|
| Status |
Public on Dec 04, 2018 |
| Title |
controlgrna18hpf1 |
| Sample type |
SRA |
| |
|
| Source name |
Trunk ventral cells
|
| Organism |
Ciona robusta |
| Characteristics |
cell type: Multipotent cardiopharyngeal progenitor cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
200 to 800 cells were directly sorted in 100µl lysis buffer included in RNAqueous®-Micro Total RNA Isolation Kit (Ambion). The total RNA extraction was performed following the manufacturer’s instruction.
250-2000 pg of total RNA was loaded as template for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with template switching technology. RNA-Seq Libraries were prepared and barcoded using Ovation® Ultralow System V2 1–16 (NuGen).
Bulk RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
reads mapping using TopHat 2.0.12
Reads count was performed using "featureCounts" functions in Rsubread1.28.1 with KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/datas/KH.KHGene.2013.gff3.zip) with default parameters.
Genome_build: Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip)
Supplementary_files_format_and_content: gene expression read counts matrices
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Dec 04, 2018 |
| Contact name |
wei wang |
| E-mail(s) |
ww39@nyu.edu
|
| Phone |
+1 2129988381
|
| Organization name |
New York University
|
| Department |
Biology
|
| Street address |
100 washington square east
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL23563 |
| Series (1) |
| GSE123295 |
Characterization of Wnt-Tcf functions during Ciona heart development |
|
| Relations |
| BioSample |
SAMN10518267 |
| SRA |
SRX5089837 |
