|
| Status |
Public on Jan 01, 2024 |
| Title |
HEK293 cells, ZNF687 WT replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human embryonic kidney
cell line: HEK293
cell type: Human embryonic kidney
genotype: Overexpressing ZNF687 WT
treatment: transient transfection
|
| Treatment protocol |
Six-well plates were seeded with 3e5 HEK293 cells overnight. The cells were transfected with ZNF687 WT, frameshift, missense variant containing plasmids and pMIG empty using Fugene6 (Promega) according to the manufacturer’s protocol. Cells were cultured and harvested for protein lysate extraction following the observation of GFP fluorescence 72h after transfection
|
| Growth protocol |
HEK293 cells were obtained from American Type Culture Collection (Manassas, VA) and cultured in DMEM medium supplemented with 10% FBS, (Atlanta Biologicals), penicillin/streptomycin (Invitrogen), and fungizone at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using the QIAGEN RNeasy Mini Kit.
Total RNA integrity was evaluated using the Bioanalyzer (Agilent). RNA-seq libraries were prepared from total RNA using the Illumina Stranded mRNA kit (Illumina). Libraries were then profiled on a TapeStation D1000 tape (Agilent) and quantified using an NGS Library Quantification Kit (Roche/Kapa) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were generated from the resulting base call files using bcl2fastq (Illumina).
The paired-end reads were aligned to hg38 (NCBI build 39) and aligned reads were analyzed using the Rsubread Package.
Differential expression analysis was performed using the deSeq2 package by FPKM (fragments of kilo- base per exon per million fragments mapped) on the human RefSeq transcript database.
iDEP platform was used for K-means clustering and generation of heat-maps.
Assembly: hg38 (NCBI build 39)
Supplementary files format and content: csv file includes cpm for each sample
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Andrew Adey |
| E-mail(s) |
adey@ohsu.edu
|
| Organization name |
Oregon Health & Science University
|
| Department |
MMG
|
| Lab |
Adey Lab
|
| Street address |
3181 S.W. Sam Jackson Park Rd, RHH, L103
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE240600 |
Identification and characterization of pathogenic ZNF687 variant in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN36940747 |
| SRA |
SRX21333372 |
