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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2019 |
| Title |
E. coli-infected wildtype mouse (#9) |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: C57/129
tissue: Liver
genotype: Wildtype
infection status: E. coli-infected
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| Treatment protocol |
All mice were housed with a 12 h alternating light-dark cycle at room temperature, and had free access to standard chow diet and water throughout the study. Mkp-1-/- and Mkp-1+/+ mice were infected with E. coli i.v., or injected with PBS. Briefly, E. coli (O55:B5, ATCC 12014), purchased from American Type Culture Collection (Manassas, VA), was grown in Luria broth at 37̊ °C for 18 h. The bacteria were pelleted by centrifugation, washed three times with phosphate-buffered saline (PBS), and finally suspended in PBS. E. coli was injected to the tail veins of mice at 2.5×107 CFU/g body weight. E. coli-infected or PBS-injected mice were euthanized 24 h later by pentobarbital over dose. The liver of each mouse was excised with a small piece preserved in formalin for histological assessment and the rest of the liver snap-frozen in liquid nitrogen prior to storage at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen liver tissues using Trizol reagent (Thermo Fisher Scientific, Waltham, MA), solubilized in UltraPure RNase/DNase-free water (Thermo Fisher Scientific), and quantified by using NanoDrop ND-1000 spectrophotometer (Marshall Scientific, Hampton, NH).
For RNA-seq analyses, 1 µg total RNA was used as starting material. First, cytoplasmic and mitochondrial ribosomal RNAs were depleted using a NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, MA), according to the manufacture’s recommendations. The RNA library was prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, RNA was fragmented, and cDNA was synthesized using random primers. The resulting double-strand cDNA was then subject to end-repair, adapter ligation, and PCR amplification to generate the library. Each library was sequenced in duplicate (two RNA-seq files per specimen).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
74c1a4008e4c5b5896a3f9a8a18431b1 = md5sum of raw file for processed data file: H_WT_9_1.count.txt
40b5606353655c15f5314f3f840030dc = md5sum of raw file for processed data file: H_WT_9_2.count.txt
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| Data processing |
RNA-seq reads were subjected to low quality read and adapter trimming using Trim Galore version 0.4.0.
RNA-seq reads were mapped to the University of California Santa Cruz mm10 Mus musculus genome assembly using TopHat2 version 2.1.0.
Raw read counts were generated using HTseq version 0.6.0.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) mapped reads. Read counts were provided separately for each technical replicate, thus there are two processed data files for each sample.
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| Submission date |
Nov 20, 2018 |
| Last update date |
Oct 02, 2019 |
| Contact name |
Irina Buhimschi |
| E-mail(s) |
irina@uic.edu
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| Phone |
3129968786
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| Organization name |
University of Illinois at Chicago College of Medicine
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| Department |
Department of Obstetrics & Gynecology
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| Lab |
Perinatal Research Laboratory
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| Street address |
820 S. Wood St.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE122741 |
The effects of Mkp-1 knockout and systemic E. coli infection on the transcriptome of the liver |
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| Relations |
| BioSample |
SAMN10450100 |
| SRA |
SRX5028997 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3484457_H_WT_9_1.count.txt.gz |
93.7 Kb |
(ftp)(http) |
TXT |
| GSM3484457_H_WT_9_2.count.txt.gz |
93.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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