|
| Status |
Public on Jul 28, 2019 |
| Title |
2C-1 |
| Sample type |
SRA |
| |
|
| Source name |
2-celled proembryo
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cell type: 2-celled proembryo
developemntal stage: 4 days after pollination
strain: SR1
|
| Growth protocol |
In greenhouse under long-day conditions (16 h light/8 h dark) at 25 °C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMARTer Ultra Low Input RNA Kit for Sequencing v3 (Clonetech) was used to generate cDNA library for sequencing
Libraries were constructed using TD503-01 TruePrep DNA Library Prep Kit V2 (Vazyme) for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Amplified with SMART-Seq Ultra Low Input RNA Kit
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Nicotiana tabacum genome Ntab-TN90 using Tophat2.
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization).
Genome_build: Nicotiana tabacum genome Ntab-TN90
Supplementary_files_format_and_content: text file including FPKM value of each gene.
|
| |
|
| Submission date |
Jun 26, 2019 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Ce Shi |
| E-mail(s) |
[email protected]
|
| Phone |
+8615271898007
|
| Organization name |
Wuhan University
|
| Street address |
Bayi Road
|
| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL25653 |
| Series (1) |
| GSE133373 |
Transcriptome anaylsis of wild type 2-celled proembryo of Nicotiana tabacum |
|
| Relations |
| BioSample |
SAMN12142969 |
| SRA |
SRX6367942 |
