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Sample GSM7496343

Query DataSets for GSM7496343

Status

Public on Jun 30, 2024

Title

Expression_bPR_2

Sample type

SRA

Source name

peripheral blood

Organism

Homo sapiens

Characteristics

tissue: peripheral blood
cell line: peripheral blood
cell type: peripheral blood
genotype: peripheral blood
treatment: NC

Extracted molecule

total RNA

Extraction protocol

A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 minG. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into 5 the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for 20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at -70°C
RNA libraries for RNA-seq were prepared using smarter mTotal RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

FPKM_allsamples.txt
counts_allsamples.txt

Data processing

Data preprocessing and genomic alignment
Transcript splicing、lncRNA prediction、and Gene quantification
Differential screening analysis and Functional Analysis
CircRNA prediction, Expression analysis and Interaction research,Gene structure optimization and New transcript prediction
Alternative splicing Analysis and SNP、INDEL Analysis
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

Submission date

Jun 16, 2023

Last update date

Jun 30, 2024

Contact name

panpan liu

E-mail(s)

liup202309@outlook.com

Phone

008613817534495

Organization name

shanghai pudong new area gongli hospital