|
| Status |
Public on Jul 06, 2023 |
| Title |
TSC2ko_hydrogel_rapamycin_rep1 [Pietrobon_S04] |
| Sample type |
SRA |
| |
|
| Source name |
TSC2ko_hydrogel_rapamycin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: teratoma-derived smooth muscle cells
genotype: TSC2-/-
culture substrate: hydrogel
treatment: 20nM rapamycin, 72 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Custom TriZOL extraction with column purification- see manuscript for details.
RNA libraries were prepared with the SMART-Seq v4 kit (Takara Bio).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Processed raw sequences with fastp to perform automatic adapter trimming and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls)
Quantified transcripts using salmon v1.4.0 with --gcBias and --validateMappings flags against an index constructed from GENCODE v35 trancripts plus Lexogen SIRV Set 3 spike-in sequences and genomic decoys
Read transcript quantification data with tximport library and summarized to gene level quantification
Normalized raw read counts using DESeq2 median of ratios method
Scaled normalized raw read counts using DEseq2 regularized log2 transformation
Genome_build: GRCh38
Supplementary_files_format_and_content: salmon transcript quantification: Quantifrication of GENCODE v35 transcripts using salmon v1.3.0
Supplementary_files_format_and_content: Comma separated matrix table includes data for every gene and every sample in three formats: 1) raw gene counts (e.g. used differential expression analysis), 2) normalized counts by DEseq2 median of ratios method (e.g. used for individual gene count visualization), 3) log transformed and regularized counts (e.g. used for dimensionality reduction and heatmap).
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Jul 06, 2023 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Ottawa Bioinformatics Core Facility
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE179044 |
Tissue-Engineered Disease Modeling of Lymphangioleiomyomatosis Exposes a Therapeutic Vulnerability to HDAC Inhibition |
|
| Relations |
| BioSample |
SAMN19918621 |
| SRA |
SRX11243536 |
