|
| Status |
Public on Apr 17, 2023 |
| Title |
MDA-MB-231 + pLV-KRAB + all 4 gRNAs, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Triple negative breast cancer
transduction (vector): pLV-KRAB
transduction (grna): All 4 gRNAs (vs ZEB1 promoter)
sequencing run: run 2
|
| Treatment protocol |
Lentiviral particles were produced using HEK293T with co-transfection using third generation VSVG (Addgene plasmid #12259), GAG/POL (Addgene plasmid #12260) and pLV dCas9-KRAB +/-gRNA as previously described [doi:10.1039/c9sc01432b & 10.1016/j.omtn.2018.12.003]. Four days following transduction, 1.25 µg/mL and 0.75 µg/mL puromycin was used to select SUM159 and MDA-MB-231, respectively.
|
| Growth protocol |
SUM159 cells were cultured in F12 Medium supplemented with 0.6% 1M Hepes, 5 µg/mL insulin, 1 µg/mL hydrocortisone, 1% Antibiotic-Antimycotic and 10% heat inactivated FBS; MDA-MB-231 cells were cultured in DMEM-Hi glucose-pyruvate + 10% heat inactivated FBS, 1% Antibiotic-Antimycotic.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed twices before RNA was harvested using QIZsol Lysis reagent (QIAGEN). Approximately 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Australian Genome Research Facility, where libraries were preprared sequenced for 50bp single-end (SE) reads on the Illumina HiSeq 2500 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B2_MDAMB231_g4_2
|
| Data processing |
RNA-seq data underwent pseudo-alignment and quantification with Salmon [10.1038/nmeth.4197] before import into R/Bioconductor using tximport [10.12688/f1000research.7563.2]
Assembly: GRCh38
Supplementary files format and content: Comma separated text files including length-scaled TPM values for each sample
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Apr 17, 2023 |
| Contact name |
Joe Cursons |
| Organization name |
Monash University
|
| Department |
Biomedicine Discovery Institute
|
| Street address |
19 Innovation Walk
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE210274 |
Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [RNA-seq] |
| GSE210277 |
Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN30088368 |
| SRA |
SRX16760933 |
