|
| Status |
Public on May 24, 2021 |
| Title |
Sample_21_2 |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 25708
gestational age: 37.3
group: Control
batch: 32
train: 1
lmp: 26-Jul-14
oper_lmp: 26-Jul-14
del_date: 13-Apr-15
gadelivery: 37.3
diagnosisga: NA
sample_date: 13-Apr-15
subgroup: TNL
d2: 0
d2interval: NA
d3: 0
d3interval: NA
|
| Growth protocol |
Plasma samples were collected and stored in PAXgene® Blood RNA collection tube (BD 762165)
|
| 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.
|
| Label |
biotin
|
| Label protocol |
100 ng of RNA was reverse transcribed and amplified using Affymetrix WT plus expression kit following manufacturer’s suggested protocol.
|
| |
|
| Hybridization protocol |
5.5ug sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit. 200ul of labeled targets were hybridized to Affymetrix Human Transcriptome Arrays (HTA) 2.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450.
|
| Scan protocol |
Affymetrix GeneChip scanner 3000. Raw intensity data were generated from array images using Affymetrix AGCC software.
|
| Description |
re-analysis of GSM3120084
|
| Data processing |
Probeset definitions are based on Brainarray’s custom CDFs version 23 and represent ENTREZ IDs. Microarray raw gene expression data was background corrected, quantile normalized and summarized at ENTREZ ID level using Robust Multi-array Average (RMA) implemented in the oligo package of Bioconductor.
|
| |
|
| Submission date |
Apr 27, 2020 |
| Last update date |
May 24, 2021 |
| Contact name |
Adi Tarca |
| E-mail(s) |
atarca@med.wayne.edu
|
| Phone |
313-577-5305
|
| Organization name |
Wayne State University
|
| Department |
Perinatology Research Branch (NIH/NICHD)
|
| Lab |
Bioinformatics and Computational Biology Unit
|
| Street address |
3990 John R.
|
| City |
Detroit |
| State/province |
Michigan |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL28460 |
| Series (2) |
| GSE149434 |
Maternal whole blood transcriptomics to assess changes with gestational age in normal pregnancy I |
| GSE149440 |
Whole blood transcriptomics data in normal pregnancy, preterm birth and early preeclampsia |
|
| Relations |
| Reanalysis of |
GSM3120084 |
