|
Status |
Public on Apr 06, 2020 |
Title |
P493-6 dCas9-sid 3 |
Sample type |
SRA |
|
|
Source name |
P493-6 Cells
|
Organism |
Homo sapiens |
Characteristics |
cell.line: P493-6 dcas9: dCas9-sid mcp: none
|
Treatment protocol |
Cells were transduced with lentiviral constructs for expression of dCas9 fusion proteins (KRAB, kPOGO, SID) and/or MCP-SID. Both, control cells and dCas9-fusion protein and/or MCP-SID expresing cells were transduced with a pooled CRISPR single-guide RNA library (MYCncLibrary) and subjected to phenotypic selection.
|
Growth protocol |
Cells were grown in RPMI1640 supplemented with 10% FBS and 1x Penicillin-Streptomycin, tetracycline-free FBS was used for P493-6 cells.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was isolated using the DNaesy Blood & Tissue kit (Qiagen). Guide sequences were PCR-amplified from genomic DNA using target specific primers with Illumina compatible adapters.
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
sid_sid_3
|
Data processing |
Library strategy: Amplicon-seq Cassava 1.8 FASTX_TOOLKIT 0.0.13 cat $infastq | fastx_barcode_splitter.pl --bcfile $barcodes --prefix sg_ --bol --suffix .fastq count_spacers.py -f $infastq -o $outcounts -i guide.sequences.csv edgeR 3.28.0 Genome_build: table_s3.xlsx
|
|
|
Submission date |
Dec 04, 2019 |
Last update date |
Apr 06, 2020 |
Contact name |
Jonathan Ross Hart |
E-mail(s) |
jhart@scripps.edu
|
Phone |
8587849725
|
Organization name |
The Scripps Research Institute
|
Department |
Molecular and Experimental Medicine
|
Lab |
Peter K. Vogt
|
Street address |
10550 North Torrey Pines Road, BCC239
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE141491 |
An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation [Amplicon-seq] |
GSE141615 |
An MXD1-derived repressor peptide identifies non-coding mediators of MYC-driven cell proliferation |
|
Relations |
BioSample |
SAMN13502256 |
SRA |
SRX7283398 |