|
| Status |
Public on Jun 01, 2020 |
| Title |
Young3: RNA4 MACS Young RNA |
| Sample type |
SRA |
| |
|
| Source name |
5 brains pooled
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Brain progenitor cells
age: 5,5 months old
strain: AB
|
| Growth protocol |
Wild-type AB strain, zebrafish were used. Animals were fed twice a day with dry food and three times a week with artemia and kept in standard conditions. After anesthesizing and decapitating the animals, brains were dissected and underwent a stem cell isolation procedure using MACS Miltenyi Biotec Neural Tissue Dissociation Kit(P). Isolated stem cells were seeded using L15 medium (supplemented with 1% P/S, 5%FBS, 20ng/ml EGF & FGF) onto the poly-D Lysin and Laminin coated culture plates (for ICC), 75cm2 Corning Cell Bind flasks (for RNA Seq.), or FalconTM Chambered Cell Culture Slides (for ICC) and were incubated at 28oC. Five to ten fish brains were pooled prior to the stem cell isolation procedure depending on the size of the culture area, in order to obtain a visible amount of stem cells in a culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After anesthesia and decapitation, whole fish brains were dissected under the stereo microscope. Total RNAs were isolated from the scraped stem cell cultures, each containing 10 fish brain isolates, using Qiagen's RNeasy Mini Kit according to the manufacturer’s instructions. The isolation protocol was followed by DNase treatment with Ambion TURBO DNA-free Kit from Thermo Fisher Scientific.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
TopHat 2.1.1: Alignment of fragments to the reference genome
Cufflinks 2.2.1: Fragments per kilobase of transcript per million mapped reads were calculated using cufflinks
Cuffmerge (Cufflinks v. 2.2.1): transcripts were merged
CuffQuant (Cufflinks v. 2.2.1): transcripts were quantified
Cuffdiff (Cufflinks v. 2.2.1): Gene expression comparisons between groups
Genome_build: Genome Reference Consortium Zebrafish Build 10
Supplementary_files_format_and_content: .FPKM_TRACKING:Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: .gtf: input assemblies merged
Supplementary_files_format_and_content: .cxb: cuffquant output
Supplementary_files_format_and_content: .DIFF: difference in gene expression. Differences in the total FPKM of transcripts sharing each gene_id are measured
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Ayca Arslan Ergul |
| E-mail(s) |
aycaergul@gmail.com
|
| Organization name |
Bilkent University
|
| Department |
UNAM
|
| Street address |
Bilkent Üniversitesi UNAM
|
| City |
ANKARA |
| State/province |
ÇANKAYA |
| ZIP/Postal code |
06800 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE133436 |
RNA sequencing data of aging zebrafish brain progenitor cells |
|
| Relations |
| BioSample |
SAMN12148437 |
| SRA |
SRX6371889 |
