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| Status |
Public on Nov 26, 2019 |
| Title |
WT CT38 RNA-Seq rep1 |
| Sample type |
SRA |
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| Source name |
LIVER
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| Organism |
Mus musculus |
| Characteristics |
gender: Male
strain: C57BJ/L6 background
age: 8-12 weeks of age
genotype/variation: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse liver tissues were collected from XBP1Flox (n=2) and XBP1LKO (n=2) mice at 2h interval for a total of 48 hours under constant darkness condition. Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions.
Extracted RNA samples underwent quality control assessment using the RNA Pico 6000 chip on Bioanalyzer 2100 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher). Strand-specific total mRNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGen) per the manufacturer’s instructions using 200ng of RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent).
The prepared libraries were pooled and sequenced using NoveSeq 6000 (Illumina), generating ~40 million 2×100 bp paired-end reads per samples. RNA-Seq library preparation and sequencing were performed at Univesity of Pittsburgh Medical Center (UPMC) Genome Center.
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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 |
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using Cufflinks (Mortazavi et al. 2008), HTSEQ and Bedtools (Quinlan et al. 2010) by default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python
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| Submission date |
May 08, 2019 |
| Last update date |
Nov 26, 2019 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
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| Organization name |
University of Pittsburgh
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| Street address |
203 Lothrop Street
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE130890 |
Time series transcritpome in wild-type mice and XBP1 liver-specific knockout mice |
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| Relations |
| BioSample |
SAMN11605124 |
| SRA |
SRX5807206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3755742_WT_CT38A_ZHU109A39_S77.wig.gz |
106.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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