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Sample GSM4586008 Query DataSets for GSM4586008
Status Public on Jan 03, 2021
Title Emo_6h_1
Sample type SRA
 
Source name lung tissue
Organism Rattus norvegicus
Characteristics tissue: lung
Treatment protocol Animals were randomized into five groups (n = 12 per group); the control group, the sham-operated group, the SAP model group, the SAP-DEX treated group, and the SAP-emodin treated group. Furthermore, each group was sub-divided into 6 h and 24 h subgroups. Briefly, SD rats were denied food for 12 h but had free access to water and were then given 1% pentobarbital sodium anesthesia (intraperitoneal injection, 40 mg/100 g body weight) prior to the surgical operation. The SAP model was induced as previously described by administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct by standard retrograde infusion. This procedure induced SAP and eventually resulted in a SAP-induced ALI, which served as the model. Sterile saline of the same volume was given to the control group of animals. The sham group of animals had surgery to marginally rotate their pancreas. DEX (10 mg/kg body weight) was intravenously administered to the DEX group of animals at 2 h and 12 h post-operation, and an equivalent volume of sterile saline was intravenously administered to the other groups of animals. Emodin (40 mg/ kg body weight) was intragastrically given to the SAP-emodin group at 2 h and 12 h post-operation. An equal volume containing 0.5% carboxymethylcellulose sodium was intragastrically given to the other groups of animals. At 6 h and 24 h post-operation, blood samples were taken via the abdominal aorta for arterial blood gas analysis and serum harvesting, and then stored at -80ºC until used
Growth protocol Sixty healthy male Sprague Dawley (SD) rats (specific pathogen-free, eight weeks old, 180–220 g) with animal license number SYXK (Liao) 2013-0003 were purchased from the Laboratory Animal Center of Dalian Medical University. Another animal license number, SCXK (Liao) 2013-0006 (with qualified number 211003700), was also acquired. The animals were housed in PVC cages. The temperature was controlled at 22 ± 2ºC in a room with 12 h light-dark cycles and free access to standard laboratory food and drinking water for one week prior to the experiments.
Extracted molecule total RNA
Extraction protocol Total RNA of each lung tissue sample was extracted using TRIzol Reagent (Ambion) according to the manufacturer’s instructions. To eliminate any DNA present, RQ1 DNase (Promega) was added to the extracted total RNA. The absorbance of the purified RNA was measured to determine the quality and concentration with a Smartspec plus (BioRad, Hercules, USA) at 260 nm/280 nm (A260/A280). Agarose gel electrophoresis (1.5%) was conducted to verify the integrity of the RNA
For RNA-seq library preparation, 10 μg of purified total RNA of each sample was purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen). Polyadenylated mRNAs were used for the construction of a directional RNA-seq library. Ion fragmentation of purified mRNAs was conducted at 95ºC following end repair and 5' adaptor ligation. The fragmented mRNAs were reverse-transcribed with RT primer, known 3' adaptors, and random hexamers. Then, purification and amplification of the cDNAs were conducted. The 200–500 bps of amplified cDNAs were collected. The cDNAs for each sample were quantified and stored at -80ºC until sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description lung tissue of rats collected at 6h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct and emodin (10 mg/kg body weight) being intragastrically given
Data processing Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: rat_ensembl_v6
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample
 
Submission date Jun 01, 2020
Last update date Jan 03, 2021
Contact name Dong Chen
Organization name ABLife, Inc.
Department Center for Genome Analysis
Street address 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
City Wuhan
State/province Hubei
ZIP/Postal code 430075
Country China
 
Platform ID GPL24688
Series (1)
GSE151572 Effect of emodin on long non-coding RNA-mRNA networks in rats with severe acute pancreatitis-induced acute lung injury
Relations
BioSample SAMN15076044
SRA SRX8449920

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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