|
| Status |
Public on Mar 20, 2018 |
| Title |
IMR32 |
| Sample type |
SRA |
| |
|
| Source name |
neuroblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: neuroblastoma cell line IMR32
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cell lines are procured from NCCS, India and maintained in MEM (IMR 32) and Hams F12K (SH-SY-5Y) growth media supplemented with 10% FBS and 1% antibiotics Pen-Strep at proper growing conditions. Total RNA was extracted from the above cell lines with the use of RNeasy Mini kit (Qiagen, USA) according to the manufacturer’s instructions. The purity of isolated RNA was evaluated using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. An aliquot of each the samples isolated from IMR-32 and SH-SY-5Y was also run on an Agilent RNA Bioanalyzer chip to check for RNA integrity number (RIN) and was found to be 8.3 and 9.2 respectively.
The RNA libraries were constructed for sequencing following Illumina TruSeq Small RNA library protocol outlined in “TruSeq Small RNA Sample Preparation Guide” (Part # 15004197; Rev. F; February 2014) and using TruSeq Small RNA sample preparation kit (Illumina, # RS-200-0012).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
small RNA
|
| Data processing |
bcl2fastq software (Illumina) was used for converting image file to FASTq format.
Sequenced reads were trimmed for adaptor sequence using srna Work bench and Quality check of the generated data was done using the FASTqc software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNAs predicted for each Sample.
|
| |
|
| Submission date |
Jul 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dr. Bibekanand Mallick |
| E-mail(s) |
vivek.iitian@gmail.com
|
| Organization name |
National Institute of Technology
|
| Department |
Department of Life Science
|
| Lab |
RNAi & Functional Genomics Lab.
|
| Street address |
NIT Rourkela
|
| City |
Rourkela |
| State/province |
Odisha |
| ZIP/Postal code |
769008 |
| Country |
India |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE83945 |
Genome-wide profiling of mature piRNAs in human Neuroblastoma (NB) cell lines |
|
| Relations |
| BioSample |
SAMN05335731 |
| SRA |
SRX1892465 |
