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| Status |
Public on Aug 01, 2019 |
| Title |
GmSIN1 OE rep1 |
| Sample type |
SRA |
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| Source name |
equal mix of root and leaf RNA
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| Organism |
Glycine max |
| Characteristics |
tissue: root, leaf
age: 2-week old
genotype: GmSIN1 over-expression
treatment: mock treatment for 6 hrs
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| Treatment protocol |
Addition of NaCl (final concentration is 150 mM) to the hydroponic solution for 6 hrs.
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| Growth protocol |
For germination, seeds of soybean were laid on moistened filter paper for 2 d at 20°C. Seedlings of uniform size were transferred to a 16-h photoperiod regime (light/dark temperature 28 °C /20 °C) under 800 µmol m-2 s-1 illumination and a relative humidity of 60% and were grown hydroponically in half-strength Hoagland solution for two weeks.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mock treated and 150 mM NaCl treated 2-week old seedlings (WEI6823 and GmSIN1 OE) using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions. The total RNA from roots and leaves was isolated separately and mixtured equaly.
The mRNA sequencing libraries were constructed with barcodes using the TrueSeq RNA Sample Preparation Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file (Cock P., et al., 2010).
Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011) computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.FPKM method is used in calculated expression level.
Genome_build: Glycine max Glycine_max_v2.0 from NCBI
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 09, 2017 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Fengning Xiang |
| E-mail(s) |
[email protected]
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| Organization name |
Shandong University
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| Department |
School of life science
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| Street address |
27, Shandanan Road
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| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250100 |
| Country |
China |
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| Platform ID |
GPL15008 |
| Series (1) |
| GSE93322 |
Transgenic and conventional cultivar comparison in response to salt stress |
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| Relations |
| BioSample |
SAMN06212816 |
| SRA |
SRX2480332 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2451229_GmSIN1_OE_rep1.txt.gz |
642.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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