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Experiment information

Accession

CRX924290

Organism

Triticum aestivum

Title

CM104_Hi-C

BioProject

PRJCA022052

BioSample

SAMC3266712

Platform

MGISEQ-2000

Library

Library name	Construction protocol	Strategy	Source	Selection	Layout
	In brief, plants were grown in a growth chamber for two weeks. Samples of 2-4 g of tender leaves were harvested, cut into pieces of ca. 2 cm2, and transferred to 50 ml tubes containing 15 ml of ice-cold nuclear isolation buffer (NBE) with 2% formaldehyde, followed by vacuum infiltration (400 mbar) and incubation with a supplemented cross-linking agent for 1 h. Cross-linking was quenched by adding 2 M glycine to a final concentration of 0.125 M with incubation for 5 min under vacuum, followed by fixation on ice. Then, the fixed leaf pieces were washed three times with sterile Milli-Q water, ground in liquid nitrogen and subjected to nucleus isolation. The isolated nuclei were purified, checked for quality and quantity and digested with 100 units of DpnII. The next steps were Hi-C specific, including marking the DNA ends with biotin-14-dATP and performing blunt-end ligation of the cross-linked fragments. After ligation, cross-linking was reversed by overnight incubation with proteinase K at 65 degrees. Biotin-14-dATP was further removed from nonligated DNA ends using the exonuclease activity of T4 DNA polymerase. DNA was purified by phenol:chloroform (1:1) extraction, precipitated and washed as previously described. The purified DNA was physically sheared to a size of 300-600 bp by sonication and was size-fractionated using standard 2% agarose gel electrophoresis to obtain fragments in the range of 300-600 bp. The fragmented ends were blunt-end repaired and A-tailed, followed by purification through biotin-streptavidin-mediated pulldown. PCR amplification was conducted using 12-15 cycles to enrich the ligation products. After the quality check, the Hi-C libraries were sequenced on the MGISEQ2000 platform at BGI (Wuhan, China).	Hi-C	GENOMIC	RANDOM	PAIRED

Processing

Planned read length (bp) for mate 1: 150
Planned read length (bp) for mate 2: 150

Release date

2024-06-07

Run

Run accession	Run data file information
Run accession	File name	File size (MB)
CRR1015127	CRR1015127_f1.fq.gz CRR1015127_r2.fq.gz	6,781.45 7,325.33
CRR1015128	CRR1015128_f1.fq.gz CRR1015128_r2.fq.gz	9,740.96 10,406.48
CRR1015129	CRR1015129_f1.fq.gz CRR1015129_r2.fq.gz	11,313.01 12,297.96
CRR1015130	CRR1015130_f1.fq.gz CRR1015130_r2.fq.gz	6,600.07 7,028.75
CRR1015131	CRR1015131_f1.fq.gz CRR1015131_r2.fq.gz	8,613.65 9,527.14
CRR1015132	CRR1015132_f1.fq.gz CRR1015132_r2.fq.gz	9,693.63 10,379.28
CRR1015133	CRR1015133_f1.fq.gz CRR1015133_r2.fq.gz	8,258.75 8,823.2
CRR1015134	CRR1015134_f1.fq.gz CRR1015134_r2.fq.gz	7,163.91 7,585.33
CRR1015135	CRR1015135_f1.fq.gz CRR1015135_r2.fq.gz	6,368.33 6,808.75
CRR1015136	CRR1015136_f1.fq.gz CRR1015136_r2.fq.gz	7,140.83 7,937.69
CRR1015137	CRR1015137_f1.fq.gz CRR1015137_r2.fq.gz	8,087.59 8,673.39
CRR1015138	CRR1015138_f1.fq.gz CRR1015138_r2.fq.gz	15,028.22 16,027.75
CRR1015139	CRR1015139_f1.fq.gz CRR1015139_r2.fq.gz	6,050.32 6,321.59
CRR1015140	CRR1015140_f1.fq.gz CRR1015140_r2.fq.gz	14,919.18 15,950.65
CRR1015141	CRR1015141_f1.fq.gz CRR1015141_r2.fq.gz	15,703.71 16,802.02
CRR1015142	CRR1015142_f1.fq.gz CRR1015142_r2.fq.gz	14,157.2 15,197.02
CRR1015143	CRR1015143_f1.fq.gz CRR1015143_r2.fq.gz	11,673.27 12,473.68
CRR1015144	CRR1015144_f1.fq.gz CRR1015144_r2.fq.gz	10,907.7 11,718.93
CRR1015145	CRR1015145_f1.fq.gz CRR1015145_r2.fq.gz	10,618.25 11,354.92
CRR1015146	CRR1015146_f1.fq.gz CRR1015146_r2.fq.gz	8,159.2 9,077.45
CRR1015147	CRR1015147_f1.fq.gz CRR1015147_r2.fq.gz	8,891.95 9,564.86
CRR1015148	CRR1015148_f1.fq.gz CRR1015148_r2.fq.gz	7,297.58 7,724.96
CRR1015149	CRR1015149_f1.fq.gz CRR1015149_r2.fq.gz	11,371.75 12,326.38
CRR1015150	CRR1015150_f1.fq.gz CRR1015150_r2.fq.gz	8,527.44 9,228.35
CRR1015151	CRR1015151_f1.fq.gz CRR1015151_r2.fq.gz	13,080.57 14,236.12
CRR1015152	CRR1015152_f1.fq.gz CRR1015152_r2.fq.gz	6,876.79 7,309.68
CRR1015153	CRR1015153_f1.fq.gz CRR1015153_r2.fq.gz	8,798.33 9,515.61
CRR1015154	CRR1015154_f1.fq.gz CRR1015154_r2.fq.gz	13,703.59 14,465.01
CRR1015155	CRR1015155_f1.fq.gz CRR1015155_r2.fq.gz	10,833.25 11,492.84
CRR1015156	CRR1015156_f1.fq.gz CRR1015156_r2.fq.gz	6,935.01 7,447.65
CRR1015157	CRR1015157_f1.fq.gz CRR1015157_r2.fq.gz	15,245.34 16,308.77
CRR1015158	CRR1015158_f1.fq.gz CRR1015158_r2.fq.gz	11,082.44 11,829.17
CRR1015159	CRR1015159_f1.fq.gz CRR1015159_r2.fq.gz	6,676.38 7,168.55
CRR1015160	CRR1015160_f1.fq.gz CRR1015160_r2.fq.gz	9,404.61 9,994.63
CRR1015161	CRR1015161_f1.fq.gz CRR1015161_r2.fq.gz	6,864.03 7,320.7
CRR1015162	CRR1015162_f1.fq.gz CRR1015162_r2.fq.gz	7,206.2 7,690.04
CRR1015163	CRR1015163_f1.fq.gz CRR1015163_r2.fq.gz	12,501.34 13,366.72
CRR1015164	CRR1015164_f1.fq.gz CRR1015164_r2.fq.gz	7,116.43 7,635.11
CRR1015165	CRR1015165_f1.fq.gz CRR1015165_r2.fq.gz	13,845.52 14,964.84
CRR1015166	CRR1015166_f1.fq.gz CRR1015166_r2.fq.gz	10,421.29 11,153.42
CRR1015167	CRR1015167_f1.fq.gz CRR1015167_r2.fq.gz	6,514 6,957.53
CRR1015168	CRR1015168_f1.fq.gz CRR1015168_r2.fq.gz	10,587.54 11,748.5
CRR1015169	CRR1015169_f1.fq.gz CRR1015169_r2.fq.gz	11,239.35 11,810.11
CRR1015170	CRR1015170_f1.fq.gz CRR1015170_r2.fq.gz	7,318.53 7,839.21
CRR1015171	CRR1015171_f1.fq.gz CRR1015171_r2.fq.gz	11,495.47 12,270.94
CRR1015172	CRR1015172_f1.fq.gz CRR1015172_r2.fq.gz	10,219.53 10,879.46
CRR1015173	CRR1015173_f1.fq.gz CRR1015173_r2.fq.gz	8,819.29 9,455.17
CRR1015174	CRR1015174_f1.fq.gz CRR1015174_r2.fq.gz	8,843.68 9,400.85
CRR1015175	CRR1015175_f1.fq.gz CRR1015175_r2.fq.gz	9,398.04 10,082.37
CRR1015176	CRR1015176_f1.fq.gz CRR1015176_r2.fq.gz	13,309.72 14,139.57
CRR1015177	CRR1015177_f1.fq.gz CRR1015177_r2.fq.gz	8,119.51 8,795.23
CRR1015178	CRR1015178_f1.fq.gz CRR1015178_r2.fq.gz	11,132.44 11,936.23
CRR1015179	CRR1015179_f1.fq.gz CRR1015179_r2.fq.gz	7,414.09 7,843.31
CRR1015180	CRR1015180_f1.fq.gz CRR1015180_r2.fq.gz	10,233.73 10,937
CRR1015181	CRR1015181_f1.fq.gz CRR1015181_r2.fq.gz	5,855.69 6,188.79
CRR1015182	CRR1015182_f1.fq.gz CRR1015182_r2.fq.gz	8,491.75 9,006.78
CRR1015183	CRR1015183_f1.fq.gz CRR1015183_r2.fq.gz	10,888.68 11,920.4
CRR1015184	CRR1015184_f1.fq.gz CRR1015184_r2.fq.gz	10,550.97 11,287.59
CRR1015185	CRR1015185_f1.fq.gz CRR1015185_r2.fq.gz	8,650.57 9,094.64
CRR1015186	CRR1015186_f1.fq.gz CRR1015186_r2.fq.gz	11,481.83 11,973.08
CRR1015187	CRR1015187_f1.fq.gz CRR1015187_r2.fq.gz	10,954.08 11,437.32
CRR1015188	CRR1015188_f1.fq.gz CRR1015188_r2.fq.gz	9,304.32 9,790.15
CRR1015189	CRR1015189_f1.fq.gz CRR1015189_r2.fq.gz	8,927.37 9,340.66
CRR1015190	CRR1015190_f1.fq.gz CRR1015190_r2.fq.gz	11,913.37 12,496.42
CRR1015191	CRR1015191_f1.fq.gz CRR1015191_r2.fq.gz	8,154.84 8,632.19
CRR1015192	CRR1015192_f1.fq.gz CRR1015192_r2.fq.gz	11,593.28 12,165.92
CRR1015193	CRR1015193_f1.fq.gz CRR1015193_r2.fq.gz	12,818.4 13,659.69
CRR1015194	CRR1015194_f1.fq.gz CRR1015194_r2.fq.gz	8,147.52 8,528.72
CRR1015195	CRR1015195_f1.fq.gz CRR1015195_r2.fq.gz	10,478.99 11,259.11
CRR1015196	CRR1015196_f1.fq.gz CRR1015196_r2.fq.gz	9,695.42 10,187.04
CRR1015197	CRR1015197_f1.fq.gz CRR1015197_r2.fq.gz	8,349.12 8,784.18
CRR1015198	CRR1015198_f1.fq.gz CRR1015198_r2.fq.gz	7,355.16 7,669.01
CRR1015199	CRR1015199_f1.fq.gz CRR1015199_r2.fq.gz	6,726.77 7,086.69
CRR1015200	CRR1015200_f1.fq.gz CRR1015200_r2.fq.gz	7,129.76 7,702.8
CRR1015201	CRR1015201_f1.fq.gz CRR1015201_r2.fq.gz	8,199.19 8,652.19

Submitter

Zehou Liu (zehouliu@163.com)

Organization

Sichuan Academy of Agricultural Sciences

Date submitted

2024-01-18

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