|
| Status |
Public on May 05, 2021 |
| Title |
3-79 at 2 DPA fiber cell replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
3-79 at 2 DPA fiber cell collected by using LCM
|
| Organism |
Gossypium barbadense |
| Characteristics |
genotype: wildtype
tissue: fiber cells
Stage: 2 DPA
|
| Growth protocol |
All plants were grown under a natural sunlight in greenhouse at The University of Texas at Austin
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
LCM epidermal and fiber tissues were subject to total RNA extraction by RNA Aqueous Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, Massachusetts)
NEB Next Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, Massachusetts)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Collected cells by using LCM
|
| Data processing |
Raw RNA-seq reads were mapped onto the Gossypium hirsutum (ZJU v2.0) and Gossypium barbadense (ZJU v1.0) by Tophat 2.1.1.
Uniquely mapped reads were extracted by using Samtools 1.5.
FPKM is analyzed by using Cufflinks 2.2.1.
Genome_build: ZJU
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples
|
| |
|
| Submission date |
Jun 22, 2020 |
| Last update date |
May 05, 2021 |
| Contact name |
Z Jeffrey Jeffrey Chen |
| E-mail(s) |
[email protected]
|
| Phone |
512-475-9327
|
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Polyploidy, Hybrid Vigor, and Epigenetics
|
| Street address |
2506 Speedway NMS 3.122 Stop A500
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1597 |
| Country |
USA |
| |
|
| Platform ID |
GPL25504 |
| Series (1) |
| GSE152995 |
New Roles of Transcriptional and Translational Regulation in Early Stages of Cotton Fiber Development |
|
| Relations |
| BioSample |
SAMN15342979 |
| SRA |
SRX8598130 |
