title: hyhGBF1OE

city: New Delhi

first: Sudip

last: Chattopadhyay

state: Delhi

address: Aruna Asaf Ali Marg, JNU Campus

department: Development Biology

country: India

institute: National Institute of Plant Genome Research

description: GBF1 ChIP-chip study in the hyhGBF1OE line normalised against the wild-type. Represents 3 biological replicates.

hyb_protocol: 7.5 microgram of fragmented and labeled DNA samples were hybridized to Arabidopsis tiling 1.0R arrays (Affymetrix) for 16 hours at 45° C at 60rpm using the Affymetrix hybridization kit and Affymetrix hybridization oven.

scan_protocol: Stained and washed arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix) controlled by GeneChip Operating Software (GCOS).

data_processing:
CEL files were analyzed using MAT software (Model-based Analysis of Tiling array (Johansan et al., 2006). The following parameters were used: Band-Width = 300, MaxGap =300, MinProbe =10 and P value = 0.001.

BAR file: Contains the MATscore for each probe.
BED file: Contains the chromosomal coordinates of all the ChIP regions with MATscore and repeat flag. TAIR9 Genome release.

organism: Arabidopsis thaliana

source_name: Anti-GBF1 ChIPed DNA from hyh GBF1OE line

label_protocol: ChIPed DNA samples were linear amplified, and incorporation of dUTP was performed as described in the Affymetrix Chromatin Immunoprecipitation Assay Protocol. Amplified DNA was fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit following the Affymetrix protocol.

growth_protocol: Wild-type, GBF1OE, hy5GBF1OE, and hyhGBF1OE Arabidopsis seeds were surface sterilized and plated on Murashige and Skoog medium supplemented with 0.8% Bactoagar (Difco) and 1% sucrose. The plates were then cold treated at 4 degrees Celsius for 4 days and transferred to light chambers maintained at 22 degrees Celsius with 20 micromol per meter square per second light intensities.

extract_protocol: 4-day-old 1.5 mg seedlings were harvested and immersed in buffer A [0.4M sucrose, 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 1 mM PMSF, 1% formaldehyde] and kept under vacuum for 10 min. Glycine was added to a final concentration of 0.25 M to stop the cross-linking. Seedlings were rinsed, dried off excess water, and frozen in liquid nitrogen. The tissues were then ground into fine powder and suspended in lysis buffer [50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 1 mM PMSF, 10 mM Sodium butyrate, and 1X Plant Protease Inhibitor (sigma)]. Chromatin was sheared to about 0.5–1.0 kb fragments by sonication. After centrifugation, the supernatant was pre-cleared and the appropriate amount (5-10 microlitre) of anti-GBF1 polyclonal antibody was added to the supernatant and incubated overnight at 4 degrees Celsius. Salmon sperm DNA/Protein A agarose was added the next day and incubated further for 2 h. The agarose beads were then washed with 1 ml of the following buffers for 3 min at 40C: 2 times with lysis buffer, 1 time with LNDET buffer (0.25 M LiCl, 1% NP40, 1% Sodium deoxycholate, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and 2 times with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). The immunocomplexes were collected from beads with 250 microlitre elution buffer (1% SDS, 0.1 M NaHCO3), and incubated at 65 degrees Celsius for 20 min with agitation. 0.3 M NaCl was added to each tube and cross-linking was reversed by incubation at 65 degrees Celsius for 6-8 hrs. Residual protein was degraded by incubation with 20 mg Proteinase K in 10 mM EDTA and 40 mM Tris-HCl pH 8.0 at 45 degrees Celsius for 1 hr, followed by phenol/chloroform/isoamylalcohol extraction and ethanol precipitation. DNA pellets were washed with 70% ethanol and suspended in 30 μl sterile water.

tag: line

value: hyh GBF1OE

tag: genotype/variation

value: hyh mutant with GBF1 over-expressor

value: whole seedling

tag: age

value: 4 days

tag: growth conditions

value: constant white light - 20 micromol/meter square/second

tag: chip antibody

value: polyclonal anti-GBF1

tag: chip antibody vendor

value: Sigma

source_name: Anti-GBF1 ChIPed DNA from wild-type (WS)

tag: ecotype

value: Wassilewskija

value: wild-type (WS)


title: Tumor 6

status: Public on Mar 24 2014

type: RNA

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

country: Spain

institute: Hospital Universitari Germans Trias i Pujol

hyb_protocol: The entire labeled RNA was hybridized on a microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA). Hybridization, washing and scanning was performed according to manufacturer's recommendations.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: CEL files were generated from DAT files using GCOS software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Tumor specimen

label_protocol: 500 ng total RNA was labeled using the FlashTag Biotin HSR Kit (Genisphere) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted with Ambion mirVanaTM miRNA Isolation Kit (CA, USA) according to the manufacturer's instructions.

treatment_protocol: Samples were frozen in liquid Nitrogen after surgical extraction and keeped at -80 until total RNA purification

tag: tissue

value: Vestibular Schwannoma

tag: batch


title: 1h_Ifnb-1_BALBc

city: Midlothian

first: Sobia

last: Raza

address: Easter Bush Campus

department: The University of Edinburgh

country: United Kingdom

institute: The Roslin Institute

description: 1h IFN-beta treated macrophage BALB/c derived replicate 1

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials, according to manufacturers reccomendations

scan_protocol: Hybridisation, washing and scanning of the arrays was performed using the Affymetrix GeneTitan instrument according to the manufacturer’s recommendations.

data_processing:
Data were processed using the Affymetrix Expression Console software version 1.1
probe group file: MoGene-1_1-st-v1.r4.pgf
meta-probeset file: MoGene-1_1-st-v1.r4.mps

label: Biotin

organism: Mus musculus

source_name: bone marrow derived macrophage

label_protocol: Replicate 250 ng samples of total RNA derived from two separate wells per time point were enzymatically fragmented and biotinylated using the Ambion Whole Transcript Expression Kit (Ambion)

growth_protocol: Bone marrow derived macrophages were prepared from femurs of 7-8 week old male BALB/c or C57BL/6 mice

extract_protocol: Total RNA was harvested from the cells using an RNeasy Plus kit (Qiagen)

treatment_protocol: On day 6 cells were harvested, counted, re-suspended in complete medium with 10,000 U/ml CSF1 and seeded into 24-well tissue culture plates at a density of 200,000 cells/well.  24 h later (day 7) cells were treated with any of LPS, interferon-beta or interferon-gamma

tag: background strain

value: BALB/c

tag: treatment type

value: Interferon-beta

tag: treatment dose

value: 10 U/ml

tag: time post treatment

value: 1 hour


title: Tumor 15


title: yFR178vsyFR116_9Myc-Srb10vsUntagged_rep1

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description: Biological replicate 1 of 2. Mediator Srb10-Cdk8-9MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR178) versus the ChIP in untagged strain (yFR116).

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 in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  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_Yeast4x180K  Set the scan as follow:  pixel size = 2Âµm;  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: 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.

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.

treatment_protocol: 9E10 anti-Myc antibody (home-prepared). Anti-mouse Dynabeads (50uL / ChIP) are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 1mL PBS + 0.5% BSA. 9E10 anti-Myc antibody (home-prepared)  is added (10uL / ChIP), and incubated overnight at 4'C in haematological mixer. Beads are washed twice with 10mL PBS + 0.5% BSA (freshly made), and resuspended in 30uL PBS + 0.5% BSA / ChIP. A mix of 250uL of cell lysate + 250uL of Lysis Buffer containing protease inhibitors are added to 30uL beads, and incubated overnight at 4'C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65'C to reverse the crosslinks. 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.

tag: strain

tag: antibody

value: 9E10 (lab stock by AF)


title: yFR178vsyFR116_9Myc-Srb10vsUntagged_rep2

description: Biological replicate 2 of 2. Mediator Srb10-Cdk8-9MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR178) versus the ChIP in untagged strain (yFR116).


title: Tumor 8


title: 0h_Con-2_BALBc

description: 0h Control BALB/c derived macrophage replicate 2

value: None -Control

value: 0 hours


title: yFR169vsyFR116_18Myc-Sin4-Med16vsUntagged_rep2

description: Biological replicate 2 of 2. MediatorSin4-Med16-18MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR169) versus the ChIP in untagged strain (yFR116).


title: Tumor 7


title: yFR169vsyFR116_18Myc-Sin4-Med16vsUntagged_rep1

description: Biological replicate 1 of 2. MediatorSin4-Med16-18MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR169) versus the ChIP in untagged strain (yFR116).


title: yFR167vsyFR116_9Myc-Srb11vsUntagged_rep2

description: Biological replicate 2 of 2. Mediator Srb11-CycC-9MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR167) versus the ChIP in untagged strain (yFR116).


title: Tumor 13


title: Tumor 12


title: flox5

city: Kumamoto

first: Ryuichi

last: Nishinakamura

address: Honjo 2-2-1

department: IMEG

country: Japan

institute: Kumamoto Univ.

description: gene expression after tamoxifen treatment

hyb_protocol: Agilent one-color gene expression hyb/wash protocol. 1.65 ug of Cy3 labeled RNA was hybridized to Agilent Whole Mouse Genome microarrays (8 x 60K: GPL10787) at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2539A Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software

data_processing: 75 Percentile Shift Normalization by using GeneSpring GX software (Agilent Technologies)

source_name: embryonic kidney

label_protocol: Agilent one-color Low RNA Fluorecent Liner Amplification kit labeling protocol. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol reagent (Life Technologies) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tamoxifen treatment was performend at E12.5. Sall1CreER E13.5 kidneys were disected and washed with PBS.

value: hybrid of 129 and C57BL/6

value: kidney

value: control


title: yFR167vsyFR116_9Myc-Srb11vsUntagged_rep1

description: Biological replicate 1 of 2. Mediator Srb11-CycC-9MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR167) versus the ChIP in untagged strain (yFR116).


title: yFR119vsyFR116_18Myc-Rox3-Med19vsUntagged_rep1

description: Biological replicate 1 of 2. Mediator Rox3-Med19-18MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR119) versus the ChIP in untagged strain (yFR116).


title: Tumor 16


title: hy5GBF1OE

description: GBF1 ChIP-chip study in the hy5GBF1OE line normalised against the wild-type. Represents 3 biological replicates.

source_name: Anti-GBF1 ChIPed DNA from hy5 GBF1OE line

value: hy5 GBF1OE

value: hy5 mutant with GBF1 over-expressor

value: whole seedling

value: 4 days


title: yFR119vsyFR116_18Myc-Rox3-Med19vsUntagged_rep2

description: Biological replicate 2 of 2. Mediator Rox3-Med19-18MYC tagged subunit occupancy, using the anti-MYC antibody, measured by the ratio of ChIP in tagged strain (yFR119) versus the ChIP in untagged strain (yFR116).


title: GBF1OE

description: GBF1 ChIP-chip study in the GBF1OE line normalised against the wild-type. Represents 3 biological replicates.

source_name: Anti-GBF1 ChIPed DNA from GBF1OE line

value: GBF1 over-expressor

value: constant white light - 20 micromol/meter square/second

value: polyclonal anti-GBF1

value: Sigma

value: Wassilewskija


title: Tumor 14

value: Vestibular Schwannoma


title: Control 2

source_name: Healthy-control tissue

value: Auricular nerve


title: Tumor 1


title: Control 3


title: Control 1

value: Hipoglossal ansa cervicalis nerve


title: CreER KO3

value: Sall1 knockout


title: CreER KO8


title: flox2


title: KO9

hyb_protocol: Agilent one-color gene expression hyb/wash protocol. 1.65 ug of Cy3 labeled RNA was hybridized to Agilent Whole Mouse Genome microarrays (4 x 44K: GPL7202) at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2539A Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software

treatment_protocol: Tamoxifen treatment was performend at E12.5. Six2CrefSall1E14.5WT, KO and Sall1CreERfSall1E14.5WT, KO kidneys were disected and washed with PBS.


title: CreER/flox5


title: E15.5Six2GFP-S1

hyb_protocol: Agilent one-color gene expression hyb/wash protocol. 1.65 ug of Cy3 labeled RNA was hybridized to Agilent Whole Mouse Genome microarrays (4 x 44K: GPL10333) at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

treatment_protocol: Six2GFP E15.5 kidneys were disected and washed with PBS. Then FACS sorting was performed to select the GFP(+) cells and the GFP(-) cells.

tag: cell type

value: nephron progenitor


title: KO7

value: hybrid of 129 and C57BL/6


title: wt/flox2

value: kidney


title: E15.5Six2GFP+S1


title: WT5

value: control


title: E15.5Six2GFP-S2


title: Cells treated by 16 µg/ml pterostilbene vs control replication-3

status: Public on Mar 23 2014

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

country: China

institute: PLA General Hospital

description: Biological replicate 3 of 3.

hyb_protocol: Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42°C and washed in a Capitalbio SlideWasher TM (CapitalBio) with two consecutive solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: A spatial and intensity dependent normalization based on the LOWESS program was employed, which is prevalent in microarray expression profiling. Each gene was represented in triplicate on each slide and the hybridization experiments were performed by dye-swap strategy.

organism: Candida albicans

source_name: C. albicans cells treated by 16 µg/ml pterostilbene

label_protocol:
cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.
In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 1 µg total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with the T7 Oligo (dT). The T7-oligo(dT) primer was provided in the kit with sequence of (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’).
After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μl elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 16 μl and subjected to 40 μl in vitro transcription reactions at 37°C for 4-14 hr using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MN).
Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 µg amplified RNA was mixed with 4 µg random nanomer, denatured at 65°C for 5min, and cooled on ice. Then, 5 μl of 4 × first-strand buffer, 2 μl of 0.1 M DTT, and 1.5 μl CbcScript II reverse transcriptase were added. The mixtures were incubated at 25°C for 10 min, then at 37°C for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μl. The cDNA was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice for 5 min. Then, 5 μl Klenow buffer, dNTP, and Cy5-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy5-dCTP. 1.2 μl Klenow enzyme was then added, and the reaction was performed at 37°C for 90 min.

growth_protocol: Candida albicans cells were propagated in RPMI 1640 medium.

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: Standardized C. albicans cells (1.0 ×10^6 cells/ml in RPMI 1640 medium) were prepared and added to 150 mm ×25 mm cell culture dishes (Corning, USA). The dishes were incubated statically at 37 °C for 90 min to allow initial adhesion and the production of germ tubes, after which the medium was removed and replaced with 80 ml pre-warmed (37 °C) fresh RPMI 1640 medium containing 16 µg/ml PTE. The dishes were further incubated statically at 37°C for 1 h. C. albicans cells were collected, washed once with PBS and stored in liquid nitrogen rapidly for further RNA isolation.

source_name: Control Candida albicans cells, untreated by pterostilbene

label_protocol:
cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.
In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 1 µg total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio) with the T7 Oligo (dT). The T7-oligo(dT) primer was provided in the kit with sequence of (5’-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT- 3’).
After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μl elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 16 μl and subjected to 40 μl in vitro transcription reactions at 37°C for 4-14 hr using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MN).
Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 µg amplified RNA was mixed with 4 µg random nanomer, denatured at 65°C for 5min, and cooled on ice. Then, 5 μl of 4 × first-strand buffer, 2 μl of 0.1 M DTT, and 1.5 μl CbcScript II reverse transcriptase were added. The mixtures were incubated at 25°C for 10 min, then at 37°C for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μl. The cDNA was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice for 5 min. Then, 5 μl Klenow buffer, dNTP, and Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy3-dCTP. 1.2 μl Klenow enzyme was then added, and the reaction was performed at 37°C for 90 min.

treatment_protocol: Standardized C. albicans cells (1.0 ×10^6 cells/ml in RPMI 1640 medium) were prepared and added to 150 mm ×25 mm cell culture dishes (Corning, USA). The dishes were incubated statically at 37 °C for 90 min to allow initial adhesion and the production of germ tubes, after which the medium was removed and replaced with 80 ml pre-warmed (37 °C) fresh RPMI 1640 medium containing 200 µl DMSO. The dishes were further incubated statically at 37°C for 1 h. C. albicans cells were collected, washed once with PBS and stored in liquid nitrogen rapidly for further RNA isolation.


title: 2007-06-15 HBE-MC-Cy5

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Boulevard

department: Microbiology

country: USA

institute: University of Texas Southwestern Medical Center

description: For more information, see our previous publication (PMID: 17620351).

hyb_protocol: Cy3- and Cy5-labeled cDNA samples were mixed, lyophilized, and then dissolved in dH2O.  Following denaturation at 94C for 3 min, these samples were kept on ice until used for DNA hybridization.  The mixture of Cy3- and Cy5-labeled cDNA in 1X Hybridization Buffer (from the kit RPN5660) was added to the DNA microarray slide and incubated at 50C overnight (~16 hours).

scan_protocol: Microarray slides were scanned by using a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA)

data_processing: Data was analyzed with GenePix and Acuity 4.0 software (Molecular Devices).

organism: Moraxella catarrhalis

source_name: M. catarrhalis-HBE cells co-culture

label_protocol: Amersham CyScribe Post-Labelling Kit (RPN5660)

growth_protocol: M. catarrhalis ATCC 43617 cells were grown attached to HBE cells in MEM (with supplementation of 10% FCS and 1% Glutamax) at 37°C in an incubator (5% CO2) for 2 hr.

extract_protocol: Extract Protocol: After 2-hours incubation period, the medium in the flask with the 16HBE14 monolayer was decanted and replaced with tissue culture medium containing 25 mM sodium azide (to protect RNA). The 16HBE14 monolayer and attached bacteria were released from the plate by scraping.  After low-speed centrifugation to collect these bronchial cells and attached bacteria, the cell pellet was re-suspended in TE containing 1% saponin (which lyses the human cells).  After a 10-min incubation at 37°C, the bacterial cells were collected by centrifugation.  Bacterial total RNA was isolated by using Qiagen RNeasy Midi Kit.

tag: M. catarrhalis ATCC 43617 cells were grown attached to a monolayer of 16HBE14 human bronchial epithelial cells.

source_name: M. catarrhalis culture

growth_protocol: M. catarrhalis ATCC 43617 cells were grown in MEM (with supplementation of 10% FCS and 1% Glutamax) at 37°C in an incubator (5% CO2) for 2 hr.

extract_protocol: An equal volume of tissue culture medium containing 25 mM sodium azide (to protect RNA) was mixed with bacterial culture. Bacterial cells were harvested by centrifugation.  The cell pellet was re-suspended in TE containing 1% saponin.  After a 10-min incubation at 37°C, the bacterial cells were collected by centrifugation.  Total RNA was extracted from bacterial cells by using the Qiagen RNeasy Midi kit.

tag: M. catarrhalis ATCC 43617 cells were grown in tissue culture flask.


title: Cells treated by 16 µg/ml pterostilbene vs control replication-2

description: Biological replicate 2 of 3.


title: WT2

tag: genotype/variation


title: 2007-06-19 HBE-MC-Cy3


title: 2007-07-02 HBE-MC-Cy5


title: 2007-05-18 HBE-MC-Cy5


title: 2007-07-02 HBE-MC-Cy3


title: Cells treated by 16 µg/ml pterostilbene vs control replication-1

description: Biological replicate 1 of 3.


title: control group 12

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

institute: Fujian Academy of Traditional Chinese Medicine

hyb_protocol: 100 μl 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: Agilent Microarray Scanner (Agilent p/n G2565BA),Scan region Scan Area (61 x 21.6 mm),Scan resolution:5μm,scanning mode Single Pass.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Add the images (.tif) to be extracted to the Agilent Feature Extraction (FE) software Project. Select Project > Start Extracting and export data to txt.Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity genes were filtered (Genes that at least 5 out of 15 samples have flags in Detected were chosen for further analysis).

source_name: human peripheral blood

label_protocol: if the yield is <1.65μg and the specific activity is <9.0 pmol Cy3 or Cy5 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: Five (5) ml of peripheral blood was taken from each patient. Mononuclear cells were isolated via lymphocyte lysing.And then add 1 ml trizol reagents.

tag: clinical phenotype

value: postmenopausal healthy

value: peripheral blood

tag: group

value: control group

tag: age

tag: Sex

value: Female


title: non-kidney deficiency 11

value: postmenopausal osteoporosis

value: non-kidney deficiency


title: control group 13


title: E16.5 Brain, Tdp2Δ1-3, biologycal replicate 2

city: Brighton

first: Fernando

last: Gomez-Herreros

address: Science Park Road, Falmer

department: GDSC

institute: University of Sussex

description: Ambion WT expression kit, followed by the Affymetrix terminal labelling kit

hyb_protocol: standard affymetrix protocol

scan_protocol: Arrays were washed and labelled using the Affymetrix hybridization wash and stain kit in a Fluidics station 450 before scanning on a 7G scanner

data_processing: Microarray quality was assessed using Affymetrix GeneChip Expression Console and CEL files were transferred to Genespring (Agilent) for differential expression analysis.

label: Affymetrix terminal labelling kit

source_name: Tdp2Δ1-3, brain

label_protocol: standard affymetrix protocol

growth_protocol: Mouse brain dissected from day 16.5 mouse embryos

extract_protocol: Samples were snap frozen in liquid N2 and mice genotyped. Whole brains (olfactory bulb, forebrain, mid-brain, hind-brain and brain stem) were homogenized in Trizol (Sigma), chloroform extracted, isopropanol precipitated and purified by RNeasy kit. Total RNA was labelled with the Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit and hybridised to GeneChip Mouse Gene 1.0 ST Arrays in an Affymetrix Hybridisation oven following the standard Affymetrix protocol.

treatment_protocol: not applicable

tag: developmental stage

value: Brain

tag: genotype


title: kidney Yang deficiency 10

tag: tissue

value: kidney Yang deficiency


title: kidney Yang deficiency 9


title: kidney Yin deficiency 7

value: kidney Yin deficiency


title: non-kidney deficiency 8


title: E16.5 Brain, Tdp2Δ1-3, biologycal replicate 3


title: kidney Yin deficiency 3


title: control group 5


title: E16.5 Brain, Wild-type, biologycal replicate 1

source_name: Wild Type, brain

value: wild-type


title: kidney Yin deficiency 4


title: day_12_replicate3

status: Public on Mar 22 2014

city: Seattle

first: Sherman

last: Ku

state: WA

address: Suite 200, 551 North 34th St

institute: Allen Institute for Brain Science

hyb_protocol: standard LC Sciences protocol (performed at third party company LC Sciences, catalog # MRA-1001)

data_processing: Lowess-normalized; ANOVA at p(adj) < 0.05 for differential expression; biophysical properties and calculations as described in the associated publication

source_name: H1 ESC, day 12 of differentiation

extract_protocol: Qiagen miRNeasy Mini kit according to manufacturer protocol

tag: cell line

tag: time

value: day 12

tag: gender

value: male

tag: nih registry number


title: E16.5 Brain, Wild-type, biologycal replicate 2


title: day_12_replicate2

scan_protocol: standard LC Sciences protocol (performed at third party company LC Sciences, catalog # MRA-1001)


title: day_9_replicate2

source_name: H1 ESC, day 9 of differentiation

label_protocol: standard LC Sciences protocol (performed at third party company LC Sciences, catalog # MRA-1001)

value: day 9


title: day_9_replicate3


title: non-kidney deficiency 2


title: E16.5 Brain, Wild-type, biologycal replicate 3


title: Analysis of the Zur regulon of Moraxella catarrhalis rep1

first: Todd

middle: C.

last: Hoopman

address: 5323 Harry Hines Blvd.

hyb_protocol: Equivalent amounts of the Cy3- and Cy5-labeled cDNA samples were mixed, lyophilized, and then dissolved in 21 microliters of H2O. After denaturation for 3 minutes at 94 degrees Celsius these samples were kept on ice until they were used for DNA hybridization. The hybridization mixture containing 15 microliters of 4X hybridization buffer (GE Healthcare), 24 microliters of formamide (40% volume/volume), and 21 microliters of the Cy3- and Cy5-labeled cDNA. The mixture was added to a DNA microarray slide and incubated at 50 degrees Celsius overnight (~ 16 hours). After hybridization the slides were washed twice in 6X SSPE containing 0.01% Tween 20 at 50 degrees Celsius for 5 min, twice in 0.8X SSPE containing 0.001% Tween 20 at 50 degrees Celsius for 5 min, and twice in 0.8X SSPE at room temperature.

scan_protocol: The slides were dried by centrifugation at 900 x g in loosely capped 50-ml conical tubes for 3 minutes. Microarray slides were scanned with a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA) and analyzed with GenePix 4.0 software (Molecular Devices).

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E wild-type cells was utilized as the baseline gene expression template. To identify those genes in the Zur mutant strain that exhibited an altered expression profile relative to the in vitro broth-grown wild-type cells , a threshold of twofold-increased or decreased expression over the baseline was utilized.

source_name: Moraxella catarrhalis strain O35E, mid-log growth in BHI

label_protocol: Ten micrograms of total RNA from the O35E cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Bacterial cells were grown in BHI broth to mid-logarithmic phase.

extract_protocol: Cells were harvested by centrifugation and processed for total RNA with the Ambion RiboPure Bacteria kit.

tag: strain background

value: wild type

source_name: Moraxella catarrhalis strain O35E non-polar ZUR mutant, mid-log growth in BHI

label_protocol: Ten micrograms of total RNA from the O35E non-polar Zur mutant cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy3 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

value: non-polar ZUR mutant


title: day_9_replicate1


title: Analysis of the Zur regulon of Moraxella catarrhalis rep2

label_protocol: Ten micrograms of total RNA from the O35E non-polar Zur mutant cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

treatment_protocol: Bacterial cells were grown in BHI broth to mid-logarithmic phase.

label_protocol: Ten micrograms of total RNA from the O35E cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy3 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.


title: E16.5 Brain, Tdp2Δ1-3, biologycal replicate 1


title: Analysis of the Zur regulon of Moraxella catarrhalis rep4


title: kidney Yang deficiency 6


title: day_12_replicate1


title: day_6_replicate1

source_name: H1 ESC, day 6 of differentiation

value: day 6


title: day_6_replicate3


title: Analysis of the Zur regulon of Moraxella catarrhalis rep3


title: day_6_replicate2


title: kidney Yin deficiency 1


title: day_3_replicate2

source_name: H1 ESC, day 3 of differentiation

value: day 3


title: day_3_replicate3


title: day_0_replicate3

source_name: H1 ESC, undifferentiated

value: day 0


title: day_3_replicate1


title: day_0_replicate2


title: control

city: MADRID

first: Erwin

middle: F

last: Wagner

address: C/ Melchor Fernández Almagro, 3

department: F-BBVA CCBP

institute: CNIO

hyb_protocol: Probe- Prehybridisation (TECAN HS4800)      Protocol for 40 domain chips:          Combine: 50µl Labeled DNA           29µl    20x SSPE          4µl 50x Denhardts solution        50µl Form amid          1.5µl   mouse block    3.5µl 20% SDS (last component to be added)         Incubate at 94°C for 2 min         Prehybridise probe for at least 1 hour at 50°C        • start prehybridization of the slides    • After prehyb of the samples and the slides pipette 135 µl onto each slide   If you have duplicates then pool and use 135µl per slide    • split and pipette 140 µl onto each slide    • Continue with hybridization on TECAN HS4800  for 12hours 45°C

scan_protocol: Scanner: GenePix 4000B

data_processing:
Image Analysis: GenPix Pro 6.0
Data were analyzed in R using the 'limma' package and background-corrected with the RMA method. Replicates were averaged.

source_name: breast epithelium cell line

label_protocol: Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647)    Thoroughly dissolve the amine-modified 4µg DNA in 5µl  nuclease free H2O (warming to 42°C for 5 min if necessary)  Add 3µl  Labeling buffer  (Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from –80°C)  Add 2µl  reactive dye to the samples, vortex briefly to mix (do not spin)  Incubate for 1 hour in the dark at room temperature

growth_protocol: DMEM supplemented with 5% FCS, 1% Pen-Strep, 1% L-Glutamine and 2% 1M HEPES pH7.3

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

value: mammary epithelial cells

source_name: breast epithelium cell line_pool_of_all_three_samples


title: day_0_replicate1


title: fra1 overexpression clone 1


title: EGFP-TS3.5 biological rep3

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

description: On MEF feeders, with FGF4/heparin/Activin A

hyb_protocol: Samples were hybridized, stained, and washed according to the Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
The expression values were summarized and normalized by the robust multiarray analysis and quantile normalization method using by Expression Console(tm) software (Affymetrix).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mod.mm9.mps

source_name: EGFP-TS3.5 TS cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on MEF feeders. TS cells were maintained in GMEM/10% FBS supplemented with 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.

extract_protocol: Total RNA was isolated using QuickGene RNA cultured cell HC kit S (Fuji Film).

treatment_protocol: Tet-inducible Oct3/4 knockout ES cells were cultured in TS cell medium supplemented with 1 ug/ml Tet for 4 days on MEF feeders.

tag: strain

value: ICR


title: EGFP-TS3.5 biological rep2


title: HT29 cells: co-cultured with HIV infected Jurkat T cells

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from HT29 epithelial cells co-cultured with HIV infected Jurkat T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2 GeneChip 3' IVT arrays. 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 dChip software, version 2010

source_name: HT29 intestinal epithelial cell line

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

tag: treatment

tag: cell type

value: intestinal epithelial cells


title: HCT116_PHF19S_sh1_1

city: Guangzhou

first: Mengfeng

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

description: HCT116 Cells transduced with pSuper Retro Neo PHF19S sh1

hyb_protocol: Hybridization was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5 m, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: The data intensities are actually gProcessed signal, which is generated by genespring with out median shift, so it is not the usual "two-color" type signal out put following the standard genespring pipeline.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: HCT116 cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol.

treatment_protocol: Retro-viral vector was co-transfected with the pIK packaging plasmid in 293FT cells by using standard calcium phosphate transfection method. Thirty-six hours after the co-transfection, supernatants were collected and incubated with cells to be infected for 24 hours in the presence of polybrene (2.5 μg/mL).  Following infection, puromycin (1.5μg/mL) was used to select stably transduced cells for 10 days.

value: PHF19S sh1


title: HCT116_PHF19L_sh1_2

description: HCT116 Cells transduced with pSuper Retro Neo PHF19L sh1

value: PHF19L sh1


title: HCT116_shRNA_Vector_1

description: HCT116 Cells transduced with pSuper Retro Neo Vector

value: shRNA Vector


title: EGFP-TS3.5 biological rep1


title: ZHBTc4-TSC biological rep2

source_name: ZHBTc4 TS cells, +Tet

value: Tet


title: HCT116_PHF19S_sh1_2


title: ZHBTc4-TSC biological rep3


title: HEK293_MOCK_2

status: Public on Mar 21 2014

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

country: Italy

institute: CBM

description: HEK293 cells stably transfected with the with the empty vector (Mock) replica 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Lumi package in R

source_name: HEK293 cells stably transfected with the empty vector (Mock)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human HEK293 were maintained in DMEM (Gibco, Invitrogen) supplemented with 10% FBS and 1% penicillin-streptomycin (Gibco, Invitrogen) and were grown in a humidified incubator with 5% CO2 at 37ºC.

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

treatment_protocol: For HEK293 stable transfections, ViraPower Lentiviral Expression kit (Invitrogen) was used for the transduction of the MLK3 wild-type and mutant P252H sequences as well as the empty vector. Lentiviral transduction was performed following the manufacturer’s instructions. Transduced cells were selected by antibiotic resistance (blasticidin, 12 μg/ml) (Gibco, Invitrogen). The expression levels of MLK3 in the different clones selected were measured by western-blot.

tag: transfection

value: with the with the empty vector


title: fra1 overexpression clone 2

value: Female


title: ZHBTc4-TSC biological rep1


title: HT29 cells: co-cultured with uninfected Jurkat T cells

description: Gene expression data from HT29 epithelial cells co-cultured with uninfected Jurkat T cells


title: HEK293_MUT_3

description: HEK293 cells stably transfected with the MLK3 P252H mutation replica 3

value: with the MLK3 P252H mutation


title: HCT116_shRNA_Vector_2


title: HCT116_PHF19L_sh1_1


title: HEK293_MOCK_3

description: HEK293 cells stably transfected with the with the empty vector (Mock) replica 3


title: HEK293_MOCK_1

description: HEK293 cells stably transfected with the with the empty vector (Mock) replica 1


title: HEK293_MUT_2

description: HEK293 cells stably transfected with the MLK3 P252H mutation replica 2


title: HEK293_MUT_1

description: HEK293 cells stably transfected with the MLK3 P252H mutation replica 1


title: HEK293_WT_3

description: HEK293 cells stably transfected with the wild-type MLK3 replicate 3

value: with the wild-type MLK3


title: HEK293_WT_2

description: HEK293 cells stably transfected with the wild-type MLK3 replicate 2


title: E15.5Six2GFP+S2

description: gene expression after tamoxifen treatment

source_name: embryonic kidney

value: hybrid of 129 and C57BL/6

value: kidney

value: nephron progenitor

tag: genotype/variation


title: HEK293_WT_1

description: HEK293 cells stably transfected with the wild-type MLK3 replicate 1


title: siHic5_2_0h_1

city: Los Angeles

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

description:
rep 1
5645326056_A

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
The data were normalized using neqc with limma (v.3.14.4) in R (v.2.15.3).
The non-normalized data matrix contains 48,210 data rows (with extra 887 rows for control probes). Control probes do not have Illumina IDs but have Probe IDs, were used in normalization, and thus removed in the dataset after normalization.

label_protocol: Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

growth_protocol: A clonal line of U2OS cells that stably express wild-type rat GRα were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.

extract_protocol: Total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using electrophoresis on an Agilent Bioanalyzer using the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 5 ug of high quality total RNA was submitted to the Southern California Genotyping Consortium at the University of California, Los Angeles.

treatment_protocol: On the next day the cells were transfected with 60 pmol of siRNA per well using Lipofectamine RNAiMAX (Invitrogen) using manufacturer’s protocol. After 2 days (24hr time point), or 3 days (2 hr and 4 hr timepoints) cells were treated with Dex for the indicated times. All treatment groups were harvested at the same time.

value: osteosarcoma cells

tag: transfected with

tag: treated with

value: dexamethasone (Dex) for 0h


title: E2P53_OSE

city: Houston

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: The mouse background is mixed (mainly C57BL/6), since there are 4 different mutant mice crossed together.

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor (v.1.8) with RMA method.

source_name: Ovarian surface epithelia cells from P53;Pten;Kras;A-cre mice treated with E2 pellet at 5 weeks and harvested at 8 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

value: mixed (mainly C57BL/6)

value: Trp53 fl/fl;Ptentm1Hwu/ Ptentm1Hwu;Krastm4Tyj/ Krastm4Tyj ; Amhr2-cre (P53;Pten;Kras;A-cre)

tag: age

value: 8 weeks

value: ovarian surface epithelia (OSE) cells


title: siHic5_2_4h_1

description:
rep 1
5645326024_C

value: dexamethasone (Dex) for 4h


title: siNS_2h_1

description:
rep 1
5645326024_E

value: nonspecific siRNA (SiNS)

value: dexamethasone (Dex) for 2h


title: siNS_24h_1

description:
rep 1
5645326056_B

value: dexamethasone (Dex) for 24h


title: siHic5_2_24h_2

description:
rep 2
5645326056_E


title: siHic5_2_2h_3

description:
rep 3
5645326024_G


title: NI_2h_2

description:
rep 2
5645326024_D

value: none (non-infected control)


title: NI_2h_3

description:
rep 3
5645326024_J


title: NI_4h_4

description:
rep 4
5645326056_C


title: siNS_2h_2

description:
rep 2
5645326024_A


title: siNS_0h_3

description:
rep 3
5645326056_I


title: siNS_0h_2

description:
rep 2
5645326023_L


title: NI_24h_2

description:
rep 2
5645326056_K


title: NI_0h_1

description:
rep 1
5645326056_G


title: siNS_2h_4

description:
rep 4
5645326024_H


title: siHic5_2_4h_2

description:
rep 2
5645326024_L


title: wild_type_OSE2

source_name: Ovarian surface epithelia cells from wild type mice

value: wild type

value: 10 weeks


title: NI_4h_2

description:
rep 2
5645326023_I


title: NI_24h_4

description:
rep 4
5645326024_F


title: HVC_intact_juvenile3

city: Sapporo

first: Kazuhiro

last: Wada

address: Room 910, Building No.5, North 10, West 8, Kita-ku

department: Biological Sciences

institute: Hokkaido University

description: Gene expression in HVC of juvenile male zebra finch

hyb_protocol: 1.65 µg of labeled cDNA from each sample was hybridized to custom designed songbird oligo arrays (Agilent Technologies) following the Agilent Gene Expression FFPE Workflow..

scan_protocol: The arrays were washed, scanned on the Agilent Microarray Scanner (G2505B) using one color scan setting for 4 x 44K array slides (scan resolution 5µm, Dye channel was set to Green), and data extracted from the scanned image using Feature Extraction version 9.1 (Agilent Technologies).

data_processing: All subsequent pre-processing and analysis were done in the Microsoft Excel (Microsoft) and the statistical software R (R Core Team 2013). Probe refers to a single probe on the array. For majority of gene-symbol identified genes, multiple probes for a single gene were present on the array. HVC and RA samples were separated and the two datasets were pre-processed separately, as follows. First, control probes were removed and probes with raw fluorescence values >3 standard deviations (SD) away from the mean of measurements across all samples for that probe were removed. To reduce noise, probes with raw fluorescence values <50 in more than 80% of samples in each nuclei were removed. A total of 41,525 and 41,340 probes (including 11,391 and 11,374 gene-symbol identified genes) in HVC and RA, respectively, fit these criteria and were processed. Arrays were quantile normalized, and fluorescence value was transformed to log2 scale.

organism: Taeniopygia guttata

source_name: HVC, intact, juvenile3

label_protocol: 1.7 µg of total amplified cDNA was converted into labeled cDNA coupled to Cy3 using Genomic DNA ULS labeling Kit (Agilent Technologies) following the Agilent Gene Expression FFPE Workflow.

growth_protocol: Subjects were deafened by cochlear extirpation during the following age spans: dph 17-23 (before fledging) for early-deafened birds. After bilateral cochlea removal, the birds were put back in their nest and kept with their parents and siblings until dph 32-41.

extract_protocol: Laser microdissected tissue was collected directly into RLT Buffer from the RNeasy Micro kit (QIAGEN) supplemented with β-mercaptoethanol. Samples were vortexed, centrifuged, and stored at -80°C until RNA purification. RNA was column purified, treated with DNase on the column to remove genomic DNA, and in order to quantify RNA quality, RNA Integrity Number (RIN) and concentration were measured by Bioanalyzer 2100 (Agilent Technologies) in randomly selected four samples (RIN; 5.9-7.1, concentration; 1.69-2.35 ng/μl). Purified RNA was amplified using TransPlex Whole Transcriptome Amplification kit (WTA2 kit, Sigma-Aldrich) in accordance with the manufacturer’s instructions. The amplified cDNA was purified for removal of residual primers and nucleotides using QIAquick PCR purification kit. To determine quality and yield of the amplified cDNA were measured by NanoDrop ND-8000 (Thermo Scien) and on electrophoresis.

treatment_protocol: For brain sampling, all animals were individually placed in a sound attenuated box at least 2 days before. Under silent and dark conditions, birds were decapitated, and brains were rapidly taken out and frozen in a plastic mold with Tissue-Tek (OCT compound, Sakura Fine Technical) placed on dry ice, then stored at -80°C until use for laser capture microdissection.

value: brain

value: male

tag: auditory


title: siHic5_2_4h_3

description:
rep 3
5645326023_F


title: siHic5_2_24h_1

description:
rep 1
5645326023_J


title: siNS_24h_2

description:
rep 2
5645326023_G


title: HVC_intact_juvenile2

source_name: HVC, intact, juvenile2


title: HVC_intact_juvenile1

source_name: HVC, intact, juvenile1


title: RA_early-deafened_old3

description: Gene expression in RA of old male zebra finch deprived auditory input

source_name: RA, early-deafened, old3


title: siNS_4h_4

description:
rep 4
5645326023_B


title: RA_intact_old2

description: Gene expression in RA of old male zebra finch

source_name: RA, intact, old2


title: siNS_4h_1

description:
rep 1
5645326021_L


title: RA_early-deafened_old2

source_name: RA, early-deafened, old2


title: HVC_early-deafened_juvenile1

description: Gene expression in HVC of juvenile male zebra finch deprived auditory input

source_name: HVC, early-deafened, juvenile1


title: RA_early-deafened_old1

source_name: RA, early-deafened, old1


title: RA_early-deafened_young5

description: Gene expression in RA of young male zebra finch deprived auditory input

source_name: RA, early-deafened, young5


title: siNS_0h_4

description:
rep 4
5645326021_D


title: siNS_4h_2

description:
rep 2
5645326021_F


title: NI_0h_4

description:
rep 4
5645326021_E


title: RA_early-deafened_young4

source_name: RA, early-deafened, young4


title: siHic5_2_0h_4

description:
rep 4
5645326023_A


title: NI_24h_3

description:
rep 3
5645326023_D


title: siHic5_2_2h_2

description:
rep 2
5645326021_K


title: siNS_2h_3

description:
rep 3
5645326020_E


title: RA_intact_old1

source_name: RA, intact, old1


title: RA_early-deafened_young2

source_name: RA, early-deafened, young2


title: NI_0h_3

description:
rep 3
5645326020_I


title: NI_2h_1

description:
rep 1
5645326021_H


title: NI_0h_2

description:
rep 2
5645326021_B


title: siHic5_2_2h_1

description:
rep 1
5645326020_G


title: siHic5_2_24h_4

description:
rep 4
5645326021_G


title: RA_intact_old3

source_name: RA, intact, old3


title: NI_24h_1

description:
rep 1
5645326020_C


title: RA_intact_young4

description: Gene expression in RA of young male zebra finch

source_name: RA, intact, young4


title: RA_intact_young5

source_name: RA, intact, young5


title: RA_early-deafened_juvenile3

description: Gene expression in RA of juvenile male zebra finch deprived auditory input

source_name: RA, early-deafened, juvenile3


title: siHic5_2_24h_3

description:
rep 3
5645326019_I


title: siNS_4h_3

description:
rep 3
5645326020_K


title: NI_4h_1

description:
rep 1
5645326019_J


title: siHic5_2_4h_4

description:
rep 4
5645326020_D


title: siNS_24h_4

description:
rep 4
5645326020_A


title: Microarrays N2 L4 stage C. elegans N2(Wt) vs. acs-3(ft5) Replicate #3

city: Santa Cruz

first: Jordan

middle: David

last: Ward

state: California

address: 1156 HIGH ST, UCSC THIMANN RECEIVING, SINSHEIMER 327

department: Molecular, Cell, and Developmental Biology

institute: University of California, Santa Cruz

hyb_protocol: acs-3 mutant and wild-type targets were co-hybridized to Washington University/Genome Sequencing Center C. elegans 23K spotted oligo arrays for 16 hours at 42 C, followed by a series of stringency washings at 42 C for 5 cycles in 2xSSC and 3 cycles in 0.1x SSC using an automated GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI, USA).

scan_protocol: Post-hybridized arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA) and image analysis was performed using GenePix Pro software.

data_processing: Arrays were normalized with the maNorm function from the marray package, which uses within-print-tip-group intensity dependent location normalization using the loess function (R stats package) and reports log-difference (M) and log-average (A) values. Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma [20] and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. We defined differential expression as |log2(ratio)| ≥0.848 with the FDR set to 5%, and p-value≤0.001.

organism: Caenorhabditis elegans

source_name: Whole animal RNA extract N2(Wt)

label_protocol: Cy5- and Cy3-labeled cDNA targets were generated from 30  g of total RNA using a reverse transcription, amino-allyl based labeling protocol

growth_protocol: Animals were synchronized by bleaching, grown to the L4 stage at 20ºC. L4 stage was determined by morphology. Animals were harvested, washed 5x in M9, flash-frozen in liquid N2, stored at -70oC.

extract_protocol: RNA was TRIZOL extracted and a Qiagen RNAeasy kit was used to clean up the RNA.  Sufficient animals to obtain 40 µg of total RNA were used.

tag: sample type

value: Strain N2 Stage L4

tag: genetic background

tag: developmental stage

value: whole organism

source_name: Whole animal RNA extract acs-3(ft5) mutant

value: Strain acs-3(ft5) mutant Stage L4

value: acs-3(ft5) mutant


title: RA_intact_young2

source_name: RA, intact, young2

tag: tissue


title: siHic5_2_0h_3

description:
rep 3
5645326021_C

tag: cell line

value: osteosarcoma cells

value: dexamethasone (Dex) for 0h


title: NI_2h_4

description:
rep 4
5645326019_H


title: Microarrays N2 L4 stage C. elegans N2(Wt) vs. acs-3(ft5) Replicate #2

tag: genotype


title: NI_4h_3

description:
rep 3
5645326019_C


title: RA_intact_juvenile3

description: Gene expression in RA of juvenile male zebra finch

source_name: RA, intact, juvenile3

tag: gender


title: siNS_0h_1

description:
rep 1
5645326019_G


title: RA_early-deafened_juvenile4

source_name: RA, early-deafened, juvenile4


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. nhr-25(RNAi) Replicate #2

description: RNAi treatment with HT1115 bacteria; carrying the nhr-25 RNAi clone (Julie Ahringer library) or the L4440 vector control; 1mM IPTG on NGM  plates

hyb_protocol: nhr-25(RNAi) and control RNAi targets were co-hybridized to Washington University/Genome Sequencing Center C. elegans 23K spotted oligo arrays for 16 hours at 42 C, followed by a series of stringency washings at 42 C for 5 cycles in 2xSSC and 3 cycles in 0.1x SSC using an automated GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI, USA).

source_name: Whole animal RNA extract control RNAi

value: control

source_name: Whole animal RNA extract nhr-25 RNAi


title: siHic5_2_2h_4

description:
rep 4
5645326019_E


title: siNS_24h_3

description:
rep 3
5645326019_K


title: Lin- BM E4bp4+/+ 6

city: London

first: Hugh

middle: JM

last: Brady

address: South Kensington

department: Life Sciences

institute: Imperial College

description: Expression in E4bp4+/+ lineage-negative bone marrow cells

hyb_protocol: 5.5ug of labelled cDNA was hybridised on GeneChip Mouse Gene 1.0 ST Array

data_processing: The data generated was imported into GeneSpring GXv11 (Agilent) and normalised using the Robust Multi-Array (RMA16) algorithm. Genes were filtered on expression value between 20th and 100th percentile to remove those with very low or no expression across all the samples. A moderated t-test was applied to the data and p values were adjusted for multiple testing using a Benjamini-Hochberg False Discovery Rate correction.

source_name: Lin- BM E4bp4+/+ 6

label_protocol: Biotinylated cDNA was prepared from 100ng RNA using Ambion WT Expression Kit and GeneChip WT Terminal Labelling and Control Kit (Affymetrix)

extract_protocol: Total RNA was extracted using Rneasy Micro Kit (Qiagen)

treatment_protocol: Total bone marrow was extracted from mouse hindlegs by crushing. Cells expressing lineage markers (NK1.1, CD2, B220, CD11b, GR1, Ter119) were magnetically depleted and the remaining lineage negative bone marrow taken through to the array.

value: Lineage-depleted bone marrow cells


title: RA_intact_juvenile1

source_name: RA, intact, juvenile1


title: Lin- BM E4bp4+/+ 2

source_name: Lin- BM E4bp4+/+ 2


title: RA_early-deafened_juvenile1

source_name: RA, early-deafened, juvenile1


title: HVC_early-deafened_old3

description: Gene expression in HVC of old male zebra finch deprived auditory input

source_name: HVC, early-deafened, old3


title: Lin- BM E4bp4+/+ 3

source_name: Lin- BM E4bp4+/+ 3


title: exocrine-pancreas-cellline_rep2

city: Paris

first: Raphael

last: Scharfmann

address: 24 Rue du Fg St Jacques

country: France

institute: INSERM U845, Research Center Growth and Signaling, Université Paris Descartes, Faculté de Médecine, Hôpital Cochin

description: SKPC-B

hyb_protocol: 3.75µg cDNA per sample were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA, USA) for 16-18 hours at 45°C and 60 rpm. EukGe_WSv4_450 was used to stain and wash the arrays.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Array Studio (Omicsoft Corp., Cary, NC, USA) using default settings and RMA as normalization method.

source_name: exocrine pancreas cell line

label_protocol: 25 ng total RNA each were amplified using the Applause 3'-Amp System and subsequently labelled with Biotin using the Encore™ Biotin Module following the manufacturer's instructions (NuGEN Technologies, San Carlos, CA, USA).

growth_protocol: EndoC-bH2 cells were grown as described in Ravassard et al. 2011 JCI 121, 3589-3597

extract_protocol: RNA was extracted using Qiagen RNeasy minikit (Qiagen) according to manufacturer instructions

treatment_protocol: Cells were transduced with a lentiviral vector expressing CRE under the control of a CMV promoter (15 ng of p24 capsid protein per 10^5 cells) and RNA was extracted 3 weeks after transduction.

value: exocrine pancreas cell line


title: Lin- BM E4bp4-/- 4

description: Expression in E4bp4-/- lineage-negative bone marrow cells

source_name: Lin- BM E4bp4-/- 4


title: exocrine-pancreas-cellline_rep3

description: SKPC-C


title: RA_intact_juvenile4

source_name: RA, intact, juvenile4


title: Lin- BM E4bp4+/+ 4

source_name: Lin- BM E4bp4+/+ 4


title: Lin- BM E4bp4+/+ 1

source_name: Lin- BM E4bp4+/+ 1


title: HVC_early-deafened_old2

source_name: HVC, early-deafened, old2


title: Lin- BM E4bp4-/- 6

source_name: Lin- BM E4bp4-/- 6


title: Lin- BM E4bp4-/- 5

source_name: Lin- BM E4bp4-/- 5


title: exocrine-pancreas-cellline_rep1

description: SKPC-A


title: Lin- BM E4bp4-/- 3

source_name: Lin- BM E4bp4-/- 3


title: Lin- BM E4bp4-/- 1

source_name: Lin- BM E4bp4-/- 1


title: HVC_intact_old3

description: Gene expression in HVC of old male zebra finch

source_name: HVC, intact, old3


title: beta-cellline_non-excised_rep3

source_name: human beta cell line containing immortalization cassette (SV40 T antigen)

value: human beta cell line


title: HVC_early-deafened_old1

source_name: HVC, early-deafened, old1


title: BS-4

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

description: pre-B cells, from VH81x transgenic Rag1-/- mice

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the mouse gene 1.0st array in a GeneChip Hyb oven 640 according to manufacturer instructions. Washing was done in a GeneChip WS-system according to manufacturer instructions.

scan_protocol: Scanning was done on a geneChip scanner 7G incl. autocaroussel using affymetrix launcher software for downstream image processing

data_processing: Normalized gene expression values were calculated using robust multi-array average (RMA)

source_name: Bone marrow B-cell fraction, B220+CD19+ pre-B

label_protocol: Total RNA was labeled using the Affymetrix GeneChip® WT (Whole Transcript) Terminal Labeling Kit, according to manufacturers instructions

growth_protocol: developing B cells were isolated directly from the bone marrow by FACS purification and processed for analysis.

extract_protocol: total RNA

treatment_protocol: RNA was extracted after one PBS wash

value: pre-B cell

value: Btk Slp KO (VH81x transgenic Rag1-/-)


title: HVC_intact_old2

source_name: HVC, intact, old2


title: BS-3


title: BS-2


title: beta-cellline_non-excised_rep2


title: Slp-4

value: Slp KO (VH81x transgenic Rag1-/-)


title: BS-1


title: Lin- BM E4bp4-/- 2

source_name: Lin- BM E4bp4-/- 2


title: beta-cellline_excised_rep3

source_name: human beta cell line after excision of immortalization cassette (SV40 T antigen)

value: immortalization cassette (SV40 T antigen) excised


title: Slp-2


title: HVC_early-deafened_young3

description: Gene expression in HVC of young male zebra finch deprived auditory input

source_name: HVC, early-deafened, young3


title: Slp-3


title: Wt-4

value: WT (VH81x transgenic Rag1-/-)


title: Btk-1

value: Btk KO (VH81x transgenic Rag1-/-)


title: beta-cellline_non-excised_rep1


title: Wt-3


title: HVC_intact_old1

source_name: HVC, intact, old1

value: brain

value: male


title: SUTI151M xeno

city: Palo Alto

first: Haiyu

last: Zhang

address: 300 Pasteur Dr.

institute: Stanford University

description: Gene expression data from metastatic TNBC patient-derived xenograft tumor SUTI151M

hyb_protocol: For each sample, 12.5ug of cRNA were hybridized for 16 hours at 45ºC for using Affymetrix GeneChip Hybridization Oven 640.

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

data_processing: For the matrix table, the data were normalized using RMA in Bioconductor using default analysis settings and logged. When multiple probe set id's mapped to a single gene symbol, the probe with the largest IQR was retained. The data was sent to TNBCtype for classification.

source_name: Patient-derived xenograft tumor from soft tissue metastasis of TNBC

label_protocol: GeneChip 3'IVT express kit (Affymetrix Inc.) was used for labeling following manufacture’s instruction.

extract_protocol: RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s instructions. The quantity and purity of the RNA sample was measured using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).


title: beta-cellline_excised_rep1


title: Btk-4


title: Slp-1


title: beta-cellline_excised_rep2


title: Btk-2


title: SUTI319T xeno

description: Gene expression data from  primary TNBC patient-derived xenograft tumor SUTI319T

source_name: Patient-derived xenograft tumor from primary TNBC


title: Selected mouse Ba/F3 cells transfected with pMSCV vector expressing the FIP1L1-PDGFRA oncogene and treated with Glivec

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression profile from selected  Ba/F3 cells expressing FIP1L1-PDGFRa oncogene and treated with Glivec for 4 hours

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: Affymetrix GCOS suite version 1.4.0 was used. 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: Ba/F3 cells

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 5 µg total mRNA.

growth_protocol: Ba/F3 cells were grown in DMEM medium supplied with 10% FBS, penicillin and streptomycin.

extract_protocol: Total mRNA was extracted using Rneasy mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Oncogene-transformed cells were selected for growth in the absence of IL3. Before RNA extraction, cells were left untreated or incubated for 4 hours with 100 nM Glivec. Samples were washed once with PBS before RNA extraction. In control condition, cells were cultured in the presence of IL3.

value: pMSCV-FIP1L1-PDGFRA vector transfection + selection + 4h Glivec treatment

value: Mouse Pro B cells


title: Btk-3


title: SUTI368 xeno

description: Gene expression data from  primary TNBC patient-derived xenograft tumor SUTI368

value: Patient-derived xenograft tumor from primary TNBC


title: Selected mouse Ba/F3 cells transfected with pMSCV vector expressing the FIP1L1-PDGFRA oncogene

description: Gene expression profile from selected  Ba/F3 cells expressing FIP1L1-PDGFRa oncogene

value: pMSCV-FIP1L1-PDGFRA vector transfection + selection


title: Wt-1


title: Wt-2


title: Microarrays N2 L4 stage C. elegans N2(Wt) vs. acs-3(ft5) Replicate #1

source_name: Whole animal RNA extract N2(Wt)

value: Strain N2 Stage L4

value: wild type

value: whole organism

source_name: Whole animal RNA extract acs-3(ft5) mutant

value: Strain acs-3(ft5) mutant Stage L4

value: acs-3(ft5) mutant


title: siHic5_2_0h_2

description:
rep 2
5645326019_F

value: osteosarcoma cells

value: dexamethasone (Dex) for 0h


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. nhr-25(RNAi) Replicate #1

source_name: Whole animal RNA extract control RNAi

value: control

source_name: Whole animal RNA extract nhr-25 RNAi


title: HVC_early-deafened_young1

source_name: HVC, early-deafened, young1


title: HVC_early-deafened_juvenile2

description: Gene expression in HVC of juvenile male zebra finch deprived auditory input

source_name: HVC, early-deafened, juvenile2


title: HVC_intact_young3

description: Gene expression in HVC of young male zebra finch

source_name: HVC, intact, young3


title: HVC_intact_young2

source_name: HVC, intact, young2


title: Selected mouse Ba/F3 cells transfected with pMSCV vector expressing the ETV6-PDGFRB oncogene and treated with Glivec

description: Gene expression profile from selected  Ba/F3 cells expressing ETV6-PDGFRB oncogene and treated with Glivec for 4 hours

value: pMSCV-ETV6-PDGFRB vector transfection + selection + 4h Glivec treatment


title: SUTI151 xeno

description: Gene expression data from  primary TNBC patient-derived xenograft tumor SUTI151


title: HVC_intact_young1

source_name: HVC, intact, young1


title: Microarrays N2 L4 stage C. elegans control(RNAi) vs. nhr-25(RNAi) Replicate #3


title: HVC_early-deafened_young2

source_name: HVC, early-deafened, young2


title: Lin- BM E4bp4+/+ 5

source_name: Lin- BM E4bp4+/+ 5

value: Lineage-depleted bone marrow cells


title: Umaydis_glucose_oil

city: Tsukuba

first: Hideaki

last: Koike

state: Ibaraki

address: Higashi 1-1-1

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol.

scan_protocol: The slide was scanned to measure the fluorescence intensity of the two fluorophores using a GenePix 4200A scanner (Axon Instruments at Molecular Devices, Sunnyvale, CA).

data_processing: The raw data (.pair files) of two dyes were merged and processed using R-BioConductor package. Two-color data with dye swap experiments were normalized and analyzed by limma module. Data was normalized by setting the baseline measurement per spot and per segment of the chip via intensity dependent (LOESS) normalization with dye swap experiment using the limma module.

organism: Mycosarcoma maydis

source_name: U. maydis grown with oil

label_protocol: Two cDNA samples labeled with Cy5 and Cy3 for each were mixed and applied onto Nimblegen Gene Expression Arrays (Roche Diagnostics, Tokyo)

growth_protocol: The strains were grown in the medium (0.03% MgSO4, 0.03% KH2PO4, 0.1% yeast extract, pH 6.0 containing 5% soybean oil or 10% glucose), at 25 °C on a rotary shaker (300 rpm) for 7 days.

extract_protocol: Total RNA was isolated from cells using ISOGEN (Wako). mRNA was purified from approximately 0.2 mg total RNA using an OligotexTM-dT30 <Super> mRNA Purification kit (Takara, Shiga, Japan)

source_name: U. maydis grown with glucose


title: Selected mouse Ba/F3 cells transfected with pMSCV vector expressing the ETV6-PDGFRB oncogene

description: Gene expression profile from selected  Ba/F3 cells expressing ETV6-PDGFRB oncogene

value: pMSCV-ETV6-PDGFRB vector transfection + selection


title: SUTI110 xeno

description: Gene expression data from  primary TNBC patient-derived xenograft tumor SUTI110


title: Rag1-1b

description: pro-B cells, non-VH81x transgenic Rag1-/-

source_name: Bone marrow B-cell fraction, B220+CD19+ pro-B

value: pro-B cell

value: control (non-VH81x transgenic Rag1-/-)


title: SUTI103 xeno

description: Gene expression data from primary TNBC patient-derived xenograft tumor SUTI103


title: Pseudozyma_glucose_oil

organism: Moesziomyces antarcticus T-34

source_name: P. antarctica grown with oil

source_name: P. antarctica grown with glucose


title: HVC_early-deafened_juvenile3

source_name: HVC, early-deafened, juvenile3

value: brain

value: male


title: MSC MSC 001

status: Public on Mar 20 2014

first: Shiyu

last: Liu

address: 2250 Alcazar Street, CSA103

institute: CCMB

description: The microarray synthesis is based on a µparafl microfluidic chip technology.

hyb_protocol: LC Sciences’ Optimized RNA Hybridization Probes are designed with normalized Tms to ensure uniform hybridization affinity to their microRNA targets under high stringency hybridization conditions enhancing both the sensitivity and specificity of the probes.

scan_protocol: LC Sciences performed the scan protocol.

data_processing: LC Sciences’ in-depth data analysis includes ANOVA and heat maps by in house software for routine array data processing.

source_name: bone marrow mesenchymal cells

label_protocol: LC Sciences uses a proprietary labeling method with Cy3, which utilizes an affinity tag for signal amplification after microRNA hybridization to the chip.

growth_protocol: The single suspension of bone marrow-derived all nucleated cells (ANCs) from femurs and tibias was seeded in 10 cm culture dishes. Colonies forming attached cells were passed once for further experimental use.

extract_protocol: Total RNA was extracted using an miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The cells were cultured in normal conditions for passage one.

value: recipient MSCs from MSCT-treated

tag: Sex

value: Female

value: 11 weeks

value: MRL/lpr

value: Bone marrow


title: C3H MSC 001

value: normal control MSCs

tag: strain


title: LPR MSC 001

value: recipient MSCs from untreated


title: SUTI097 xeno

description: Gene expression data from primary TNBC patient-derived xenograft tumor SUTI097

source_name: Patient-derived xenograft tumor from primary TNBC


title: Tsetse_fly_midgut-Infected_20days-sample7

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

institute: UMR 177 IRD-CIRAD

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 20 days after infected blood meal, sample 7

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was added to 250 ml of 2x Agilent hybridization buffer and hybridized to Agilent Sodalis glossinidius custom Oligo Microarrays (earray Design ID = 041518; earray Slide Layout = IS-15744-8-V1) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09GE1_107_Sep09 and Grid: 041518_D_F_20120607) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

organism: Sodalis glossinidius

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 5µg RNA using the Chipshot Direct labeling and Clean-Up System kit (Promega) according to the manufacturer's instructions

extract_protocol: Total RNA was extracted from fly midgut by TRIzol (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Flies were exposed to Trypanosoma brucei gambiense infected mices.

tag: status

value: Infected

tag: timepoint

value: 20 days after infected blood meal

value: infected blood meal

tag: source gender

value: female fly

tag: source tissue

value: Tsetse fly midgut


title: Mouse Ba/F3 cells transfected with pMSCV empty vector supplied with IL3 and treated with Glivec

description: Gene expression profile from  Ba/F3 cells expressing control vector treated with Glivec for 4 hours and kept in culture with the presence of IL3

source_name: Ba/F3 cells

tag: treatment

value: pMSCV empty vector transfection + cuture in the presence of IL3 + 4h treatment with Glivec

tag: cell type

value: Mouse Pro B cells


title: Tsetse_fly_midgut-Infected_20days-sample4

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 20 days after infected blood meal, sample 4

tag: treated with


title: Rag1-1

value: pro-B cell

tag: genotype/variation

value: control (non-VH81x transgenic Rag1-/-)


title: Tsetse_fly_midgut-Infection_self_cleared_20days-sample12

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 20 days after infected blood meal, sample 12

value: Infection self cleared


title: Tsetse_fly_midgut-Infected_20days-sample5

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 20 days after infected blood meal, sample 5


title: Tsetse_fly_midgut-Infected_20days-sample3

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 20 days after infected blood meal, sample 3


title: Tsetse_fly_midgut-Infection_self_cleared_20days-sample18

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 20 days after infected blood meal, sample 18


title: Tsetse_fly_midgut-Infection_self_cleared_20days-sample21

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 20 days after infected blood meal, sample 21


title: Tsetse_fly_midgut-Infection_self_cleared_20days-sample25

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 20 days after infected blood meal, sample 25


title: Mouse Ba/F3 cells transfected with pMSCV empty vector supplied with IL3

description: Gene expression profile from  Ba/F3 cells expressing control vector and kept in culture with the presence of IL3

value: pMSCV empty vector transfection + cuture in the presence of IL3


title: Tsetse_fly_midgut-Infected_10days-sample2

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 10 days after infected blood meal, sample 2

value: 10 days after infected blood meal


title: Tsetse_fly_midgut-Infected_10days-sample4

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 10 days after infected blood meal, sample 4


title: Tsetse_fly_midgut-Infected_10days-sample1

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 10 days after infected blood meal, sample 1


title: Tsetse_fly_midgut-Infected_10days-sample3

description: total RNA Glossina palpalis gambiensis infected by Trypanosoma brucei gambiense, 10 days after infected blood meal, sample 3


title: Tsetse_fly_midgut-Infection_self_cleared_10days-sample5

description: total RNA Glossina palpalis gambiensis Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 5


title: Rag1-2

description: pro-B cells, non-VH81x transgenic Rag1-/-


title: Tsetse_fly_midgut-Infection_self_cleared_10days-sample4

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 4


title: Stable FLAG-HA-CSB and FLAG-CSB-PGBD3 co-expression, biological replicate 2

city: Seattle

first: Lucas

middle: T

last: Gray

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB and FLAG-CSB-PGBD3 to test the effects of coexpression of CSB and CSB-PGBD3, as in normal (not UVSS1KO) cells
UVSS1KO_CSB_CSB-PGBD3_2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The 12 datasets were normalized using the Probe Logarithmic Intensity Error (PLIER) program of the Affymetrix Expression Console v1.1.1. using the Significance Analysis for Microarrays (SAM) program of the MeV v4.4 software suite.

source_name: UVSS1KO cells stably transfected using linearized pFLAG-HA-CSB-IREShyg and pFLAG-CSB-PGBD3-IRESneo

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated by using RNeasy midi spin columns (Qiagen) and enriched for polyA+ RNA on Oligotex polydT beads (Qiagen).

treatment_protocol: pFLAG-HA-CSB-IREShyg3, pFLAG-HA-CSB-PGBD3-IREShyg3, and the empty vector pFLAG-HA-IREShyg3 were linearized with XhoI just downstream from the poly(A) site, and transfected using TransIT-LT1 reagent (Mirus) into UVSS1KO cells grown in DMEM. Selection with 100, 150 and 200 µg/ml hygromycin (Invitrogen) was begun after 24 h, and both drug and media were refreshed every 48–72 h. Confluent wells containing 50–100 colonies were trypsinized and passaged thereafter as pools. To generate doubly-transfected cells, the singly-transfected hygromycin-resistant pools were transfected with pFLAG-CSB-PGBD3-neo linearized by PvuI within the ampR gene. G418 selection was increased from 200 to 600 µg/ml while continuing 200 µg/ml hygromycin selection.

tag: selection

value: hygromycin (FLAG-HA-CSB) and neomycin (FLAG-CSB-PGBD3)

tag: immortalization

value: CSB-null UV-sensitive syndrome cells (UVSS1KO) cells

value: fibroblast


title: Stable FLAG-HA-CSB expression, biological replicate 3

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB to test the effects of CSB alone
UVSS1KO_CSB_3

source_name: UVSS1KO cells stably transfected using linearized pFLAG-HA-CSB-IREShyg

value: hygromycin

value: CSB


title: Stable FLAG-HA-CSB and FLAG-CSB-PGBD3 co-expression, biological replicate 3

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB and FLAG-CSB-PGBD3 to test the effects of coexpression of CSB and CSB-PGBD3, as in normal (not UVSS1KO) cells
UVSS1KO_CSB_CSB-PGBD3_3


title: Stable FLAG-HA-CSB-PGBD3 expression, biological replicate 2

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB-PGBD3 to test the effects of the CSB-PGBD3 fusion protein alone
UVSS1KO_CSB-PGBD3_2

source_name: UVSS1KO cells stably transfected using linearized pFLAG-HA-CSB-PGBD3-IREShyg


title: Tsetse_fly_midgut-Infection_self_cleared_3days-sample3

description: total RNA Glossina palpalis gambiensis, 3 days after non infected blood meal, sample 3

value: 3 days after uninfected blood meal

value: uninfected blood meal


title: Stable FLAG-HA-CSB-PGBD3 expression, biological replicate 3

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB-PGBD3 to test the effects of the CSB-PGBD3 fusion protein alone
UVSS1KO_CSB-PGBD3_3


title: Tsetse_fly_midgut-Infection_self_cleared_3days-sample4

description: total RNA Glossina palpalis gambiensis, 3 days after non infected blood meal, sample 4


title: Stable FLAG-HA expression, biological replicate 2

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA tags as a negative control
UVSS1KO_TAGS_2

source_name: UVSS1KO cells stably transfected using linearized pFLAG-HA-IREShyg

value: control


title: Stable FLAG-HA expression, biological replicate 1

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA tags as a negative control
UVSS1KO_TAGS_1


title: Stable FLAG-HA-CSB expression, biological replicate 2

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB to test the effects of CSB alone
UVSS1KO_CSB_2


title: Tsetse_fly_midgut-Infection_self_cleared_10days-sample2

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 2

value: infected blood meal

value: female fly


title: Tsetse_fly_midgut-Infection_self_cleared_3days-sample2

description: total RNA Glossina palpalis gambiensis, 3 days after non infected blood meal, sample 2

value: Tsetse fly midgut


title: Stable FLAG-HA expression, biological replicate 3

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA tags as a negative control
UVSS1KO_TAGS_3


title: Tsetse_fly_midgut-Infection_self_cleared_10days-sample1

description: total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 1


title: Stable FLAG-HA-CSB-PGBD3 expression, biological replicate 1

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB-PGBD3 to test the effects of the CSB-PGBD3 fusion protein alone
UVSS1KO_CSB-PGBD3_1


title: Stable FLAG-HA-CSB expression, biological replicate 1

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB to test the effects of CSB alone
UVSS1KO_CSB_1


title: Stable FLAG-HA-CSB and FLAG-CSB-PGBD3 co-expression, biological replicate 1

description:
Gene expression data from CSB-null UVSS1KO cells expressing exogenous FLAG-HA-CSB and FLAG-CSB-PGBD3 to test the effects of coexpression of CSB and CSB-PGBD3, as in normal (not UVSS1KO) cells
UVSS1KO_CSB_CSB-PGBD3_1


title: MSC MSC 001

description: MeDIP-Sequencing Service

hyb_protocol: Corresponding IP (experimental) and Input (control) samples were co-hybridized to a 385K array using the approproate protocol, according to the NimbleGen Guide. The proximal regions of gene promoters and additional CpG islands were covered by close-set 50 base oligonucleotides (approx. -1,500 to + 800 bp around TSS).

scan_protocol: The two-color (IP-Cy5/Input-Cy3) arrays were scanned applying the Nimblescan 2.4 software.

data_processing: Raw data was extracted from Nimblescan files and computed to scaled and centered log2-Cy5/Cy3 values for each oligonucleotide probe, coverted into graphic data set (.gff files with SignalMap software). All steps from labelling to data processing have been performed as a service of NimbleGen, according to NimbleGen Arrays User’s Guide for Epigenetic Arrays.

source_name: MeDIP DNA from bone marrow mesenchymal cells

label_protocol: 1 µg of whole-genome.amplified MeDIP DNA (IP) and genomic input DNA (Input) were labeled with Cy5 or Cy3 nonamers, respectively (via Klenow Fragment).

extract_protocol: Total DNA from cells at passage one was extracted using a DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

tag: sample type

value: recipient MSCs from MSCT-treated

value: Female

tag: age

value: 11 weeks

value: MRL/lpr

value: Bone marrow

tag: antibody

value: 5-methyl-cytosine (IP)

source_name: input DNA from bone marrow mesenchymal cells


title: Tsetse_fly_midgut-Infection_self_cleared_3days-sample1

description: total RNA Glossina palpalis gambiensis, 3 days after non infected blood meal, sample 1

value: Infection self cleared