|
| Status |
Public on Oct 07, 2024 |
| Title |
NTKO-5D-2 |
| Sample type |
SRA |
| |
|
| Source name |
KMS11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMS11
genotype: NSD2-high
timepoint: Day 5 Post Transduction
biorep: 2
|
| Treatment protocol |
Cells weere transduced with the Brunello Library and selected in puromycing for 5 days
|
| Growth protocol |
Advanced RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% pen/strep in humidified incubator with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Blood and Cell Culture DNA Maxi Kit (Qiagen) from cell samples collected at Day 5 and Day 23 (NTKO) or Day 25 (TKO)
PCR using primers with Illumina adapters and multiplexing barcodes
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: Amplicon seq
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the Brunello library using Bowtie2.
Quantifcation of sgRNA hits was performed with custom scripts.
Assembly: GRCh38
Supplementary files format and content: Counts of hits to each guide RNA in each sample
|
| |
|
| Submission date |
Oct 12, 2023 |
| Last update date |
Oct 07, 2024 |
| Contact name |
Alberto Riva |
| E-mail(s) |
ariva@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
ICBR
|
| Lab |
Bioinformatics Core
|
| Street address |
2033 Mowry Rd
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32605 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE245148 |
NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2 [AS_CR] |
| GSE245150 |
NSD2 Overexpression in Myeloma Enhances Dependency on Mitochondrial High Energy Phosphate Transport Facilitated by Adenylate Kinase 2. |
|
| Relations |
| BioSample |
SAMN37791145 |
| SRA |
SRX22070575 |
