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| Status |
Public on Nov 06, 2014 |
| Title |
TIL15_TGGAT.PL15 |
| Sample type |
SRA |
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| Source name |
ear tissue from parent TIL15,biological replicate 2
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| Organism |
Zea mays |
| Characteristics |
cultivar: TIL15
genotype: teosinte
tissue: ear
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| Treatment protocol |
Fifty to 100 milligram samples of the immature ear, leaf, and seedling stem were harvested for RNA extraction during this time. Leaf and seedling stem (including the shoot apical meristem) tissue was collected at the v4 leaf stage. Single ears from maize and F1 hybrid plants were collected when the ears weighed 50 to 100 milligrams with silks just beginning to be visible. Teosinte ears were also collected when silks just started to appear, however, due to the small size of teosinte ears 7 to 16 ears (average of 11.27) from each plant were pooled to obtain ~50 milligrams of tissue.
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| Growth protocol |
Plants were grown in growth chambers with a 12 hour dark-light cycle for up to 6 weeks, after which they were moved to a greenhouse.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from the plant tissues using a standard TRIzol protocol, quantified by spectrophotometer, and normalized to 1 ììin nuclease free water.
We generated polyA selected, strand specific, barcoded RNAseq libraries using a five minute fragmentation time and 12 PCR amplification cycles. Library adapters used balanced barcode sequences of four and five base pairs. Pools of 14 (F1s) or 15 (parents) libraries were sequenced on one Illumina lane each
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Tissue captured from ear of parent TIL15
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Pseudotranscriptomes were constructed for all parents by inserting SNPs and short indels into the B73 reference transcriptome (AGP v2).
RNA-Seq reads were aligned to pseudotranscriptomes using Bowtie 1
Counts of reads perfectly aligning to different alleles were obtained for each gene within each pair of species
Read counts were used in downstream statisctical analysis
Genome_build: B73_Refgenv2
Supplementary_files_format_and_content: Files *.snpspt_trn list maize- and teosinte-specific read counts (columns 11 and 12, respectively) at sites segregating between the two parents in a cross (the cross is specified in the beginning of the file name). Columns 1-10 contain: gene, transcript, position on B73 transcript, allele on B7 3 transcript, position on maize pseudotranscript, allele on maize pseudotranscript, position on teosinte pseudotranscript, allele on teosinte pseudotranscript, chromosome, position on the chromosome,
Supplementary_files_format_and_content: Files *.snpspt_unnorm list read counts (column 9) for a given parent at all sites segregating between this parent and any other parent it is crossed with in this study. Columns 1-8 contain: gene, transcript, position on B73 transcript, allele on B7 3 transcript, position on parent's pseudotranscript, allele on parent's pseudotranscript, chromosome, position on the chromosome
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| Submission date |
Sep 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
John Doebley |
| E-mail(s) |
jdoebley@wisc.edu
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| Organization name |
University of Wisconsin - Madison
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| Department |
Genetics Department
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| Lab |
Laboratory of Genetics
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| Street address |
425-G Henry Mall
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| City |
Madison; |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL15463 |
| Series (1) |
| GSE61810 |
The Role of cis Regulatory Evolution in Maize Domestication |
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| Relations |
| BioSample |
SAMN03082047 |
| SRA |
SRX711037 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1514551_TIL15_TGGAT.PL15.snpspt_unnorm.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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