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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Ground Control, Root Rep. 3 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517005","a100001samplename":"GSM2517005","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0009005\" title=\"Commonly thought of as one of the three basic parts of the seed plant body. 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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Spaceflight, Root Rep. 1 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517006","a100001samplename":"GSM2517006","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0009005\" title=\"Commonly thought of as one of the three basic parts of the seed plant body. 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The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Ground Control, Leaf Rep. 2 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517010","a100001samplename":"GSM2517010","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0025034\" title=\"A phyllome (PO:0006001) that is not associated with a reproductive structure. hoja (Spanish), \u8449 (Japanese)\" source=\"PAE\">leaf </a>","a100011factorvaluespaceflight":"Ground Control ","a100014characteristicsmaterialtype":"leaf","a100015protocolref":"growth protocol","a100016parametervaluelightsource":"<a target=\"_blank\" href=\"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C49923\" title=\"A type of diode designed to emit light when a current passes through it. 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The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Ground Control, Leaf Rep. 3 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517011","a100001samplename":"GSM2517011","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0025034\" title=\"A phyllome (PO:0006001) that is not associated with a reproductive structure. hoja (Spanish), \u8449 (Japanese)\" source=\"PAE\">leaf </a>","a100011factorvaluespaceflight":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D013026\" title=\"Travel beyond the earth&#x27;s atmosphere. 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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Spaceflight, Leaf Rep. 1 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517012","a100001samplename":"GSM2517012","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0025034\" title=\"A phyllome (PO:0006001) that is not associated with a reproductive structure. hoja (Spanish), \u8449 (Japanese)\" source=\"PAE\">leaf </a>","a100011factorvaluespaceflight":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D013026\" title=\"Travel beyond the earth&#x27;s atmosphere. 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The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Spaceflight, Leaf Rep. 2 [BS]","a100048commentoriginalsubmittedsamplename":"Not applicable "},{"a100000sourcename":"GSM2517013","a100001samplename":"GSM2517013","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0025034\" title=\"A phyllome (PO:0006001) that is not associated with a reproductive structure. hoja (Spanish), \u8449 (Japanese)\" source=\"PAE\">leaf </a>","a100011factorvaluespaceflight":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D013026\" title=\"Travel beyond the earth&#x27;s atmosphere. 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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. 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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. 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A plant stucture that is usually underground and does not bear leaves and only rarely shoots, is usually more or less positively geotropic, is endogenous in origin, indeterminate in growth and often with secondary thickening. A plant axis (PO:0025004) that is part of a root system (PO:0025025). radices, \u6839 (Japanese), radix, ra&amp;#237z (Spanish), climbing root, aerial root\" source=\"PAE\">root </a>","a100011factorvaluespaceflight":"<a target=\"_blank\" href=\"http://purl.bioontology.org/ontology/MESH/D013026\" title=\"Travel beyond the earth&#x27;s atmosphere. Space Travels\" source=\"MESH\">Space Flight </a>","a100014characteristicsmaterialtype":"root","a100015protocolref":"growth protocol","a100016parametervaluelightsource":"<a target=\"_blank\" href=\"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C49923\" title=\"A type of diode designed to emit light when a current passes through it. 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The centigrade scale has its zero at 273.15 K.&quot; [NIST:NIST] C\" source=\"UO\">-80 degree Celsius</a>","a100046commentseedsource":"ABRC stock CS915 (www.arabidopsis.org)","a100047commentsamplenamenotes":"Spaceflight, Root Rep. 1","a100048commentoriginalsubmittedsamplename":"GSM2516797 "},{"a100000sourcename":"Atha_Ws_root_FLT_Rep2","a100001samplename":"Atha_Ws_root_FLT_Rep2","a100002characteristicsorganism":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/NCBITaxon_3702\" title=\"thale-cress, mouse-ear cress, Arbisopsis thaliana, thale cress, Arabidopsis thaliana (thale cress)\" source=\"EFO\">Arabidopsis thaliana </a>","a100005characteristicsecotype":"<a target=\"_blank\" href=\"http://www.ebi.ac.uk/efo/EFO_0005156\" title=\"Wassilewskija is an Arabidopsis ecotype.\" source=\"CCONT\">Wassilewskija ecotype </a>","a100008factorvalueorganismpart":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/PO_0009005\" title=\"Commonly thought of as one of the three basic parts of the seed plant body. 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RNALater\" source=\"NCIT\">RNAlater </a>","a100042parametervaluesamplestoragetemperature":"<a target=\"_blank\" href=\"http://purl.obolibrary.org/obo/UO_0000027\" title=\"&quot;A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. 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The authors also thank the APEX-03-2 support team at Kennedy Space Center, and the on-obit operations and expertise of astronaut Butch Wilmore."},{"name":"DOI","value":"10.26030/f05z-e688"},{"name":"Data Source Accession","value":"GSE95646"},{"name":"Data Source Link","value":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95646"},{"name":"Experiment Platform","value":"Vegetable Production System (VPS/Veggie)"},{"name":"Flight Program","value":"International Space Station (ISS)"},{"name":"Funding","value":"This work was funded by grants NNX12AN69G and NNX14AT24G to RF and AP from NASA Space Life and Physical Sciences, managed through Kennedy Space Center."},{"name":"Identifiers","value":""},{"name":"Managing NASA Center","value":"Kennedy Space Center (KSC)"},{"name":"Mission End","value":"11-Feb-2015"},{"name":"Mission Link","value":"https://lsda.jsc.nasa.gov/Mission/miss/1370"},{"name":"Mission Name","value":"SpaceX-5"},{"name":"Mission Start","value":"10-Jan-2015"},{"name":"Project Identifier","value":""},{"name":"Project Link","value":"https://lsda.jsc.nasa.gov/Experiment/exper/13840"},{"name":"Project Title","value":"Molecular Biology of Growth and Cell Remodeling within the Spaceflight Environment"},{"name":"Project Type","value":"Spaceflight Study"},{"name":"Space Program","value":"NASA"},{"name":"Study Grant Number","value":""}],"description":"When germinated and grown on-board the ISS (International Space Station), plant do not exhibit abnormal structures but they do have altered growth habits and this project aims to investigate the molecular mechanisms that provide the foundation for the altered growth habits observed in orbit. 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Between 100-250 ng of this material was used for Illumina sequencing library construction using the NEBnext Ultra DNA Illumina construction kit (Cat# E7370S, NEB) in conjunction with Illumina-specific methylated and barcoded adaptors (Cat# E7535S, NEB) from the same source. This particular library construction kit was chosen because it contains reagents that have been optimized for relatively low-input DNA in the library construction process. At the end of the end-repair, 3'-adenylation, and adaptor-ligation steps, 75-150 ng of clean, adaptor-ligated DNA fragments (Illumina library) were recovered in Tris-HCl, pH 8.0. It should be noted that the libraries were not PCR-amplified at this stage, as it would normally be done in the most typical Illumina library construction protocol. Libraries were quantitated using a QUBIT fluorometer (Life Technologies).Illumina libraries (containing methylated adaptors) were subjected to sodium bisulfite treatment using the EZ DNA Methylation Direct kit (ZYMO Research, Cat #D5020) according to the manufacturer's instructions. The resulting libraries were enriched by a 13-15 cycle amplification using an uracil-insensitive polymerase (EpiMark hot start Taq polymerase, NEB, Cat#M0490S). The amplified library products were separated on a 2% agarose gel from which library fragments in the 250-500 bp range were excised (QIAquick gel extraction kit, Cat# 28704, QIAGEN) and AMPure purified (Cat# A63881, Beckman Coulter). Gel staining was done with SYBR safe (Life Technologies) and visualized on a blue light transilluminator (Life Technologies) in order to avoid UV damage of DNA. The final libraries were quantitated by the QUBIT fluorometer, and by qPCR with the Kapa SYBR Fast qPCR reagents (Cat# KK4824, Kapa Biosystems) with monitoring on an ABI7900HT real-time PCR system (LifeTechnologies). The average library size was 350 bp. In preparation for sequencing on the HiSeq3000 Illumina sequencer, barcoded libraries were normalized to 2.5 nM and pooled (equimolarly). Up to 6 samples were pooled for sequencing on a single HiSeq3000 flow cell lane, using a 2x101 cycle multiplex, paired-end configuration. Typically, the PhiX library is used for a spike-in (at 20%) in order to correct for the low base diversity of bisulfite-converted genomic libraries. Alternatively, bisulfite-converted libraries were sequenced alongside RNA-seq libraries (60%:40% ratio of RNA-seq vs Bisulfite-converted libraries), without a PhiX spike-in. Library pools were processed according the Illumina protocol (HiSeq3000) for clustering on the cBOT machine. The final pool concentration for clustering was 0.25 nM, following denaturation, neutralization, and mixing with the ExAmp reagent.","name":"Bisulfite-Seq library construction","parameters":[{"@id":"#140424987571056","parameterName":{"@id":"yMlcs211WCEcGEHzemgRoKGcDTBqNdphSogqkFTH","annotationValue":"library strategy","comments":[],"termAccession":"","termSource":""}},{"@id":"#140424987572544","parameterName":{"@id":"4a5FiDbDQsdVjo0pSH9bDjaOpun5U1omQLtGKcSM","annotationValue":"library selection","comments":[],"termAccession":"","termSource":""}},{"@id":"#140424987573024","parameterName":{"@id":"IGq9rbNXpEWfC8vEpombTe2NvK8MUiWnl5X0tOmQ","annotationValue":"library layout","comments":[],"termAccession":"","termSource":""}}],"protocolType":{"@id":"H95EZHIeDCnH0crlNn20OQAkQ0J2YeXug6ap62U3","annotationValue":"Bisulfite-Seq library construction","comments":[],"termAccession":"","termSource":""},"uri":"","version":""},{"@id":"#140424987570864","comments":[],"components":[],"description":"DNA was extracted using a modified phenol/chloroform protocol as previously described [105], as residual components from the RNAlater preservation interfered with spin-column based gDNA kits. 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