|
| Status |
Public on Aug 05, 2013 |
| Title |
MGC3 (miRNA) |
| Sample type |
SRA |
| |
|
| Source name |
mural granulosa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mural granulosa cells
stimulation protocol: GnRH antagonist, rFSH, hCG
etiology of infertility: male factor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Small RNA fraction (< 200nt) was eluted separately from large RNA fraction.
Small RNA libraries were prepared using Bioo Scientific NEXTflex Small RNA Sequencing Kit and NEXTflex small RNA Barcode Primer Set A (Bioo Scientific Corporation) following the manufacturer’s protocol. Size selection of 140-160 bp fragments corresponding to mature miRNAs and adapters was carried out by gel electrophoresis with 10% Mini-PROTEAN TBE Precast gels (Bio-Rad Laboratories). 0.66 pM of individual indexed samples were pooled for template hybridization and clustering/amplification was performed using TruSeq SR Cluster Kit v2-cBot-GA (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base calling and filtering was done using instrument software real time analysis (RTA v 1.9.35) with default parameters.
Raw filtered data was submitted to miRDeep2 software (30) that integrates adapter trimming, sequence alignment and miRNA annotation according to miRBase version 18.
Differential miRNA expression analysis was performed using the R/Bioconductor package EdgeR.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: miRNA counts for each sample generated by miRDeep2. Data from technical replicates has been summed.
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Agne Velthut-Meikas |
| Organization name |
Tallinn University of Technology
|
| Department |
Department of Chemistry and Biotechnology
|
| Street address |
Akadeemia tee 15
|
| City |
Tallinn |
| ZIP/Postal code |
12618 |
| Country |
Estonia |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE46489 |
Small RNA sequencing of human preovulatory cumulus and mural granulosa cells |
| GSE46508 |
Small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes |
|
| Relations |
| BioSample |
SAMN02087546 |
| SRA |
SRX272865 |
