|
| Status |
Public on Jun 16, 2019 |
| Title |
pT2N1: Ulcerative Adenocarcinoma |
| Sample type |
SRA |
| |
|
| Source name |
greater gastric curvature
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: stomach
cell_type: Ulcerative Adenocarcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the TruSeq Kit (Illumina, Inc.) with modifications. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Poly-T oligo-attached magnetic beads (Illumina, Inc.) were used to remove residual poly-A RNA. All other steps were performed according to the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For circRNA expression analysis, the reads were to mapped genome using 1.the STAR (58) and DCC (59) was used to identify the cirRNA and to estimate the circRNA expression
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Shan Kong |
| E-mail(s) |
1816310060@yjs.ntu.edu.cn
|
| Phone |
+8618860976895
|
| Organization name |
Affiliated Hospital of Nantong University
|
| Department |
Department of Laboratory Medicine
|
| Lab |
Research Center of Clinical Medicine
|
| Street address |
NO.20, Xisi Road
|
| City |
Nantong |
| State/province |
Jiangsu |
| ZIP/Postal code |
226001 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE131414 |
High-throughput sequencing identifies 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, in gastric cancer tissues |
|
| Relations |
| BioSample |
SAMN11671014 |
| SRA |
SRX5855871 |
