|
| Status |
Public on Mar 17, 2023 |
| Title |
26Tet2OE |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampal neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Neurons
genotype: Tet2 OE
|
| Treatment protocol |
Mice were maintained for 60 days after injection and then euthanized for neuronal isolation
|
| Growth protocol |
3 month old mice were stereotactically injected with lentivirus with either GFP or Tet2 expression cassettes under the control of the synapsin promoter
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from hippocampi followed by FACS isolation of neuronal nuclei. DNA was extracted from neuronal nuclei.
Equal amounts of DNA were sonicated to 300-500bp followed by end cleanup and NEB-Next adapter ligation. DNA was treated with USER enzyme followed by DNA cleanup. DNA was denatured, and subjected to immunoprecipitation with a 5-hydroxymethylcytosine antibody (ActiveMotif) followed by extensive washing. Captured DNA was amplified by PCR and purified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
library strategy: hMeDIP-Seq
FASTQ reads were aligned to the mouse genome (mm10) using Bowtie2 with default parameters.
MACS2 callpeak was used to find peaks between the conditions using the BAM output.
Bedgraph files were outputted from MACS2 for each condition.
Assembly: mm10
Supplementary files format and content: Bedgraph files of combined samples from each condition
|
| |
|
| Submission date |
Mar 17, 2022 |
| Last update date |
Mar 17, 2023 |
| Contact name |
Jeremy Michael Shea |
| Organization name |
University of California, San Francisco
|
| Department |
Anatomy
|
| Lab |
Villeda
|
| Street address |
513 Parnassus Avenue
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE198910 |
hMeDIP-Seq of Tet2 overexpressing hippocampal neurons |
|
| Relations |
| BioSample |
SAMN26755089 |
| SRA |
SRX14495592 |
