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| Status |
Public on Sep 01, 2013 |
| Title |
10R |
| Sample type |
SRA |
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| Source name |
maize root
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| Organism |
Zea mays |
| Characteristics |
genotype: wide type DH4866
developmental stage: Three-leaf stage
growth condition: osmotic stress treatment with 18% (w/v) polyethyleneglycol-6000 (PEG-6000) for 24 hours
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extract 6ug total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 95bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
We take all CATG*** tags in a gene, not only the 3' end one, as its reference tags.
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| Data processing |
Unique tag consolidation: Raw sequences were extracted from the resulting image files using the open source Firecrest and Bustard applications (Illumina). Data were consolidated by read counts for unique sequences. The consolidated, unfiltered sequence tags and raw read counts are provided as processed data files for each sample (lane of sequence).All downstream analyses are performed by BGI. Co., Ltd (Shenzhen, China).
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| Submission date |
Sep 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiuxia Liu |
| E-mail(s) |
liuxiuxia2007@gmail.com
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| Organization name |
Shandong University
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| Street address |
27 Shanda South Road
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| City |
Jinan |
| ZIP/Postal code |
86-531 |
| Country |
China |
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| Platform ID |
GPL9141 |
| Series (1) |
| GSE31944 |
The differences of the transcriptional profile between wide-type maize and transgenic ZmPIS maize (drought tolerance) by the assay of digital gene expression profile data |
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| Relations |
| SRA |
SRX096148 |
| BioSample |
SAMN00715923 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM791596_10R_TagCopyNumber.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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