Accession | CRX017983 |
Organism | Mus musculus |
Title | HoxB a viewpoint E7.5 4Cseq |
BioProject | PRJCA000241 |
BioSample | SAMC013112 |
Platform | Illumina HiSeq X Ten |
Library |
Library name |
Construction protocol |
Strategy |
Source |
Selection |
Layout |
|
Low-amount 4C library generation was performed with some modification according to the procedures described in detail elsewhere(Splinter et al., 2012) . We used about 50,000 cells for 4C-seq. The primary digestion enzyme is HindIII. All the DNA was digested with second restriction endonuclease DpnII in 25 ul total reaction volume (2.5 ul 10x DpnII restriction buffer; 2.5U DpnII ) at 37°C for 5h, inactive the enzyme at 65°C for 30min. Then perform second ligation in 150 ul total reaction volume (15 ul 10x ligation buffer; 0.5 μl of 400 U/ μl T4 DNA Ligase). Then incubate at 16 °C overnight. Add 6μl 20 mg/ml proteinase K and incubate at 65 °C for 5 hours and 75 °C for 30 minutes to inactivate the protease K. Purify the DNA with AgencourtAMPure XP beads. The 4C template is now ready for PCR.<br/>All reads were validated and reads that did not match the primary restriction enzyme sequence or the primer sequence were discarded. After clipping the primer sequence from each read, all remaining reads were mapped to a corresponding reference (mm10) using bowtie2 (Langmead and Salzberg, 2012). After mapping, we remove the undigested and self-ligated fragment and generate visualization track. |
OTHER |
GENOMIC |
unspecified |
PAIRED
|
|
Processing |
Planned read length (bp) for mate 1: 150
Planned read length (bp) for mate 2: 150
|
Release date | 2017-07-13 |
Run |
Run accession |
Run data file information |
File name | File size (MB) |
CRR019680 |
CRD039132
CRD039133
|
1,867.34
2,633.67
|
|
Submitter | Xuepeng Chen (chenxp@big.ac.cn) |
Organization | Beijing Institute of Genomics, Chinese Academy of Sciences |
Date submitted | 2017-05-29 |