run_metadata: 44529
This data as json
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| 44529 | SRR6261577 | SRX3367859 | SRS2665539 | SRP124289 | PRJNA417290 | Drop seq analysis of wild type TLAB zebrafish embryos from high to 6 somite stage 12 timepoints | GSE106474 | Transcriptome Analysis | Wild type zebrafish embryos were mechanically dissociated and profiled using Drop seq Overall design: Drop seq was performed on 28 groups of 20 40 visually staged mechanically dissociated embryos. Samples were combined and sequenced in batches DS2 DS5. | parent bioproject:PRJNA417291 | pubmed:29700225 | WT zebrafish embryo zfs:0000015 Rep 1 | GSM2838506 | tissue:Wild type TLAB Embryo|developmental stage:zfs:0000015|hpf batch:DS5 | WT zebrafish embryo zfs:0000015 Rep 1 | Data was processed using Drop seq tools v1.01 according to Drop seq protocol v3.1 http://www.dropseq.org/ Base calling was performed with bcl2fastq v2.17.1.14 Read 2 was aligned with Bowtie2 v 2.2.1 to Ensembl Zv10 release 82. Each aligned read was tagged with its mate pair UMI and cell barcode which comprise Read 1 Each aligned exonic read was tagged with a gene name ZFIN name preferred over Ensembl name Cell barcodes were corrected for synthesis errors A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells and rows are genes The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample Genome build: dr82 Supplementary files format and content: tab delimited text file of UMI counts | Wild type TLAB Embryo | Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. | Tupful longfin / AB TLAB fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging. | developmental stage:zfs:0000015|hpf batch:DS5 | GSM2838506 | GSM2838506: WT zebrafish embryo zfs:0000015 Rep 1; Danio rerio; RNA Seq | GSM2838506 | 1 | Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated using a standard Drop seq apparatus. Lysis occurred in droplets in Drop seq lysis buffer . Libraries were prepared according to Drop seq Protocol v3.1 12/28/2015 with 12–13 cycles of PCR amplification and 50–100 STAMPs per PCR reaction. | GEO Accession:GSM2838506 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP124289 | dangling references:treat as unmapped | ZF30-DS5.bam | bam | 1506806977.0 | 25842795.0 | GSM2838506 r1 | 0:58.31 | A:477897847;C:307865773;G:330036592;T:390748777;N:257988 | 58 | 477897847 | 307865773 | 330036592 | 390748777 | 257988 | SRX3367859 | SRS2665539 | SRA628740 | GEO | Schier Lab, Molecular and Cellular Biology, Harvard University | 1 | 0.90526 | 0.05376 | 0.8644 | 0.75191 | 43 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | dropseq | United States | 2017-11-02 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |