|
| Status |
Public on Jan 01, 2023 |
| Title |
SFO_ASPL |
| Sample type |
SRA |
| |
|
| Source name |
human ASPS tumor
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: ASPSCR1
tissue: human ASPS tumor
patient id (city where they are from): SFO
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
paired-end 50bp sequencing on an Illumina HiSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using novoalign-4.00.01
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a normalized pileup signal
|
| |
|
| Submission date |
Dec 01, 2020 |
| Last update date |
Jan 01, 2023 |
| Contact name |
Jinxiu Li |
| Organization name |
China Agricutural University
|
| Department |
College of biological sciences
|
| Lab |
State key laboratories of Agrobiotechnology
|
| Street address |
Yuanmingyuan west road 2#
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE162478 |
ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [hASPS_ChIP, ASPL_VCP_Pol2] |
| GSE162609 |
ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP |
|
| Relations |
| BioSample |
SAMN16974676 |
| SRA |
SRX9616652 |
