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| Status |
Public on Jun 03, 2013 |
| Title |
Mo17_RNA_rep1 |
| Sample type |
SRA |
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| Source name |
5-day-old coleoptyle
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| Organism |
Zea mays |
| Characteristics |
tissue: 5-day-coleoptyle
strain: Mo17
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| Growth protocol |
Seeds were grown in the incubator at 25°C in darkness on wet paper towels set in glass Pyrex dish. After 5 days coleoptiles were excised and stored at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared by grinding tissue in TRIzol reagent (Invitrogen 15596-026) on dry ice and processed following the protocol provided by manufacturer. To remove DNA, an aliquot of total RNA was treated with RQ1 DNase (Promega M6101), followed by phenol/chloroform/ iso-amyl alcohol extraction, chloroform/iso-amyl alcohol extraction and ethanol precipitation. Total RNA (20 μg) was used for poly(A)+ selection using oligo(dT) magnetic beads (Invitrogen 610-02), eluted in water and used for RNA-seq library construction with ScriptSeqTM kit (Epicentre SS10906) or mRNA-seq Sample Prep kit (Illumina RS-100-0801) according to the manufacturer’s protocol. DNA concentrations were quantified on a Bioanalyzer (Agilent), diluted to 10 nM and loaded on flow cells to generate clusters. Libraries were sequenced on Illumina GAII or HiSeq2000 machines using the paired-end 50 cycle protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Base call and quality scores were generated using the standard Illumina Pipeline.
BS-seq reads were trimmed for adaptor sequence and low quality base call, then aligned to ZmB73 4a.53 genome assembly using rmap V2.03 with parameters -Q -v -m 4
Then the C/T counts from aligned BS-seq reads for each cytosine in reference genome were saved in CT count file
RNA-seq reads were aligned to ZmB73 4a.53 and calculated FPKM using Tophat v1.3.2/Cufflinks v1.1.0
smRNA-seq reads were aligned to ZmB73 4a.53 genome aeembly using rmap V2.03 with parameters -Q -v -m 2, then the mapped 21/22/24 nt smRNA-seq reads were counted in each 1M bin in whole genome
Genome_build: ZmB73 4a.53
Please note that the bed files for B73 DNA rep 1,2,3 and M017 DNA rep 1,2,3,4 Samples are on the Series record.
Supplementary_files_format_and_content: The CT count files have the first 6 columns the same as bed file, the 7th col is count of C, the 8th col is count of T, the 9th col is the 3 nt in reference genome, the 10th col is the context of cytosine
Supplementary_files_format_and_content: The FPKM tracking file format is described in http://cufflinks.cbcb.umd.edu/manual.html
Supplementary_files_format_and_content: The BED from smRNA-seq data contains the count of mapped smRNA-seq reads in each 1M bin in the whole genome
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| Submission date |
Jul 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenyuan Lu |
| Organization name |
Cold Spring Harbor Laboratory
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| Lab |
Doreen Ware
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL9141 |
| Series (1) |
| GSE39232 |
The maize methylome modulates mRNA splicing and reveals widespread paramutation guided by small RNA. |
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| Relations |
| SRA |
SRX159567 |
| BioSample |
SAMN01087451 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM958907_GERALD_04-03-2011_ghibane.s_6_sequence.genes.fpkm_tracking.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
| GSM958907_GERALD_04-03-2011_ghibane.s_7_sequence.genes.fpkm_tracking.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSM958907_GERALD_04-03-2011_ghibane.s_8_sequence.genes.fpkm_tracking.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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