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| Status |
Public on Mar 28, 2013 |
| Title |
pbx2/4-MO rep3 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Danio rerio |
| Characteristics |
developmental stage: 10 somites
strain: AB
genotype: pbx2/4-MO; prdm1+/+
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| Treatment protocol |
Embryos were injected with pbx2/4 morpholinos or control morpholinos at the 1 cell stage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from individual embryos was isolated using the RNAqueous Micro Kit (Ambion). Samples were genotyped, pooled, then further cleaned and concentrated using the RNeasy MinElute Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were aligned by tophat 1.4
gene counts are collected using Bioconductor Rsamtools package. Reads mapped to M locations are counted as 1/M at each occurrence.
differentential gene expression detection was performed by edgeR.
Genome_build: Zv9 release 63
Supplementary_files_format_and_content: GSE45532_gene.counts.csv: Read counts extracted by Bioconductor packages for each ENSEMBL genes. Reads that mapped to M locations are counted as 1/M for each occurrence. The columns are: gene name, ENSEMBL ID, and read counts for all samples.
Supplementary_files_format_and_content: GSE45532_double.genes.csv: Differential expressed genes between Double knockout pbx2/4-MO;prdm1-/- vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.
Supplementary_files_format_and_content: GSE45532_pbx.genes.csv: Differential expressed genes between pbx2/4-MO vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.
Supplementary_files_format_and_content: GSE45532_prdm.genes.csv: Differential expressed genes between prom1-/- vs. control. Differential genes are detected by edgeR at 1.5 fold change cutoff and 0.05 pvalue cutoff. The columns are gene name, ENSEMBL gene.id, edgeR pvalue, edgeR log fold change.
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| Submission date |
Mar 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Tapscott |
| E-mail(s) |
stapscot@fredhutch.org
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| Organization name |
Fred Hutch Cancer Research Center
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| Department |
Human Biology
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| Lab |
Tapscott
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| Street address |
1100 Fairview N. Ave
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| City |
Seattle |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98103 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE45532 |
Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish |
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| Relations |
| SRA |
SRX255752 |
| BioSample |
SAMN01992805 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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