|
| Status |
Public on Mar 30, 2019 |
| Title |
Wei-plate3 |
| 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 |
SAMN11289172 |
| SRA |
SRX5604646 |
