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opencc-by-4.0Apr 2019View details →

Supplementing data and code for: "Correlation of mRNA delivery timing and protein expression in lipid-based transfection"

Supplementary data and code for Reiser et al.: Correlation of mRNA delivery timing and protein expression in lipid-based transfection. 2019, <a href="https://doi.org/10.1093/intbio/zyz030">doi:10.1093/intbio/zyz030</a>. See `README.pdf` for further details.

opencc-by-4.0Apr 2019View details →

Characterizing Novel Olfactory Receptors Expressed in the Murine Renal Cortex: Supplemental Table S2

Olfactory receptors selected for study. Olfactory receptors (ORs) selected for study based on mapped reads in at least 7 out of 8 murine renal cortex samples. Murine samples are listed as A - M. Samples A - G were fed high fat diet, while samples I - M were fed control diet. (mm10) FPKM counts for ORs selected for study based on the GRCm30/mm10 genome build using previously published OR coordinates. ORs are listed using the "Olfr" gene names, as well as the "CUFFOR" names as determined by Ibarra-Soria X et al. (mm9) FPKM counts for ORs selected for study based on the NCBI37/mm9 genome build using established coordinates. ORs listed in green were identified and cloned from kidney RNA previously.   Data accessible at NCBI GEO database, accession number GSE117249 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117249

Supplementary data for: Detection of expressed mutations in acute myeloid leukemia cells using single cell RNA-sequencing

Supplemental data for the publication: Detection of expressed mutations in acute myeloid leukemia cells using single cell RNA-sequencing  Contents:  - expression_matrices.tar  - Gene/Barcode expression matrices from `cellranger count` - *.seurat.rds  - R object files with Seurat analyses and data structures for each sample - scrna_mutations.tar.gz  - copy of a git repository containing additional scripts and data - also hosted at <a href="https://github.com/genome/scrna_mutations">https://github.com/genome/scrna_mutations</a> (snapshot as of May 20, 2019)

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.

Figure 2 in Identification and expression of Dmrt1 and Sox9 during the gonadal differentiation of Rana chensinensis

Figure 2. Nucleotides and deduced amino acids of rcDmrt1. The DM domain is boxed in shaded rectangles, while the male-specific motifs and P/S-rich element are underlined with a solid and dotted line, respectively. Cysteines and histidines that coordinate Zn2+ are aligned as two intertwined binding sites: site I (circles) and site II (boxes). The stop codon is marked by an asterisk.

Figure 1 in Identification and expression of Dmrt1 and Sox9 during the gonadal differentiation of Rana chensinensis

Figure 1. Images of undifferentiated gonads and differentiated testes and ovaries of R. Chensinensis tadpoles. A, Stage 28; B, stage 46, testis; C, stage 46, ovary. Wd, Wolffian duct; Gmc, gonad-mesonephros complex; Pe, perisome; Ki, kidney; Te, testis; Ov, ovary.

Figure 6. rcDmrt1 and rcSox9 in Identification and expression of Dmrt1 and Sox9 during the gonadal differentiation of Rana chensinensis

Figure 6. rcDmrt1 and rcSox9 expression in various tissues of adult R. chensinensis. Upper two panels, RT-PCR using rcDmrt1 and rcSox9 gene-specific primers, respectively; lower panel, control RT-PCR using rpl8 gene-specific primers.

Figure 4 in Identification and expression of Dmrt1 and Sox9 during the gonadal differentiation of Rana chensinensis

Figure 4. The neighbor-joining phylogenetic trees of Dmrt1 and Sox9. Phylogenetic tree was constructed on the basis of alignment of the amino acid sequences of Dmrt1 and Sox9 homologs, showing the evolutionary relationship of rcDmrt1 (A) and rcSox9 (B) with other species of the Dmrt1 and Sox9 family. Numbers at branch nodes are percentages of bootstrap confidence values derived from 2000 replications. GenBank Accession Nos. of various species are shown in Table 2.