|
| Status |
Public on Dec 31, 2020 |
| Title |
Primed rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Rhesus ESCs
|
| Organism |
Macaca mulatta |
| Characteristics |
cell type: Rhesus ESCs
type: Primed cells
protocol: Primed
|
| Growth protocol |
Cells were grown in culture conditions as described in original protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed in Triizol and subjected to the RNeasy mini kit (Qiagen). 200ng of RNA were used to genrated libraries for sequencing.
The libraries were prepared using 200 ng of RNA with NextFlex Rapid Directional mRNA-Seq kit (Bioo-Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were sequenced on a NextSeq500 sequencing machine (Illumina) as single-reads of 75bp.
The bcl2fastq conversion software was used for demultiplexing (Illumina) and data trimming was performed using Cutadapt.
Sequencing depth for each sample was about 30 millions of reads.
Reads were then mapped to the Mmul8 rhesus macaque genome using HISAT2 alignment program and quantified with the HTseq script.
Genome_build: Mmul8 macaca mulatta
Supplementary_files_format_and_content: TPM values for each sample
|
| |
|
| Submission date |
Mar 02, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Irene Aksoy |
| E-mail(s) |
[email protected]
|
| Organization name |
Stem Cell and Brain Research Institute
|
| Street address |
18 avenue du Doyen Lepine
|
| City |
Lyon |
| ZIP/Postal code |
69500 |
| Country |
France |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE146178 |
Transcriptomic profiling of primed and naive primate pluripotent stem cells by RNA-sequencing |
|
| Relations |
| BioSample |
SAMN14257754 |
| SRA |
SRX7826781 |
