run_metadata: 52954

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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
52954	SRR9609653	SRX6373047	SRS5034104	SRP212225	PRJNA551501	Single cell RNA sequencing of zebrafish thyroid cells	GSE133466	Transcriptome Analysis	The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes surrounded by thyroid follicular epithelial cells or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes we performed droplet based next generation sequencing of individual thyrod gland cells. Using unsupervised clustering we could identify all the major cell types present in the thyroid gland. Moreover we could define sub populations within the major cell types demonstrating the presence of molecular heterogeneity within nominally homogenous cell populations. Overall design: We used 10x Genomics to profile thyroid cells from zebrafish. Thyroid gland was enzymatically dissociated and single cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired end mode R1: 26 cycles; I1: 8 cycles; R2: 57 cycles thus generating 45 mio fragments. The raw sequencing data was then processed with the 'count' command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ' expect cells' set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the 'mkgtf' command of Cell Ranger options: ' attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense'. Genome sequence and filtered annotation were then used as input to the 'mkref' command of Cell Ranger to build the appropriate Cellranger Reference.				2mpf Thyroid	GSM3909771		tissue:thyroid gland\|treatment:2mpf\|strain:Tgtg:mVenus T2A NTR\|tag:Normal	2mpf Thyroid	The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v2.1.0 provided by 10X Genomics with the option ‘ expect cells’ set to 6000 all other options were used as per default. To build the reference for Cell Ranger zebrafish genome GRCz10 as well as gene annotation Ensembl 87 were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger options: ‘ attribute=gene biotype:protein coding attribute=gene biotype:lincRNA –attribute=gene biotype:antisense’. Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference. Genome build: Zebrafish GRCz10 Supplementary files format and content: Matrix with rows as genes and columns as cells.	thyroid gland		Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer’s instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer’s protocol.		treatment:2mpf\|strain:Tgtg:mVenus T2A NTR\|tag:Normal	GSM3909771	GSM3909771: 2mpf Thyroid; Danio rerio; RNA Seq	GSM3909771		1	Enzymatic Dissociation The single cell suspension was adjusted to a concentration of about 800 cells per microliter and diluted with nuclease free water according to the manufacturer's instructions to yield 12000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system Zheng et al. 2016. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The cDNA was amplified with 10 cycles following the guidelines of the 10x Genomics user manual. The 10X Genomics single cell RNA seq library preparation involving fragmentation dA Tailing adapter ligation and indexing PCR – was performed based on the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP212225			L38695_Track-76231_R2.fastq.gz L38695_Track-76231_R1.fastq.gz	fastq fastq	9092057268.0	108238777.0	GSM3909771 r1	0:28 1:56	A:2584354341;C:1956113829;G:2086486284;T:2461142498;N:3960316	28	56			2584354341	1956113829	2086486284	2461142498	3960316	SRX6373047	SRS5034104	SRA914541	GEO	Singh Lab, IRIBHM	2	0.01005	0.87575	0.00435	0.23392	0.99192	0.80344	0.39812	0.53402	28	56	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Belgium	2019-06-27	Juvenile	Juvenile	Thyroid	Endocrine System