|
| Status |
Public on Jul 27, 2022 |
| Title |
786-O_ZHX2_shCtrl_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-O
condition: shCtrl
shRNA: shCtrl
|
| Treatment protocol |
USP13 shRNA (43 and 45) were purchased from Sigma Aldrich. USP13 siRNA were purchased from Dharmacon (D006064). SgRNA targeting USP13 were inserted into CRISPR-V2 lentivirus vector. ShRNA targeting USP13 were cloned into tet-on puro vector to generate doxycycline-inducible shUSP13 plasmids. ShRNA and sgRNA sequences: Sg1: AGCGCCGGGGCGCCCTGTT. Sg2: AATAGCACTACCAAATATTG. Sg3: TGTATGCATGAATACATTTT. Sg4: TGCCCACGATCCGCGTGCCC. Sh50: CGCCTGATGAACCAATTGATA. Sh52: CCGGTGAAATCTGAACTCATT.
|
| Growth protocol |
The 786-0, UMRC-2, UMRC-6, OS-RC-2, RCC-4, Caki-1, 293T and HKC cells were bought from the American Type Culture Collection (ATCC) or Sigma-Aldrich. The above cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco 11965118) with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin (PS). All cells were cultured in incubator at 37℃ with 5% CO2. All cells were verified by short tandem repeat testing. Mycoplasma detection was used to ensure cells were Mycoplasma free.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 786-O cells (triplicates) was extracted by using RNeasy kit with on column DNase digestion (Qiagen).
Libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500 with paired-end 150 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were then filtered for adapter contamination using cutadapt (v1.12) and filtered using FASTX-Toolkit (v0.0.14) such that at least 90% of bases of each read had a Phred score > 20.
Reads were aligned to the reference genome (hg19) using STAR (v2.5.2b) retaining only primary alignments. Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon (v0.11.3), and differential expression was detected using DESeq2 (v1.14.1).
Genome_build: hg19
Supplementary_files_format_and_content: sf files contain the per-gene transcript-per-million (TPM) data. The Excel table contains the full list of differential genes.
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Jul 28, 2022 |
| Contact name |
Austin J Hepperla |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Street address |
7018B Mary Ellen Jones Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE186717 |
USP13 Promotes Deubiquitination of ZHX2 and Tumorigenesis in Kidney Cancer |
|
| Relations |
| BioSample |
SAMN22608724 |
| SRA |
SRX12802010 |
