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Sample GSM4811731

Query DataSets for GSM4811731

Status

Public on Oct 01, 2020

Title

Sample type

SRA

Source name

MXSG group

Organism

Rattus norvegicus

Characteristics

strain: Sprague-Dawley
Sex: male
treatment: Ma Xing Shi Gan (MXSG) Decoction
tissue: lung

Treatment protocol

The pneumonia model group and MXSG group were received given 0.5 mg/mL LPS nebulization intervention, 30 min per day for three consecutive days. After 3 days, the MXSG group were intragastrically administered of MXSG once a day for 3 consecutive days (According to clinical guidelines, all doses were converted according to the equivalent dose of 0.018 for human and rat). The model group and the control group received an equal volume of saline accordingly.

Growth protocol

Eight or nine-week-old Male SD rats (110±10 g) were maintained under specific pathogen-free conditions according to agency guidelines. The rats were kept with a 12-h light/dark cycle and with access to water and food ad libitum. After three days of adaptive breeding, 30 rats were randomly divided into three groups (n=10): normal group, pneumonia model group, Ma Xing Shi Gan Decoction (MXSG) group.

Extracted molecule

total RNA

Extraction protocol

Add 600 μL Lysis/Binding Buffer to the 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 .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. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. 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. 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. 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 min. 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. 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. 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.
the library was detected by Agilent 2100 Bioanalyzer, Illumina HiSeqTM 2 sequencer was used to sequence the library, and 125bp or 150bp double-ended data were generated.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Sample_65

Data processing

DESeq software was used to standardize the counts of each sample gene (the basement value is used to estimate the expression quantity), calculate the multiple difference. NB (negative binomial distribution test) was used to test the different significance of reads numbers. Finally, significantly DEGs were screened according to the difference in multiple and different significance test results. P value<0.05 and fold Change>2 or fold Change<0.5 was set as the selection condition. Pathway analysis of differential expression was performed using the KEGG database (combined with KEGG annotation results), and the hypergeometric distribution test was used to calculate the significance of enrichment of DEGs in each pathway entry.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Sep 30, 2020

Last update date

Oct 01, 2020

Contact name

qianqian li

E-mail(s)

lqq@bucm.edu.cn

Organization name

Beijing University of Chinese Medicine

Department

School of Traditional Chinese Medicine