|
| Status |
Public on Jul 12, 2023 |
| Title |
NeuroD1_BMP2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreatic islets
strain: C57BL/6NRj
Sex: male
age: 12 weeks
treatment: Ctrl 10d
chip antibody: NeuroD1 antibody (Cat#4373, Cell Signaling).
|
| 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 |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext® UltraTM DNA library Kit for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data was mapped to the UCSC mouse genome NCBI37/mm10
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.
Assembly: mm10
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 |
GPL19057 |
| Series (2) |
| GSE216232 |
Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding [NeuroD1 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 |
SAMN31391623 |
| SRA |
SRX17970164 |
