|
| Status |
Public on Jun 23, 2020 |
| Title |
EC109_shScr |
| Sample type |
SRA |
| |
|
| Source name |
human esophageal squamous carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: EC109
cell type: esophageal squamous carcinoma cell line
shRNA: shScr
|
| Treatment protocol |
Human ESCC cells were treated with specific shRNAs for silencing DAP3.
|
| Growth protocol |
RPMI medium 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted using Qiagen RNeasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Scramble shRNA treated
Strand-specific RNA-Seq
processed data file: dap3_kd_specific_editing_sites_in_escc.xlsx
|
| Data processing |
Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SAOPnuke software.
Clean reads were then mapped to reference genome (hg19) using bwa (v0.7.15-r1140). PCR duplicates were removed with samtools (v1.4.1). The reads with mapping quality score less than 20 were discarded.
Variants were called with an in-house variant caller (Perl script) from the samtools mpileup data.
Candidate editing sites were filtered as the following: SNPs from different databases (1000 Genomes Project, NHLBI GO Exome Sequencing Project (http://evs.gs.washington.edu/EVS/), dbSNP v138) were removed, sites within the first 6 bases of the reads were excluded. For sites not located in Alu elements, the candidates within the 4 bases of a splice junction on the intronic side, and those residing in the homopolymeric regions and in the simple repeats were all removed. Candidate variants located in the reads that map to the non-unique regions of the genome by using BLAT were also excluded. Only A-to-G editing sites based on the strand information were retained.
To obtain high confidence editing events, the candidate sites were required to be supported by at least 20 reads of which at least 2 are edited and both shDAP3 knockdown treatments to result in at least 10% change in the editing level in the same direction.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: dap3_kd_specific_editing_sites_in_escc.xlsx: Excel sheet includes DAP3 knockdown specific high confidence editing events in 2 different ESCC cell lines.
|
| |
|
| Submission date |
Nov 27, 2018 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Polly Leilei Chen |
| E-mail(s) |
polly_chen@nus.edu.sg
|
| Phone |
+6565168435
|
| Organization name |
Cancer Science Institute of Singapore NUS
|
| Department |
Department of Anatomy
|
| Lab |
PLC Lab
|
| Street address |
#12-01, MD6, 14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE123020 |
Suppression of adenosine-to-inosine (A-to-I) RNA editome by death associated protein 3 (DAP3) promotes cancer progression |
|
| Relations |
| BioSample |
SAMN10486411 |
| SRA |
SRX5066985 |
