|
| Status |
Public on Jun 09, 2017 |
| Title |
Exp 4 Control rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
NuLi cells (cell line)
|
| Organism |
Homo sapiens |
| Characteristics |
batch: 4
condition: Control
cell type: lung epithelium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from NuLi cells using the ReliaPrep™ RNA Cell Miniprep System (Promega Corporation) following the manufacturer’s instructions. RNA was eluted in 30 µL of RNAse-free water and stored at -80°C. RNA was quantified using a NanoDrop™ UV Spectrophotometer (Thermo Fisher Scientific Inc) and quality assessed using the Experion™ Automated Electrophoresis System (Bio-Rad Laboratories Pty Ltd). All RNA integrity numbers (RIN) for the analysed samples ranged from 9.7 to 10.
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used for Experiment 4. The six RNA-Seq libraries in Experiment 4 were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: Exp4_PE_count_matrix.txt, Exp4_SE_count_matrix.txt, Exp4_NS_count_matrix.txt,
|
| Data processing |
The reads for Experiment 4 were mapped to the Ensembl Home sapiens genome (GRCh38). Mapping was performed with Tophat2 (v 2.0.12) [14] calling Bowtie2 (v 2.1.0)
The featureCounts function of Subread was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 annotation gtf file.
Comparison of controls in the PE, and SE datasets was performed using edgeR (v3.14.0). Comparison of the controls versus treated samples in each of the four experiments was performed using functions in the edgeR (v 3.14.0) [23] and limma (v 3.28.17) [17] Bioconductor packages
genome build: Ensembl Homo sapiens genome (GRCh38)
processed data files format and content: Tab-delimited text file with read count for each sample.
|
| |
|
| Submission date |
Apr 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Corley |
| E-mail(s) |
s.corley@unsw.edu.au
|
| Phone |
+61 02 9385 8853
|
| Organization name |
UNSW
|
| Department |
Biotechnology & Biomolecular Sciences
|
| Lab |
Systems Biology Initiative
|
| Street address |
D26, Kensignton Campus
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE97471 |
Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols |
|
| Relations |
| BioSample |
SAMN06693597 |
| SRA |
SRX2714844 |
