|
| Status |
Public on Oct 12, 2022 |
| Title |
N1 |
| Sample type |
SRA |
| |
|
| Source name |
Stomach
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Matched adjacent tissue
donor: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNeasy Plus Mini Kit with QIAshredder columns (Qiagen) following manufacturer's instructions.
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 |
Expression_FPKM_Transcript.txt
|
| Data processing |
Solexa pipeline version 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 whole genome using Hisat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Expression_FPKM_Transcript.txt: Tab-delimited text file includes RPKM values for each Sample (FPKM >= 0.5).
|
| |
|
| Submission date |
Apr 13, 2021 |
| Last update date |
Oct 12, 2022 |
| Contact name |
shouyu wang |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing university medical school
|
| Street address |
22 Hankou Road
|
| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE172032 |
RNA-Seq in four pairs of human gastric cancer and matched adjacent normal tissue specimens |
|
| Relations |
| BioSample |
SAMN18737503 |
| SRA |
SRX10597169 |
