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Sample GSM838494 Query DataSets for GSM838494
Status Public on Nov 23, 2011
Title dRNA-seq of Green barley plastids without TEX treatment
Sample type SRA
 
Source name plastids of primary leaves from 11-day-old green albostrians seedlings
Organism Hordeum vulgare
Characteristics strain: cv. "Haisa"; albostrians mutant
tissue: primary leaves of green seedlings
development stage: Mixed stage
treatment: no TEX
Growth protocol The barley mutant line albostrians was grown for 11 days in soil at 23 °C in a growth chamber with a photoperiod of 16h (light intensity: 150 mE s-1 m-2). The first leaves from completely green and white seedlings were used for plastid isolation.
Extracted molecule total RNA
Extraction protocol Total RNA from green and white plastids was cleaned from genomic DNA contamination by gDNA Wipeout buffer (QIAGEN). For depletion of processed transcripts, 7 ug of RNA from each sample was treated with TerminatorTM 5’-phosphate-dependent exonuclease (TEX; Epicentre #TER51020) or in buffer alone for 60 min at 30 °C. 1 unit TEX was used per 1 ug total chloroplast RNA. Following organic extraction (25:24:1 v/v phenol/chloroform/isoamyalcohol), RNA was recovered by overnight precipitation with 2.5 volumes of ethanol/0.1M sodium acetate (pH 6.5). RNA was further treated with 1 unit TAP (tobacco acid pyrophosphatase; Epicentre, #T19100) for 1 hour at 37 °C to generate 5’-mono-phosphates for linker ligation, and again purified by organic extraction and precipitation as described above. After addition of specific 5'linkers (with unique tags for each library) and polyA-tailing, the RNA was converted into a cDNA library. The cDNA libraries were sequenced on a Roche FLX sequencer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS FLX
 
Data processing For the mapping of the sequence reads, 5-linker and poly-A-tails clipped reads larger or equal to 18 nt were aligned to the barley chloroplast genome (NC_008590) using WU Blast 2.0 (http://blast.wustl.edu/) with the following parameters: -B=1 -V=1 -m=1 -n=-3 -Q=3 -R=3 -gspmax=1 -hspmax=1 -mformat=2 -e=0.0001. For each library, graphs representing the number of mapped reads per nucleotide were calculated as previously described (Sittka et al.,2008).
 
Submission date Nov 22, 2011
Last update date May 15, 2019
Contact name Konrad U. Förstner
E-mail(s) foerstner@zbmed.de
Organization name ZB MED - Information Centre for Life Sciences
Department Information Services
Lab Förstner Lab
Street address Gleueler Str. 60
City Cologne
State/province North Rhine-Westphalia
ZIP/Postal code 50931
Country Germany
 
Platform ID GPL14919
Series (1)
GSE33773 The primary transcriptome of barley (Hordeum vulgare L.) chloroplasts
Relations
SRA SRX109244
BioSample SAMN00760751

Supplementary file Size Download File type/resource
GSM838494_Green-minus_TEX-_plus_strand.bedgraph.gz 93.8 Kb (ftp)(http) BEDGRAPH
GSM838494_Green-minus_TEX-minus_strand.bedgraph.gz 68.3 Kb (ftp)(http) BEDGRAPH
GSM838494_Green-minus_TEX.fasta.gz 1.4 Mb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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