|
| Status |
Public on Oct 18, 2022 |
| Title |
Atg7Hmgb1DKO1-Tum |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Atg7KO; Hmgb1KO
tissue type: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from liver tissues using a GeneTET RNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling and quality scoring were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq4000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5.3a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered by keeping read count per million 10 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: raw count
|
| |
|
| Submission date |
Oct 21, 2019 |
| Last update date |
Oct 18, 2022 |
| Contact name |
Xiao-Ming Yin |
| Organization name |
Indiana University
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
975 W Walnut St IB411/406
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE139153 |
RNA-Seq Transcriptomic analysis in tumor and non-tumor tissues of Atg7-/- and Atg7-/-/Hmgb1-/- livers |
|
| Relations |
| BioSample |
SAMN13067709 |
| SRA |
SRX7027902 |
