|
| Status |
Public on Oct 23, 2014 |
| Title |
shield stage, sectioned from right to left |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
Stage: shield stage
sectioning direction: right-left
section thickness: 18 µm
embedding strategy: intact embryo
|
| Treatment protocol |
Unfixed samples (zebrafish embryos or mouse forelimbs) were embedded in tissue freezing medium. Blocks were cryosectioned, and individual slices were transferred to Eppendorf tubes on dry ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by TRIzol extraction
mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript (Table S1). The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
Genome_build: mm10 and zv9 (with improved 3' annotation)
Supplementary_files_format_and_content: text files: read count matrices in which rows correspond to genes and columns to sections
|
| |
|
| Submission date |
Jul 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jan Philipp Junker |
| Organization name |
Hubrecht Institute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE59873 |
Genome-wide RNA tomography in the zebrafish embryo |
|
| Relations |
| BioSample |
SAMN02944971 |
| SRA |
SRX665242 |
