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| Status |
Public on Mar 23, 2023 |
| Title |
lin5.4w.b3 |
| Sample type |
SRA |
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| Source name |
lin-5 4wpi
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| Organism |
Medicago truncatula |
| Characteristics |
tissue: nodule
genotype: 4 wpi
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| Treatment protocol |
Collecting nodule using liquid nitrogen
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| Growth protocol |
Medicago incubated with S. meliloti Rm1021 nifH::GUS for 2 week or 4week
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated isolated using RNAiso Plus (Takara Japen)
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA by using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
Data mapping to the reference genome of medicago (https://plants.ensembl.org/Medicago_truncatula/Info/Index).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 18, 2023 |
| Last update date |
Mar 23, 2023 |
| Contact name |
FENG zhan Gao |
| E-mail(s) |
gaofz487@nenu.edu.cn
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| Organization name |
Hunan university
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| Department |
College of Biology
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| Street address |
no
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| City |
changsha |
| State/province |
hunan |
| ZIP/Postal code |
410000 |
| Country |
China |
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| Platform ID |
GPL30272 |
| Series (1) |
| GSE227642 |
The change of gene expression between late- and early stage lin-5 nodules |
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| Relations |
| BioSample |
SAMN33813281 |
| SRA |
SRX19716132 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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