title: epithelium_tumor_sample_060_rep2

description:
part of dyeswap pair
060E_rep2


title: EXP-520: P9407_C08

status: Public on May 12 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: infant ALL case

value: Pheresis

tag: gender

value: Male

tag: age

tag: race

value: WHITE

tag: ethnicity

value: Not Hispanic or Latino

tag: gene

tag: pg

tag: karyotype

tag: treatment

tag: cohort

value: COHORT 3


title: EWS#1

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

scan_protocol: scanning of HuEx1.0 microarrays was carried out following the manufacturer’s instructions

data_processing:
Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software (Partek, St. Louis, MO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: tumor biopsy

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: Qiagen miRNA easy

tag: tissue

value: local tumor, pre-chemo


title: 11-0047

city: Stanford

first: Timothy

middle: E

last: Sweeney

state: California

address: 1265 Welch Road, MSOB

department: Biomedical Informatics

institute: Stanford University

description: gcRMA normalized

hyb_protocol: See original GSEs for clinical and technical information.

data_processing: All samples here were downloaded as .CEL files and re-normalized together using gcRMA using R package 'affy'.

source_name: Whole Blood

value: whole blood

tag: disease

value: SIRS


title: 07-0005

description: gcRMA normalized

scan_protocol: See original GSEs for clinical and technical information.


title: 11-0051

description: gcRMA normalized

label_protocol: See original GSEs for clinical and technical information.


title: EWS#4


title: 11-0049

description: gcRMA normalized

extract_protocol: See original GSEs for clinical and technical information.


title: 11-0045

description: gcRMA normalized

treatment_protocol: See original GSEs for clinical and technical information.


title: 11-0059

description: gcRMA normalized


title: 11-0041

description: gcRMA normalized


title: 04-0007

description: gcRMA normalized


title: 10-0027

description: gcRMA normalized


title: 10-0022

description: gcRMA normalized


title: 14-0001

description: gcRMA normalized


title: 11-0016

description: gcRMA normalized


title: 01-0046

description: gcRMA normalized


title: 11-0060

description: gcRMA normalized


title: 10-0023

description: gcRMA normalized


title: 15-0010

description: gcRMA normalized


title: epithelium_tumor_sample_022_rep1

city: Montreal

first: Morag

last: Park

state: Quebec

address: 1160 Ave. des Pins O.

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

description:
part of dyeswap pair
022E_rep2

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (500 ng) were subjected to fragmentation followed by 18 h hybridization, washing, and scanning (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90030). Samples were hybridized against Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA). Duplicate hybridizations were performed for all samples using reverse-dye labeling

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3) from Agilent with the default parameters

data_processing: Outlier features on arrays were flagged by the software. Arrays were required to have an average raw signal intensity of 800 in each channel, and a signal to noise ratio above 16 per channel. MvA plots were examined for signs of hybridization or labeling problems. Replicate arrays were required to have a concordance above 0.90. This level was established empirically using sets of known good replicate arrays in our database.  Data preprocessing and normalization were automated using the BIAS system. Raw feature intensities were background corrected using the RMA background correction algorithm. Resulting expression estimates were converted to log2-ratios. Within array normalization was performed using spatial and intensity-dependent loess. Median absolute deviation scale normalization was used to normalize between arrays.

source_name: microdissected breast tumor epithelium

label_protocol: Sample RNA was subjected to two rounds of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and labeled with Cy3 and Cy5 dyes according to the manufacturer’s procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA). Reference RNA  RNA was subjected to one round of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and then processed as per the procedure described above.

growth_protocol: Breast tumor tissue samples were obtained at primary surgery from patients providing written informed consent.

extract_protocol: Total RNA was extracted from each population of microdissected cells using a GITC (guanidinium isothiocyanate) extraction protocol. Briefly, LCM caps were incubated for 5 minutes (room temperature) in 200 μl GITC extraction buffer (4 M GITC, 25 mM sodium citrate pH 7.0, 0.1 M β-mercaptoethanol, 0.5% N-lauroylsarcosine) supplemented with 1.6 μl β-mercaptoethanol. Subsequently, 20 μl of 2 M NaOAc, pH 4.0, 220 μl of water-saturated phenol and 60 μl of chloroform-isoamyl alcohol (23:1) were added to the extraction buffer. Following 15 minutes incubation on ice and centrifugation (12,000 rpm, 15 minutes) the aqueous phase was removed and RNA was precipitated with 2 μl glycogen (GenHunter, Nashville, Tennessee, USA) and 200 μl isopropanol. Samples were placed at -80°C for 30 minutes and centrifuged at 4°C (12,000 rpm) for 30 minutes to pellet RNA. Pellets were washed with 70% ethanol, air dried and subjected to DNAseI treatment (Roche, Basel, Switzerland). DNAseI treatment was performed in the presence of an RNase inhibitor (Invitrogen, Carlsbad, California, USA). Subsequently, samples were re-extracted as described above and re-suspended in 10 μl of diethylpyrocarbonate-treated water. RNA was quantified using a RiboGreen assay (Molecular Probes, Carlsbad, California, USA).

treatment_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours following tissue staining.

tag: tissue type

value: epithelium

tag: sample id

source_name: Reference

tag: sample type


title: 11-0040

description: gcRMA normalized


title: 01-0063

description: gcRMA normalized


title: 11-0046

description: gcRMA normalized


title: 01-0037

description: gcRMA normalized


title: yFR1298_sic1D_Htz1vsH2B_SPIKE-IN_Rep2

type: genomic

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

institute: IRCM

description: Biological replicate 2 of 2. H2A.Z occupancy in sic1D mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

hyb_protocol: Hybridization: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA). Put at 95°C for 5 minutes. Put at 42°C for 10 min (Keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42°C 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 slides in Wash buffer #2 preheated at 31°C for 5 minutes at room temperature 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. 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). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) 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. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 5 ml of this 1M solution in 1L Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180. Set the scan as follow: Pixel Size = 2µm; Speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto.  Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing: Correction = Foreground-Background; Normalisation = limma loess (subgrid)

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 ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 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 -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice. Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C.    Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.    Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. 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 ddH2O).  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, wash the columns only once, and elute twice with 30uL 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. 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, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness.      Phosphate Wash Buffer (100mL):  0.5mL 1M KPO4, pH 8.5  15.25mL ddH2O  84.25mL 95% EtOH  Solution will be cloudy upon mixing.    Phosphate Elution Buffer (10mL):  0.04mL 1M KPO4, pH 8.5  9.96mL ddH2O    1M KPO4, pH 8.5 (10mL):  9.5mL 1M K2HPO4  0.5mL 1M KH2PO4    1M Sodium Carbonate Buffer, pH 9.0 (100mL):  10.8g Na2CO3  80mL ddH2O  pH to 9.0 with concentrated HCl  Adjust volume to 100mL with ddH2O  DILUTE 1:10 WHEN USING!  Solution will change composition over time. Use only if less than a month old.

growth_protocol: YEP-Glu_37C-80min. YEP+2%Glucose is inoculated at OD600 of 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reachs OD600=0.6. Cell cultures are switched to 37°C and allowed to grow for additional 80 min. Culture is poured/divided in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80°C

extract_protocol:
Cells are thawed on ice, and resuspended in 700uL lysis buffer with protease inhibitors (solution composition detailed at the end). 500uL of acid-washed glass beads (Sigma) are added, and the cells are lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates is centrifuge for 5 min at 4'C max speed and supernatant used immediately for ChIP (or saved and frozen at -80'C). Lysis buffer: 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.
The following amounts of antibody per immunoprecipitation were used: HA (Santa Cruz, F7, 3µg), Myc (9E11, a gift from A. Verreault, 5μg), H2A.Z (Active Motif, 39647, 2µL), H2B (Abcam, ab1790, 5µg), H4 (a gift from A. Verreault, 2µl), Spt16 (a gift from T. Formosa, 1μL), FRB (mTor, human FRB domain from Enzo Life Sciences, ALX-215-065, 5μL), rabbit IgG (Cell Signaling Technology, 2729, 5µg). All comercial antibodies have been validated for ChIP (see manufacturers’ web sites). The Myc, H4 and Spt16 antibodies have been described before (Drouin et al., 2010; Duina et al., 2007).

treatment_protocol: 80min at 37°C

tag: strain

tag: genotype/variation

value: MATa leu2∆0 ura3∆0 his3∆0 lys2∂ sic1::KanMX4

tag: spike dna

value: 300 ng of sonicated bacteriophage phiX174 DNA (Thermo Scientific) was added to the extract prior to immunoprecipitation

tag: antibody

value: Htz1 (Active Motif_39647)

value: H2B (Abcam ab1790)


title: yFR1297_spt16-197_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197 mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa leu2∆0 ura3∆0 lys2∆0 spt16-197


title: yFR1298_sic1D_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in sic1D mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: 04-0008

description: gcRMA normalized


title: yFR1297_spt16-197_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197 mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1296_WT_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa leu2∆0 ura3∆0 his3∆0 lys2∂


title: Heart A

source_name: Affymetrix tissue data

value: normal tissue


title: yFR1296_WT_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR974_spt6ts_80min37C_Htz1vsInput_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: 06-0002

description: gcRMA normalized


title: 10-0007

description: gcRMA normalized


title: yFR971_WT_80min37C_Htz1vsInput_20140328_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).

value: MAT*, leu2D1


title: 10-0015

description: gcRMA normalized


title: yFR1295_spt16-197_sic1D_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197_sic1D double-mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa leu2∆0 ura3∆0 lys2∆0 spt16-197 sic1::KanMX4


title: yFR973_spt16ts_80min37C_Htz1vsInput_20140328_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: 10-0006

description: gcRMA normalized


title: yFR972_WT_80min37C_Htz1vsInput_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).

value: MATa, leu2D1, lys2-128d, trp1D63, ura3-52


title: 10-0010

description: gcRMA normalized


title: yFR974_spt6ts_80min37C_Htz1vsInput_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: yFR1295_spt16-197_sic1D_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197_sic1D double-mutant cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR974_spt6ts_Htz1vsMock_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.

value: rabbit IgG


title: EWS#20


title: yFR972_WT_Htz1vsMock_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: yFR972_WT_Htz1vsMock_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: 10-0002

description: gcRMA normalized


title: yFR973_spt16ts_80min37C_Htz1vsInput_20140328_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: yFR971_WT_Htz1vsMock_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: 11-0031

description: gcRMA normalized


title: 05-0002

description: gcRMA normalized


title: yFR973_spt16ts_Htz1vsMock_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation.H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: yFR973_spt16ts_Htz1vsMock_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation.H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: yFR974_spt6ts_Htz1vsMock_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: yFR1480_Spt6-AA_T90minRapa_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy inSpt6-AA cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

growth_protocol: YEP-Glu_kinetics_Rapamycin-1µg/ml. 400mL of YEP+2%Glucose media is inoculated at OD600=0.1 from an overnight preculture in the appropriate media and allowed to grow until it reaches OD600=0.6. An aliquot of 50mL (T=0) is then poured in  a Falcon tube containing 1.4mL of 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min.  The remaining cell culture (350mL) is treated with 1 microg/ml of Rapamycin and allowed to grow. Aliquots of 50mL of cell culture are taken and crosslinked as mentioned above after different time points of treatment with rapamycin. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80°C.

value: MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1 SPT6-FRB::kanMX6


title: yFR971_WT_Htz1vsMock_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against a Mock ChIP sample (Cy3-labeled), using rabbit IgG.


title: yFR971_WT_80min37C_Htz1vsInput_20140328_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: yFR972_WT_80min37C_Htz1vsInput_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against Input DNA (Cy3-labeled).


title: yFR1480_Spt6-AA_T90minRapa_Htz1vsH2B_SPIKE-IN_20140326_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy inSpt6-AA cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1480_Spt6-AA_T0_Htz1vsH2B_SPIKE-IN_20140312_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in Spt6-AA cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1480_Spt6-AA_T0_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in Spt6-AA cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1478_Spt16-AA_T90minRapa_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy inSpt16-AA cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1 SPT16-FRB::kanMX6


title: SPT16-WT_80min37C_SWR1-HAvsUntagged_yFR1574vs971_20140404_rep2

description: Biological replicate 2 of 2. Swr1 occupancy in SPT16 cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MAT*, leu2D1, SWR1::6xHA(KanMX4)

value: F7 (anti-HA)


title: yFR1478_Spt16-AA_T0_Htz1vsH2B_SPIKE-IN_20140312_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in Spt16-AA cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1478_Spt16-AA_T0_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in Spt16-AA cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: spt16-197_80min37C_SWR1-HAvsUntagged_yFR1575vs973_20140404_rep2

description: Biological replicate 2 of 2. Swr1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MAT*, leu2D1, spt16-197, SWR1::6xHA(KanMX4)


title: yFR1512_spt6-1004_80min37C_H4vsInput_20140704_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GAL1pr-flo8-HIS3, FLAG-spt6-1004

value: RYH4 (A.Verreault)


title: yFR1478_Spt16-AA_T90minRapa_Htz1vsH2B_SPIKE-IN_20140326_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy inSpt16-AA cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: 300 ng of sonicated bacteriophage phiX174 DNA (Thermo Scientific) was added to the extract prior to immunoprecipitation


title: yFR1511_WT_80min37C_H4vsInput_20140704_Rep2

description: Biological replicate 2 of 2. H4 occupancy in WT cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GAL1pr-flo8-HIS3


title: 11-0036

description: gcRMA normalized

value: whole blood

value: SIRS


title: yFR1513_spt16-197_80min37C_H4vsInput_20140405_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GAL1pr-flo8-HIS3, spt16-197


title: spt16-197_80min37C_SWR1-HAvsUntagged_yFR1575vs973_20140404_rep1

description: Biological replicate 1 of 2. Swr1 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).


title: yFR1321_WT_T90_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATα ade2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1

value: Htz1 (Active Motif_39647)

value: H2B (Abcam ab1790)


title: SPT6-WT_80min37C_SWR1-HAvsUntagged_yFR1601vs972_20140404_rep2

description: Biological replicate 2 of 2. Swr1 occupancy in SPT6 cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MATa, leu2D1, lys2-128d, trp1D63, ura3-52, SWR1::6xHA(KanMX4)


title: SPT16-WT_80min37C_SWR1-HAvsUntagged_yFR1574vs971_20140404_rep1

description: Biological replicate 1 of 2. Swr1 occupancy in SPT16 cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MAT*, leu2D1


title: yFR1764_spt6-1004-htz1D_80min37C_H4vsInput_20140704_Rep2

description: Biological replicate 2 of 2. H4 occupancy in spt6-1004/htz1D double-mutant cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GALpr-flo8-HIS3, FLAG-spt6-1004, htz1::klURA3


title: yFR1764_spt6-1004-htz1D_80min37C_H4vsInput_20140704_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt6-1004/htz1D double-mutant cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: yFR1546_spt16-197-htz1D_80min37C_H4vsInput_20140704_Rep2

description: Biological replicate 2 of 2. H4 occupancy in spt16-197/htz1D double-mutant cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GALpr-flo8-HIS3, spt16-197, htz1::klURA3


title: SPT6-WT_80min37C_SWR1-HAvsUntagged_yFR1601vs972_20140404_rep1

description: Biological replicate 1 of 2. Swr1 occupancy in SPT6 cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MATa, leu2D1, lys2-128d, trp1D63, ura3-52


title: yFR1512_spt6-1004_80min37C_H4vsInput_20140405_Rep2

description: Biological replicate 2 of 2. H4 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: yFR1321_WT_T90_Htz1vsH2B_SPIKE-IN_20140404_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT cells treated 90 minutes with 1µg/ml rapamycin (T=90). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1512_spt6-1004_80min37C_H4vsInput_20140704_Rep2


title: yFR1321_WT_T0_Htz1vsH2B_SPIKE-IN_20140312_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR1546_spt16-197-htz1D_80min37C_H4vsInput_20140704_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt16-197/htz1D double-mutant cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: yFR1513_spt16-197_80min37C_H4vsInput_20140405_Rep2

description: Biological replicate 2 of 2. H4 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: yFR1511_WT_80min37C_H4vsInput_20140704_Rep1

description: Biological replicate 1 of 2. H4 occupancy in WT cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: spt6-1004_80min37C_SWR1-HAvsUntagged_yFR1603vs974_20140404_rep1

description: Biological replicate 1 of 2. Swr1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).

value: MAT*, his3D200, leu2D1, lys2-128d, ura3-52, spt6-1004-FLAG, SWR1::6xHA(KanMX4)

value: F7 (anti-HA)


title: yFR1321_WT_T0_Htz1vsH2B_SPIKE-IN_20140404_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT cells before treatment to rapamycin (T=0). SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: spt6-1004_80min37C_SWR1-HAvsUntagged_yFR1603vs974_20140404_rep2

description: Biological replicate 2 of 2. Swr1 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. Swr1 ChIP sample (Cy5-labeled) was performed from a HA-tagged Swr1 strain using the anti-HA antibody and hybridized against a similar ChIP sample performed from an isogenic strain where the SWR1 gene is not tagged (Cy3-labeled).


title: yFR1513_spt16-197_80min37C_H4vsInput_20140704_Rep2


title: yFR1511_WT_80min37C_H4vsInput_20140405_Rep1


title: yFR987_Htz1vsH2B_rtt106delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in rtt106D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

growth_protocol: Standard_YEPD_50mL. 50mL of YEP+2% Glucose is inoculated at OD600= 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reach OD600= 0.6-1.0. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

value: MATa his3Δ 1 leu2Δ 0 met15Δ 0 ura3Δ 0 rtt106::KanMx


title: yFR1512_spt6-1004_80min37C_H4vsInput_20140405_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GAL1pr-flo8-HIS3, FLAG-spt6-1004

value: RYH4 (A.Verreault)


title: yFR1513_spt16-197_80min37C_H4vsInput_20140704_Rep1

description: Biological replicate 1 of 2. H4 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).


title: yFR971_WT_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: 300 ng of sonicated bacteriophage phiX174 DNA (Thermo Scientific) was added to the extract prior to immunoprecipitation


title: yFR987_Htz1vsH2B_rtt106delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in rtt106D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR972_WT_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR982_Htz1vsH2B_chz1delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in chz1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa his3Δ 1 leu2Δ 0 met15Δ 0 ura3Δ 0 chz1::KanMx


title: yFR1511_WT_80min37C_H4vsInput_20140405_Rep2

description: Biological replicate 2 of 2. H4 occupancy in WT cells treated 80 minutes at 37°C. H4 ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H4 and hybridized against Input DNA (Cy3-labeled).

value: MATa, arg4-12, his3D200, lys2-128, ura3-52, kanMX-GAL1pr-flo8-HIS3


title: yFR973_spt16ts_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Effector memory T cell, biological rep4

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

country: Japan

institute: Keio University

description: Gene expression data from Tem cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45℃ on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetryx GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Effector memory T cell

label_protocol: Biotinylated cDNA were prepared using NuGEN Encore Biotin Module from 5ug of amplified cDNA.

growth_protocol: Human healthy volunteer

extract_protocol: Total RNA from sorted cells were extracted using miRCURY RNA Isolation Kit (Exiqon),  purified by RNeasy MinElute Cleanup Kit (Qiagen), and amplified with Ovation Pico WTA System V2 (NuGEN Technologies).

treatment_protocol: Peripheral mononuclear cells were isolated by density gradient centrifugation, and CD4+ T cell were purified from them using CD4+ T Cell Isolation Kit. Cells were sorted by FACS Aria Ⅲ. Tn, Tscm, Tcm, and Tem cells were defined as CD45RO-CCR7+CD95-, CD45RO-CCR7+CD95+, CD45RO+CCR7+, and CD45RO-CCR7-, respectively.

tag: gender

value: female

tag: age

tag: cell population

value: Effector memory T cell


title: yFR972_WT_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: Htz1 (Active Motif_39647)


title: yFR981_Htz1vsH2B_nap1delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in nap1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa his3Δ 1 leu2Δ 0 met15Δ 0 ura3Δ 0 nap1::KanMx

value: H2B (Abcam ab1790)


title: yFR973_spt16ts_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Effector memory T cell, biological rep6

description: Gene expression data from Tem cells


title: yFR982_Htz1vsH2B_chz1delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in chz1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR971_WT_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MAT*, leu2D1


title: Effector memory T cell, biological rep2

description: Gene expression data from Tem cells


title: yFR986_Htz1vsH2B_hir1delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in hir1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa his3Δ 1 leu2Δ 0 met15Δ 0 ura3Δ 0 hir1::KanMx


title: yFR974_spt6ts_Htz1vsH2B_SPIKE-IN_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Effector memory T cell, biological rep5

description: Gene expression data from Tem cells


title: yFR986_Htz1vsH2B_hir1delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in hir1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR974_spt6ts_Htz1vsH2B_SPIKE-IN_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. SPIKE DNA was added to the extract prior to immunoprecipitation. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Effector memory T cell, biological rep1

description: Gene expression data from Tem cells


title: yFR981_Htz1vsH2B_nap1delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in nap1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR974_Htz1vsH2B_spt6ts_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Effector memory T cell, biological rep3

description: Gene expression data from Tem cells


title: Central memory T cell, biological rep5

description: Gene expression data from Tcm cells

source_name: Central memory T cell

value: Central memory T cell


title: yFR974_Htz1vsH2B_spt6ts_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Central memory T cell, biological rep6

description: Gene expression data from Tcm cells


title: Central memory T cell, biological rep3

description: Gene expression data from Tcm cells


title: Stem cell memory T cell, biological rep5

description: Gene expression data from Tscm cells

source_name: Stem cell memory T cell

value: Stem cell memory T cell


title: Stem cell memory T cell, biological rep4

description: Gene expression data from Tscm cells


title: yFR973_Htz1vsH2B_spt16ts_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Naive T cell, biological rep6

description: Gene expression data from Tn cells

source_name: Naive T cell

value: Naive T cell


title: Central memory T cell, biological rep1

description: Gene expression data from Tcm cells


title: yFR745_Htz1vsH2B_asf1delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in asf1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR745_Htz1vsH2B_asf1delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in asf1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Naive T cell, biological rep5

description: Gene expression data from Tn cells


title: Central memory T cell, biological rep4

description: Gene expression data from Tcm cells


title: Stem cell memory T cell, biological rep1

description: Gene expression data from Tscm cells


title: yFR741_Htz1vsH2B_cac1delta_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in cac1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Stem cell memory T cell, biological rep3

description: Gene expression data from Tscm cells


title: Stem cell memory T cell, biological rep6

description: Gene expression data from Tscm cells


title: Stem cell memory T cell, biological rep2

description: Gene expression data from Tscm cells


title: yFR972_Htz1vsH2B_WT_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa, leu2D1, lys2-128d, trp1D63, ura3-52


title: yFR117_Htz1vsH2B_WT_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (S288C) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR116_Htz1vsH2B_WT_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR741_Htz1vsH2B_cac1delta_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in cac1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Central memory T cell, biological rep2

description: Gene expression data from Tcm cells


title: yFR972_Htz1vsH2B_WT_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT6 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR973_Htz1vsH2B_spt16ts_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR117_Htz1vsH2B_WT_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (S288C) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: yFR116_Htz1vsH2B_WT_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Survivor+VHSV Rep4

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

description: Zebrafish that have survived two challenges with VHSV and were challenged for a third time two days before the sampling

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

organism: Danio rerio

source_name: head kidney and spleen of 3 zebrafish VHSV infected survivors rep 4

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Adult wild type zebrafish were obtained from a local pet shop and maintained in a 30 l aquarium provided with biological filter, 23ºC, pH 8.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: We defined VHSV survivors as fishes which have survived two consecutive challenges.For each viral infection experiment, groups of zebrafish were moved to 2 l aquaria provided with biological filters. Zebrafish were infected by bath immersion with a final dose of 106 pfu/ml  for 90 minutes.   Mock-infected zebrafish were incubated with cell culture medium.

tag: disease state

value: Wild type

tag: developmental stage

value: Adult


title: Control Rep1

description: Zebrafish control

source_name: head kidney and spleen of 3 zebrafish WT control rep 1

value: control non-infected


title: Control Rep2

description: Zebrafish control

source_name: head kidney and spleen of 3 zebrafish WT control rep 2


title: Survivor control Rep4

description: Zebrafish that have survived two challenges with VHSV and were mock-infected two days before sampling

source_name: head kidney and spleen of 3 zebrafish control survivors rep 4


title: Braak α-synuclein 3-4 BR34_6SN

city: Amsterdam

first: Anke

middle: Akke

last: Dijkstra

address: Van der Boechorststraat 7

department: Anatomy and neurosciences

country: Netherlands

institute: Vu Medical center

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U 133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: The data were analyzed with Partek, using GC-RMA normalization.

source_name: Substantia nigra

label_protocol: One-Cycle cDNA synthesis kit and the GeneChip ® IVT labeling kit

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

treatment_protocol: dissected based on surrounding structures

tag: braak stage

tag: rin

value: substantia nigra

value: Parkinson's disease


title: yFR971_Htz1vsH2B_WT_Rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Survivor+VHSV Rep1

source_name: head kidney and spleen of 3 zebrafish VHSV infected survivors rep 1

value: survived two challenges with VHSV and were challenged for a third time two days before the sampling


title: Control Rep3

description: Zebrafish control

source_name: head kidney and spleen of 3 zebrafish WT control rep 3


title: Control Rep4

description: Zebrafish control

source_name: head kidney and spleen of 3 zebrafish WT control rep 4


title: Survivor+VHSV Rep2

source_name: head kidney and spleen of 3 zebrafish VHSV infected survivors rep 2


title: Braak α-synuclein stages 5-6  BR56_1SN


title: Braak α-synuclein 3-4 BR34_5SN


title: Survivor+VHSV Rep3

source_name: head kidney and spleen of 3 zebrafish VHSV infected survivors rep 3


title: Braak α-synuclein stages 5-6  BR56_4SN


title: Braak α-synuclein stages 5-6  BR56_5SN


title: Braak α-synuclein stages 5-6  BR56_8SN


title: yFR971_Htz1vsH2B_WT_Rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in SPT16 cells treated 80 minutes at 37°C. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Braak α-synuclein stages 5-6  BR56_7SN


title: Braak α-synuclein stages 5-6  BR56_2SN


title: Naive T cell, biological rep4

description: Gene expression data from Tn cells

value: female


title: Braak α-synuclein 3-4 BR34_7SN


title: Braak α-synuclein 3-4 BR34_3SN


title: Braak α-synuclein stages 5-6  BR56_3SN


title: Braak α-synuclein stages 5-6  BR56_6SN


title: Infectado por bacterias Rep3

description: Zebrafish naturally infected by Aeromonas hydrophila and Vibrio fluvialis

source_name: head kidney and spleen of 3 zebrafish bacteria infected rep 3


title: Infectado por bacterias Rep1

source_name: head kidney and spleen of 3 zebrafish bacteria infected rep 1

value: infected by Aeromonas hydrophila and Vibrio fluvialis


title: Infectado por bacterias Rep4

source_name: head kidney and spleen of 3 zebrafish bacteria infected rep 4


title: Naive T cell, biological rep2

description: Gene expression data from Tn cells


title: Survivor control Rep3

source_name: head kidney and spleen of 3 zebrafish control survivors rep 3

value: survived two challenges with VHSV and were mock-infected two days before sampling


title: Survivor control Rep2

source_name: head kidney and spleen of 3 zebrafish control survivors rep 2


title: Naive T cell, biological rep1

description: Gene expression data from Tn cells


title: Braak α-synuclein 3-4 BR34_4SN


title: Naive T cell, biological rep3

description: Gene expression data from Tn cells


title: Infectado por bacterias Rep2

source_name: head kidney and spleen of 3 zebrafish bacteria infected rep 2


title: SM036 12.4 10^5 MA15 B6NJ d7 RNA

city: Richland

first: Katrina

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

organism: Mus musculus

source_name: WT, Lung tissue, MA15-inoculated, 7 days, bioreplicate 4

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

value: WT

value: 10 weeks

tag: infection

value: MA15 virus

tag: time

value: 7 dpi

value: lung


title: Survivor control Rep1

source_name: head kidney and spleen of 3 zebrafish control survivors rep 1


title: DKO1 brain

city: Setagaya

first: Seiichi

last: Kanzaki

institute: NCCHD

description: SD (Hexb -/-) mice; C57BL/6X129/Sv background were bred in a closed colony over 30 generations; therefore, the mice were inbred for both C57BL/6- and 129/Sv-divered genes.   -Synuclein knockout mice (ASyn -/- mice) with the C57BL/6 background were bred with Hexb -/- mice to obtain double-heterozygous mice (Hexb +/- ASyn +/-). To minimize variations due to differences in their genetic backgrounds, all genotypes used in this study were derived from these cross-breedings and the sibling pairs were used as comparisons.

hyb_protocol: Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 C for 5 minutes and immediately chill on ice for 30 minutes. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 24 h at 37 C. Transfer the bioarray to the 0.75× TNT, and incubate at 46 C for 1 h.

scan_protocol: The array was scanned with GenePix® 4000B (Molecular Devices, Inc). Settings; wavelength:635 nm, PMT voltage:600 V, laser power:100%.

data_processing: The data was analysed with CodeLink™ Expression Analysis v5.0 (Applied Microarrays, Inc)

source_name: whole brain

label_protocol: Biotin-labelled cRNA target is prepared by a linear amplification method. The poly(A)+ RNA subpopulation is primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5′ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA.

extract_protocol: Total RNA of each brains were extracted with trizol reagent and purified with qiagen RNeasy mini column.

tag: tissue

value: whole brain

tag: genotype

value: hexb-/- ASyn-/-

value: 14 weeks-old


title: Braak α-synuclein stage 1-2 BR12_5SN

value: incidental Lewy body disease


title: DKO2 brain


title: Braak α-synuclein 3-4 BR34_1SN


title: Braak α-synuclein 3-4 BR34_2SN


title: SD1 brain

value: hexb-/- ASyn+/+


title: SM036 11.2 Mock B6NJ d7 RNA

source_name: WT, Lung tissue, mock-inoculated, 7 days, bioreplicate 2

value: mockulum


title: SM036 12.3 10^5 MA15 B6NJ d7 RNA

source_name: WT, Lung tissue, MA15-inoculated, 7 days, bioreplicate 3


title: SM036 12.2 10^5 MA15 B6NJ d7 RNA

source_name: WT, Lung tissue, MA15-inoculated, 7 days, bioreplicate 2


title: SM036 12.1 10^5 MA15 B6NJ d7 RNA

source_name: WT, Lung tissue, MA15-inoculated, 7 days, bioreplicate 1


title: SM036 11.3 Mock B6NJ d7 RNA

source_name: WT, Lung tissue, mock-inoculated, 7 days, bioreplicate 3


title: Braak α-synuclein stage 1-2 BR12_4SN

source_name: Substantia nigra

value: substantia nigra


title: SD2 brain


title: SM036 11.4 Mock B6NJ d7 RNA

source_name: WT, Lung tissue, mock-inoculated, 7 days, bioreplicate 4


title: WT2 brain

value: hexb+/+ ASyn+/+


title: Braak α-synuclein stage 1-2 BR12_2SN


title: SM036 10.5 10^5 MA15 TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 7 days, bioreplicate 5


title: SM036 10.4 10^5 MA15 TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 7 days, bioreplicate 4


title: Braak α-synuclein stage 1-2 BR12_3SN


title: WT1 brain


title: Braak α-synuclein stage 1-2 BR12_1SN


title: SM036 10.2 10^5 MA15 TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 7 days, bioreplicate 2


title: SM036 10.3 10^5 MA15 TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 7 days, bioreplicate 3


title: SM036 9.2 Mock TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 7 days, bioreplicate 2


title: SM036 11.1 Mock B6NJ d7 RNA

source_name: WT, Lung tissue, mock-inoculated, 7 days, bioreplicate 1


title: ZF-4 cells: MOCK vs NNV infected

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction (FE) Software (version10.5.1.1).

data_processing: Agilent Feature Extraction Software (v10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: NNV infected

label_protocol: Agilent's Quick Amp Labeling Kit denerates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Cells were grown at 28℃ in RPMI 1640 medium (containing RPMI1640 powder, 10% FBS, 2g sodium bicarbonate, 10ml P/S, 10ml sodium pyruvate and 10ml L-G).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: ZF-4 cells were seeded in 12 well plates, and were inoculated with NNV. Cells were incubated with NNV at different 5 MOI for 1 hour. The cells were then wash to remove the unbound viral particles and further cultured at 28℃ then collected at 6 hpi.

tag: cell line

tag: time point

value: 6 hpi

source_name: MOCK


title: Control Braak α- synuclein Stage 0 C8SN

value: CTRL

value: control


title: SM036 10.1 10^5 MA15 TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 7 days, bioreplicate 1

tag: strain


title: SM036 9.3 Mock TLR3 d7 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 7 days, bioreplicate 3

tag: genotype/variation


title: Mouse postnatal day 10 heart wild type [268]

city: Durahm

first: Nancy

last: Andrews

state: NC

address: 450 Research Drive

institute: Duke University

description: Heart P10 268

hyb_protocol: Targets were hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array in the Affymetrix Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G System.

data_processing: partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set. Multi-way ANOVA and fold change were performed to identify target genes that were differentially expressed between WT and Tfr1 heart KO mice.

label: Biotin

source_name: postnatal day 10 heart wild type

label_protocol: The labeling, hybridization, scanning, and data processing was performed by the Duke University Genomics Microarray facility. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: WT and Tfr1 heart conditional KO mice were kept with their mother until P5 or P10.

extract_protocol: Total RNA was extracted from the heart using the Qiagen Rneasy isolation kit according to the manufacturer’s instructions.

treatment_protocol: Heart tissues were collected immediately after decapitaion of the mice and snap frozen in the liquid nitrogen.

tag: strain  background

value: mixed 129 and C57BL6

value: Wild type

value: 10 day old

value: heart


title: Mouse postnatal day 10 heart KO [290]

description: Heart p10 290

source_name: postnatal day 10 heart KO

value: Tfr1 KO


title: SM036 8.5 10^5 MA15 B6NJ d4 RNA

source_name: WT, Lung tissue, MA15-inoculated, 4 days, bioreplicate 5

value: WT

value: 10 weeks

value: MA15 virus

value: 4 dpi

value: lung


title: Mouse postnatal day 10 heart wild type [291]

description: Heart P10 291


title: SM036 8.2 10^5 MA15 B6NJ d4 RNA

source_name: WT, Lung tissue, MA15-inoculated, 4 days, bioreplicate 2


title: SM036 8.1 10^5 MA15 B6NJ d4 RNA

source_name: WT, Lung tissue, MA15-inoculated, 4 days, bioreplicate 1


title: Control Braak α- synuclein Stage 0 C5SN

source_name: Substantia nigra


title: Control Braak α- synuclein Stage 0 C6SN


title: SM036 8.4 10^5 MA15 B6NJ d4 RNA

source_name: WT, Lung tissue, MA15-inoculated, 4 days, bioreplicate 4


title: ZF-4 cells: controle morpholino-NNV infection cells vs. rig1 morpholino-infection cells

source_name: rig1 morpholino-NNV infection

treatment_protocol: ZF-4 cells were seeded in 12 well plates, and transfected with 20uM rig1 MOs. After 24 hours post transfection, cells were inoculated with NNV. Cells were incubated with NNV at different 5 MOI for 1 hour. The cells were then wash to remove the unbound viral particles and further cultured at 28℃ then collected at 6 hpi.

source_name: controle morpholino-NNV infection


title: Mouse postnatal day 10 heart KO [265]

description: Heart P10 265


title: SM036 7.3 Mock B6NJ d4 RNA

source_name: WT, Lung tissue, mock-inoculated, 4 days, bioreplicate 3


title: Control Braak α- synuclein Stage 0 C7SN


title: SM036 7.2 Mock B6NJ d4 RNA

source_name: WT, Lung tissue, mock-inoculated, 4 days, bioreplicate 2


title: Control Braak α- synuclein Stage 0 C4SN


title: SM036 7.5 Mock B6NJ d4 RNA

source_name: WT, Lung tissue, mock-inoculated, 4 days, bioreplicate 5


title: Mouse postnatal day 10 heart wild type [233]

description: Heart P10 233


title: SM036 7.4 Mock B6NJ d4 RNA

source_name: WT, Lung tissue, mock-inoculated, 4 days, bioreplicate 4


title: SM036 6.5 10^5 MA15 B6NJ d2 RNA

source_name: WT, Lung tissue, MA15-inoculated, 2 days, bioreplicate 5

value: 2 dpi


title: Control Braak α- synuclein Stage 0 C2SN


title: Mouse postnatal day 10 heart wild type [230]

description: Heart P10 230


title: Metaphase II_4

city: Valencia

first: Juan

last: Moreno-Moya

address: Catedrático Agustín Escardino

institute: FIVI

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII_4

hyb_protocol: After H2O resuspended, samples were mixed with another Spike, mixed with blocking agent and Hi-RPM hybridization buffer and heated at 100C for 5' and cooled at 4ºC. Then samples were loaded onto gaskets slides and microarrays slides were put on them. Finally Samples were hybridized for 20h at 55C.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel

data_processing: Median intensity value of each spot data was normalized and log2 transformed using R software and libraries from bioconductor database. The intensity values were logarithmically and quartile normalized using R software and the Bioconductor libraries ‘limma’ and ‘tkrplot’. Next, replicated probes were further merged by mean using GEPAS.

source_name: Metaphase II_follicular fluid

label_protocol: 100ng of total RNA were mixed with spike and treated with phosphatase for 30' at 37º then cooled at 4C. Next DMSO was added and heated at 100ºC for 7.5' then cooled at 4ºC. Next mixed with Cy3-pCp and T4 RNA Ligase for 2 hours at 16C and cooled at 4ºC. Samples were dried in a vacuum for 3h at 45C. Then H2O added.

extract_protocol: To ensure that miRNA fraction will be recovered we performed RNA extraction using the miRNeasy Kit (Qiagen, Valencia, CA, USA). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the proportion of miRNAs was evaluated using the Small RNA LabChip BioAnalyzer 2100,  (Agilent Technologies Inc, DE, USA)

treatment_protocol:
Ovarian stimulation and egg retrieval: A control ovarian hyperstimulation (COH) protocol with human recombinant FSH (Gonal-F, Merck Serono S.A., Madrid, Spain) and hMG-HP (Menopur, Ferring S.A., Madrid, Spain) was initiated on menstrual cycle day 2 or 3 at a variable dose depending of age, body mass index (BMI) and antral follicular count (AFC). Pituitary suppression was achieved by daily s.c. administration of 0.25 mg of cetrorelix acetate (Cetrotide, Merck Serono, S.A., Madrid, Spain) when at least one follicle exceeded a mean diameter of 14 mm or estradiol was >400pg/mL. Ovulation was triggered by s.c administration of 6500U of hCG (Ovitrelle®, Merk-Serono, S.A., Madrid, Spain). Transvaginal oocyte retrieval was performed 36 hours after hMG trigger administration and ICSI was performed in all cases. Embryo quality was recorded according to ASEBIR criteria [27].  Luteal phase was supported by 400 mg/day of vaginal micronized progesterone (Progeffik, Lab. Effik, Madrid, Spain) starting at the day of embryo transfer. Pregnancy was defined as a positive pregnancy test; clinical pregnancy was defined as intrauterine sac visualization in transvaginal ecography.
Collection of follicular fluid and granulosa cells: Follicular fluid (FF) were collected individually, after independent follicular puncture. FF and cumulus oophorus-oocyte complexes (COC) were subsequently separated after oocyte retrieval. Follicular fluid-derived cells were separated from erythrocytes by density gradient centrifugation on equal v/v of Histopaque (Sigma-Aldrich, St. Louis, USA) for 30min at 600g. Following centrifugation, three layers could be distinguished: a top layer containing the follicular fluid, a bottom layer containing erythrocytes and, in the middle, a ring-like layer containing the cells-derived from the follicular fluid. This middle layer was collected, washed by centrifugation for 10 min at 600g and resuspended in 1-ml phosphate-buffered saline (PBS). We use the cell strainer methodology to separate granulose cells, based on the fact that GCs form large cell aggregates in such a way that clusters can be retained by 40-µm pore cell strainers while erythrocytes and other blood contaminants (such as single cells and aggregates of a smaller size) pass through the strainer. Following the cell strainer methodology but with some modifications [PMID 10831550; 19001513; 22454458] the aspirates were first filtered through a 40-µm cell strainer (BD Biosciences) and the clusters of GCs were retained. The strainer was rinsed with 12-ml PBS in order to remove the last traces of blood contaminants and the strainer was then back washed with PBS to collect the ‘hypothetical’ GCs. The acquired suspension was incubated for several minutes and repeatedly aspirated through Pasteur pipettes stretched to different diameters to break up aggregates mechanically. The suspension was then filtered through a 70-µm cell strainer (BD Biosciences) to remove unwanted undispersed material, which was retained in the filter. The cell suspension, collected after filtering the sample, was subsequently washed by centrifugation for 5min at 600g, after which the supernatant was removed and the pellet was resuspended in 1 ml PBS.

tag: oocyte maturation stage

value: metaphase II

value: follicular fluid


title: SM036 7.1 Mock B6NJ d4 RNA

source_name: WT, Lung tissue, mock-inoculated, 4 days, bioreplicate 1

value: mockulum


title: SM036 6.4 10^5 MA15 B6NJ d2 RNA

source_name: WT, Lung tissue, MA15-inoculated, 2 days, bioreplicate 4


title: SM036 6.3 10^5 MA15 B6NJ d2 RNA

source_name: WT, Lung tissue, MA15-inoculated, 2 days, bioreplicate 3


title: Control Braak α- synuclein Stage 0 C1SN

value: substantia nigra


title: SM036 6.2 10^5 MA15 B6NJ d2 RNA

source_name: WT, Lung tissue, MA15-inoculated, 2 days, bioreplicate 2


title: Control Braak α- synuclein Stage 0 C3SN

value: CTRL


title: SM036 5.5 Mock  B6NJ d2 RNA

source_name: WT, Lung tissue, mock-inoculated, 2 days, bioreplicate 5


title: Mouse postnatal day 10 heart KO [229]

description: Heart P10 229

source_name: postnatal day 10 heart KO


title: SM036 6.1 10^5 MA15 B6NJ d2 RNA

source_name: WT, Lung tissue, MA15-inoculated, 2 days, bioreplicate 1


title: Mouse postnatal day 5 heart KO [629]

description: Heart P5 629

source_name: postnatal day 5 heart KO

value: 5 day old


title: SM036 5.3 Mock  B6NJ d2 RNA

source_name: WT, Lung tissue, mock-inoculated, 2 days, bioreplicate 3


title: SM036 5.4 Mock  B6NJ d2 RNA

source_name: WT, Lung tissue, mock-inoculated, 2 days, bioreplicate 4


title: Metaphase II_3

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII_3


title: SM036 5.2 Mock  B6NJ d2 RNA

source_name: WT, Lung tissue, mock-inoculated, 2 days, bioreplicate 2


title: Mouse postnatal day 5 heart KO [567]

description: Heart P5 567

value: mixed 129 and C57BL6


title: Metaphase II_2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII_2


title: Mouse postnatal day 5 heart KO [625]

description: Heart P5 625


title: Germinal Vesicle 4

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
GV4

source_name: Germinal Vesicle_follicular fluid

value: germinal vesicle


title: Mouse postnatal day 5 heart KO [564]

description: Heart P5 564


title: Metaphase II_1

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII_1


title: SM036 4.2 10^5 MA15 TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 4 days, bioreplicate 2


title: Germinal Vesicle 2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
GV2


title: Germinal Vesicle 3

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
GV3


title: Mouse postnatal day 5 heart wild type [600]

description: Heart P5 600

source_name: postnatal day 5 heart wild type

value: Wild type


title: Mouse postnatal day 10 heart KO [228]

description: Heart P10 228

value: 10 day old

value: heart


title: Mouse postnatal day 5 heart wild type [628]

description: Heart P5 628


title: SM036 5.1 Mock  B6NJ d2 RNA

source_name: WT, Lung tissue, mock-inoculated, 2 days, bioreplicate 1

value: WT


title: SM036 4.4 10^5 MA15 TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 4 days, bioreplicate 4

value: 10 weeks


title: SM036 4.3 10^5 MA15 TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 4 days, bioreplicate 3

value: MA15 virus


title: SM036 3.4 Mock TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 4 days, bioreplicate 4

value: 4 dpi


title: SM036 3.3 Mock TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 4 days, bioreplicate 3

value: lung


title: SM036 2.5 10^5 MA15 TLR3  d2 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 2 days, bioreplicate 5

value: 2 dpi


title: Mouse postnatal day 5 heart wild type [568]

description: Heart P5 568


title: SM036 4.1 10^5 MA15 TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 4 days, bioreplicate 1


title: Mouse postnatal day 5 heart wild type [589]

description: Heart P5 589


title: Metaphase II  3

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII3

source_name: Metaphase II_follicular fluid

value: metaphase II


title: SM036 3.1 Mock TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 4 days, bioreplicate 1


title: SM036 2.2 10^5 MA15 TLR3 d2 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 2 days, bioreplicate 2


title: Metaphase II  2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII2

value: follicular fluid


title: Germinal Vesicle 1

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
GV1


title: SM036 3.2 Mock TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 4 days, bioreplicate 2

value: mockulum


title: SM036 2.3 10^5 MA15 TLR3  d2 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 2 days, bioreplicate 3


title: SM036 2.4 10^5 MA15 TLR3  d2 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 2 days, bioreplicate 4


title: Metaphase I  3

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MI3

source_name: Metaphase I_follicular fluid

value: metaphase I


title: SM036 1.4 Mock TLR3  d2 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 2 days, bioreplicate 4


title: SM036 2.1 10^5 MA15 TLR3  d2 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 2 days, bioreplicate 1


title: Metaphase II  1

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MII1


title: Metaphase I  1

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MI1


title: SM036 1.1 Mock TLR3 d2 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 2 days, bioreplicate 1


title: SM036 1.3 Mock TLR3 d2 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 2 days, bioreplicate 3


title: Metaphase I  2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
MI2


title: SM036 1.2 Mock TLR3 d2 RNA

source_name: TLR3-/-, Lung tissue, mock-inoculated, 2 days, bioreplicate 2


title: LI_macrophage_IL10p_rep02

city: LA JOLLA

first: Jason

last: Greenbaum

state: CA

address: 9420 Athena Circle

department: Bioinformatics Core Facility

institute: LIAI

description: Mus musculus, large instestinal macrophages, IL10+

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's instructions

scan_protocol: Wash, Stain and Scan protocol using GeneChip Hybridization Wash and Stain Kit according to manufacturer's instructions

data_processing: Data were normalized with the 'rma' function of the Bioconductor package, along with several GEO (GSM616132, GSM616136, GSM616140, GSM868296, GSM868297, GSM868298) and ArrayExpress (E-MEXP-3216: 04-M2WT, 05-M2WT, 06-M2WT) datasets.RMA normalized signals for all data sets are available in the file "Complete_data_set.txt" located on the series level.

label_protocol: Affymetrix GeneChip IVT Express Kit according to the manufactuer's instructions

extract_protocol: RNA was isolated using QIAGEN Rneasy mini kit according to the manufacturer's instructions and amplified using NuGen Ovation amplificationsystem V2

tag: il10 status

value: positive


title: LI_macrophage_IL10m_rep02

description: Mus musculus, large instestinal macrophages, IL10-

value: negative


title: LI_macrophage_IL10m_rep01

data_processing: Data were normalized with the 'rma' function of the Bioconductor package, along with several GEO (GSM616132, GSM616136, GSM616140, GSM868296, GSM868297, GSM868298) and ArrayExpress (E-MEXP-3216: 04-M2WT, 05-M2WT, 06-M2WT) datasets. RMA normalized signals for all data sets are available in the file "Complete_data_set.txt" located on the series level.

source_name: Mus musculus, large instestinal macrophages, IL10-


title: LI_macrophage_IL10p_rep01

source_name: Mus musculus, large instestinal macrophages, IL10+


title: Myc-Htz1vsHA-H2B_swr1DyFR881_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in swr1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.

tag: spike dna

tag: antibody

value: Myc 9E11 (Verreault)

value: F7 (anti-HA)


title: advanced age (AA; >36 years old)  5

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
AA5

source_name: advanced age_follicular fluid

tag: age

value: advanced; >36 yrs


title: Myc-Htz1vsHA-H2B_WTyFR488_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: Myc-Htz1vsHA-H2B_WTyFR488_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: CHL-1020

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Hybridize Hu-6 V3

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Pediatric influenza patient

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions.

tag: disease status

value: FLU

tag: race

value: Black

tag: gender

value: Female

value: Whole Blood


title: advanced age (AA; >36 years old)  3

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
AA3


title: MTB/TICNX_96h_rep4

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: RMA

source_name: MTB/TICNX inguinal mammary gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

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

treatment_protocol: 48h or 96h induction with 2mg/mL doxycycline + 5% sucrose starting at 6 weeks of age

value: FVB

value: 6 weeks

value: Mammary gland

value: MMTV-rtTA; TetO-NICD1

tag: treatment

value: Doxycycline


title: advanced age (AA; >36 years old)  4

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
AA4

value: metaphase II

value: follicular fluid


title: MTB/TICNX_96h_rep2

tag: time


title: Myc-Htz1vsHA-H2B_swr1DyFR881_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in swr1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: MTB/TICNX_96h_rep3

tag: tissue


title: Myc-Htz1vsHA-H2B_isw2DyFR883_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in isw2D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: CHL-765

value: Hispanic


title: advanced age (AA; >36 years old)  2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
AA2


title: young age (YA; <36 years old) 5

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
YA5

source_name: young age_follicular fluid

value: young; <36 yrs


title: CHL-755

value: White

value: Male


title: Myc-Htz1vsHA-H2B_isw2DyFR883_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in isw2D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.

value: Myc 9E11 (Verreault)

value: F7 (anti-HA)


title: CHL-1047

value: FLU


title: MTB/TICNX_96h_rep1

tag: genotype


title: Myc-Htz1vsHA-H2B_isw1DyFR882_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in isw1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: ACC-1049

value: Other


title: young age (YA; <36 years old) 4

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
YA4


title: MTB/TICNX_48h_rep4

value: Female


title: Myc-Htz1vsHA-H2B_isw1DyFR882_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in isw1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: young age (YA; <36 years old) 1

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
YA1


title: TICNX_96h_rep3

source_name: TICNX inguinal mammary gland

value: TetO-NICD1 (control)


title: young age (YA; <36 years old) 2

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
YA2


title: MTB/TICNX_48h_rep3

value: FVB


title: SM036 4.5 10^5 MA15 TLR3 d4 RNA

source_name: TLR3-/-, Lung tissue, MA15-inoculated, 4 days, bioreplicate 5

value: 10 weeks

tag: infection

value: MA15 virus

value: 4 dpi

value: lung


title: CHL-771

value: Black

value: Whole Blood


title: MTB/TICNX_48h_rep2

value: 6 weeks

value: Mammary gland

value: MMTV-rtTA; TetO-NICD1

value: Doxycycline


title: MTB/TICNX_48h_rep1


title: abHtz1vsabH2B_WTyFR934_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (JS91.15-23) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATalpha ura3 leu2 trp1 his3 can1

value: Htz1 (Active Motif_39647)

value: H2B (Abcam ab1790)


title: Myc-Htz1vsHA-H2B_chd1DyFR884_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in chd1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.

value: Myc 9E11 (Verreault)

value: F7 (anti-HA)


title: CHL-1013

value: FLU

value: Hispanic

value: Female


title: CHL-759

value: Male


title: abHtz1vsabH2B_WTyFR934_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (JS91.15-23) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: CHL-801


title: Myc-Htz1vsHA-H2B_chd1DyFR884_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in chd1D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using anti-Myc antibody against Myc-tagged H2A.Z and hybridized against HA-tagged H2B ChIP sample (Cy3-labeled), also performed on the some extract using an anti-HA antibody.


title: TICNX_96h_rep2

value: FVB

value: TetO-NICD1 (control)


title: TICNX_96h_rep1


title: CHL-781

value: White


title: CHL-1012

value: Whole Blood