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Sample GSM617302 Query DataSets for GSM617302
Status Public on Feb 05, 2011
Title [E-MTAB-75] Cell culture 1
Sample type SRA
 
Source name Cell culture 1
Organism Saccharomyces cerevisiae
Characteristics material type: whole_organism
strainorline: BY4742
genotype: MAT_ ura3_0 leu2_0 his3_1 lys2_0
Growth protocol grow | Cells were grown to mid-exponential phase in YPD for a wild type strain (condition 1) and in YPD supplemented with doxycycline (10µg/ml) for 16h for the mutant strain (condition 2).
Extracted molecule total RNA
Extraction protocol nucleic_acid_extraction | Poly(A)+-enriched RNA from the wild type strain was purified using Dynabeads Oligo (dT)25 (Dynal, Invitrogen). RNA from the CUT fraction was obtained by Cbp20 TAP purification.
TETRATAGS CONSTRUCTION | 3'Long-SAGE tags were obtained by an improved 3' Long-SAGE technique adapted from Wei et al, PNAS, 2004. The 18nt-long 3' tags resulted from MmeI cleavage were ligated into tetratags. These tetratags correspond to 2 ditags and 3 delimiting linkers. First linkers bears a barcode sequence to distinguish the two conditions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS
 
Data processing Sequences in FASTA format were analyzed and header from condition 1 (CGCCATCAGCGTCGAC) and condition 2 (CGCCATCAGTCATATG) were identified. Then tag sequences were found by identifiing the linkers positions. Tags were the 18 bp sequences downstream of each linker. The found tags were aligned in genome using BLAST.
 
Submission date Nov 03, 2010
Last update date Oct 19, 2011
Organization European Bioinformatics Institute
E-mail(s) miamexpress@ebi.ac.uk
Lab ArrayExpress
Street address Wellcome Trust Genome Campus
City Hinxton
State/province Cambridgeshire
ZIP/Postal code CB10 1SD
Country United Kingdom
 
Platform ID GPL11160
Series (1)
GSE25132 [E-MTAB-75] Cryptic unstable transcripts in yeast

Supplementary data files not provided
Processed data are available on Series record
Raw data are available on Series record

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