|
| Status |
Public on Oct 10, 2021 |
| Title |
337_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Root tip
|
| Organism |
Cenchrus americanus |
| Characteristics |
line: 337
phenotype: Low primary root growth
tissue: Primary root tip (2 cm apex)
developmental stage: 15 days after germination
growth condition: Hydropony
|
| Growth protocol |
Plants were grown in hydropony in 1/2 Hoagland solution at 27 °C (12 h light/12 h dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted using the RNeasy kit (Qiagen).
Libraries were constructed with the TruSeq Stranded mRNA Sample Preparation (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pennisetum glaucum
|
| Data processing |
Illumina RTA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Splice junction mapping using TopHat2.
Counting using HTSeq-count.
Mapping was performed against predicted CDS available as PM.genechr.trans.cds.txt.
Genome_build: Pearl millet genome of reference IDs: ASM217483v2 (1532771 [UID] 5927848 [GenBank])
Supplementary_files_format_and_content: Lignee337_vs_Lignee249_Raw_Counts_RNA-Seq.txt: Matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Oct 07, 2021 |
| Last update date |
Oct 10, 2021 |
| Contact name |
Laurent Laplaze |
| E-mail(s) |
laurent.laplaze@ird.fr
|
| Organization name |
IRD
|
| Department |
DIADE
|
| Lab |
CERES
|
| Street address |
911 avenue Agropolis
|
| City |
Montpellier |
| ZIP/Postal code |
34394 |
| Country |
France |
| |
|
| Platform ID |
GPL30824 |
| Series (1) |
| GSE185517 |
Comparison of the root tip transcriptome of 2 pearl millet lines with contrasted primary root growth |
|
| Relations |
| BioSample |
SAMN22133042 |
| SRA |
SRX12515403 |
