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| Status |
Public on Jul 01, 2014 |
| Title |
tbh_rep2 |
| Sample type |
SRA |
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| Source name |
tbh mutant_fruit spine
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| Organism |
Cucumis sativus |
| Characteristics |
strain: R1407
genotype/variation: tbh mutant
developmental stage: 4 days before anthesis
tissue: fruit spine
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Huayueyang RNA extraction kit (China)
6ug total RNA was used in library construction.Double-stranded cDNAs were synthesized using oligo(dT) beads (Invitrogen).The cDNAs were then digested with an anchoring restriction enzyme (NlaIII) and ligated to a 5' adapter, which contains a recognition site for the type IIS restriction enzyme MmeI (New England Biolabs). Following MmeI digestion, 3' adapter was ligated. Tags flanked by both adapters were enriched by PCR for 15 cycles. The PCR products were run on a 6% PAGE gel, and the 105-bp DNA band was excised and purified. The DNA samples were sequenced on an Illumina HiSeq 2000 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 4
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| Data processing |
library strategy: Digital Gene Expression
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adapter sequence. Only 21nt tags without any 'N' nucleotide and with count > 1 in a library were kept as clean tags.
Counts of tags were normalized to transcript per million (TPM) according to total number of clean tags in each library
Genome_build: v2i available at http://cucumber.genomics.org.cn/
Supplementary_files_format_and_content: Each file contains three columns: tag sequence, raw count, normalized count (transcript per million, TPM)
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| Submission date |
Aug 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Renyi Liu |
| E-mail(s) |
rliu.bicomp@gmail.com
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| Phone |
02157078228
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| Organization name |
Shanghai Center for Plant Stress Biology
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| Department |
Bioinformatics
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| Street address |
3888 Chenhua Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
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| Platform ID |
GPL16310 |
| Series (1) |
| GSE49607 |
Transcriptome profiling reveals roles of meristem regulators and polarity genes during multicellular fruit trichome development in cucumber (Cucumis sativus L.). |
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| Relations |
| BioSample |
SAMN02303665 |
| SRA |
SRX332273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1202548_tbh_rep2_TagCopyNumber.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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