cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10837056
title: Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line PD2)

description: Data repository for publication: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (PD line 2)
description: The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

PD line 2: (TS5_R1_001.fastq.gz, TS5_R2_001.fastq.gz, TS5_R1_001.fastq.gz.md5, TS5_R2_001.fastq.gz.md5, TS5.counts.txt)

PD line 2 TNFalpha+IL-1beta (TS11_R1_001.fastq.gz, TS11_R2_001.fastq.gz, TS11_R1_001.fastq.gz.md5, TS11_R2_001.fastq.gz.md5, TS11.counts.txt)

PD line 2 TNFalpha (TS17_R1_001.fastq.gz, TS17_R2_001.fastq.gz, TS17_R1_001.fastq.gz.md5, TS17_R2_001.fastq.gz.md5, TS17.counts.txt)
description: Line information



Genotype: LRRK2 G2019S

Reference: Holmqvist et al. 2016


Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments



Nonexposed (TS5)

4 h TNFalpha+IL-1beta exposed (TS11)

4 h TNFalpha exposed (TS17)


RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
DOI: 10.5281/zenodo.10837057
title: Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line PD2)

description: Data repository for publication: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (PD line 2)
description: The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

PD line 2: (TS5_R1_001.fastq.gz, TS5_R2_001.fastq.gz, TS5_R1_001.fastq.gz.md5, TS5_R2_001.fastq.gz.md5, TS5.counts.txt)

PD line 2 TNFalpha+IL-1beta (TS11_R1_001.fastq.gz, TS11_R2_001.fastq.gz, TS11_R1_001.fastq.gz.md5, TS11_R2_001.fastq.gz.md5, TS11.counts.txt)

PD line 2 TNFalpha (TS17_R1_001.fastq.gz, TS17_R2_001.fastq.gz, TS17_R1_001.fastq.gz.md5, TS17_R2_001.fastq.gz.md5, TS17.counts.txt)
description: Line information



Genotype: LRRK2 G2019S

Reference: Holmqvist et al. 2016


Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments



Nonexposed (TS5)

4 h TNFalpha+IL-1beta exposed (TS11)

4 h TNFalpha exposed (TS17)


RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
DOI: 10.5281/zenodo.10837071
title: Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line PD3)

description: Data repository for publication: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (PD line 3)
description: The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

PD line 3: (TS6_R1_001.fastq.gz, TS6_R2_001.fastq.gz, TS6_R1_001.fastq.gz.md5, TS6_R2_001.fastq.gz.md5, TS6.counts.txt)

PD line 3 TNFalpha+IL-1beta (TS12_R1_001.fastq.gz, TS12_R2_001.fastq.gz, TS12_R1_001.fastq.gz.md5, TS12_R2_001.fastq.gz.md5, TS12.counts.txt)

PD line 3 TNFalpha (TS18_R1_001.fastq.gz, TS18_R2_001.fastq.gz, TS18_R1_001.fastq.gz.md5, TS18_R2_001.fastq.gz.md5, TS18.counts.txt)
description: Line information



Genotype: LRRK2 G2019S

Reference: Holmqvist et al. 2016


Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments



Nonexposed (TS6)

4 h TNFalpha+IL-1beta exposed (TS12)

4 h TNFalpha exposed (TS18)


RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
DOI: 10.5281/zenodo.10837072
title: Data Repository: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (line PD3)

description: Data repository for publication: LRRK2 G2019S mutation affects human iPSC-derived endothelial cells (PD line 3)
description: The blood-brain barrier (BBB) serves as an interface between the periphery and central nervous system. It limits the movement of molecules and immune cells, regulates the entry of nutrients, and removes waste products from the brain. The dysfunction of the BBB has been identified in Parkinson´s disease (PD) but the role of the BBB and endothelial cells (ECs) has not been well studied. LRRK2 G2019S mutation is the most common PD causing mutation with similar pathophysiology than in sporadic cases. How the mutation affects EC function has not been investigated previously in patient’s cells. In the study, we used iPSC-derived ECs from PD patients with the LRRK2 mutation as well as cells from healthy individuals. We report that PD ECs have higher levels of α-synuclein, altered mitochondrial respiration and response to inflammatory exposure, especially to TNFα. In addition, transcriptomic analysis showed upregulation of fatty acid synthesis related pathways in PD ECs and downregulation of lncRNA MEG3, both of which have been associated with PD. Altogether, PD ECs manifest some of the PD related hallmarks and are likely to contribute to the pathogenesis of PD.
description: RNA sequencing of human induced pluripotent stem cell (hiPSC) derived endothelial cells (ECs).

raw data files (.fastq.gz), processed data files (.txt), MD5 files for raw data (.md5)

PD line 3: (TS6_R1_001.fastq.gz, TS6_R2_001.fastq.gz, TS6_R1_001.fastq.gz.md5, TS6_R2_001.fastq.gz.md5, TS6.counts.txt)

PD line 3 TNFalpha+IL-1beta (TS12_R1_001.fastq.gz, TS12_R2_001.fastq.gz, TS12_R1_001.fastq.gz.md5, TS12_R2_001.fastq.gz.md5, TS12.counts.txt)

PD line 3 TNFalpha (TS18_R1_001.fastq.gz, TS18_R2_001.fastq.gz, TS18_R1_001.fastq.gz.md5, TS18_R2_001.fastq.gz.md5, TS18.counts.txt)
description: Line information



Genotype: LRRK2 G2019S

Reference: Holmqvist et al. 2016


Cell culturing: hiPSCs were cultured in matrigel (Corning) coated dishes in E8 (Gibco) media. EC were differentiated according to previously published protocol (Harding et al. 2017).

Treatments



Nonexposed (TS6)

4 h TNFalpha+IL-1beta exposed (TS12)

4 h TNFalpha exposed (TS18)


RNA sequencing: Cells were lysed on ice (Buffer RLT + β-mercaptoethanol 10 µl/ml), and RNA was extracted directly after lysis with the Qiagen RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen). 1-4 µg of RNA were sent for library preparation and sequencing (performed by Azenta). Quality was evaluated with FastQC, and sequencing was done with Illumina NovaSeq, PE 2x150. Sequence reads were trimmed by using Trimmomatic v.0.36 to remove possible adaptor sequences and nucleotides of poor quality. Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
DOI: 10.6084/m9.figshare.25435927
title: Formononetin alleviate myocardial no reflow through antioxi-dant by affecting metabolites to regulate gut microbiota- electrocardiogram

description: Formononetin alleviate myocardial no reflow through antioxi-dant by affecting metabolites to regulate gut microbiota- electrocardiogram.
DOI: 10.6084/m9.figshare.25435927.v1
title: Formononetin alleviate myocardial no reflow through antioxi-dant by affecting metabolites to regulate gut microbiota- electrocardiogram

description: Formononetin alleviate myocardial no reflow through antioxi-dant by affecting metabolites to regulate gut microbiota- electrocardiogram.
DOI: 10.6084/m9.figshare.25436062
title: HIV64148 source code

description: Archived code as at time of publication.
DOI: 10.6084/m9.figshare.25436062.v1
title: HIV64148 source code

description: Archived code as at time of publication.
DOI: 10.17871/try.99
title: Weeds and crops leaf C,N,S content

description: Leaf Nitrogen, Carbon and Sulfur content from weeds and crops (wheat, barley, oilseed rape, pea) growing in an agronomical experiment in NE France
Taxonomic coverage: 	Poacea, Fabaceae, Brassicaceae, Polygonaceae, Asteraceae, Chenopodiaceae, Convolvulaceae, Rubiaceae
Field list: 	Species, Latitude, Longitude, Altitude, Sampling date, Exposition, Health status, Physiological leaf age, Canopy position, surface, SLA, LDMC, LNC, LCC, LSC, C/N, C/S, Comment
DOI: 10.14473/csda/bj3qnn/2cac63
title: 09_JC kraj - volby do PS 2013_data_opr.tab

description: Data_CSDA00189
DOI: 10.14473/csda/bj3qnn/laqrjw
title: OM_CSDA00181-CSDA00194.pdf

description: Ostatní materiály_CSDA00181-CSDA00194
DOI: 10.14473/csda/bj3qnn/hnwxhn
title: TI_CSDA00181-CSDA00194.pdf

description: Technická informace_CSDA00181-CSDA00194
DOI: 10.7925/drs1.duchas_4922026
title: Pallaskenry

description: A collection of folklore and local history stories from Pallaskenry (school) (Pallaskenry, Co. Limerick), collected as part of the Schools' Folklore Scheme, 1937-1938 under the supervision of teacher Tomás Midheach.
description: Weather-Lore / Barry, John -- Local Heroes / Barry, John -- Local Ruins / Barry, John -- Local Happenings / Fitzgerald, William -- Food in Olden Times / Barry, John -- Local Graveyards / Barry, John -- Festival Customs / Barry, John -- My Home District / Barry, John -- Potato Crop / Barry, John -- Local Fairs / Barry, John -- Local Place Names / Barry, John -- Local Cures / Fitzgerald, Mary -- Old Cures / Slattery, Jeremiah -- Great Storms / Staff, Nora -- Old Schools / Staff, Nora -- Thatcher / Fitzgerald, Mary -- Fairy Forts / Rourke, Minnie O -- Landlords / Fitzgerald, Mary
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4922027
title: Shountrade, Adare

description: A collection of folklore and local history stories from Shountrade, Adare (school) (Shantraud, Co. Limerick), collected as part of the Schools' Folklore Scheme, 1937-1938 under the supervision of teacher Máire, Bean Uí Fhloinn.
description: Creagán na hOla Graveyard in the Parish of Adare / Murphy, Kitty -- How Creagán na hOla Got Its Name / Murphy, Kitty -- Creagán na hOla / Hickey, Mary -- Desmonds' Castle, Adare / Hickey, Mary -- St Brigid's Well / Fennell, Brigid -- My School District - Shountrade / Fennell, Brigid -- Seanbheann, Rour, Adare / Monckton, Mary -- Old Relic of the Fenian Movement of '67 / Monckton, Mary -- Giants of Knockfierna / Monckton, Mary -- Croppies / Monckton, Kathryn -- Dead by Night / Kinevane, Annie -- Tale of the Locality / Kinevane, Annie -- Old Protestant Church of Croagh / Kinevane, Annie -- Men Executed in Adare in 1821 / Bourke, Kitty -- Dead Hunt, Tuogh, Adare / Fennell, Brigid -- Ghost of Arban, Ardare / Dillon, Chrissie -- Protestant Church of Croagh / Conway, Nora -- Ghost of Ardban / Fennell, Brigid -- Old School of Shountrade / Dillon, Chrissie -- St James' Well, Croagh / Browne, Nora -- Knockfierna - The Hill of the Fairies / Browne, Nora -- Tale of Local Whiteboys / Browne, Nora -- Battle between the Fairies of Clare and Limerick / Fennell, Thomas -- Interesting Finds in the Locality / Bourke, Mary -- Soup-Houses of 1820 / Bourke, Stephen -- Tale of the Bruíon Caorthainn / Bourke, Stephen -- Some Incidents in the District Connected with '67 Rising / Bourke, Stephen -- Fairy Wind / Monckton, Kathryn -- Magic Saddle / Nash, Peggy -- Another Story of the Sean Bheann / Mahon, Thomas Mc -- Kilnockan Forth / Mahon, Thomas Mc -- Potato and Its Message / Kinevane, Annie -- Lios na Muc in the District of Shountrade / Bourke, Mary -- Ballinvira Holy Well Croagh / Bourke, Mary -- Deeper You Dig the More You Find / Monckton, Kathryn -- Ghost of Clorane / Fennell, Brigid -- Haunted House at Adare / Bourke, Mary -- Kilnockan Fort / Fennell, Brigid -- Dolmens in the Locality / Kinevane, Annie -- De Veres of Curragh Chase / Bourke, Mary -- Franciscan Abbey Adare and Tradition Connected with It / Bourke, Mary -- Some Facts Connected with the Village of Adare / Bourke, Mary -- Scourge of Landlordism in Rour Mor and Tuagh in the Parish of Adare / Mahon, Thomas Mc -- Dead Hunt in Tuogh / Mahon, Thomas Mc -- Tale of the Copey Wood in the Parish of Adare / Mahon, Thomas Mc -- Some Facts Connecting with the Village of Adare / Mahon, Thomas Mc -- Clonshire House / Bourke, Stephen
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4922029
title: Áth Dara (C.)

description: A collection of folklore and local history stories from Áth Dara (C.) (school) (Adare, Co. Limerick), collected as part of the Schools' Folklore Scheme, 1937-1938 under the supervision of teacher Máire Boardman.
description: Adare National School - List of Irish Words and Phrases that Have Been Adopted into the Popular English Speech of the District -- Adare - 1798 -- Legend of St Patrick / #missing, -- Local History -- Weather-Lore -- Local Superstitions -- Local Handicrafts -- Nail Manufacture -- Boot Manufacture -- Drinking Vessels -- Rush Lights and Dip Candles -- Local Superstitions -- Old Irish Sayings -- Old Proverbs -- True Fairy Story / Long, Ruby -- Wedding Customs -- Funeral Customs -- Birth Customs -- Old Story / Knott, David G. -- Bird-Lore -- Festival Customs - Hallow Eve Customs / Alfred, Kitty -- Festival Customs - Christmas Eve Customs / Alfred, Clarrie -- Festival Customs - Christmas Day Customs / Ruttle, Mary -- Festival Customs - St Stephen's Day / Knott, David G. -- Festival Customs - New Year's Eve and New Years Day / Chamberlain, James -- Festival Customs - Epiphany / Miller, Phyllis -- Festival Customs - St Brighid's Day / Shine, Olive -- Festival Customs - Candlemas Day / Alfred, Kitty -- Festival Customs - Shrove Tuesday / Alfred, Clarrie -- Festival Customs - Ash Wednesday / Knott, David G. -- Festival Customs - St Patrick's Day / Miller, Phyllis -- Festival Customs - Palm Sunday / Miller, Phyllis -- Festival Customs - Holy Week / Shine, Olive -- Festival Customs - May Day / Alfred, Clarrie -- Festival Customs - Midsummer Day / Miller, Patricia -- Festival Customs - St Swinthin's Day / Miller, Patricia -- Festival Customs - Lady Day in August / Miller, Patricia -- Festival Customs - St Martin's Day / Alfred, Kitty
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4922030
title: Bánóg

description: A collection of folklore and local history stories from Bánóg (school) (Banoge, Co. Limerick), collected as part of the Schools' Folklore Scheme, 1937-1938 under the supervision of teacher Pádraig Ó Riordáin.
description: Hidden Treasure - Crag an Óir -- Funny Stories -- Funny Stories -- Riddles -- Weather-Lore -- Old Crafts -- Penal Times -- Place Names -- Travelling Folk -- Place Names -- Famine Times -- Potato Crop -- The Care of our Farm Animals -- My Home District -- Local Ruins -- Old Customs -- Nature -- Riddles -- There is an old man, aged 72 years in the district who takes a few 'jars' (drinks) as he says himself. -- If my mother was milking a heifer that would be inclined to kick with her right hind leg... / Kelly, Dan -- My mother also says Gráidhín and Gráidhín chroidhe when milking a young cow... / Kelly, Dan -- Ghost Story -- Shee-geehe -- 'You should never open an umbrella inside a house.' -- 'You should never carry a spade or fork or any other implement into or out of a house.' -- When you hear or see the whirlwind you should through up a piece of grass or hay... -- Matchmaking -- Old Cures -- Marriage Customs -- Old Story
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4927877
title: Old Crafts and Craftsmen

description: Story collected by a student at Dún Gar (Frenchpark) school (Frenchpark, Co. Roscommon) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Tomás Mac Mághnuis.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.