|
| Status |
Public on Jun 03, 2015 |
| Title |
Control 23 |
| Sample type |
SRA |
| |
|
| Source name |
control_placenta
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: normotensive pregnant women
tissue: Placental biopsy
molecule subtype: Enriched small RNA fraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The placental biopsies were subjected to mechanical homogenization, and the enriched small RNA fraction was isolated using a mirVanaTM miRNA Isolation Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer's specifications.
Libraries were constructed according to the TruSeq Small RNA Sample Prep Kit Set A protocol (Illumina) using a total of 50 ng of small RNA in the 5’ and 3’ RNA adapters ligation step. cDNA synthesis was performed using the SuperScript ® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by 15 PCR cycles to enrich the sample. The first quality control step for the libraries was performed using a High Sensitivity DNA Analysis kit on the 2100 Bioanalyzer System (both Agilent Technologies). Libraries were selected (fraction of ~145-160 bp) by non-denaturing polyacrylamide gel electrophoresis using 6% of acrylamide gels followed by a concentration step with a standard ethanol/sodium acetate/glycoblue protocol. A second quality control step for the libraries was performed using a High Sensitivity DNA Analysis Kit/2100 Bioanalyzer system. The libraries were quantified using the dsDNA HS Assay Kit (Invitrogen) on a Qubit fluorometer and were each adjusted to a concentration of 20 pM. In the clonal amplification of the libraries, bridge PCR was performed using the TruSeq SR Cluster v5 kit on a Cluster Station (Illumina). The sequencing was performed on the Illumina GAIIx platform with a configuration of 36 cycles for single-end reads. Each sample was sequenced on 1/3 lanes of a flow cell, resulting in a range of 7 to 13 million reads.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Control Placenta_3 CB_1023
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Clean Adapter performed using custom script in perl.
Aligmnent perfomed using smalt version 0.7.5
Coverage of sequence alignments performed using coverageBed function from BEDTools version 2.16.2
Data were filtered removing miRNA's without at least 1 read per million in 3 of the samples, using a custom R script
Normalization and differential expression process were performed with edgeR v.3.4.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values and gene expresion for each Sample, performed with edgeR v.3.4.2. Please note that colums 6 to 19 correspond to raw counts and from columns 20 to 33 correspond to normalized counts.
|
| |
|
| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Veronica Jimenez-Jacinto |
| E-mail(s) |
vjimenez@ibt.unam.mx
|
| Phone |
+52(777) 3291719
|
| Organization name |
Universidad Nacional Autonoma de Mexico
|
| Department |
Unidad Universitaria de Secuenciación Masiva y Bioinformática
|
| Street address |
Av. Universidad 2001. Col. chamilpa
|
| City |
Cuernavaca |
| State/province |
Morelos |
| ZIP/Postal code |
62130 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE69452 |
GLOBAL ANALYSIS OF CIRCULATING AND PLACENTAL MICRORNA SIGNATURES AND PREECLAMPSIA DEVELOPMENT |
|
| Relations |
| BioSample |
SAMN03742239 |
| SRA |
SRX1043140 |
