|
| Status |
Public on Nov 13, 2013 |
| Title |
MZdicer 6h 430_duplex |
| Sample type |
SRA |
| |
|
| Source name |
MZdicer mutant micoinjected with miR-430 duplex
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Whole embryo
strain: MZdicer (hu896/hu896)
Stage: 6-hpf (shield)
treatment: miR430_duplex
|
| Treatment protocol |
Treated MZdicer embryos were injected at 1-cell with 1 nl of a 25 microMolar stock solution of miR-430 duplex, miR-430 (Ago2-haripin) and miR-430 (Ago2-hairpin 3xPhosphorothioate)
|
| Growth protocol |
Embryos are incubated at 28C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from 15 embryos was extracted using Trizol (Invitrogen) for each experimental condition.
TruSeq strand-specific libraries were constructed according to standard protocols. For mRNA-Seq, polyA+ RNA was selected with oligodT beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
dcr_2b_dup_005
|
| Data processing |
Base calling was performed using CASAVA-1.8.2.
For mRNA-Seq, raw reads were aligned strand-specific to the Zebrafish Zv9 (UCSC danRer7) genome sequence using Tophat v2.0.8 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 annotations for uniquely, aligned twice and without limit aligning reads, normalizing against the total number of aligned exonic reads in the sample.
Genome_build: Ensembl 70 / UCSC danRer7
Supplementary_files_format_and_content: Count (uniquely map reads: “count_1”; max twice mapped reads “count_2”; all reads mapped: “count_all”) and RPKM tables (uniquely map reads: “rpkm_1”; max twice mapped reads “rpkm_2”; all reads mapped: “rpkm_all”)
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Antonio Giraldez |
| E-mail(s) |
antonio.giraldez@yale.edu
|
| Organization name |
Yale
|
| Department |
Genetics
|
| Street address |
333 Cedar street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE51036 |
PARN mediates 3'-end trimming of Argonaute-cleaved precursor microRNAs |
|
| Relations |
| BioSample |
SAMN02360468 |
| SRA |
SRX357079 |
