|
| Status |
Public on Feb 07, 2019 |
| Title |
A549_T40 |
| Sample type |
SRA |
| |
|
| Source name |
Lung cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: non-small cell lung cancer cell line
passage: 42-45
treatment: 40uM epigallocatechin gallate (EGCG)
|
| Treatment protocol |
A549 cells were treated with 40 micromolar or 100 micromolar EGCG concentration for 24h and was processed for small RNA sequencing.
|
| Growth protocol |
A549 cancer cells were grown in F-12K medium with 10% FBS and 1% 100X Antibiotic-Antimycotic solution at 37 degrees Celsius with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol method for total RNA isolation was used.
NEBNext® Multiplex Small RNA Library Prep Set for Illumina.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
T40 treatment for 24h.
processed data files:
Rawcounts_known.csv
Rawcounts_novel.csv
Normalized_known.csv
Normalized_novel.csv
|
| Data processing |
Reads were preprocessed to remove adapter and low quality bases. srna-workbenchV3.0_ALPHA1 was used to trim the 3' adapter sequences.
Trimmed reads were filtered based on the length criteria (minimum length 16bp and maximum 40 bp).
The filtered reads were aligned to Homo sapiens GRCh38 using bowtie-1.1.1.
Other non-coding RNAs (rRNA, tRNA, snRNA, snoRNA and piRNA) were filtered.
MiRBase21 was used for known miRNA identification. Further putative novel miRNA sequences were predicted by ncbi-blast-2.2.304 at e-4.
Genome_build: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary_files_format_and_content: Rawcounts_*.csv: Comma-separate text files include raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_*.csv: Comma-separate text files include RPKM for each Sample.
|
| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Abul Kalam Azad Mandal |
| E-mail(s) |
akamandal@rediffmail.com
|
| Phone |
9443758596
|
| Organization name |
VELLORE INSTITUTE OF TECHNOLOGY
|
| Department |
BIOTECHNOLOGY, SCHOOL OF BIOSCIENCES AND TECHNOLOGY
|
| Street address |
VELLORE
|
| City |
VELLORE |
| State/province |
Tamil Nadu |
| ZIP/Postal code |
632014 |
| Country |
India |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE110514 |
EGCG-treated non-small cell lung cancer associated signature miRNA expression analysis: NGS approach for novel miRNA sequence detection |
|
| Relations |
| BioSample |
SAMN08522684 |
| SRA |
SRX3686942 |
