|
| Status |
Public on Oct 13, 2020 |
| Title |
mRNA_GF4 |
| Sample type |
SRA |
| |
|
| Source name |
germ-free mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumor tissue
tumor model: Lung-metastasis model of mice
injected cell line: Lewis lung carcinoma (LLC)
Sex: male
|
| Treatment protocol |
Lung-metastasis model of mice: One million Lewis lung carcinoma (LLC) cells in 100 ul sterile PBS were injected into mice via tail vein.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA quality and quantity was measured by using nanodrop spectrophotometer
Total RNA of each sample was used to prepare the RNA sequencing library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.
|
| |
|
| Submission date |
Nov 22, 2019 |
| Last update date |
Oct 13, 2020 |
| Contact name |
X XX |
| Organization name |
university
|
| Street address |
Road 89
|
| City |
X |
| ZIP/Postal code |
11 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE140885 |
Gut microbiota regulates tumor via circRNA/miRNA networks III |
| GSE140887 |
Gut microbiota regulates tumor via circRNA/miRNA networks |
|
| Relations |
| BioSample |
SAMN13354000 |
| SRA |
SRX7202814 |
