|
| Status |
Public on Jun 28, 2016 |
| Title |
miR_NOG3 |
| Sample type |
SRA |
| |
|
| Source name |
animal caps, noggin
|
| Organism |
Xenopus laevis |
| Characteristics |
strain/background: NXR
developmental stage: mid-gastrula embryo
tissue: animal caps
treatment: noggin
ip antibody: none
|
| Treatment protocol |
Embryos were injected at the 2-cell stage, and animal caps were isolated manually when the embryos reached stg. 8. Isolated animal caps were maintained in 1X MMR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For small RNAs and total RNAs: Tissue samples were lysed in Trizol, and RNA was extracted and treated with DNaseI using the Direct-zol RNA mini-prep kit (Zymo).
For AGO IP RNA: Ago-RNP immunoprecipitations were carried out as a modification of Keene et al. (2006).
RNA samples were processed for library preparation using the NEBNext Multiplex Small RNA Library Prep Set for Illumina kit according to manufacturer's instructions.
Sequencing libraries were prepared from the immunoprecipitated RNA samples using the ScriptSeqTM Complete Gold Kit - Low Input (Epicentre Technologies), with rRNA depleted protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Small RNA
|
| Data processing |
Sequences were trimmed and quality was checked using fastQC.
For small RNA-seq: Trimmed reads are aligned to Xenopus laevis genome assembly 9.1. For Ago-IP- & total RNA-seq: Trimmed reads are aligned to Xenopus laevis transcriptome using bowtie-2.
For small RNA-seq: Reads were re-aligned to miRBase 21 using miRdeep2. For Ago-IP- & total RNA-seq: Aligned reads were counted using Express.
For Ago-IP & total RNA-seq: Read counts were analyzed using DESeq package for R.
Genome_build: Xenopus laevis v9.1
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts using Express tool.
|
| |
|
| Submission date |
Jun 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vrutant V Shah |
| E-mail(s) |
vvshah@mdanderson.org
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
EMC
|
| Lab |
Michelle Barton
|
| Street address |
1515 Holcombe Blvd #1000
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL17682 |
| Series (1) |
| GSE83784 |
Identification of microRNAs and microRNA targets in Xenopus ectoderm |
|
| Relations |
| BioSample |
SAMN05296706 |
| SRA |
SRX1880840 |
