|
| Status |
Public on Jan 16, 2023 |
| Title |
mASPS_JQ1_Brd4 |
| Sample type |
SRA |
| |
|
| Source name |
Alveolar soft part sarcoma
|
| Organism |
Mus musculus |
| Characteristics |
cell type/genotype: ASPSCR1-TFE3-expressing murine alveolar soft part sarcoma cells
strain/cell line: Balb/c
antibody: Brd4 (Bethyl Laboratories, A301-985A100, lot 7)
treatment: mASPS cells treated with JQ1
|
| Treatment protocol |
Mouse ASPS cells were treated with 100 nM JQ1 for 48 hours. Small interfering RNA-mediated gene silencing of human ASPS cells was performed.
|
| Growth protocol |
Mouse and human ASPS cells were grown in IMDM supplemented with 10% fetal bovine serum (FBS) and RPMI-1640 supplemented with 10% FBS, respectively.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Base calls were performed using Bowtie 2.
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9 (mouse) and hg19 (human)
Supplementary_files_format_and_content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Jan 16, 2023 |
| Contact name |
Takuro Nakamura |
| E-mail(s) |
takuro-ind@umin.net
|
| Phone |
81-3-3570-0462
|
| Organization name |
Japanese Foundation for Cancer Research
|
| Department |
The Cancer Institute
|
| Lab |
Carcinogenesis
|
| Street address |
3-8-31 Ariake, Koto-ku
|
| City |
Tokyo |
| ZIP/Postal code |
135-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE189163 |
ASPSCR1-TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN23296641 |
| SRA |
SRX13171711 |
