|
| Status |
Public on Apr 05, 2016 |
| Title |
36hpf PGC |
| Sample type |
SRA |
| |
|
| Source name |
germ cells_36hpf
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
tissue: embryo
cell type: germ cell
developmental stage: 36 hpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PGCs and somatic cells were FACSed and total RNA was extacted using Arcturus RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
processed data file: HT data 36hpf.xls
|
| Data processing |
The reads were filtered and trimmed for low quality reads and then mapped to transcriptome using seqmap for 7hpf samples (bowtie for the 36hpf samples) and generated expression value using rseq.
Differential expression was detected using DEseq package of bioconductor.
Genome_build: Zv8
Supplementary_files_format_and_content: Excel files with Gene Ids and RNA abundance for each sample
|
| |
|
| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Katsiaryna Tarbashevich |
| E-mail(s) |
k.tarbashevich@uni-muenster.de
|
| Phone |
+4917620089474
|
| Organization name |
Institute for Cell Biology
|
| Street address |
Von-Esmarch Str 56
|
| City |
Muesnter |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE77077 |
Control of progenitor cell positioning and organ patterning during embryogenesis |
|
| Relations |
| BioSample |
SAMN04432767 |
| SRA |
SRX1539608 |
