|
| Status |
Public on Nov 05, 2020 |
| Title |
Group A_3 |
| Sample type |
SRA |
| |
|
| Source name |
Group A MSCs-derived NPCs (EGF+bFGF), Replicate 3
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: bone marrow
passage: Passage 3
treatment: EGF+bFGF
cell type: Mesenchymal stem cell
|
| Growth protocol |
Group A and Group B MSCs-derived NPCs were maintained in their respective microenvironment for 3 days prior to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted using miRNeasy mini kit (Qiagen) according to manufacturer's protocol. Starting material (300 ng) of total RNA was used the construction of sequencing library.
The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina Inc).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8, FASTQ files are generated using the appropriate bcl2fastq software (Illumina Inc.)
Tophat aligns the sequencing reads to the rat reference genome using the sequence aligner Bowtie2
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome.
The Cufflinks assembles aligned reads into different transcript isoforms based on exon usage and also determines the transcriptional start sites (TSSs).
Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
Genome_build: Ensembl (Rattus norvegicus)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 03, 2017 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Amir Ali Khan |
| E-mail(s) |
amkhan@sharjah.ac.ae
|
| Organization name |
University of Sharjah
|
| Department |
Department of Applied Biology
|
| Lab |
College of Sciences
|
| Street address |
Emirates of Sharjah
|
| City |
Sharjah |
| ZIP/Postal code |
PO Box 27272 |
| Country |
United Arab Emirates |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE104548 |
Transcriptomic RNA sequence analysis of bone marrow mesenchymal stem cells derived neural progenitor-like cells under the influence of different growth factor combinations |
|
| Relations |
| BioSample |
SAMN07735242 |
| SRA |
SRX3241416 |
