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| Status |
Public on Aug 18, 2016 |
| Title |
endosperm_12DAP_r1 |
| Sample type |
SRA |
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| Source name |
endosperm 12 days after pollination
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| Organism |
Zea mays |
| Characteristics |
tissue: endosperm 12 days after pollination
genotype: B73
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq libraries were prepared as follows. Approximately four micrograms of total RNA was used as input. Each sequencing library was constructed using the TruSeq RNA Sample Prep Kit V2 (Illumina, San Diego, CA) according to manufacturer’s instructions with the following modifications to confer strand-specificity. The polyA-selected RNA was used for first strand synthesis and the resulting cDNA:RNA hybrid was purified using RNAClean XP beads (Beckman, Brea, CA). The second strand synthesis was performed using a dNTP mix containing dUTPs (10mM dATPs, 10mM dGTPs, 10mM dCTPs, and 20mM dUTPs) and DNA Polymerase I (New England Biolabs, Ipswich, MA). The purified ligation products were incubated with Uracil DNA Glycosylase (Fermentas) before PCR amplification.
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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 |
Data were mapped to the ZmB73_RefGen_v2 reference genome and the ZmB73_5a.59_WGS_exons.tfp was used for annotations of gene models
RNA-Seq RPKM data were generated using Bowtie version 2.1.0 and Tophat version 2.0.8b (flags = –F 0 -i 30 -M). Gene expression values were calculated using Cufflinks version 2.1.1 (flags = -u --library-type fr-firststrand -b)
Genome_build: ZmB73_RefGen_v2
Supplementary_files_format_and_content: The processed data for the FPKM.tsv file contains a row of headers indicating the sample name. this first colum is the unique gene identifier and the all of columns represent the expression value represented in Fragments per Kilobase of exons per gene per million reads. This is a tab delimited file.
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| Submission date |
Aug 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
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| Phone |
8584534100
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| Organization name |
HHMI-Salk-Institute
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| Department |
Genomic Analysis Laboratory
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| Lab |
Ecker lab
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| Street address |
10010 North Torrey Pines Road
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE50191 |
Maize proteome and transcriptome atlas |
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| Relations |
| BioSample |
SAMN02334471 |
| SRA |
SRX339756 |
| 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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