|
Status |
Public on Mar 30, 2019 |
Title |
Wei-plate5 |
Sample type |
SRA |
|
|
Source name |
TVC progeny
|
Organism |
Ciona robusta |
Characteristics |
developmental stage: Stage 38 juveniles cell type: FACS purified Mesp+ cells
|
Growth protocol |
Juvenile cultured in FASW in agarose coated plastic Petri dishes at 18°C.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA libraries were prepared for sequencing SMART-seq 2 protocol.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Barcodes in Read1 fastq files. Sequenced reads were mapped to JoinedScaffold (http://ghost.zool.kyoto-u.ac.jp/datas/JoinedScaffold.zip) whole genome using star/intel/2.5.2b with default parameters. Reads count were calculated using featureCounts function in Rsubread package with parameters as annot.ext="KH.KHGene.2013.gtf",isGTFAnnotationFile = TRUE,GTF.featureType = "exon",GTF.attrType = "gene_id" Supplementary_files_format_and_content: Expression matrix ready for single cell RNA-seq analysis.tab-delimited text files include raw FPKMs for each gene per cell. Rows:Gene_id, Columns: cell_id.
|
|
|
Submission date |
Mar 29, 2019 |
Last update date |
Mar 31, 2019 |
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 (2) |
GSE99846 |
A single cell transcriptional roadmap for cardiopharyngeal fate diversification |
GSE129074 |
scRNA-seq of Ciona juvenile heart |
|
Relations |
BioSample |
SAMN11289170 |
SRA |
SRX5604648 |