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SRX9908781: GSM5028846: TM-1-leaf-Iuput_clean; Gossypium hirsutum; ChIP-Seq
1 ILLUMINA (HiSeq X Ten) run: 11.4M spots, 2.9G bases, 893.2Mb downloads

Submitted by: NCBI (GEO)
Study: Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (ChIP-Seq)
show Abstracthide Abstract
Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. In this study, we conducted H3K4me3 and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating expression of genes between A and D subgenome, respectively. Expression of H3K4me3-H3K27me3 bivalent genes was regulated by combinatorial actions of both marks and may be dominantly controlled by H3K4me3. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. In addition, H3K4me3, H3K27me3 and bivalent mark can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression between A and D subgenome in cotton. Overall design: RNA-seq, ChIP-seq
Sample: TM-1-leaf-Iuput_clean
SAMN17469081 • SRS8087017 • All experiments • All runs
Library:
Instrument: HiSeq X Ten
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction 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)
Experiment attributes:
GEO Accession: GSM5028846
Links:
Runs: 1 run, 11.4M spots, 2.9G bases, 893.2Mb
Run# of Spots# of BasesSizePublished
SRR1349677811,357,3702.9G893.2Mb2021-12-01

ID:
12968073

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