|
| Status |
Public on May 27, 2021 |
| Title |
CDH2 shRNA_CSC_1 |
| Sample type |
SRA |
| |
|
| Source name |
Breast Cancer Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
knocked down: CDH2
|
| Treatment protocol |
The CSCs from MDA-MB-231 with CDH2, Cx43 and Scramble knockdown were sorted using Flow cytometry. Cells were then incubated overnight at 37C / 5% CO2
|
| Growth protocol |
The CSCs from MDA-MB-231 with CDH2, Cx43 and Scramble knockdown cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen). Ribosomal RNA was depleted with Ribo-Zero gold from Illumina (San Diego, CA)
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Lognormal shrinkage was used to remove batch effect between runs and one of the outlier, Cx43 shRNA_CSC_3, was removed from further analysis.
Counts with a maximum of less than 1 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes RPKM values for each sample
|
| |
|
| Submission date |
Oct 04, 2019 |
| Last update date |
May 27, 2021 |
| Contact name |
Pranela Rameshwar |
| E-mail(s) |
rameshwa@njms.rutgers.edu
|
| Organization name |
Rutgers NJ Medical School
|
| Department |
Medicine
|
| Lab |
Stem Cell and Translational Medicine
|
| Street address |
185 South Orange Avenue
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE138434 |
CDH2 and Cx43 knockdown CSCs compaired with scramble (control) in breast cancer |
|
| Relations |
| BioSample |
SAMN12912117 |
