|
| Status |
Public on Mar 01, 2019 |
| Title |
094_Head_000_A |
| Sample type |
SRA |
| |
|
| Source name |
Homeostatic apical region (head), subtentacular section
|
| Organism |
Hydra vulgaris |
| Characteristics |
strain: Jussy
time point: Homeostatic apical region (subtentacular cut)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
3 feedings per week
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy, polyA enrichment
Illumina TruSeq, directional
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Homeostatic apical region (subtentacular cut), replicate A
|
| Data processing |
Adapter and removal of known trans-spliced leader: Cutadapt 1.11 (--trim-n -m 50 -q 5)
Generation of pseudo counts: Salmon 0.7.2 (--libType SR --seqBias --gcBias)
Normalization using DESeq2
Genome_build: Hv_Jussy_transcriptome.fasta.gz
Supplementary_files_format_and_content: counts2017_reg.csv.gz: Raw abundance measurements (estimated counts)
Supplementary_files_format_and_content: normacounts_reg2017.csv.gz: Normalized abundance measurements (estimated counts)
|
| |
|
| Submission date |
Mar 07, 2018 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Yvan Wenger |
| E-mail(s) |
yvan.wenger@gmail.com
|
| Organization name |
University of Geneva
|
| Department |
Genetics and Evolution
|
| Lab |
B. Galliot
|
| Street address |
30 Quai Ernest-Ansermet
|
| City |
Geneva |
| State/province |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19551 |
| Series (2) |
| GSE111531 |
Gene expression time course analysis during apical and basal regeneration in Hydra |
| GSE111534 |
Generic and context-dependent gene modulations during Hydra whole body regeneration |
|
| Relations |
| BioSample |
SAMN08648352 |
| SRA |
SRX3771991 |
