|
| Status |
Public on Feb 06, 2022 |
| Title |
Hi-C_WT_E14_MN_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Motor neurons
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESC-derived cervical motor neurons
genotype: wild type
developmental stage: E14
|
| Growth protocol |
mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)). For motor neuron (MN) differentiation, the previously described protocol in Narendra et. al. (2015) was applied. Briefly, ESCs were differentiated into embryoid bodies in 2 days (Day 0) in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol). Medium was exchanged on Day 2 of differentiation, and further patterning of embryoid bodies was induced by supplementing the ANDFK media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested, and 1 M cells were fixed in 2% formaldehyde (Fisher Chemical) according to the ARIMA-HiC protocol.
Libraries were prepared according to ARIMA-HiC protocol by NYU Genome Technology Center.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Hoxa5-P2A-mCherry/Hoxa7-P2A-eGFP reporter cells
|
| Data processing |
Overall processing by HiC-bench pipeline
Align to mm10 reference genome internally using bowtie2 2.3.5.1
Create contact matrix in hic format using Juicer 1.5
Genome_build: mm10
Supplementary_files_format_and_content: Contact matrix in hic format
|
| |
|
| Submission date |
Aug 30, 2020 |
| Last update date |
Feb 06, 2022 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
Danny.Reinberg@nyulangone.org
|
| Phone |
212-263-9036
|
| Organization name |
New York University School of Medicine
|
| Department |
Biochemistry
|
| Lab |
Reinberg Lab
|
| Street address |
522 First Avenue, 2nd floor, Room 211
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157136 |
CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters [Hi-C] |
| GSE157139 |
CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters |
|
| Relations |
| BioSample |
SAMN15942049 |
| SRA |
SRX9036156 |
