|
| Status |
Public on Mar 01, 2012 |
| Title |
embryo_1dpf_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
the whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB*WT
developmental stage: 1dpf
tissue: the whole embryos
|
| Growth protocol |
Embryos were raised at 28°C in egg water (0.03% Instant Ocean marine salt mix) for the initial several hours of development
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish embryos were collected at the 256-cell stage, sphere stage, shield stage, and 1dpf. Total RNA was isolated from embryos using Trizol. RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15-30 nucleotides were excised and purified. cDNA libraries were generated using specific linkers and RT/PCR, as previously described. Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm, which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "_x" and the reads counts. e.g. unique ID_x counts.
alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm, which allows one mismatch in the linker sequences. Small RNAs with perfect matches to the zebrafish genome (Zv8) from Ensembl (http://www.ensembl.org) were retrieved using megaBLAST (http://www.ncbi.nlm.nih.gov/blast/megablast.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/tutorial.shtml). To identify piRNAs, consensus sequences from zebrafish repetitive elements were retrieved from Repbase (http://www.girinst.org/repbase/index.html) and Repeat Maskers using the UCSC genome browser (http://genome.ucsc.edu). Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence.
fasta files description: small RNA 15-30 nt
alignment file description: piRNA map to repetitive elements
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunyao Wei |
| E-mail(s) |
weic@molbio.mgh.harvard.edu
|
| Organization name |
Mass General Hospital
|
| Department |
Molecular Biology
|
| Lab |
Lee Lab
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE27722 |
Transcriptome-wide analysis of small RNA expression in early zebrafish development |
|
| Relations |
| BioSample |
SAMN02196997 |
| SRA |
SRX336218 |
