rbbt-marq 1.0.0

data/install_scripts/GEO/series/GSE1975.yaml

@@ -0,0 +1,65 @@
+--- 
+:arrays: 
+  GSM35315: 
+    condition: BY diploid
+  GSM35304: 
+    condition: BYxRM diploid
+  GSM35316: 
+    condition: BY diploid
+  GSM35305: 
+    condition: BYxRM diploid
+  GSM35294: 
+    condition: BY haploid
+  GSM35317: 
+    condition: RM diploid
+  GSM35306: 
+    condition: BY-RM mixture
+  GSM35295: 
+    condition: BY haploid
+  GSM35318: 
+    condition: RM diploid
+  GSM35307: 
+    condition: BY-RM mixture
+  GSM35296: 
+    condition: BY haploid
+  GSM35319: 
+    condition: RM diploid
+  GSM35308: 
+    condition: BY-RM mixture
+  GSM35297: 
+    condition: RM haploid
+  GSM35320: 
+    condition: Segregant diploid hybrid
+  GSM35309: 
+    condition: BY-RM mixture
+  GSM35298: 
+    condition: RM haploid
+  GSM35321: 
+    condition: Segregant diploid hybrid
+  GSM35310: 
+    condition: BY-RM mixture
+  GSM35299: 
+    condition: RM haploid
+  GSM35311: 
+    condition: BY-RM mixture
+  GSM35300: 
+    condition: BYxRM diploid
+  GSM35312: 
+    condition: Segregant
+  GSM35301: 
+    condition: BYxRM diploid
+  GSM35313: 
+    condition: Segregant
+  GSM35302: 
+    condition: BYxRM diploid
+  GSM35314: 
+    condition: BY diploid
+  GSM35303: 
+    condition: BYxRM diploid
+:title: Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression
+:description: |-
+  By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains.  We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM.  A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments.  The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003).  We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium.  We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays.  In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed.
+  Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821).
+  The results are part of Ronald et al. (in press) describing a novel use of oligonucleotide expression arrays to perform genotyping.   This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.
+  Keywords: other
+:platform: GPL90

data/install_scripts/GEO/series/GSE20.yaml

@@ -0,0 +1,24 @@
+--- 
+:title: Manipulation in phospate levels
+:description: |-
+  The arrays were used to study the effects of modifying phosphate levels in yeast, either through mutation, or chemical manipulation.
+  This study is described in more detail in Ogawa N et al.(2000) Mol Biol Cell 11:4309-21
+  Keywords: other
+:arrays: 
+  GSM885: 
+    condition: DBY7286 LowPi vs High-Pi
+  GSM886: 
+    condition: PHO81 vs wt
+  GSM866: 
+    condition: NBW7.lowPi vs HighPi
+  GSM867: 
+    condition: PHO81 vs wt
+  GSM869: 
+    condition: PHO85 vs wt
+  GSM870: 
+    condition: PHO80 vs wt
+  GSM871: 
+    condition: PHO4 vs wt
+  GSM894: 
+    condition: NBW7.lowPi vs HighPi
+:platform: GPL66

data/install_scripts/GEO/series/GSE2107.yaml

@@ -0,0 +1,14 @@
+--- 
+:arrays: 
+  GSM37889: 
+    mutant: hog1  RC
+  GSM37890: 
+    mutant: hog1  RC
+  GSM37891: 
+    mutant: hog1  RC
+  GSM37892: 
+    mutant: hog1  RC
+:title: Hog1 mutant 4 hours exposure to congo red (cell wall chip)
+:description: "S. cerevisiae hog1 mutant strain was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 \xC2\xB0C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 \xC2\xB0C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 \xC2\xB5g/ml. Cells were collected at 4hours of growth, frozen at -80 \xC2\xB0C and processed for RNA extraction.\n\
+  Keywords: repeat sample"
+:platform: GPL1433

data/install_scripts/GEO/series/GSE2159.yaml

@@ -0,0 +1,31 @@
+--- 
+:arrays: 
+  GSM38947: 
+    condition: SAN1 YC
+  GSM38938: 
+    condition: SAN1 YEPD
+  GSM38939: 
+    condition: SAN1 YEPD
+  GSM38940: 
+    condition: SAN1 YEPD
+  GSM38941: 
+    condition: SAN1 YEPD
+  GSM38942: 
+    condition: SAN1 YC
+  GSM38943: 
+    condition: SAN1 YC
+  GSM38932: 
+    condition: SAN1 YEPD
+  GSM38944: 
+    condition: SAN1 YC
+  GSM38933: 
+    condition: SAN1 YEPD
+  GSM38945: 
+    condition: SAN1 YC
+  GSM38946: 
+    condition: SAN1 YC
+:title: SAN1/san1 YEPD/YC transcript arrays
+:description: |-
+  comparison of SAN1/san1 cells in YEPD and YC
+  Keywords: other
+:platform: GPL1797

data/install_scripts/GEO/series/GSE2246.yaml

@@ -0,0 +1,157 @@
+--- 
+:arrays: 
+  GSM41267: 
+    condition: WT_Gal_N2_0.25
+  GSM41288: 
+    condition: WT_Gal_N2_5.0
+  GSM41303: 
+    condition: WT_Gal_Air_6.1
+  GSM41289: 
+    condition: WT_Gal_N2_5.0
+  GSM41304: 
+    condition: WT_Gal_Air_6.1
+  GSM41268: 
+    condition: WT_Gal_N2_0.25
+  GSM41290: 
+    condition: WT_Gal_N2_5.0
+  GSM41305: 
+    condition: WT_Gal_Air_6.1
+  GSM41270: 
+    condition: WT_Gal_N2_0.38
+  GSM41269: 
+    condition: WT_Gal_N2_0.25
+  GSM41291: 
+    condition: WT_Gal_N2_6.0
+  GSM41306: 
+    condition: WT_Gal_Air_6.13
+  GSM41271: 
+    condition: WT_Gal_N2_0.38
+  GSM41292: 
+    condition: WT_Gal_N2_6.0
+  GSM41307: 
+    condition: WT_Gal_Air_6.13
+  GSM41272: 
+    condition: WT_Gal_N2_0.38
+  GSM41293: 
+    condition: WT_Gal_N2_6.0
+  GSM41308: 
+    condition: WT_Gal_Air_6.13
+  GSM41252: 
+    condition: WT_Gal_N2_0
+  GSM41273: 
+    condition: WT_Gal_N2_0.5
+  GSM41294: 
+    condition: WT_Gal_Air_6.0
+  GSM41310: 
+    condition: WT_Gal_Air_6.2
+  GSM41309: 
+    condition: WT_Gal_Air_6.2
+  GSM41253: 
+    condition: WT_Gal_N2_0
+  GSM41274: 
+    condition: WT_Gal_N2_0.5
+  GSM41295: 
+    condition: WT_Gal_Air_6.0
+  GSM41311: 
+    condition: WT_Gal_Air_6.2
+  GSM41254: 
+    condition: WT_Gal_N2_0
+  GSM41275: 
+    condition: WT_Gal_N2_0.5
+  GSM41296: 
+    condition: WT_Gal_Air_6.0
+  GSM41255: 
+    condition: WT_Gal_N2_0.04
+  GSM41276: 
+    condition: WT_Gal_N2_1.0
+  GSM41297: 
+    condition: WT_Gal_Air_6.03
+  GSM41312: 
+    condition: WT_Gal_Air_6.3
+  GSM41256: 
+    condition: WT_Gal_N2_0.04
+  GSM41277: 
+    condition: WT_Gal_N2_1.0
+  GSM41298: 
+    condition: WT_Gal_Air_6.03
+  GSM41313: 
+    condition: WT_Gal_Air_6.3
+  GSM41278: 
+    condition: WT_Gal_N2_1.0
+  GSM41299: 
+    condition: WT_Gal_Air_6.03
+  GSM41314: 
+    condition: WT_Gal_Air_6.3
+  GSM41257: 
+    condition: WT_Gal_N2_0.04
+  GSM41315: 
+    condition: WT_Gal_Air_6.4
+  GSM41258: 
+    condition: WT_Gal_N2_0.08
+  GSM41280: 
+    condition: WT_Gal_N2_2.0
+  GSM41279: 
+    condition: WT_Gal_N2_2.0
+  GSM41316: 
+    condition: WT_Gal_Air_6.4
+  GSM41260: 
+    condition: WT_Gal_N2_0.08
+  GSM41259: 
+    condition: WT_Gal_N2_0.08
+  GSM41281: 
+    condition: WT_Gal_N2_2.0
+  GSM41317: 
+    condition: WT_Gal_Air_6.4
+  GSM41261: 
+    condition: WT_Gal_N2_0.13
+  GSM41282: 
+    condition: WT_Gal_N2_3.0
+  GSM41340: 
+    condition: WT_Gal_Air_7.6
+  GSM41339: 
+    condition: WT_Gal_Air_7.6
+  GSM41318: 
+    condition: WT_Gal_Air_6.6
+  GSM41262: 
+    condition: WT_Gal_N2_0.13
+  GSM41283: 
+    condition: WT_Gal_N2_3.0
+  GSM41341: 
+    condition: WT_Gal_Air_7.6
+  GSM41320: 
+    condition: WT_Gal_Air_6.6
+  GSM41319: 
+    condition: WT_Gal_Air_6.6
+  GSM41263: 
+    condition: WT_Gal_N2_0.13
+  GSM41284: 
+    condition: WT_Gal_N2_3.0
+  GSM41321: 
+    condition: WT_Gal_Air_6.8
+  GSM41300: 
+    condition: WT_Gal_Air_6.06_Generations
+  GSM41264: 
+    condition: WT_Gal_N2_0.19
+  GSM41285: 
+    condition: WT_Gal_N2_4.0
+  GSM41322: 
+    condition: WT_Gal_Air_6.8
+  GSM41265: 
+    condition: WT_Gal_N2_0.19
+  GSM41286: 
+    condition: WT_Gal_N2_4.0
+  GSM41301: 
+    condition: WT_Gal_Air_6.06_Generations
+  GSM41323: 
+    condition: WT_Gal_Air_6.8
+  GSM41266: 
+    condition: WT_Gal_N2_0.19
+  GSM41287: 
+    condition: WT_Gal_N2_4.0
+  GSM41302: 
+    condition: WT_Gal_Air_6.06_Generations
+:title: JM43_Galactose_Air_N2_Air_Shift
+:description: |-
+  The yeast cells were grown aerobically on galactose medium. At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, 3, 4, 5 and 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control), 6.03, 6.06, 6.1, 6.13, 6.2, 6.3, 6.4, 6.6, 6.8, and 7.6 generations.
+  Keywords: time-course
+:platform: GPL1535

data/install_scripts/GEO/series/GSE2263.yaml

@@ -0,0 +1,57 @@
+--- 
+:arrays: 
+  GSM41752: 
+    condition: SP 130seg
+  GSM41741: 
+    condition: SP 20seg
+  GSM41753: 
+    condition: SP 140seg
+  GSM41742: 
+    condition: SP 30seg
+  GSM41754: 
+    condition: SP 150seg
+  GSM41743: 
+    condition: SP 40seg
+  GSM41755: 
+    condition: SP 160seg
+  GSM41744: 
+    condition: SP 50seg
+  GSM42238: 
+    condition: SP 0seg
+  GSM41756: 
+    condition: SP 170seg
+  GSM41745: 
+    condition: SP 60seg
+  GSM42239: 
+    condition: SP 0seg
+  GSM41757: 
+    condition: SP 180seg
+  GSM41746: 
+    condition: SP 70seg
+  GSM42240: 
+    condition: SP 0seg
+  GSM41758: 
+    condition: SP 300seg
+  GSM41747: 
+    condition: SP 80seg
+  GSM42241: 
+    condition: SP 0seg
+  GSM41748: 
+    condition: SP 90seg
+  GSM42242: 
+    condition: SP 0seg
+  GSM41749: 
+    condition: SP 100seg
+  GSM41750: 
+    condition: SP 110seg
+  GSM41739: 
+    condition: SP 0seg
+  GSM41751: 
+    condition: SP 120seg
+  GSM41740: 
+    condition: SP 10seg
+:title: 10s oxidative stress
+:description: |-
+  This series represents the rapid response to oxidative stress
+  Keywords: time-course
+:platform: GPL1859

data/install_scripts/GEO/series/GSE2267.yaml

@@ -0,0 +1,155 @@
+--- 
+:arrays: 
+  GSM41817: 
+    condition: WT_Glu_N2_4
+  GSM41840: 
+    condition: WT_Glu_Air_6.13
+  GSM41820: 
+    condition: WT_Glu_N2_5
+  GSM41818: 
+    condition: WT_Glu_N2_4
+  GSM41841: 
+    condition: WT_Glu_Air_6.20
+  GSM41839: 
+    condition: WT_Glu_Air_6.13
+  GSM41800: 
+    condition: WT_Glu_N2_0.25
+  GSM41821: 
+    condition: WT_Glu_N2_5
+  GSM41819: 
+    condition: WT_Glu_N2_4
+  GSM41842: 
+    condition: WT_Glu_Air_6.20
+  GSM41785: 
+    condition: WT_Glu_N2_0
+  GSM41801: 
+    condition: WT_Glu_N2_0.25
+  GSM41822: 
+    condition: WT_Glu_N2_5
+  GSM41843: 
+    condition: WT_Glu_Air_6.20
+  GSM41786: 
+    condition: WT_Glu_N2_0
+  GSM41802: 
+    condition: WT_Glu_N2_0.25
+  GSM41823: 
+    condition: WT_Glu_N2_6
+  GSM41844: 
+    condition: WT_Glu_Air_6.30
+  GSM41787: 
+    condition: WT_Glu_N2_0
+  GSM41803: 
+    condition: WT_Glu_N2_0.38
+  GSM41824: 
+    condition: WT_Glu_N2_6
+  GSM41845: 
+    condition: WT_Glu_Air_6.30
+  GSM41788: 
+    condition: WT_Glu_N2_0.04
+  GSM41804: 
+    condition: WT_Glu_N2_0.38
+  GSM41825: 
+    condition: WT_Glu_N2_6
+  GSM41846: 
+    condition: WT_Glu_Air_6.30
+  GSM41790: 
+    condition: WT_Glu_N2_0.04
+  GSM41789: 
+    condition: WT_Glu_N2_0.04
+  GSM41805: 
+    condition: WT_Glu_N2_0.5
+  GSM41826: 
+    condition: WT_Glu_Air_6.0
+  GSM41847: 
+    condition: WT_Glu_Air_6.40
+  GSM41791: 
+    condition: WT_Glu_N2_0.08
+  GSM41827: 
+    condition: WT_Glu_Air_6.0
+  GSM41848: 
+    condition: WT_Glu_Air_6.40
+  GSM41792: 
+    condition: WT_Glu_N2_0.08
+  GSM41850: 
+    condition: WT_Glu_Air_6.60
+  GSM41849: 
+    condition: WT_Glu_Air_6.40
+  GSM41793: 
+    condition: WT_Glu_N2_0.08
+  GSM41806: 
+    condition: WT_Glu_N2_0.5
+  GSM41851: 
+    condition: WT_Glu_Air_6.60
+  GSM41794: 
+    condition: WT_Glu_N2_0.13
+  GSM41807: 
+    condition: WT_Glu_N2_0.5
+  GSM41830: 
+    condition: WT_Glu_Air_6.03
+  GSM41828: 
+    condition: WT_Glu_Air_6.0
+  GSM41852: 
+    condition: WT_Glu_Air_6.60
+  GSM41795: 
+    condition: WT_Glu_N2_0.13
+  GSM41810: 
+    condition: WT_Glu_N2_1
+  GSM41808: 
+    condition: WT_Glu_N2_1
+  GSM41831: 
+    condition: WT_Glu_Air_6.03
+  GSM41829: 
+    condition: WT_Glu_Air_6.03
+  GSM41853: 
+    condition: WT_Glu_Air_6.80
+  GSM41811: 
+    condition: WT_Glu_N2_2
+  GSM41809: 
+    condition: WT_Glu_N2_1
+  GSM41832: 
+    condition: WT_Glu_Air_6.06
+  GSM41796: 
+    condition: WT_Glu_N2_0.13
+  GSM41854: 
+    condition: WT_Glu_Air_6.80
+  GSM41812: 
+    condition: WT_Glu_N2_2
+  GSM41833: 
+    condition: WT_Glu_Air_6.06
+  GSM41797: 
+    condition: WT_Glu_N2_0.19
+  GSM41855: 
+    condition: WT_Glu_Air_6.80
+  GSM41813: 
+    condition: WT_Glu_N2_2
+  GSM41834: 
+    condition: WT_Glu_Air_6.06
+  GSM41798: 
+    condition: WT_Glu_N2_0.19
+  GSM41856: 
+    condition: WT_Glu_Air_7.60
+  GSM41814: 
+    condition: WT_Glu_N2_3
+  GSM41835: 
+    condition: WT_Glu_Air_6.10
+  GSM41799: 
+    condition: WT_Glu_N2_0.19
+  GSM41857: 
+    condition: WT_Glu_Air_7.60
+  GSM41815: 
+    condition: WT_Glu_N2_3
+  GSM41836: 
+    condition: WT_Glu_Air_6.10
+  GSM41858: 
+    condition: WT_Glu_Air_7.60
+  GSM41816: 
+    condition: WT_Glu_N2_3
+  GSM41837: 
+    condition: WT_Glu_Air_6.10
+  GSM41838: 
+    condition: WT_Glu_Air_6.13
+:title: JM43_Glucose_Air_N2_Air_Shift
+:description: |-
+  The yeast cells were grown aerobically on glucose medium. At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, 3, 4, 5 and 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control), 6.03, 6.06, 6.1, 6.13, 6.2, 6.3, 6.4, 6.6, 6.8, and 7.6 generations.
+  Keywords: time-course
+:platform: GPL1535