|
| Status |
Public on Jul 01, 2021 |
| Title |
78780-Brg1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: TATcre;SS18-SSX+ and Snf5-/-
chip antibody: Brg1
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei was isolated from snap frozen samples. Lysates were clarified from sonicated nuclei and BAF-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 |
| |
|
| Description |
Combined_ChIPBrg1.log2FE.bw
|
| Data processing |
paired-end 50bp sequencing on an Illumina NovaSeq platform
ChIP-seq reads were aligned to the mm10 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: mm10
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a log2 fold enrichment
|
| |
|
| Submission date |
Jul 06, 2020 |
| Last update date |
Jul 01, 2021 |
| 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 |
GPL24247 |
| Series (1) |
| GSE153857 |
Tumor transcriptomes profiling of SS18-SSX, Smarcb1-/- and combination of SS18-SSX and Smarcb1-/- driven tumor |
|
| Relations |
| BioSample |
SAMN15457944 |
| SRA |
SRX8673286 |
