREADS)
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Apr 07, 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 |
GPL24676 |
| Series (1) |
| GSE148716 |
Tau aggregates are RNA-protein assemblies that mis-localize multiple nuclear speckle components |
|
| Relations |
| BioSample |
SAMN18633287 |
| SRA |
SRX10522387 |
