|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jun 23, 2022 |
Title |
GX100-2 1h root rep3 |
Sample type |
SRA |
|
|
Source name |
root
|
Organism |
Gossypium hirsutum |
Characteristics |
tissue: root treatment: 150 mM NaCl developmental stage: 1h
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from the roots of seedlings with an improved CTAB–ammonium acetate method (Zhao et al. 2012) RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
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 TM-1 whole genome using HISAT v2.0 with default parameters. Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Florea et al., F1000Res, 2013. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: TM-1
|
|
|
Submission date |
Oct 25, 2021 |
Last update date |
Jun 23, 2022 |
Contact name |
Anhui Guo |
E-mail(s) |
guoah@cau.edu.cn
|
Organization name |
College of Agronomy and Biotechnology, China Agricultural University
|
Street address |
College of Agronomy and Biotechnology,
|
City |
Beijing |
State/province |
China |
ZIP/Postal code |
100193 |
Country |
China |
|
|
Platform ID |
GPL16485 |
Series (1) |
GSE186533 |
Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton |
|
Relations |
BioSample |
SAMN22561558 |
SRA |
SRX12771117 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|