|
| Status |
Public on Mar 26, 2024 |
| Title |
T_27_BP |
| Sample type |
SRA |
| |
|
| Source name |
T_BP = Placental biopsy of a control patient during delivery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Placental biopsy taken from the umbilical cord axis
experimental group: T_BP = Placental biopsy of a control patient during delivery
|
| Treatment protocol |
N/A
|
| Growth protocol |
Total blood sample (PAXgene tube, PreAnalytiX) was taken at the time of preeclampsia diagnosis (and matched on gestational age at inclusion for controls) and was repeated 4 to 6 weeks postpartum. PAXgene tubes were stored at 4°C for 24 hours, before freezing for 24 hours at -20°C and then permanently stored at -80°C. At-term placental biopsy was also performed at the time of delivery for each of the included women. Placental biopsy was defined as a macroscopically placental area of 2x2 cm including both chorionic and basal membranes. Biopsies were immediately preserved in RNAlater (Thermo Fisher Scientific) for 24 hours at 4°C, before freezing for 24 hours at -20°C, then permanently at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs from total blood samples were extracted using the PAXgene Blood RNA kit according to the procedure recommended by the manufacturer (Qiagen). Briefly, total blood was lyzed using proteinase K and the nucleic acids were precipitated by the addition of ethanol. DNA was digested with DNase I RNase-free for 15 minutes at room temperature. Total RNAs were eluted and then incubated at 65°C for 5 minutes before being placed at -80°C. Total RNAs from placenta biopsies were extracted using the RNeasy Mini Kit according to the procedure recommended by the manufacturer (Qiagen). After dissolution of placental tissue with RLT-β-mercapto-ethanol, nucleic acids were precipitated with the addition of ethanol. DNA was digested with DNase I RNase-free for 15 minutes at room temperature. Total RNAs were eluted before being placed at -80°C. The quality and quantity of the extracted RNAs were evaluated using the Bioanalyzer 2100 (Agilent Technologies) and by NanoDrop Spectrophotometer (Nanodrop Technologies).
None
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D586T138
|
| Data processing |
Nextflow, FastQC, Trimgalore, Fastp, MultiQC
Assembly: NCBI
Supplementary files format and content: Raw data, annotations of RNA-seq
|
| |
|
| Submission date |
Mar 21, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Jonatane Andrieu |
| E-mail(s) |
jonataneandrieu@gmail.com
|
| Phone |
0687955104
|
| Organization name |
ADES EFS CNRS
|
| Department |
Recherche
|
| Lab |
GENGLOBE
|
| Street address |
14 rue de chanterac
|
| City |
Marseille |
| ZIP/Postal code |
13003 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE262147 |
Dual specificity phosphate 1 (DUSP1) has a key non-invasive predictive marker in preeclampsia |
|
| Relations |
| BioSample |
SAMN40568538 |
| SRA |
SRX24015838 |
