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| Status |
Public on Jun 06, 2019 |
| Title |
RNA-seq_Wt DP-R1med rep1 |
| Sample type |
SRA |
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| Source name |
aortic endothelium
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| Organism |
Danio rerio |
| Characteristics |
age: 28-30 hpf
cell isolation: FACS isolated cells
tissue: aortic endothelium
genotype/variation: non-injected
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| Treatment protocol |
double transgenic embryos were collected, batches were split in half and were either injected or non-injected with a runx1-morpholino
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| Growth protocol |
TgBAC(runx1P2:Citrine);Tg(kdrl:mCherry) double-transgenic zebrafish embryos, were raised to 28-30 hpf.
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| Extracted molecule |
total RNA |
| Extraction protocol |
whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN, Cat No. 74034).
High quality RNA (RIN > 8.0) was sent for RNAseq to the Wellcome Trust Centre for Human Genetics (WTCHG). 2.2 ng of total RNA was used for to generate SMARTer libraries for low-input RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
double positive *runx1*-medium mCherry+Citrinemed
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| Data processing |
Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol.
Sequenced reads were checked for base qualities, trimmed where 20% of the bases were below quality score 20, and filtered to exclude adapters using Trimmomatic (Version 0.32).
Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads (QC-passed reads count) has been obtain using Samtools mapping statistics (flagstat tool).
RAW data files represent the trimmed sequencing reads in separated lanes.
Genome_build: Zv10
Supplementary_files_format_and_content: Wt-DP-R1hi_Wt-DP-R1lo Differential analysis between Wt DP-R1hi and Wt DP-R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene_id, Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.
Supplementary_files_format_and_content: Wt-DP-R1hi_MO-DP-R1hi Differential analysis between Wt DP-R1hi and MO DP-R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene_id, Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.
Supplementary_files_format_and_content: Wt-DN_MO-DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene_id, Counts Per Million, gene_name, end value of each sample, log FC (wt/mo), P value and FDR value.
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| Submission date |
Jun 05, 2019 |
| Last update date |
Jun 06, 2019 |
| Contact name |
Florian Bonkhofer |
| Organization name |
Oxford University
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| Street address |
John Radcliffe Hospital/Headley Way
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| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
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| Platform ID |
GPL21741 |
| Series (2) |
| GSE132259 |
RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
| GSE132260 |
ATACseq and RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28-20 hours post fertilization |
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| Relations |
| BioSample |
SAMN11962921 |
| SRA |
SRX5978254 |
| 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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