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| Status |
Public on Jan 10, 2022 |
| Title |
VvMYB13_PN94-B_r2 |
| Sample type |
SRA |
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| Source name |
young leaf
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Pinot Noir (clone PN-94)
protein: VvMYB13
gene id vcost: Vitvi05g01732
gene id v1: VIT_05s0049g01010
protein family: MYB
protein source: Vitis vinifera
protein affinity tag: HALO
expression system: rabbit reticulocyte lysate
dna source: PN94-B
replicate: r2
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| Treatment protocol |
Leaf material was collected and flash frozen with liquid nitrogen prior gDNA isolation.
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| Growth protocol |
Leaf material (1-2 in) was collected from a single plant of cv. ‘Pinot Noir’ clone PN94 located in the Foundation Plant Services Facility-UCDavis, California.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted following procedure described in Chin et al., 2016 (Chin, CS., Peluso, P., Sedlazeck, F. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13, 1050–1054 (2016). https://doi.org/10.1038/nmeth.4035). DAP-seq experiment was performed as described in Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055). The DAP-Seq DNA library is prepared from fragmented naked genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter. Separately, a construct containing a HALO-tagged transcription factor is translated by in vitro (rabbit reticulocyte) expression system. The affinity-tagged protein is immobilized on the appropriate affinity resin. The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The eluted DNA fragments are PCR amplified with a full-length indexed TruSeq primer and directly sequenced on the Illumina NextSeq 500.
DAP-Seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
DAPSeq-MYB_rr-VvMYB13_PN94-B-pn_GEM_events.narrowPeak
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| Data processing |
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using TrimGalore 0.4.4 wrapper for Cutadapt 1.16 with the following parameter: "-q 20".
Trimmed reads were aligned by bowtie2 version 2.3.2 against the Vitis vinifera genome assembly PN40024_12X.2 with default parameters, and additionally filter for alignments with MAPQ score of at least 30.
Peaks were called using GEM peak caller version 3.4 with the default version read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode with the pIXHALO samples as control, and parameters " --q 1 --t 1 --f BAM --outNP --outBED --outJASPAR --outMEME --outHOMER --k_min 6 --k_max 20 --k_seqs 600 --k_neg_dinu_shuffle".
Genome_build: Vitis vinifera genome assembly PN40024_12X.2
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.
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| Submission date |
Jul 20, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Shao-shan Carol Huang |
| Organization name |
New York University
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| Department |
Biology
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| Street address |
12 Waverly Pl
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL24368 |
| Series (1) |
| GSE180450 |
Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine |
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| Relations |
| BioSample |
SAMN20326015 |
| SRA |
SRX11504286 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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