|
Status |
Public on Jul 12, 2023 |
Title |
NeuroD1_Ctrl_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 |
SAMN31391625 |
SRA |
SRX17970162 |