Comment[ArrayExpressAccession]	E-GEOD-46508
MAGE-TAB Version	1.1	
Public Release Date	2013-08-05
Investigation Title	Small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes	
Comment[Submitted Name]	Small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series	
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl
Person Last Name	Velthut-Meikas	
Person First Name	Agne	
Person Email	geo@ncbi.nlm.nih.gov	
Person Affiliation	Competence Centre on Reproductive Medicine and Biology	
Person Address	Competence Centre on Reproductive Medicine and Biology, Tiigi 61B, Taru, Estonia	
Person Roles	submitter	
Protocol Name	P-GSE46508-2	P-GSE46508-1
Protocol Description	Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerM-bM-^@M-^Ys instructions. RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturerM-4s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample).	Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerM-bM-^@M-^Ys 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 manufacturerM-bM-^@M-^Ys 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).
Protocol Type	nucleic acid library construction protocol	nucleic acid library construction protocol
Experimental Factor Name	CELL TYPE	
Experimental Factor Type	cell type	
Publication Title	Research Resource: Small RNA-seq of Human Granulosa Cells Reveals miRNAs in FSHR and Aromatase Genes.	
Publication Author List	Velthut-Meikas A, Simm J, Tuuri T, Tapanainen JS, Metsis M, Salumets A	
PubMed ID	23660593	
Publication DOI	10.1210/me.2013-1058	
Comment[SecondaryAccession]	GSE46508	
Comment[GEOReleaseDate]	2013-08-05	
Comment[ArrayExpressSubmissionDate]	2013-04-30	
Comment[GEOLastUpdateDate]	2013-08-05	
Comment[AEExperimentType]	RNA-seq of coding RNA	
Comment[AEExperimentType]	RNA-seq of non coding RNA	
SDRF File	E-GEOD-46508.sdrf.txt