|
| Status |
Public on Oct 28, 2019 |
| Title |
Patient_01_cancer |
| Sample type |
SRA |
| |
|
| Source name |
ESCC tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue_type: ESCC
sample_type: cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ESCC tissues using TRIzol reagent (Invitrogen) for construction of RNA-seq libraries.
The sequencing library was prepared from 1 ug of total RNA using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (RS-122-2203).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
To control RNA-seq data quality, the RNA-seq reads with Phred base quality ≥ 20 were filtered using Sickle (version 1.33).
The remaining reads were mapped to human reference genome (CRCh37/hg19) using STAR (version 2.5.2b) with parameters "--alignIntronmin 61 --alignIntronMax 265006 --outFilterMultiMapNmax 20 --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0.90 --outFilterMatchNminOverLread 0.90".
Read counts were estimated with BAM files using featureCounts (version 1.5.1) with parameters "--minOverlap 60 -s 2 -p -B -C".
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each samples.
|
| |
|
| Submission date |
Apr 19, 2019 |
| Last update date |
Oct 28, 2019 |
| Contact name |
Jin-Wu Nam |
| E-mail(s) |
[email protected]
|
| Phone |
+82 2-2220-2428
|
| Organization name |
Hanyang University
|
| Department |
Department of Life Science
|
| Street address |
Seongdong-Gu Hangdang-dong
|
| City |
Seoul |
| ZIP/Postal code |
133-791 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE130078 |
A Novel LincRNA HERES Epigenetically Regulates Wnt Signaling Pathway via Interaction with EZH2 in Esophageal Squamous Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN11467211 |
| SRA |
SRX5712729 |
