|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Oct 15, 2021 |
Title |
heart, LPS-stressed 24 h mice_2 |
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 |
SAMN22228503 |
SRA |
SRX12580383 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|