|
| Status |
Public on Apr 06, 2020 |
| Title |
Ramos dCas9-sid 2 |
| Sample type |
SRA |
| |
|
| Source name |
Ramos Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell.line: Ramos
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 |
rsid_sid_2
|
| 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 |
SAMN13502265 |
| SRA |
SRX7283392 |
