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| Status |
Public on Sep 02, 2020 |
| Title |
JEK16230_HFD + PFOA |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: 29-30 weeks
treatment: HFD + PFOA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed, flash frozen in liquid nitrogen, and total RNA was isolated using Qiagen Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard BGI protocols (non-stranded).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Data included 16 single-read fastq libraries (raw read length 50 nt). Base-calling was done bcl2fastq v2.20.0.422.
Reads were quality filtered using Trimmomatic ver. 0.33 (http://www.usadellab.org/cms/?page=trimmomatic), with the cutoff threshold for average base quality score set at 20 over a window of 3 bases.
Reads shorter than 20 bases post-trimming were excluded.
Cleaned reads were mapped to Mus musculus genome reference (GRCm38) using STAR version STAR_2.5.2b.
Number of reads aligned to the exon regions of each of the annotated genes (gencode M16) were generated using featureCounts tool of subread package version 1.6.0 (https://doi.org/10.1093/bioinformatics/btt656).
Read alignments were considered unstranded. Multiple mapped reads and reads overlapping with multiple features were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of each gene for each sample
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| Submission date |
Sep 04, 2018 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Xilin Li |
| E-mail(s) |
[email protected]
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| Phone |
8624858599
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| Organization name |
Indiana University
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| Street address |
2719 E 10th street Rm230
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| City |
Bloomington |
| State/province |
Indiana |
| ZIP/Postal code |
47408 |
| Country |
USA |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE119441 |
The effects of perfluorooctanoate on high fat diet induced non-alcoholic fatty liver disease in mice |
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| Relations |
| BioSample |
SAMN09951437 |
| SRA |
SRX4637990 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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