|
| Status |
Public on Dec 16, 2020 |
| Title |
sgMYCenhancer_2_-_22RV1 |
| Sample type |
SRA |
| |
|
| Source name |
sgMYCenhancer_22RV1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: 22Rv1
source tissue: Prostate
genotype/variation: sgRNAs against the MYC enhancer
|
| Treatment protocol |
22Rv1 and V16A dCas9-KRAB stable cells were transduced individually with lentiviral particles containing two sgRNAs against the MYC enhancer, MYC promoter or a non-target region (Luciferase and LacZ).
|
| Growth protocol |
24hrs post-transduction, cells were selected with completed medium containing puromycin for 72hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (74106, QIAGEN)
Following on-column DNase digestion RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sgMYCenhancer_2_-_22RV1_CRISPRi_S4_L001
|
| Data processing |
The raw sequencing data were mapped to human genome assembly Hg19 using TopHat2 version 2.1.0 (Kim et al., 2013) in its default setting.
The reads per gene were counted using HTSeq version 0.7.2 (Anders et al., 2015) against refGene gene annotation
The differential expression analyses were performed using DESeq2 package in R
Genome_build: Hg19
Supplementary_files_format_and_content: Raw count matrix of refGene genes in all samples
|
| |
|
| Submission date |
Jan 01, 2020 |
| Last update date |
Dec 16, 2020 |
| Contact name |
Musaddeque Ahmed |
| E-mail(s) |
[email protected]
|
| Organization name |
University health Network
|
| Lab |
He Lab
|
| Street address |
101 College St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE142809 |
CRISPRi screen of prostate cancer associated risk cis-regulatory elements [RNA-seq] |
| GSE142811 |
CRISPRi screen of prostate cancer associated risk cis-regulatory elements |
|
| Relations |
| BioSample |
SAMN13705318 |
| SRA |
SRX7484907 |
