run_metadata: 30663

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
30663	SRR28125660	SRX23770349	SRS20595836	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 SRX13397705 SAMN24007732 lck eGFP Thymus 1 .filtered feature bc matrix.h5 GSM5732078 Adult Thymus 2 SRX13397706 SAMN24007733 lck eGFP Thymus 2 .filtered feature bc matrix.h5 GSM5732079 Juvenile Thymus 1 SRX13397707 SAMN24007734 4wpfThymus 1.filtered feature bc matrix.h5 GSM5732080 Juvenile Thymus 2 SRX13397708 SAMN24007735 4wpfThymus 3.filtered feature bc matrix.h5 GSM5732081 Juvenile Thymus 3 SRX13397709 SAMN24007736 4wpfThymus 5.filtered feature bc matrix.h5 GSM5732082 Juvenile Thymus 4 SRX13397710 SAMN24007737 4wpfThymus 6.filtered feature bc matrix.h5				adult thy liberase 2	GSM8115868		tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115868	GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq	GSM8115868 r1	GSM8115868	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP492124		loader:fastq load.py	adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz	fastq fastq fastq	64816880653.0	510369139.0	GSM8115868 r1	0:8 1:28 2:91	A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488	8	28	91		12985717325	10400471721	10926930853	12129907262	564488	SRX23770349	SRS20595836			Oncology/Hematology, Boston Children's Hospital	1	0.90014		0.13619		0.81103		0.54906		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined