{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and experiment.platform = \"DNBSEQ\"", "rows": [[35816, "SRR33052294", "SRX28317427", "SRS24656196", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "WT", "GSM8898657", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "WT", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898657", "GSM8898657: WT; Danio rerio; RNA Seq", "GSM8898657 r1", "GSM8898657", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "WT_L01_read_1.fq.gz WT_L01_read_2.fq.gz", "fastq fastq", 74425524705.0, 551300183.0, "GSM8898657 r1", "0:35 1:100", "A:19898122181;C:17423066656;G:16942100032;T:20160847006;N:1388830", 35, 100, null, null, 19898122181, 17423066656, 16942100032, 20160847006, 1388830, "SRX28317427", "SRS24656196", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35817, "SRR33052295", "SRX28317426", "SRS24656195", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD5", "GSM8898656", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD5", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898656", "GSM8898656: AD5; Danio rerio; RNA Seq", "GSM8898656 r1", "GSM8898656", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD5_L01_read_1.fq.gz AD5_L01_read_2.fq.gz", "fastq fastq", 84955633785.0, 629300991.0, "GSM8898656 r1", "0:35 1:100", "A:22736382740;C:20123949961;G:19583698932;T:22509389862;N:2212290", 35, 100, null, null, 22736382740, 20123949961, 19583698932, 22509389862, 2212290, "SRX28317426", "SRS24656195", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35818, "SRR33052296", "SRX28317425", "SRS24656194", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD4", "GSM8898655", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD4", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898655", "GSM8898655: AD4; Danio rerio; RNA Seq", "GSM8898655 r1", "GSM8898655", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD4_L01_read_1.fq.gz AD4_L01_read_2.fq.gz", "fastq fastq", 44786077200.0, 331748720.0, "GSM8898655 r1", "0:35 1:100", "A:11725098079;C:10594300338;G:10327407801;T:12138018161;N:1252821", 35, 100, null, null, 11725098079, 10594300338, 10327407801, 12138018161, 1252821, "SRX28317425", "SRS24656194", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35819, "SRR33052297", "SRX28317424", "SRS24656193", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish  providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3  AD4  AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD3", "GSM8898654", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD3", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files  matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898654", "GSM8898654: AD3; Danio rerio; RNA Seq", "GSM8898654 r1", "GSM8898654", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI  China surface and incubated at 37\u2103 for 3 minutes. Then  the sections were fixed in methanol and incubated for 40 minutes at  20\u2103 before Stereo seq library preparation. Where indicated  the same sections were stained with nucleic acid dye Thermo fisher  Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L  tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma  P7000 in 0.01 M HCl buffer  incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo  AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB  M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen  18064 014  10 U/ml reverse transcriptase  1 mM dNTPs  1 M betaine solution PCR reagent  7.5 mM MgCl2  5 mM DTT  2 U/ml RNase inhibitor  2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription  tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl  25 mM EDTA  100 mM NaCl  0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme  cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo  Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes  post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product  1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer  0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes  13 cycles of 98\u2103 20 seconds  58\u2103 20 seconds and 72\u2103 30 seconds  and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153  used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD3_L01_read_1.fq.gz AD3_L01_read_2.fq.gz", "fastq fastq", 60591288060.0, 448824356.0, "GSM8898654 r1", "0:35 1:100", "A:15920282345;C:14771409856;G:14276809765;T:15621229410;N:1556684", 35, 100, null, null, 15920282345, 14771409856, 14276809765, 15621229410, 1556684, "SRX28317424", "SRS24656193", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [71409, "SRR21590947", "SRX17592668", "SRS15130333", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 WT 7dpi", "GSM6586115", null, "source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing", "danRer11 WT 7dpi", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi", "GSM6586115", "GSM6586115: danRer11 WT 7dpi; Danio rerio; RNA Seq", "GSM6586115 r1", "GSM6586115", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample4_S1_L001_R2_001.fastq.gz KP_VC_sample4_S1_L001_R1_001.fastq.gz", "fastq fastq", 50454681480.0, 423988920.0, "GSM6586115 r1", "0:28 1:91", "A:14159328348;C:10820572193;G:11486998159;T:13985883249;N:1899531", 28, 91, null, null, 14159328348, 10820572193, 11486998159, 13985883249, 1899531, "SRX17592668", "SRS15130333", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.00753, 0.88935, 0.00224, 0.18283, 0.98528, 0.77656, 0.24704, 0.5609, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71410, "SRR21590948", "SRX17592667", "SRS15130332", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 WT sham", "GSM6586114", null, "source name:spinal cord|genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing", "danRer11 WT sham", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:WT|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham", "GSM6586114", "GSM6586114: danRer11 WT sham; Danio rerio; RNA Seq", "GSM6586114 r1", "GSM6586114", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample3_S1_L001_R1_001.fastq.gz KP_VC_sample3_S1_L001_R2_001.fastq.gz", "fastq fastq", 49434606578.0, 415416862.0, "GSM6586114 r1", "0:28 1:91", "A:13689985840;C:10750469002;G:11165716773;T:13825714788;N:2720175", 28, 91, null, null, 13689985840, 10750469002, 11165716773, 13825714788, 2720175, "SRX17592667", "SRS15130332", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.01019, 0.90181, 0.00309, 0.16838, 0.98522, 0.78459, 0.27523, 0.51926, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71411, "SRR21590949", "SRX17592666", "SRS15130331", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 hbegfaKO 7dpi", "GSM6586113", null, "source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi|geo loc name:missing|collection date:missing", "danRer11 hbegfaKO 7dpi", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:7dpi", "GSM6586113", "GSM6586113: danRer11 hbegfaKO 7dpi; Danio rerio; RNA Seq", "GSM6586113 r1", "GSM6586113", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample2_S1_L001_R1_001.fastq.gz KP_VC_sample2_S1_L001_R2_001.fastq.gz", "fastq fastq", 48346471411.0, 406272869.0, "GSM6586113 r1", "0:28 1:91", "A:13278513523;C:10826562396;G:11318717473;T:12918171753;N:4506266", 28, 91, null, null, 13278513523, 10826562396, 11318717473, 12918171753, 4506266, "SRX17592666", "SRS15130331", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.01379, 0.89003, 0.00446, 0.1909, 0.97808, 0.78415, 0.32888, 0.6007, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [71412, "SRR21590950", "SRX17592665", "SRS15130330", "SRP397443", "PRJNA880627", "Single cell sequencing of WT and hb egfaKO zebrafish spinal cord  at 1 week post sham or transection injury.", "GSE213435", "Transcriptome Analysis", "We identified hb egfa as a secreted factor necessary and sufficient for spinal cord regeneration in zebrafish. To elucidate the Hb egfa mechanism of action  we perforemd single cell sequencing of WT and hb egfaKO zebrafish spinal cord. Overall design: Adult zebrafish were subjected to spinal cord transection. 2 mm rostral and caudal to the transection site were collected at 1 xxx post injury. Spinal cord of sham injured animals was collected as control. Samples were and subjected to the 10X Genomics pipeline for single cell sequencing 4 samples in total  WT 1 wpi  WT sham  hb egfaKO 1 wpi  hb egfaKO sham.", null, "pubmed:37567873", null, "danRer11 hbegfaKO sham", "GSM6586112", null, "source name:spinal cord|genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham|geo loc name:missing|collection date:missing", "danRer11 hbegfaKO sham", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danRer11 Supplementary files format and content: h5 files for count table", "spinal cord", null, "Samples were processed following the 10X Chromium platform following the manufacturer\u2019s guidelines  using 10X Single Cell 3\u2019 v3 chemistry 10X Genomics  Pleasanton  USA.", null, "genotype:hbegfaKO|tissue:spinal cord|strain:Ekkwill EK|age:6 month|treatment:sham", "GSM6586112", "GSM6586112: danRer11 hbegfaKO sham; Danio rerio; RNA Seq", "GSM6586112 r1", "GSM6586112", "1", "Samples were processed following the 10X Chromium platform following the manufacturer's guidelines  using 10X Single Cell three prime v3 chemistry 10X Genomics  Pleasanton  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP397443", null, null, "KP_VC_sample1_S1_L001_R1_001.fastq.gz KP_VC_sample1_S1_L001_R2_001.fastq.gz", "fastq fastq", 50009919813.0, 420251427.0, "GSM6586112 r1", "0:28 1:91", "A:13721824199;C:11296818044;G:11807686254;T:13179637678;N:3953638", 28, 91, null, null, 13721824199, 11296818044, 11807686254, 13179637678, 3953638, "SRX17592665", "SRS15130330", "SRA1500311", "Cell biology, Duke University", "Poss, Cell Biology, Duke University", 2, 0.01254, 0.83945, 0.00371, 0.16358, 0.98378, 0.80728, 0.25895, 0.57907, 28, 91, "T", "B", "sc-like readlen", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-09-15", "Adult", "Adult", "Spinal Cord", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 8, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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[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 from run_metadata where \"experiment.library_source\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC SINGLE CELL", "p1": "DNBSEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.platform=DNBSEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 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"truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.platform=DNBSEQ", "results": [{"value": "Adult", "label": "Adult", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.platform=DNBSEQ&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&experiment.platform=DNBSEQ&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": 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