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| Status |
Public on Mar 01, 2020 |
| Title |
124_r2: TF124 Zm00001d005892 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
Leaf protoplast
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| Organism |
Zea mays |
| Characteristics |
cultivar: B73
tissue: Leaf protoplast
transcription factor: Zm00001d005892
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| Treatment protocol |
PEG mediated protoplast transformation
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| Growth protocol |
Leaf protoplast from 1-2 weeks old maize seedlings
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with streptavidin dynabeads.
Libraries were prepared according to Illumina's instructions using purified HS-Tn5 transposase, Tn5-MEA/B adapter as well as N5xx and N7xx PCR primers.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Description |
Contain genome coverage bigwig files for each replicates and the peak file generated by IDR
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| Data processing |
For mapping, we aligned the raw reads to the unmasked maize genome (B73 RefGen_v4) using Bowtie 2 (version 2.2.5) under the default parameters with the 3’ 100 bp trimming option. Reads with mapping quality >= 10 were kept and PCR duplicates are removed using SAMTools (version 1.3). Deeptools bamcoverage was used to convert the BAM to bigwig files for viewing.
For peak calling, BAM files of biological replicates were used to call peaks with the SPP peak caller using relaxed parameters “-i = <INPUT BAM file>”, “-npeak = 300,000”, with input as control. Peaks in the transformed TF genebody itself are removed. Reproducible peaks were obtained with the IDR (Irreproducible discovery rate) statistical framework (version 2.0.3), as implemented in the PhantomPeakQualTools package, using 1% IDR as the threshold (cut-off).
To identify the high confident target genes of each TF, we used the probabilistic model TIP (Cheng et al., Bioinformatics, 2011, 3221–3227) with FDR 0.05 as cutoff.
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: peak and bigwig files
Supplementary_files_format_and_content: TF_target_TIP.txt: High cofident TF target genes called by TIP
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| Submission date |
Sep 25, 2019 |
| Last update date |
Mar 02, 2020 |
| Contact name |
Silin Zhong |
| E-mail(s) |
zhonglab.cuhk@gmail.com
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| Organization name |
CUHK
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| Department |
School of Life Sciences
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| Street address |
Shatin, N.T.
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| City |
Hong Hong |
| ZIP/Postal code |
NA |
| Country |
China |
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| Platform ID |
GPL25842 |
| Series (1) |
| GSE137972 |
Decoding the regulatory architecture of the maize leaf |
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| Relations |
| BioSample |
SAMN10867730 |
| SRA |
SRX5327874 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4095424_124_r2.s.r.bam.bw |
23.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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