|
| Status |
Public on Apr 24, 2024 |
| Title |
168_WT_H3K4me1_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer
|
| Organism |
Mus musculus |
| Characteristics |
tissue: breast cancer
cell line: 168FARN
cell type: cell line
genotype: WT
chip antibody: H3K4me1 (abcam, ab8895)
|
| Growth protocol |
DMEM, 10% FBS, 1x Pen/Strep, 1x Glutamin, 1x Non-essential amino acids, 5% CO2, 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyd for 10 minutes. Then, cells were collected, nuclei were isolated and lysed and chromatin was sheared with an ultrasonicator (Covaris E220)
ChIPseq libraries were prepared using xGen DNA library prep reagents (IDT) on a Biomek i7 (Beckman Coulter) liquid handling platform from approximately 1ng of DNA with 14 cycles of PCR amplification according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq data was processed using CoBRA pipeline (https://bitbucket.org/cfce/cobra/src/master/).
Steps include alignment using BWA mem, filtering for uniquely mapped read and sorting bam files.
Peaks were called using macs2 with default settings (-broad mode for H3K4me1 and H3K27me3)
Output bedgraph files were then used to generate bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Jul 14, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE237390 |
Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 [ChIP-seq] |
| GSE237392 |
Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3 |
|
| Relations |
| BioSample |
SAMN36451706 |
| SRA |
SRX21024131 |
