|
| Status |
Public on Jun 01, 2024 |
| Title |
HEK-293R, dCas9-VP64-FUS_gScramble_RNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK-293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK-293T
cell type: Human embryonic kidney
genotype: TetO-GFP reporter
treatment: Transfected by dCas9-VP64-FUS fusion protein and scrambled gRNA
|
| Growth protocol |
HEK-293T cells were cultured in DMEM medium with addition of 10% FBS and 1% PS at 37°C and 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol™ reagent (Invitrogen, #15596018).
Sequencing libraries were prepared using the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (Yeasen, #12309), with 2 μg of total RNA input.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For RNA-seq data analysis, clean reads were aligned to human reference genome (hg38) supplemented with GFP sequence by HISAT2. Aligned reads were inputted into featureCounts for counting the read number of coding genes and GFP. The genome annotation gtf file was obtained from Ensemble v105 and only coding genes and addition GFP annotation were used for count. The differential expression genes were identified using DEseq2.
Assembly: hg38 supplemented with GFP sequence
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Nov 23, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Rui Chen |
| E-mail(s) |
12131298@mail.sustech.edu.cn
|
| Phone |
13149905923
|
| Organization name |
Southern University of Science and Technology
|
| Lab |
Chenwei lab
|
| Street address |
Southern University of Science and Technology
|
| City |
ShenZhen |
| State/province |
GuangDong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248523 |
Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [RNA-seq] |
| GSE249351 |
Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping. |
|
| Relations |
| BioSample |
SAMN38391729 |
| SRA |
SRX22629174 |
