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| Status |
Public on Apr 09, 2018 |
| Title |
WT rep1 |
| Sample type |
SRA |
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| Source name |
kernel
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| Organism |
Zea mays |
| Characteristics |
tissue: kernel
age: 15 DAP
genotype: Wild-type
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3.24 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: reads mapped to mapped to B73 RefGen_v3.24; Ensembl plants release-24 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Fan Feng |
| E-mail(s) |
fengfan_102@outlook.com
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| Phone |
18817395283
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| Organization name |
Shanghai University
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| Street address |
333 Nanchen Road
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| City |
Shanghai |
| ZIP/Postal code |
200444 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE97422 |
Next Generation Sequencing Facilitates Quantitative Analysis of WT and o11 mutant Transcriptomes |
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| Relations |
| BioSample |
SAMN06688735 |
| SRA |
SRX2710005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2564305_WT_rep1.txt.gz |
444.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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