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| Status |
Public on Apr 22, 2010 |
| Title |
thaliana_inflorescence_rep2 |
| Sample type |
SRA |
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| Source name |
inflorescences
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/subspecies: Col-0
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| Growth protocol |
A. thaliana plants were grown at ~22C under 16hr. days for about 8 weeks prior to harvest of inflorescences and RNA extraction. A. lyrata plants were grown at ~22C under 16hr. days for about 12 weeks, then vernalized at ~6C for 6 weeks under 8 hr. days, followed by return to ~22C, 16hr. days to induce flowering
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Tri-reagent and polyA+ RNA purified. The untreated polyA+ RNA was used in conjunction with the ABI SOLiD RNAseq kit, except the fragmentation with RNAseIII was omitted. This results in adapter ligation only to the 5' ends of RNAs with a 5'-monophosphate. Further steps in library construction were per the manufacturer's suggestion, except that size selection of the final amplicons prior to emulsion PCR was very broad (~80nt to ~3kb). The library was sequenced only from the 5' adapter, resulting in 35color tags representing the 5' ends of uncapped, polyA+ messages.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Description |
5' ends of uncapped polyA mRNA.
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| Data processing |
alignment (.shrimp, SHRiMP-rmapper-cs format) files were created as follows: Raw 35color .csfasta reads were mapped to the appropriate transcriptome using rmapper-cs (from the SHRiMP package), using non-default settings -o 10000 -M 35bp,fast. The initial, "raw" shrimp results were then filtered as follows: a) for each read, only the alignments with the minimum alignment score were retained (i.e., only the best mapping position(s) of each read were kept, b) The maximum overall edit distance allowed for an aligned read was 6 (1 point for insertions, deletions, substitutions, or colorspace cross-overs), c) nucleotides 1-6 of the read had to exactly match the transcript in question., d) the alignment had to extend to at least position 29 of the read, and e) the alignment must be to the sense strand of the transcript in question.
degradome density files were generated from the filtered shrimp files by tallying the abundances of the 1st position of aligned reads (thus, the 5' ends of the underlying uncapped RNAs) at each position on each transcript. For each transcript, the data are presented in 5 tab-delimited fields. 1) the position along the transcript, 2) the number of raw reads with 5' ends at that position, 3) the repeat-normalized number of reads with 5' ends at that positon (accounts for reads which mapped to more than one transcript), 4) the number of uniquely mapped reads with 5' ends at that position, and 5) the 'degradome category' of that position. Cat 0: Category 0: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript Category 1: >1 raw read at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript Category 2: >1 raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript Category 3: >1 raw read at the position, abundance at position is equal to or less than the median for the transcript Category 4: Only 1 raw read at the position.
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| Submission date |
Feb 22, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael J Axtell |
| E-mail(s) |
mja18@psu.edu
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| Organization name |
Pennsylvania State University
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| Department |
Biology
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| Lab |
Axtell
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| Street address |
280 Mueller Lab
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL10088 |
| Series (1) |
| GSE20451 |
Arabidopsis thaliana and Arabidopsis lyrata degradomes |
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| Relations |
| SRA |
SRX018530 |
| BioSample |
SAMN00010701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM512879_AT2_degradome_density.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
| GSM512879_AT2_filtered_shrimp.txt.gz |
162.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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