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| Status |
Public on Mar 19, 2013 |
| Title |
smRNA-seq_B73_shoot |
| Sample type |
SRA |
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| Source name |
smRNA-seq_B73_shoot
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| Organism |
Zea mays |
| Characteristics |
line: B73
tissue: shoot
developmental stage: 14 day old seedling
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| Growth protocol |
Maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrids (B73 x Mo17 and Mo17 x B73) were used in this study. Seeds were grown in soil under controlled environmental conditions (15 hours light at 25oC, and 9 hours dark at 20oC) in a growth chamber. After 14 days, seedling shoots and roots were harvested, respectively, frozen in liquid nitrogen and stored at -80oC for DNA and total RNA isolations, or processed directly for ChIP assays after harvesting.
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-seq, smRNA-seq, McrBC-seq and ChIP-seq libraries were all prepared for sequencing using standard Illumina protocols. Total RNAs were isolated using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (New England Biolabs) to remove any contaminating genomic DNA. mRNA extraction was performed using Dynabeads oligo(dT) (Invitrogen Dynal). Double-stranded cDNAs were synthesized using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries. Genomic DNAs were isolated using a DNeasy plant maxi kit (Qiagen). Isolated gDNAs were then digested with McrBC (New England Biolabs) followed by gel purification to enrich methylated genomic DNAs. The McrBC-seq libraries were generated following the standard Illumina protocol. The ChIP-seq libraries were generated by immunoprecipitating chromatin with antibodies against H3K4me3 (Abcam), H3K9ac (Upstate), or H3K36me3 (Abcam), as described previously (Gendrel et al., 2005). The eluted ChIP DNAs from the three ChIP reactions were pooled to generate ChIP-seq libraries for Illumina sequencing following the manufacturer’s protocol. sRNAs were gel-purified from total RNAs and were subsequently ligated with 3′ and 5′ adapters, followed by reverse transcription using 3′ RT primer. The cDNAs were then amplified by PCRs using primers specific to sRNAs (Mi et al., 2008). After gel purification, the sRNA-seq libraries were subjected to Illumina sequencing following the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
small RNA gel isolated
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| Data processing |
Raw sequencing reads from all libraries were mapped to the reference genome of the maize inbred line B73 (version 2; ZmB73_RefGen_v2) (http://ftp.maizesequence.org/current/assembly/) (Schnable et al., 2009) using Bowtie software (Langmead et al., 2009). Sequencing reads from mRNA-seq were also mapped to Mo17 whole-genome shotgun sequences (ftp://ftp.jgi-psf.org/pub/JGI_data/Zea_mays_Mo17/) using the same software. For the data of mRNAs, histone modifications and DNA methylation, up to two mismatches per read were allowed during the alignment procedure. For small RNA data, the 3’ adapter sequences were removed by a custom Perl script before alignment, and adapter-trimmed small RNA reads which were perfectly matched to the reference genome were retained. Small RNA sequencing reads matched to tRNAs, rRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) were also excluded from further analysis. For all sequencing data, the reads mapped equally well to multiple locations in the genome without mismatch or with identical mismatches were assigned to one position at random.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples, read counts for ChIP and McrBC seq peaks, and read counts for small RNA seq clusters.
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| Submission date |
Dec 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
1706380435@pku.edu.cn
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| Organization name |
Peiking University
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| Street address |
5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL9141 |
| Series (1) |
| GSE43142 |
Conservation and Divergence of Transcriptomic and Epigenomic Variations in Maize Hybrids |
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| Relations |
| SRA |
SRX212637 |
| BioSample |
SAMN01860773 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1057326_BS.sm.peaks.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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