|
Status |
Public on Feb 06, 2022 |
Title |
Hi-C_Maz_KO_ESC_rep1 |
Sample type |
SRA |
|
|
Source name |
Embryonic stem cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic stem cells genotype: Maz -/- 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 |
SAMN15942052 |
SRA |
SRX9036153 |