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| Status |
Public on Nov 20, 2014 |
| Title |
lbl1, mRNA, rep1 |
| Sample type |
SRA |
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| Source name |
maize vegetative apex, lbl1 mutant, mRNA
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| Organism |
Zea mays |
| Characteristics |
line/background: B73
genotype: LBL1 -/-
age: 2 weeks
tissue: leaf apex
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| Growth protocol |
Families segregating the lbl1-rgd1 allele (Nogieira, et al., 2007) introgressed at least three times into B73 were grown in growth-chambers at 16 hour 28 C/light and 8 hour 24 C/dark cycles. Shoot apices including the meristem and up to 5 leaf primordia were dissected from 2-week-old plants.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the mirVana RNA isolation kit (Life Techologies).
Libraries were prepared using TruSeq RNA Sample Prep Kits (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
rnaseq-lbl1-Cuffdiff_gene_expression.txt
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| Data processing |
The mRNA sequencing data were aligned to the B73 RefGen_v2 genome (release 5a.57) and the annotated exon junctions (version 5b_AGPv2) using TopHat v1.2.0.
mRNA differential expression was determined using Cuffdiff v1.0.3 with default parameters, except that the "minimum alignment count" (-c) which was set to 50.
Genome_build: Maize B73 RefGen_v2 genome (release 5a.57) and the annotated exon junctions (version 5b_AGPv2).
Supplementary_files_format_and_content: Small RNA: DatasetS1_smallRNA_counts.xls: All counts, fold changes and P-values are given for the hundreds of DE species (rather than the 100,000s of all small RNAs mapped).
Supplementary_files_format_and_content: mRNA: rnaseq-lbl1-Cuffdiff_gene_expression.txt: Cuffdiff output of RPKM values is given for all RNA-seq data.
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| Submission date |
Sep 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Molly Gale Hammell |
| E-mail(s) |
[email protected]
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| Phone |
516-367-5009
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| Organization name |
Cold Spring Harbor Lab
|
| Department |
Quantitative Biology
|
| Lab |
Molly Hammell
|
| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL15463 |
| Series (1) |
| GSE50557 |
Genome-wide analysis of leafbladeless1-regulated and phased small RNAs provides new insights into the tas3 pathway in maize- |
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| Relations |
| BioSample |
SAMN02343718 |
| SRA |
SRX343582 |
| 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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