 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 04, 2018 |
| Title |
R1 |
| Sample type |
SRA |
| |
|
| Source name |
Red-flowered mutant
|
| Organism |
Trifolium repens |
| Characteristics |
strain: Red-flowered mutant
tissue: Petal
flower color: Red
|
| Treatment protocol |
At the pre-flowering stage, the plants with many flower buds were divided into two groups, a control group and treatment group. The plants from the control group were placed in the field for growth, and the plants from the treatment group grew under shaded conditions, which were created by covering the top of plants with a cubic shading net to prevent sunlight from irradiating the flowers.
|
| Growth protocol |
The experimental materials grew under natural conditians in the field until squaring stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted with the column plant RNAout kit (Tiandz Technology, Beijing, China).The RNA quality was detected by 1.5% agarose gels, and these bands that have not been degraded and contaminated were used to later test. The RNA concentration was quantified using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Data filtering,SOAPnuke,v1.5.2,default parameters with '-l 15 -q 0.5 -n 0.05 --seqType 0'
Transcriptome assembly,Trinity,v2.0.6,default parameters with '--min_contig_length 150 --CPU 10 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr'
Gene functional annotation,Blast,v2.2.23,default parameters with evalue =1e-5
Quantification of gene expression levels,RSEM,v1.2.12,default parameters
CDS predict,ESTscan,v3.0.2,default parameters
GO enrichment,Blast2GO,v2.5.0,default parameters
KEGG enrichment,Blast2GO,v2.5.0,default parameters
SSR ,MISA,v1.0,default parameters with '1-12,2-6,3-5,4-5,5-4,6-4 100 150'
Differential expression analysis,DESeq R package,(1.10.1)
Transcription factor predict,Hmmsearch,v3.0,default parameters
Genome_build: de novo assembly; FASTA file is available on the series record.
Supplementary_files_format_and_content: text format files including FPKM values for each Sample
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Heshan Zhang |
| E-mail(s) |
sdzhanghs@163.com
|
| Phone |
+86-27-87680959
|
| Organization name |
Hubei Academy of Agricultural Sciences
|
| Department |
Institute of Animal Husbandry and Veterinary science
|
| Street address |
Southern Lake Street, Hongshan District, Wuhan city, China
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL23680 |
| Series (1) |
| GSE101059 |
Transcriptome analysis of a red-flowered white clover mutant |
|
| Relations |
| BioSample |
SAMN07338935 |
| SRA |
SRX2993309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2698807_R1.genes.fpkm.txt.gz |
995.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
