|
| Status |
Public on Jul 01, 2010 |
| Title |
MZdicer mutant1 hu715 |
| Sample type |
SRA |
| |
|
| Source name |
48hpf embryo, Mzdicer mutant
|
| Organism |
Danio rerio |
| Characteristics |
strain: mixed AB, TU, TL,TLF background
developmental stage: 48h post-fertilization embryo
genotype: MZdicer hu715/hu715
|
| 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 |
SRX020024 |
| BioSample |
SAMN00012355 |
