 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 25, 2020 |
| Title |
stage2 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
floral meristems
|
| Organism |
Aquilegia coerulea |
| Characteristics |
cultivar: Kiragami
tissue: floral meristems
developmental stage: developmental stage2
genotype: wild-type
|
| Treatment protocol |
all wild-type
|
| Growth protocol |
Seeds of Aquilegia coerulea ‘Kiragami’ were purchased from Swallowtail Garden Seeds (Santa Rosa, CA, USA). Seeds were germinated in wet soil and seedlings were grown under conditions of 16h daylight at 18˚C and 8 h dark at 13˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Once the plants developed approx. six true leaves, they were transferred into vernalization conditions (16h daylight at 6˚C and 8h dark at 6˚C) for three to four weeks, and subsequently moved back to the regular growth condition. Once the inflorescences started to develop, axillary FMs were quickly dissected on ice using surgical needles and flash frozen in liquid nitrogen. Three sepals were removed from every floral bud collected. The total RNA of all samples was extracted using the RNeasy Micro Kit (Qiagen, Netherlands).
Sequencing libraries were prepared by the Bauer Core facility of Harvard University using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc., CA, USA) for cDNA synthesis and Illumina Nextera XT (Illumina) for library preparation. Libraries were fragmented to an average size of 350 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
staminode primordia finish initiating
|
| Data processing |
Sequencing was conducted at Novogene (Beijing, China) using the 150 bp paired-end Illumina HiSeq4000 sequencing platform.
The raw sequencing reads were filtered by removing adapters and low-quality reads using Trim Galored v0.6.5 17 (quality Phred score cutoff = 20) and mapped to the Aquilegia coerulea ‘Goldsmith’ v3.1 reference transcriptome (https://phytozome.jgi.doe.gov/) using Kallisto v0.46.118.
Supplementary_files_format_and_content: Tab Separated Value files including estimated counts and tpm for each sample.
|
| |
|
| Submission date |
Sep 24, 2020 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Ya Min |
| E-mail(s) |
minyaaa9058@gmail.com
|
| Organization name |
Harvard University
|
| Street address |
16 Divinity Ave.
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL29181 |
| Series (1) |
| GSE158507 |
Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea |
|
| Relations |
| BioSample |
SAMN16243442 |
| SRA |
SRX9176296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4801855_W4.tsv.gz |
402.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
