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| Status |
Public on Sep 19, 2019 |
| Title |
ChIP_Rice_7days_leaf_H3K4me1 |
| Sample type |
SRA |
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| Source name |
DNA
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| Organism |
Oryza sativa |
| Characteristics |
accession: Nipponbare
tissue: leaf
age: 7days
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| Growth protocol |
Arabidopsis thaliana (accession Col-0) were grown on 1/2MS plates under 25°C and continues light for 7 days. Leaves were collected for the experiments. Spirodela polyrhiza (accession 7498) were grown in liquid bases (Schenk and Hilldebrandt basak salt mixture) under 25°C and continuous light. Whole seedlings were collected 3 days after transferring to a new basis. Eutrema salsugineum (accession Shandong) and Asparagus officinalis (accession Gijnlim) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). All the young leaves were collected for the experiments. Phaseolus vulgaris (accession G19833) and Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. Brachypodium distachyon (accession Bd21), Oryza sativa (accession Nipponbare), Setaria viridis (accession A10), Sorghum bicolor, Zea mays (accession B73), and Hordeum vulgare (accession Morex) were grown in soil for ~6-7days under 25°C, 16 hours of light/8 hours of dark. The inner second leaves—which contains the third and fourth leaves sheathed inside—were used for experiments. Populus trichocarpa leaves were collected from the tree and flash-frozen with liquid N2 immediately for the following experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP-seq: ChiP-seq was performed following the methods of Zhang et al (2007) (https://www.ncbi.nlm.nih.gov/pubmed/17439305). Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.
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| Library strategy |
ChIP-Seq |
| Library source |
transcriptomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA-seq: analysis was performed using Tophat v2.1.1 and cufflinks v2.2.1
ChIP-seq: analysis was performed using bowtie1.1.1
ATAC-seq:analysis was performed using bowtie1.1.1, macs2
Genome_build: Arabidopsis thaliana, Eutrema salsugineum, Phaseolus vulgaris, Glycine max, Brachypodium distachyon, Oryza sativa, Setaria viridis, Populus trichocarpa, Sorghum bicolor genomes were from JGI (phytozome version 11) ; Zea mays from maizeGDB AGP_v4; Hordeum vulgare from ensemble (version 42) ; Asparagus officinalis from Asparagus genome project (http://asparagus.uga.edu/tripal/); Spirodela polyrhiza from Michael et al..
Supplementary_files_format_and_content: *BED file, the identified regulatory regions, tab delimited text file, see ACR_column_header.txt for column headers
Supplementary_files_format_and_content: *BIGWIG , the genome coverage of each sample
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| Submission date |
Mar 18, 2019 |
| Last update date |
Sep 19, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL21087 |
| Series (1) |
| GSE128434 |
The prevalence, evolution and chromatin signatures of plant regulatory elements |
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| Relations |
| BioSample |
SAMN11158823 |
| SRA |
SRX5534520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3674685_ChIP_Rice_7days_leaf_H3K4me1.bw |
288.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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