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Sample GSM434586 Query DataSets for GSM434586
Status Public on Dec 31, 2009
Title isy1-null expression profile
Sample type RNA
 
Channel 1
Source name Total RNA from an isy1 null mutant
Organism Saccharomyces cerevisiae
Characteristics strain: Y3656
Growth protocol Cell cultures were grown to an early mid-log phase (OD600 0.8) in rich medium (YPD) at 30C while shaking.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from yeast cells by vortexing with glass beads in the presence of hot acid phenol and cleaned by phenol:chlorophorm extraction followed by ethanol precipitation. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 25 ug of total RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen) in the presence of 6 μg/ml Actinomycin D to prevent antisense artifacts. RNA was subsequently removed by hydrolysis and cDNA was cleaned up and concentrated on MinElute PCR purification columns (Qiagen).
Label biotin
Label protocol cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ーC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.
 
Channel 2
Source name Total RNA from wild-type yeast
Organism Saccharomyces cerevisiae
Characteristics strain: Y3656
Growth protocol Cell cultures were grown to an early mid-log phase (OD600 0.8) in rich medium (YPD) at 30C while shaking.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from yeast cells by vortexing with glass beads in the presence of hot acid phenol and cleaned by phenol:chlorophorm extraction followed by ethanol precipitation. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 25 ug of total RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen) in the presence of 6 μg/ml Actinomycin D to prevent antisense artifacts. RNA was subsequently removed by hydrolysis and cDNA was cleaned up and concentrated on MinElute PCR purification columns (Qiagen).
Label Biotin
Label protocol cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ーC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.
 
 
Hybridization protocol 6 μg of biotinylated cDNA was hybridized at 45C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned in an Affymetrix 7G scanner.
Description isy1-null expression profile
Data processing Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. Treatment and control samples were quantile normalized in pairs using only perfect match probes with a bandwidth of 20.
 
Submission date Jul 29, 2009
Last update date Jul 29, 2009
Contact name Harm van Bakel
E-mail(s) harm.vanbakel@mssm.edu
Organization name Mount Sinai School of Medicine
Department Genetics and Genomic Sciences
Lab Bakel Lab
Street address One Gustave L. Levy Place, Box 1498
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL7070
Series (1)
GSE17395 A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300

Supplementary file Size Download File type/resource
GSM434586_ISY1-null_vs_WT_forward.bar.gz 8.3 Mb (ftp)(http) BAR
GSM434586_ISY1-null_vs_WT_reverse.bar.gz 8.3 Mb (ftp)(http) BAR
GSM434586_ISY1_null.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM434586_WT.CEL.gz 29.0 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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