|
| Status |
Public on Nov 11, 2019 |
| Title |
UCS2 control Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Fbxw7-/-; Pten-/- uterine carcisnosarcoma cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: endometrial carcinosarcoma
genotype: Fbxw7-/-; Pten-/-
genotype/variation: Cells stably expressing pLVX and TetON vector
|
| Treatment protocol |
UCS1 and UCS2 cells were transduced with A) lentivirus expressing Fbxw7 under a Tet inducible promoter (FBXW7) or B) lentivirus with vector only (PLVX) AND c) with lentivirus expressing TetON. Cells were selected with puromycin (pLVX) and G418 (tetON).
|
| Growth protocol |
UCS1 and UCS2 cells were grown in DMEM +10% FBS in the presence of doxycycline 500ng/ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNeasy Mini Kit (Qiagen #74104). RNA was treated with RNAse-free DNAse (Qiagen #79254) and Qubit quantified for library preparation
4 ug of total DNAse-treated RNA was prepared with TruSeq Stranded Total RNA LT Sample Prep kit (Illumina). Poly-A-RNA was purified and fragmented before strand specific cDNA synthesis. cDNA was poly A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples were quantified by Qubit before normalization and pooling. Samples were sequenced on the Illumina NextSeq 500 with read configuration as 75 bp, single end reads. 25-40 million reads were generated per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene
|
| |
|
| Submission date |
Oct 07, 2019 |
| Last update date |
Nov 11, 2019 |
| Contact name |
Ileana C Cuevas |
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Pathology
|
| Lab |
Castrillon
|
| Street address |
5323 Harry hines Blvd. NB6.112
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE138490 |
FBXW7 is a defining driver of uterine carcinosarcoma by promoting epithelial-mesenchymal transition |
|
| Relations |
| BioSample |
SAMN12930532 |
| SRA |
SRX6956891 |
