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| Status |
Public on Nov 29, 2021 |
| Title |
TM-1-leaf-K27me3_clean |
| Sample type |
SRA |
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| Source name |
TM-1-leaf
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| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: leaf
chip antibody: H3K27me3(Sigma)
age: 20 days
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| Treatment protocol |
none
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| Growth protocol |
The allotetraploid cotton cultivar Gossypium hirsutum was used in this study. Cotton seeds were soaked in water for 24 h, then transferred to soil in pots to continue to grow in a greenhouse with 60 % humidity at 28/25°C and 16/8-h light/dark cycle. Two and three true leaves were collected from 20-old plants and ground into fine powder using liquid nitrogen
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 d-old cotton leaves were used for nuclei preparation. The nuclei were extracted using nuclei isolation buffer (NIB, pH 5.0, 1.0 M Glucose, 0.1 M citric acid, 80 mM KCl, 10 mM EDTA, adding fresh Triton X-100 to final 1% just before use). The nuclei were purified using 1x nuclei washing buffer (NWB, pH 5.0, 1 M Glucose, 0.1 M Na-citrate, adding fresh Triton X-100 to final 1% just before use). The purified nuclei were resuspended using 600 µl MNB buffer (50 % w/v Sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2) for MNase digestion at 37°C for 10 min. Centrifuge the digestion mix at 13,000 rpm for 10 min at 4°C and transferred supernatant into a new 1.5 ml tube. The digested nuclei pellet was resuspended in lysis buffer (1 mM Tris-HCl, pH 7.5, 0.1 mM PMSF, 2 % v/v Complete Mini) and leave it on ice for 1 h. After centrifugation, the supernatant was transferred into the 1.5 m tube containing digested chromatin. ChIP incubation buffer was added to the digested chromatin to make 1.7 ml total. The remaining steps were followed the published procedures (Zhang et al., 2012), including antibody incubation followed by adding protein A-sepharose beads, beads washing and ChIPed DNA elution, purification of ChIPed DNA for library preparation and sequencing on Illumina platform.
The final purified DNA was used for ChIP-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina purchased from NEB (Cat#: E7645S)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads ChIP-seq data were mapped to the G. hirsutum reference genome with Bowtie2 aligner (Langmead and Salzberg, 2012).
Any PCR duplicates were removed using Picard. Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
H3K27me3 peaks were called with ‘--broad’ parameter on (-f BAM -g 2.3e+9 --nomodel -q 0.01 --broad --broad-cutoff 0.1) and H3K4me3 peaks were called with off (-f BAM -g 2.3e+9 --nomodel -q 0.01) using the MACS2 software (Zhang et al., 2008)
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: bed files were generated using MACS2
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| Submission date |
Jan 21, 2021 |
| Last update date |
Nov 29, 2021 |
| Contact name |
Li Wen Zhang |
| E-mail(s) |
wzhang25@njau.edu.cn
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| Organization name |
Nanjing Agricultural University
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| Street address |
No.1 Weigang
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL29633 |
| Series (2) |
| GSE165243 |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (ChIP-Seq) |
| GSE165245 |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton |
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| Relations |
| BioSample |
SAMN17469076 |
| SRA |
SRX9908779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5028847_TM-1-leaf-K27me3.bed.gz |
194.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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