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opencc-by-4.0Sep 2019View details →

Human-specific tandem repeat expansion and differential gene expression during primate evolution

THIS DATASET IS PART OF THE FOLLOWING STUDY: <a href="https://www.pnas.org/content/early/2019/10/22/1912175116">https://www.pnas.org/content/early/2019/10/22/1912175116</a>   THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056</a> ORIGINAL UPLOAD: 09/06/2019 UPDATES: 10/28/2019; 01/27/2020 DESCRIPTION: Contigs were assembled using Phased-SV (<a href="https://www.nature.com/articles/s41467-018-08148-z">Chaisson et al, Nature Communications 2019</a>) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified  21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in <a href="https://science.sciencemag.org/content/360/6393/eaar6343">Kronenberg et al, Science 2018</a>. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.

opencc-by-4.0Nov 2019View details →

Processed RNA expression count data from Groen et al.: The strength and pattern of natural selection on rice gene expression

We assessed transcriptome variation in populations of 216 accessions of rice, Oryza sativa, which represented all major varietal groups including indica and japonica. During the 2016 Philippines dry season the accessions were planted in triplicate (with two accessions planted in triplicate three times as replicated checks) in identical alpha-lattice layouts of 660 plots in two fields: a continuously wet paddy, and a field where plants were exposed to intermittent drought in the vegetative and reproductive stages. We measured transcript levels in leaf blades of 50-day-old plants at 33 days after seedling transplant, and 17 days after withholding water in the dry field, using a liquid automation-based 3’ mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library. Raw sequencing data are available at the SRA in BioProject accession number PRJNA588478. A key to the raw sequencing data in this BioProject can be found in the metadata of the processed RNA expression count data here.

Figure 2 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 2. Nucleotide and deduced aa sequences of rcPRLR. The predicted site of signal peptide cleavage is marked by a triangle. The conserved cysteine residues are circled. Three potential N-glycosylation sites are underlined by dotted lines. The WS motif is boxed and TMD is underlined with a solid line. Within the ICD, boxes 1 and 2 are underlined with a double line and a wavy line, respectively. The stop codon is marked by an asterisk.

Figure 7 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 7. Expression analysis of rcPRLR by qRT-PCR in liver (A), skin (B), tail (C), and kidneys (D) of different stages. The data for rcPRLR mRNA levels were normalized by those for rpl8 mRNA levels and expressed relative to the value for stage 43 tissue, respectively. The experiments were repeated 3 times using 3 independent biological samples. Each bar represents mean ± SD. Those with different letters were regarded as statistically significant at the 5% level (Duncan test).

Figure 6 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 6. Detection of rcPRL and rcPRLR in tadpoles by RT-PCR. (A) and (B): Upper panel, RT-PCR using rcPRL and rcPRLR gene-specific primers, respectively; lower panel, control RT-PCR using rpl8 gene-specific primers.

Figure 1 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 1. Nucleotide and deduced aa sequences of rcPRL. The predicted site of signal peptide cleavage is marked by a triangle. The conserved cysteine residues are circled and the potential phosphorylation site is boxed, while the four α-helical domains are boxed in shaded rectangles. The stop codon is marked by an asterisk.

Figure 5 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 5. Construction of neighbor-joining tree based on aa sequences of PRL (A) and PRLR (B). The sequences used above are: Rana catesbeiana (CAA34199.1, BAD14941.1), Xenopus laevis (AAH75216.1, AAI70439.1), Chelonia mydas (XP_007059983.1, EMP31801.1), Anser anser (ADG03649.1, ABW74516.1), Sus scrofa (NP_999091.1, ABA41035.1), Mus musculus (P06879.1, CAA51789.1), Homo sapiens (NP_001157030.1, NP_000940.1), Oncorhynchus mykiss (NP_001118205.1, NP_001118071.1), Danio rerio (AAH92358.1, AAI63012.1), Bufo japonicus (BAF75354.1), and Cynops pyrrhogaster (BAB61107.1). Bootstrap percentage values are indicated for each node.

Figure 4 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 4. Alignment of aa sequences of various PRLRs. Conserved cysteines are circled; 3 potential N-glycosylation sites (His 212; WS motif, Box 1; and DSGRGS motif) are marked by boxes; Trp165 and Tyr609 are marked by triangles. Dots (·) represent spaces inserted to maximize similarity, and small letters represent the conserved amino acids in that position.

Figure 3 in Characteristic analysis of prolactin and its receptor genes from Rana chensinensis and expression pattern during metamorphosis

Figure 3. Alignment of aa sequences of various PRLs. Conserved cysteines are boxed, while motifs 1 and 2 are marked by arrows.

Figure 4 in Identification of thyroid hormone receptors α and β genes and their expression profiles during metamorphosis in Rana chensinensis*

Figure 4. The levels of rcTRα and rcTRβ mRNA in several (n = 6) tadpoles as assessed by qRT-PCR. Different letters indicate significant differences (P <0.05) between developmental stages.

Figure 2 in Identification of thyroid hormone receptors α and β genes and their expression profiles during metamorphosis in Rana chensinensis*

Figure 2. Phylogenetic relationship of TRs among R. chensinensis and other species. Numbers at the branches are the bootstrap values.

Figure 3 in Identification of thyroid hormone receptors α and β genes and their expression profiles during metamorphosis in Rana chensinensis*

Figure 3. Organ-specific expression of rcTRα and rcTRβ in tadpoles during stages 33–46 by RT-PCR. M: DL2000 DNA marker.

Figure 1 in Identification of thyroid hormone receptors α and β genes and their expression profiles during metamorphosis in Rana chensinensis*

Figure 1. Alignment of TR polypeptide sequences in a few species of Rana. The A/B, DBD, D, and LBD domains are separated by arrows. Two conserved zinc fingers are boxed. Asterisks indicate conserved amino acid and hyphens represent spaces inserted to maximized similarity.

opencc-by-4.0Sep 2019View details →

Figure 3 in Validation of reference genes for quantitative expression analysis by qPCR in various tissues of date mussel (Lithophaga lithophaga)

Figure 3. Pairwise variation (V-value) of candidate reference genes in date mussel (L. lithophaga) using geNorm.

opencc-by-4.0Dec 2023View details →

Fig. 1. Differentially expressed genes between infected and uninfected P in Subtle transcriptomic response of Eurasian perch (Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection

Fig. 1. Differentially expressed genes between infected and uninfected P. fluviatilis in a) spleen and b) liver tissues. Filled-in and empty boxes on the top of each plot represent infected and uninfected individuals, respectively. N/A indicates unknown protein.

FIGURE 1 in Characterization and expression of the gene glucose transporter 2 (GLUT2) in embryonic, larval and adult Bay snook Petenia splendida (Cichliformes: Cichlidae)

FIGURE 1 | Partial sequence of nucleotides and amino acids (AA) encoding glut2 (glucose transporter 2) from Petenia splendida taken from Gen Bank to design specific oligonucleotides for qPCR.

FIGURE 3 in Characterization and expression of the gene glucose transporter 2 (GLUT2) in embryonic, larval and adult Bay snook Petenia splendida (Cichliformes: Cichlidae)

FIGURE 3 | Phylogenetic tree based on the sequence of glut2 (glucose transporter 2) from Petenia splendida and other teleosts using the neighbor-joining (NJ) method. Values at branch points represent percentage frequencies for tree topology after 1,000 interations.

FIGURE 4 in Characterization and expression of the gene glucose transporter 2 (GLUT2) in embryonic, larval and adult Bay snook Petenia splendida (Cichliformes: Cichlidae)

FIGURE 4 | Relative expression of glut2 in kidney (K), liver (L), muscle (M), brain (B), pancreas (P), gill (G), heart (H), intestine (I), stomach (S) and testis (T) of adult Petenia splendida (mean ± SEM; n = 3). Lowercase letters indicate significant differences between the expression level in the tissues (p <0.05).

FIGURE 2 in Characterization and expression of the gene glucose transporter 2 (GLUT2) in embryonic, larval and adult Bay snook Petenia splendida (Cichliformes: Cichlidae)

FIGURE 2 | Amino acid sequence of glut2 in Petenia splendida aligned with other species other species of teleost fish. Identical amino acids are presented in black, and the high and less conserved amino acids are presented in gray and period, respectively.

FIGURE 5 in Characterization and expression of the gene glucose transporter 2 (GLUT2) in embryonic, larval and adult Bay snook Petenia splendida (Cichliformes: Cichlidae)

FIGURE 5 | Relative expression of glut2 during the early ontogeny of Petenia splendida. Lowercase letters indicate significant differences in the expression of glut2 as a function of developmental time (p <0.05). AN: Artemia nauplii (3–10 dph), CF: cofeeding (Artemia nauplii and tilapia feed) (11–13 dph), TF: trout feed (14–30 dph) (mean ± SEM; n = 3).