title: colon cancer (GRUBER_CRC_168)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_284)

status: Public on Apr 07 2011

type: RNA

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

country: USA

institute: UT MD Anderson Cancer Center

description: amplified using Nugen WT-Ovation™

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
Expression levels were measured in two batches using Affymetrix U133A and U133A Plus 2.0 arrays (Santa Clara, CA). Expression analyses were carried out in the R-software using the package Bioconductor. Expression data in both batches were first subjected for quality assessment by creating the density plot of the log-intensity and RNA degradation plot corresponding to each sample. After preprocessing and quality assessment the two batches were aligned. Probes of the U133A array present in the U133A Plus 2.0 were selected and quantile normalized to mimic the distribution of the U133A array. Five samples had been hybridize in both arrays and served to verify that the correlation of the expression was adequate for the majority of the probes. A total of 331 samples and 419,473 probe sets were subjected to further analysis. Two class comparison of MSI versus MSS tumors were carried out by two-sample t-test to yield a list of differentially expressed probe sets, discriminating between the two biologic states of interest under consideration. We had information on MSI status available from 300 patients and the data set was subsequently reduced to this 300 patients. Then we examined only the expression levels of those genes integrated in the KEGG pathway hsa03440 corresponding to the homologous recombination (a total of 31 genes and their correponding 49 probe sets) using data from a total of 300 CRCs. The issue of multiple testing was addressed by using adjusted P-values after controlling for the overall false discovery rate by Benjamini and Hochberg method (BH-adjusted P-values). We also evaluated the local false discovery rate associated with our probe selection procedure by using the locfdr package in R.
For all 331 samples, MAS 5.0-calculated signal intensities were normalized using the quantile normalization procedure implemented in robust multiarray analysis and the normalized data were log 2 transformed.  Sample specific median centering and scaling by the standard deviation were additionally applied. Filtering was done to exclude probe sets that were not expressed or probe sets that exhibited low variability across samples. Expression values were required to be above the lower quartile of all expression measurements in at least 25% of samples, and the interquartile range across the samples on  log 2 scale was required to be at least 0.5.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colon cancer tissue

label_protocol: The RNA samples were labeled with IVT labelling kit according to manufacturer's instructions.

extract_protocol: RNA isolation and Microarray procedures. Primary tumors were obtained at the time of surgical resection, then they were snap frozen in liquid nitrogen at -80C, embedded in optimum cutting temperature freezing media (Miles Scientific, Naperville, IL), cryotome sectioned, stained with H&E, and evaluated by a surgical pathologist. Areas with >70% tumor cellularity were identified for RNA isolation. Selected sections of tumor samples were homogenized in Trizol (Invitrogen, Carlsbad, CA), and total cellular RNA was purified according the instructions of the manufacturer, with additional purification using RNeasy spin columns (Qiagen, Valencia, CA). RNA quality was assessed by 1% agarose gel electrophoresis, and samples were included only if the 18S and 28S bands were discrete and approximately equal.

tag: age

tag: gender

value: Female

tag: microsatellite instability (msi) status

value: Stable [MSS]


title: colon cancer (GRUBER_CRC_265)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_268)

description: amplified using Nugen WT-Ovation™

value: Male


title: colon cancer (GRUBER_CRC_141)

description: amplified using Nugen WT-Ovation™

value: Low [MSI-L]


title: colon cancer (GRUBER_CRC_262)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_144)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_259)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_261)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_253)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_254)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_244)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_145)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_257)

description: amplified using Nugen WT-Ovation™

value: Unknown


title: colon cancer (GRUBER_CRC_156)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_243)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_167)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_148)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_130)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_140)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_143)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_136)

description: amplified using Nugen WT-Ovation™

value: High [MSI-H]


title: colon cancer (GRUBER_CRC_127)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_241)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_139)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_242)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_129)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_126)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_133)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_124)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_234)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_231)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_235)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_228)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_125)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_119)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_201)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_111)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_112)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_194)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_120)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_221)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_114)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_113)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_118)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_117)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_229)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_110)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_208)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_198)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_123)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_195)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_115)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_109)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_180)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_108)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_107)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_185)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_191)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_179)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_166)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_170)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_106)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_173)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_160)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_174)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_190)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_169)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_162)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_164)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_165)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_161)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_97)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_104)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_227)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_100)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_163)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_96)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_158)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_102)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_92)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_91)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_155)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_153)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_154)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_159)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_146)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_137)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_87)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_147)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_246)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_150)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_138)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_157)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_89)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_134)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_131)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_263)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_83)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_135)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_152)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_128)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_82)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_132)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_81)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_80)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_149)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_85)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_88)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_142)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_122)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_116)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_79)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_121)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_105)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_75)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_99)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_103)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_73)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_101)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_98)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_95)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_74)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_151)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_70)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_93)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_67)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_86)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_77)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_94)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_64)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_63)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_71)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_65)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_78)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_69)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_72)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_68)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_61)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_59)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_58)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_84)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_66)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_62)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_53)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_76)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_60)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_90)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_57)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_56)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_52)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_55)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_54)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_48)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_51)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_49)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_44)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_45)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_42)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_40)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_47)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_50)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_38)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_39)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_37)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_33)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_29)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_36)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_43)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_32)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_26)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_35)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_34)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_27)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_20)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_41)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_31)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_23)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_28)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_30)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_46)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_16)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_18)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_25)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_21)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_15)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_22)

description: amplified using Nugen WT-Ovation™


title: DatasetN1_3hr

status: Public on Mar 07 2011

type: SRA

city: New York

first: Scott

last: Keeney

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing: For mapping of the Illumina reads (1–9 million reads per dataset) to both the SGD and SK1 genomes, the rmapper-ls program from SHRiMP was used with more stringent “gapless” parameters:  -s 111101111 -o 10001 -n 1 -m 1 -i -6 -g -5000 -e -5000 -h 24.   The match score was 1, mismatches were -6 and gap openings and extensions were 5,000 which effectively make them infinite on this scale. The Smith-Waterman cutoff was 24; so a read would need at least 24 matches (with zero mismatches) to pass. We recorded 10,001 optimal hits. This number was chosen to insure that all multiple mappings were enumerated and we checked the mapping results to verify that the most degenerate multiple mapping read was below this threshold.  The mapping data were then post-processed following previously described methods (Kaplan et al., Nature 2009). We first looked across all datasets to identify regions containing reads that mapped to other locations as well. These regions, extended by 150 bp on each side are denoted as MASK (a 0 in the MASK field means not masked). We next computed a histogram of distances by taking for each read the distances to all other reads that were downstream and on the opposite strand. The first mode of this distribution of distances was defined as the mononucleosome DNA length (Lnuc). Each read was extended to length Lnuc, then an occupancy table was computed by summing at each base pair the number of extended reads that overlapped that base pair.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Synchronized meiotic culture

growth_protocol: Synchronized meiotic diploid cultures of S. cerevisiae of strain background SK1 (NKY611: MATα/MATa, ho::LYS2/”, lys2/“, ura3/”, leu2::hisG/”) were set up as follows: A saturated YPD culture was used to inoculate 200 ml liquid YPA medium (1% yeast extract, 2% Bacto peptone, 1% potassium acetate) to OD600 = 0.2 and grown in 2-liter unbaffled Erlenmeyer flasks at 250 rpm at 30°C for 14 hrs. Cells were harvested, washed once in sterile water, resuspended in sporulation medium to OD600 ~1.9 (in 0.3% potassium acetate for Dataset N1) or to OD600 ~6.5 (in 2% potassium acetate at for Dataset N2) and incubated in 2-liter unbaffled Erlenmeyer flasks at 250 rpm at 30°C.

extract_protocol: Samples of 50 ml were harvested at 0, 1, 2, 3 or 4 hr after transfer to sporulation conditions, and immediately crosslinked by addition of formaldehyde to 1% and incubation for 15 min at room temperature. Glycine was then added to a final concentration of 125 mM, cells were pelleted and resuspended in 18.5 ml Buffer Z (0.5 M sorbitol, 50 mM Tris-HCl, pH 7.4, 10 mM β-mercaptoethanol) containing 5 mg zymolyase 100T (US Biological) and incubated at 30°C for 30 min. Spheroplasted cells were pelleted, supernatants removed, and treated with a dilution series of micrococcal nuclease (MNase) from 5 to 80 Units (Worthington Biochemical, Corp.) in NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 0.5 mM spermidine, 1 mM β-mercaptoethanol, 0.075% NP-40) and incubated at 37°C for 20 min. Digestions were stopped by the addition of 5% SDS and 50 mM EDTA followed by the addition of 100 μg proteinase K (Fisher Scientific) and incubated at 65°C for 18 hr. DNA was then extracted with 1.5 M ammonium acetate, pH 5.5 and 500 μl of phenol-chloroform-isoamyl alcohol (25:24:1), washed with 100% isopropanol and then 70% ethanol, and treated with RNase. Mononucleosome-sized DNA generated by treatment with 20 (Dataset N1) or 40 (Dataset N2) units MNase was then purified by size fractionation on agarose gels and prepared for sequencing using the Genomic DNA Sample Prep Kit (Illumina, Inc.) and sequenced using the Illumina Genome Analyzer Systems at the MIT Biopolymers Facility (Dataset N1) or at the Genomics Resource Center at The Rockefeller University (Dataset N2).

tag: time in meiosis (hr)

tag: strain


title: colon cancer (GRUBER_CRC_9)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_10)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_17)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_24)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_12)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_14)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_11)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_13)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_19)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_7)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_6)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_8)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_5)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_4)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_3)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_2)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_1)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_236)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_270)

description: amplified using Nugen WT-Ovation™


title: colon cancer (GRUBER_CRC_196)

description: amplified using Nugen WT-Ovation™