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| Status |
Public on Jan 19, 2016 |
| Title |
Col_H3K27me3_ChIPseq |
| Sample type |
SRA |
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| Source name |
Arabidopsis thaliana 2-week-old seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 2-week old seedlings without roots
ecotype: Col
chip antibody: H3K27me3
chip antibody manufacturer: Upstate
chip antibody catalog #: 07-449
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| Treatment protocol |
No treatment applied.
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| Growth protocol |
16h light, 8h dark, 21°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin or RNA was extracted from 2-week-old seedlings, using standard protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000 following the manufacturer's instructions (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The sequencing reads were cleaned, including removing bases with low quality score (<20) and irregular GC content based on FastQC, cutting sequencing adaptor followed by filtering short reads.
The cleaned reads were mapped to Arabidopsis thaliana genome (TAIR10) using BOWTIE2.0 for DNA sequencing and TOPHATv2.0.8 for RNA sequencing, both with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
For ChIP-seq, MACS1.4 was used to identify read enriched regions (peaks) and MAnorm was applied to characterize the change of genome-wide H3K27me3 profile. For RNA-seq, HTSeq-count was used to preprocess the RNA-seq alignments and deseq was used to detect the differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: In ChIP-seq, peak files was provided; In RNA-seq, read counts for genes (TAIR10) was provided.
Supplementary_files_format_and_content: RNA_seq.deseq.log2fc.p.txt: Contains the ratio between mutant and wild-type for both replicates. The number of read in each gene is counted by DEseq-count.
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| Submission date |
Mar 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
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| Organization name |
Fudan University
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| Department |
Biochemistry
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| Lab |
Functional Epigenomics Group
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| Street address |
2005 Songhu Road
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| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE67322 |
Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements |
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| Relations |
| BioSample |
SAMN03448560 |
| SRA |
SRX969887 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1644813_macs.nomodel.Col_H3K27me3_vs_Neg_peaks.xls.gz |
73.6 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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