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Sample GSM5623246 Query DataSets for GSM5623246
Status Public on Oct 15, 2021
Title heart, LPS-stressed 24 h mice_1
Sample type SRA
 
Source name heart
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Heart
age: 8 weeks old
stress: LPS
Extracted molecule total RNA
Extraction protocol Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, FPKMs
 
Submission date Oct 12, 2021
Last update date Oct 15, 2021
Contact name Xiaoping Wang
E-mail(s) XiaopingWang726@outlook.com
Phone +8617702206558
Organization name Beijing University of Chinese Medicine
Street address No. 11, North 3rd Ring East Road, Chaoyang District, Beijing
City Beijing
State/province Beijing
ZIP/Postal code 100029
Country China
 
Platform ID GPL24247
Series (1)
GSE185754 Cardiomyocyte TLR4 regulates autophagy through TRAF6-mediated TFEB ubiquitination in sepsis-associated cardiac dysfunction
Relations
BioSample SAMN22228501
SRA SRX12580382

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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