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| Status |
Public on Jan 04, 2018 |
| Title |
ChIPseq_AGO1_WT_Flg22control_ChIP_rep2 |
| Sample type |
SRA |
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| Source name |
seedling, WT, Flg22 control
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Col-0
genotype/variation: WT
tissue: seedling
age: 10 days
substrate: 1/2 MS
treatment: Flg22 control
chip antibody: AGO1
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| Treatment protocol |
Ten-day-old seedlings were exposed to one of the following treatments: 50 μM of MeJA for 1 h, 10 μM of flg22 for 3 h, 40 μM of BTH for 24 h and 4 °C (cold) for 6 h. For IAA treatment, 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days. Then they were grown on 1/2 MS containing 20 μM IAA for 1 h. Plants grown under the same condition were treated with the buffers and served as controls.
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| Growth protocol |
Plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). Other growth conditions for specific tissues/organs are in the 'description' field.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as previously described (Fang et al., 2015), using antibodies against AGO1 (Qi et al., 2005), myc (Abcam, ab32), Pol II (Abcam, ab817), Pol II Ser2P (Abcam, ab5095), Pol II Ser5P (Abcam, ab5131), or IgG (Abmart, B30011). For GRO-seq, ~5X10^6 nuclei were run on for 5 min at 30 °C. The reactions were stopped by addition of Trizol and RNAs were extracted. After digestion with Terminator exonuclease (Epicentre) and fragmentation, nascent RNAs were enriched twice for 5-bromo-UTP (BrUTP) by immunoprecipitation. For RNA-seq, total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN). For sRNA-seq, nuclei were isolated from 10-day-old Col-0 and coi1-1 seedlings without or with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008). To characterize nuclear AGO1-associated sRNAs, sRNAs were extracted from the immunoprecipitates as described (Mi et al., 2008).
Libraries for ChIP-seq were generated using the NEXTflex ChIP-seq Kit (Bioo Scientific) according to the manufacturer's instructions; Libraries for GRO-seq were performed as described (Wang et al., 2011a); Libraries for RNA-seq were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) or NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions; Libraries for sRNA-seq were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with water for 3h.
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| Data processing |
Reads were mapped with Bowtie for all data; Peaks were called with MACS2 for ChIP-seq; Gene expressions were calculated with Cuffdiff for RNA-seq; GRO-seq data was analysed by HOMER software.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph for ChIP-seq; expression matrix for RNA-seq; bigwig for GRO-seq; raw read counts for sRNA-seq.
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| Submission date |
Mar 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@mail.tsinghua.edu.cn
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| Organization name |
Tsinghua University
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| Department |
School of Life Sciences
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| Street address |
NO.1 Qinghuayuan
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| City |
Beiing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE95301 |
Chromatin-Bound ARGONAUTE 1 Promotes Gene Transcription in Response to Various Stimuli in Arabidopsis |
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| Relations |
| BioSample |
SAMN06480095 |
| SRA |
SRX2613466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2522216_ChIPseq_AGO1_WT_Flg22control_ChIP_rep2.bedgraph.gz |
177.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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