|
| Status |
Public on May 28, 2019 |
| Title |
MCF10A_satb1_CHIP_seq |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A expressing satb1 fusion
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: human mammary gland epithelial cell line
genotype/variation: expressing Satb1 full length protein
chip antibody: Anti-GFP antibody (Abcam, Ab290)
|
| Growth protocol |
MCF10A expressing satb1 fusion are maintained in DMEM/F12 with supplements as described. Vl3 cells are maintained in RPMI supplemented with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are fixed, washed, and lysed to purify the nuceli. Then chromatin were fragmented with Covaris, and mixed with antibody and beads to pull down the bound fraction as described in the manuscript
Standard CHIP-seq libraries made using NEBnext Ultra II kit from chipped DNA
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
reads are filtered and trimed with Cutadapt
reads are aligned to genome using Bowtie2
MACS2 is used for peak calling
Differential binding in CHIP-seq was performed with DESeq2 package in r.
Genome_build: hg19 and mm10
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
May 30, 2019 |
| Contact name |
Jan Liphardt |
| E-mail(s) |
jan.liphardt@stanford.edu
|
| Phone |
6504983560
|
| Organization name |
Stanford university
|
| Department |
Bioengineering
|
| Street address |
443 Via Ortega, Shriram Center 020
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE123292 |
Satb1 integrates DNA sequence, shape, motif density and torsional stress to selectively bind a subset of putative targets in nucleosome-dense regions of the genome |
|
| Relations |
| BioSample |
SAMN10517919 |
| SRA |
SRX5089783 |
