|
| Status |
Public on Sep 27, 2023 |
| Title |
iSLK-RGB-pCDH-RFP_rep3-input |
| Sample type |
SRA |
| |
|
| Source name |
iSLK-RGB-pCDH-RFP_input
|
| Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
| Characteristics |
cell type: iSLK-RGB
genotype/variation: pCDH-RFP-flag
treatment: treated with Doxycycline for 72 h
rip-antibody: DDDDK-tag (MBL,M185-3L)
|
| Treatment protocol |
Doxycycline treatment for 72 h.
|
| Growth protocol |
Four iSLK cells were routinely cultured in 10% FBS DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standared RNA extraction protocol
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina®
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then clean reads were aligned to the GRCh38 and NC_009333.1 genome assembly using STAR version 2.5.3a with default parameters
Data were filtered using the following specifications:abs(log2FC>1),pvalue<0.05.We selected proteins up-regulated in IP relative to input as genes that NAT10 may combine with.
peaks were called using exomePeak version 3.8 and peaks were annotated using bedtools Version 2.25.0.
Genome_build: Homo_sapiens.GRCh38
Genome_build: NC_009333.1
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Liuxue Sheng |
| E-mail(s) |
shengliuxue@gmail.com
|
| Organization name |
Nanjing Medical University
|
| Street address |
Tian Yuan East Road
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
211166 |
| Country |
China |
| |
|
| Platform ID |
GPL30065 |
| Series (1) |
| GSE173889 |
RIP-seq of NAT10 interacted cellular and KSHV transcripts in iSLK-KSHV cells |
|
| Relations |
| BioSample |
SAMN19021831 |
| SRA |
SRX10779306 |
