|
| Status |
Public on Feb 02, 2023 |
| Title |
Se1_Severe TBI, replicate_1 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
gender: M
age: 23
condition: traumatic brain injury
|
| Treatment protocol |
Freshly drawn peripheral blood from 12 TBI and 4 healthy volunteers was collected, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Blood RNA Purification kit (Qiagen, USA) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-ND-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression within 24hr in TBI human blood
|
| Data processing |
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.
|
| |
|
| Submission date |
Jan 19, 2023 |
| Last update date |
Feb 02, 2023 |
| Contact name |
Ping Zheng |
| E-mail(s) |
[email protected]
|
| Phone |
13917664347
|
| Organization name |
Shanghai Pudong New area People's Hospital
|
| Department |
Neurosurgery
|
| Street address |
490 South Chuanhuan Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201299 |
| Country |
China |
| |
|
| Platform ID |
GPL33038 |
| Series (1) |
| GSE223245 |
Integrated single-cell multiomics reveals novel immune candidate markers for post-traumatic coagulopathy |
|
