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| Status |
Public on Aug 03, 2020 |
| Title |
H3C_WT_Rep1 |
| Sample type |
SRA |
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| Source name |
Aerial parts of two-weeks old seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Aerial parts of two-weeks old seedlings
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| Growth protocol |
All Arabidopsis seedlings were grown on soil or half-strength Murashige and Skoog (1/2 MS) solid medium containing 1% (w/v) sucrose in a growth chamber (16-h day, 8-h night, 22 °C; 100 μE m-2s-1)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, chromatin was sonicated and immunoprecipitated with the respective antibody; For RNA-seq, total RNA were isolated using TRIzol reagent, DNA and ribosomal RNA were removed using the Ribo-Zero rRNA Removal Reagents (Plant Leaf)(Epicentre, USA).
ChIP-seq libraries and RNA-seq were prepared using NEBNext Ultra II DNA library prep kit for Illumina (E7645, New England Biolabs) and NEBNext Ultra Directional RNA library prep kit for Illumina (E7420, New England Biolabs) according to the manufacturer’s instruction respectively.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For ChIP-seq, raw reads quality was first analyzed using FastQC, and any base with a quality score below 25 or N was trimmed using Sickle. Trimmed reads were then mapped to the A. thaliana genome (TAIR 10) using BWA 0.7.15-r1140 with mem option default parameters. Uniquely mapped reads were further filtered for calculating H3K9me2 coverage in transcript, while unfiltered reads were used for calculating H3K9me2 coverage in transposable elements.
For both RNA-seq,the quality of raw reads was analyzed using FastQC. The first 10 bases and the last base were trimmed. Contaminating adaptor reads, reads that were unpaired, bases below 25 and Ns, and reads shorter than 18 bases are also filtered using Sickle.All trimmed reads were mapped to A. thaliana genome (TAIR 10) using HISAT2 v2.1.0 with a known splice site file, built from Araport annotation file v11, and strand information parameter, --rna-strandness RF. Coverage values for each transcript was calculated using BEDTools with –split, -D, and -S parameters.
For genome browser tracks, read coverage per nucleotide is calculated using BEDTools. Coverage values were then normalized per million mapped reads.
Genome_build: TAIR 10
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| Submission date |
Dec 24, 2017 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Xueqing Maggie Lu |
| E-mail(s) |
maggieqqlu@gmail.com
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| Phone |
8186878070
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| Organization name |
University of California, Riverside
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| Department |
Cell Biology
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| Lab |
Le Roch
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| Street address |
3401 Watkins Drive, Genomics, Room 2126
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE108487 |
Genome-wide profilings of EDM2-mediated effects on H3K9me2 and transcripts in Arabidopsis thaliana |
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| Relations |
| BioSample |
SAMN08238141 |
| SRA |
SRX3508944 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2901541_flowcell429_all_pair1_GTGGCC.H3C_WT_Rep1.nonunique.normalized.bed.gz |
358.2 Mb |
(ftp)(http) |
BED |
| GSM2901541_flowcell429_all_pair1_GTGGCC.H3C_WT_Rep1.unique.normalized.bed.gz |
357.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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