|
| Status |
Public on Feb 26, 2015 |
| Title |
4C.HOXA10.MN.Δ5|6 |
| Sample type |
SRA |
| |
|
| Source name |
Differentiated Motor Neurons (Day 4 post RA/SAG)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Δ5|6
bait name: 4C.HOXA7-3
bait coordinate: chr6:52187161
|
| Growth protocol |
mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated 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) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the 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 |
10 million cells were trypsinized and crosslinked in 2% formaldehyde and 10% FBS in PBS for 10 min at room temperature. The primary restriction enzyme used was DpnII. The secondary enzyme was Csp6I. Template DNA (1ug) was amplified using inverse primers containing barcoded illumina sequencing adapters on either end.
Libraries were constructed by adding barcoded illumine adapters to the 5’ end of each primer. PCR reactions were performed using the Expand Long Template PCR System (Roche), and 100-700bp DNA was gel purified and quantified before sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: 4C-Seq
Fastq was demultiplexed and primer sequence was removed from each read
Reads were mapped to mm9 using 4cseqpipe (http://compgenomics.weizmann.ac.il/tanay/?page_id=99)
Median and 20/80% contact intensity across chr6:52075000-52250000 were calculated in 1kb bins using 4cseqpipe
Genome_build: mm9
Supplementary_files_format_and_content: Median and 20/80% contact intensity across chr6:52075000-52250000 were calculated in 2kb windows centered about 1kb bins. Medians across windows of increasing size from 2-50kb are also presented.
|
| |
|
| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
reinbd01@nyumc.org
|
| Phone |
212-263-9036
|
| Organization name |
NYU School of Medicine / HHMI
|
| Street address |
522 First Avenue, 2nd floor Rm 211
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE60227 |
CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [4C-Seq] |
| GSE60240 |
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation |
|
| Relations |
| BioSample |
SAMN02978988 |
| SRA |
SRX672310 |
