cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25444/nhlbi.20483757
title: Flow dependence of gene expression in cultured mIMCD cells

description: Bioinformatic analysis of data from Mohammed SG, Arjona FJ, Verschuren EHJ, Bakey Z et al. Primary cilia-regulated transcriptome in the renal collecting duct. FASEB J 2018 Jul;32(7):3653-3668. PMID: 29452568. https://doi.org/10.1096/fj.201701228r Authors' methods: IMCD3 cells were cultured in DMEM/F-12 1:1 v/v medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 1 mM sodium pyruvate, 10% v/v fetal calf serum, and 10 µg/ml ciproxin, at 37°C and 5% v/v CO2. Cells were seeded into 6-channel ibiTreat-coated μ-Slide chambers (ibidi, Martinsried, Germany) at a cell suspension density of ~0.7 × 106 cells/ml. The medium was refreshed twice a day. To induce ciliogenesis, cells were grown to confluency for 2 d, followed by an additional 1 d in serum-deprived medium prior to the flow experiment (Fig. 1A). See: https://faseb.onlinelibrary.wiley.com/doi/epdf/10.1096/fj.201701228R#f1 (DOI: 10.1096/fj.201701228R) Application of Flow. After 1 d of culture in serum-deprived medium, cells were incubated under static conditions or exposed to fluid flow for 3 h at 37°C. To apply fluid flow, the ibidi μ-Slide chamber was connected to a peristaltic pump (Ismatec, Wertheim, Germany) with a series of tubes and connectors extending to a reservoir (see Supplemental Fig. S1A for schematic representation). Each well was perfused with serum-deprived medium at a physiologic rate of 0.45 ml/min. The fluid flow rate was set to generate a physiologic stress of 0.6 dyn/cm2, a force within the ciliary bending profile reported in previous studies (16, 17). For static condition, medium was refreshed. Next, cells were lysed for RNA isolation and RNA-seq analysis. See original paper. Knepper lab curated the data to make it accessible for the community at a user friendly web site: https://esbl.nhlbi.nih.gov/Databases/IMCD3_flow_effect/RD.htm
DOI: 10.25444/nhlbi.20483757.v1
title: Flow dependence of gene expression in cultured mIMCD cells

description: Bioinformatic analysis of data from Mohammed SG, Arjona FJ, Verschuren EHJ, Bakey Z et al. Primary cilia-regulated transcriptome in the renal collecting duct. FASEB J 2018 Jul;32(7):3653-3668. PMID: 29452568. https://doi.org/10.1096/fj.201701228r Authors' methods: IMCD3 cells were cultured in DMEM/F-12 1:1 v/v medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 1 mM sodium pyruvate, 10% v/v fetal calf serum, and 10 µg/ml ciproxin, at 37°C and 5% v/v CO2. Cells were seeded into 6-channel ibiTreat-coated μ-Slide chambers (ibidi, Martinsried, Germany) at a cell suspension density of ~0.7 × 106 cells/ml. The medium was refreshed twice a day. To induce ciliogenesis, cells were grown to confluency for 2 d, followed by an additional 1 d in serum-deprived medium prior to the flow experiment (Fig. 1A). See: https://faseb.onlinelibrary.wiley.com/doi/epdf/10.1096/fj.201701228R#f1 (DOI: 10.1096/fj.201701228R) Application of Flow. After 1 d of culture in serum-deprived medium, cells were incubated under static conditions or exposed to fluid flow for 3 h at 37°C. To apply fluid flow, the ibidi μ-Slide chamber was connected to a peristaltic pump (Ismatec, Wertheim, Germany) with a series of tubes and connectors extending to a reservoir (see Supplemental Fig. S1A for schematic representation). Each well was perfused with serum-deprived medium at a physiologic rate of 0.45 ml/min. The fluid flow rate was set to generate a physiologic stress of 0.6 dyn/cm2, a force within the ciliary bending profile reported in previous studies (16, 17). For static condition, medium was refreshed. Next, cells were lysed for RNA isolation and RNA-seq analysis. See original paper. Knepper lab curated the data to make it accessible for the community at a user friendly web site: https://esbl.nhlbi.nih.gov/Databases/IMCD3_flow_effect/RD.htm
DOI: 10.25444/nhlbi.20533536
title: Identifying Circadian Transcripts in Mouse Proximal Tubule

description: Rationale: To provide a guide for physiological studies on the kidney proximal tubule, we have now created a data resource consisting of expression levels for all measurable mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. This approach employs small-sample RNA-sequencing (RNA-seq) applied to microdissected renal proximal tubules [33769951], including both S1 proximal convoluted tubules and S2 proximal straight tubules. The data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/. Methods: The study was done in mice (male C57BL/6,4-6 weeks) maintained in an environmentally controlled animal room with a 12hr:12hr light:dark cycle. Three animals were selected at each of 6 time points starting at 8 a.m. (lights on, Zeitgeber 0) and then at every-four-hour junctures. Each of thethree animals in at each time point were studied on separate days. They mice were rapidly euthanized, kidneys were perfused with a physiological solution containing collagenase, followed by manual microdissection as described by Wright and Knepper [2074757] to obtain S1 proximal convoluted tubules and S2 proximal straight tubules. The S1 segments were distinguished by their attachments to glomeruli. The S2 segments originated from the outer cortex. After washing by dragging through clean dissection solution, the tubules were processed for small-sample RNA-seq as described by Chen et al. [33769951]. Each time point was represented by 3 samples for both S1 and S2 segments, each from a different mouse. RNA-Seq used the NEBNext(TM) low Input RNA library preparation kit and a NovaSeq6000 DNA sequencer. Transcripts per million (TPM) values were calculated for each sample. The data were filtered to include only transcripts with a maximum TPM&gt;7 to remove noisy, low abundance mRNAs. The data were analyzed using JTK-Cycle (20876817) to detect periodicity. For this analysis, circadian genes were those with a period 20 or 24 hours, and a curve fit significance level of P&lt;0.05 by nonparametric test described by Hughes et al [20876817]. Analyzed data were shared via user-friendly web pages accessible at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/
DOI: 10.25444/nhlbi.20533536.v1
title: Identifying Circadian Transcripts in Mouse Proximal Tubule

description: Rationale: To provide a guide for physiological studies on the kidney proximal tubule, we have now created a data resource consisting of expression levels for all measurable mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. This approach employs small-sample RNA-sequencing (RNA-seq) applied to microdissected renal proximal tubules [33769951], including both S1 proximal convoluted tubules and S2 proximal straight tubules. The data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/. Methods: The study was done in mice (male C57BL/6,4-6 weeks) maintained in an environmentally controlled animal room with a 12hr:12hr light:dark cycle. Three animals were selected at each of 6 time points starting at 8 a.m. (lights on, Zeitgeber 0) and then at every-four-hour junctures. Each of thethree animals in at each time point were studied on separate days. They mice were rapidly euthanized, kidneys were perfused with a physiological solution containing collagenase, followed by manual microdissection as described by Wright and Knepper [2074757] to obtain S1 proximal convoluted tubules and S2 proximal straight tubules. The S1 segments were distinguished by their attachments to glomeruli. The S2 segments originated from the outer cortex. After washing by dragging through clean dissection solution, the tubules were processed for small-sample RNA-seq as described by Chen et al. [33769951]. Each time point was represented by 3 samples for both S1 and S2 segments, each from a different mouse. RNA-Seq used the NEBNext(TM) low Input RNA library preparation kit and a NovaSeq6000 DNA sequencer. Transcripts per million (TPM) values were calculated for each sample. The data were filtered to include only transcripts with a maximum TPM&gt;7 to remove noisy, low abundance mRNAs. The data were analyzed using JTK-Cycle (20876817) to detect periodicity. For this analysis, circadian genes were those with a period 20 or 24 hours, and a curve fit significance level of P&lt;0.05 by nonparametric test described by Hughes et al [20876817]. Analyzed data were shared via user-friendly web pages accessible at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/
DOI: 10.25444/nhlbi.20632092
title: Curation of vasopressin-regulated phosphorylation sites in collecting duct

description: Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. This document details the step-by-step process followed to identify the vasopressin-regulated phosphorylation sites that change in both mpkCCD cells and in native inner medullary collecting duct cells.
DOI: 10.25444/nhlbi.20632092.v1
title: Curation of vasopressin-regulated phosphorylation sites in collecting duct

description: Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. This document details the step-by-step process followed to identify the vasopressin-regulated phosphorylation sites that change in both mpkCCD cells and in native inner medullary collecting duct cells.
DOI: 10.25444/nhlbi.21218180
title: Vasopressin-Regulated Protein Phosphorylation in Kidney Collecting Duct

description: Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. Among these sites are 23 consensus protein kinase A (PKA) sites that are increased in response to vasopressin, consistent with a central role for PKA in vasopressin signaling. The remaining sites are predicted to be phosphorylated by other kinases, most notably ERK1/2 which accounts for decreased phosphorylation at sites with a X-p(S/T)-P-X motif. Additional protein kinases that undergo vasopressin-induced changes in phosphorylation are Camkk2, Cdk18, Erbb3, Mink1 and Src, which also may be activated directly or indirectly by PKA. The regulated phosphoproteins are mapped to processes that hypothetically can account for vasopressin-mediated control of AQP2 trafficking, cytoskeletal alterations, and <em>Aqp2</em> gene expression, providing grist for future studies.
DOI: 10.25444/nhlbi.21218180.v1
title: Vasopressin-Regulated Protein Phosphorylation in Kidney Collecting Duct

description: Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. Among these sites are 23 consensus protein kinase A (PKA) sites that are increased in response to vasopressin, consistent with a central role for PKA in vasopressin signaling. The remaining sites are predicted to be phosphorylated by other kinases, most notably ERK1/2 which accounts for decreased phosphorylation at sites with a X-p(S/T)-P-X motif. Additional protein kinases that undergo vasopressin-induced changes in phosphorylation are Camkk2, Cdk18, Erbb3, Mink1 and Src, which also may be activated directly or indirectly by PKA. The regulated phosphoproteins are mapped to processes that hypothetically can account for vasopressin-mediated control of AQP2 trafficking, cytoskeletal alterations, and <em>Aqp2</em> gene expression, providing grist for future studies.
DOI: 10.15156/bio/sh1229765.08fu
title: SH1229765.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th029471
title: TH029471
title: Picrodendraceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th029472
title: TH029472
title: Ochnaceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.25549/one-c4-50103
title: S. Judd Gee, letters (1959-1966)

description: S. Judd Gee, letters including handwritten letters praising ONE, mentioning his cat's interference with his writing, and his unsubscribing in 1966 (1959-1966)
DOI: 10.15156/bio/sh1229766.08fu
title: SH1229766.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229767.08fu
title: SH1229767.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229768.08fu
title: SH1229768.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th029473
title: TH029473
title: Caryocaraceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th029474
title: TH029474
title: Putranjivaceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th029475
title: TH029475
title: Chrysobalanaceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.