|
| Status |
Public on Aug 04, 2022 |
| Title |
IgG_KCl_0min_exp2 |
| Sample type |
SRA |
| |
|
| Source name |
E15.5 C57BL/6 embryonic mouse cortices
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E15.5
cell type: primary corticol neurons
antibody used for cut&run: Millipore PP64B (Lot#3229748)
|
| Treatment protocol |
For CUT&RUN experiments, mouse cortical neurons were plated at an approximate density of 2 × 10^6 on 35-mm dishes. Neurons were plated in 2 mL neuronal medium. One ml of the medium was replaced with 1 ml fresh warm medium on Day3 and Day6. Prior to KCl depolarization, neurons were silenced with 1 μM tetrodotoxin on Day6 (TTX; Fisher). Neurons were subsequently stimulated on Day7 by adding warmed KCl depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2 and 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)) directly to the neuronal culture to a final concentration of 31% in the neuronal culture medium within the culture plate or well for the indicated time.
|
| Growth protocol |
Neurons were grown in neuronal medium consisting of Neurobasal medium containing B27 supplement (2%; Thermo Fisher), penicillin-streptomycin (50 g/mL) and Glutamax (1x; Thermo Fisher). Neurons were subsequently plated and placed in a cell culture incubator that maintained a temperature of 37 °C and a CO2 concentration of 5%. Ten minutes after plating neurons, the medium was completely aspirated from cells and replaced with fresh warm neuronal medium. Neurons were grown in vitro until Day7.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using CUTANA™ CUT&RUN Protocol [www.epicypher.com] which is an optimized version of that previously described. For each sample, 5x105 cells were immobilized onto Concanavalin-A beads (EpiCypher #21-1401) and incubated overnight (4ºC with gentle rocking) with 0.5 µg of antibody.
CUT&RUN enriched DNA was purified, and 10 ng used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, bed
|
| |
|
| Submission date |
Oct 11, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Yuliang Tan |
| E-mail(s) |
yut020@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
School of Medicine
|
| Street address |
Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037-0648 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE135808 |
Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers |
| GSE185649 |
Topo1cc siganls are presented at the KCl induced acutely activated enhancers [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN22213297 |
| SRA |
SRX12569203 |
