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| Status |
Public on Mar 19, 2023 |
| Title |
H1527 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain background: C57BL/6J
genotype: Pi*Z
treatment: LPS
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) from Pi*M and Pi*Z liver samples (n=6). The quantity and quality of the RNA were determined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads were trimmed or removed. The high quality reads were then mapped to GRCm38 using STAR 2.7.6a
Fragments Per Kilobase of exon per Megabase of library size (FPKM), Transcript Per Million (TPM) and extimated read counts were calculated using RSEM 1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jun 22, 2022 |
| Last update date |
Mar 19, 2023 |
| Contact name |
Tongjun Gu |
| E-mail(s) |
tgu@ufl.edu
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| Organization name |
The University of Florida
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| Department |
ICBR
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| Street address |
2033 Mowry Road
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE206619 |
Comprehensive characterization of hepatic inflammatory changes in a mouse model of alpha-1 antitrypsin deficiency |
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| Relations |
| BioSample |
SAMN29234382 |
| SRA |
SRX15821845 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6258238_H1527_expr.genes.results.txt.gz |
957.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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