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| Status |
Public on Feb 04, 2019 |
| Title |
Sample_11 [RNA-Seq 2] |
| Sample type |
SRA |
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| Source name |
Maternal Blood
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| Organism |
Homo sapiens |
| Characteristics |
individual: mi548
group: TIL
gestational age: 34.7
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| 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.
The DriverMap™ Human Genome-Wide Gene Expression Profiling Assay (hDM18Kv2) from Cellecta, Inc (Mountain View, CA) was used to measure the expression level of 18,559 protein coding genes by combining highly multiplexed RT-PCR amplification with Next-Generation Sequencing (NGS) quantitation. Sample processing was performed per manufacturer protocols available at https://www.cellecta.com/technology-portfolio/targeted-expression-profiling-driver-map-assay/. cDNA products amplified in the assay were analyzed on an Illumina NextSeq 500 sequencer using a NextSeq 500/550 High Output v2 kit (75 cycles).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample_11
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| Data processing |
Representation of gene-specific amplicons in amplified cDNA products was analyzed using a custom gene enumeration software developed at Cellecta, Inc. With this method, only reads that align to the gene specific amplicon are counted. The alignment uses only the 36 nucleotides started by forward primer position and 36 nucleotides region ended by reverse primer. Any reads from the middle portion of the amplicons are not counted. Alignment used the DriverMap Reference Database (hGWDv2) .
Supplementary_files_format_and_content: Raw count matrix in .csv format.
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| Submission date |
May 04, 2018 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Adi Tarca |
| E-mail(s) |
atarca@med.wayne.edu
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| Phone |
3135775305
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| Organization name |
Wayne State University
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| Department |
Perinatology Research Branch (NIH/NICHD)
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| Street address |
3990 John R
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| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48188 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE113966 |
Maternal whole blood expression changes with gestational age and labor in normal pregnancy |
| GSE114037 |
Targeted sequencing based maternal whole blood expression changes with gestational age and labor in normal pregnancy |
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| Relations |
| BioSample |
SAMN09069707 |
| SRA |
SRX4040855 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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