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| Status |
Public on Oct 30, 2021 |
| Title |
VvCARPO_500_leaf_r1 |
| Sample type |
SRA |
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| Source name |
young leaf
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Syrah
protein: CARPO (NAC60)
gene id vcost: Vitvi08g01843
gene id v1: VIT_08s0007g07670
protein family: NAC
protein source: Vitis vinifera
protein affinity tag: HALO
expression system: rabbit reticulocyte lysate
dna source: Syrah
replicate: r1
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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 was collected and pooled from fruiting cuttings of cv. ‘Syrah’.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted following procedure described in Thomas et al., 1993 (Thomas MR, Scott NS. 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theoretical and Applied Genetics. 86(8):985-90. doi: 10.1007/BF00211051. PMID: 24194007). 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
library strategy: DAP-seq
Base calling was done with Illumina Offline Base Caller (OLB 1.9.4).
Raw reads were trimmed using fastp version 0.21.0 with the following parameters: " -w 16 --n_base_limit 5 cut_front_window_size 1 cut_front_mean_quality 30 --cut_front cut_tail_window_size 1 cut_tail_mean_quality 30 --cut_tail -l 20 -i "
Trimmed reads were aligned by bowtie2 version 2.0-beta7 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 3.4 read distribution, PN40024_12X.2 genome sequences, in multi-replicate mode when it was possible and with the GST samples as control, and parameters “–q 1 –t 1 –k_min 6 –kmax 20 –k seqs 600 –k_neg_dinu_shuffle”, limited to nuclear chromosomes.
Peak summits called by GEM were associated with the closest gene model in the custom annotation file using the BioConductor package ChIPpeakAnno (16) with default parameters (i.e., NearestLocation).
Supplementary_files_format_and_content: Peak regions in narrowPeak format were created by GEM.
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| Submission date |
Oct 27, 2021 |
| Last update date |
Oct 30, 2021 |
| Contact name |
José Tomás Matus |
| E-mail(s) |
tomas.matus@gmail.com
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| Organization name |
Institute for Integrative Systems Biology
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| Lab |
TOMSbiolab
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| Street address |
Carrer del Catedràtic Agustín Escardino Benlloch
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| City |
Paterna |
| State/province |
Valencia |
| ZIP/Postal code |
46980 |
| Country |
Spain |
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| Platform ID |
GPL24368 |
| Series (1) |
| GSE186656 |
Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor |
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| Relations |
| BioSample |
SAMN22600410 |
| SRA |
SRX12797775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5658622_NAC60_r1_r2.GEM_events.narrowPeak.gz |
250.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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