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Sample GSM1316816 Query DataSets for GSM1316816
Status Public on Jan 29, 2014
Title Dre_155_2hpf_PAL
Sample type SRA
 
Source name zebrafish embryo
Organism Danio rerio
Characteristics strain: AB
developmental stage: 2 hours post-fertilization
Treatment protocol RNA-seq: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Subtelny et al., 2014 (GSE52809). PAL-seq: Polyadenylated ends in total RNA were ligated to a biotinylated adaptor, then partially digested with RNase T1. The resulting fragments were size-selected (104-750 nt), captured on streptavidin beads, and used for library preparation.
Growth protocol Each sample was grown or maintained in accordance with standard protocols.
Extracted molecule cytoplasmic RNA
Extraction protocol Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description PAL-Seq
cytoplasmically-enriched RNA
processed data file: Dre_155_2hpf.txt
processed data file: Dre_155_2hpf_PAL_norm_intensities.txt.gz
processed data file: Dre_155_2hpf_PAL_raw_intensities.txt.gz
Data processing Raw read files were stripped of adaptor and mapped to the appropriate species' genome and/or transcriptome.
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. Poly(A)-tail length measurements were generated using PAL-seq tags that mapped within the 3' UTR of an annotated gene.
Genome_build: Human: hg18; Mouse: mm9; Zebrafish: danRer7; Drosophila: dm3; Arabidopsis: tair10; S. cerevisiae: sacCer3; S. pombe: Spombe1; Xenopus: Unigene
Supplementary_files_format_and_content: One set of processed data files contains abundance and poly(A)-tail length measurements for each gene. Another set contains raw fluorescence intensities for each base for each cycle of sequencing-by-synthesis and streptavidin flow-in for each sequencing cluster. Another set contains normalized streptavidin fluorescence intensities for each sequencing cluster.
 
Submission date Jan 29, 2014
Last update date May 15, 2019
Contact name Stephen Eichhorn
E-mail(s) eichhorn@wi.mit.edu
Organization name Whitehead Institute for Biomedical Research
Department Biology
Lab Bartel
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9319
Series (1)
GSE52809 Poly(A)-tail profiling reveals an embryonic switch in translational control
Relations
BioSample SAMN02598806
SRA SRX451693

Supplementary file Size Download File type/resource
GSM1316816_Dre_155_2hpf_PAL_norm_intensities.txt.gz 97.0 Mb (ftp)(http) TXT
GSM1316816_Dre_155_2hpf_PAL_raw_intensities.txt.gz 2.6 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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