Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco

Brockmöller, Thomas; Ling, Zhihao; Li, Dapeng; Gaquerel, Emmanuel; Baldwin, Ian T.; Xu, Shuqing

doi:10.1186/s12864-016-3465-9

Table 3 Overview of RNA-Seq data

From: Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco

Library ID/ SRA ID	Tissue	Treatment/development stage	# of expressed genes	Additional note on sampling procedure
NA1498ROT SRX1804895	Root	Rosette stage plants, treated with 5 μL 1:1 diluted M. sexta oral secretion three times in leaves	15,499	Roots of rosette stage plants that were treated three times on leaves were collected for RNA extraction. The treatments were performed at 10 am and 6 pm on the day before sampling and 10 am on the day of sampling. Samples were collected at 11 am.
NA1500LET SRX1804896	Leaf	Rosette stage plants, treated with 5 μL 1:1 diluted M. sexta oral secretion three times in leaves	12,179	Local leaves of rosette stage plants that were treated three times on leaves were collected for RNA extraction. The treatments were performed at10 am, 6 pm on the day before sampling and 10 am on the day of sampling. Samples were collected at 11 am.
NA1717LEC SRX1804554	Leaf	Rosette stage plants, no treatment	11,840	Rosette stage leaves were collected for RNA extraction. Samples were collected at 11 am.
NA1504STT SRX1804900	Stem	Rosette stage plants, treated with 5 μL 1:1 diluted M. sexta oral secretion three times in leaves	14,682	Stems of rosette stage plants that were treated three times on leaves were collected for RNA extraction. The treatments were performed at 10 am, 6 pm on the day before sampling and 10 am on the day of sampling. Samples were collected at 11 am.
NA1505COE SRX1804901	Corolla	Early developmental stage, no treatment	13,662	Samples were collected in the afternoon, 60 samples were pooled.
NA1515COL SRX1804913	Corolla	Late developmental stage, no treatment	13,486	Samples were collected at 6 pm (open flowers) and 9 am (closed flower after opening), 4-10 samples were pooled.
NA1506STI SRX1804902	Stigma	Mature stigma, no treatment	14,485	Stigma samples were collected in the afternoon, 40 samples were pooled.
NA1507POL SRX1804903	Pollen tube	No treatment	3,490	Pollen tubes were pooled.
NA1508SNP SRX1804904	Style	Mature style without pollination	13,492	Styles were collected at 7 am, anthers were removed one day before, and 50 samples were pooled.
NA1509STO SRX1804905	Style	Mature style, pollinated with pollens from different genotype	13,365	Styles were collected at two hours after pollination, at 7 am. Anthers were removed one day before, and 30 samples were pooled.
NA1510STS SRX1804906	Style	Mature style, self-pollinated	13,533	Styles were collected at two hours after pollination, at 7 am. Anthers were removed one day before, and 30 samples were pooled.
NA1511NEC SRX1804907	Nectary	Mature nectary, no treatment	12,928	Samples were collected in the afternoon, 60 samples were pooled.
NA1512ANT SRX1804908	Anther	Mature anther no treatment	11,550	Samples were collected in the afternoon, 60 samples were pooled.
NA1513OVA SRX1804909	Ovary	Mature ovary, no treatment	13,960	Samples were collected in the afternoon, 60 samples were pooled.
NA1514PED SRX1804910	Pedicel	Mature pedicel, no treatment	14,550	Samples collected at 9 am (heading down) and 4 pm (heading up) were pooled.
NA1516OFL SRX1804911	Flower	Fully opened flowers, no treatment	14,390	Both morning (7 am) and evening (6 pm) flowers were collected, 1 sample of each were pooled.
NA1517FLB SRX1804912	Flower bud	Two early developmental stages of flowers, no treatment	14,543	Samples were collected at 6 pm, 1 bud and 1 middle stage flower were collected. Sepals were removed from the samples.
NA1501SES SRX1804897	Seed	Treated with liquid smoke	9,227	100 mg seeds treated with 1:50 diluted liquid smoke solution for 9-15 min were used for RNA extraction.
NA1502SEW SRX1804898	Seed	Treated with water	8,872	100 mg seeds treated with water for 9-15 min were used for total RNA extraction.
NA1503SED SRX1804899	Seed	Dry seeds	8,681	100 mg dried seeds directly used for total RNA extraction.

The raw reads information and methods used for generating these data are available under NCBI accession number PRJNA317743

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