|
| Status |
Public on Apr 08, 2014 |
| Title |
Mit1 [py4144-pombe1.0FR] |
| Sample type |
RNA |
| |
|
| Source name |
Mit1 deletion
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: h- mit1D::NatMX6 ade6-210 arg3-D4 his3-D1 leu1-32 ura4-D18
|
| Treatment protocol |
Not appplicable.
|
| Growth protocol |
Yeast were grown to exponential growth phase at 30°C in YES media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by hot phenol:chloroform method.
|
| Label |
Biotin
|
| Label protocol |
Seven micrograms of total RNA was converted to cDNA, fragmented and biotin-labeled according to the Affymetrix Eukaryotic Double Strand Whole Transcript protocol for yeast tiling arrays (Affymetrix P/N703064 Rev1).
|
| |
|
| Hybridization protocol |
Biotinylated cDNA was hybridized to an Affymetrix GeneChip S.pombe Tiling 1.0FR array for 16 hours at 45 C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G
|
| Data processing |
Data were analyzed using the Affymetrix Tiling Analysis Software v1.1.02 (2006). The genomic map file used was Sp20b_M_v04.bpmap, and the GRC file used was Sp20b_M_v04.grc from the 2004 genome build of S. pombe. Probe signals on the arrays were quantile normalized and scaled to an average value of 500. Comparison between Mit1-deletion and WT samples were performed using duplicate samples. A two-sided Wilcoxon signed-rank test was performed using probes summarized over a window of 101 nucleotides (software setting: bandwith = 50). BAR files of the summarized log2 signal differences and -10logP of the Wilcoxon signed-rank test are provided. Text (TXT) files of the summarized log2 signal differences and -10logP of the Wilcoxon signed-rank test are also provided.
Mit1_vs_WT_log2ratio.txt, Mit1_vs_WT_pvalue.txt, Mit1_vs_WT_2fold_up.bed, Mit1_vs_WT_2fold_down.bed, Mit1_vs_WT_p05.bed
Mit1_vs_WT_log2ratio.txt and Mit1_vs_WT_pvalue.txt are TEXT versions of the BAR files generated in the Tiling Analysis Software. Following summarization of signal differences, genomic interval analysis was also performed using the Tiling Analysis Software. The thresholds for significance were set to greater than 2-fold difference (up-regulated or down-regulated) or with p-value <0.05 by the 2-sided Wilcoson signed-rank test. The distance thresholds applied were maximum gap <100 bases and minimum run of >150 bases. The BED files contain regions across the genome that passed these thresholds. A separate BED file is provided for up-regulated regions (Mit1_vs_WT_2fold_up.bed), down-regulated regions (Mit1_vs_WT_2fold_down.bed), and significant regions (Mit1_vs_WT_p05.bed).
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| |
|
| Submission date |
May 06, 2013 |
| Last update date |
Apr 08, 2014 |
| Contact name |
Geoffrey Neale |
| E-mail(s) |
geoffrey.neale@stjude.org
|
| Organization name |
St Jude Childrens Research Hospital
|
| Department |
Hartwell Center
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE46649 |
The Mi-2 homolog, Mit1, actively positions nucleosomes within heterochromatic domains to suppress transcription |
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