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Sample GSM1690275 Query DataSets for GSM1690275
Status Public on Mar 17, 2016
Title Gh1e rep 2
Sample type SRA
 
Source name stem tip
Organism Gossypium hirsutum
Characteristics strain: 3798
tissue: shoot apical
age: seedling stage, have two 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 ā€˜Nā€™), 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 SAMN03701476
SRA SRX1032899

Supplementary file Size Download File type/resource
GSM1690275_Gh1e-2.Gene.rpkm.txt.gz 885.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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