| Library |
| Library name |
Construction protocol |
Strategy |
Source |
Selection |
Layout |
|
The 1×10^6 cells were cross-linked with a final concentration of 4% formaldehyde for 30min at room temperature and followed by quenching with glycine in a final concentration of 0.25 mol/L. Mixtures were next centrifuged at 1,500×g for 10min at room temperature, and separated supernatant were added lysis buffer and incubate 15 min on ice. The mixture was then centrifuged at 5,000×g for 10 min in room temperature. The sediment was washed with 100μL 1×NEBuffer 2. The mixture was added with SDS in a final concentration of 0.1% and incubate 10min at 65°C, then added with TritonX-100 in a final concentration of 1% and incubate 15min at 37°C, thus nuclei of cells were permeabilized. DNA was digested with 200 units of DpnII (a 4-cutter restriction enzyme) for one hour at 37°C. The restriction fragment overhangs were filled and labeled by biotinylated nucleotides and then ligated in a small volume. After crosslink reversal, DNA were purified and sonicated to fragments about 300-500 bp by applying Covaris S220 sonicator, at which point ligated fragments were pulled down with Dynabeads™ M-280 Streptavidin (Invitrogen, Cat.N: 11206D) and also were end repaired and A-tailed. Adaptors were next ligated and DNA fragments were PCR amplified using KAPA Hyper Prep Kit (Roche, Cat.N: KK8504) for 8-10 cycles. These fragments were then performed double-size selected using AMPure XP Beads (Beckman, Cat.N: A63882) in order to isolate fragments between 300 and 800bp, which were prepped for sequencing at BGISEQ-500 platform to provided 100 bp paired-end reads. Consequently, we generated a total of ~10.91-billion valid contacts of 16 Hi-C libraries (~681.95 M contacts per library) for pEpiSCs, and a total of ~14.34-billion valid contacts of 16 Hi-C libraries (~895.96 M contacts per library) for pEFs. |
Hi-C |
GENOMIC |
RANDOM |
PAIRED
|
|
| Run |
| Run accession |
Run data file information |
| File name | File size (MB) |
|---|
| CRR271389 |
CRR271389_f1.fastq.gz
CRR271389_r2.fastq.gz
|
101,266.81
103,308.91
|
| CRR271390 |
CRR271390_f1.fastq.gz
CRR271390_r2.fastq.gz
|
95,263.15
101,500.97
|
| CRR271391 |
CRR271391_f1.fastq.gz
CRR271391_r2.fastq.gz
|
100,978.89
104,319.3
|
| CRR271392 |
CRR271392_f1.fastq.gz
CRR271392_r2.fastq.gz
|
98,101.56
101,277.35
|
| CRR271393 |
CRR271393_f1.fastq.gz
CRR271393_r2.fastq.gz
|
108,294.79
112,912.94
|
| CRR271394 |
CRR271394_f1.fastq.gz
CRR271394_r2.fastq.gz
|
104,561.78
110,982.05
|
| CRR271395 |
CRR271395_f1.fastq.gz
CRR271395_r2.fastq.gz
|
88,393.27
95,027.08
|
| CRR271396 |
CRR271396_f1.fastq.gz
CRR271396_r2.fastq.gz
|
104,200.41
109,448.79
|
| CRR271397 |
CRR271397_f1.fastq.gz
CRR271397_r2.fastq.gz
|
89,453.01
94,006.49
|
| CRR271398 |
CRR271398_f1.fastq.gz
CRR271398_r2.fastq.gz
|
110,408.02
117,543.41
|
| CRR271399 |
CRR271399_f1.fastq.gz
CRR271399_r2.fastq.gz
|
99,217.44
107,911.45
|
| CRR271400 |
CRR271400_f1.fastq.gz
CRR271400_r2.fastq.gz
|
94,816.21
100,902.33
|
| CRR271401 |
CRR271401_f1.fastq.gz
CRR271401_r2.fastq.gz
|
99,110.77
104,727.85
|
| CRR271402 |
CRR271402_f1.fastq.gz
CRR271402_r2.fastq.gz
|
109,920.16
114,772.55
|
| CRR271403 |
CRR271403_f1.fastq.gz
CRR271403_r2.fastq.gz
|
99,951.98
100,654.08
|
| CRR271404 |
CRR271404_f1.fastq.gz
CRR271404_r2.fastq.gz
|
117,673.68
119,603.53
|
|
