|
| Status |
Public on Feb 04, 2019 |
| Title |
Sample_8 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Maternal Blood
|
| Organism |
Homo sapiens |
| Characteristics |
individual: mi058
group: TIL [Term in Labor (with labor)]
gestational age (weeks): 26.1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from PAXgene® Blood RNA collection tube (BD 762165) as described in the PAXgene® Blood miRNA Kit Handbook (December, 2015). Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean) and quality assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation.
Starting with 500 ng of total RNA, cDNA library templates were synthesized using the Illumina TruSeq® Stranded Total RNA LT (Set A) Kit with Ribo-Zero Globin rRNA reduction, as described in the TruSeq® Stranded Total RNA Sample Preparation Guide (Rev. E, October 2013). Libraries were validated using the HS D1000 ScreenTape on the Agilent 2200 TapeStation, and quantified on the Qubit® 2.0 Fluorometer by the Qubit® dsDNA HS Assay (ThermoFisher). The Illumina HiSeq 2500 instrument was used to cluster the samples onto the flow cell.
The pools were put on at 10pM and run in rapid mode at 2×100 paired end. Illumina HiSeq Rapid PE Cluster kit V2 and HiSeq Rapid SBS kit v2 200 cycles was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_8
|
| Data processing |
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner (version 0.9.1) in quasi-mapping-based mode using these command options: "--seqBias --gcBias --useVBOpt --vbPrior"
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package
Genome_build: Ensembl GRCh37.75 (hg19)
Supplementary_files_format_and_content: Count matrix from "scaledTPM" from tximport (v. 1.6.0) were save in .csv format
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Adi Tarca |
| E-mail(s) |
atarca@med.wayne.edu
|
| Phone |
3135775305
|
| Organization name |
Wayne State University
|
| Department |
Perinatology Research Branch (NIH/NICHD)
|
| Street address |
3990 John R
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48188 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE113964 |
Sequencing based maternal whole blood expression changes with gestational age and labor in normal pregnancy |
| GSE113966 |
Maternal whole blood expression changes with gestational age and labor in normal pregnancy |
|
| Relations |
| BioSample |
SAMN09011933 |
| SRA |
SRX4022892 |
