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Sample GSM540643 Query DataSets for GSM540643
Status Public on Jul 01, 2010
Title WT1
Sample type SRA
 
Source name 48hpf embryo, WT
Organism Danio rerio
Characteristics strain: mixed AB, TU, TL,TLF background
developmental stage: 48h post-fertilization embryo
genotype: wild type
Growth protocol Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hours post-fertilization, embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions (Part # 1004239 Rev. A) accompanying the small RNA Sample Kit. Briefly, total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18-35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Description RNA size from 18 to 35 nt.
Data processing Alignment: Sequence reads were mapped to Zebrafish (Zv8/danRer6) precursor miRNA sequences using Bowtie software (version 0.12.1) with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.
 
Submission date May 04, 2010
Last update date May 15, 2019
Contact name Antonio J. Giraldez
E-mail(s) antonio.giraldez@yale.edu
Phone 203 785 5423
Organization name Yale University
Department Genetics
Lab Giraldez Lab
Street address 333 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06510
Country USA
 
Platform ID GPL10164
Series (1)
GSE21503 A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity
Relations
SRA SRX020025
BioSample SAMN00012356

Data table header descriptions
SEQUENCE Unique sequence
COUNT Sequence count

Data table
SEQUENCE COUNT
TCTTTGGTTATCTAGCTGTATCTGTATCAACC 1
CACATTCATTGCTGTCGGTGGGTCTTTCGGCC 19
TGGAATGTAAGGCAGTGTGTGGCTGTCGGGACC 1
CAAAGTGCTCACAGTGCAGATCCAGTAATAACAG 1
AAAGTGCTATCAAGTTGGGAGAGATATAGTGAA 1
TACCCTGTAGAACCGACGTTGTG 3
TTGCATAGTCACAAACCTGAGCA 1
TGGAATGTAAGGACGTGTGTGGCTGTTGGCTCC 2
TGGAATGAAAGGCAGTGTGT 1
TAAGGTGCATCTTGTGTCGTTCG 18
TACCCTGTAGATCCGGATTTGTCTGTCGGTCCC 1
TAAGGCACGCGGTGAATGCCACAGTCGGCACAAT 1
TGGAATGTAGGGAAGAGTGTGGCTGGAGGTCTC 1
TAAGTGCTATTTGTTGGGTTAGCTGTAGTAAAC 1
TAAAGTGCTTATAGTGCAGGTAGCATAATTCAG 1
AGGCGGAGACTTGGGCAGCTGAC 1
TCTTTGGTTCTCTATCTGTATGCTGTATGTCCC 1
AACATTCAACGCTGTCGGTGAGTTCTATATGCA 1
TGGAATGTAAGGAAGTGGGTGGCTGGAAGCA 1
TCTTTGGTTATCTCGCTTTATGCTGTCTGCCCC 2

Total number of rows: 120232

Table truncated, full table size 3956 Kbytes.




Supplementary file Size Download File type/resource
GSM540643.out.txt.gz 46.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data included within Sample table
Processed data provided as supplementary file
Raw data are available in SRA
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