run_metadata: 43699
This data as json
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| 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 |