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| Status |
Public on Jan 25, 2023 |
| Title |
smk7a_12D_bio rep1 |
| Sample type |
SRA |
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| Source name |
maize kernels
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| Organism |
Zea mays |
| Characteristics |
tissue: maize kernels
genotype: smk7a
development stages: kernels 12 days after polination
time: 12 DAP
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total ribonucleic acid (RNA) was isolated from the kernels of WT and smk7a collected at 12 and 20 DAP using a RNA Easy Fast Extraction Kit (DP452, Tiangen, Beijing, China)
RNA libraries for RNA-seq were prepared using a TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
smk7a_12D_1_FPKM
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| Data processing |
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the maize reference genome RefGen_V4 (ftp://ftp.ensemblgenomes.org/pub/plants/release-32/gff3/zea_mays/) using HISAT2
The gene expression levels were estimated using the fragments per kilobase of the transcript per million fragments (FPKM) mapped
Supplementary files format and content: FPKM value of expressed genes for all samples
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| Submission date |
Dec 22, 2022 |
| Last update date |
Jan 25, 2023 |
| Contact name |
xiaojiao Hu |
| E-mail(s) |
huxiaojiao@caas.cn
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| Organization name |
Institute of crop science, Chinese academy of agricultural science
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| Street address |
No.12 Zhongguancun South Main Street, Haidian District
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| City |
beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE221594 |
Characterization and transcriptome analysis of maize small kernel mutant smk7a in different development stages |
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| Relations |
| BioSample |
SAMN32369540 |
| SRA |
SRX18826364 |
| 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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