run_metadata: 35819

This data as json

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
35819	SRR33052297	SRX28317424	SRS24656193	SRP577565	PRJNA1248471	P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß 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.				AD3	GSM8898654		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		Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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℃ 5 minutes 13 cycles of 98℃ 20 seconds 58℃ 20 seconds and 72℃ 30 seconds and 1 cycle of 72℃ 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.		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℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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℃ 5 minutes 13 cycles of 98℃ 20 seconds 58℃ 20 seconds and 72℃ 30 seconds and 1 cycle of 72℃ 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.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP577565			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			15920282345	14771409856	14276809765	15621229410	1556684	SRX28317424	SRS24656193	SRA2109204	ShanTou University	ShanTou University												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc	unknown	unknown		China	2025-04-09	Undetermined	Undetermined	Brain	Nervous System