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| Status |
Public on Jun 01, 2011 |
| Title |
total amplified RNA, 2-to-4 cells Ler/Col embryos, sample # LerCol_7 |
| Sample type |
SRA |
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| Source name |
embryos (dissected)
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| Organism |
Arabidopsis thaliana |
| Characteristics |
Stage: 2-to-4 cells embryo stage with suspensor (partial)
maternal strain: Landsberg erecta (Ler)
maternal genotype/variation: wildtype
paternal strain: Columbia_0 (Col0)
paternal genotype/variation: wildtype
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| Growth protocol |
Plants were grown under 16h light.
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| Extracted molecule |
total RNA |
| Extraction protocol |
1-RNA extraction: PicoPure RNA Isolation Kit (Arcturus). 2-RNA amplification: WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies, USA) producing single-stranded cDNA. 3- Second strand synthesis: poly-A tails added using Terminal Transferase (New England Biolabs, USA) in presence of dATPs (1 PCR cycle using Ex Taq Polymerase , (TaKaRa, Japan), and oligo(dT)12-18 primers (Invitrogen). 4-Library preparation: from 500 ng ds cDNA, Covaris S2 system (Covaris, Inc.), sheared into 80–130 bp fragments , DNA ends were repaired and ligated to SOLiD P1 and P2 adaptors, followed by enrichment by PCR (7 cycles) and a size selection on gel
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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 |
linear amplified
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| Data processing |
50 base reads generated by SOLiD v3 were aligned to the TAIR8.0 version of the Arabidopsis Col genome using the SOLiD™ System Analysis Pipeline Tool (Corona Lite 4.0r2.0, Applied Biosystems, USA), allowing up to 4 color-space mismatches with the additional rule “count valid adjacent errors as single errors”. For transcriptome profiles, reads were excluded if they mapped to more than one genomic position, mapped at splice junctions or were partially overlapping. Consequently, full-length reads uniquely mapping inside a transcript were taken.
Processed data file contains transcript coverage, read count (full-length), transcript type
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| Submission date |
Sep 17, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc William Schmid |
| E-mail(s) |
contact@mwschmid.ch
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| Organization name |
MWSchmid GmbH
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| Street address |
Hauptstrasse 34
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| City |
Glarus |
| ZIP/Postal code |
8750 |
| Country |
Switzerland |
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| Platform ID |
GPL10088 |
| Series (1) |
| GSE24198 |
Deep-sequencing of total RNA from manually dissected wild-type and kyp-2m/KYPp Arabidopsis embryos |
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| Relations |
| SRA |
SRX037074 |
| BioSample |
SAMN00189366 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM595272_2_4cells_WT_unique_read_count.txt.gz |
337.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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