 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 08, 2024 |
| Title |
MH-seq data of spikelet |
| Sample type |
SRA |
| |
|
| Source name |
bread wheat
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar: Chinese Spring (CS)
tissue: spikelet
developmental stage: booting stage
genotype: WT
|
| Treatment protocol |
none
|
| Growth protocol |
Common wheat (Tritium aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C. The germinated seeds with residual endosperm were transferred to soil (1:1:3 mixture of vermiculite: perlite: peat soil) or Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2-3 g of ten-day-old whole seedlings or spikelet from Chinese spring (CS) were collected for a 10 min cross-link in 1% of formaldehyde fixation buffer (27.4 g sucrose + 2 ml 1M Tris-HCl pH8.0 + 400 μl 500 mM EDTA + 5.6 ml 36% Formaldehyde) under vacuum at 23-25℃. After adding 125 mM of Glycine to quench the excessive formaldehyde, the cross-linked leaves were washed three time with excessive autoclave ddH2O. The air-dry cross-linked leaves or spikelet were ground into a fine powder in liquid nitrogen and used for nuclei preparation
the purified nuclei pellet was digested in MNase digestion buffer (20 mM Tris-HCl, 4 mM MgCl2, 1mM CaCl2, 60 mM KCl, pH 7.5) with the amount of MNase (M0247, 2,000 gels units/μl, NEB) as 0 unit (U), 90 U, 100 U, 700 U and 900 U, respectively. Each enzymatic reaction was stopped by adding 16 μl 0.5 M EDTA (pH 8.0). Each digested nuclei were reversely cross-linked at 65℃ overnight for reverse cross-linking. MNased DNA was recovered by sequentially extracting using 1 volume of phenol, phenol:chloroform mixture and chloroform, then followed by ethanol precipitation. 40-100 bp small-sized DNA fragments were recovered from running 2% of agarose gel in 1xTBE buffer and used for MH-seq library preparation. MH-seq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). The MH-seq library was finally sequenced using Illumina NovaSeq platform.
Mnase-seq small sizes
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fasp to remove the adapter. only reads length greater than 50 bp were retained
All clean reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) using bowtie2 (Langmead and Salzberg 2012) with parameter -N 1
Duplicated reads were removed using Sambamba (Tarasov et al. 2015). Reads with mapping quality equal to or greater than 20 were retained for further analyses.
The MACS2 (Zhang et al. 2008)(version 2.0) program with parameters “--SPMR –g 14e9 -q 0.01 --nomodel” was used for calling MHS peaks.
Genome_build: International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0)
Supplementary_files_format_and_content: bigwig files, were generated using " bamCoverage --binSize 20 --normalizeUsing RPKM "
Supplementary_files_format_and_content: peak txt file
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Oct 08, 2024 |
| Contact name |
dongyang Zheng |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing Agricultural University
|
| Department |
college of agriculture
|
| Lab |
wenliZhang
|
| Street address |
NJAU Wei gang No.1
|
| City |
Nanjing |
| State/province |
Jiang su |
| ZIP/Postal code |
210018 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN22602060 |
| SRA |
SRX12798607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5659038_spikelet_MH.bigwig |
2.1 Gb |
(ftp)(http) |
BIGWIG |
| GSM5659038_spikelet_Peak.txt.gz |
7.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
