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Sample GSM1448814 Query DataSets for GSM1448814
Status Public on Oct 23, 2014
Title 15 somite stage, sectioned from left to right
Sample type SRA
 
Source name whole embryo
Organism Danio rerio
Characteristics Stage: 15 somites
sectioning direction: left-right
section thickness: 18 ┬Ám
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 SAMN02944986
SRA SRX665257

Supplementary file Size Download File type/resource
GSM1448814_dr_15ss_LR.txt.gz 472.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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