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Sample GSM7657450 Query DataSets for GSM7657450
Status Public on Apr 23, 2024
Title DIS-16-T2
Sample type SRA
 
Source name serum
Organism Homo sapiens
Characteristics time point: T2
patient id: 16
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_H04
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 SAMN36679104
SRA SRX21126434

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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