| 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) |
|---|
| CRR271373 |
CRR271373_f1.fastq.gz
CRR271373_r2.fastq.gz
|
50,275.04
52,831.05
|
| CRR271374 |
CRR271374_f1.fastq.gz
CRR271374_r2.fastq.gz
|
118,154.78
124,911.6
|
| CRR271375 |
CRR271375_f1.fastq.gz
CRR271375_r2.fastq.gz
|
90,167.6
95,289.81
|
| CRR271376 |
CRR271376_f1.fastq.gz
CRR271376_r2.fastq.gz
|
74,184.96
78,017.94
|
| CRR271377 |
CRR271377_f1.fastq.gz
CRR271377_r2.fastq.gz
|
76,122.94
80,257.3
|
| CRR271378 |
CRR271378_f1.fastq.gz
CRR271378_r2.fastq.gz
|
90,290.27
94,751.45
|
| CRR271379 |
CRR271379_f1.fastq.gz
CRR271379_r2.fastq.gz
|
90,316.19
96,063.6
|
| CRR271380 |
CRR271380_f1.fastq.gz
CRR271380_r2.fastq.gz
|
75,052.33
78,147.97
|
| CRR271381 |
CRR271381_f1.fastq.gz
CRR271381_r2.fastq.gz
|
83,433.79
89,297.59
|
| CRR271382 |
CRR271382_f1.fastq.gz
CRR271382_r2.fastq.gz
|
87,612.11
94,404.66
|
| CRR271383 |
CRR271383_f1.fastq.gz
CRR271383_r2.fastq.gz
|
80,962.39
86,644.91
|
| CRR271384 |
CRR271384_f1.fastq.gz
CRR271384_r2.fastq.gz
|
89,834.7
96,408.65
|
| CRR271385 |
CRR271385_f1.fastq.gz
CRR271385_r2.fastq.gz
|
70,590.51
74,792
|
| CRR271386 |
CRR271386_f1.fastq.gz
CRR271386_r2.fastq.gz
|
101,483.64
106,748.16
|
| CRR271387 |
CRR271387_f1.fastq.gz
CRR271387_r2.fastq.gz
|
92,465.47
97,248.7
|
| CRR271388 |
CRR271388_f1.fastq.gz
CRR271388_r2.fastq.gz
|
78,143.27
82,630.34
|
|
