|
| Status |
Public on Nov 12, 2020 |
| Title |
TDMD screen_CYRANO KO-2_sorted |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: miR-7 reporter, CYRANO-/-
sgrna received: brunello library
cell line: K562
|
| Growth protocol |
K562 cells were grown in RPMI supplemented with 10% FBS and Antibiotic-Antimycotic solution
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets using either a gDNA isolation method that has been previously described Golden et al., Nature, 2017 for the sorted cells or the MasterPureTM Complete DNA Purification Kit (Lucigen) for the unsorted cells.
PCR amplicon libraries were generated as described in the manuscript.
CRISPR/Cas9-mediated loss of function screening.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sgRNA sequence amplified out of genomic DNA
|
| Data processing |
Reads were mapped to Brunello library sgRNA reference files.
Reads from run1 and run2 were combined, and normalized read counts were calculated as described in Shalem et al., Science, 2014.
MAGeCK (Li et al., Genome Biology, 2014) was used to assign significance to each gene targeted by the sgRNAs in the Brunello library.
Genome_build: Brunello library sgRNA reference files obtained from Addgene
Supplementary_files_format_and_content: A table of normalized read counts for each sgRNA in each sample (run1 and run2 combined) is provided.
|
| |
|
| Submission date |
May 31, 2020 |
| Last update date |
Nov 12, 2020 |
| Contact name |
Joshua Mendell |
| E-mail(s) |
joshua.mendell@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Molecular Biology
|
| Street address |
6000 Harry Hines Blvd., NA6.200A
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE151516 |
A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming [TDMD] |
| GSE151517 |
A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming |
|
| Relations |
| BioSample |
SAMN15065976 |
| SRA |
SRX8432481 |
