|
| Status |
Public on Nov 22, 2021 |
| Title |
293T cells, PRCC-TFE3 transduced replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic kidney
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: 293T
genotype: PRCC-TFE3
tissue: kidney
|
| Treatment protocol |
293T cells were seeded in 6-well plates at 2 x 105 cells per well and after 24 hours were transfected with 500 ng of plasmids encoding ASPSCR1-TFE3, NONO-TFE3, PRCC-TFE3, SFPQ-TFE3, wild type (WT) TFE3, or an empty vector control (all in pLX313). All transfections were performed in three biological replicates. Cells were harvested 48 hours after transfection.
|
| Growth protocol |
Cell lines were grown in base media of DMEM, supplemented with 10% FBS, 100 U mL-1 penicillin, 100 μg mL-1 streptomycin, 2 mM L-glutamine, and 100 μg mL-1 Normocin (Invivogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the RNeasy Plus Mini Kit (QIAGEN, #74136).
Sequencing libraries were prepared with poly(A) selection using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Paired-end sequencing reads were aligned to the human genome reference build hg38 using STAR v2.7.2
Quantification was performed using RSEM v1.3.2
Expected counts and Transcripts-Per-Million (TPM) were generated using RSEM v1.3.2
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary table 3a.txt - tab-delimited text file containing expected counts for all samples and all genes
Supplementary_files_format_and_content: Supplementary table 3a.txt - tab-delimited text file containing Transcript-Per-Million (TPM) for all samplesa and all genes
Supplementary_files_format_and_content: Tab-delimited text file for each file containing expected counts, TPMs, and FPKMs for all genes
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Nov 22, 2021 |
| Contact name |
Ziad Bakouny |
| E-mail(s) |
ziad_elbakouny@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Lab |
Viswanathan Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE188885 |
Integrative Clinical and Molecular Characterization of Translocation Renal Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN23167799 |
| SRA |
SRX13143650 |
