title: Oneut-2 knockout duodenum, day 15, biological replicate 2


title: Primary_Colorectal_Cancer_Patient_No.8

status: Public on Jul 07 2010

type: genomic

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

description:
HD522-Tu
US22502683_156723_S01_A01.gpr

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 h at 37°C. Slides were washed with 2x SSC/0.05% Tween-20 at 37°C for one cycle, 2x SSC/0.05% Tween-20 at 44°C for two cycles, 50% formamide/2x SSC/0.1% Tween-20 at 44°C for 3 cycles, 2x SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1x PBS/0.05% Tween-20 at 25°C for two cycles. Slides were dried by centrifugation

scan_protocol: Arrays were scanned with an Agilent DNA microarray scanner (Agilent Technologies, Palo Alto, USA), Images were quantified using GenePix Pro 6.0 software (Axon Instruments, Burlingame, USA)

data_processing: Data were filtered consistently according to spot signal/local background ratio (>3.0), mean/median spot intensity (<0.3) and spot replicate standard deviation (<0.25), and normalized globally by print-tip loess

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Colorectal Cancer

label_protocol: 300 ng of genomic DNA was labeled with Cy5 or Cy5 using the Bioprime Labelling Kit (Invitrogen, Karlsruhe, Germany) according to the manufactures' instructions

extract_protocol: Extraction of high molecular weight DNA and RNA from frozen HCC samples was carried out by ultracentrifugation in cesium chloride as previously described in van den Boom et al., 2003 Am J Pathol.

source_name: lymphocyte pool of six healthy male controls


title: Primary_Colorectal_Cancer_Patient_No.7

description:
HD482-Tu
US22502683_156883_S01_A01.gpr

source_name: lymphocyte pool of six healthy female controls


title: TIME +KSHV, 13 h.p.i. (P-type strain study)

type: RNA

city: San Francisco

first: Sanjay

last: Chandriani

state: CA

address: 513 Parnassus Avenue

country: USA

institute: UCSF

hyb_protocol: Samples were hybridized to the custom tiling microarrays according the manufacturer’s protocol (Agilent). Hybridized microarrays were washed according to the manufacturer’s protocol (Agilent),

scan_protocol: Microarrays were scanned on the GenePix 4000B scanner (Axon instruments) and all feature intensities collected using the GenePix Pro 6.0 software.

data_processing:
TIFF images of scanned slides were analyzed using Feature Extraction Software version 9.5.3 (Agilent) using a custom grid file (017577_D_F_20070822). LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Data of identical probes were averaged.
Data were subject to a further linear normalization step by the average of the features detecting the spike-in transcripts. Only features that did not have any feature non-uniformity or population outlier flags contributed to the averages used for determining the normalization factor.
Remove any data that failed any of the following spot quality filters: 1. gIsFound = 1 AND rIsFound = 1; 2. no PopnOL or NonUnifOL detected; 3. g OR r IsWellAboveBackground.
Data of every probe was centered to the average of the corresponding control samples.
Data for host genes were removed and probes against viral sequences were ordered by position in genome.

molecule: total RNA

source_name: TIME +KSHV, 13 h.p.i.

label_protocol: The Quick Amp labeling kit (Agilent) was used according to the manufacturer’s protocol to generate Cy5/Cy3 labeled cRNA from 450ng of total RNA, which contains mix of spike-in transcripts A + B (Agilent). An equal amount of hte spike-in transcript mix are added to both Cy5 and Cy3 labeled samples. The spike-in transcripts are detected by E1A probes on the array and are used for a linear normalization subsequent to the LOWESS normalization performed by the Agilent feature extraction software.

extract_protocol: All samples were harvested in RLT buffer and RNA was isolated using the RNeasy Mini kit according to the manufacturer’s protocol (Qiagen)

tag: cell type

value: TIME

tag: virus

value: KSHV (P-type strain)

tag: infection status

value: Acute, latent

source_name: Common reference: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME), both infected and uninfected.

value: All infections were performed with either BCBL-1-derived KSHV or rKSHV.219.

value: both infected and uninfected


title: Unaffected (healthy control): 95-1680-B

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

description:
4564612037_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

hyb_protocol: Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation28 DNA Analysis bead chip

scan_protocol: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chip  Standard Illumina protocol for Human Methylation29 DNA Analysis bead chip

data_processing: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chipAverage normalization was used to rescale intensities across multiple chips (Methylation, 3.1.0, BeadStudio Methylation Analysis Module). Beta value represents methylation level of the CpG locus using the ratio of intensities between methylated and unmethylated alleles. ß-value was processed by BeadStudio using the implemented procedures. A ß-value of 0-1.0 was reported significant percent methylation, from 0% to 100%, respectively, for each CpG site.  We re-processed the BeadStudio output later on using log2 [β /(1- β )] for further analysis: log2 [β /(1- β )] values given only for the 63 experimental samples.

label: Biotin

source_name: Unaffected (healthy control)

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

growth_protocol: Lymphoblastoid cell lines (LCL) were grown uniformly in RPMI 1640 with 20% fetal bovine serum (FBS), 100 U penicillin/mL, 100 μg streptomycin/mL sulfate, and 1% L-glutamine as described previously.  All 63 cell lines were grown anonymously and processed randomly.

extract_protocol: DNA was extracted from actively growing lymphoblastoid cells using kit from Gentra Systems following the manufacturer’s instruction.

treatment_protocol: Prior to hybridization, bisulfite conversion of DNA samples was done using the EZ DNA methylation kit (Zymo Research).  500ng DNA was used,  a thermocycling program with a short denaturation step included for bisulfite conversion (16 cycles of 95ºC for 30 seconds fol¬lowed by 50ºC for 1 hour)

tag: gender

value: M

tag: disease severity

tag: gene mutation

tag: mutation type

tag: id


title: Unaffected (healthy control): CDL-227-05F

description:
4564612037_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: TIME replicate 2 (P-type strain study)

source_name: TIME replicate 2

value: Mock

value: mix of several different cell types (BJAB, BCBL, SLK, HFF, HUVEC, TIME)


title: Unaffected (healthy control): CDL-145-03S

description:
4564612037_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F


title: Liver_Metastasis_Patient_No.7

description:
HD482-LM
US22502683_156884_S01_A01.gpr

source_name: Liver metastasis of Colorectal Cancer

tag: lymphocyte pool of six healthy female controls


title: Unaffected (healthy control): 27574-B

description:
4564612037_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Oneut-2 knockout duodenum, day 15, biological replicate 1

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description: Mice during postnatal developmental phase of intestine, day 15

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 18 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450-0007). Stained with R-Phycoerythrin Stepavidin (Molecular Probes) and probed with anti-streptavidin biotinylated goat antibody (Vector Laboratories).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G and GeneChip Operating Software.

data_processing: The CEL files were processed through the Affymetrix Expression Console software (ver. 1.1).  These were RMA normalized and the intensity values were used in Genespring GX 7.3.1 to create the experiments.

label: biotin

organism: Mus musculus

source_name: Mouse duodenum, Onecut-2 knockout, day 15

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA .

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: tissue

value: Duodenum

tag: genotype

value: Onecut-2 knockout

tag: strain

tag: age

value: Postnatal day 15

value: Mixed


title: TIME replicate 1 (P-type strain study)

source_name: TIME replicate 1


title: HUVEC +KSHV, 48 h.p.i. (P-type strain study)

source_name: HUVEC +KSHV, 48 h.p.i.

value: HUVEC


title: Primary_Colorectal_Cancer_Patient_No.6

description:
HD469-Tu
US22502683_156877_S01_A01.gpr

tag: lymphocyte pool of six healthy male controls


title: HUVEC +KSHV, 36 h.p.i. (P-type strain study)

source_name: HUVEC +KSHV, 36 h.p.i.


title: Control_Unmethylation DNA_b1

description:
4564612037_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Unmethylation DNA


title: mildly affected NIPBL mutant CdLS proband: CDL-109-00P

description:
4564612037_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Mild

value: NIPBL

value: Missense


title: HUVEC replicate 2 (P-type strain study)

source_name: HUVEC replicate 2


title: Primary_Colorectal_Cancer_Patient_No.4

description:
HD346-Tu
US22502683_203971_S01_A01.gpr


title: Primary_Colorectal_Cancer_Patient_No.5

description:
HD406-Tu
US22502683_156634_S01_A01.gpr


title: Liver_Metastasis_Patient_No.5

description:
HD406-LM
US22502683_156286_S01_A01.gpr


title: Liver_Metastasis_Patient_No.6

description:
HD469-LM
US22502683_156879_S01_A01.gpr


title: HUVEC +KSHV, 14 h.p.i. (P-type strain study)

source_name: HUVEC +KSHV, 14 h.p.i.


title: RBS44 (Roberts syndrome proband): RBS44

description:
4564612037_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: RBS44 (Roberts syndrome proband)

value: M?

value: unknown


title: HUVEC replicate 1 (P-type strain study)

source_name: HUVEC replicate 1


title: mildly affected NIPBL mutant CdLS proband: CDL-114-P

description:
4564612034_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: HUVEC +KSHV, 24 h.p.i. (P-type strain study)

source_name: HUVEC +KSHV, 24 h.p.i.

value: KSHV (P-type strain)

value: Acute, latent


title: severly affected NIPBL mutant CdLS proband: CDL-001-98-P

description:
4564612037_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Severe

value: Frameshift


title: Liver_Metastasis_Patient_No.4

description:
HD346-LM
US22502683_022388_S01_A01.gpr


title: CVMMS126R_8WG16_N2_L4_1 extraction1_array2

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Ab:8WG16:JL:CVMMS126R;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing:
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard zscore:JL:2 protocol. ChIP-chip_normalization_standard_zscore_v2   First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained for each probe by standardizing the data by subtracting the mean and dividing by the standard deviation of all probes.  Processed data are obtained using following parameters: genome version is WS180

label: Cy5 dye

organism: Caenorhabditis elegans

growth_protocol: Worm_L4_growth_and_harvest_vSE1.doc. Worms were grown in standard S-basal media liquid culture. The culture was synchronized by starving hatched embryos at L1 stage and grown at 20C in liquid culture until they reach L4 stage. Worms were collected over 34 uM Nitex membrane, and washed with M9 Buffer + protease inhibitors (Calbiochem). Worms were resuspended in 1 pellet volume of M9, frozen as ?popcorn? in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_germlineless_adult_soma_extract_v2.2. Frozen worms were ground to a powder using mortar and pestle. Worm powder was diluted in M9 + 1% formaldehyde+1mM PMSF and fixed 5 or 10 minutes. Fixing was quenched by the addition of 125 mM glycine for 5 minutes. Cells were collected by centrifuging 5 minutes at 4000 g at 4C. Samples were washed and resuspended in FA Buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC and taking the supernatant. Protein concentration was determined by Bradford Assay and 10 mgs were used per ChIP.
Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit.
Worm_Whole_Genome_Amplification_for_ChIP-chip_v2. Samples were amplified using a modified Whole Genome Amplification Kit protocol (Sigma).

tag: developmental stage

value: L4 Larva

value: wild type

tag: sex

value: mixed Male and Hermaphrodite population

label: Cy3 dye


title: severly affected NIPBL mutant CdLS proband: CDL-064-99P

description:
4564612034_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M

value: Nonsense


title: Control_Unmethylation DNA_b2

description:
4564612034_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Unmethylation DNA_b2


title: Primary_Colorectal_Cancer_Patient_No.3

description:
HD324-Tu
US22502683_156368_S01_A01.gpr

source_name: Primary Colorectal Cancer

source_name: lymphocyte pool of six healthy male controls


title: Liver_Metastasis_Patient_No.3

description:
HD324-LM
US22502683_156369_S01_A01.gpr


title: Primary_Colorectal_Cancer_Patient_No.2

description:
HD323-Tu
US22502683_156370_S01_A01.gpr


title: NA_MES4FLAG_EEMB_1 extraction1_array3

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: No Antibody Control;target name: Not Applicable;host: None-Control;antigen: NONE;clonal: None-Control;purified: None-Control;company: None-Control;catalog: Not Applicable;reference: Not Applicable;short description: Specific Antibodies were omitted from this immunoprecipitation reaction (as a negative control).;
channel ch2 is input DNA;

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

growth_protocol: Worm_embryo_growth_and_harvest_vSS1. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 1.85% formaldehyde for 30 minutes at room temperature. Embryos were then washed twice with M9 Buffer, once with 100mM Tris-HCl pH 7.5  and once with FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vSS1. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) + protease inhibitors. Sample was dounced 30 times using tight pestle at 4ºC, then sonicated 4 times on ice at the following settings: 30 sec; 20% power output; 0.7 duty cycle. Cell debris was removed by centrifuging at 13,000rpm for 15 minutes at 4ºC and taking the supernatant. Supernatants were filtered through Millipore Ultrafree-MC 0.45 ?m filter units (cat. UFC30HV0S) at 13,000rpm, 4?C for 1 minute to remove lipids.  Protein concentration was determined, and extracts were aliquoted and stored at -80ºC. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vSS1. Protein A or G-coupled Dynal magnetic beads from 20 ul of slurry were washed 3 times in 1ml of 5mg/ml IgG-Free BSA in PBS (wash buffer). Beads were resuspended in 100ul of the wash buffer and rotated with 5ug of the appropriate antibody overnight at 4 oC. Beads were further washed 2 times in the wash buffer and resuspended in 30ul of the wash buffer. Before beginning IP, 5% of starting material of protein (3-6mg) was saved as "input" at -20 oC. The antibody-conjugated Dynal beads were mixed with 3-6mg of protein and nutated for 2hrs at 4 oC. After washing the beads, captured proteins were eluted by incubating beads in 300 ul of TE with 1% SDS and 250mM NaCl for 2 times 15 minutes at 65 oC. Samples were treated with proteinase K and reverse-crosslinked at 65 oC overnight. DNA was purified using Zymo DNA purification column and eluted in in 43ul dH2O. RNA was digest for 1 hour at 37 oC with RNase One (Promega). For a detailed protocol see http://www.modencode.org/.
Worm_LM-PCR_Amplification_for_ChIP-chip_vSS1. ChIP DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from FlyChip protocol version 1.2 from R. Auburn:  http://www.flychip.org.uk/protocols/chip/lm_pcr.php. For a detailed protocol see http://www.modencode.org/.

value: MES4FLAG tagged by Bombard)

value: Early Embryo

value: mes-4(bn73); bnIs15[mes-3 promoter::MES-4::GFP::3xFLAG::mes-4 3' region

tag: transgene

value: mes-3 promoter::MES-4 coding sequence::GFP::3xFLAG::mes-4 3' sequence


title: CVMMS126R_8WG16_N2_L4_1 extraction1_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: Ab:8WG16:JL:CVMMS126R;target name: RNA polII CTD domain unphosophorylated;host: Mouse;antigen: Native RNA Polymerase II purified from wheat germ;clonal: Monoclonal;purified: Size;company: Covance;catalog: Covance (MMS126R);short description: A mouse monoclonal antibody which recognizes primarily the unphosphorylated RNA Pol II CTD (8WG16) obtained from Covance (MMS126R) was used for ChIP.;


title: severly affected NIPBL mutant CdLS proband: CDL-066-99P

description:
4564612034_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: NIPBL


title: NA_MES4FLAG_EEMB_2 extraction2_array3


title: Liver_Metastasis_Patient_No.2

description:
HD323-LM
US22502683_022387_S01_A01.gpr


title: SMC3 mutant CdLS proband: CDL-057-99P

description:
4564612034_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: SMC3 mutant CdLS proband

value: mild

value: Missense


title: SMC1A mutant CdLS proband: CDL-203-04P

description:
4564612034_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: SMC1A mutant CdLS proband

value: F


title: severly affected NIPBL mutant CdLS proband: CDL-364-06P

description:
4564612034_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: NA_MES4FLAG_EEMB_2 extraction2_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: No Antibody Control;target name: Not Applicable;host: None-Control;antigen: NONE;clonal: None-Control;purified: None-Control;company: None-Control;catalog: Not Applicable;reference: Not Applicable;short description: Specific Antibodies were omitted from this immunoprecipitation reaction (as a negative control).;


title: NHE4_stomach

first: Gary

last: Shull

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

description: 6 wild-type and 6 NHE4-knockout stomach RNA samples were compared. Total RNA was collected from both male and female adult (between 8 and 12 weeks of age) wild-type and NHE4-null mice on a mixed 129 Black Swiss background. With the exception of one, all comparisons were done between wild-type and NHE4-null samples from littermate age- and gender-matched siblings.

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min.  For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.  The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.  To test for differentially expressed genes, a hierarchical Bayes procedure, IBMT (Sartor et al., BMC Bioinf, 2006) was used.

source_name: total RNA from whole stomach

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

growth_protocol: Mice had access to normal chow and water ad libitum.

extract_protocol: Total RNA was extracted from whole colon using Tri-Reagent as per the manufacturer's instructions.

value: 129 Black Swiss (mixed)

value: 186 WT FEMALE

value: 524 WT FEMALE

value: 554 KO MALE

value: 569 KO FEMALE

value: 570 KO FEMALE

value: 193 WT MALE

value: 183 KO FEMALE

value: 523 KO MALE

value: 553 WT MALE

value: 568 WT FEMALE

value: 571 WT FEMALE

value: 194 KO MALE


title: c2N_autogamy_N8_T36

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

description: Population of cells at 2000 cells per mL, 36 hours after T0, with 47% of autogamy (anlagen) and 53% caryonides

hyb_protocol: Hybridization by NimbleGen company

scan_protocol: Scanning by NimbleGen company

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450440.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450440_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

organism: Paramecium tetraurelia

source_name: N8 (36 hours after T0), with dsRNA

label_protocol: SuperScript Invitrogen (double strand labeling)

growth_protocol:
Strain 51 is an entirely homozygous Paramecium tetraurelia strain. Its mating type was checked to be O (=mt7) before autogamy. Cells were grown in feeding medium. Feeding media were prepared by inoculating pre-cultures of the appropriate feeding strains into WGP Paramecium medium containing Ampicillin at 0.1 mg/ml and growing them overnight with shaking at 37°C. On the next day, the culture was diluted 4-fold into the same medium. After 1 hr of incubation at 37°C, IPTG was added at a final concentration of 0.5 mM to induce the synthesis of with dsRNA, and the culture was incubated 4 hours at 37°C. The medium was cooled to 27°C and supplemented with 0.8 mg/l of β-sitosterol just before use. Cells were maintained at 27°C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.
ND7 is a non-essential gene involved in the regulated discharge of trichocysts; the loss of function of this gene by with dsRNA feeding results in a mutant phenotype: non-discharge of trichocysts (Skouri and Cohen 1997).

extract_protocol: Trizol and Ambion column (ref AM1924)

treatment_protocol: 400 mL of Paramecium cells were centrifuged at 200 xg for 1 min and total RNA was extracted from unwashed cell pellets.

value: 51 new mt7

value: Wild type mating type VII

tag: caryonide

value: monocaryonide

tag: medium

value: Escherichia coli WGP

value: autogamy competent


title: c2N_autogamy_N7_T15.5

description: Population of cells at 2000 cells per mL, 15.5 hours after T0, with 3% of meiosis 97% of autogamy (7% skeins, 10% fragmented macs, 80% anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450439.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450439_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: N7 (15.5 hours after T0), with dsRNA


title: Primary_Colorectal_Cancer_Patient_No.1

description:
HD301-Tu
US22502683_156902_S01_A01.gpr


title: c2N_vegetative cells

description: Vegetative cells at 673 cells per mL

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450436.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450436_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Vegetative cell before autogamy, with dsRNA

value: log-phase growth


title: Control_Methylation DNA_2

description:
4564612034_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Methylation DNA_2


title: severly affected NIPBL mutant CdLS proband: CDL-056-99P

description:
4564612034_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M

value: Severe

value: NIPBL

value: Frameshift


title: NA_MES4FLAG_EEMB_1 extraction1_array1

value: MES4FLAG tagged by Bombard)

value: Early Embryo

value: mes-4(bn73); bnIs15[mes-3 promoter::MES-4::GFP::3xFLAG::mes-4 3' region

value: mixed Male and Hermaphrodite population

value: mes-3 promoter::MES-4 coding sequence::GFP::3xFLAG::mes-4 3' sequence


title: CVMMS126R_8WG16_N2_L4_1 extraction1_array1

value: L4 Larva

value: wild type


title: c2N_autogamy_N3_T0

description: T0 = Population of cells at 2113 cells per mL with 30% of meiosis and 3% autogamy (skeins)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450437.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450437_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: N3 (reference point in autogamy time course), with dsRNA

value: 51 new mt7


title: c2K_autogamy_K7_T30

description: Population of cells at 2000 cells per mL, 30 hours after T0, with 70% of autogamy (anlagen) and 30% caryonides

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450435.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450435_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: K7 (30 hours after T0)

growth_protocol: Strain 51 is an entirely homozygous Paramecium tetraurelia strain. Its mating type was checked to be O (=mt7) before autogamy. Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae bacteria, and supplemented with 0.8 µg/L of beta-sitosterol (Merck, Darmstadt, FRG). Cells were maintained at 27¡C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

value: Wild type mating type VII

value: Klebsiella pneumoniae WGP


title: SRYS1 (Roberts syndrome proband): SRYS1

description:
4564612037_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: SRYS1 (Roberts syndrome proband)

value: M?

value: unknown


title: NA_MES4FLAG_EEMB_1 extraction1_array2


title: NA_MES4FLAG_EEMB_2 extraction2_array2


title: severly affected NIPBL mutant CdLS proband: CDL-018-98-P

description:
4564612034_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F

value: Nonsense


title: c2N_autogamy_N6_T7.5

description: Population of cells at 2000 cells per mL, 7.5 hours after T0, with 23% of meiosis 62% of autogamy (10% skeins, 48% fragmented macs, 4% anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450438.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450438_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: N6 (7.5 hours after T0), with dsRNA

value: monocaryonide

value: Escherichia coli WGP

value: autogamy competent


title: severly affected NIPBL mutant CdLS proband: CDL-035-99P

description:
4564612034_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Severe

value: NIPBL


title: Liver_Metastasis_Patient_No.1

description:
HD301-LM
US22502683_156885_S01_A01.gpr

source_name: Liver metastasis of Colorectal Cancer


title: severly affected NIPBL mutant CdLS proband: CDL-038-99P

description:
4564612034_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Frameshift


title: severly affected NIPBL mutant CdLS proband: CDL-013-98-P

description:
4564612032_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M


title: c2K_autogamy_K6_T19.5

description: Population of cells at 2000 cells per mL, 19.5 hours after T0, with 98% of autogamy (anlagen) and 2% caryonides

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450434.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450434_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: K6 (19.5 hours after T0)


title: severly affected NIPBL mutant CdLS proband: CDL-152-03P

description:
4564612032_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: severly affected NIPBL mutant CdLS proband: CDL-015-98-P

description:
4564612032_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: RFP R4

city: Oklahoma City

first: Igor

middle: M

last: Dozmorov

state: OK

address: 825 NE 13th Street

department: Arthritis & Immunology

institute: OMRF

description:
RFP R4
Jurkat cells - control transfection replicate 4

hyb_protocol: hybridization to the HumanWG-6 v3.0 Expression BeadChips.

scan_protocol: scanned on an Illumina BeadArray Reader.

data_processing:
All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Two-step normalization procedure (1). The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”.     The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.

source_name: Jurkat T cells transfected with an lentiviral vector expressing control (RFP or Lin28)

label_protocol: RNA was prepared and labeled with the Ambion TotalPrep kit

growth_protocol: The Jurkat human leukemia cell line was cultured in RPMI 1640 containing 100 mL/L newborn calf serum, 2 mmol/L of L-glutamine, 1 x 105 IU/L penicillin, 100 mg/L of streptomycin at 37°C in a humidified atmosphere of 5% carbon dioxide/95% air.

extract_protocol: RNA was extracted from GFP+ or RFP+ FACS-sorted Jurkat T cells transfected LV-GFP-Pbx1-d or LV-RFP, as well as non-transfected cells in 4 independent transfections per group.

treatment_protocol: Jurkat T cells (5 x 105 cells/ml) were transfected with an lentiviral (LV) vector expressing either control (RFP or Lin28) or Pbx1-d-GFP.  Pbx1 expression was detected with a polyclonal Ab (Cell Signaling).

tag: cell line

value: CD4+ Jurkat leukemic T-cell line

tag: transfection

value: RFP-transfected control


title: RFP R3

description:
RFP R3
Jurkat cells - control transfection replicate 3


title: RFP R2

description:
RFP R2
Jurkat cells - control transfection replicate 2


title: RFP R1

description:
RFP R1
Jurkat cells - control transfection replicate 1


title: mildly affected NIPBL mutant CdLS proband: 126P

description:
4564612032_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

tag: gender

tag: disease severity

value: Mild

value: Missense


title: PBX1 R3

description:
PBX1 R3
Jurkat cells - transfected with PBX1 replicate 3

source_name: Jurkat T cells transfected with an lentiviral vector expressing Pbx1-d-GFP

value: PBX1 transfected


title: PBX1 R2

description:
PBX1 R2
Jurkat cells - transfected with PBX1 replicate 2


title: c3_autogamy_T5

description: Population of cells at 5500 cells per mL, 5 hours after T0,  with 5% of meiosis and 92% of autogamy (6% skeins, 35% fragmented macs, 51% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450412.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM4504012_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T5 (5 hours after T0)

growth_protocol: Strain 51 is an entirely homozygous Paramecium tetraurelia strain. Its mating type was checked to be E (=mt8) before autogamy. Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae bacteria, and supplemented with 0.8 µg/L of beta-sitosterol (Merck, Darmstadt, FRG). Cells were maintained at 27¡C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

treatment_protocol: At each time-point, 200 to 400 mL of Paramecium cells were centrifuged at 170 to 200 xg for 1 min and total RNA was extracted from unwashed cell pellets.

value: 51 new mt8

value: Wild type mating type VIII

value: Klebsiella pneumoniae WGP


title: mildly affected NIPBL mutant CdLS proband: CDL-156-04P

description:
4564612032_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F

tag: gene mutation

tag: mutation type


title: c2K_autogamy_K4_T7.5

description: Population of cells at 2213 cells per mL, 7.5 hours after T0, with 29% of meiosis 48% of autogamy (7% skeins, 38% fragmented macs, 3% anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450433.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450433_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: K4 (7.5 hours after T0)

value: 51 new mt7

value: Wild type mating type VII


title: PBX1 R4

description:
PBX1 R4
Jurkat cells - transfected with PBX1 replicate 4


title: c2K_autogamy_K1_T0

description: T0 = Population of cells at 1826 cells per mL with 21% of meiosis

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450431.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450431_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: K1 (T0, first point in autogamy time course)

value: monocaryonide


title: PBX1 R1

description:
PBX1 R1
Jurkat cells - transfected with PBX1 replicate 1


title: c3_autogamy_T15

description: Population of cells at 5500 cells per mL, 5 hours after T15,  with 95% of autogamy (2.5% fragmented macs, 92.5% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450413.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450413_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T15 (15 hours after T0)

value: autogamy competent


title: severly affected NIPBL mutant CdLS proband: CDL-157-04P

description:
4564612032_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

data_processing: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chipAverage normalization was used to rescale intensities across multiple chips (Methylation, 3.1.0, BeadStudio Methylation Analysis Module). Beta value represents methylation level of the CpG locus using the ratio of intensities between methylated and unmethylated alleles. ß-value was processed by BeadStudio using the implemented procedures. A ß-value of 0-1.0 was reported significant percent methylation, from 0% to 100%, respectively, for each CpG site.  We re-processed the BeadStudio output later on using log2 [β /(1- β )] for further analysis: log2 [β /(1- β )] values given only for the 63 experimental samples.

value: Severe

value: Nonsense

tag: id


title: c3_autogamy_Tm25

description: Population of cells at 4000 cells per mL, 3.5 hours before T0, with 31% of meiosis and 35% of autogamy (19% skeins, 16% fragmented macs)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450410.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450410_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Tm25 (autogamy competent cells, 3.5 hours before T0)


title: c2K_vegetative cells

description: Vegetative cells at 1000 cells per mL

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450430.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450430_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: Vegetative cell before autogamy

value: log-phase growth


title: autogamy_T11

description: Population of cells at 4000 cells per mL, 11 hours after T0, with 99% of autogamy (1% sleins, 57% fragmented macs, 41% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450406.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450406_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T11 (11 hours after T0)

growth_protocol: Strain d4-2 is an entirely homozygous Paramecium tetraurelia derivative of strain 51. Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae bacteria, and supplemented with 0.8 µg/L of beta-sitosterol (Merck, Darmstadt, FRG). Cells were maintained at 27¡C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

extract_protocol: Trizol

value: d4-2 6A2a Paris


title: c2K_autogamy_K3_T5

description: Population of cells at 2200 cells per mL, 5 hours after T0, with 31% of meiosis 32% of autogamy (16% skeins, 16% fragmented macs)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM450432.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450432_RMA.txt file contains the signals after background correction, but before applying between-array normalization.

source_name: K3 (5 hours after T0)


title: c3_autogamy_T0

description: Population of cells at 5500 cells per mL with 20% of meiosis and 65% of autogamy (11% skeins, 37% fragmented macs, 17% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450411.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450411_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T0 (reference point in autogamy time course)


title: severly affected NIPBL mutant CdLS proband: CDL-132-01P

description:
4564612032_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: NIPBL


title: severly affected NIPBL mutant CdLS proband: CDL-054-99P

description:
4564612032_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: mildly affected NIPBL mutant CdLS proband: 134P

description:
4564612032_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M


title: N R3

description:
N R3
control Jurkat cells replicate 3

source_name: Jurkat T cells

value: CD4+ Jurkat leukemic T-cell line

value: non-transfected control


title: N R4

description:
N R4
control Jurkat cells replicate 4


title: autogamy_T20

description: Population of cells at 4000 cells per mL, 20 hours after T0, with 97% of autogamy (8% fragmented macs, 89% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450407.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450407_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T20 (20 hours after T0)


title: severly affected NIPBL mutant CdLS proband: CDL-049-99P

description:
4564612032_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: autogamy_T0

description: Population of cells at 4000 cells per mL with 56% of autogamy (23% skeins, 32% fragmented macs, 1% visible anlagen)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450405.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450405_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T0 (first point in autogamy time course)


title: c3_starved cells

description: Population of cells at 5500 cells per mL, 6 hours before T0, with 27% of meiosis and 8% of autogamy (5% skeins, 3% fragmented macs)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450409.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450409_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Starved cells (6 hours before T0)


title: SMC1A mutant CdLS proband: CDL-107-00P

description:
4564612032_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: SMC1A mutant CdLS proband

value: mild

value: missense


title: Control_Methylation DNA_3

description:
4564612025_L

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Methylation DNA_3


title: c3_vegetative cells

description: Vegetative cells at 400 cells per mL

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450408.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450408_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

value: 51 new mt8

value: Wild type mating type VIII


title: vegetative cells

description: Vegetative cells at 1253 cells per mL

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450404.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450404_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

value: Klebsiella pneumoniae WGP


title: N R2

description:
N R2
control Jurkat cells replicate 2


title: severly affected NIPBL mutant CdLS proband: CDL-129-01P

description:
4564612032_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: Unaffected (healthy control): AGS-248-S

description:
4564612025_K

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Unaffected (healthy control)

value: M?


title: N R1

description:
N R1
control Jurkat cells replicate 1


title: autogamy_T5, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 2% vegetative cells; 5% meiotic cells; 9% cells with skeins; 50% cells with fragmented old macronucleus and no visible anlagen; 35% of cells with two anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450358.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450358_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

growth_protocol: Strain 51 is an entirely homozygous Paramecium tetraurelia strain. Its mating type was checked to be E (=mt8) before autogamy. Cells were grown in a wheat grass powder (Pines International Co., Lawrence, USA) infusion medium bacterized the day before use with Klebsiella pneumoniae bacteria, and supplemented with 0.8 µg/L of beta-sitosterol (Merck, Darmstadt, FRG). Cells were maintained at 27°C during vegetative growth and starvation. Cell growth was monitored by manual counting of cells in 1 mL aliquots of the culture. During starvation, the progression of autogamy through the different stages of nuclear reorganization was monitored by DAPI staining of cells.

value: stock 37c09


title: SMC1A mutant CdLS proband: 94-3852-P

description:
4564612025_J

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: F

value: Missense


title: SMC1A mutant CdLS proband: CDL-074-99P

description:
4564612025_I

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: PC3 PDGF-D cells, passage 20

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The arrays were scanned using Illumina's BeadStudio Software suite (v 3.1, Illumina) according to standard Illumina scanning protocol.

data_processing: The data were normalised using the function normalize.quantiles from the package preprocessCore (version 1.2.0) under the R statistical language (version 2.7.0).

source_name: bone metastasis of prostate cancer

label_protocol: Biotinylated cRNA were prepared using Illumina Totalprep RNA Amplification Kit  for Illumina arrays

growth_protocol: Stable PC3 Neo and PC3 PDGF-D cells were coltured in RPMI 1640 medium supplemented with 5% FBS for 3 days and then total RNA was isolated.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: bone metastasis of prostate cancer

tag: genotype/variation

value: PDGF-D

tag: cell passage


title: PC3 PDGF-D cells, passage 10


title: autogamy_T11, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 0% vegetative cells; 0% meiotic cells; 2% cells with skeins; 13% cells with fragmented old macronucleus and no visible anlagen; 82% of cells with two anlagen; 3% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450359.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450359_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

tag: strain

value: monocaryonide

value: autogamy competent


title: Control_Unmethylation DNA_a1

description:
4564612025_H

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Unmethylation DNA_a1


title: SMC1A mutant CdLS proband: CDL-060-99P

description:
4564612025_G

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.


title: starved cells, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 1960 cells/mL; 45% vegetative cells; 32% meiotic cells; 18% cells with skeins; 5% cells with fragmented old macronucleus and no visible anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450356.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450356_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: Starved cells


title: 7 day old seedlings, 35SPaWRKY1-3

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

department: Biology

country: Taiwan

institute: National Changhua University of Education

description: Gene expression data from transgenic Arabidopsis 35S-PaWRKY1 plants biological rep 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The data was further normalized by the RMA algorithm.

organism: Arabidopsis thaliana

source_name: 7 day old seedlings in full-strength MS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: 7 day old seedlings in full-strength MS

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Empty-vector control and transgenic PaWRKY1 Arabidopsis

tag: tissues

value: Seedlings including shoot and root

tag: age

value: 2day seed vernalization and 7 day old seedling

tag: genotype

value: Transgenic 35S-PaWRKY1 Arabidopsis


title: PC3 Neo cells, passage 20

value: Neo


title: PC3 Neo cells, passage 10


title: PC3 PDGF-D cells, passage 7


title: PC3 Neo cells, passage 7


title: Control_Unmethylation DNA_a3

description:
4564612025_E

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

source_name: Control_Unmethylation DNA_a3


title: severly affected NIPBL mutant CdLS proband: CDL-276-05P

description:
4564612025_F

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M

value: Severe

value: NIPBL

value: Frameshift


title: Genotyping data from one patient with autism spectrum disorder and a deletion of SHANK2 gene

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

institute: The Hospital for Sick Children

description: Genomic DNA extracted from whole blood from patient with autism spectrum disorder was genotyped using Illumina 1M array.

hyb_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip

data_processing: Genomic DNA extracted whole blood was genotyped using Infinium 1M-single Genotyping BeadChips (Illumina). For CNV calling on the Illumina 1M platform we used combinations of QuantiSNP, iPattern and PennCNV.

label: C-Bio and A-DNP

extract_protocol: Standard DNA isolation Kit from whole blood with promega maxwell-technology.

tag: disease

value: Male

tag: tissue

value: whole blood

tag: subject

value: patient

tag: alternate id


title: autogamy_T11, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 1% vegetative cells; 1% meiotic cells; 0% cells with skeins; 25% cells with fragmented old macronucleus and no visible anlagen; 73% of cells with two anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450353.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450353_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

value: 51 new mt8

value: stock 37c09

tag: caryonide

tag: medium

value: Klebsiella pneumoniae WGP


title: 7 day old seedlings, Vector-3

description: Gene expression data from empty-vector control plants biological rep 3

value: Empty-vector control pCAMBIA 1302


title: 7 day old seedlings, Vector-1

description: Gene expression data from empty-vector control plants biological rep 1


title: Unaffected (healthy control): AGS-222-S

description:
4564612025_D

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

data_processing: Standard Illumina protocol for Human Methylation29 DNA Analysis bead chipAverage normalization was used to rescale intensities across multiple chips (Methylation, 3.1.0, BeadStudio Methylation Analysis Module). Beta value represents methylation level of the CpG locus using the ratio of intensities between methylated and unmethylated alleles. ß-value was processed by BeadStudio using the implemented procedures. A ß-value of 0-1.0 was reported significant percent methylation, from 0% to 100%, respectively, for each CpG site.  We re-processed the BeadStudio output later on using log2 [β /(1- β )] for further analysis: log2 [β /(1- β )] values given only for the 63 experimental samples.

tag: gender

value: F

tag: disease severity


title: 7 day old seedlings, Vector-2

description: Gene expression data from empty-vector control plants biological rep 2


title: autogamy_T20, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 0% vegetative cells; 0% meiotic cells; 0% cells with skeins; 11% cells with fragmented old macronucleus and no visible anlagen; 85% of cells with two anlagen; 4% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450354.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450354_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

value: monocaryonide

value: autogamy competent


title: severly affected NIPBL mutant CdLS proband: CDL-006-98-P

description:
4564612025_C

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

tag: gene mutation

tag: mutation type


title: severly affected NIPBL mutant CdLS proband: CDL-095-00P

description:
4564612025_B

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: Splice site

tag: id


title: autogamy_T20, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 0% vegetative cells; 0% meiotic cells; 0% cells with skeins; 9% cells with fragmented old macronucleus and no visible anlagen; 91% of cells with two anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450360.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450360_RMA.txt file contains the signals after background correction, but before applying across-array normalization.


title: 7 day old seedlings, 35SPaWRKY1-2

description: Gene expression data from transgenic Arabidopsis 35S-PaWRKY1 plants biological rep 2

value: Seedlings including shoot and root

value: 2day seed vernalization and 7 day old seedling

value: Transgenic 35S-PaWRKY1 Arabidopsis


title: Genotyping data from one mother of a patient with autism spectrum disorder and a deletion of SHANK2 gene

description: Genomic DNA extracted from whole blood from mother of a patient with autism spectrum disorder was genotyped using Illumina 1M array.

scan_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip

value: Female

tag: relation to patient

value: mother


title: vegetative cells, biological rep2

description: 51 new mt8 in Klebsiella pneumoniae; 730 cells/mL; 98% vegetative cells, 1% cells with fragmented old macronucleus and no visible anlagen; 1% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450355.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450355_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

value: log-phase growth


title: autogamy_T5, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 0% vegetative cells; 3% meiotic cells; 5% cells with skeins; 56% cells with fragmented old macronucleus and no visible anlagen; 37% of cells with two anlagen; 0% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450352.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450352_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

source_name: T5 (5 hours after T0)


title: Genotyping data from one father of a patient with autism spectrum disorder and a deletion of SHANK2 gene

description: Genomic DNA extracted from whole blood from father of a patient with autism spectrum disorder was genotyped using Illumina 1M array.

label_protocol: Standard Illumina protocol for Infinium 1M-single Beadchip

value: Male

value: father


title: OD00079_HCP3_N2_MXEMB_3 extraction3_array4

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;
channel ch2 is input DNA;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: ChIP-chip_scanning_nimblegen_v2. Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User?s Guide.

data_processing:
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180
ChIP-chip normalization standard nimblegen:JL:1 protocol. ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User?s Guide and chapter 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen.  Processed data are obtained using following parameters: genome version is WS180

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l.  Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added.  50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 °C.  Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C.  Eluates were incubated over night at 65 °C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 °C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 °C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 °C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.

tag: developmental stage

value: Mixed Embryo

value: wild type

tag: sex

value: mixed Male and Hermaphrodite population


title: autogamy_T0, biological rep1

description: 51 new mt8 in Klebsiella pneumoniae; 32% vegetative cells; 20% meiotic cells; 7% cells with skeins; 40% cells with fragmented old macronucleus and no visible anlagen; 1% post autogamous cells

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

The supplementary GSM450351.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The GSM450351_RMA.txt file contains the signals after background correction, but before applying across-array normalization.

tag: strain

value: 51 new mt8

value: stock 37c09

value: Klebsiella pneumoniae WGP


title: OD00079_HCP3_N2_MXEMB_2 extraction2_array4

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: OD00079 HCP3;target name: HCP-3;host: Rabbit;antigen: N-terminal histone tail of HCP-3;clonal: Polyclonal;purified: Affinity;company: Other;catalog: Desai Lab;reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55;short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen;

label_protocol: ChIP-chip_label_hyb_nimblegen_v2. DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: OD00079_HCP3_N2_MXEMB_4 extraction4_array4


title: 7 day old seedlings, 35SPaWRKY1-1

description: Gene expression data from transgenic Arabidopsis 35S-PaWRKY1 plants biological rep 1

tag: tissues

tag: age


title: ABAB5408_4H8_N2_MXEMB_2 extraction2_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;antigen: Synthetic peptide YSPTSpPS;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: ab5408;reference: Abcam website and references therein;short description: This antibody recognises the C-terminal repeat of the largest subunit of RNA polymerase II.  It recognises both unphosphorylated and phosphorylated forms.;
channel ch2 is input DNA;

tag: genotype


title: SMC1A mutant CdLS proband: CDL-017-98-P

description:
4564612025_A

Genomic DNA extracted from lymphoblastoid cell lines (LCLs) was treated with sodium bisulfite then was genotyped on Illumina?s Infinium HumanMethylation27 BeadChip. A pair of bead-bound probes is used to detect the presence of T or C by hybridization followed by single-base extension with a labeled nucleotide.

value: M

value: mild

value: Missense


title: HD945-NL-Normal_Liver_Control_No.5

hyb_protocol: According to the Illumina® Protocol for Human Sentrix-6 Beat-Chips

data_processing: Data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. All data was then used for the mean expression value calculation within one array. Next, outliers were removed when their expression value dropped below a threshold of median + 3*MAD expression of all negative control beads. Individual bead types were also flagged as filtered when their bead replicate count dropped below 17. Finally, we discarded a bead type when the bead type’s filter flag was set across all samples. 18.184 features passed quality controls and further data analysis was done by variance stabilization and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

source_name: Normal Liver Tissue

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: Extraction of high molecular weight DNA and RNA from frozen CRC and liver metastases samples was carried out by ultracentrifugation in cesium chloride as previously described in van den Boom et al., 2003 Am J Pathol.

tag: normal liver tissue


title: HD940-NL-Normal_Liver_Control_No.3

scan_protocol: According to the Illumina® Protocol for Human Sentrix-6 Beat-Chips


title: HD935-NL-Normal_Liver_Control_No.1


title: HD938-NL-Normal_Liver_Control_No.2


title: ABAB5408_4H8_N2_MXEMB_1 extraction1_array1

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: ab5408;target name: RNA polymerase II CTD repeat YSPTSPS;host: Mouse;antigen: Synthetic peptide YSPTSpPS;clonal: Monoclonal;purified: Protein A/G;company: Abcam;catalog: ab5408;reference: Abcam website and references therein;short description: This antibody recognises the C-terminal repeat of the largest subunit of RNA polymerase II.  It recognises both unphosphorylated and phosphorylated forms.;


title: trichocyst_discharge_T0, biological rep4

description: Time point before trichocyst discharge.

hyb_protocol: Hybridization by NimbleGen company.

scan_protocol: Scanning by NimbleGen company.

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM447194.txt file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

source_name: Time point before trichocyst discharge

treatment_protocol: A pellet of living paramecia (routinely 0.5 ml) is transferred drop by drop in a small beaker containing 5 ml of aminoethyl dextran 0.05%  in TrisHCl 10mM pH 7.2, CaCl2 1mM under mild rotary agitation, diluted to 100 ml of the same buffer without aminoethyl dextran and centrifuged 1 min. 1000g. The pellet is essentially composed of living paramecia having discharged all of their trichocysts (secretory granules) that are transferred to fresh culture medium. Aliquots are taken and pelleted at desired times after the treatment for total RNA extraction.

value: 7s d4-2 self VB mt7-2A

value: Wild type

value: polycaryonide

value: Klebsiella pneumoniae BHB

value: stationary phase


title: HD779-Tu-Primary_Colorectal_Cancer_Patient_No.18

source_name: Primary Colorectal Cancer


title: HD941-NL-Normal_Liver_Control_No.4


title: OD00079_HCP3_N2_MXEMB_1 extraction1_array1