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50 rows where technology = "fluidigm" and tissue_curation = "Undetermined"

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  • Undetermined · 50 ✖

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  • fluidigm · 50 ✖

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Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
43663 43663 SRR6025626 SRX3176118 SRS2505881 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 33775 GSM2779358   tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 33775 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive bulk cells   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779358 GSM2779358: Sample 33775; Danio rerio; RNA Seq GSM2779358   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779358 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s33775_R1.fastq.gz s33775_R2.fastq.gz fastq fastq 13661182750.0 54644731.0 GSM2779358 r1 0:125 1:125 A:3950172269;C:2838736020;G:2884461639;T:3801586863;N:186225959 125 125     3950172269 2838736020 2884461639 3801586863 186225959 SRX3176118 SRS2505881 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.3904 0.36122 0.09478 0.08957 0.84609 0.8744 0.59399 0.59594 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43664 43664 SRR6025625 SRX3176117 SRS2505880 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 33774 GSM2779357   tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 33774 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive bulk cells   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779357 GSM2779357: Sample 33774; Danio rerio; RNA Seq GSM2779357   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779357 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s33774_R1.fastq.gz s33774_R2.fastq.gz fastq fastq 20456842250.0 81827369.0 GSM2779357 r1 0:125 1:125 A:5563992445;C:4574332893;G:4653958315;T:5384278584;N:280280013 125 125     5563992445 4574332893 4653958315 5384278584 280280013 SRX3176117 SRS2505880 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.31701 0.30885 0.06888 0.06856 0.87685 0.90228 0.64144 0.64023 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43665 43665 SRR6025624 SRX3176116 SRS2505879 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 33773 GSM2779356   tissue:OMP positive bulk cells|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 33773 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive bulk cells   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779356 GSM2779356: Sample 33773; Danio rerio; RNA Seq GSM2779356   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779356 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s33773_R1.fastq.gz s33773_R2.fastq.gz fastq fastq 16320124000.0 65280496.0 GSM2779356 r1 0:125 1:125 A:4965742539;C:3472731005;G:3562901570;T:4084584782;N:234164104 125 125     4965742539 3472731005 3562901570 4084584782 234164104 SRX3176116 SRS2505879 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.33805 0.33895 0.08212 0.0862 0.92659 0.93628 0.67629 0.68777 125 125 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43666 43666 SRR6025623 SRX3176115 SRS2505878 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23575 GSM2779355   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23575 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779355 GSM2779355: Sample 23575; Danio rerio; RNA Seq GSM2779355   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779355 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23575_R1.fastq.gz s23575_R2.fastq.gz fastq fastq 12544724200.0 62723621.0 GSM2779355 r1 0:100 1:100 A:3618844414;C:2653220939;G:2611261038;T:3661178111;N:219698 100 100     3618844414 2653220939 2611261038 3661178111 219698 SRX3176115 SRS2505878 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93157 0.92953 0.58399 0.58725 0.94836 0.9499 0.53141 0.54357 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43667 43667 SRR6025622 SRX3176114 SRS2505877 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23574 GSM2779354   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23574 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779354 GSM2779354: Sample 23574; Danio rerio; RNA Seq GSM2779354   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779354 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23574_R1.fastq.gz s23574_R2.fastq.gz fastq fastq 12628944800.0 63144724.0 GSM2779354 r1 0:100 1:100 A:3604039692;C:2698993964;G:2661293369;T:3664381683;N:236092 100 100     3604039692 2698993964 2661293369 3664381683 236092 SRX3176114 SRS2505877 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92997 0.92999 0.56527 0.57132 0.95394 0.9554 0.49391 0.49038 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43668 43668 SRR6025621 SRX3176113 SRS2505876 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23573 GSM2779353   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23573 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779353 GSM2779353: Sample 23573; Danio rerio; RNA Seq GSM2779353   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779353 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23573_R1.fastq.gz s23573_R2.fastq.gz fastq fastq 11247992600.0 56239963.0 GSM2779353 r1 0:100 1:100 A:3267497015;C:2352817279;G:2318570280;T:3308902561;N:205465 100 100     3267497015 2352817279 2318570280 3308902561 205465 SRX3176113 SRS2505876 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92371 0.92218 0.48304 0.49128 0.92957 0.93178 0.50806 0.51052 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43669 43669 SRR6025620 SRX3176112 SRS2505875 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23572 GSM2779352   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23572 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779352 GSM2779352: Sample 23572; Danio rerio; RNA Seq GSM2779352   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779352 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23572_R2.fastq.gz s23572_R1.fastq.gz fastq fastq 11219692000.0 56098460.0 GSM2779352 r1 0:100 1:100 A:3258674288;C:2339096536;G:2306091995;T:3315620058;N:209123 100 100     3258674288 2339096536 2306091995 3315620058 209123 SRX3176112 SRS2505875 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.91678 0.91488 0.61703 0.61868 0.94696 0.94966 0.50994 0.50873 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43670 43670 SRR6025619 SRX3176111 SRS2505874 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23571 GSM2779351   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23571 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779351 GSM2779351: Sample 23571; Danio rerio; RNA Seq GSM2779351   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779351 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23571_R1.fastq.gz s23571_R2.fastq.gz fastq fastq 13030579800.0 65152899.0 GSM2779351 r1 0:100 1:100 A:3722290207;C:2782988880;G:2744142531;T:3780916231;N:241951 100 100     3722290207 2782988880 2744142531 3780916231 241951 SRX3176111 SRS2505874 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93208 0.93215 0.57822 0.58304 0.9572 0.9586 0.46862 0.48068 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43671 43671 SRR6025618 SRX3176110 SRS2505873 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23570 GSM2779350   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23570 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779350 GSM2779350: Sample 23570; Danio rerio; RNA Seq GSM2779350   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779350 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23570_R1.fastq.gz s23570_R2.fastq.gz fastq fastq 12121714600.0 60608573.0 GSM2779350 r1 0:100 1:100 A:3516410174;C:2524668105;G:2487242768;T:3593167208;N:226345 100 100     3516410174 2524668105 2487242768 3593167208 226345 SRX3176110 SRS2505873 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.91432 0.91459 0.68729 0.68793 0.95799 0.95994 0.6103 0.61469 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43672 43672 SRR6025617 SRX3176109 SRS2505871 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23569 GSM2779349   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23569 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779349 GSM2779349: Sample 23569; Danio rerio; RNA Seq GSM2779349   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779349 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23569_R1.fastq.gz s23569_R2.fastq.gz fastq fastq 13109319000.0 65546595.0 GSM2779349 r1 0:100 1:100 A:3781614875;C:2765399267;G:2726180320;T:3835879250;N:245288 100 100     3781614875 2765399267 2726180320 3835879250 245288 SRX3176109 SRS2505871 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92553 0.92363 0.61103 0.61504 0.95047 0.95256 0.51779 0.51905 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43673 43673 SRR6025616 SRX3176108 SRS2505872 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23568 GSM2779348   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23568 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779348 GSM2779348: Sample 23568; Danio rerio; RNA Seq GSM2779348   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779348 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23568_R1.fastq.gz s23568_R2.fastq.gz fastq fastq 10809849800.0 54049249.0 GSM2779348 r1 0:100 1:100 A:3099873624;C:2301570943;G:2269311103;T:3138901271;N:192859 100 100     3099873624 2301570943 2269311103 3138901271 192859 SRX3176108 SRS2505872 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93288 0.93209 0.54983 0.55527 0.95122 0.95286 0.54032 0.54826 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43674 43674 SRR6025615 SRX3176107 SRS2505869 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23567 GSM2779347   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23567 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779347 GSM2779347: Sample 23567; Danio rerio; RNA Seq GSM2779347   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779347 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23567_R1.fastq.gz s23567_R2.fastq.gz fastq fastq 10856209000.0 54281045.0 GSM2779347 r1 0:100 1:100 A:3101117015;C:2322206669;G:2293577151;T:3139111242;N:196923 100 100     3101117015 2322206669 2293577151 3139111242 196923 SRX3176107 SRS2505869 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93023 0.92872 0.64291 0.6459 0.95793 0.95962 0.47236 0.51474 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43675 43675 SRR6025614 SRX3176106 SRS2505870 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23566 GSM2779346   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23566 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779346 GSM2779346: Sample 23566; Danio rerio; RNA Seq GSM2779346   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779346 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23566_R1.fastq.gz s23566_R2.fastq.gz fastq fastq 6524402000.0 32622010.0 GSM2779346 r1 0:100 1:100 A:1637781661;C:1626426425;G:1602187410;T:1657893406;N:113098 100 100     1637781661 1626426425 1602187410 1657893406 113098 SRX3176106 SRS2505870 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.95 0.94842 0.59579 0.59362 0.96453 0.96587 0.50083 0.50284 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43676 43676 SRR6025613 SRX3176105 SRS2505868 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23565 GSM2779345   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23565 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779345 GSM2779345: Sample 23565; Danio rerio; RNA Seq GSM2779345   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779345 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23565_R1.fastq.gz s23565_R2.fastq.gz fastq fastq 10387462200.0 51937311.0 GSM2779345 r1 0:100 1:100 A:2936142531;C:2240421768;G:2216761959;T:2993930182;N:205760 100 100     2936142531 2240421768 2216761959 2993930182 205760 SRX3176105 SRS2505868 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.91926 0.91982 0.66756 0.67009 0.95548 0.95737 0.53908 0.53171 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43677 43677 SRR6025612 SRX3176104 SRS2505867 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23564 GSM2779344   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23564 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779344 GSM2779344: Sample 23564; Danio rerio; RNA Seq GSM2779344   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779344 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23564_R1.fastq.gz s23564_R2.fastq.gz fastq fastq 14979643000.0 74898215.0 GSM2779344 r1 0:100 1:100 A:4264810263;C:3191982840;G:3161599788;T:4360950298;N:299811 100 100     4264810263 3191982840 3161599788 4360950298 299811 SRX3176104 SRS2505867 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92995 0.93129 0.6183 0.62251 0.95917 0.95978 0.52498 0.52445 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43678 43678 SRR6025611 SRX3176103 SRS2505866 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23563 GSM2779343   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23563 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779343 GSM2779343: Sample 23563; Danio rerio; RNA Seq GSM2779343   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779343 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23563_R1.fastq.gz s23563_R2.fastq.gz fastq fastq 13158024200.0 65790121.0 GSM2779343 r1 0:100 1:100 A:3783048488;C:2775938640;G:2744155512;T:3854621841;N:259719 100 100     3783048488 2775938640 2744155512 3854621841 259719 SRX3176103 SRS2505866 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92923 0.92877 0.56994 0.57248 0.9486 0.94925 0.53538 0.53999 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43679 43679 SRR6025610 SRX3176102 SRS2505865 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23562 GSM2779342   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23562 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779342 GSM2779342: Sample 23562; Danio rerio; RNA Seq GSM2779342   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779342 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23562_R1.fastq.gz s23562_R2.fastq.gz fastq fastq 12449365000.0 62246825.0 GSM2779342 r1 0:100 1:100 A:3533715755;C:2668392844;G:2636217587;T:3610782967;N:255847 100 100     3533715755 2668392844 2636217587 3610782967 255847 SRX3176102 SRS2505865 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92882 0.92935 0.65434 0.65647 0.95889 0.95986 0.54424 0.54695 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43680 43680 SRR6025609 SRX3176101 SRS2505864 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23561 GSM2779341   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23561 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779341 GSM2779341: Sample 23561; Danio rerio; RNA Seq GSM2779341   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779341 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23561_R1.fastq.gz s23561_R2.fastq.gz fastq fastq 12799216000.0 63996080.0 GSM2779341 r1 0:100 1:100 A:3688996768;C:2684674464;G:2656843614;T:3768443466;N:257688 100 100     3688996768 2684674464 2656843614 3768443466 257688 SRX3176101 SRS2505864 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.91822 0.91905 0.60422 0.60709 0.95475 0.95574 0.56585 0.56751 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43681 43681 SRR6025608 SRX3176100 SRS2505863 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23560 GSM2779340   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23560 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779340 GSM2779340: Sample 23560; Danio rerio; RNA Seq GSM2779340   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779340 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23560_R1.fastq.gz s23560_R2.fastq.gz fastq fastq 13605105600.0 68025528.0 GSM2779340 r1 0:100 1:100 A:3874286570;C:2892667747;G:2852156877;T:3985718797;N:275609 100 100     3874286570 2892667747 2852156877 3985718797 275609 SRX3176100 SRS2505863 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92952 0.92911 0.77695 0.77662 0.97254 0.97339 0.54961 0.55378 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43682 43682 SRR6025607 SRX3176099 SRS2505862 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23559 GSM2779339   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23559 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779339 GSM2779339: Sample 23559; Danio rerio; RNA Seq GSM2779339   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779339 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23559_R1.fastq.gz s23559_R2.fastq.gz fastq fastq 14038482800.0 70192414.0 GSM2779339 r1 0:100 1:100 A:3960290719;C:3025074892;G:2994349007;T:4058483161;N:285021 100 100     3960290719 3025074892 2994349007 4058483161 285021 SRX3176099 SRS2505862 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93175 0.9329 0.62025 0.62495 0.96658 0.96739 0.49279 0.49477 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43683 43683 SRR6025606 SRX3176098 SRS2505861 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23558 GSM2779338   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23558 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779338 GSM2779338: Sample 23558; Danio rerio; RNA Seq GSM2779338   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779338 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23558_R1.fastq.gz s23558_R2.fastq.gz fastq fastq 13003254800.0 65016274.0 GSM2779338 r1 0:100 1:100 A:3758329047;C:2708543092;G:2677214324;T:3858903008;N:265329 100 100     3758329047 2708543092 2677214324 3858903008 265329 SRX3176098 SRS2505861 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.91853 0.91806 0.65078 0.65255 0.94961 0.95071 0.50517 0.51058 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43684 43684 SRR6025605 SRX3176097 SRS2505860 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23557 GSM2779337   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23557 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779337 GSM2779337: Sample 23557; Danio rerio; RNA Seq GSM2779337   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779337 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23557_R1.fastq.gz s23557_R2.fastq.gz fastq fastq 15313320600.0 76566603.0 GSM2779337 r1 0:100 1:100 A:4308598805;C:3312393284;G:3270540620;T:4421477194;N:310697 100 100     4308598805 3312393284 3270540620 4421477194 310697 SRX3176097 SRS2505860 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93231 0.93219 0.77055 0.77158 0.98046 0.98094 0.56595 0.56298 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43685 43685 SRR6025604 SRX3176096 SRS2505859 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23556 GSM2779336   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23556 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779336 GSM2779336: Sample 23556; Danio rerio; RNA Seq GSM2779336   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23556_R1.fastq.gz s23556_R2.fastq.gz fastq fastq 12817928800.0 64089644.0 GSM2779336 r1 0:100 1:100 A:3636940808;C:2743921783;G:2720083561;T:3716727753;N:254895 100 100     3636940808 2743921783 2720083561 3716727753 254895 SRX3176096 SRS2505859 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93256 0.93098 0.54622 0.54805 0.94541 0.9472 0.48073 0.47781 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43686 43686 SRR6025603 SRX3176095 SRS2505858 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23555 GSM2779335   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23555 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779335 GSM2779335: Sample 23555; Danio rerio; RNA Seq GSM2779335   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779335 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23555_R1.fastq.gz s23555_R2.fastq.gz fastq fastq 13164248800.0 65821244.0 GSM2779335 r1 0:100 1:100 A:3699423154;C:2864617193;G:2832369173;T:3767574718;N:264562 100 100     3699423154 2864617193 2832369173 3767574718 264562 SRX3176095 SRS2505858 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93457 0.93477 0.56712 0.56973 0.95538 0.95635 0.49943 0.46846 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43687 43687 SRR6025602 SRX3176094 SRS2505857 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23554 GSM2779334   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23554 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779334 GSM2779334: Sample 23554; Danio rerio; RNA Seq GSM2779334   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779334 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23554_R1.fastq.gz s23554_R2.fastq.gz fastq fastq 7262209400.0 36311047.0 GSM2779334 r1 0:100 1:100 A:1907583588;C:1714326211;G:1698764389;T:1941393648;N:141564 100 100     1907583588 1714326211 1698764389 1941393648 141564 SRX3176094 SRS2505857 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93648 0.9356 0.50734 0.50884 0.94272 0.94373 0.47032 0.47653 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43688 43688 SRR6025601 SRX3176093 SRS2505856 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23553 GSM2779333   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23553 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779333 GSM2779333: Sample 23553; Danio rerio; RNA Seq GSM2779333   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779333 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23553_R1.fastq.gz s23553_R2.fastq.gz fastq fastq 11822418400.0 59112092.0 GSM2779333 r1 0:100 1:100 A:3118571640;C:2785354873;G:2752046165;T:3166220124;N:225598 100 100     3118571640 2785354873 2752046165 3166220124 225598 SRX3176093 SRS2505856 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.94518 0.94357 0.55971 0.56137 0.95948 0.95962 0.45789 0.45663 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43689 43689 SRR6025600 SRX3176092 SRS2505855 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23552 GSM2779332   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23552 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779332 GSM2779332: Sample 23552; Danio rerio; RNA Seq GSM2779332   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779332 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23552_R1.fastq.gz s23552_R2.fastq.gz fastq fastq 15618525200.0 78092626.0 GSM2779332 r1 0:100 1:100 A:4331214340;C:3464419077;G:3419272596;T:4403312389;N:306798 100 100     4331214340 3464419077 3419272596 4403312389 306798 SRX3176092 SRS2505855 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.94354 0.94207 0.64763 0.64745 0.96765 0.96885 0.52121 0.50469 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43690 43690 SRR6025599 SRX3176091 SRS2505854 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23551 GSM2779331   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23551 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779331 GSM2779331: Sample 23551; Danio rerio; RNA Seq GSM2779331   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779331 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23551_R1.fastq.gz s23551_R2.fastq.gz fastq fastq 13523929400.0 67619647.0 GSM2779331 r1 0:100 1:100 A:3761044627;C:2980561485;G:2940766088;T:3841300096;N:257104 100 100     3761044627 2980561485 2940766088 3841300096 257104 SRX3176091 SRS2505854 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93802 0.93656 0.78828 0.78689 0.97585 0.97617 0.64659 0.63139 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43691 43691 SRR6025598 SRX3176090 SRS2505853 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23550 GSM2779330   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23550 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779330 GSM2779330: Sample 23550; Danio rerio; RNA Seq GSM2779330   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779330 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23550_R1.fastq.gz s23550_R2.fastq.gz fastq fastq 13773520400.0 68867602.0 GSM2779330 r1 0:100 1:100 A:3781789884;C:3087914097;G:3047563316;T:3855981298;N:271805 100 100     3781789884 3087914097 3047563316 3855981298 271805 SRX3176090 SRS2505853 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.9435 0.94327 0.63355 0.63638 0.96684 0.96735 0.51875 0.52302 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43692 43692 SRR6025597 SRX3176089 SRS2505852 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23549 GSM2779329   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23549 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779329 GSM2779329: Sample 23549; Danio rerio; RNA Seq GSM2779329   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779329 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23549_R1.fastq.gz s23549_R2.fastq.gz fastq fastq 13833565400.0 69167827.0 GSM2779329 r1 0:100 1:100 A:3871499806;C:3039772666;G:2996616126;T:3925408591;N:268211 100 100     3871499806 3039772666 2996616126 3925408591 268211 SRX3176089 SRS2505852 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93554 0.93467 0.54178 0.54255 0.95156 0.95177 0.53446 0.54157 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43693 43693 SRR6025596 SRX3176088 SRS2505851 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23548 GSM2779328   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23548 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779328 GSM2779328: Sample 23548; Danio rerio; RNA Seq GSM2779328   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779328 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23548_R1.fastq.gz s23548_R2.fastq.gz fastq fastq 13820952200.0 69104761.0 GSM2779328 r1 0:100 1:100 A:3860273103;C:3045401890;G:2998258507;T:3916751954;N:266746 100 100     3860273103 3045401890 2998258507 3916751954 266746 SRX3176088 SRS2505851 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93826 0.93761 0.62803 0.62906 0.95913 0.96004 0.5438 0.54591 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43694 43694 SRR6025595 SRX3176087 SRS2505850 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23547 GSM2779327   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23547 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779327 GSM2779327: Sample 23547; Danio rerio; RNA Seq GSM2779327   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779327 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23547_R1.fastq.gz s23547_R2.fastq.gz fastq fastq 11366785600.0 56833928.0 GSM2779327 r1 0:100 1:100 A:3214019580;C:2456125449;G:2428331610;T:3268085490;N:223471 100 100     3214019580 2456125449 2428331610 3268085490 223471 SRX3176087 SRS2505850 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92317 0.92291 0.5299 0.53266 0.94113 0.94217 0.51651 0.52118 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43695 43695 SRR6025594 SRX3176086 SRS2505849 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23546 GSM2779326   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23546 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779326 GSM2779326: Sample 23546; Danio rerio; RNA Seq GSM2779326   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779326 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23546_R1.fastq.gz s23546_R2.fastq.gz fastq fastq 12174866600.0 60874333.0 GSM2779326 r1 0:100 1:100 A:3452417750;C:2615757090;G:2585494526;T:3520960685;N:236549 100 100     3452417750 2615757090 2585494526 3520960685 236549 SRX3176086 SRS2505849 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92674 0.9259 0.59418 0.5966 0.9526 0.95408 0.47877 0.4871 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43696 43696 SRR6025593 SRX3176085 SRS2505848 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23545 GSM2779325   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23545 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779325 GSM2779325: Sample 23545; Danio rerio; RNA Seq GSM2779325   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779325 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23545_R1.fastq.gz s23545_R2.fastq.gz fastq fastq 12332102000.0 61660510.0 GSM2779325 r1 0:100 1:100 A:3455012273;C:2700750069;G:2667784512;T:3508316711;N:238435 100 100     3455012273 2700750069 2667784512 3508316711 238435 SRX3176085 SRS2505848 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.93462 0.93428 0.44648 0.45292 0.94397 0.94491 0.48987 0.49012 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43697 43697 SRR6025592 SRX3176084 SRS2505847 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23544 GSM2779324   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23544 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779324 GSM2779324: Sample 23544; Danio rerio; RNA Seq GSM2779324   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779324 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23544_R1.fastq.gz s23544_R2.fastq.gz fastq fastq 11495965400.0 57479827.0 GSM2779324 r1 0:100 1:100 A:3239277586;C:2499452258;G:2466282264;T:3290731467;N:221825 100 100     3239277586 2499452258 2466282264 3290731467 221825 SRX3176084 SRS2505847 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.92887 0.92785 0.50244 0.50529 0.94379 0.94406 0.47153 0.47993 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43698 43698 SRR6025591 SRX3176083 SRS2505846 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 23543 GSM2779323   tissue:OMP positive cell|strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 23543 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:ERCC|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779323 GSM2779323: Sample 23543; Danio rerio; RNA Seq GSM2779323   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779323 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s23543_R1.fastq.gz s23543_R2.fastq.gz fastq fastq 12269933200.0 61349666.0 GSM2779323 r1 0:100 1:100 A:3285868097;C:2845990394;G:2808031165;T:3329810665;N:232879 100 100     3285868097 2845990394 2808031165 3329810665 232879 SRX3176083 SRS2505846 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.94094 0.94004 0.54712 0.54678 0.95444 0.95491 0.50258 0.51231 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43699 43699 SRR6025590 SRX3176082 SRS2505845 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20599 GSM2779322   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20599 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779322 GSM2779322: Sample 20599; Danio rerio; RNA Seq GSM2779322   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779322 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20599_R1.fastq.gz s20599_R2.fastq.gz fastq fastq 13570689150.0 64830571.0 GSM2779322 r1 0:104.66 1:104.66 A:3746382385;C:3035431532;G:3017617207;T:3766655416;N:4602610 104 104     3746382385 3035431532 3017617207 3766655416 4602610 SRX3176082 SRS2505845 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.68337 0.68693 0.21707 0.22287 0.9598 0.96112 0.49497 0.51067 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43700 43700 SRR6025589 SRX3176081 SRS2505844 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20595 GSM2779321   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20595 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779321 GSM2779321: Sample 20595; Danio rerio; RNA Seq GSM2779321   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779321 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20595_R1.fastq.gz s20595_R2.fastq.gz fastq fastq 11070127350.0 52852383.0 GSM2779321 r1 0:104.73 1:104.73 A:2982708297;C:2554784552;G:2519746253;T:3009345413;N:3542835 104 104     2982708297 2554784552 2519746253 3009345413 3542835 SRX3176081 SRS2505844 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.60906 0.61457 0.36125 0.3667 0.9582 0.96059 0.51449 0.50705 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43701 43701 SRR6025588 SRX3176080 SRS2505843 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20566 GSM2779320   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20566 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779320 GSM2779320: Sample 20566; Danio rerio; RNA Seq GSM2779320   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779320 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20566_R1.fastq.gz s20566_R2.fastq.gz fastq fastq 13606761150.0 65046784.0 GSM2779320 r1 0:104.59 1:104.59 A:3665640421;C:3135272778;G:3111565962;T:3689671946;N:4610043 104 104     3665640421 3135272778 3111565962 3689671946 4610043 SRX3176080 SRS2505843 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.66341 0.66751 0.25233 0.25854 0.95696 0.9587 0.49264 0.50014 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43702 43702 SRR6025587 SRX3176079 SRS2505841 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20565 GSM2779319   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20565 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779319 GSM2779319: Sample 20565; Danio rerio; RNA Seq GSM2779319   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779319 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20565_R1.fastq.gz s20565_R2.fastq.gz fastq fastq 13510104100.0 64509618.0 GSM2779319 r1 0:104.71 1:104.71 A:3690515096;C:3059445453;G:3040155086;T:3715724132;N:4264333 104 104     3690515096 3059445453 3040155086 3715724132 4264333 SRX3176079 SRS2505841 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.67247 0.67728 0.30104 0.30816 0.95753 0.95868 0.50785 0.50355 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43703 43703 SRR6025586 SRX3176078 SRS2505842 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20556 GSM2779318   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20556 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779318 GSM2779318: Sample 20556; Danio rerio; RNA Seq GSM2779318   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779318 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20556_R1.fastq.gz s20556_R2.fastq.gz fastq fastq 12979896450.0 61997072.0 GSM2779318 r1 0:104.68 1:104.68 A:3360577219;C:3127516743;G:3108274254;T:3379692612;N:3835622 104 104     3360577219 3127516743 3108274254 3379692612 3835622 SRX3176078 SRS2505842 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.71027 0.71422 0.16443 0.16968 0.94688 0.94771 0.45596 0.466 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43704 43704 SRR6025585 SRX3176077 SRS2505840 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20545 GSM2779317   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20545 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779317 GSM2779317: Sample 20545; Danio rerio; RNA Seq GSM2779317   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779317 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20545_R1.fastq.gz s20545_R2.fastq.gz fastq fastq 12989935500.0 62257631.0 GSM2779317 r1 0:104.32 1:104.32 A:3572227261;C:2914841466;G:2894234446;T:3604038426;N:4593901 104 104     3572227261 2914841466 2894234446 3604038426 4593901 SRX3176077 SRS2505840 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.68046 0.68257 0.24349 0.25017 0.96098 0.96146 0.49722 0.49929 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43705 43705 SRR6025584 SRX3176076 SRS2505838 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20544 GSM2779316   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20544 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779316 GSM2779316: Sample 20544; Danio rerio; RNA Seq GSM2779316   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779316 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20544_R1.fastq.gz s20544_R2.fastq.gz fastq fastq 10850415100.0 51845962.0 GSM2779316 r1 0:104.64 1:104.64 A:2883478486;C:2540887534;G:2532673572;T:2889737674;N:3637834 104 104     2883478486 2540887534 2532673572 2889737674 3637834 SRX3176076 SRS2505838 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.75352 0.75587 0.27675 0.2836 0.94454 0.9455 0.4848 0.48686 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43706 43706 SRR6025583 SRX3176075 SRS2505839 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20535 GSM2779315   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20535 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779315 GSM2779315: Sample 20535; Danio rerio; RNA Seq GSM2779315   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779315 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20535_R1.fastq.gz s20535_R2.fastq.gz fastq fastq 11095624100.0 53041376.0 GSM2779315 r1 0:104.59 1:104.59 A:2935149963;C:2612483606;G:2588444487;T:2955689662;N:3856382 104 104     2935149963 2612483606 2588444487 2955689662 3856382 SRX3176075 SRS2505839 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.66175 0.66467 0.28361 0.28982 0.95446 0.95637 0.4427 0.46855 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43707 43707 SRR6025582 SRX3176074 SRS2505837 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 20534 GSM2779314   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 20534 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779314 GSM2779314: Sample 20534; Danio rerio; RNA Seq GSM2779314   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779314 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248   loader:fastq load.py s20534_R1.fastq.gz s20534_R2.fastq.gz fastq fastq 9279270400.0 44312137.0 GSM2779314 r1 0:104.70 1:104.70 A:2257778518;C:2383104726;G:2364686021;T:2270914797;N:2786338 104 104     2257778518 2383104726 2364686021 2270914797 2786338 SRX3176074 SRS2505837 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.75658 0.75749 0.03939 0.03975 0.95465 0.95633 0.43347 0.45305 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43708 43708 SRR6025581 SRX3176073 SRS2505836 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 18931 GSM2779313   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 18931 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779313 GSM2779313: Sample 18931; Danio rerio; RNA Seq GSM2779313   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779313 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s18931_R2.fastq.gz s18931_R1.fastq.gz fastq fastq 10382332600.0 51911663.0 GSM2779313 r1 0:100 1:100 A:2908734493;C:2273168729;G:2245788132;T:2952822006;N:1819240 100 100     2908734493 2273168729 2245788132 2952822006 1819240 SRX3176073 SRS2505836 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.67976 0.68217 0.31458 0.31819 0.95726 0.95763 0.48306 0.47976 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43709 43709 SRR6025580 SRX3176072 SRS2505835 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 18930 GSM2779312   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 18930 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779312 GSM2779312: Sample 18930; Danio rerio; RNA Seq GSM2779312   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779312 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s18930_R1.fastq.gz s18930_R2.fastq.gz fastq fastq 13527577200.0 67637886.0 GSM2779312 r1 0:100 1:100 A:3738123002;C:3017390941;G:2980829526;T:3788876926;N:2356805 100 100     3738123002 3017390941 2980829526 3788876926 2356805 SRX3176072 SRS2505835 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.72022 0.72046 0.30139 0.30255 0.94679 0.94744 0.48588 0.48782 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43710 43710 SRR6025579 SRX3176071 SRS2505834 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 18928 GSM2779311   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 18928 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779311 GSM2779311: Sample 18928; Danio rerio; RNA Seq GSM2779311   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779311 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s18928_R1.fastq.gz s18928_R2.fastq.gz fastq fastq 11247464600.0 56237323.0 GSM2779311 r1 0:100 1:100 A:3119559722;C:2500776647;G:2474446157;T:3150698487;N:1983587 100 100     3119559722 2500776647 2474446157 3150698487 1983587 SRX3176071 SRS2505834 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.645 0.64814 0.2583 0.26292 0.95741 0.9586 0.47386 0.48835 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43711 43711 SRR6025578 SRX3176070 SRS2505833 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 18927 GSM2779310   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 18927 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779310 GSM2779310: Sample 18927; Danio rerio; RNA Seq GSM2779310   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779310 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s18927_R1.fastq.gz s18927_R2.fastq.gz fastq fastq 10683045600.0 53415228.0 GSM2779310 r1 0:100 1:100 A:2868542756;C:2476008591;G:2434571227;T:2902046467;N:1876559 100 100     2868542756 2476008591 2434571227 2902046467 1876559 SRX3176070 SRS2505833 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.55065 0.55754 0.24721 0.25312 0.96883 0.96978 0.5382 0.5322 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined
43712 43712 SRR6025577 SRX3176069 SRS2505832 SRP117248 PRJNA404067 Distinct OR specific subsets of axon guidance molecules govern early olfactory map formation GSE103692 Transcriptome Analysis We have discovered subsets of axon guidance molecules and transcription factors that are enriched in specific subsets of olfactory sensory neurons. We have demonstrated guidance activity for three of the candidate axon guidance genes we identified suggesting that this approach is an efficient method for characterizing guidance systems relevant to olfactory axon targeting. Overall design: Single cell RNASeq of OMP expressing olfactory sensory neurons was performed by capture on Fluidigm C1 followed by sequencing on Illumina HiSeq2500   pubmed:29385124   Sample 18926 GSM2779309   tissue:OMP positive cell|strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit Sample 18926 Illumina Casava 1.8.2 was used for basecalling Low confidence nucleotides with Phred score less than 20 were treated as unknown and replaced with Ns. Unknown nucleotides Ns at the ends of reads were trimmed. Poly A and method specific adapter sequences were trimmed from the 3’ end of reads using in house software. Reads were aligned to the danio rerio reference genome build GRCz10 and to spike in transcript sequences using STAR Spliced Transcripts Alignment to a Reference aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice junction loci database for use in alignment. We retained reads that aligned to at least 40% paired end of trimmed length or 30bp whichever was greater. In addition we discarded reads with greater than 30% mismatched positions in trimmed length. Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike in transcripts using Verse which functions identically to HTSeq's htseq counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non empty method. Genome build: GRCz10 Supplementary files format and content: all data files are tab delimited text files containing gene abundence measurements OMP positive cell   Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit   strain:Tu/TLF|spike in:Fluidigm|single cell amplification protocol used:Clontech SMARTer Ultralow RNA kit GSM2779309 GSM2779309: Sample 18926; Danio rerio; RNA Seq GSM2779309   1 Cells were isolated on a C1 Fluidigm platform libraries made using Illumina's Nextera kit GEO Accession:GSM2779309 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP117248     s18926_R1.fastq.gz s18926_R2.fastq.gz fastq fastq 9785632200.0 48928161.0 GSM2779309 r1                       SRX3176069 SRS2505832 SRA606958 GEO Junhyong Kim, Biology, University of Pennsylvania 2 0.56035 0.54079 0.19973 0.19425 0.95905 0.95988 0.50309 0.50507 100 100 B B biological fallback assumption illumina hiseq_era full_length poly_a smarter sc single_cell_plate fluidigm   United States 2017-09-11 Undetermined Undetermined Undetermined Undetermined

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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");;