|
| Status |
Public on Jul 18, 2024 |
| Title |
MA_PC3M_X2_siJMJD6_MG132 |
| Sample type |
SRA |
| |
|
| Source name |
PC3M
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3M
cell type: Prostate cancer cells
genotype: siJMJD6
treatment: MG132 2.5uM, 4h
|
| Treatment protocol |
Cells were transfected with siNT or siJMJD6 for 72h, then were treated with DMSO or MG132 for 4h or heat shocked for 1h
|
| Growth protocol |
Cells were grown at 37°C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit according to supplied protocol.
Libraries were prepared from 100 ng RNA using the Lexogen QuantSeq FWD kit for Illumina sequencing , according to supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq: Sequence quality was assessed with FastQC v0.11.2, Fastq files were trimmed using bbduk from BBTools v35.92 according to Lexogen QuantSeq manufacturer parameters, mapped to hg38 using STAR v2.6.0 and gene annotations from Ensembl 78. HTSeq was used to count uniquely mapped reads.
Assembly: hg38
Supplementary files format and content: htseq counts tables provide counts of uniquely mapped RNAseq reads
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Marc L Mendillo |
| E-mail(s) |
[email protected]
|
| Phone |
3125034862
|
| Organization name |
Northwestern University
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Marc Mendillo
|
| Street address |
303 East Superior Street Simpson Querrey, 7th Floo
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE270672 |
An HSF1-JMJD6-HSP feedback circuit promotes cell adaptation to proteotoxic stress [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN42017744 |
| SRA |
SRX25035087 |
