|
| Status |
Public on May 15, 2022 |
| Title |
128651.tumor.INPUT |
| Sample type |
SRA |
| |
|
| Source name |
128651.tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Balb/c
genotype/variation: PyMT;Rag1KO
treatment: injected with CD4+ T cells
tissue: Breast tumor
|
| Treatment protocol |
10-30 mg of tumor was cut on dry ice and minced on ice with a razor blade. Samples were then resuspended in 1ml cold PBS and fixed in 1% formaldehyde for 15 minutes at room temperature. Glycine was added for 5 minutes at room temperature. Samples were washed and resuspended in cold PBS and homogenized with a syringe.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin extracted from formalin-fixed cells was fragmented with a Branson 250 sonifier, solubilized and immunoprecipitated with H3K27ac antibody (Active Motif, Inc., Carlsbad, CA) overnight at 4°C. Antibody-chromatin complexes were pulled down with protein G-Dynabeads (Life Technologies), washed, and eluted.
Immunoprecipitated DNA was extracted with AMP Pure beads (Beckman Coulter) after crosslink reversal, RNase A, and proteinase K treatment. ChIP DNA was quantified with Qubit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment: BWA
Density map: IGV Density tool
ChIP seq coverage analyis: IGV
Peaks identification: MACS2peak caller
Pathway Erichment analysis: GSEA
Genome_build: mm10
Supplementary_files_format_and_content: list of EMT genes upregulated in tumor vs. cyst
Supplementary_files_format_and_content: all enhancers up or downregulated in tumor vs cyst
|
| |
|
| Submission date |
Aug 12, 2020 |
| Last update date |
May 15, 2022 |
| Contact name |
Margherita Boieri |
| E-mail(s) |
mboieri@mgh.harvard.edu, margherita.boieri@gmail.com
|
| Organization name |
Masachusetts General Hospital
|
| Street address |
55 Fruit Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE156117 |
Analysis of the effect of TSLP stimulated CD4+T cells on epigenetic markers in PyMT primary tumors |
|
| Relations |
| BioSample |
SAMN15803462 |
| SRA |
SRX8934315 |
