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| Status |
Public on Aug 16, 2013 |
| Title |
col0_1 |
| Sample type |
SRA |
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| Source name |
unopened flower buds
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: wild-type
ecotype: Col-0
replicates: 1
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| Growth protocol |
Plants were grown on soil in 16 hours of light and 8 hours of dark
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, RNA-seq libraries were produced using the whole transcriptome sequencing kit (ABI, Foster City, CA) as per manufacturerâs instruction. RNA-seq libraries were sequenced using the AB SOLiD 3+ (ABI, Foster City, CA) as per manufacturerâs instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System |
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| Description |
total RNA from wild-type Col-0 plants
AB SOLiD System 3
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| Data processing |
Raw RNA-seq reads in color space were first converted into pseudo-base space reads using in-house Perl script. To map pseudobase-space reads, the Arabidopsis genome was also converted into pseudo-bases using MAQ program (http://maq.sourceforge.net/); it is of note that the plus and minus strands of the genome were converted into pseudo-bases independently, as their sequences in pseudo-base space are dependent on their first bases and not complementary to each other. In pseudo-base space, the RNA-seq reads were then mapped to the genome (both strands) using a modified pipeline as described previously (Zheng et al., 2010), where no adaptor-trimming process was involved and reads were required to align no less than 39 nt (40 nt in real space) from the 5' end with a maximum of 8% mismatches allowed. The clone-abundance and alignment information were loaded into local MySQL database for further queries.
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| Submission date |
Apr 11, 2011 |
| Last update date |
Aug 16, 2013 |
| Contact name |
Qi Zheng |
| E-mail(s) |
qi.zheng@nemours.org
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| Phone |
3026515778
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| Organization name |
Nemours Children's Health
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| Street address |
1701 Rockland Road
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| City |
Wilmington |
| State/province |
DE |
| ZIP/Postal code |
19803 |
| Country |
USA |
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| Platform ID |
GPL13396 |
| Series (2) |
| GSE28509 |
DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (RNA-seq) |
| GSE28524 |
DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis |
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| Relations |
| BioSample |
SAMN02052646 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM706237_col0_1_NR_TAIR9_loc.txt.gz |
106.2 Mb |
(ftp)(http) |
TXT |
| GSM706237_col0_1_mapped_NR_info.txt.gz |
50.7 Mb |
(ftp)(http) |
TXT |
| GSM706237_col0_1_mapped_NR_seq.fasta.gz |
145.7 Mb |
(ftp)(http) |
FASTA |
| Processed data provided as supplementary file |
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