|
| Status |
Public on Mar 20, 2024 |
| Title |
EV, Suicide male, MDD20 |
| Sample type |
SRA |
| |
|
| Source name |
Anterior cingulate cortex-derived Evs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Anterior cingulate cortex-derived Evs
gender: male
sample type: MDD
|
| Treatment protocol |
For each subject, 200-400 mg of brain tissue were cut into very fine pieces while still partially frozen. The tissue was then incubated in Hibernate E medium (800 µL / 100 mg of tissue) in the presence of 75 U/mL of collagenase type III at 37 oC for 20 min with gentle shaking. The reaction was then halted using protease (PI) and phosphatase (PS) inhibitors (1X) , and the sample was centrifuged at 300g for 5 min. The pellet was homogenized in phosphate buffered saline (PBS) with 1X PI/PS, while the supernatant was collected and centrifuged at 2,000g for 10 min. The supernatant was collected again and centrifuged at 10,000g for 30 min. The supernatant was overlaid on a size exclusion column for extracellular vesicle (EV) separation according to the manufacturer’s protocol. Samples were then concentrated using Amicon centrifugal filters. EVs were treated with Proteinase K at 37 °C for 30 min, then with PureLink RNAseA at room temperature for 2 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAzol lysis reagent was added at 5X to each sample, which were then incubated at room temperature for 5 min. 1X of chloroform was added, and the samples were incubated at room temperature for 3 min. They were centrifuged at 12000g at 4 °C for 15 min, and the aqueous phase was collected. 1.5 volumes of 100 % ethanol were added and mixed gently. The mixture was then added to QIAGEN MinElute columns, and the MiRNeasy Micro Kit was used according to the manufacturer’s protocol (QIAGEN).
Libraries were constructed follwing the Galas Lab - 4N library prep - Version 1.0 protocol
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Data trimmed with cutadapt
Extracellular RNA Communication Consortium’s (ERCC) exceRpt small RNA-Seq pipeline (v.4.6.3)
no mismatch allowed during alignment
filter: excluded miRNAs with less than 10 counts in 70% of subjects per group
Assembly: hg38
Supplementary files format and content: csv file contains filtered raw read counts
|
| |
|
| Submission date |
Feb 09, 2024 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Gustavo Turecki |
| E-mail(s) |
gustavo.turecki@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Psychiatry
|
| Lab |
McGill Group for Suicide Studies
|
| Street address |
6875 Boulevard LaSalle
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4H 1R3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE255478 |
Title: Profiling Small RNA from Brain Extracellular Vesicles in Individuals with Depression |
|
| Relations |
| BioSample |
SAMN39904049 |
| SRA |
SRX23585639 |
