metadata: run_metadata: 14 rows where devstage_curation_coarse = "Undetermined" and technology = "indrops"

14 rows where devstage_curation_coarse = "Undetermined" and technology = "indrops"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
48402	48402	SRR7240617	SRX4146448	SRS3360068	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	cell line B fish	GSM3167490	tissue:melanoma cell line cells in a fish\|time:NA\|type:CEL Seq	cell line B fish	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	melanoma cell line cells in a fish	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:NA\|type:CEL Seq	GSM3167490	GSM3167490: cell line B fish; Danio rerio; RNA Seq	GSM3167490	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167490	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	Efish_R2_001.fastq.gz Efish_R1_001.fastq.gz	fastq fastq	7254277529.0	93829840.0	GSM3167490 r1	0:21.77 1:55.55	A:2013320976;C:1304302014;G:1275408938;T:2658668719;N:2576882	21	55	2013320976	1304302014	1275408938	2658668719	2576882	SRX4146448	SRS3360068	SRA713129	GEO	Yanai, NYU	2	0.35315	0.81249	0.33399	0.25257	0.99222	0.89526	0.4613	0.58245	26	58	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48403	48403	SRR7240616	SRX4146447	SRS3360067	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	cell line B cultured	GSM3167489	tissue:melanoma cell line cells\|time:NA\|type:CEL Seq	cell line B cultured	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	melanoma cell line cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:NA\|type:CEL Seq	GSM3167489	GSM3167489: cell line B cultured; Danio rerio; RNA Seq	GSM3167489	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167489	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	Edish_R1_001.fastq.gz Edish_R2_001.fastq.gz	fastq fastq	3315328468.0	40362508.0	GSM3167489 r1	0:24.95 1:57.19	A:870288472;C:583199815;G:546968405;T:1313319011;N:1552765	24	57	870288472	583199815	546968405	1313319011	1552765	SRX4146447	SRS3360067	SRA713129	GEO	Yanai, NYU	2	0.4358	0.77687	0.41224	0.1804	0.98673	0.92372	0.39048	0.55564	26	58	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48404	48404	SRR7240615	SRX4146446	SRS3360066	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	cell line A fish	GSM3167488	tissue:melanoma cell line cells in a fish\|time:NA\|type:CEL Seq	cell line A fish	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	melanoma cell line cells in a fish	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:NA\|type:CEL Seq	GSM3167488	GSM3167488: cell line A fish; Danio rerio; RNA Seq	GSM3167488	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167488	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	Afish_R1_001.fastq.gz Afish_R2_001.fastq.gz	fastq fastq	1760981184.0	27515331.0	GSM3167488 r1	0:13 1:51	A:527501645;C:354257934;G:378832308;T:500290272;N:99025	13	51	527501645	354257934	378832308	500290272	99025	SRX4146446	SRS3360066	SRA713129	GEO	Yanai, NYU	2	0.0	0.86857	0.0	0.2721	1.0	0.84869		0.53458	13	51	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48405	48405	SRR7240614	SRX4146445	SRS3360065	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	cell line A cultured	GSM3167487	tissue:melanoma cell line cells\|time:NA\|type:CEL Seq	cell line A cultured	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	melanoma cell line cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:NA\|type:CEL Seq	GSM3167487	GSM3167487: cell line A cultured; Danio rerio; RNA Seq	GSM3167487	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167487	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	Adish_R1_001.fastq.gz Adish_R2_001.fastq.gz	fastq fastq	2758577088.0	43102767.0	GSM3167487 r1	0:13 1:51	A:901840607;C:537128308;G:580843998;T:738597709;N:166466	13	51	901840607	537128308	580843998	738597709	166466	SRX4146445	SRS3360065	SRA713129	GEO	Yanai, NYU	2	0.0	0.73258	0.0	0.1063	1.0	0.85865		0.58942	13	51	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48406	48406	SRR7240613	SRX4146444	SRS3360064	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF3 ST	GSM3167486	tissue:tumor tissue section\|time:NA\|type:ST	ZF3 ST	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor tissue section	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:NA\|type:ST	GSM3167486	GSM3167486: ZF3 ST; Danio rerio; RNA Seq	GSM3167486	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167486	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00715A_S4_R1_001.fastq.gz BS00715A_S4_R2_001.fastq.gz	fastq fastq	8346596335.0	108397355.0	GSM3167486 r1	0:31 1:46	A:2031003864;C:1619238171;G:2052969755;T:2622927017;N:20457528	31	46	2031003864	1619238171	2052969755	2622927017	20457528	SRX4146444	SRS3360064	SRA713129	GEO	Yanai, NYU	2	0.0219	0.7716	0.01972	0.18796	0.99429	0.83086	0.55276	0.5937	31	46	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48407	48407	SRR7240612	SRX4146443	SRS3360063	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF2 time point 2	GSM3167485	tissue:tumor cells\|time:2017 06 08\|type:inDrop	ZF2 time point 2	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 08\|type:inDrop	GSM3167485	GSM3167485: ZF2 time point 2; Danio rerio; RNA Seq	GSM3167485	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167485	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00418A_S2_R1_001.fastq.gz BS00418A_S2_R2_001.fastq.gz	fastq fastq	18879921248.0	219533968.0	GSM3167485 r1	0:35 1:51	A:4915572934;C:4065059620;G:5109553396;T:4789479927;N:255371	35	51	4915572934	4065059620	5109553396	4789479927	255371	SRX4146443	SRS3360063	SRA713129	GEO	Yanai, NYU	2	0.22339	0.01677	0.04998	0.01242	0.904	0.99795	0.64786	0.76205	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48408	48408	SRR7240611	SRX4146442	SRS3360062	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF2 time point 1	GSM3167484	tissue:tumor cells\|time:2017 05 25\|type:inDrop	ZF2 time point 1	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 05 25\|type:inDrop	GSM3167484	GSM3167484: ZF2 time point 1; Danio rerio; RNA Seq	GSM3167484	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167484	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00417A_S1_R1_001.fastq.gz BS00417A_S1_R2_001.fastq.gz	fastq fastq	15195762260.0	176694910.0	GSM3167484 r1	0:35 1:51	A:3730288221;C:3100069649;G:3917397047;T:4447806244;N:201099	35	51	3730288221	3100069649	3917397047	4447806244	201099	SRX4146442	SRS3360062	SRA713129	GEO	Yanai, NYU	2	0.45584	0.02194	0.10866	0.01434	0.8508	0.99594	0.56562	0.74387	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48409	48409	SRR7240610	SRX4146441	SRS3360061	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 2 time point 3	GSM3167483	tissue:tumor cells\|time:2017 06 22\|type:inDrop	ZF1 tumor 2 time point 3	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 22\|type:inDrop	GSM3167483	GSM3167483: ZF1 tumor 2 time point 3; Danio rerio; RNA Seq	GSM3167483	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167483	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00516A_S3_R1_001.fastq.gz BS00516A_S3_R2_001.fastq.gz	fastq fastq	9387695500.0	109159250.0	GSM3167483 r1	0:35 1:51	A:1996385781;C:1819073805;G:2713262409;T:2858501572;N:471933	35	51	1996385781	1819073805	2713262409	2858501572	471933	SRX4146441	SRS3360061	SRA713129	GEO	Yanai, NYU	2	0.78336	0.12929	0.17042	0.07562	0.83116	0.98196	0.62361	0.7167	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48410	48410	SRR7240609	SRX4146440	SRS3360060	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 2 time point 2	GSM3167482	tissue:tumor cells\|time:2017 06 15\|type:inDrop	ZF1 tumor 2 time point 2	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 15\|type:inDrop	GSM3167482	GSM3167482: ZF1 tumor 2 time point 2; Danio rerio; RNA Seq	GSM3167482	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167482	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00515A_S2_R1_001.fastq.gz BS00515A_S2_R2_001.fastq.gz	fastq fastq	7645768166.0	88904281.0	GSM3167482 r1	0:35 1:51	A:1659830380;C:1483879485;G:1955626018;T:2546036303;N:395980	35	51	1659830380	1483879485	1955626018	2546036303	395980	SRX4146440	SRS3360060	SRA713129	GEO	Yanai, NYU	2	0.78059	0.04637	0.15414	0.03167	0.81156	0.99125	0.5786	0.82113	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48411	48411	SRR7240608	SRX4146439	SRS3360059	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 2 time point 1	GSM3167481	tissue:tumor cells\|time:2017 06 02\|type:inDrop	ZF1 tumor 2 time point 1	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 02\|type:inDrop	GSM3167481	GSM3167481: ZF1 tumor 2 time point 1; Danio rerio; RNA Seq	GSM3167481	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167481	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	BS00514A_S1_R1_001.fastq.gz BS00514A_S1_R2_001.fastq.gz	fastq fastq	9759139906.0	113478371.0	GSM3167481 r1	0:35 1:51	A:2243979852;C:1912724883;G:2573948349;T:3027979990;N:506832	35	51	2243979852	1912724883	2573948349	3027979990	506832	SRX4146439	SRS3360059	SRA713129	GEO	Yanai, NYU												B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48412	48412	SRR7240607	SRX4146438	SRS3360058	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 1 time point 4	GSM3167480	tissue:tumor cells\|time:2017 06 22\|type:inDrop	ZF1 tumor 1 time point 4	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 22\|type:inDrop	GSM3167480	GSM3167480: ZF1 tumor 1 time point 4; Danio rerio; RNA Seq	GSM3167480	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167480	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	t4_R1.fastq.gz t4_R2.fastq.gz	fastq fastq	13285828250.0	154486375.0	GSM3167480 r1	0:35 1:51	A:3106404784;C:2642499289;G:3548717541;T:3987624595;N:582041	35	51	3106404784	2642499289	3548717541	3987624595	582041	SRX4146438	SRS3360058	SRA713129	GEO	Yanai, NYU	2	0.588	0.04697	0.13733	0.02918	0.8308	0.99119	0.59025	0.75017	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48413	48413	SRR7240606	SRX4146437	SRS3360057	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 1 time point 3	GSM3167479	tissue:tumor cells\|time:2017 06 15\|type:inDrop	ZF1 tumor 1 time point 3	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 15\|type:inDrop	GSM3167479	GSM3167479: ZF1 tumor 1 time point 3; Danio rerio; RNA Seq	GSM3167479	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167479	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	t3_R1.fastq.gz t3_R2.fastq.gz	fastq fastq	12949174972.0	150571802.0	GSM3167479 r1	0:35 1:51	A:3045479995;C:2532873724;G:3340677661;T:4029571801;N:571791	35	51	3045479995	2532873724	3340677661	4029571801	571791	SRX4146437	SRS3360057	SRA713129	GEO	Yanai, NYU	2	0.56814	0.02383	0.11626	0.01895	0.82599	0.99569	0.55364	0.73492	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48414	48414	SRR7240605	SRX4146436	SRS3360056	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 1 time point 2	GSM3167478	tissue:tumor cells\|time:2017 06 09\|type:inDrop	ZF1 tumor 1 time point 2	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 09\|type:inDrop	GSM3167478	GSM3167478: ZF1 tumor 1 time point 2; Danio rerio; RNA Seq	GSM3167478	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167478	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	t2_R1.fastq.gz t2_R2.fastq.gz	fastq fastq	24232410834.0	281772219.0	GSM3167478 r1	0:35 1:51	A:5863941889;C:4979860831;G:6744452007;T:6643024623;N:1131484	35	51	5863941889	4979860831	6744452007	6643024623	1131484	SRX4146436	SRS3360056	SRA713129	GEO	Yanai, NYU	2	0.36566	0.03272	0.07206	0.03013	0.85719	0.99673	0.55683	0.65034	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
48415	48415	SRR7240604	SRX4146435	SRS3360055	SRP149420	PRJNA473915	Single cell analysis of tumor progression reveals the function structure and evolution of cancer archetypes	GSE115140	Transcriptome Analysis	The classic cancer evolution model posits that driver mutations sweep the population sequentially as the complete set of hallmarks are assembled by the neoplastic clone. However recent work has challenged this model revealing that most tumors contain highly complex dynamics with genetic diversity reflecting distinct clonal architectures. The functional and phenotypic heterogeneity also has been shown to have a crucial influence on the fate of the tumor5–10. However it is not well understood how distinct tumor clonal populations coexist and function. Here we study tumor architecture at the level of individual cells by sampling a zebrafish melanoma tumor over time and space. We found that cancer transcriptional programs can be classified to three archetypes each exploiting the existing neural crest mature melanocytes and stress modules and distinct intra tumor locations. Strikingly these archetypes are conserved in human melanoma. Further we found that the cancer cells are comprised of two distinct clones where one expresses a unique archetype. Over time we found that the cells of this clone adapt by exhibiting a more similar profile to the corresponding archetype. Overall design: Single cell RNA sequencing of zebrafish tumor cells from 2 zebrafish at multiple time points.	ZF1 tumor 1 time point 1	GSM3167477	tissue:tumor cells\|time:2017 06 02\|type:inDrop	ZF1 tumor 1 time point 1	Illumina RTA v2 software was used for basecalling and quality determination. Raw sequencing data obtained from the inDrop method was processed using a custom built pipeline available at https://github.com/flo compbio/singlecell. Briefly the location of the known “W1” adapter sequence of the inDrop RT primer was located in the barcode read read 2. Reads for which the W1 sequence could not be detected were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read which can range from 8 11 bp as well as the start position of the second part of the inDrop cell barcode which is 8 bp long. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally UMI sequence was extracted and reads with low confidence base calls for the six bases comprising the UMI sequence minimum PHRED score less than 20 were discarded. The reads containing the mRNA sequence read 1 were mapped using STAR with parameter “—outSAMmultNmax 1” and default settings otherwise27. Expression was quantified by counting the number of reads mapped to each gene and correcting for UMI as described previously Grün et al. 2014 The genome and gff file used included the zebrafish genome and the BRAF human vector. Single cell transcriptomes with UMIs>750 mitochondrial transcripts < 20% and ribosomal transcripts < 30% were retained for analysis. Raw sequencing data obtained from the Spatial Transcriptomics ST method were processed using a publicly available pipeline https://github.com/jfnavarro/st pipeline. Briefly quality trimming is performed to remove low quality bases and reads with long nucleotide stretches > 15. Read 2 transcript sequence is mapped with STAR 2.5.1 and Read 1 spatial barcode is demultiplexed with Taggd. Reads that contain both a valid spatial barcode and are correctly map are kept. UMIs are then counted with htseq …	tumor cells	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	time:2017 06 02\|type:inDrop	GSM3167477	GSM3167477: ZF1 tumor 1 time point 1; Danio rerio; RNA Seq	GSM3167477	1	For inDrop and CEL Seq samples were obtained using a dissecting forceps and placing the desired tissue sample in 1.5 mL Eppendorf tube followed by addition of 500 uL 0.25% Trypsin EDTA for digestion. The digestion was carried out at 37ºC in thermomixer for 15 30 min to soften tissue every 5 minutes mashing the tissue using a disposable pestle to break up softened tissue. Upon completion of incubation at 37ºC 500 uL of DMEM10 were added to deactivate the trypsin. Cells were washed three times by spinning down the sample at 500 rcf for 5 minutes and resuspended in PBS. Then sample was filtered twice using 5 mL polystyrene round bottom tube with 35um cell strainer. Viability and single cell consistency were checked prior to encapsulation of the cells using the inDrop system for each biopsy taken. For the ST sample sections from zebrafish melanoma tumors were obtained by sectioning the entire tumor with its surrounding. Tissue was gently washed with cold 1X PBS and 4 5 mm3 cubes were removed with a scalpel for OCT embedding. Tissue was transferred from 1X PBS to a dry sterile 10 cm dish and gently dried prior to equilibration in cold OCT for 2 minutes. The tissue was then transferred to a tissue mold with OCT and snap frozen in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C until further use. Prior to cryosectioning the cryostat was cleaned with 100% ethanol and equilibrated to an internal temperature of 18°C for 30 minutes. Once equilibrated OCT embedded tissue blocks were mounted onto the chuck and equilibrated to the cryostat temperature for 15 20 minutes prior to trimming. ST slide was also placed inside cryostat to keep the slide cold and minimize RNase activity. Sections were cut at 10 µm sections and mounted onto the ST arrays and stored at 80°C until use maximum of two weeks. Prior to fixation and staining the ST array was removed from the 80C and into a RNase free biosafety hood for 5 minutes to bring to room temperature followed by warming on a 37°C heat block for 1 mi…	GEO Accession:GSM3167477	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP149420	t1_R1.fastq.gz t1_R2.fastq.gz	fastq fastq	9252930920.0	107592220.0	GSM3167477 r1	0:35 1:51	A:2335222288;C:1982182390;G:2612836318;T:2322125944;N:563980	35	51	2335222288	1982182390	2612836318	2322125944	563980	SRX4146435	SRS3360055	SRA713129	GEO	Yanai, NYU	2	0.23022	0.0283	0.05144	0.02308	0.90254	0.99608	0.58852	0.70642	35	51	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	indrops	United States	2018-05-31	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor

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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");;