|
| Status |
Public on Jan 30, 2018 |
| Title |
Screen1-4round GFP negative |
| Sample type |
SRA |
| |
|
| Source name |
Jurakat Cells
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: transduced sgRNAs pre-selection
tissue: Peripheral Blood
disease: Acute T Cell Leukemia
|
| Treatment protocol |
Cells were transduced with sgRNA lentivirus
|
| Growth protocol |
Cells were grown under standard laboratory conditions and stably transfected with CRISPR components.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers.PCR amplified libraries were generated with independent barcodes to allow multiplexing. 50% PhiX DNA was included in the sequencing run, as low diversity libraries were expected.
qiagen_PCR
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Double Lane Sequencing
|
| Data processing |
The Trimmomatic-0.33 software was used to remove the double-end sequences respectively: the base with the tail mass less than 25 was removed; the 20bp sliding window was set at the same time and 1bp was moved with the average mass of the bases in the window not less than 25; A sequence of less than 80 bp in length.
High-quality double-stranded sequences were linked using flash-1.2.11 software, with the smallest overlap region of 10 bp and the overlap region bases not mismatched ( the mismatch rate was 0)
The forward and backward primersw were removed, leaving a sequence with a length of 5 bp or more.
Genome_build: Gecko V2.0
Supplementary_files_format_and_content: Scores represent different length of the sequence frequency
|
| |
|
| Submission date |
Jan 29, 2018 |
| Last update date |
Jan 30, 2018 |
| Contact name |
SHAN JIN |
| E-mail(s) |
jinshasally@163.com
|
| Phone |
13122601610
|
| Organization name |
FUDAN University
|
| Street address |
Scientific Research Center 2901 Cao Lang Road, Jin Shan District, Shanghai, P.R.China
|
| City |
Shanghai |
| ZIP/Postal code |
201508 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE109808 |
Genome-wide CRISPR screen identifies TSC1 and DEPDC5 that control HIV-1 latency via the mTOR Signaling pathway |
|
| Relations |
| BioSample |
SAMN08432417 |
| SRA |
SRX3626620 |
