|
| Status |
Public on Jul 12, 2023 |
| Title |
H3K4me3_ChIPseq_BMP2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreatic islets
strain: C57BL/6NRj
Sex: male
age: 12 weeks
treatment: BMP2 10d
chip antibody: H3K4me3 (Cat#04-745 Milipore)
|
| Treatment protocol |
Islets were cultured in the absence or presence of 50ng/ml BMP2
|
| Growth protocol |
Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and BMP2 were
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After sonication chromatin immunoprecipitation was performed using ChIP-IT High Sensitivit (Active Motif). Histone-DNA complexes were isolated with the corresponding antibody.
Libraries were prepared using KAPA DNA Library Preparation Kits for Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Data was mapped to the UCSC mouse genome NCBI37/mm9 (July 2007).
Bowtie 2 was used to map data to the genome with the following settings: the seed length was set as 33 with a maximum number of 2 mismatches allowed in the seed region, and reads aligning to multiple locations were discarded. Duplicate reads were removed using samtools
In homer, function "makeUCSCfile" was used to generate bigWig file
Assembly: mm9
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Jul 12, 2023 |
| Contact name |
Matthew Wortham |
| E-mail(s) |
mwortham@ucsd.edu
|
| Phone |
8582460588
|
| Organization name |
University of California, San Diego
|
| Lab |
Maike Sander
|
| Street address |
2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE216230 |
Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding [Histone ChIP-seq] |
| GSE216233 |
Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding |
|
| Relations |
| BioSample |
SAMN31391503 |
| SRA |
SRX17970155 |
