GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM8390317

Query DataSets for GSM8390317

Status

Public on Jul 15, 2024

Title

Vessel,T48h control, 03

Sample type

SRA

Source name

cerebral artery

Organism

Homo sapiens

Characteristics

tissue: cerebral artery
treatment: NA

Treatment protocol

HB vessels for 48 hours treatment was employed with Human Hb (64,500 Da; Sigma-Aldrich, St. Louis, Missouri, USA) in culture. We have prepared stock in 1X PBS and diluted to 25uM by using culture media, media changed once after 24 hours.

Extracted molecule

total RNA

Extraction protocol

Total RNA isolation was performed using RNeasy® Mini Kit (Qiagen CatNo:74104), for which the initial sample mincing was carried out on dry ice with sterilized, pre-chilled blade and pipette tips to avoid degradation of RNA, then transferred to RLT lysis buffer containing beta-mercaptoethanol. Other than this initial set of sample processing, the rest of the steps, including DNase I treatment, were followed as instructed in the protocol.
Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) , library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq X

Data processing

Fastq files generated were analyzed manually using the RNA Detector platform HISAT2 alignment has been executed and mapping reads of all files were ≥79%, then differential expression performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab limited file contain normalised counts for each samples

Submission date

Jul 10, 2024

Last update date

Jul 15, 2024

Contact name

Shafeeque Mohammedali

E-mail(s)

Shafeeque.C.MohammedAli@uth.tmc.edu

Phone

8326753380

Organization name

UTH Health Houston