|
| Status |
Public on Dec 22, 2018 |
| Title |
CPP injected GFP(+) 48 hpi rep2 |
| Sample type |
SRA |
| |
|
| Source name |
CPP injected, 48 hpi, zebrafish brain
|
| Organism |
Danio rerio |
| Characteristics |
tissue: brain
age: 6 mpf
|
| Treatment protocol |
Fish brains were injected with CPP or AB-42 peptides.
|
| Growth protocol |
Fish were cultured at 28 °C at a 14:10 h light:dark cycle in a recirculating tank system.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish brains from Tg(her4.1:EGFP) were dissected after control or TR-Aβ42 injections at 48 hpi. Cells were dissociated with Miltenyi Neural Tissue Dissociation Kit as described (Kyritsis et al., 2012). Cells were sorted with BD Aria II FACS machine, RNA was isolated using Norgen Total RNA Purification Kit.
Complete cDNA was synthesized from the obtained mRNA with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase. After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75bp single-end sequencing on the Illumina HiSeq2000 platform providing on average 31 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CPP-GFP-P_R2
|
| Data processing |
The FastQ files from sequencing were aligned to zebrafish genome (GRCz10/danRer10) using bwa (bwa-0.7.12) with default options. The read counts for each gene were calculated using featureCounts and GTF file from ensemble genome browser (Danio_rerio.GRCz10.82.gtf).
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: The processed data files contain read counts calculated by featureCounts. The first 6 columns is information about the gene (ensembl gene id, chromosome, start, end, strand, length), and the remaining columns contain read counts of each gene in the corresponding sample.
|
| |
|
| Submission date |
Oct 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Caghan Kizil |
| E-mail(s) |
ck2893@cumc.columbia.edu
|
| Phone |
4752570197
|
| Organization name |
Columbia University Irving Medical Center
|
| Street address |
650 W 168th St.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE74326 |
Amyloid-β42-induced neurodegeneration enhances stem cell plasticity and neurogenesis in adult zebrafish brain |
|
| Relations |
| BioSample |
SAMN04211716 |
| SRA |
SRX1372117 |
