|
| Status |
Public on Sep 11, 2023 |
| Title |
Mesenchymal chondrosarcoma, Runx3 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal chondrosarcoma
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
cell type: HEY1-NCOA2-expressing murine mesenchymal chondrosarcoma cells
chip antibody: RUNX3 (Cell Signaling, 9647, lot 2)
|
| Treatment protocol |
HEY1-NCOA2 was introduced by retrovirus-mediated gene transfer
|
| Growth protocol |
Sarcoma cells were maintained in IMDM supplemented with 10% FBS
|
| 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 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Assembly: mm9
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 |
Mar 14, 2022 |
| Last update date |
Sep 11, 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 (2) |
| GSE163585 |
HEY1-NCOA2 interacts with RUNX2 to induce mesenchymal chondrosarcoma [ChIP-seq] |
| GSE163588 |
HEY1-NCOA2 interacts with RUNX2 to induce mesenchymal chondrosarcoma |
|
| Relations |
| BioSample |
SAMN26656998 |
| SRA |
SRX14462224 |
