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864 rows where devstage_curation = "Undetermined" and tissue_curation_coarse = "Nervous System"

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experiment.library_selection 6

devstage_curation_coarse 5

tissue_curation 3

experiment.platform 3

experiment.library_strategy 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Nervous System · 864 ✖

devstage_curation 1

  • Undetermined · 864 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
38 38 DRR408248 DRX393854 DRS407179 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 3 zebrafish ENCDC replicate 3 SAMD00529468   sample name:zebrafish ENCDC replicate 3|biological replicate:enteric neural crest derived cells 3|strain:Tgsox10:cre; EF3alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529468 DRX393854 190326ENvsNC N706 5day;NeuralCrestDerivedCell;rep3 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529468       3803721121.0 24526633.0 DRR408248 0:77.54 1:77.54 A:999106107;C:897663781;G:921501114;T:979486853;N:5963266 77 77     999106107 897663781 921501114 979486853 5963266 DRX393854 DRS407179 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
39 39 DRR408247 DRX393853 DRS407178 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 2 zebrafish ENCDC replicate 2 SAMD00529467   sample name:zebrafish ENCDC replicate 2|biological replicate:enteric neural crest derived cells 2|strain:Tgsox10:cre; EF2alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529467 DRX393853 190326ENvsNC N705 5day;NeuralCrestDerivedCell;rep2 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529467       3436798274.0 22156202.0 DRR408247 0:77.56 1:77.56 A:900848174;C:812031426;G:832960423;T:885671203;N:5287048 77 77     900848174 812031426 832960423 885671203 5287048 DRX393853 DRS407178 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
40 40 DRR408246 DRX393852 DRS407177 DRP012042 PRJDB14275 Zebrafish EN/ENCDC RNA seq DRP012042 Transcriptome Analysis A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs and isolated GFP+ ENs and dsRed+ ENCDCs. Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.     zebrafish 5 day DsRed positive enteric neural crest derived cells replicate 1 zebrafish ENCDC replicate 1 SAMD00529466   sample name:zebrafish ENCDC replicate 1|biological replicate:enteric neural crest derived cells 1|strain:Tgsox10:cre; EF1alpha:loxP gfp loxP dsred                 NextSeq 550 paired end sequencing of SAMD00529466 DRX393852 190326ENvsNC N704 5day;NeuralCrestDerivedCell;rep1 1 1   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP012042 NextSeq 550 paired end sequencing of SAMD00529466       3582073512.0 23135170.0 DRR408246 0:77.41 1:77.42 A:943152815;C:841972211;G:863627245;T:927361159;N:5960082 77 77     943152815 841972211 863627245 927361159 5960082 DRX393852 DRS407177 DRA014886 NIBB|NIBB core research facilities, National Institute for Basic Biology University of Hyogo                       B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Japan 2024-09-22 Undetermined Larval Brain Nervous System
147 147 DRR051067 DRX045959 DRS057267 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as h62A GFP plus Tel GFP cells from telencephalon of hspGFF62A;UAS:GFP transgenic zebrafish SAMD00044994   sample name:h62A GFP minus Tel|tissue type:brain|genotype:hspGFF62A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044994 DRX045959 h62A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v3 > Library prep : Illumina Nextera XT DNA Library Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044994       17913873600.0 89569368.0 DRR051067 0:100 1:100 A:5009629866;C:3957379257;G:3797879751;T:5144366288;N:4618438 100 100     5009629866 3957379257 3797879751 5144366288 4618438 DRX045959 DRS057267 DRA004277 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89075 0.89087 0.23044 0.23295 0.69493 0.69769 0.5366 0.54852 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified nextera bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
151 151 DRR051063 DRX045955 DRS057266 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.     These cells are from the same fish as 120A GFP plus Tel GFP cells from telencephalon of SAGFFLF120A;UAS:GFP transgenic zebrafish SAMD00044987   sample name:120A GFP minus Tel|tissue type:brain|genotype:SAGFFLF120A;UAS:GFP                 Illumina HiSeq 2500 paired end sequencing of SAMD00044987 DRX045955 120A GFP minus Tel 1 cDNA synthesis : clontech SMARTer v2 > Library prep : Illumina TrunSeq DNA Sample Preparation Kits   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 2500 paired end sequencing of SAMD00044987       15411400120.0 76294060.0 DRR051063 0:101 1:101 A:4583085286;C:3082552426;G:3134669086;T:4606055524;N:5037798 101 101     4583085286 3082552426 3134669086 4606055524 5037798 DRX045955 DRS057266 DRA004273 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 2 0.89184 0.8842 0.30246 0.30334 0.69232 0.705 0.52824 0.51492 101 101 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   Japan 2018-01-06 Undetermined Undetermined Brain Nervous System
8076 8076 ERR2304209 ERX2355537 ERS2201745 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged mutant biorep3 SAMEA104590463 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590463|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep3|common name:zebrafish|sample name:Aged mutant biorep3                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 12 9 psen1K97Gfshet 24mth 13 03 2014 S3 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 9_psen1K97Gfshet_24mth_13_03_2014_S3_fem_R1.fastq.gz 9_psen1K97Gfshet_24mth_13_03_2014_S3_fem_R2.fastq.gz fastq fastq 9318039088.0 38360343.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 12 0:121.17 1:121.74 A:2583644589;C:2091813317;G:2105322994;T:2536795040;N:463148 121 121     2583644589 2091813317 2105322994 2536795040 463148 ERX2355537 ERS2201745 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.93003 0.92836 0.26254 0.26157 0.68992 0.69593 0.48246 0.48292 134 134 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8077 8077 ERR2304208 ERX2355536 ERS2201744 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged mutant biorep2 SAMEA104590462 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590462|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep2|common name:zebrafish|sample name:Aged mutant biorep2                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 11 8 psen1K97Gfshet 24mth 13 03 2014 S2 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 8_psen1K97Gfshet_24mth_13_03_2014_S2_fem_R1.fastq.gz 8_psen1K97Gfshet_24mth_13_03_2014_S2_fem_R2.fastq.gz fastq fastq 8559244581.0 35608377.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 11 0:119.87 1:120.50 A:2397336730;C:1892236963;G:1910506310;T:2358778868;N:385710 119 120     2397336730 1892236963 1910506310 2358778868 385710 ERX2355536 ERS2201744 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92422 0.92311 0.30514 0.30437 0.69578 0.7008 0.49054 0.48857 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8078 8078 ERR2304207 ERX2355535 ERS2201743 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged mutant biorep1 SAMEA104590461 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590461|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged mutant biorep1|common name:zebrafish|sample name:Aged mutant biorep1                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 10 7 psen1K97Gfshet 24mth 13 03 2014 S1 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 7_psen1K97Gfshet_24mth_13_03_2014_S1_fem_R1.fastq.gz 7_psen1K97Gfshet_24mth_13_03_2014_S1_fem_R2.fastq.gz fastq fastq 6521711648.0 27182062.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 10 0:119.65 1:120.27 A:1831722484;C:1434689482;G:1449266189;T:1805677755;N:355738 119 120     1831722484 1434689482 1449266189 1805677755 355738 ERX2355535 ERS2201743 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92564 0.92498 0.29344 0.29212 0.69327 0.69964 0.48557 0.48942 86 86 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8079 8079 ERR2304206 ERX2355534 ERS2201742 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged wild type biorep3 SAMEA104590460 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590460|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep3|common name:zebrafish|sample name:Aged wild type biorep3                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 9 3 non mutant K97Gfs 24mth 13 03 2014 S3 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 3_non_mutant_K97Gfs_24mth_13_03_2014_S3_fem_R1.fastq.gz 3_non_mutant_K97Gfs_24mth_13_03_2014_S3_fem_R2.fastq.gz fastq fastq 6865452019.0 28646225.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 9 0:119.50 1:120.16 A:1903309108;C:1535570672;G:1550661363;T:1875578941;N:331935 119 120     1903309108 1535570672 1550661363 1875578941 331935 ERX2355534 ERS2201742 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92997 0.92904 0.26949 0.26497 0.69485 0.70072 0.49378 0.50075 96 96 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8080 8080 ERR2304205 ERX2355533 ERS2201741 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged wild type biorep2 SAMEA104590459 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590459|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep2|common name:zebrafish|sample name:Aged wild type biorep2                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 8 2 non mutant K97Gfs 24mth 13 03 2014 S2 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 2_non_mutant_K97Gfs_24mth_13_03_2014_S2_fem_R1.fastq.gz 2_non_mutant_K97Gfs_24mth_13_03_2014_S2_fem_R2.fastq.gz fastq fastq 8418868343.0 34905186.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 8 0:120.29 1:120.91 A:2334515884;C:1885784857;G:1900432559;T:2297775998;N:359045 120 120     2334515884 1885784857 1900432559 2297775998 359045 ERX2355533 ERS2201741 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.93078 0.92967 0.25478 0.25365 0.69372 0.69938 0.4988 0.49709 132 132 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8081 8081 ERR2304204 ERX2355532 ERS2201740 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Aged wild type biorep1 SAMEA104590458 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590458|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Aged wild type biorep1|common name:zebrafish|sample name:Aged wild type biorep1                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 7 1 non mutant K97Gfs 24mth 13 03 2014 S1 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 1_non_mutant_K97Gfs_24mth_13_03_2014_S1_fem_R1.fastq.gz 1_non_mutant_K97Gfs_24mth_13_03_2014_S1_fem_R2.fastq.gz fastq fastq 6628468736.0 27477727.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 7 0:120.31 1:120.92 A:1839014115;C:1487750495;G:1497160978;T:1804205119;N:338029 120 120     1839014115 1487750495 1497160978 1804205119 338029 ERX2355532 ERS2201740 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92916 0.92783 0.28453 0.28375 0.69798 0.70289 0.48132 0.48227 125 125 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8082 8082 ERR2304203 ERX2355531 ERS2201739 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young mutant biorep3 SAMEA104590457 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590457|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep3|common name:zebrafish|sample name:Young mutant biorep3                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 6 12 psen1K97Gfshet 6mth 10 03 2016 S3 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 12_psen1K97Gfshet_6mth_10_03_2016_S3_fem_R1.fastq.gz 12_psen1K97Gfshet_6mth_10_03_2016_S3_fem_R2.fastq.gz fastq fastq 11485397100.0 38284657.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 6 0:150 1:150 A:3206707597;C:2539306860;G:2721427816;T:3015264084;N:2690743 150 150     3206707597 2539306860 2721427816 3015264084 2690743 ERX2355531 ERS2201739 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92853 0.92813 0.26757 0.26433 0.68487 0.68903 0.47708 0.47074 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8083 8083 ERR2304202 ERX2355530 ERS2201738 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young mutant biorep2 SAMEA104590456 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590456|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep2|common name:zebrafish|sample name:Young mutant biorep2                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 5 11 psen1K97Gfshet 6mth 10 03 2016 S2 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 11_psen1K97Gfshet_6mth_10_03_2016_S2_fem_R1.fastq.gz 11_psen1K97Gfshet_6mth_10_03_2016_S2_fem_R2.fastq.gz fastq fastq 13258122000.0 44193740.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 5 0:150 1:150 A:3781076311;C:2868334319;G:3063279426;T:3542309854;N:3122090 150 150     3781076311 2868334319 3063279426 3542309854 3122090 ERX2355530 ERS2201738 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.91552 0.91659 0.32337 0.32168 0.69546 0.698 0.4697 0.47295 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8084 8084 ERR2304201 ERX2355529 ERS2201737 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young mutant biorep1 SAMEA104590455 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590455|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young mutant biorep1|common name:zebrafish|sample name:Young mutant biorep1                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 4 10 psen1K97Gfshet 6mth 10 03 2016 S1 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 10_psen1K97Gfshet_6mth_10_03_2016_S1_fem_R1.fastq.gz 10_psen1K97Gfshet_6mth_10_03_2016_S1_fem_R2.fastq.gz fastq fastq 11724649800.0 39082166.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 4 0:150 1:150 A:3304100658;C:2560616667;G:2779636286;T:3077545106;N:2751083 150 150     3304100658 2560616667 2779636286 3077545106 2751083 ERX2355529 ERS2201737 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.92121 0.91893 0.28263 0.27928 0.69073 0.6953 0.47174 0.46157 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8085 8085 ERR2304200 ERX2355528 ERS2201736 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young wild type biorep3 SAMEA104590454 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590454|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep3|common name:zebrafish|sample name:Young wild type biorep3                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 3 6 non mutant K97Gfs 6mth 10 03 2016 S3 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R1.fastq.gz 6_non_mutant_K97Gfs_6mth_10_03_2016_S3_fem_R2.fastq.gz fastq fastq 24923212200.0 83077374.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 3 0:150 1:150 A:7077378299;C:5398402396;G:5838059014;T:6604505033;N:4867458 150 150     7077378299 5398402396 5838059014 6604505033 4867458 ERX2355528 ERS2201736 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.91973 0.92144 0.29148 0.29015 0.69587 0.69994 0.46145 0.47047 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8086 8086 ERR2304199 ERX2355527 ERS2201735 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young wild type biorep2 SAMEA104590453 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590453|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep2|common name:zebrafish|sample name:Young wild type biorep2                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 2 5 non mutant K97Gfs 6mth 10 03 2016 S2 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R1.fastq.gz 5_non_mutant_K97Gfs_6mth_10_03_2016_S2_fem_R2.fastq.gz fastq fastq 7840317153.0 39006553.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 2 0:101 1:100 A:2200490653;C:1718458832;G:1730278863;T:2188900320;N:2188485 101 100     2200490653 1718458832 1730278863 2188900320 2188485 ERX2355527 ERS2201735 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.91783 0.91983 0.32092 0.32105 0.67714 0.67691 0.47312 0.47481 101 100 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
8087 8087 ERR2304198 ERX2355526 ERS2201734 ERP106721 PRJEB24858 Zebrafish modelling familialAlzheimer's disease using heterozygous K97fs mutation in locus psen1 ena-STUDY-Adelaide Bioinformatics Hub-08-02-2018-04:47:34:743-1099 Other RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from the whole brains of mutant and wild type zebrafish when they were either 6 mpf young adult or 24 mpf infertile adult. Mutant zebrafish possess a heterozygous K97fs mutation at the endogenous zebrafish psen1 locus while wild type zebrafish do not. ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 02 08     Young wild type biorep1 SAMEA104590452 Adelaide Bioinformatics Hub ENA first public:2018 05 11|ENA last update:2018 02 14|External Id:SAMEA104590452|INSDC center alias:Adelaide Bioinformatics Hub|INSDC center name:Adelaide Bioinformatics Hub|INSDC first public:2018 05 11T17:03:03Z|INSDC last update:2018 02 14T06:16:03Z|INSDC status:public|Submitter Id:Young wild type biorep1|common name:zebrafish|sample name:Young wild type biorep1                 NextSeq 500 paired end sequencing ena EXPERIMENT Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 1 4 non mutant K97Gfs 6mth 10 03 2016 S1 fem RNA seq analysis of whole brains from zebrafish possessing a heterozygous K97fs mutation in psen1 to model familial Alzheimer's disease Total RNA was extracted from whole brains using the mirVana miRNA isolation kit ThermoFisher using the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA NextSeq 500   ERP106721 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 05 11|ENA LAST UPDATE:2018 11 16 4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R1.fastq.gz 4_non_mutant_K97Gfs_6mth_10_03_2016_S1_fem_R2.fastq.gz fastq fastq 13910901600.0 46369672.0 ena RUN Adelaide Bioinformatics Hub 15 02 2018 04:44:34:534 1 0:150 1:150 A:3994738757;C:2957179645;G:3191379676;T:3764325893;N:3277629 150 150     3994738757 2957179645 3191379676 3764325893 3277629 ERX2355526 ERS2201734 ERA1210082 Adelaide Bioinformatics Hub|European Nucleotide Archive Adelaide Bioinformatics Hub 2 0.91399 0.9166 0.3202 0.31818 0.6942 0.698 0.46902 0.47111 150 150 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Australia 2018-02-08 Undetermined Adult Brain Nervous System
10170 10170 ERR375749 ERX348126 ERS337052 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168448 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#3 7941068 Illumina sequencing of library 7941068 constructed from sample accession ERS337052 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence TTAGGC. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#3.cram cram 11298599000.0 56492995.0 SC RUN 10586 2#3 0:100 1:100 A:3356877540;C:2323057831;G:2299363865;T:3303865798;N:15433966 100 100     3356877540 2323057831 2299363865 3303865798 15433966 ERX348126 ERS337052 ERA267455 SC Wellcome Sanger Institute 2 0.91061 0.90958 0.1659 0.16567 0.68398 0.68645 0.53954 0.54231 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10171 10171 ERR375748 ERX348125 ERS337051 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168447 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#2 7941067 Illumina sequencing of library 7941067 constructed from sample accession ERS337051 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence CGATGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#2.cram cram 10462424000.0 52312120.0 SC RUN 10586 2#2 0:100 1:100 A:3035632557;C:2208885147;G:2197231235;T:3006145790;N:14529271 100 100     3035632557 2208885147 2197231235 3006145790 14529271 ERX348125 ERS337051 ERA267455 SC Wellcome Sanger Institute 2 0.91417 0.91329 0.15428 0.15477 0.66882 0.66896 0.52191 0.51898 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10172 10172 ERR375747 ERX348124 ERS337050 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168446 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 2#1 7941066 Illumina sequencing of library 7941066 constructed from sample accession ERS337050 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 2. This submission includes reads tagged with the sequence ATCACG. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_2#1.cram cram 10377603200.0 51888016.0 SC RUN 10586 2#1 0:100 1:100 A:3021582125;C:2187474575;G:2170525378;T:2983668309;N:14352813 100 100     3021582125 2187474575 2170525378 2983668309 14352813 ERX348124 ERS337050 ERA267455 SC Wellcome Sanger Institute 2 0.90978 0.90815 0.15565 0.15454 0.67322 0.67476 0.52923 0.51842 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10173 10173 ERR375746 ERX348123 ERS337052 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168448 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168448|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE3 sc 2013 08 12T10:36:21Z 1677721|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#3 7941068 Illumina sequencing of library 7941068 constructed from sample accession ERS337052 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence TTAGGC. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#3.cram cram 11455059800.0 57275299.0 SC RUN 10586 1#3 0:100 1:100 A:3406564785;C:2353388363;G:2329218644;T:3351844154;N:14043854 100 100     3406564785 2353388363 2329218644 3351844154 14043854 ERX348123 ERS337052 ERA267455 SC Wellcome Sanger Institute 2 0.91087 0.90879 0.16647 0.16616 0.6832 0.68436 0.54098 0.53604 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10174 10174 ERR375745 ERX348122 ERS337051 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168447 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:13Z|External Id:SAMEA2168447|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:13Z|INSDC status:public|Submitter Id:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE2 sc 2013 08 12T10:36:20Z 1677720|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#2 7941067 Illumina sequencing of library 7941067 constructed from sample accession ERS337051 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence CGATGT. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#2.cram cram 10636681200.0 53183406.0 SC RUN 10586 1#2 0:100 1:100 A:3088549841;C:2244455059;G:2232424530;T:3058125106;N:13126664 100 100     3088549841 2244455059 2232424530 3058125106 13126664 ERX348122 ERS337051 ERA267455 SC Wellcome Sanger Institute 2 0.9134 0.91251 0.15433 0.154 0.66849 0.66949 0.52089 0.53096 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10175 10175 ERR375744 ERX348121 ERS337050 ERP003756 PRJEB4464 Zebrafish olfactory transcriptomics Zebrafish_olfactory_transcriptomics-sc-2013-08-12T10:32:48Z-2742 Transcriptome Analysis The olfactory gene repertoire is largely species specific shaped by the nature and necessity of chemosensory information for survival in each species' niche. The relative expression of olfactory receptors can be quantified by RNA sequencing. We investigated the olfactory transcriptome of zebrafish because : i of its phylogenetic location in the vertebrate tree ii it has only one olfactory organ yet it has representatives of all the mammalian chemosensory receptor families iii its biology is well known iv is a commonly used model organism and it is suitable for subsequent functional analysis.         SAMEA2168446 SC ArrayExpress Genotype:Wildtype|ArrayExpress OrganismPart:Olfactory epithelium|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 11 25T10:18:08Z|ENA LAST UPDATE:2018 03 08T16:38:06Z|External Id:SAMEA2168446|INSDC center name:SC|INSDC first public:2013 11 25T10:18:08Z|INSDC last update:2018 03 08T16:38:06Z|INSDC status:public|Submitter Id:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|common name:zebrafish|sample description:RNA from OE|sample name:ZF OE1 sc 2013 08 12T10:36:17Z 1677719|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing SC EXP 10586 1#1 7941066 Illumina sequencing of library 7941066 constructed from sample accession ERS337050 for study accession ERP003756. This is part of an Illumina multiplexed sequencing run 10586 1. This submission includes reads tagged with the sequence ATCACG. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP003756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2013 11 25|ENA LAST UPDATE:2018 11 16 10586_1#1.cram cram 10534775800.0 52673879.0 SC RUN 10586 1#1 0:100 1:100 A:3069581091;C:2219273001;G:2202030288;T:3030929981;N:12961439 100 100     3069581091 2219273001 2202030288 3030929981 12961439 ERX348121 ERS337050 ERA267455 SC Wellcome Sanger Institute 2 0.91028 0.90986 0.15668 0.15607 0.67456 0.67472 0.52998 0.49845 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2013-11-25 Undetermined Undetermined Brain Nervous System
10391 10391 ERR8516975 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R 0:51 1:51 A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852 51 51     1077092958 949537387 955020348 1099432979 20556852 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.9053 0.9259 0.21658 0.22155 0.69369 0.69179 0.50726 0.50871 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10392 10392 ERR8516976 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R 0:51 1:51 A:972081222;C:890179393;G:888655698;T:998443264;N:18934747 51 51     972081222 890179393 888655698 998443264 18934747 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86107 0.87807 0.22063 0.23029 0.70859 0.70561 0.51656 0.51946 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10393 10393 ERR8516977 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R 0:51 1:51 A:728798881;C:962223604;G:958876331;T:735449513;N:17094231 51 51     728798881 962223604 958876331 735449513 17094231 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.54616 0.55881 0.13313 0.14036 0.84295 0.84185 0.64193 0.59762 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10394 10394 ERR8516972 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R 0:51 1:51 A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786 51 51     837274632 1062368015 1049892288 853310517 19213786 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.5726 0.57788 0.13781 0.14082 0.80616 0.80452 0.61581 0.60389 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10395 10395 ERR8516973 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R 0:51 1:51 A:897813231;C:796012893;G:794839496;T:923696030;N:17221274 51 51     897813231 796012893 794839496 923696030 17221274 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.92095 0.94156 0.18892 0.20024 0.6901 0.68905 0.49377 0.50086 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10396 10396 ERR8516974 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R 0:51 1:51 A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248 51 51     951912827 1107150666 1086060798 973791571 20785248 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.63792 0.62667 0.18547 0.18671 0.78756 0.78549 0.59274 0.55478 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10397 10397 ERR8516969 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R 0:51 1:51 A:925784769;C:934445856;G:959155668;T:924080408;N:18878983 51 51     925784769 934445856 959155668 924080408 18878983 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.59503 0.61112 0.1947 0.20225 0.76512 0.76337 0.54584 0.54345 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10398 10398 ERR8516970 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R 0:51 1:51 A:991755033;C:864808531;G:892202564;T:992188806;N:18881958 51 51     991755033 864808531 892202564 992188806 18881958 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86612 0.88689 0.26181 0.2728 0.7094 0.7091 0.53639 0.53906 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10399 10399 ERR8516971 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R 0:51 1:51 A:766707527;C:798667604;G:818782599;T:773280942;N:15938306 51 51     766707527 798667604 818782599 773280942 15938306 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.88811 0.92834 0.21869 0.22669 0.72878 0.72604 0.55598 0.57831 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10400 10400 ERR8516966 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R 0:51 1:51 A:774360373;C:720215184;G:719479745;T:796239200;N:15182374 51 51     774360373 720215184 719479745 796239200 15182374 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.79643 0.81194 0.25554 0.2603 0.72236 0.72021 0.51775 0.51678 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10401 10401 ERR8516967 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R 0:51 1:51 A:739921027;C:667375549;G:663864111;T:764302396;N:14288091 51 51     739921027 667375549 663864111 764302396 14288091 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.90817 0.92909 0.23387 0.24814 0.70088 0.69842 0.51238 0.51267 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10402 10402 ERR8516968 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R 0:51 1:51 A:882831441;C:935213418;G:957033335;T:879085993;N:18444957 51 51     882831441 935213418 957033335 879085993 18444957 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.76218 0.7682 0.18357 0.18521 0.74444 0.74272 0.46714 0.55518 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
19493 19493 ERR14085264 ERX13487656 ERS22622156 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 1 Replicate 3 Day 1 Replicate 3 SAMEA117549392 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009436 Day 1 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009436 Day 1 Replicate 3|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9517 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19137_1dpl3_R1.fastq.gz 19138_1dpl3_R2.fastq.gz fastq fastq 9165478634.0 30349267.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9517 0:151 1:151 A:2646232308;C:1796801479;G:2124056448;T:2588021406;N:10366993 151 151     2646232308 1796801479 2124056448 2588021406 10366993 ERX13487656 ERS22622156 ERA31046063 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19494 19494 ERR14085263 ERX13487655 ERS22622154 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 1 Replicate 2 Day 1 Replicate 2 SAMEA117549391 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009435 Day 1 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009435 Day 1 Replicate 2|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9516 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19135_1dpl2_R1.fastq.gz 19136_1dpl2_R2.fastq.gz fastq fastq 9442039362.0 31265031.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9516 0:151 1:151 A:2725446078;C:1808614751;G:2223018565;T:2675393466;N:9566502 151 151     2725446078 1808614751 2223018565 2675393466 9566502 ERX13487655 ERS22622154 ERA31046062 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19495 19495 ERR14085271 ERX13487663 ERS22622318 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 7 Replicate 3 Day 7 Replicate 3 SAMEA117549418 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009442 Day 7 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009442 Day 7 Replicate 3|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9523 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19149_7dpl5_R1.fastq.gz 19150_7dpl5_R2.fastq.gz fastq fastq 9932206502.0 32888101.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9523 0:151 1:151 A:2877130874;C:2050638794;G:2165950578;T:2827301936;N:11184320 151 151     2877130874 2050638794 2165950578 2827301936 11184320 ERX13487663 ERS22622318 ERA31046070 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19496 19496 ERR14085261 ERX13487653 ERS22622089 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 1 Replicate 1 Day 1 Replicate 1 SAMEA117549390 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009434 Day 1 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009434 Day 1 Replicate 1|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9515 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19133_1dpl1_R1.fastq.gz 19134_1dpl1_R2.fastq.gz fastq fastq 9389201442.0 31090071.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9515 0:151 1:151 A:2731715362;C:1816017173;G:2148260573;T:2683133097;N:10075237 151 151     2731715362 1816017173 2148260573 2683133097 10075237 ERX13487653 ERS22622089 ERA31046060 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19497 19497 ERR14085274 ERX13487666 ERS22622321 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Control Replicate 3 Control Replicate 3 SAMEA117549421 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009445 Control Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009445 Control Replicate 3|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9526 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19155_C7_R1.fastq.gz 19156_C7_R2.fastq.gz fastq fastq 9909221282.0 32811991.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9526 0:151 1:151 A:2850780132;C:1946613930;G:2307229799;T:2793332914;N:11264507 151 151     2850780132 1946613930 2307229799 2793332914 11264507 ERX13487666 ERS22622321 ERA31046073 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19498 19498 ERR14085268 ERX13487660 ERS22622316 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 7 Replicate 1 Day 7 Replicate 1 SAMEA117549416 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009440 Day 7 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009440 Day 7 Replicate 1|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9521 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19145_7dpl1_R1.fastq.gz 19146_7dpl1_R2.fastq.gz fastq fastq 9208706914.0 30492407.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9521 0:151 1:151 A:2666375656;C:1820213036;G:2101314534;T:2611250093;N:9553595 151 151     2666375656 1820213036 2101314534 2611250093 9553595 ERX13487660 ERS22622316 ERA31046067 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19499 19499 ERR14085276 ERX13487668 ERS22622315 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 4 Replicate 3 Day 4 Replicate 3 SAMEA117549415 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009439 Day 4 Replicate 3|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009439 Day 4 Replicate 3|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9520 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19143_4dpl4_R1.fastq.gz 19144_4dpl4_R2.fastq.gz fastq fastq 9313489740.0 30839370.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9520 0:151 1:151 A:2667044089;C:1836529353;G:2193641971;T:2605720804;N:10553523 151 151     2667044089 1836529353 2193641971 2605720804 10553523 ERX13487668 ERS22622315 ERA31046075 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19500 19500 ERR14085272 ERX13487664 ERS22622319 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Control Replicate 1 Control Replicate 1 SAMEA117549419 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009443 Control Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009443 Control Replicate 1|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9524 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19151_C5_R1.fastq.gz 19152_C5_R2.fastq.gz fastq fastq 13295515874.0 44024887.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9524 0:151 1:151 A:3841326329;C:2750684077;G:2915049240;T:3777029141;N:11427087 151 151     3841326329 2750684077 2915049240 3777029141 11427087 ERX13487664 ERS22622319 ERA31046071 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19501 19501 ERR14085265 ERX13487657 ERS22622177 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 4 Replicate 1 Day 4 Replicate 1 SAMEA117549413 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009437 Day 4 Replicate 1|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009437 Day 4 Replicate 1|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9518 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19139_4dpl2_R1.fastq.gz 19140_4dpl2_R2.fastq.gz fastq fastq 12509373332.0 41421766.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9518 0:151 1:151 A:3636942004;C:2502487228;G:2790329437;T:3565530654;N:14084009 151 151     3636942004 2502487228 2790329437 3565530654 14084009 ERX13487657 ERS22622177 ERA31046064 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19502 19502 ERR14085266 ERX13487658 ERS22622210 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 4 Replicate 2 Day 4 Replicate 2 SAMEA117549414 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009438 Day 4 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009438 Day 4 Replicate 2|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9519 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19141_4dpl3_R1.fastq.gz 19142_4dpl3_R2.fastq.gz fastq fastq 9691702460.0 32091730.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9519 0:151 1:151 A:2791714294;C:1934967288;G:2210755028;T:2743302083;N:10963767 151 151     2791714294 1934967288 2210755028 2743302083 10963767 ERX13487658 ERS22622210 ERA31046065 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19503 19503 ERR14085269 ERX13487661 ERS22622317 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Day 7 Replicate 2 Day 7 Replicate 2 SAMEA117549417 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009441 Day 7 Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009441 Day 7 Replicate 2|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9522 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19147_7dpl4_R1.fastq.gz 19148_7dpl4_R2.fastq.gz fastq fastq 9862024420.0 32655710.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9522 0:151 1:151 A:2841799545;C:2048598598;G:2166200803;T:2794242657;N:11182817 151 151     2841799545 2048598598 2166200803 2794242657 11182817 ERX13487661 ERS22622317 ERA31046068 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
19504 19504 ERR14085273 ERX13487665 ERS22622320 ERP167301 PRJEB83711 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration inda-STUDY-IIT-Delhi,Indraprastha Institute of Information Technology Shilpi Minocha, KSBS, IIT-Delhi New Delhi,India-2024-12-18 14:20:14.533-243 Other Regeneration of damaged brain tissue is a complex biological process that varies significantly across species. Zebrafish possess a remarkable ability to regenerate central nervous system structures making them an invaluable model for studying the molecular and cellular mechanisms underlying neuroregeneration. In this study we employed a previously standardized telencephalic stab wound injury model to investigate transcriptional and cellular responses during zebrafish brain regeneration. This well characterized model allows for precise analysis of injury induced regenerative processes by comparing different temporal stages of recovery. Using RNA sequencing at four key time points: control 1 day post lesion 4 dpl and 7 dpl we identified dynamic changes in gene expression and revealed critical signaling pathways associated with regeneration. Among these the p38 MAPK signaling cascade emerged as a key regulator. Our findings underscore the multifaceted role of p38 MAPK which modulates progenitor cell proliferation differentiation and neurogenesis during regeneration. These insights align with known roles of p38 MAPK in neural stem cell biology while highlighting its distinct contributions in a regenerative context. This work provides a comprehensive overview of early transcriptional events and highlights novel molecular players involved in CNS repair further establishing the zebrafish as a robust model for regenerative research. Our findings open avenues for applying these pathways to develop therapeutic strategies aimed at enhancing brain repair in humans. ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19   RNA seq Control Replicate 2 Control Replicate 2 SAMEA117549420 Indian Institute of Technology Delhi,Indraprastha Institute of Information Technology ENA first public:2024 12 19|INSDC center name:Indian Institute of Technology Delhi Indraprastha Institute of Information Technology|INSDC status:public|Submitter Id:SAMIN0009444 Control Replicate 2|broker name:IBDC|collection date:2022 12 23|common name:zebrafish|geographic location country and/or sea:India|geographic location region and locality:New Delhi India|sample name:SAMIN0009444 Control Replicate 2|scientific name:Danio rerio                 From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP167301 Illumina NovaSeq 6000 paired end sequencing; From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration ENA FIRST PUBLIC:2024 12 19|ENA LAST UPDATE:2024 12 19 19153_C6_R1.fastq.gz 19154_C6_R2.fastq.gz fastq fastq 11398526732.0 37743466.0 RUN From injury to recovery: Transcriptomic dynamics in Zebrafish brain regeneration 9525 0:151 1:151 A:3315198872;C:2268180334;G:2561003095;T:3244771542;N:9372889 151 151     3315198872 2268180334 2561003095 3244771542 9372889 ERX13487665 ERS22622320 ERA31046072 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-19 Undetermined Undetermined Brain Nervous System
26386 26386 SRR25917801 SRX21637674 SRS18807763 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02953 GSM7761847   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing 22 02953 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5 GSM7761847 GSM7761847: 22 02953; Danio rerio; RNA Seq GSM7761847 r1 GSM7761847 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02953_S24_L01_R1_001.fastq.gz 22-02953_S24_L01_R2_001.fastq.gz fastq fastq 1889616596.0 9640901.0 GSM7761847 r1 0:98 1:98 A:502776047;C:437946838;G:435110760;T:512766381;N:1016570 98 98     502776047 437946838 435110760 512766381 1016570 SRX21637674 SRS18807763 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9328 0.92722 0.09638 0.09803 0.70285 0.70345 0.50688 0.50192 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26387 26387 SRR25917802 SRX21637674 SRS18807763 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02953 GSM7761847   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing 22 02953 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5 GSM7761847 GSM7761847: 22 02953; Danio rerio; RNA Seq GSM7761847 r1 GSM7761847 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02953_S24_L02_R1_001.fastq.gz 22-02953_S24_L02_R2_001.fastq.gz fastq fastq 2862274828.0 14603443.0 GSM7761847 r2 0:98 1:98 A:757126187;C:668245308;G:664888408;T:771615407;N:399518 98 98     757126187 668245308 664888408 771615407 399518 SRX21637674 SRS18807763 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94091 0.93645 0.09729 0.09803 0.70309 0.7041 0.51085 0.50502 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26388 26388 SRR25917803 SRX21637674 SRS18807763 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02953 GSM7761847   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing 22 02953 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5 GSM7761847 GSM7761847: 22 02953; Danio rerio; RNA Seq GSM7761847 r1 GSM7761847 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02953_S24_L03_R1_001.fastq.gz 22-02953_S24_L03_R2_001.fastq.gz fastq fastq 2584726676.0 13187381.0 GSM7761847 r3 0:98 1:98 A:684660799;C:601450975;G:598598564;T:699408337;N:608001 98 98     684660799 601450975 598598564 699408337 608001 SRX21637674 SRS18807763 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94069 0.93734 0.09389 0.09545 0.70264 0.70254 0.49261 0.50213 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26389 26389 SRR25917804 SRX21637674 SRS18807763 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02953 GSM7761847   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing 22 02953 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.5 GSM7761847 GSM7761847: 22 02953; Danio rerio; RNA Seq GSM7761847 r1 GSM7761847 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02953_S24_L04_R1_001.fastq.gz 22-02953_S24_L04_R2_001.fastq.gz fastq fastq 4100821760.0 20922560.0 GSM7761847 r4 0:98 1:98 A:1082079470;C:958686210;G:956517599;T:1103432545;N:105936 98 98     1082079470 958686210 956517599 1103432545 105936 SRX21637674 SRS18807763 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94702 0.94327 0.09591 0.09712 0.70252 0.70402 0.51264 0.51319 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26390 26390 SRR25917805 SRX21637673 SRS18807762 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02952 GSM7761846   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing 22 02952 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8 GSM7761846 GSM7761846: 22 02952; Danio rerio; RNA Seq GSM7761846 r1 GSM7761846 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02952_S23_L01_R1_001.fastq.gz 22-02952_S23_L01_R2_001.fastq.gz fastq fastq 1992642428.0 10166543.0 GSM7761846 r1 0:98 1:98 A:531507040;C:460525641;G:457631907;T:541925633;N:1052207 98 98     531507040 460525641 457631907 541925633 1052207 SRX21637673 SRS18807762 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93066 0.92518 0.10299 0.10378 0.7067 0.70735 0.49353 0.49352 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26391 26391 SRR25917806 SRX21637673 SRS18807762 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02952 GSM7761846   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing 22 02952 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8 GSM7761846 GSM7761846: 22 02952; Danio rerio; RNA Seq GSM7761846 r1 GSM7761846 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02952_S23_L02_R1_001.fastq.gz 22-02952_S23_L02_R2_001.fastq.gz fastq fastq 2995445852.0 15282887.0 GSM7761846 r2 0:98 1:98 A:793690840;C:697826413;G:694428368;T:809079956;N:420275 98 98     793690840 697826413 694428368 809079956 420275 SRX21637673 SRS18807762 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93866 0.93421 0.10232 0.10415 0.7038 0.70496 0.49446 0.49935 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26392 26392 SRR25917807 SRX21637673 SRS18807762 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02952 GSM7761846   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing 22 02952 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8 GSM7761846 GSM7761846: 22 02952; Danio rerio; RNA Seq GSM7761846 r1 GSM7761846 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02952_S23_L03_R1_001.fastq.gz 22-02952_S23_L03_R2_001.fastq.gz fastq fastq 2558248644.0 13052289.0 GSM7761846 r3 0:98 1:98 A:678550810;C:594295508;G:591607450;T:693175940;N:618936 98 98     678550810 594295508 591607450 693175940 618936 SRX21637673 SRS18807762 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93834 0.93526 0.10036 0.10226 0.70443 0.70565 0.49418 0.4945 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26393 26393 SRR25917808 SRX21637673 SRS18807762 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02952 GSM7761846   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing 22 02952 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8 GSM7761846 GSM7761846: 22 02952; Danio rerio; RNA Seq GSM7761846 r1 GSM7761846 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02952_S23_L04_R1_001.fastq.gz 22-02952_S23_L04_R2_001.fastq.gz fastq fastq 3963250536.0 20220666.0 GSM7761846 r4 0:98 1:98 A:1045663273;C:926206212;G:924140110;T:1067139742;N:101199 98 98     1045663273 926206212 924140110 1067139742 101199 SRX21637673 SRS18807762 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94449 0.94083 0.10086 0.10197 0.70469 0.70569 0.4991 0.49202 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26394 26394 SRR25917809 SRX21637672 SRS18807761 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02951 GSM7761845   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing 22 02951 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7 GSM7761845 GSM7761845: 22 02951; Danio rerio; RNA Seq GSM7761845 r1 GSM7761845 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02951_S22_L01_R1_001.fastq.gz 22-02951_S22_L01_R2_001.fastq.gz fastq fastq 2029687408.0 10355548.0 GSM7761845 r1 0:98 1:98 A:538688097;C:471579919;G:470623522;T:547765689;N:1030181 98 98     538688097 471579919 470623522 547765689 1030181 SRX21637672 SRS18807761 SRA1706756 The University of Adelaide The University of Adelaide 2 0.92721 0.92969 0.09472 0.09676 0.70423 0.70276 0.49981 0.49898 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26395 26395 SRR25917810 SRX21637672 SRS18807761 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02951 GSM7761845   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing 22 02951 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7 GSM7761845 GSM7761845: 22 02951; Danio rerio; RNA Seq GSM7761845 r1 GSM7761845 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02951_S22_L02_R1_001.fastq.gz 22-02951_S22_L02_R2_001.fastq.gz fastq fastq 3072360760.0 15675310.0 GSM7761845 r2 0:98 1:98 A:810685642;C:719109817;G:718137072;T:824036555;N:391674 98 98     810685642 719109817 718137072 824036555 391674 SRX21637672 SRS18807761 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9358 0.93813 0.09385 0.09614 0.70341 0.70303 0.49098 0.49194 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26396 26396 SRR25917811 SRX21637672 SRS18807761 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02951 GSM7761845   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing 22 02951 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7 GSM7761845 GSM7761845: 22 02951; Danio rerio; RNA Seq GSM7761845 r1 GSM7761845 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02951_S22_L03_R1_001.fastq.gz 22-02951_S22_L03_R2_001.fastq.gz fastq fastq 2765019432.0 14107242.0 GSM7761845 r3 0:98 1:98 A:730929526;C:644675885;G:644121852;T:744649936;N:642233 98 98     730929526 644675885 644121852 744649936 642233 SRX21637672 SRS18807761 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93375 0.93756 0.0926 0.09517 0.70429 0.70358 0.50064 0.50166 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26397 26397 SRR25917812 SRX21637672 SRS18807761 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02951 GSM7761845   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing 22 02951 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7 GSM7761845 GSM7761845: 22 02951; Danio rerio; RNA Seq GSM7761845 r1 GSM7761845 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02951_S22_L04_R1_001.fastq.gz 22-02951_S22_L04_R2_001.fastq.gz fastq fastq 4491524436.0 22915941.0 GSM7761845 r4 0:98 1:98 A:1183373286;C:1051469132;G:1052482979;T:1204083766;N:115273 98 98     1183373286 1051469132 1052482979 1204083766 115273 SRX21637672 SRS18807761 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94091 0.94403 0.09318 0.09521 0.70374 0.70234 0.49577 0.49187 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26398 26398 SRR25917813 SRX21637671 SRS18807760 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02949 GSM7761844   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing 22 02949 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7 GSM7761844 GSM7761844: 22 02949; Danio rerio; RNA Seq GSM7761844 r1 GSM7761844 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02949_S21_L01_R1_001.fastq.gz 22-02949_S21_L01_R2_001.fastq.gz fastq fastq 2534565376.0 12931456.0 GSM7761844 r1 0:98 1:98 A:674884849;C:586725099;G:584045434;T:687552587;N:1357407 98 98     674884849 586725099 584045434 687552587 1357407 SRX21637671 SRS18807760 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93278 0.9279 0.10047 0.10166 0.70506 0.70461 0.51365 0.5138 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26399 26399 SRR25917814 SRX21637671 SRS18807760 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02949 GSM7761844   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing 22 02949 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7 GSM7761844 GSM7761844: 22 02949; Danio rerio; RNA Seq GSM7761844 r1 GSM7761844 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02949_S21_L02_R1_001.fastq.gz 22-02949_S21_L02_R2_001.fastq.gz fastq fastq 3889732308.0 19845573.0 GSM7761844 r2 0:98 1:98 A:1029905526;C:906662466;G:903535838;T:1049088768;N:539710 98 98     1029905526 906662466 903535838 1049088768 539710 SRX21637671 SRS18807760 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94166 0.93609 0.09893 0.10006 0.70313 0.70439 0.51404 0.50855 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26400 26400 SRR25917815 SRX21637671 SRS18807760 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02949 GSM7761844   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing 22 02949 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7 GSM7761844 GSM7761844: 22 02949; Danio rerio; RNA Seq GSM7761844 r1 GSM7761844 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02949_S21_L03_R1_001.fastq.gz 22-02949_S21_L03_R2_001.fastq.gz fastq fastq 3291066380.0 16791155.0 GSM7761844 r3 0:98 1:98 A:872393079;C:764845510;G:762405303;T:890638586;N:783902 98 98     872393079 764845510 762405303 890638586 783902 SRX21637671 SRS18807760 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94062 0.93691 0.09836 0.0996 0.70416 0.70461 0.51782 0.50965 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26401 26401 SRR25917816 SRX21637671 SRS18807760 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02949 GSM7761844   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing 22 02949 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7 GSM7761844 GSM7761844: 22 02949; Danio rerio; RNA Seq GSM7761844 r1 GSM7761844 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02949_S21_L04_R1_001.fastq.gz 22-02949_S21_L04_R2_001.fastq.gz fastq fastq 5366313988.0 27379153.0 GSM7761844 r4 0:98 1:98 A:1415961559;C:1253439804;G:1252742067;T:1444033449;N:137109 98 98     1415961559 1253439804 1252742067 1444033449 137109 SRX21637671 SRS18807760 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94568 0.94293 0.09906 0.10054 0.70402 0.7052 0.51461 0.52073 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26402 26402 SRR25917817 SRX21637670 SRS18807759 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02948 GSM7761843   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02948 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761843 GSM7761843: 22 02948; Danio rerio; RNA Seq GSM7761843 r1 GSM7761843 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02948_S20_L01_R1_001.fastq.gz 22-02948_S20_L01_R2_001.fastq.gz fastq fastq 2053905168.0 10479108.0 GSM7761843 r1 0:98 1:98 A:547671134;C:475089537;G:473080534;T:556992811;N:1071152 98 98     547671134 475089537 473080534 556992811 1071152 SRX21637670 SRS18807759 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93522 0.9298 0.10197 0.10238 0.70339 0.70421 0.50454 0.50393 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26403 26403 SRR25917818 SRX21637670 SRS18807759 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02948 GSM7761843   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02948 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761843 GSM7761843: 22 02948; Danio rerio; RNA Seq GSM7761843 r1 GSM7761843 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02948_S20_L02_R1_001.fastq.gz 22-02948_S20_L02_R2_001.fastq.gz fastq fastq 3144952300.0 16045675.0 GSM7761843 r2 0:98 1:98 A:832655138;C:733701092;G:731348360;T:846811030;N:436680 98 98     832655138 733701092 731348360 846811030 436680 SRX21637670 SRS18807759 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94365 0.93984 0.10028 0.10124 0.70398 0.70565 0.50353 0.50505 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26404 26404 SRR25917819 SRX21637670 SRS18807759 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02948 GSM7761843   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02948 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761843 GSM7761843: 22 02948; Danio rerio; RNA Seq GSM7761843 r1 GSM7761843 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02948_S20_L03_R1_001.fastq.gz 22-02948_S20_L03_R2_001.fastq.gz fastq fastq 2460170244.0 12551889.0 GSM7761843 r3 0:98 1:98 A:651706233;C:572474025;G:570982999;T:664399947;N:607040 98 98     651706233 572474025 570982999 664399947 607040 SRX21637670 SRS18807759 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9411 0.93886 0.09891 0.10006 0.70485 0.70362 0.50337 0.50208 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26405 26405 SRR25917820 SRX21637670 SRS18807759 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02948 GSM7761843   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02948 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761843 GSM7761843: 22 02948; Danio rerio; RNA Seq GSM7761843 r1 GSM7761843 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02948_S20_L04_R1_001.fastq.gz 22-02948_S20_L04_R2_001.fastq.gz fastq fastq 3890916344.0 19851614.0 GSM7761843 r4 0:98 1:98 A:1025556861;C:910441322;G:909593603;T:1045230061;N:94497 98 98     1025556861 910441322 909593603 1045230061 94497 SRX21637670 SRS18807759 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94835 0.94517 0.09781 0.09849 0.70274 0.70374 0.5027 0.5008 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26406 26406 SRR25917821 SRX21637669 SRS18807758 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02947 GSM7761842   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing 22 02947 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6 GSM7761842 GSM7761842: 22 02947; Danio rerio; RNA Seq GSM7761842 r1 GSM7761842 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02947_S19_L01_R1_001.fastq.gz 22-02947_S19_L01_R2_001.fastq.gz fastq fastq 1696563848.0 8655938.0 GSM7761842 r1 0:98 1:98 A:453186259;C:391677304;G:390304899;T:460508753;N:886633 98 98     453186259 391677304 390304899 460508753 886633 SRX21637669 SRS18807758 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9329 0.92803 0.10284 0.10415 0.70611 0.70664 0.49615 0.49305 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26407 26407 SRR25917822 SRX21637669 SRS18807758 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02947 GSM7761842   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing 22 02947 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6 GSM7761842 GSM7761842: 22 02947; Danio rerio; RNA Seq GSM7761842 r1 GSM7761842 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02947_S19_L02_R1_001.fastq.gz 22-02947_S19_L02_R2_001.fastq.gz fastq fastq 2634385040.0 13440740.0 GSM7761842 r2 0:98 1:98 A:699185241;C:613094915;G:611213748;T:710534569;N:356567 98 98     699185241 613094915 611213748 710534569 356567 SRX21637669 SRS18807758 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94184 0.93645 0.10113 0.10207 0.70268 0.70345 0.50894 0.50924 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26408 26408 SRR25917823 SRX21637669 SRS18807758 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02947 GSM7761842   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing 22 02947 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6 GSM7761842 GSM7761842: 22 02947; Danio rerio; RNA Seq GSM7761842 r1 GSM7761842 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02947_S19_L03_R1_001.fastq.gz 22-02947_S19_L03_R2_001.fastq.gz fastq fastq 2356722424.0 12024094.0 GSM7761842 r3 0:98 1:98 A:626784832;C:546121522;G:545024526;T:638243477;N:548067 98 98     626784832 546121522 545024526 638243477 548067 SRX21637669 SRS18807758 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94068 0.93749 0.09906 0.10122 0.7039 0.70449 0.50662 0.51119 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26409 26409 SRR25917824 SRX21637669 SRS18807758 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02947 GSM7761842   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing 22 02947 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6 GSM7761842 GSM7761842: 22 02947; Danio rerio; RNA Seq GSM7761842 r1 GSM7761842 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02947_S19_L04_R1_001.fastq.gz 22-02947_S19_L04_R2_001.fastq.gz fastq fastq 3824206372.0 19511257.0 GSM7761842 r4 0:98 1:98 A:1013047237;C:890237600;G:890115590;T:1030706585;N:99360 98 98     1013047237 890237600 890115590 1030706585 99360 SRX21637669 SRS18807758 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9463 0.94321 0.10017 0.1014 0.7038 0.70437 0.50533 0.51168 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26410 26410 SRR25917825 SRX21637668 SRS18807757 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02946 GSM7761841   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing 22 02946 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5 GSM7761841 GSM7761841: 22 02946; Danio rerio; RNA Seq GSM7761841 r1 GSM7761841 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02946_S18_L01_R1_001.fastq.gz 22-02946_S18_L01_R2_001.fastq.gz fastq fastq 2024888936.0 10331066.0 GSM7761841 r1 0:98 1:98 A:542606378;C:466454644;G:464323282;T:550429046;N:1075586 98 98     542606378 466454644 464323282 550429046 1075586 SRX21637668 SRS18807757 SRA1706756 The University of Adelaide The University of Adelaide 2 0.933 0.92706 0.10233 0.10303 0.70429 0.70465 0.49443 0.48878 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26411 26411 SRR25917826 SRX21637668 SRS18807757 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02946 GSM7761841   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing 22 02946 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5 GSM7761841 GSM7761841: 22 02946; Danio rerio; RNA Seq GSM7761841 r1 GSM7761841 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02946_S18_L02_R1_001.fastq.gz 22-02946_S18_L02_R2_001.fastq.gz fastq fastq 3069224368.0 15659308.0 GSM7761841 r2 0:98 1:98 A:816848746;C:712756904;G:710416167;T:828782508;N:420043 98 98     816848746 712756904 710416167 828782508 420043 SRX21637668 SRS18807757 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94117 0.93483 0.10216 0.10274 0.70467 0.7051 0.50931 0.51613 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26412 26412 SRR25917827 SRX21637668 SRS18807757 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02946 GSM7761841   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing 22 02946 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5 GSM7761841 GSM7761841: 22 02946; Danio rerio; RNA Seq GSM7761841 r1 GSM7761841 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02946_S18_L03_R1_001.fastq.gz 22-02946_S18_L03_R2_001.fastq.gz fastq fastq 2612758008.0 13330398.0 GSM7761841 r3 0:98 1:98 A:695834172;C:605270278;G:603512924;T:707518532;N:622102 98 98     695834172 605270278 603512924 707518532 622102 SRX21637668 SRS18807757 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94095 0.93716 0.09929 0.10092 0.70343 0.70396 0.49363 0.50028 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26413 26413 SRR25917828 SRX21637668 SRS18807757 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02946 GSM7761841   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing 22 02946 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5 GSM7761841 GSM7761841: 22 02946; Danio rerio; RNA Seq GSM7761841 r1 GSM7761841 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02946_S18_L04_R1_001.fastq.gz 22-02946_S18_L04_R2_001.fastq.gz fastq fastq 4163040196.0 21240001.0 GSM7761841 r4 0:98 1:98 A:1104116525;C:968916166;G:968183447;T:1121718793;N:105265 98 98     1104116525 968916166 968183447 1121718793 105265 SRX21637668 SRS18807757 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94611 0.94219 0.09973 0.10107 0.70303 0.70394 0.51684 0.51536 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26414 26414 SRR25917829 SRX21637667 SRS18807756 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02945 GSM7761840   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing 22 02945 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2 GSM7761840 GSM7761840: 22 02945; Danio rerio; RNA Seq GSM7761840 r1 GSM7761840 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02945_S17_L01_R1_001.fastq.gz 22-02945_S17_L01_R2_001.fastq.gz fastq fastq 2619858892.0 13366627.0 GSM7761840 r1 0:98 1:98 A:705166138;C:600115338;G:598330950;T:714861086;N:1385380 98 98     705166138 600115338 598330950 714861086 1385380 SRX21637667 SRS18807756 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93476 0.92831 0.09718 0.09862 0.70457 0.70567 0.4957 0.52808 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26415 26415 SRR25917830 SRX21637667 SRS18807756 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02945 GSM7761840   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing 22 02945 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2 GSM7761840 GSM7761840: 22 02945; Danio rerio; RNA Seq GSM7761840 r1 GSM7761840 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02945_S17_L02_R1_001.fastq.gz 22-02945_S17_L02_R2_001.fastq.gz fastq fastq 3955690816.0 20182096.0 GSM7761840 r2 0:98 1:98 A:1058443729;C:912805409;G:911028821;T:1072858146;N:554711 98 98     1058443729 912805409 911028821 1072858146 554711 SRX21637667 SRS18807756 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94318 0.93872 0.09645 0.0973 0.70613 0.70715 0.52714 0.52457 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26416 26416 SRR25917831 SRX21637667 SRS18807756 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02945 GSM7761840   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing 22 02945 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2 GSM7761840 GSM7761840: 22 02945; Danio rerio; RNA Seq GSM7761840 r1 GSM7761840 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02945_S17_L03_R1_001.fastq.gz 22-02945_S17_L03_R2_001.fastq.gz fastq fastq 3434879028.0 17524893.0 GSM7761840 r3 0:98 1:98 A:919933771;C:790247133;G:789182712;T:934693677;N:821735 98 98     919933771 790247133 789182712 934693677 821735 SRX21637667 SRS18807756 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94324 0.93862 0.09659 0.09728 0.70571 0.70583 0.52686 0.53004 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26417 26417 SRR25917832 SRX21637667 SRS18807756 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02945 GSM7761840   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing 22 02945 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2 GSM7761840 GSM7761840: 22 02945; Danio rerio; RNA Seq GSM7761840 r1 GSM7761840 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02945_S17_L04_R1_001.fastq.gz 22-02945_S17_L04_R2_001.fastq.gz fastq fastq 5433098048.0 27719888.0 GSM7761840 r4 0:98 1:98 A:1449452101;C:1255780383;G:1256728807;T:1470998035;N:138722 98 98     1449452101 1255780383 1256728807 1470998035 138722 SRX21637667 SRS18807756 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94785 0.94392 0.09527 0.09667 0.70556 0.70676 0.52907 0.52805 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26418 26418 SRR25917833 SRX21637666 SRS18807755 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02942 GSM7761839   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02942 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6 GSM7761839 GSM7761839: 22 02942; Danio rerio; RNA Seq GSM7761839 r1 GSM7761839 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02942_S16_L01_R1_001.fastq.gz 22-02942_S16_L01_R2_001.fastq.gz fastq fastq 1924129256.0 9816986.0 GSM7761839 r1 0:98 1:98 A:513816169;C:444302395;G:442002444;T:522987233;N:1021015 98 98     513816169 444302395 442002444 522987233 1021015 SRX21637666 SRS18807755 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93541 0.9292 0.09209 0.09323 0.70496 0.70595 0.50865 0.51472 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26419 26419 SRR25917834 SRX21637666 SRS18807755 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02942 GSM7761839   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02942 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6 GSM7761839 GSM7761839: 22 02942; Danio rerio; RNA Seq GSM7761839 r1 GSM7761839 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02942_S16_L02_R1_001.fastq.gz 22-02942_S16_L02_R2_001.fastq.gz fastq fastq 3006370892.0 15338627.0 GSM7761839 r2 0:98 1:98 A:798357725;C:699049238;G:696286354;T:812267336;N:410239 98 98     798357725 699049238 696286354 812267336 410239 SRX21637666 SRS18807755 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94371 0.93809 0.09 0.09081 0.70429 0.7054 0.50485 0.50657 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26420 26420 SRR25917835 SRX21637666 SRS18807755 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02942 GSM7761839   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02942 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6 GSM7761839 GSM7761839: 22 02942; Danio rerio; RNA Seq GSM7761839 r1 GSM7761839 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02942_S16_L03_R1_001.fastq.gz 22-02942_S16_L03_R2_001.fastq.gz fastq fastq 2569908488.0 13111778.0 GSM7761839 r3 0:98 1:98 A:683489191;C:595497651;G:593400486;T:696913366;N:607794 98 98     683489191 595497651 593400486 696913366 607794 SRX21637666 SRS18807755 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94243 0.93803 0.0901 0.09173 0.70601 0.70595 0.5082 0.50536 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26421 26421 SRR25917836 SRX21637666 SRS18807755 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02942 GSM7761839   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02942 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6 GSM7761839 GSM7761839: 22 02942; Danio rerio; RNA Seq GSM7761839 r1 GSM7761839 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02942_S16_L04_R1_001.fastq.gz 22-02942_S16_L04_R2_001.fastq.gz fastq fastq 4090784012.0 20871347.0 GSM7761839 r4 0:98 1:98 A:1082885031;C:953380881;G:951809866;T:1102604651;N:103583 98 98     1082885031 953380881 951809866 1102604651 103583 SRX21637666 SRS18807755 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9483 0.94389 0.08825 0.08951 0.70575 0.70642 0.5123 0.50956 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26422 26422 SRR25917837 SRX21637665 SRS18807754 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02941 GSM7761838   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02941 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6 GSM7761838 GSM7761838: 22 02941; Danio rerio; RNA Seq GSM7761838 r1 GSM7761838 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02941_S15_L01_R1_001.fastq.gz 22-02941_S15_L01_R2_001.fastq.gz fastq fastq 1451986424.0 7408094.0 GSM7761838 r1 0:98 1:98 A:390918596;C:332118752;G:330611037;T:397580767;N:757272 98 98     390918596 332118752 330611037 397580767 757272 SRX21637665 SRS18807754 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93162 0.92627 0.10255 0.10375 0.7067 0.70741 0.48748 0.50266 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26423 26423 SRR25917838 SRX21637665 SRS18807754 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02941 GSM7761838   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02941 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6 GSM7761838 GSM7761838: 22 02941; Danio rerio; RNA Seq GSM7761838 r1 GSM7761838 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02941_S15_L02_R1_001.fastq.gz 22-02941_S15_L02_R2_001.fastq.gz fastq fastq 2226903784.0 11361754.0 GSM7761838 r2 0:98 1:98 A:595644295;C:513538924;G:511376888;T:606030075;N:313602 98 98     595644295 513538924 511376888 606030075 313602 SRX21637665 SRS18807754 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94004 0.93541 0.09921 0.10033 0.70374 0.70471 0.50851 0.50748 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26424 26424 SRR25917839 SRX21637665 SRS18807754 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02941 GSM7761838   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02941 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6 GSM7761838 GSM7761838: 22 02941; Danio rerio; RNA Seq GSM7761838 r1 GSM7761838 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02941_S15_L03_R1_001.fastq.gz 22-02941_S15_L03_R2_001.fastq.gz fastq fastq 1835563128.0 9365118.0 GSM7761838 r3 0:98 1:98 A:491600256;C:421963198;G:420470403;T:501084604;N:444667 98 98     491600256 421963198 420470403 501084604 444667 SRX21637665 SRS18807754 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93909 0.93552 0.09787 0.10025 0.7063 0.70668 0.49667 0.49612 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26425 26425 SRR25917840 SRX21637665 SRS18807754 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02941 GSM7761838   source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing 22 02941 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6 GSM7761838 GSM7761838: 22 02941; Danio rerio; RNA Seq GSM7761838 r1 GSM7761838 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02941_S15_L04_R1_001.fastq.gz 22-02941_S15_L04_R2_001.fastq.gz fastq fastq 3014378668.0 15379483.0 GSM7761838 r4 0:98 1:98 A:802870126;C:697333543;G:696291116;T:817807708;N:76175 98 98     802870126 697333543 696291116 817807708 76175 SRX21637665 SRS18807754 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94458 0.94088 0.0997 0.10084 0.70542 0.70615 0.49847 0.50128 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26426 26426 SRR25917841 SRX21637664 SRS18807753 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02938 GSM7761837   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing 22 02938 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2 GSM7761837 GSM7761837: 22 02938; Danio rerio; RNA Seq GSM7761837 r1 GSM7761837 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02938_S14_L01_R1_001.fastq.gz 22-02938_S14_L01_R2_001.fastq.gz fastq fastq 1991261020.0 10159495.0 GSM7761837 r1 0:98 1:98 A:532249087;C:459160151;G:456558143;T:542243720;N:1049919 98 98     532249087 459160151 456558143 542243720 1049919 SRX21637664 SRS18807753 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93301 0.92619 0.10156 0.10145 0.70203 0.70354 0.50217 0.50319 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26427 26427 SRR25917842 SRX21637664 SRS18807753 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02938 GSM7761837   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing 22 02938 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2 GSM7761837 GSM7761837: 22 02938; Danio rerio; RNA Seq GSM7761837 r1 GSM7761837 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02938_S14_L02_R1_001.fastq.gz 22-02938_S14_L02_R2_001.fastq.gz fastq fastq 3089219896.0 15761326.0 GSM7761837 r2 0:98 1:98 A:820946080;C:717486845;G:714242053;T:836115769;N:429149 98 98     820946080 717486845 714242053 836115769 429149 SRX21637664 SRS18807753 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93958 0.93485 0.09922 0.10087 0.70297 0.70374 0.48594 0.48787 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26428 26428 SRR25917843 SRX21637664 SRS18807753 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02938 GSM7761837   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing 22 02938 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2 GSM7761837 GSM7761837: 22 02938; Danio rerio; RNA Seq GSM7761837 r1 GSM7761837 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02938_S14_L03_R1_001.fastq.gz 22-02938_S14_L03_R2_001.fastq.gz fastq fastq 2646575652.0 13502937.0 GSM7761837 r3 0:98 1:98 A:704124909;C:612713176;G:610276201;T:718835355;N:626011 98 98     704124909 612713176 610276201 718835355 626011 SRX21637664 SRS18807753 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93984 0.93514 0.09825 0.09978 0.70368 0.70364 0.50476 0.5062 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26429 26429 SRR25917844 SRX21637664 SRS18807753 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02938 GSM7761837   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing 22 02938 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2 GSM7761837 GSM7761837: 22 02938; Danio rerio; RNA Seq GSM7761837 r1 GSM7761837 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02938_S14_L04_R1_001.fastq.gz 22-02938_S14_L04_R2_001.fastq.gz fastq fastq 4235942788.0 21611953.0 GSM7761837 r4 0:98 1:98 A:1121922192;C:986087720;G:984166129;T:1143659828;N:106919 98 98     1121922192 986087720 984166129 1143659828 106919 SRX21637664 SRS18807753 SRA1706756 The University of Adelaide The University of Adelaide 2 0.94454 0.94039 0.09757 0.09901 0.70035 0.70138 0.49729 0.48826 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26430 26430 SRR25917845 SRX21637663 SRS18807752 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02937 GSM7761836   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing 22 02937 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3 GSM7761836 GSM7761836: 22 02937; Danio rerio; RNA Seq GSM7761836 r1 GSM7761836 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02937_S13_L01_R1_001.fastq.gz 22-02937_S13_L01_R2_001.fastq.gz fastq fastq 1825781944.0 9315214.0 GSM7761836 r1 0:98 1:98 A:489329069;C:419397972;G:418043678;T:498054837;N:956388 98 98     489329069 419397972 418043678 498054837 956388 SRX21637663 SRS18807752 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93216 0.9269 0.10415 0.10514 0.70696 0.70713 0.50133 0.50188 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26431 26431 SRR25917846 SRX21637663 SRS18807752 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02937 GSM7761836   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing 22 02937 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3 GSM7761836 GSM7761836: 22 02937; Danio rerio; RNA Seq GSM7761836 r1 GSM7761836 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02937_S13_L02_R1_001.fastq.gz 22-02937_S13_L02_R2_001.fastq.gz fastq fastq 2831655708.0 14447223.0 GSM7761836 r2 0:98 1:98 A:753926233;C:655777502;G:654115498;T:767448178;N:388297 98 98     753926233 655777502 654115498 767448178 388297 SRX21637663 SRS18807752 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93913 0.93449 0.10226 0.10403 0.70623 0.70698 0.50808 0.5015 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26432 26432 SRR25917847 SRX21637663 SRS18807752 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02937 GSM7761836   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing 22 02937 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3 GSM7761836 GSM7761836: 22 02937; Danio rerio; RNA Seq GSM7761836 r1 GSM7761836 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02937_S13_L03_R1_001.fastq.gz 22-02937_S13_L03_R2_001.fastq.gz fastq fastq 2309829816.0 11784846.0 GSM7761836 r3 0:98 1:98 A:615504790;C:533456596;G:532490021;T:627819856;N:558553 98 98     615504790 533456596 532490021 627819856 558553 SRX21637663 SRS18807752 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93883 0.93641 0.10187 0.10383 0.70615 0.70593 0.49921 0.49159 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26433 26433 SRR25917848 SRX21637663 SRS18807752 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02937 GSM7761836   source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing 22 02937 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3 GSM7761836 GSM7761836: 22 02937; Danio rerio; RNA Seq GSM7761836 r1 GSM7761836 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02937_S13_L04_R1_001.fastq.gz 22-02937_S13_L04_R2_001.fastq.gz fastq fastq 3731146944.0 19036464.0 GSM7761836 r4 0:98 1:98 A:989277206;C:866724233;G:866705291;T:1008347419;N:92795 98 98     989277206 866724233 866705291 1008347419 92795 SRX21637663 SRS18807752 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9451 0.94176 0.10033 0.10187 0.70494 0.70571 0.49807 0.49112 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26434 26434 SRR25917849 SRX21637662 SRS18807751 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02936 GSM7761835   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02936 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761835 GSM7761835: 22 02936; Danio rerio; RNA Seq GSM7761835 r1 GSM7761835 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02936_S12_L01_R1_001.fastq.gz 22-02936_S12_L01_R2_001.fastq.gz fastq fastq 2087585416.0 10650946.0 GSM7761835 r1 0:98 1:98 A:557206023;C:482369335;G:479442541;T:567486868;N:1080649 98 98     557206023 482369335 479442541 567486868 1080649 SRX21637662 SRS18807751 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93131 0.92508 0.10425 0.10495 0.70715 0.70796 0.49956 0.48457 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26435 26435 SRR25917850 SRX21637662 SRS18807751 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02936 GSM7761835   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02936 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761835 GSM7761835: 22 02936; Danio rerio; RNA Seq GSM7761835 r1 GSM7761835 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02936_S12_L02_R1_001.fastq.gz 22-02936_S12_L02_R2_001.fastq.gz fastq fastq 3225005756.0 16454111.0 GSM7761835 r2 0:98 1:98 A:855605850;C:750757069;G:747157352;T:871043603;N:441882 98 98     855605850 750757069 747157352 871043603 441882 SRX21637662 SRS18807751 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93771 0.93339 0.10257 0.10429 0.70601 0.70727 0.50591 0.50179 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26436 26436 SRR25917851 SRX21637662 SRS18807751 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02936 GSM7761835   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02936 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761835 GSM7761835: 22 02936; Danio rerio; RNA Seq GSM7761835 r1 GSM7761835 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02936_S12_L03_R1_001.fastq.gz 22-02936_S12_L03_R2_001.fastq.gz fastq fastq 2793582512.0 14252972.0 GSM7761835 r3 0:98 1:98 A:742243213;C:648028314;G:645258591;T:757391700;N:660694 98 98     742243213 648028314 645258591 757391700 660694 SRX21637662 SRS18807751 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9379 0.9345 0.10089 0.10292 0.70887 0.70907 0.48756 0.50559 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26437 26437 SRR25917852 SRX21637662 SRS18807751 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02936 GSM7761835   source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing 22 02936 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5 GSM7761835 GSM7761835: 22 02936; Danio rerio; RNA Seq GSM7761835 r1 GSM7761835 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02936_S12_L04_R1_001.fastq.gz 22-02936_S12_L04_R2_001.fastq.gz fastq fastq 4412090144.0 22510664.0 GSM7761835 r4 0:98 1:98 A:1166366926;C:1029504824;G:1027522438;T:1188583356;N:112600 98 98     1166366926 1029504824 1027522438 1188583356 112600 SRX21637662 SRS18807751 SRA1706756 The University of Adelaide The University of Adelaide 2 0.9434 0.94005 0.10109 0.10212 0.70565 0.70627 0.49953 0.49393 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26438 26438 SRR25917853 SRX21637661 SRS18807750 SRP458896 PRJNA1013345 Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome GSE242370 Transcriptome Analysis Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA       22 02935 GSM7761834   source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing 22 02935 fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts whole brain   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3 GSM7761834 GSM7761834: 22 02935; Danio rerio; RNA Seq GSM7761834 r1 GSM7761834 1 RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   loader:fastq load.py 22-02935_S11_L01_R1_001.fastq.gz 22-02935_S11_L01_R2_001.fastq.gz fastq fastq 1425260256.0 7271736.0 GSM7761834 r1 0:98 1:98 A:380769821;C:328986720;G:327546654;T:387200001;N:757060 98 98     380769821 328986720 327546654 387200001 757060 SRX21637661 SRS18807750 SRA1706756 The University of Adelaide The University of Adelaide 2 0.93263 0.92464 0.09384 0.0946 0.70145 0.70159 0.50261 0.49541 98 98 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;