|
| Status |
Public on Apr 23, 2024 |
| Title |
DIS-04-T1 |
| Sample type |
SRA |
| |
|
| Source name |
serum
|
| Organism |
Homo sapiens |
| Characteristics |
time point: T1
patient id: 4
tissue: serum
diagnosis: CD
fraction: small RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Serum EVs were then isolated via precipitation using “ExoQuick™ - Exosome Precipitation Kit” (#EXOQ20A-1, Biozol, Eching, Germany) according to manufacturer’s protocol from 500µL aliquots. The pellet containing precipitated EVs was suspended in 100µL of PBS. 50µL of this suspension were subjected to small RNA extraction using of the “SeraMir™ Exosome RNA Amplification Kit” (#RA808A-1, Biozol, Eching, Germany) with an adapted protocol for extracellular RNA isolation14. The isolates were eluted in 30µL elution buffer and miRNA concentration was quantified using the “Qubit™ microRNA Assay Kit” (#Q32880, Invitrogen™, Waltham, MA) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using the TruSeq® RNA seq Library Prep Kit v2 according to the Illumina TruSeq® messenger (mRNA) sequencing protocol. The RNA-seq libraries were sequenced on the Illumina HiSeq 3000/4000 (1 x 50bp).
miRNA-sequencing libraries were prepared according to the manufacturer’s protocol of the NEXTFLEX® Small RNA-Seq Kit v3 (#NOVA-5132-06, PerkinElmer, Waltham, MA) and sequenced on SP lanes on an Illumina NovaSeq 6000 (1 × 50 bp).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
21Feb18_G01
mature_counts.csv
hairpin_counts.csv
|
| Data processing |
Reads were processed by the nf-core/smrnaseq (v 1.1.0) pipeline
Reads were trimmed with Trim Galore! (v 0.6.5). Reads were first clipped by 4 bases on the 5’ and 3’ ends followed by adapter trimming.
Reads were then mapped to annotated miRbase (release 22) miRNAs with Bowtie1(v 1.3.1). Reads were first mapped to annotated mature miRNAs with unmapped reads subsequently mapped to annotated hairpin miRNAs.
Count estimation was done using Samtools (v 1.12)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include hairpin and mature miRNA counts
|
| |
|
| Submission date |
Jul 21, 2023 |
| Last update date |
Apr 23, 2024 |
| Contact name |
Neha Mishra |
| E-mail(s) |
n.mishra@ikmb.uni-kiel.de
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE237994 |
Dynamic Changes in Extracellular Vesicle-Associated miRNAs Elicited by Abdominal Ultrasound in Peripheral Blood of Inflammatory Bowel Disease Patients |
|
| Relations |
| BioSample |
SAMN36679113 |
| SRA |
SRX21126425 |
