title: yFR116_3E8_W303_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: yFR116_3E8_W303_P-Ser5_Rep2

status: Public on Feb 01 2012

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

hyb_protocol: Hybridization: Add 110uL of hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA) to the resuspended (mixed) colored pellet. Put at 95C for 5 minutes, centrifuge briefly and transfer at 42C for 10 min (Keep samples at 42C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42C in Agilent hybridization oven at 20 rpm rotation speed.    Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.    Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1) Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Submerge the rack with slides (from 1 to 10) in stripping buffer and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2) Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations.

scan_protocol: Scanner Axon GenePix4000B and GenePix Pro (version 6.1.0.4) extraction software were used for scanning and features quantification. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0uM. Set the minimal intensity (histogram preview) to 3000-5000. Adjust PMTs so that approximately 5-10% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 (when possible).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL mQH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 400ng of DNA diluted to 40uL with mQH2O. Incubate 20 minutes at 12C. Add 12uL of a the following mix: 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -20'C for at least 30 min, then spin 20 minutes at 4C. Wash the pellet with 700uL -20'C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL mQH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice (or in cold room). Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL mQH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20'C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (visible as a smear on the side of the tube) with 700uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL mQH2O.    Labeling: Add 15uL of PCR aa-dUTP mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL mQH2O) to resuspended ligation samples. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL mQH2O)(Pause program if necessary). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C. Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also elute twice with 40uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO (Use DMSO store in vacuum with desiccant). Resuspended dyes are store in the dark at -80?C. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, elute twice in 40uL.  Speed-vac until ~10uL is left, or to dryness (corresponding Cy3 and Cy5 samples can be mixed before speed-vac in order to avoid DNA loss upon later resuspension).  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.

growth_protocol: Culture were done at 30C in YEP+2% Glucose media (50 to 200mL) inoculated at OD600 0.1 from an overnight preculture in YEP+2% Glucose media. Culture were allowed to grow until it reach OD600 0.6-1.0, poured in 50mL Falcon tubes containing 1.4mL 37% formaldehyde for crosslinking (1% final), and incubate on rotating wheel for 30 min at room temperature. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (~125mM final). Crosslinked cells were pelleted at 4 C, 3000 rpm ( in Beckman centrifuge (GS 6R Rotor 3.8)), resuspended in 40mL ice cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells snap-freeze in liquid nitrogen. Cells were store at -80 C. Ref: Bataille A.R., Robert F. Methods in Enzymology 2009

extract_protocol: Cells are thawed on ice, and resuspended in 700mL lysis buffer with protease inhibitors (50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate; 1mM PMSF; 1mM Benzamidine; 10ug/mL Aprotinin; 1ug/mL Leupeptin; 1ug/mL Pepstatin). 500uL of acid-washed glass beads (Sigma) are added, and the cells lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle and place in 2mL collection tubes to allow transfer of lysate, but not beads, with a brief centrifugation. The lysates are then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4 C max speed and supernatant used immediately for ChIP (or snap-freeze in liquid nitrogen and saved frozen at -80C).    For immunoprecipitation, Dynabeads (details at the end of the section) (50uL / ChIP) are washed twice with PBS + 0.5% BSA (freshly made), and resuspended in PBS + 0.5% BSA. Antibody are added (Concentration and souce at the end of the section), and incubated overnight at 4 C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody are added to 400-600uL of lysate, and incubated overnight at 4 C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors)(50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate ), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA), and once with ice cold TE. Remaining liquid is removed by pipetting after 1 min centrifugation at 4 C (max speed). 50uL TE + 1% SDS is added and beads are incubated overnight at 65 C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks with the ChIP samples.  For this study the anti-myc (9E10) was a kind gift from Alain Verreault. The anti-Flag (M2) was from Sigma. The 3E8, 3E10 and 4E12 antibodies were purchased from Helmholtz Zentrum in Munich. The H5 (P-Ser2) and H14 (P-Ser5) were purchased from Covance. The anti-Rpb3 (W0012) was purchased from Neoclone Biotechnology. The 8WG16 (Ab817) antibody was purchased from Abcam.The following amounts of antibody per immunoprecipitation were used: 3E8 (5μL), 3E10 (5μL), 4E12 (5μL), 8WG16 (2μg), H14 (15μg), H5 (15μg), W0012 (3μL), 9E10 (5μg), M2 (5μg). The antibodies were coupled to Dynabeads (Invitrogen) coated with protein G (3E8, 3E10, 4E12), IgG Pan mouse antibodies (8WG16, H14, W0012, 9E10, M2) or Sheep anti-mouse IgG (H5).    To clean up the DNA, beads are spun down and supernatant is transfered to a new 1.5mL tube. 350uL of a solution of 345uL TE / 3uL RNAse A (10mg/mL) / 2uL Glycogen (20mg/mL) is added to the supernatant and samples incubated at 37C for 2 hours. 15uL of 10% SDS and 7.5uL Proteinase K are then added and the tubes incubated for another 2 hours at 37 C. The samples are then extracted twice with 400uL phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 14uL of 5M NaCl (for about 350uL of extracted sample) and 1mL of freezing 100% EtOH (-20 C). Pellets are washed with 700uL 70% EtOH (-20 C) and left to air dry for few minutes before they are resuspended in 50uL TE. Stored ChIP samples at -20 C.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.


title: EBSC_CTL7

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

country: USA

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

organism: Homo sapiens

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: cell type

value: leukocyte

tag: sample id

tag: gender

value: Female

tag: sentrix id

tag: sentrix position

value: G

tag: experiment

tag: group


title: L189_555 environment 2

type: RNA

city: Ithaca

first: Jesse

middle: D.

last: Munkvold

state: NY

address: 240 Emerson

department: Plant Breeding and Genetics

institute: Cornell University

description: array batch 20202

hyb_protocol: Prehybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

scan_protocol: Scanning was done using an Axon 6000B scanner with automatic PMT gain, 100% laser power, and 10um resolution.

data_processing: Array, block, and spot detection was done automatically and inspected by hand. Bad spots were automatically and hand-flagged.Background was calculated by morphological opening followed by closing using the GenePix 6 software.

label: Alexa 555

molecule: total RNA

organism: Triticum aestivum

source_name: CxC Line 189, embryo at physiological maturity

label_protocol: 10ug of total RNA were amplified using the amino allyly MessageAmp II aRNA Amplification kit (Ambion). Alexa 555 or 647 (Invitrogen #A32755) dyes were coupled according to accompanying protocols. Dye incorporation was measured using photospectrometry.

growth_protocol: Plants were grown in the  field (Ketola 2005) near Ithaca, NY. Spike samples were harvested at physiological maturity as described in Munkvold et al. 2009. TAG. 119. Samples were stored at -20C for two months while embryo samples were harvested. Primary and secondary position seeds were selected from five spikes and embryos (~100) were isolated by hand, frozen in liquid nitrogen, and stored at -80C.

extract_protocol: Total RNA extraction from isolated embryos was done using the Trizol reagent with only slight modifications to the manufacturer protocol. Total RNA was treated with RQ1 DNAse and cleaned using Qiagen Rneasy columns.

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: embryo at physiological maturity

label: Alexa 647

source_name: Pre-anthesis spike bulk

value: Pre-anthesis spike bulk


title: 11052.s1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

value: Male

value: L

tag: family

tag: distribution

tag: site

value: oi

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white


title: yFR116_3E10_W303_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

tag: strain

tag: antibody

tag: vendor


title: 11227.s1

tag: cell type

tag: sample id

tag: gender

tag: sentrix id

value: H

value: hv


title: yFR116_4E12_W303_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells


title: 11289.s1

tag: sentrix position

value: E

tag: experiment

tag: group

value: kr

value: asian


title: yFR116_4E12_W303_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

value: Helmholtz Zentrum


title: L176_555 environment 2

description: array batch 20202

source_name: CxC Line 176, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue


title: 11156.s1

value: leukocyte

tag: family

tag: distribution

tag: site

value: pb

tag: cpea dx


title: 11011.s1

value: J

value: sb

tag: age at collection (months)

tag: ethnicity


title: yFR1004_W0012_fcp1-1_Rpb3_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

tag: strain

tag: antibody

tag: vendor

value: Neoclone Biotechnology


title: 11346.s1

tag: cell type

tag: sample id

tag: gender

tag: sentrix id

value: kc


title: L169_555 environment 2

description: array batch 20202

source_name: CxC Line 169, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11399.s1

value: Male

tag: sentrix position

value: B

tag: experiment

tag: group

value: xm

value: white


title: EBSC_CTL6

value: Female

value: F


title: 11462.s1

tag: family


title: 11018.s1

value: C

tag: distribution

value: ox


title: L175_555 environment 2

description: array batch 20574

source_name: CxC Line 175, embryo at physiological maturity

tag: field location

tag: year

tag: tissue


title: L167_555 environment 2

description: array batch 20202

source_name: CxC Line 167, embryo at physiological maturity


title: yFR1004_W0012_fcp1-1_Rpb3_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells


title: yFR1004_H5_fcp1-1_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

value: H5 (Ser2)

value: Covance


title: yFR116_3E10_W303_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR116 W303 Wt cells

value: Helmholtz Zentrum


title: 11325.s1

value: leukocyte

value: L

tag: site

value: xx

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: yFR1004_H5_fcp1-1_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

tag: strain

tag: antibody

tag: vendor


title: EBSC_CTL4

tag: cell type

tag: sample id

tag: gender

tag: sentrix id

value: D


title: 11026.s1.1

tag: sentrix position

value: H

tag: experiment

tag: group

value: hv


title: L162_555 environment 2

description: array batch 20556

source_name: CxC Line 162, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L168_555 environment 2

description: array batch 20202

source_name: CxC Line 168, embryo at physiological maturity

tag: year

tag: tissue


title: 11417.s1

value: Male

value: B

tag: family

tag: distribution

tag: site

value: kc

tag: cpea dx

value: asian


title: yFR1004_4E12_fcp1-1_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

tag: strain

tag: antibody


title: EBSC_CTL5

tag: cell type

value: Female

value: E


title: yFR1004_8WG16_fcp1-1_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

value: 8WG16 (CTD)

tag: vendor

value: Abcam


title: 11307.s1

value: leukocyte

tag: sample id

tag: gender

value: F

value: fl

tag: age at collection (months)

tag: ethnicity

value: white


title: L166_555 environment 2

description: array batch 20556

source_name: CxC Line 166, embryo at physiological maturity


title: yFR1004_8WG16_fcp1-1_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells


title: 11108.s1

tag: sentrix id

tag: sentrix position

value: H

tag: experiment

tag: group


title: L155_555 environment 2

description: array batch 20556

source_name: CxC Line 155, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

tag: field location

tag: year

tag: tissue


title: L158_555 environment 2

description: array batch 20574

source_name: CxC Line 158, embryo at physiological maturity

value: Ketola, Cornell University, Ithaca, NY


title: yFR1004_4E12_fcp1-1_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

value: Helmholtz Zentrum


title: L153_555 environment 2

description: array batch 20574

source_name: CxC Line 153, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11303.s1

value: Male

tag: family

tag: distribution

tag: site

value: xx

tag: cpea dx


title: 11057.s1

tag: cell type

value: J

value: kr


title: 11484.s1

tag: sample id

value: G

value: xm


title: 11561.s1

tag: gender


title: EBSC_CTL3

value: Female

value: C


title: L147_555 environment 2

description: array batch 20556

source_name: CxC Line 147, embryo at physiological maturity


title: 11256.s1

value: leukocyte

value: I

value: hv

tag: age at collection (months)


title: 11252.s1

value: F

value: sb

tag: ethnicity

value: white


title: 11333.s1

tag: sentrix id


title: L143_555 environment 2

description: array batch 20556

source_name: CxC Line 143, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY


title: 11201.s1

tag: sentrix position

value: H


title: EBSC_CTL2

value: B

tag: experiment


title: L142_555 environment 2

description: array batch 20574

source_name: CxC Line 142, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11257.s1

value: Male

value: K

tag: group


title: yFR1004_3E8_fcp1-1_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

tag: strain

tag: antibody

tag: vendor

value: Helmholtz Zentrum


title: L138_555 environment 2

description: array batch 20556

source_name: CxC Line 138, embryo at physiological maturity

tag: population

tag: field location

tag: year

tag: tissue


title: 11077.s1

source_name: leukocyte

tag: family

tag: distribution

tag: site

tag: cpea dx


title: 11242.s1

tag: cell type

tag: sample id

tag: gender

value: L

value: xx

tag: age at collection (months)


title: yFR1004_3E10_fcp1-1_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells


title: yFR1004_3E10_fcp1-1_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells


title: yFR1003_H5_FCP1wt_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells

value: H5 (Ser2)

value: Covance


title: 11597.s1

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

value: leukocyte

tag: sentrix id

tag: sentrix position

value: J

tag: experiment

value: xm

tag: ethnicity


title: L129_555 environment 2

description: array batch 20202

source_name: CxC Line 129, embryo at physiological maturity


title: L128_555 environment 2

description: array batch 20556

source_name: CxC Line 128, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: L130_555 environment 2

description: array batch 20556

source_name: CxC Line 130, embryo at physiological maturity


title: yFR1004_3E8_fcp1-1_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR1004 fcp1-1 cells

tag: strain

tag: antibody

tag: vendor


title: yFR1003_H5_FCP1wt_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using H5 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: 11557.s1.1

tag: group

value: kc

value: more-than-one-race


title: 11094.s1

value: G

value: hv

value: white


title: yFR1003_W0012_FCP1wt_Rpb3_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells

value: Neoclone Biotechnology


title: yFR1003_8WG16_FCP1wt_CTD_Rep2

description: Biological replicate 2 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells

value: 8WG16 (CTD)

value: Abcam


title: EBSC_CTL1

value: Female

value: A


title: L135_555 environment 2

description: array batch 20202

source_name: CxC Line 135, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Ketola, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: 11299.s1

value: leukocyte

value: Male

value: B

tag: family

tag: distribution

tag: site

value: oi

tag: cpea dx

value: other


title: L119_555 environment 2

description: array batch 20556

source_name: CxC Line 119, embryo at physiological maturity


title: L118_555 environment 2

description: array batch 20556

source_name: CxC Line 118, embryo at physiological maturity


title: L132_555 environment 2

description: array batch 20556

source_name: CxC Line 132, embryo at physiological maturity


title: yFR1003_4E12_FCP1wt_P-Ser7_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells

value: Helmholtz Zentrum


title: L117_555 environment 2

description: array batch 20556

source_name: CxC Line 117, embryo at physiological maturity


title: L125_555 environment 2

description: array batch 20202

source_name: CxC Line 125, embryo at physiological maturity


title: yFR1003_4E12_FCP1wt_P-Ser7_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser7 occupancy, using 4E12 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: yFR1003_8WG16_FCP1wt_CTD_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using 8WG16 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: yFR1003_3E8_FCP1wt_P-Ser5_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: yFR1003_W0012_FCP1wt_Rpb3_Rep1

description: Biological replicate 1 of 2. RNAPII occupancy, using W0012 (anti-Rpb3) antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: L124_555 environment 2

description: array batch 20202

source_name: CxC Line 124, embryo at physiological maturity


title: L115_555 environment 2

description: array batch 20202

source_name: CxC Line 115, embryo at physiological maturity


title: L112_555 environment 2

description: array batch 20202

source_name: CxC Line 112, embryo at physiological maturity


title: HeLa DGCR8 siRNA #3, miRNA

city: New York

first: Scott

middle: H

last: Olejniczak

address: 417 E68th St

institute: Memorial Sloan Kettering Cancer Center

description: miRNA expression data from DGCR8 siRNA #3-transfected HeLa cells.

hyb_protocol: Biotin-labeled microRNAs were hybridized according to the manufacturer's recommendations.

scan_protocol: An Affymetrix GCS3000 laser scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix miRNA QCTool was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: biotin

source_name: HeLa cells, DGCR8 siRNA-3

label_protocol: 2ug of total RNA was labeled using the microRNA FlashTag Biotin HSR kit following the manufacturer's instructions.

growth_protocol: HeLa cells were grown in DMEM containing 10% FCS.

extract_protocol: Total RNA was isolated using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: HeLa cells were transfected with siRNAs using RNAiMAX (Invitrogen) according to the manufacturer's recommendations.

tag: cell line

value: HeLa

tag: cell type

value: cervical adenocarcinoma

tag: treatment

value: DGCR8 siRNA-3


title: A375 16R6-4 9B–10 nM GSK212 + 1 uM GSK436-2

city: Collegeville

first: Vivian

last: Zhang

state: PA

address: 1250 S. Collegeville Rd

department: Oncology Translational Research

institute: GlaxoSmithKline

description: 10 nM GSK212 + 1 uM GSK436-2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip  Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data was normalized in Microarray Suite version 5.0 (MAS 5.0) with the trimmed mean target intensity of each array arbitrarily set to 150. Further analysis was conducted with Array Studio V5.0

source_name: A375 Melanoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA

growth_protocol: Grow A375 and A375 16R6-4 cells in RPMI1640 supplemented with 10% Fetal Bovin Serum

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

treatment_protocol: Cells were treated with compounds for 24hrs at 37°C

value: GSK436 resistant clone

value: 10 nM GSK212 + 1 uM GSK436


title: L111_555 environment 2

description: array batch 20202

source_name: CxC Line 111, embryo at physiological maturity


title: HeLa DGCR8 siRNA #1, miRNA

description: miRNA expression data from DGCR8 siRNA #1-transfected HeLa cells.

source_name: HeLa cells, DGCR8 siRNA-1

value: DGCR8 siRNA-1


title: HeLa DGCR8 siRNA #2, miRNA

description: miRNA expression data from DGCR8 siRNA #2-transfected HeLa cells.

source_name: HeLa cells, DGCR8 siRNA-2

value: DGCR8 siRNA-2


title: A375 16R6-4 8B–10 nM GSK212 + 0.1 uM GSK436-2

description: 10 nM GSK212 + 0.1 uM GSK436-2


title: L114_555 environment 2

description: array batch 20202

source_name: CxC Line 114, embryo at physiological maturity

value: Cayuga x Caledonia, DH


title: L109_555 environment 2

description: array batch 20556

source_name: CxC Line 109, embryo at physiological maturity

value: Ketola, Cornell University, Ithaca, NY

source_name: Pre-anthesis spike bulk


title: yFR1003_3E10_FCP1wt_P-Ser2_Rep2

description: Biological replicate 2 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: A375 16R6-4 9A–10 nM GSK212 + 1 uM GSK436-1

description: 10 nM GSK212 + 1 uM GSK436-1


title: A375 16R6-4 2B–10 nM GSK212-2

description: 10 nM GSK212-2

value: 10 nM GSK212


title: A375 16R6-4 9C–10 nM GSK212 + 1 uM GSK436-3

description: 10 nM GSK212 + 1 uM GSK436-3


title: A375 16R6-4 5C–1 uM GSK436-3

description: 1 uM GSK436-3

value: 1 uM GSK436


title: L102_555 environment 2

description: array batch 20574

source_name: CxC Line 102, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: A375 16R6-4 5B–1 uM GSK436-2

description: 1 uM GSK436-2


title: HeLa Ars2 siRNA #3, miRNA

description: miRNA expression data from Ars2 siRNA #3-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-3

value: Ars2 siRNA-3


title: yFR1003_3E10_FCP1wt_P-Ser2_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser2 occupancy, using 3E10 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells


title: A375 16R6-4 2C–10 nM GSK212-3

description: 10 nM GSK212-3


title: A375 16R6-4 8C–10 nM GSK212 + 0.1 uM GSK436-3

description: 10 nM GSK212 + 0.1 uM GSK436-3


title: A375 1C–DMSO-3

value: Parental cells

value: DMSO


title: A375 16R6-4 3A–30 nM GSK212-1

description: 30 nM GSK212-1

value: 30 nM GSK212


title: A375 16R6-4 3B–30 nM GSK212-2

description: 30 nM GSK212-2


title: L104_555 environment 2

description: array batch 20202

source_name: CxC Line 104, embryo at physiological maturity


title: A375 16R6-4 2A–10 nM GSK212-1

description: 10 nM GSK212-1


title: A375 16R6-4 8A–10 nM GSK212 + 0.1 uM GSK436-1

description: 10 nM GSK212 + 0.1 uM GSK436-1


title: HeLa Ars2 siRNA #1, miRNA

description: miRNA expression data from Ars2 siRNA #1-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-1

value: HeLa

value: Ars2 siRNA-1


title: A375 16R6-4 5A–1 uM GSK436-1

description: 1 uM GSK436-1


title: HeLa Ars2 siRNA #2, miRNA

description: miRNA expression data from Ars2 siRNA #2-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-2

value: cervical adenocarcinoma

value: Ars2 siRNA-2


title: yFR1003_3E8_FCP1wt_P-Ser5_Rep1

description: Biological replicate 1 of 2. RNAPII CTD P-Ser5 occupancy, using 3E8 antibody, measured by the IP/input ratio in yFR1003 (wt for yFR1004 fcp1-1) cells

value: Helmholtz Zentrum


title: L98_555 environment 2

description: array batch 20556

source_name: CxC Line 98, embryo at physiological maturity


title: A375 16R6-4 4C–0.1 uM GSK436-3

description: 0.1 uM GSK436-3

value: GSK436 resistant clone


title: Normal reactive lymph node #6

city: Seoul

first: Sang Yun

last: Ha

state: Seoul

address: Ilwondong Kangnamgu

department: Pathology

country: South Korea

institute: Samsung Medical center

description:
Raw data file: normal_EBVPTCL6.txt
Normal reactive lymph node #6
Agilent 4x44K(01485)
Normal-6

hyb_protocol: After labeling, cRNA was purified with Qiagen’s RNeasy Mini-spin columns (QIAGEN, Germantown, MD) and quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer for cyanine 3 dye concentration, RNA absorbance ratio (260 nm/280 nm), and cRNA concentration. Cyanine 3-labled linearly amplified cRNA was mixed with 10X blocking agent, nuclease-free water, and 25X fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies), and incubated for 30 min at 60oC to fragment RNA. After adding 2X GEx hybridization buffer Hi-RPM, the amplified fragmented RNA was hybridized on a 4 x 44K or 8 x 60K Whole Human Genome Oligo Microarray Chip (Agilent Technologies) using a SureHyb DNA Microarray Hybridization Chamber in a DNA Microarray Hybridization Oven (Agilent Technologies) at 10 rpm, 65oC for 17 hours.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffers 1 and 2 for 1 min each and then scanned with an Agilent DNA microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies).

data_processing:
Feature Extraction Software v9 (Agilent Technologies) was used to extract and analyze the signals. To validate the amplification process, amplified and unamplified RNAs were labeled, hybridized and compared.
For combined analysis of two different types of microarray kits (Agilent chip 4x44K and 8x60K), we chose common probes from two kits and total 18,565 probes were used for analysis. Normalization (Quantile method in Genespring software) was performed after choosing common probes. The VALUE is defined as normalized signal intensity.

source_name: Normal reactive lymph node #6

label_protocol: 0.1 ug of total RNA was amplified and labeled using Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted using trizol-chloroform extraction.

value: Normal reactive lymph node


title: L96_555 environment 2

description: array batch 20202

source_name: CxC Line 96, embryo at physiological maturity

value: Cayuga x Caledonia, DH


title: A375 9C–10 nM GSK212 + 1 uM GSK436-3

description: 10 nM GSK212 + 1 uM GSK436-3

value: 10 nM GSK212 + 1 uM GSK436


title: A375 9B–10 nM GSK212 + 1 uM GSK436-2

description: 10 nM GSK212 + 1 uM GSK436-2


title: A375 16R6-4 4A–0.1 uM GSK436-1

description: 0.1 uM GSK436-1


title: HeLa ctl siRNA, biological replicate 1, miRNA

description: miRNA expression data from control siRNA-transfected HeLa cells, biological replicate #1.

source_name: HeLa cells, control siRNA

value: control siRNA


title: A375 3B–30 nM GSK212-2

description: 30 nM GSK212-2


title: A375 8B–10 nM GSK212 + 0.1 uM GSK436-2

description: 10 nM GSK212 + 0.1 uM GSK436-2


title: HeLa ctl siRNA, biological replicate 2, miRNA

description: miRNA expression data from control siRNA-transfected HeLa cells, biological replicate #2.


title: A375 16R6-4 1B–DMSO-2


title: A375 16R6-4 3C–30 nM GSK212-3

description: 30 nM GSK212-3


title: HeLa ctl siRNA, biological replicate 3, miRNA

description: miRNA expression data from control siRNA-transfected HeLa cells, biological replicate #3.


title: A375 8C–10 nM GSK212 + 0.1 uM GSK436-3

description: 10 nM GSK212 + 0.1 uM GSK436-3


title: Normal reactive lymph node #5

description:
Raw data file: normal_EBVPTCL5.txt
Normal reactive lymph node #5
Agilent 4x44K(01485)
Normal-5

source_name: Normal reactive lymph node #5


title: A375 8A–10 nM GSK212 + 0.1 uM GSK436-1

description: 10 nM GSK212 + 0.1 uM GSK436-1

source_name: A375 Melanoma cell line


title: L95_555 environment 2

description: array batch 20202

source_name: CxC Line 95, embryo at physiological maturity

value: Ketola, Cornell University, Ithaca, NY


title: A375 16R6-4 1A–DMSO-1


title: A375 9A–10 nM GSK212 + 1 uM GSK436-1

description: 10 nM GSK212 + 1 uM GSK436-1


title: L107_555 environment 2

description: array batch 20574

source_name: CxC Line 107, embryo at physiological maturity

value: embryo at physiological maturity


title: L88_555 environment 2

description: array batch 20556

source_name: CxC Line 88, embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L87_555 environment 2

description: array batch 20574

source_name: CxC Line 87, embryo at physiological maturity


title: L90_555 environment 2

description: array batch 20574

source_name: CxC Line 90, embryo at physiological maturity


title: A375 5B–1 uM GSK436-2

description: 1 uM GSK436-2

value: 1 uM GSK436


title: A375 2A–10 nM GSK212-1

description: 10 nM GSK212-1

value: Parental cells

value: 10 nM GSK212


title: L93_555 environment 2

description: array batch 20202

source_name: CxC Line 93, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: A375 3C–30 nM GSK212-3

description: 30 nM GSK212-3

value: 30 nM GSK212


title: A375 16R6-4 4B–0.1 uM GSK436-2

description: 0.1 uM GSK436-2


title: L86_555 environment 2

description: array batch 20202

source_name: CxC Line 86, embryo at physiological maturity


title: Normal reactive lymph node #4

description:
Raw data file: normal_EBVPTCL4.txt
Normal reactive lymph node #4
Agilent 4x44K(01485)
Normal-4

source_name: Normal reactive lymph node #4


title: A375 4C–0.1 uM GSK436-3

description: 0.1 uM GSK436-3


title: A375 2B–10 nM GSK212-2

description: 10 nM GSK212-2


title: Normal reactive lymph node #2

description:
Raw data file: normal_EBVPTCL2.txt
Normal reactive lymph node #2
Agilent 4x44K(01485)
Normal-2

source_name: Normal reactive lymph node #2


title: A375 5C–1 uM GSK436-3

description: 1 uM GSK436-3


title: A375 2C–10 nM GSK212-3

description: 10 nM GSK212-3


title: L85_555 environment 2

description: array batch 20556

source_name: CxC Line 85, embryo at physiological maturity


title: L92_555 environment 2

description: array batch 20556

source_name: CxC Line 92, embryo at physiological maturity


title: A375 1B–DMSO-2

value: DMSO


title: Normal reactive lymph node #1

description:
Raw data file: normal_EBVPTCL1.txt
Normal reactive lymph node #1
Agilent 4x44K(01485)
Normal-1

source_name: Normal reactive lymph node #1


title: A375 4B–0.1 uM GSK436-2

description: 0.1 uM GSK436-2


title: L82_555 environment 2

description: array batch 20574

source_name: CxC Line 82, embryo at physiological maturity


title: A375 1A–DMSO-1


title: L81_555 environment 2

description: array batch 20574

source_name: CxC Line 81, embryo at physiological maturity


title: EBV positive PTCL-U case#1

description:
Raw data file: EXPRE_EBV_PTCL1.txt
EBV positive PTCL-U case#1
Agilent 4x44K(01485)
Tumor-1

source_name: EBV positive PTCL-U case#1

value: EBV positive PTCL-U


title: L80_555 environment 2

description: array batch 20574

source_name: CxC Line 80, embryo at physiological maturity


title: EBV positive PTCL-U case#2

description:
Raw data file: EXPRE_EBV_PTCL2.txt
EBV positive PTCL-U case#2
Agilent 4x44K(01485)
Tumor-2

source_name: EBV positive PTCL-U case#2


title: VCS2 DHT 24h 1

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street, PMCRT 11-305

department: Medical Biophysics

institute: UNIVERSITY HEALTH NETWORK

hyb_protocol: standard Affymetrix 3' array hybridyzation protocol

scan_protocol: standard Affymetrix confocal laser scanner protocol

data_processing: RMA was used to process the data

source_name: prostate cancer

label_protocol: standard Affymetrix biotin label protocol

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit following manufacturer's instruction

treatment_protocol: Cells were incubated in DMEM supplemented with 5%  charcoal/dextran-treated FBS for 3 days, and then treated with 10nM DHT or Ethanol for 24h

tag: gender

value: male

value: DHT


title: L79_555 environment 2

description: array batch 20574

source_name: CxC Line 79, embryo at physiological maturity


title: UCLA liver non-tolerance 17

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

description: test set

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

scan_protocol: We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used for background subtraction GeneSpring was used for normalization

source_name: pediatric liver, UCLA

label_protocol: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions

extract_protocol: The blood was drawn in the presence of sodium heparin. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).

value: peripheral blood

tag: phenotype

value: liver operational non-tolerance

source_name: human reference total RNA pool

tag: sample type

value: 10 human cell lines


title: VCS2 Veh 1

value: vehicle


title: VCaP DHT 24h 1

value: VCaP


title: L75_555 environment 2

description: array batch 20574

source_name: CxC Line 75, embryo at physiological maturity

value: Cayuga x Caledonia, DH


title: Normal reactive lymph node #3

description:
Raw data file: normal_EBVPTCL3.txt
Normal reactive lymph node #3
Agilent 4x44K(01485)
Normal-3

source_name: Normal reactive lymph node #3

value: Normal reactive lymph node


title: L68_555 environment 2

description: array batch 20202

source_name: CxC Line 68, embryo at physiological maturity

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: UCLA liver non-tolerance 8

description: test set


title: L69_555 environment 2

description: array batch 20202

source_name: CxC Line 69, embryo at physiological maturity

value: Pre-anthesis spike bulk


title: UCLA liver non-tolerance 6

description: test set


title: L66_555 environment 2

description: array batch 20556

source_name: CxC Line 66, embryo at physiological maturity


title: UCLA liver non-tolerance 15

description: test set


title: VCaP Veh 1


title: L65_555 environment 2

description: array batch 20202

source_name: CxC Line 65, embryo at physiological maturity


title: UCLA liver non-tolerance 10

description: test set


title: UCLA liver non-tolerance 5

description: test set


title: UCLA liver tolerance 21

description: test set

value: liver operational tolerance


title: L73_555 environment 2

description: array batch 20202

source_name: CxC Line 73, embryo at physiological maturity


title: L64_555 environment 2

description: array batch 20556

source_name: CxC Line 64, embryo at physiological maturity


title: L63_555 environment 2

description: array batch 20202

source_name: CxC Line 63, embryo at physiological maturity


title: UCLA liver tolerance 12

description: test set


title: UCLA liver tolerance 22

description: test set


title: L54_555 environment 2

description: array batch 20202

source_name: CxC Line 54, embryo at physiological maturity


title: UCLA liver tolerance 20

description: test set


title: v2 aCGH GSY2238

first: Barbara

last: Dunn

department: Genetics

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85717.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: Agilent Feature Extraction

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

label_protocol: not provided

extract_protocol: not provided

tag: test

source_name: 55 ng sonicated genomic DNA of GSY 2238

tag: lab database strain name

tag: type

value: Wine - commercially produced strain

tag: strain


title: L59_555 environment 2

description: array batch 20556

source_name: CxC Line 59, embryo at physiological maturity

tag: population

tag: field location


title: UCLA liver tolerance 9

description: test set

tag: tissue


title: v2 aCGH GSY2214

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85738.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2214

value: SYR


title: L56_555 environment 2

description: array batch 20202

source_name: CxC Line 56, embryo at physiological maturity

tag: year


title: UCLA liver tolerance 4

description: test set

source_name: pediatric liver, UCLA

source_name: human reference total RNA pool


title: L51_555 environment 2

description: array batch 20556

source_name: CxC Line 51, embryo at physiological maturity


title: L50_555 environment 2

description: array batch 20556

source_name: CxC Line 50, embryo at physiological maturity


title: UCLA liver tolerance 3

description: test set


title: UCLA liver tolerance 2

description: test set


title: v2 aCGH GSY2175-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86248.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2175

value: BDX


title: v2 aCGH GSY2213

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85732.gif

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2213


title: v2 aCGH GSY2299 Sklu

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86485.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2299 S. kluyveri

value: GSY2299 S. kluyveri

value: Laboratory


title: v2 aCGH GSY2174

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85716.gif

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2174


title: v2 aCGH GSY219

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86569.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY219

value: Bread


title: UCLA liver tolerance 1

description: test set

value: peripheral blood

value: 10 human cell lines


title: v2 aCGH GSY2228

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85727.gif

source_name: 55 ng sonicated genomic DNA of GSY 2228

value: CSM


title: v2 aCGH GSY2197

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86338.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2197


title: v2 aCGH GSY860

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86577.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY860

value: Wine - native or "wild"


title: v2 aCGH GSY2179

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86345.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2179


title: v2 aCGH GSY2234

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85740.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2234

value: SimiWhite


title: v2 aCGH GSY2192-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86339.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2192-2


title: v2 aCGH GSY2229

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85711.gif

source_name: 55 ng sonicated genomic DNA of GSY 2229


title: Stanford liver non-tolerance 14

description: training set

source_name: pediatric liver, Stanford

value: liver operational non-tolerance

source_name: human reference total RNA pool


title: L47_555 environment 2

description: array batch 20574

source_name: CxC Line 47, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: v2 aCGH GSY2235

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85729.gif

source_name: 55 ng sonicated genomic DNA of GSY 2235

value: Wine - commercially produced strain


title: v2 aCGH GSY2182-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86482.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2182-2


title: L48_555 environment 2

description: array batch 20556

source_name: CxC Line 48, embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L46_555 environment 2

description: array batch 20556

source_name: CxC Line 46, embryo at physiological maturity


title: L45_555 environment 2

description: array batch 20574

source_name: CxC Line 45, embryo at physiological maturity


title: v2 aCGH GSY2199

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86249.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2199


title: v2 aCGH GSY2196

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85725.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2196


title: Stanford liver non-tolerance 10

description: training set


title: Stanford liver non-tolerance 11

description: training set


title: v2 aCGH GSY2201

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85720.gif

source_name: 55 ng sonicated genomic DNA of GSY 2201


title: L44_555 environment 2

description: array batch 20202

source_name: CxC Line 44, embryo at physiological maturity


title: v2 aCGH GSY1216 Sbay

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86484.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY1216 S. bayanus

value: GSY1216 S. bayanus


title: v2 slide000 self ctrl

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85769.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool


title: v2 aCGH GSY2217

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85773.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2217


title: v2 aCGH GSY2236

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85733.gif

source_name: 55 ng sonicated genomic DNA of GSY 2236

value: F-champ


title: Stanford liver non-tolerance 8

description: training set

source_name: pediatric liver, Stanford

source_name: human reference total RNA pool


title: v2 slide002 self ctrl

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85715.gif


title: L43_555 environment 2

description: array batch 20574

source_name: CxC Line 43, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: Stanford liver non-tolerance 7

description: training set


title: v2 aCGH GSY2184

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85713.gif

source_name: 55 ng sonicated genomic DNA of GSY 2184


title: v2 aCGH GSY2237

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85741.gif

source_name: 55 ng sonicated genomic DNA of GSY 2237

value: LalvinAC


title: L37_555 environment 2

description: array batch 20202

source_name: CxC Line 37, embryo at physiological maturity


title: v2 S288c only

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85765.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY S288c

value: GSY S288c

value: Laboratory


title: L36_555 environment 2

description: array batch 20556

source_name: CxC Line 36, embryo at physiological maturity


title: Stanford liver non-tolerance 5

description: training set

value: peripheral blood

value: 10 human cell lines


title: v2 aCGH GSY2176

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85718.gif

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2176

value: BGY


title: v2 slide001 self ctrl

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85772.gif


title: L35_555 environment 2

description: array batch 20202

source_name: CxC Line 35, embryo at physiological maturity


title: Stanford liver non-tolerance 4

description: training set


title: L34_555 environment 2

description: array batch 20202

source_name: CxC Line 34, embryo at physiological maturity


title: v2 aCGH GSY2188-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86344.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2188-2


title: Stanford liver non-tolerance 3

description: training set


title: L32_555 environment 2

description: array batch 20556

source_name: CxC Line 32, embryo at physiological maturity


title: v2 aCGH Scer only ref pool

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85768.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool


title: L29_555 environment 2

description: array batch 20202

source_name: CxC Line 29, embryo at physiological maturity


title: Stanford liver non-tolerance 9

description: training set

source_name: pediatric liver, Stanford


title: Stanford liver non-tolerance 2

description: training set

source_name: human reference total RNA pool


title: v2 aCGH GSY2220

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85746.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2220


title: v2 aCGH GSY707

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86563.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY707

value: Ale - commercially produced strain


title: L24_555 environment 2

description: array batch 20574

source_name: CxC Line 24, embryo at physiological maturity

value: Cayuga x Caledonia, DH

source_name: Pre-anthesis spike bulk


title: v2 aCGH GSY704

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86568.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY704


title: Stanford liver non-tolerance 12

description: training set

value: liver operational non-tolerance


title: Stanford liver non-tolerance 13

description: training set


title: L21_555 environment 2

description: array batch 20202

source_name: CxC Line 21, embryo at physiological maturity

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity


title: v2 aCGH GSY2193-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86343.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2193-2

value: Wine - commercially produced strain


title: L20_555 environment 2

description: array batch 20556

source_name: CxC Line 20, embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L19_555 environment 2

description: array batch 20202

source_name: CxC Line 19, embryo at physiological maturity


title: Stanford liver tolerance 2

description: training set

value: liver operational tolerance


title: v2 aCGH GSY269

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86574.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY269

value: "Wine - native or ""wild"" strain"


title: v2 aCGH GSY2172

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85726.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2172


title: v2 aCGH GSY2298 Scas

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86480.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2298 S. castellii

value: GSY2298 S. castellii


title: v2 aCGH GSY2225

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85744.gif

source_name: 55 ng sonicated genomic DNA of GSY 2225

value: Will-Sel


title: v2 aCGH GSY2175-3

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86254.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2175

value: BDX


title: v2 aCGH GSY2210

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85745.gif

source_name: 55 ng sonicated genomic DNA of GSY 2210


title: Stanford liver non-tolerance 1

description: training set

source_name: pediatric liver, Stanford

value: peripheral blood

source_name: human reference total RNA pool


title: v2 aCGH GSY2204

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85724.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2204

value: Primeur


title: v2 aCGH GSY239

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86564.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY239

value: Fuel Ethanol


title: Stanford liver tolerance 5

description: training set

value: 10 human cell lines


title: L18_555 environment 2

description: array batch 20556

source_name: CxC Line 18, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: L12_555 environment 2

description: array batch 20574

source_name: CxC Line 12, embryo at physiological maturity


title: Stanford liver tolerance 4

description: training set


title: v2 aCGH GSY2171

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85722.gif

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2171


title: L11_555 environment 2

description: array batch 20574

source_name: CxC Line 11, embryo at physiological maturity


title: v2 aCGH GSY2211

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85735.gif

source_name: 55 ng sonicated genomic DNA of GSY 2211


title: Stanford liver tolerance 6

description: training set


title: Stanford liver tolerance 8

description: training set


title: Stanford liver tolerance 7

description: training set


title: v2 aCGH GSY2170-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86334.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY 2170-2


title: L9_555 environment 2

description: array batch 20574

source_name: CxC Line 9, embryo at physiological maturity


title: v2 aCGH GSY2221

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85728.gif

source_name: 55 ng sonicated genomic DNA of GSY 2221


title: v2 aCGH GSY2230

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85736.gif

source_name: 55 ng sonicated genomic DNA of GSY 2230


title: Stanford liver tolerance 3

description: training set


title: v2 aCGH GSY2186

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85770.gif

source_name: 55 ng sonicated genomic DNA of GSY 2186

value: EPII


title: v2 aCGH GSY2176-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86252.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2176

value: BGY


title: v2 aCGH GSY2205

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85723.gif

source_name: 55 ng sonicated genomic DNA of GSY 2205


title: v2 aCGH GSY328

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86562.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY328


title: Healthy Control 6

description: training set

source_name: controls

value: control

source_name: human reference total RNA pool


title: L1_555 environment 2

description: array batch 20556

source_name: CxC Line 1, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Ketola, Cornell University, Ithaca, NY

value: embryo at physiological maturity


title: Healthy Control 5

description: training set


title: v2 aCGH GSY166 Skud

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85766.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 166

value: GSY 166

value: Laboratory


title: v2 aCGH GSY2178-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86347.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2178-2

value: Wine - commercially produced strain


title: L3_555 environment 2

description: array batch 20202

source_name: CxC Line 3, embryo at physiological maturity

source_name: Pre-anthesis spike bulk

value: Pre-anthesis spike bulk


title: v2 aCGH GSY2198

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86348.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2198


title: Healthy Control 4

description: training set


title: v2 aCGH GSY2177-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86247.gif

source_name: 165 ng sonicated genomic DNA from GSY2177


title: L10_555 environment 2

description: array batch 20556

source_name: CxC Line 10, embryo at physiological maturity


title: L173_647

description: Array Batch: 20050

hyb_protocol: Perhybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

label_protocol: 10ug of total RNA were reverse transcribed using anchored poly-T primers and a 2:3 amino-allyl dUTP:dTTP ratio. RNA was hydrolyzed with NaOH and the amino-allyl cDNA was cleaned with a Qiagen Qiaquick column and phosphate buffers. Alexa 555 or 647 (Invitrogen #A32755) dyes were coupled according to accompanying protocols. Labeled cDNA  was cleaned using a Qiaquick column and incorporation was measured by spectrophotometry.

growth_protocol: Plants were grown in the  field (Helfer 2004) near Ithaca, NY. Spike samples were harvested at physiological maturity as described in Munkvold et al. 2009. TAG. 119. Samples were stored at -20C for two months while embryo samples were harvested. Primary and secondary position seeds were selected from five spikes and embryos (~100) were isolated by hand, frozen in liquid nitrogen, and stored at -80C.

value: Helfer, Cornell University, Ithaca, NY

source_name: CxC Line 173, embryo at physiological maturity


title: L167_647

description: Array Batch: 20038

source_name: CxC Line 167, embryo at physiological maturity


title: Healthy Control 3

description: training set


title: Healthy Control 2

description: training set


title: Healthy Control 1

description: training set


title: v2 aCGH GSY2212

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85714.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2212


title: L158_647

description: Array Batch: 20050

source_name: CxC Line 158, embryo at physiological maturity


title: v2 aCGH GSY2289

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86576.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY2289

value: Fuel Ethanol - commercially produced strain

value: EtOHRedFuel


title: v2 aCGH GSY2223

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85739.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2223


title: v2 aCGH GSY168 Smik

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86479.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY168 S. mikatae

value: GSY168 S. mikatae


title: L169_647

description: Array Batch: 20050

source_name: CxC Line 169, embryo at physiological maturity


title: v2 aCGH GSY2222

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85776.gif

source_name: 55 ng sonicated genomic DNA of GSY 2222


title: L157_647

description: Array Batch: 20038

source_name: CxC Line 157, embryo at physiological maturity


title: v2 aCGH OtherSppCompletePool control

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86478.gif

source_name: 975 ng sonicated complete other spp DNA pool


title: L153_647

description: Array Batch: 20038

source_name: Pre-anthesis spike bulk

source_name: CxC Line 153, embryo at physiological maturity


title: 252665510805-1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing (10.7.3.1); LOG2(signal) with interslide quantile normalization performed with R (bioconductor).

organism: Mus musculus

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski

value: CD43 positive lymphomas

tag: genotype/variation

value: c-myc-3'RR IgA

tag: amount in (µg)

tag: rin number


title: v2 aCGH GSY2183-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86337.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2183-2


title: L152_647

description: Array Batch: 20050

source_name: CxC Line 152, embryo at physiological maturity


title: 252665510805-2


title: v2 aCGH GSY2189-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86333.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY GSY2189-2

value: GSY GSY2189-2


title: v2 aCGH GSY2226

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85743.gif

source_name: 55 ng sonicated genomic DNA of GSY 2226


title: v2 aCGH GSY2207

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86335.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2207


title: v2 aCGH GSY2194-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86481.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2194-2


title: v2 aCGH GSY275

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86565.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY275

value: "Wine - native or ""wild"" strain"


title: v2 aCGH GSY2202

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85775.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2202

value: PC


title: v2 aCGH GSY2102

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86566.gif

source_name: 165 ng HaeIII-cut genomic DNA of GSY2102

value: Bread - commercially produced strain


title: v2 slide012 self cntrl

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86342.gif


title: L166_647

description: Array Batch: 20050

value: Cayuga x Caledonia, DH

source_name: CxC Line 166, embryo at physiological maturity

value: embryo at physiological maturity


title: L151_647

description: Array Batch: 20050

source_name: CxC Line 151, embryo at physiological maturity


title: 252665510805-4


title: L145_647

description: Array Batch: 20050

source_name: CxC Line 145, embryo at physiological maturity


title: v2 aCGH GSY2208

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85748.gif

source_name: 55 ng sonicated genomic DNA of GSY 2208


title: 252665510804-1

value: CD43 negative lymphomas


title: L142_647

description: Array Batch: 20038

source_name: Pre-anthesis spike bulk

source_name: CxC Line 142, embryo at physiological maturity


title: BM_Rep2

first: Lei

last: Ding

institute: Columbia University Medical Center

description: Gene expresion data from whole bone marrow cells isolated from young adult wild type mice

hyb_protocol: 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

scan_protocol: The chips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Whole bone marrow cells from wild-type mice.

label_protocol: cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN).

growth_protocol: 5,000 bone marrow Scf-GFP+ cells from Scf-GFP knockin heterozygous mice were double-sorted into Trizol (Invitroen). 5,000 whole bone marrow cells from wild-type mice were sorted into Trizol (Invitrogen).

extract_protocol: Total RNA was extracted using Trizol with 25 µg/ml linear acrylamide (Ambion). The extracted RNA (10 µl volume) was treated with 2 Units of RNase-free recombinant DNase I (Ambion) for 15 min at 25C, followed by 15 min at 37C to remove any contaminating genomic DNA. The DNA-free RNA samples were purified using the RNA Clean & Concentrator™-5 from Zymo Research and eluted in 10 µl of nuclease-free water. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer's instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN).

tag: strain background

tag: genotype

value: wild type

tag: age

value: young adult

value: Whole bone marrow cells


title: L147_647

description: Array Batch: 20038

value: Helfer, Cornell University, Ithaca, NY

value: Pre-anthesis spike bulk

source_name: CxC Line 147, embryo at physiological maturity


title: L138_647

description: Array Batch: 20038

source_name: CxC Line 138, embryo at physiological maturity


title: BM_Rep3

tag: cell type


title: 252665510805-3


title: v2 aCGH GSY2215

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85737.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2215

value: Wine - commercially produced strain


title: 252665510804-2


title: v2 aCGH GSY2200

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86341.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2200


title: v2 aCGH GSY1124 Spar

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85767.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng in-complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 1124

value: Laboratory


title: Scf-GFP_Rep3

description: Gene expresion data from Scf-GFP+ cells isolated from young adult Scf-GFP knockin heterozygous mice

source_name: Bone marrow Scf-GFP+ cells from Scf-GFP knockin mice.

value: Scf-GFP knockin heterozygous mice.

value: Bone marrow Scf-GFP+ cells


title: 252665510804-3

value: c-myc-3'RR IgA


title: v2 aCGH GSY2206

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86250.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng sonicated genomic DNA from GSY2206


title: v2 aCGH GSY2185-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86336.gif

source_name: 165 ng HaeIII-cut genomic DNA from GSY2185-2


title: BM_Rep1


title: v2 aCGH GSY2180

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85721.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2180


title: L131_647

description: Array Batch: 20050

source_name: CxC Line 131, embryo at physiological maturity


title: L130_647

description: Array Batch: 20038

source_name: CxC Line 130, embryo at physiological maturity


title: L137_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 137, embryo at physiological maturity


title: L135_647

description: Array Batch: 20038

source_name: CxC Line 135, embryo at physiological maturity


title: Scf-GFP_Rep2


title: 252665510707-3

value: Anaplastic lymphoma


title: L129_647

description: Array Batch: 20050

source_name: CxC Line 129, embryo at physiological maturity


title: Scf-GFP_Rep1


title: L126_647

description: Array Batch: 20050

source_name: CxC Line 126, embryo at physiological maturity


title: 252665510804-4


title: Universal

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14062

hyb_protocol: Affymetrix standard protocol The arrays were washed and stained using the Affymetrix Fluidics Station 450.  Fluidics Protocol FS450-0007. Amount labeled  target hybridization to array: Approximately 2.5 µg into the hybridization cocktail, approximately 2.1 µg were hybridized to the array.

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix GeneChip Command Console (AGCC) Software version 3.1.1.

data_processing:
Analysis method: Partek
GCOS Tgt value: 500

label: Biotin

source_name: P0 mouse (from Steve Potter)

label_protocol: Nugen Encore Biotin Module (4200)

treatment_protocol:
Pooled sample: Yes
Pool size: 8 whole embryos (4 male and 4 female)
Dissection method:
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.

tag: gene reported

value: wild-type

value: Both

tag: sex

value: both

tag: developmental stage

tag: theiler stage


title: 252665510707-1


title: 13Sox9M2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14060

source_name: Gonad, Embryo 13.5 dpc male Sertoli cells

treatment_protocol:
Pooled sample: Yes
Pool size: one or more litters
Dissection method: Dissected out the gonad, trypsinized and FACS sorted.  Capel protocol: FACS Protocol
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.

value: Tg(Sox9-ECFP)2Capl / PMID:17940049

value: Progeny of CD-1 crossed to C57BL/6J

value: male


title: 13Sox9M3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14061


title: 252665510706-1

value: Burkitt lymphoma


title: 13SryF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14058

source_name: Gonad, Embryo 13.5 dpc female supporting cell precursors (follicle cells/pre-Granulosa cells)

tag: Sex

value: female


title: 13Sox9M1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14059

tag: strain


title: 252665510707-4


title: 252665510707-2


title: v2 aCGH GSY2216

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85730.gif

tag: test

source_name: 55 ng sonicated genomic DNA of GSY 2216

tag: lab database strain name

tag: type


title: 252665510706-2


title: L123_647

description: Array Batch: 20050

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Helfer, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: Pre-anthesis spike bulk

source_name: CxC Line 123, embryo at physiological maturity

value: embryo at physiological maturity


title: 252665510706-4

tag: genotype/variation

tag: amount in (µg)

tag: rin number


title: L124_647

description: Array Batch: 20050

source_name: CxC Line 124, embryo at physiological maturity


title: L119_647

description: Array Batch: 20050

source_name: CxC Line 119, embryo at physiological maturity


title: v2 aCGH GSY2218

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85774.gif

value: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2218

value: Wine - commercially produced strain


title: v2 aCGH GSY2190-2

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86483.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA from GSY2190-2


title: 13SmaaM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14054

source_name: Gonad, Embryo 13.5 dpc male interstitial cells

value: Tg(Acta2-EYFP)Jll / PMID:18769072

value: FVB


title: 13SmaaM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14055


title: 13SryF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14056


title: 13SryF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14057


title: L111_647

description: Array Batch: 20038

source_name: CxC Line 111, embryo at physiological maturity


title: 13SmaaM1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14053


title: L116_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 116, embryo at physiological maturity


title: L115_647

description: Array Batch: 20050

source_name: CxC Line 115, embryo at physiological maturity


title: v2 aCGH GSY2203

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85771.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2203

value: PDM


title: 13SmaaF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14052

source_name: Gonad, Embryo 13.5 dpc female vascular associated mesenchymal stromal cells


title: 13SmaaF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14051


title: v2 aCGH GSY2209

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85731.gif

source_name: 55 ng sonicated genomic DNA of GSY 2209


title: 252665510706-3

tag: cell type


title: L110_647

description: Array Batch: 20050

source_name: CxC Line 110, embryo at physiological maturity


title: v2 aCGH GSY2224

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85742.gif

source_name: 55 ng sonicated genomic DNA of GSY 2224


title: v2 aCGH GSY2227

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85749.gif

source_name: 55 ng sonicated genomic DNA of GSY 2227


title: L105_647

description: Array Batch: 20050

source_name: CxC Line 105, embryo at physiological maturity


title: L106_647

description: Array Batch: 20050

source_name: CxC Line 106, embryo at physiological maturity


title: L107_647

description: Array Batch: 20050

source_name: CxC Line 107, embryo at physiological maturity


title: v2 aCGH GSY2191

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85777.gif

source_name: 55 ng sonicated genomic DNA of GSY 2191


title: 13OctM3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14049

source_name: Gonad, Embryo 13.5 dpc male germ cells

tag: gene reported


title: L125_647

description: Array Batch: 20050

source_name: CxC Line 125, embryo at physiological maturity


title: 13SmaaF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14050

tag: sex


title: L102_647

description: Array Batch: 20050

source_name: CxC Line 102, embryo at physiological maturity


title: v2 aCGH GSY2169

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85712.gif

source_name: 55 ng HaeIII-cut genomic DNA of GSY 2169


title: DE cells, biological replicate 1

city: Philadelphia

first: Paul

last: Gadue

address: 3501 Civic center Blvd, CTRB 5012

institute: Children's Hospital of Philadelphia

description: Gene expression data from human embryonic stem cell-derived definitive endoderm cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA normalization method through Affymetrix expression console.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells were growing in human ES media containg 20% knockout serum and 10 ng/ml bFGF. DE cells were cultured in high activin media and EP cells were in high BMP media.

extract_protocol: Total RNA was extracted and purified with Qiangen Rneasy Micro Kit  according to the manufacturer's instructions.

treatment_protocol: ES cells were sorted with SSEA3 and SSEA4. DE and EPC cells were sorted with CXCR4 and CD117.


title: v2 aCGH GSY267

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86570.gif

source_name: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY267

value: "Wine - native or ""wild"" strain"


title: v2 aCGH GSY855

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86567.gif

value: 165 ng sonicated complete S. cerevisiae DNA pool plus 975 ng complete other spp DNA pool

source_name: 165 ng HaeIII-cut genomic DNA of GSY855

value: Wine - native or "wild"


title: DE cells, biological replicate 3

source_name: human embryonic stem cell-derived definitive endoderm cells


title: 13OctF3

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14046

source_name: Gonad, Embryo 13.5 dpc female meiotic germ cells

tag: developmental stage


title: v2 aCGH GSY2231

description:
Simple annotation: Wine, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-11/85719.gif

source_name: 55 ng sonicated complete S. cerevisiae DNA pool plus 325 ng complete other spp DNA pool

source_name: 55 ng sonicated genomic DNA of GSY 2231


title: 13OctF2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14045

tag: theiler stage


title: L100_647

description: Array Batch: 20050

source_name: Pre-anthesis spike bulk

source_name: CxC Line 100, embryo at physiological maturity


title: L101_647

description: Array Batch: 20050

source_name: CxC Line 101, embryo at physiological maturity


title: DE cells, biological replicate 2

value: human embryonic stem cell-derived definitive endoderm cells


title: L97_647

description: Array Batch: 20050

source_name: CxC Line 97, embryo at physiological maturity


title: 13OctM2

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14048

value: Progeny of CD-1 crossed to C57BL/6J

tag: Sex


title: 13OctF1

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:14044

tag: strain


title: EP cells, biological replicate 1

description: Gene expression data from human endodermal progenitor cells

source_name: human endodermal progenitor cell

value: human endodermal progenitor cell