metadata: run_metadata: 15 rows where experiment.platform = "ILLUMINA", technology = "celseq" and tissue_curation

15 rows where experiment.platform = "ILLUMINA", technology = "celseq" and tissue_curation_coarse = "Surface Structure"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.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
32858	32858	SRR29482326	SRX24993370	SRS21694834	SRP515140	PRJNA1126247	Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]	GSE270356	Other	Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.		Internal melanocytes	GSM8340241	source name:Internal melanocytes\|tissue:Internal melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP\|geo loc name:missing\|collection date:missing	Internal melanocytes	BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq	Internal melanocytes	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.	mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues	tissue:Internal melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP	GSM8340241	GSM8340241: Internal melanocytes; Danio rerio; OTHER	GSM8340241 r1	GSM8340241	1	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP515140	HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz	fastq fastq	2957975418.0	34395063.0	GSM8340241 r1	0:26 1:60	A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268	26	60	738954503	560052455	520746060	1137116132	1106268	SRX24993370	SRS21694834	SRA1904773	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	2	0.11637	0.84116	0.10894	0.31188	0.98851	0.71526	0.6688	0.60221	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	small_rna	trueseq	sc	single_cell_plate	celseq	United States	2024-06-20	Undetermined	Adult	Skin	Surface Structure
32859	32859	SRR29482327	SRX24993369	SRS21694833	SRP515140	PRJNA1126247	Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq]	GSE270356	Other	Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.		Cutaneous melanocytes	GSM8340240	source name:Cutaneous melanocytes\|tissue:Cutaneous melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP\|geo loc name:missing\|collection date:missing	Cutaneous melanocytes	BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq	Cutaneous melanocytes	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.	mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues	tissue:Cutaneous melanocytes\|cell type:melanocytes\|genotype:mitfa / ; roy / fish injected with mitfa:GFP	GSM8340240	GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER	GSM8340240 r1	GSM8340240	1	Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP515140	HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz	fastq fastq	2680460212.0	31168142.0	GSM8340240 r1	0:26 1:60	A:704357434;C:519158361;G:467098420;T:988838604;N:1007393	26	60	704357434	519158361	467098420	988838604	1007393	SRX24993369	SRS21694833	SRA1904773	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	2	0.11679	0.81545	0.10693	0.5033	0.9808	0.76404	0.44749	0.57623	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	small_rna	trueseq	sc	single_cell_plate	celseq	United States	2024-06-20	Undetermined	Adult	Skin	Surface Structure
41278	41278	SRR6039223	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate01_R1.fastq.gz FinC_plate01_R2.fastq.gz	fastq fastq	4156649914.0	27498834.0	GSM2781033 r1	0:75.66 1:75.50	A:1184667722;C:812111779;G:946047137;T:1213491214;N:332062	75	75	1184667722	812111779	946047137	1213491214	332062	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.13191	0.2761	0.11086	0.21281	0.97997	0.9586	0.48699	0.512	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41279	41279	SRR6039224	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinE_plate07_R1.fastq.gz FinE_plate07_R2.fastq.gz	fastq fastq	7045442122.0	46667895.0	GSM2781033 r10	0:75.65 1:75.32	A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774	75	75	1992737539	1481998828	1584855122	1984679859	1170774	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.08863	0.2093	0.07731	0.18045	0.97934	0.95655	0.51176	0.52167	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41280	41280	SRR6039225	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinE_plate08_R1.fastq.gz FinE_plate08_R2.fastq.gz	fastq fastq	18530449971.0	122665653.0	GSM2781033 r11	0:75.68 1:75.38	A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121	75	75	4667348302	4333487274	4681098112	4848415162	101121	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.05595	0.12249	0.04637	0.10243	0.98415	0.96451	0.51093	0.52879	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41281	41281	SRR6039226	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate02_R1.fastq.gz FinC_plate02_R2.fastq.gz	fastq fastq	5961095878.0	39431358.0	GSM2781033 r2	0:75.66 1:75.51	A:1678045732;C:1185915367;G:1391829821;T:1704836561;N:468397	75	75	1678045732	1185915367	1391829821	1704836561	468397	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.13015	0.27027	0.11023	0.2177	0.97985	0.95964	0.5491	0.51821	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41282	41282	SRR6039227	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate03_R1.fastq.gz FinC_plate03_R2.fastq.gz	fastq fastq	6170232577.0	40846092.0	GSM2781033 r3	0:75.56 1:75.50	A:1866777846;C:1148020988;G:1151073641;T:2003993265;N:366837	75	75	1866777846	1148020988	1151073641	2003993265	366837	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.21215	0.40881	0.18316	0.33198	0.95919	0.91102	0.49711	0.53044	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41283	41283	SRR6039228	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate04_R1.fastq.gz FinC_plate04_R2.fastq.gz	fastq fastq	11725606474.0	77611342.0	GSM2781033 r4	0:75.62 1:75.46	A:3255674293;C:2567072026;G:2847190480;T:3054954945;N:714730	75	75	3255674293	2567072026	2847190480	3054954945	714730	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.06975	0.13988	0.05976	0.119	0.98533	0.97165	0.50512	0.46229	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41284	41284	SRR6039229	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate05_R1.fastq.gz FinC_plate05_R2.fastq.gz	fastq fastq	10721896827.0	71080622.0	GSM2781033 r5	0:75.44 1:75.41	A:3568478635;C:1747554798;G:1675757438;T:3729472140;N:633816	75	75	3568478635	1747554798	1675757438	3729472140	633816	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.32303	0.52716	0.2796	0.43703	0.94276	0.90057	0.51543	0.52404	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41285	41285	SRR6039230	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinC_plate06_R1.fastq.gz FinC_plate06_R2.fastq.gz	fastq fastq	4861560177.0	32218130.0	GSM2781033 r6	0:75.46 1:75.44	A:1606516776;C:766379277;G:687731226;T:1800636189;N:296709	75	75	1606516776	766379277	687731226	1800636189	296709	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.40204	0.66185	0.35053	0.55748	0.94637	0.89148	0.48866	0.50482	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41286	41286	SRR6039231	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinE_plate02_R1.fastq.gz FinE_plate02_R2.fastq.gz	fastq fastq	7812360278.0	51697480.0	GSM2781033 r7	0:75.54 1:75.58	A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950	75	75	2098454376	1641311761	1943503636	2128270555	819950	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.0105	0.02592	0.00852	0.02011	0.99626	0.98754	0.33762	0.53206	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41287	41287	SRR6039232	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinE_plate03_R1.fastq.gz FinE_plate03_R2.fastq.gz	fastq fastq	6704494628.0	44436630.0	GSM2781033 r8	0:75.49 1:75.39	A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167	75	75	2087008571	1124579474	1252171872	2240541544	193167	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.24968	0.47949	0.2198	0.40276	0.95154	0.89238	0.48976	0.54355	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
41288	41288	SRR6039233	SRX3187382	SRS2515225	SRP082370	PRJNA339266	Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations	GSE85755	Other	In many gene expression studies cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here we applied single cell mRNA sequencing scRNA seq to muscle stem cells and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly we detected similar subpopulations in other single cell datasets suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins respectively. For cell extraction traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed and live cells were subsequently sorted into plates using FACS. Next single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see "Cel seq barcodes 96.csv"; some primes numbers are bulk samples see "BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library"; Spike ins included see "ERCC92.fa"; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; "Merged CEL Seq AllMiceAndLibrariesMerged.csv" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y where Z = mouse x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Sate…	pubmed:28960196	SORT Seq zebrafish fin merged	GSM2781033	tissue:All cells from caudal fin\|strain:Wildtype	SORT Seq zebrafish fin merged	Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see "Cel seq barcodes 384" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see "ERCC92.fa" Supplementary files format and content: .coutt.csv TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome…	All cells from caudal fin	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.		strain:Wildtype	GSM2781033	GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq	GSM2781033		1	Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius post which SORT Seq Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017 was applied. As in SORT Seq protocol Muraro et al. 2016 with minor modifications as desribed in Supplementary Methods of van den Brink et al. 2017.	GEO Accession:GSM2781033	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP082370	FinE_plate04_R2.fastq.gz FinE_plate04_R1.fastq.gz	fastq fastq	8402262674.0	55692887.0	GSM2781033 r9	0:75.48 1:75.39	A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856	75	75	2618499207	1444061167	1613776766	2725680678	244856	SRX3187382	SRS2515225	SRA453335	GEO	Alexander van Oudenaarden, Hubrecht Institute	2	0.26069	0.43322	0.23296	0.36903	0.95663	0.90542	0.50653	0.52921	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2017-09-12	Undetermined	Adult	Fin	Surface Structure
44015	44015	SRR6211474	SRX3320751	SRS2626325	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.	pubmed:29644996	Time course 10h24h mRNA	GSM2830047	source name:Full organism\|strain/background:Zebrabow M\|tissue:Whole body\|developmental stage:Embryo\|time point:10h 24h	Time course 10h24h mRNA	Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1 2 3 4 6 8 10 and 24 hours 2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample we calculated the percentage of unscarred RFP. We fit a negative exponential to this data assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode.	Full organism	Trizol extraction of RNA. CEL seq		strain/background:Zebrabow M\|tissue:Whole body\|developmental stage:Embryo\|time point:10h 24h	GSM2830047	GSM2830047: Time course 10h24h mRNA; Danio rerio; OTHER	GSM2830047		1	Trizol extraction of RNA. CEL seq	GEO Accession:GSM2830047	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	dyn_RNA_10h24h_S13_R2_001.fastq.gz dyn_RNA_10h24h_S13_R1_001.fastq.gz	fastq fastq	1456176300.0	9707842.0	GSM2830047 r1	0:100 1:50	A:216943159;C:398650961;G:516656316;T:323899428;N:26436	100	50	216943159	398650961	516656316	323899428	26436	SRX3320751	SRS2626325	SRA623333	GEO	Max Delbrück Center	2	3e-05	0.00111	0.0	0.0011	0.99995	1.0	0.75		100	50	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_plate	celseq	Germany	2017-10-24	Undetermined	Embryo	Trunk	Surface Structure
44016	44016	SRR6211473	SRX3320750	SRS2626324	SRP121343	PRJNA415636	Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars	GSE106121	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.	pubmed:29644996	Time course 3h6h8h mRNA	GSM2830046	source name:Full organism\|strain/background:Zebrabow M\|tissue:Whole body\|developmental stage:Embryo\|time point:3h 6h 8h	Time course 3h6h8h mRNA	Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1 2 3 4 6 8 10 and 24 hours 2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample we calculated the percentage of unscarred RFP. We fit a negative exponential to this data assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode.	Full organism	Trizol extraction of RNA. CEL seq		strain/background:Zebrabow M\|tissue:Whole body\|developmental stage:Embryo\|time point:3h 6h 8h	GSM2830046	GSM2830046: Time course 3h6h8h mRNA; Danio rerio; OTHER	GSM2830046		1	Trizol extraction of RNA. CEL seq	GEO Accession:GSM2830046	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500	SRP121343	dyn_RNA_3h6h8h_S12_R1_001.fastq.gz dyn_RNA_3h6h8h_S12_R2_001.fastq.gz	fastq fastq	1382400000.0	9216000.0	GSM2830046 r1	0:100 1:50	A:219040774;C:378529638;G:475287684;T:309516830;N:25074	100	50	219040774	378529638	475287684	309516830	25074	SRX3320750	SRS2626324	SRA623333	GEO	Max Delbrück Center	2	5e-05	0.00116	0.0	0.00115	0.99987	1.0	0.5		100	50	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	other	unknown	sc	single_cell_plate	celseq	Germany	2017-10-24	Undetermined	Embryo	Trunk	Surface Structure

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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");;