|
| Status |
Public on May 31, 2021 |
| Title |
SUDS3 RNAi knockdown replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cells with SUDS3 RNAi knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
|
| Treatment protocol |
HEK293T cells were transfected with Ambion Silencer™ Select siRNAs targeting SUDS3 (siRNA i.d. s34740), PHF12 (siRNA i.d. s33518), or Silencer™ Select Negative Control No. 2 at final concentrations of 10 nM with Lipofectamine™ RNAiMAX Transfection Reagent for 36 h.
|
| Growth protocol |
HEK293T cells were cultured in DMEM + 10 % FBS + GlutaMAX™ Supplement at 37 °C and 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HEK293T total RNA was isolated using TRIzol™ Reagent. Isolates were DNAseI treated, then extracted with TRIzol™ Reagent a second time.
Illumina TruSeq RNA library prep kit
poly-A stranded RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence with Trimmomatic version 0.36
Reads were mapped to genome using Hisat2 version 2.1.0
Read counts were calculated with htseq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count .csv file and TPM .csv file
|
| |
|
| Submission date |
May 03, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Gaye L Hattem |
| Organization name |
Stowers Institute
|
| Department |
Proteomics
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE130676 |
Analysis of PHF12/SUDS3 functions within HEK293T cells. |
|
| Relations |
| BioSample |
SAMN11569479 |
| SRA |
SRX5784966 |
