|
| Status |
Public on Jun 03, 2019 |
| Title |
Ern1-LKO biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver from Ern1-LKO mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Liver
age: 8 weeks of age
genotype: Liver specific Ern1 knockout mouse
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver were harvested and flash frozen in liquid nitrogen, and total RNA was isolated using RNAiso reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 μg of total RNA for librariesgeneration. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Liver total RNA from Ern1 liver specific knockout mouse
|
| Data processing |
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.
|
| |
|
| Submission date |
Jun 22, 2017 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Zhenji Gan |
| E-mail(s) |
ganzj@nju.edu.cn
|
| Organization name |
Nanjing University
|
| Department |
Model Animal Research Center of Nanjing University
|
| Street address |
12 Xuefu Road
|
| City |
Nanjing |
| ZIP/Postal code |
210061 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE100358 |
RNA-seq analysis of liver transcriptomes from wild type and Ern1-LKO mice |
|
| Relations |
| BioSample |
SAMN07269028 |
| SRA |
SRX2946733 |
