|
| Status |
Public on Jun 13, 2017 |
| Title |
EPH4_AU1_CHIPSEQ_CMYC |
| Sample type |
SRA |
| |
|
| Source name |
Eph4 Cell Line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Established Cell Line
cell line: Eph4
strain: Balb/C
gender: Female
|
| Treatment protocol |
Eph4 cell line was treated for 24 hours with AU-1 (5uM) or DMSO
|
| Growth protocol |
Eph4 Cells were grown in DMEM with 5% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin fraction obtained from Eph4 cells or FACS-sorted mammary epithelial cells were incubated with antibodies that recognize mouse histone H3K27ac or mouse c-Myc protein. 1/10 of chromatin fraction was saved as Input. Chromatin-antibody were isolated with magnetic beads. DNA purified with ChIP DNA kit (Zymo) according the manufacturer's instruction
ChIP library samples were amplified and barcoded using Clontech DNA Smart Chipseq kit and Clontech Indexing set in accordance with the manufacturer’s instructions, then pooled for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Chromatin IP purified DNA
|
| Data processing |
Reads were mapped to the indexed mm9 genome using bowtie short-read aligner tool with an allowable mismatch limit set to 2 and the --best and --strata options used to report best alignments and suppress suboptimal alignments.
MACS peak-calling program was used to identify enriched genomic regions in this data by comparing the pulldown ChIP data to the control (Input) data, using a tag size of 25 bp and a p-value cutoff of 1.00e-3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wesley D. Frey |
| E-mail(s) |
[email protected]
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
One Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE98002 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells [ChIP-Seq] |
| GSE98004 |
Bptf maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells |
|
| Relations |
| BioSample |
SAMN06768570 |
| SRA |
SRX2748804 |
