|
| Status |
Public on Sep 27, 2023 |
| Title |
iSLK-puro_rep2-IP |
| Sample type |
SRA |
| |
|
| Source name |
iSLK-puro
|
| Organisms |
Homo sapiens; Human gammaherpesvirus 8 |
| Characteristics |
cell type: iSLK-puro
treatment: treated with Doxycycline for 72 h
acrip: EpiTM ac4C immunoprecipitation kit (Epibiotek, cat. no R1815)
|
| 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 |
Standard RNA extraction protocol
The stranded RNA sequencing library was constructed by using EpiTM mini longRNA-seq kit
acRIP-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Puro_peak_ann.xls
|
| 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 HISAT2 version 2.1.0 with the following parameters:--rna-strandness RF
peaks were called using exomePeak version 2.13.2 with the following setting: PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200,and ac peaks were annotated.
Genome_build: GRCh38_Ensembl91_year_2017
Genome_build: NC_009333.1
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table of ac peak annotation
|
| |
|
| Submission date |
May 10, 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) |
| GSE174161 |
ac4C-seq of cellular and KSHV transcripts in iSLK-Puro, iSLK-KSHV (i.e. iSLK-RGB), iSLK-KSHV (WT), iSLK-KSHV (Ξ”NAT10) cells |
|
| Relations |
| BioSample |
SAMN19093042 |
| SRA |
SRX10828262 |
