GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2552387 Query DataSets for GSM2552387
Status Public on Mar 30, 2017
Title T8.P.2670085
Sample type SRA
Source name Whole-blood
Organism Homo sapiens
Characteristics time point (weeks): T8
treatment: Placebo
response: NRES
Extracted molecule total RNA
Extraction protocol Peripheral blood samples were collected in PAXgene blood RNA tubes (PreAnalytix). PAXgene tubes were frozen using a sequential freezing process: tubes were stored at room temperature for 3hrs, transferred to 4°C overnight, followed by 6-8 hrs at -20°C, then final storage at -80°C. Total RNA (including the miRNA fraction) was isolated from whole-blood using the PAXgene Blood miRNA Kit (Qiagen, Canada), according to manufacturer’s instructions. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
All libraries were prepared using the Illumina TruSeq Small RNA protocol following the manufacturer's instructions with 12 cycles of PCR amplification after ligation of the 3' and 5' adapters, as described elsewhere5. Libraries were purified using biotinylated magnetic AMPure beads that allow for selection of specified cDNA products bound to streptavidin. A total of 50µl of amplified cDNA were mixed and purified twice with AMPure XP beads at a 1.8:1 ratio (beads:sample). This ratio allows for optimal selection of all products higher than 100nt. Library qualities were assessed using an Agilent 2100 Bioanalyzer High Sensitivity DNA chip, as well as qRT-PCR with the KAPA library quantification kit (Kapa Biosystems, USA). Samples were sequenced at the McGill University and Genome Quebec Innovation Centre (Montreal, Canada) using the HiSeq2500 Illumina sequencer with 50nt single-end reads.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Data processing All sequencing data were processed using CASAVA 1.8+34 and extracted from FASTQ files. The Fastx_toolkit was used to trim the Illumina adapter sequences. Additional filtering based on defined cut-offs was applied in order to obtain high quality data. These filters included: 1) Phred quality (Q) mean scores higher than 30, 2) reads between 15-40nt in length, 3) adapter detection based on perfect-10nt match, and 4) removal of reads without detected adapter. Additionally, we used Bowtie 35 to align reads to the human genome (GRCh37)36 and ncPRO-seq37 in combination with miRBase (V20) to match them to known miRNA sequences38,39. We used a detection threshold of 10 counts per miRNA (present at least in 80% of libraries tested). A total of 281 miRNAs survived our criteria and were included in the analysis. All small RNA sequencing data was normalized with the Bioconductor – DESeq2 package using the Variance Stabilizing Transformation (VST) method40. To identify significant microRNAs based on differential expression changes across time, we used significance analysis of microarrays method, adapted for small RNA sequencing data (SAMSeq)41. SAMSeq was implemented using a two-class paired model which accounts for changes not only between groups, but also within subjects as there is a one-to-one pairing between subjects across time. We used the Benjamini–Hochberg, false discovery rate (FDR) correction for multiple testing set at 5%, which corrects for the proportion of miRNAs likely to have been identified by chance as being significant (adjusted P values < 0.05). We also tested for potential confounding effects of age, gender, race, and RNA integrity (RIN) but found no significant differences across groups or time.
Genome_build: Human genome (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text file includes miRNA count values for each sample
Submission date Mar 28, 2017
Last update date May 15, 2019
Contact name Juan Pablo Lopez
Phone 514 7616131
Organization name McGill University
Department Human Genetics
Lab McGill Group for Suicide Studies (MGSS)
Street address 6875 La Salle Blvd
City Montreal
State/province Quebec
ZIP/Postal code H4H1R3
Country Canada
Platform ID GPL16791
Series (1)
GSE97154 MicroRNAs 146a/b-5p, 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes
BioSample SAMN06649078
SRA SRX2682853

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap