run_metadata: 33652
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 33652 | SRR30353610 | SRX25811745 | SRS22442016 | SRP528282 | PRJNA1151637 | Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq] | GSE275537 | Transcriptome Analysis | Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow. | pubmed:39548947 | WT rep1 | GSM8479117 | source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing | WT rep1 | Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes features and matrix files | Whole kidney marrow | Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics. | tissue:Whole kidney marrow|genotype:wild type | GSM8479117 | GSM8479117: WT rep1; Danio rerio; RNA Seq | GSM8479117 r1 | GSM8479117 | 1 | Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP528282 | WT_rep1_S1_L001_R2_001.fastq.gz WT_rep1_S1_L001_R1_001.fastq.gz | fastq fastq | 26909031908.0 | 231974413.0 | GSM8479117 r1 | 0:27 1:89 | A:7272478752;C:6312728360;G:6433038501;T:6890198195;N:588100 | 27 | 89 | 7272478752 | 6312728360 | 6433038501 | 6890198195 | 588100 | SRX25811745 | SRS22442016 | SRA1954153 | Horsfield, Pathology, University of Otago | Horsfield, Pathology, University of Otago | 2 | 0.00366 | 0.93902 | 0.00134 | 0.0858 | 0.99318 | 0.82769 | 0.35 | 0.51885 | 27 | 89 | T | B | sc-like readlen | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | New Zealand | 2024-08-23 | Adult | Adult | Kidney | Renal System |