|
| Status |
Public on Feb 08, 2019 |
| Title |
Control_RNA-seq_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: Human mammary epithelial cell line
|
| Treatment protocol |
shRNA plasmids for UBR7 with pLKO.1-puro backbone (Sigma Aldrich) were screened for efficient knock-down.Two out seven shRNAs were selected for subsequent experiments. Four micrograms of shRNA and packaging vectors were transfected and cells were selected using puromycin (10 μg / ml) (Sigma) for 3 days.
|
| Growth protocol |
MCF10A cells were maintained in DMEM / Ham’s F12 supplemented with 5% horse serum (Gibco), EGF, insulin, hydrocortisone, cholera toxin (Sigma) and 1% antibiotic-antimycotic.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini Kit and quantified using a Bioanalyzer 1000.
Libraries for Illumina sequencing were generated using the TruSeq RNA Library Prep Kit according to manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq reads for all RNA-seq experiments were aligned to the hg19 reference genome using TopHat version 2.0.14 with a Bowtie2 version 2.2.3 index based on UCSC annotations using the following criteria: -G -g 1 -r 150 --mate-std-dev 50 --library-type fr-unstranded.
Raw counts were obtained by assigning reads at the gene level across the UCSC hg19 reference genome using featureCounts in the Rsubread package. DESeq2 was employed for normalization and identification of DEGs between UBR7-shRNA and Control samples.
deepTools version 2.4.0 was used to generate bigWig files by scaling the bam files to RPKM. Scaled bigWig files were then converted to bedGraph files using the bigWigToBedGraph tool.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files containing normalized counts for all genes and DEGs identified using DESeq2. bigWig files of Forward and Reverse strand for Control and UBR7-shRNA samples
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kunal Rai |
| E-mail(s) |
[email protected]
|
| Phone |
713-792-6809
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Genomic Medicine
|
| Lab |
Rai Lab
|
| Street address |
1801 East Rd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE93758 |
UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [RNA-Seq] |
| GSE93759 |
UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer |
|
| Relations |
| BioSample |
SAMN06237760 |
| SRA |
SRX2499870 |
