|
| Status |
Public on Apr 02, 2019 |
| Title |
LLC1 |
| Sample type |
SRA |
| |
|
| Source name |
lewis lung cancinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
agent: LLC-RFP alone
tissue: primary cancer sites
|
| Treatment protocol |
subcutaneously injected with LLC-RFP alone or subcutaneously injected with LLC-RFP with BMSCs
|
| Growth protocol |
water and sunlight and air and food
|
| Extracted molecule |
total RNA |
| Extraction protocol |
flow cytometry cell sorting,and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
the red fluorescent protein positive LLC cells were collected from the tumor sites by flow cytometry cell sorting and subjected to RNA sequencing analysis
|
| Data processing |
Sequencing data filtering
After obtaining clean reads, we compared clean reads to reference genome sequences using HISAT
Using StringTie,Each sample is reconstructed with a transcript, which is then reconstructed with a Cuffcompare (one of the Cufflinks tools).The new transcripts were obtained by referring to the annotation information, and the coding potential of the new transcripts was predicted with the CPC software.
We use GATK to test each sample SNP and INDEL information, the final result is stored in VCF format
Detection of differential splicing genes (DSG) between samples using rMATS
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include Fpkm values for each Sample ...
|
| |
|
| Submission date |
Sep 23, 2018 |
| Last update date |
Apr 02, 2019 |
| Contact name |
xina zhang |
| E-mail(s) |
[email protected]
|
| Phone |
+8618711148647
|
| Organization name |
Central South University
|
| Department |
Cancer Research Institute
|
| Lab |
The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education
|
| Street address |
110 XiangYa Road
|
| City |
ChangSha |
| State/province |
HuNan |
| ZIP/Postal code |
410078 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE120349 |
RNA sequencing in LLCs from co-injected mice or LLC injection alone. |
|
| Relations |
| BioSample |
SAMN10106136 |
| SRA |
SRX4730172 |
