|
| Status |
Public on Jun 22, 2020 |
| Title |
siB/siM-3 |
| Sample type |
SRA |
| |
|
| Source name |
epithelial breast cancer cell line; derived from metasatic pleural effusion
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: siB/siM-3
cell line: MDA-MB-231
|
| Treatment protocol |
cells were tranfected with either 100nM non-targeting siRNA (siNS), or 100nM SMARTpool siRNAs targeting either BCL11A, MBNL1 or the combination of both BCL11A and MBNL1 at 50nM each.
|
| Growth protocol |
MDA-MB-231 cells were cultured in RPMI-1640 supplmented with 10% fetal bovine serum and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold for rRNA removal was used. Illumina TruSeq libraries were tagged with unique adapter-indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qPCR (KAPA Biosystems Illumina Library Quantification Kit) and pooled at equimolar ratios
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA isolated 48h post transfection
146_Double_KD_sensitive_exons
|
| Data processing |
fastq files were aligned to version hg19 using Olego (Wu et al., 2013)
The Quantas pipeline was used to infer transcript structure and quantify alternative splicing and gene expression (Yan et al., 2015)
Genes expressed at RPKM>=2 in one group and had a fold change expression of 2 or greater and adjusted p-value < 0.01 were considered signficantly differentially expressed.
Signficant splicing changes were determined using a FDR<0.05, adjusted p value < 0.05 and average RPKM across biological replicates >=1 in both conditions.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Apr 27, 2020 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Darcie D Seachrist |
| E-mail(s) |
dds8@case.edu
|
| Phone |
2163685924
|
| Organization name |
Case Western Reserve University
|
| Street address |
2109 Adelbert Rd,, Pharmacology Department SOM RT300
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106-4965 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE149435 |
The transcriptional repressor, BCL11A, promotes breast cancer metastasis |
|
| Relations |
| BioSample |
SAMN14738736 |
| SRA |
SRX8181925 |
