|
| Status |
Public on May 31, 2018 |
| Title |
Nematostella ELAV positive cells ATACseq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult polyps
|
| Organism |
Nematostella vectensis |
| Characteristics |
stage/cell type: Polyps
strain: ELAV::mOrange reporter transgenic line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq experiments were performed starting from 200,000 fresh cells, following the ATAC protocol originally described in Buenrostro et al. 2013 (10.1038/nmeth.2688)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read_1 files were mapped into Nematostella genome assembly v1.0 (http://genome.jgi.doe.gov/Nemve1/Nemve1.download.html) using bowtie2, using default parameters.
Duplicate reads were removed using samtools.
The starting position of each read was moved +4 (in positive strand) or -5 (negative strand) to compensate for the 9bp insertion of Tn5 transposase.
deepTools bamCoverage was used to generate bigWig coverage files, using a total extension of 50bps from the read start position, and a scaleFactor parameter of 0.1
|
| |
|
| Submission date |
Jan 19, 2018 |
| Last update date |
May 31, 2018 |
| Contact name |
Arnau Sebe-Pedros |
| E-mail(s) |
arnau.sebe@crg.es
|
| Organization name |
Centre for Genomic Regulation
|
| Department |
Systems Biology
|
| Lab |
Sebe-Pedros lab
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23029 |
| Series (1) |
| GSE95723 |
Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis |
|
| Relations |
| BioSample |
SAMN08379114 |
| SRA |
SRX3591596 |
