|
| Status |
Public on May 24, 2024 |
| Title |
SS-HA |
| Sample type |
SRA |
| |
|
| Source name |
neonatal skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: skin fibroblasts
cell line: BJ
genotype: wild type
chip antibody: CST no 3724S
treatment: SS18-SSX1-HA overexpression
|
| Treatment protocol |
overexpression by lentiviral infection.
|
| Growth protocol |
BJ fibroblasts were cultured by 10% FBS medium (DMEM, 10%FBS, NEAA, GlutaMAX)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP DNA library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme) according to manufacturer’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
|
| |
|
| Submission date |
Aug 09, 2023 |
| Last update date |
May 24, 2024 |
| Contact name |
kuang junqi |
| E-mail(s) |
kuangjunqi@westlake.edu.cn
|
| Organization name |
westlake University
|
| Street address |
No.18 Shilongshan Road
|
| City |
hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE211456 |
Enhanced Phase Separation Mediated Oncogenicity |
| GSE240464 |
Enhanced Phase Separation Mediated Oncogenicity [ChIP-Seq, 2] |
|
| Relations |
| BioSample |
SAMN36912175 |
| SRA |
SRX21313898 |
