|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 17, 2016 |
Title |
Gh3e rep2 |
Sample type |
SRA |
|
|
Source name |
stem tip
|
Organism |
Gossypium hirsutum |
Characteristics |
strain: 3798 tissue: shoot apical age: the budding stage,twelve pieces of leaf genotype: nulliplex-branch
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using Plant RNA EASYspin Plus Kit(Aidlab, Peking, China). RNA and miRNA 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 Casava1.7 software used for basecalling. Reads were aligned to cotton genome no more than 5 mismatches using the SOAP aligner/SOAP2 software after low-quality reads (reads with unknown sequences āNā), adaptor sequence fragments, and empty reads were removed Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. The GeneIDs in the processed data files represent (e.g. CotAD_22466, CotAD_64340, etc.), The cotton genome and cds sequences we download form http://cgp.genomics.org.cn (Free to register to use). The reference :(Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J et al: Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Genome_build: ASM98774v1; NCBI WGS Project: LBLM01 (Gossypium hirsutum) Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
|
|
Submission date |
May 19, 2015 |
Last update date |
May 15, 2019 |
Contact name |
quan sun |
E-mail(s) |
sunquan@cqupt.edu.cn
|
Organization name |
Chongqing University of Posts and Telecommunications
|
Department |
College of Bioinformation
|
Street address |
Chongwen road 2#
|
City |
Chongqing |
ZIP/Postal code |
400065 |
Country |
China |
|
|
Platform ID |
GPL16485 |
Series (1) |
GSE69025 |
To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages |
|
Relations |
BioSample |
SAMN03701488 |
SRA |
SRX1032911 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1690287_Gh3e-2.Gene.rpkm.txt.gz |
920.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|