|
Status |
Public on Dec 04, 2018 |
Title |
tcfgrna18h1 |
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 |
SAMN10518263 |
SRA |
SRX5089841 |