title: AML patient sample number 200 set2 plate 2

city: TOULOUSE

first: DAVID

last: Laure

address: 2 avenue Hubert CURIEN

country: France

institute: Cancer Research Center of Toulouse

description:
Sample name: 200_serie2_2
thawed samples of cells from acute myeloid leukemia patients

data_processing: Values presented in the matrix non normalized data file are issues from relative quantification cycles that were calculated from the mean Cq (quantification cycle) obtained for each gene :raw data obtained from the system’s software, using the auto detector function to establish the threshold setting (BioMark Realtime PCR Analysis V2.1.1, Fluidigm), were checked using the graphical representation of the plate layout. Among all reactions investigated, 0 were rejected due to bubbles or instable ROX (Carboxy-X-Rhodamin) signal. All amplification curves were displayed for each well of the calibrator sample. When the threshold for cycle did not meet quality criteria (that is the threshold occurred in the linear phase of the amplification curve instead of the exponential phase), the threshold value was set manually. The threshold established for the first Dynamic Array were applied to the 4 other Dynamic Arrays. Wells with very high (> 26), absent (999), or very low (< 2) endogenous Ct were excluded. These raw data are then normalized with the data obtained with the housekeeping genes. Then we performed the inter-plate calibration using the qbase+ algorithm as described (Hellemans, 2007). Among the 9 housekeeping genes tested [GUSB (Hs99999908_m1), ACTB (Hs99999903_m1), ABL1 (Hs01104728_m1), G6PD (Hs00166169_m1), TBP (Hs00427621_m1), GAPDH (Hs03929097_g1), HMBS (Hs00609293_g1), B2M (Hs00984230_m1), UBC (Hs00824723_m1)], GeNorm algorithm determined the four most stable, which were GAPDH, GUSB, TBP and ABL1, and were used to calculate the gene expression normalization factor. Expression values are given in CNRQ (2^ - deltaCT).

label: FAM

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse

label_protocol: cDNA was generated from 1 µg of RNA with the SuperScript VILO cDNA Synthesis Kit (Invitrogen) for reverse transcription-PCR following the manufacturer’s suggestions. In order to ensure a good quality reverse transcription step, one part of each cDNA was used to check ABL1 (“TaqMan Gene Expression Assay”, Applied Biosystems, Hs01104728_m1) expression using ABI Prism 7300 HT (Applied Biosystems, Carlsbad, CA, USA). The other part of each cDNA was diluted in water to 5 ng/µl and used for target amplification by Biomark Dynamic Arrays (Fluidigm, BioMark, Pueblo, CO, USA). Inventoried TaqMan assays (Applied Biosystems) were pooled using 84 probes and primers pairs (72 DNA replication genes, 9 housekeeping genes - ABL, ACTB, B2MC, G6PD, GAPDH, GUSB, HPBS, TBP, UBC -, and BAALC, ERG, and MN1 genes) to a final concentration of 0.2X for each of the 84 assays. To increase sensitivity, a multiplexed pre-amplification process was performed for the pool on every 1.25 µl cDNA using 14 cycles cDNA pre-amplification step (95°C for 15s and 60°C 4 min) and Taqman PreAmp Master Mix (Applied Biosystems) in a standard PCR Thermocycler. Pre-amplified cDNA was diluted 1:5 in 10 mmol/L Tris, 1 mmol/L EDTA. Diluted cDNA (2.25 µl) was added to 2.5 µl Taqman Universal PCR Master Mix (Applied Biosystems) and 0.25 µl GE Sample Loading Reagent (Fluidigm). In a separate tube, 3.5 µl of Taqman Assay was added to 3.5 µl Sample Loading Reagent. 5 µl cDNA samples were loaded into the sample inlet wells, and 5 µl assay samples were loaded into assay detector inlets. Because 198 samples were to be analyzed in duplicated, five 96.96 Dynamic Arrays (Fluidigm) were used. For each plate, 1 well was loaded with H2O as a control for contamination. Genomic DNA (gDNA) from 3 different patients was loaded in order to check if TaqMan assays can also amplify gDNA. To verify STA (Specific Target Amplification) efficiency, a sample control gDNA and assay control RNAse P Taqman probe was treated (Lifetech PN 4316844), pre-amplified and quantified using the same master mix from the kit. The expected value cq (quantification cycle) was between 12 and 13.  To perform inter-plate calibration, a sample calibrator made of cDNA from the patient #1 was included in duplicate in each plate. The chip was primed and placed into the NanoFlex Integrated fluidic circuit controller where 8 nl of cDNA and 1 nl of Assay were mixed. Real time PCR analysis was completed on the BioMark System (Fluidigm).

extract_protocol: Total RNA were extracted from frozen cells (7 to 15 million of cells) stored in 1 ml of Tri Reagent RNA/DNA/protein isolation reagent (Molecular Research Center). The extraction was done by adding 200 µl of cold Ready Red-Chloroform isoamyl alcohol (MP Biomedicals, France) and vigorously shaking for 15 s using a vortex, then the sample was incubated on ice for at least 5 min. After centrifugation at 13 000 rpm for 15 min at 4°C, the upper aqueous phase was transferred into a new vial. One volume of isopropanol was added, the sample was vortexed and incubated for one hour at -20°C. After centrifugation at 13 000 rpm for 15 min at 4°C, the pellet was dried and 1 ml of cold 75% ethanol added. After centrifugation at 8000 rpm for 10 min at 4°C, the pellet was dried and incubated for 4 min at 65°C. The pellet was resuspended in 30 µl of RNAse-free water with RiboLock RNase Inhibitor (40U, Fermentas, France). RNA concentration was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc, Thermo Scientific, Brebières, France). RNA quality and purity was assessed on the Agilent 2100 BioAnalyser by using the Agilent RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA). Only RNA presenting a RIN (RNA Integrity Number) > 6.5 were selected for expression analysis (~ 90% of the samples had a RIN > 8).

value: acute myeloid leukemia

value: leukemic cells

value: bone marrow


title: AML patient sample number 204 set2 plate 2

status: Public on Sep 21 2016

type: RNA

description:
Sample name: 204_serie2_2
thawed samples of cells from acute myeloid leukemia patients

molecule: total RNA

organism: Homo sapiens

tag: diagnosis

tag: cell type

tag: tissue


title: control2

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using quantilenormalization by using GenomeStudio software v.3 (Illumina).

organism: Mus musculus

source_name: mouse, stellate cell, control,2

extract_protocol: RNA was isolated from primary mouse hepatic stellate cell (Passage 0) with Triazol reagent (Invitrogen) followed by a cleanup procedure using QIAGEN RNeasy minicolumns according to manufacturer’s protocol.

treatment_protocol: Six week-old female IL-15RaKO and wild type (WT) B6/129 mice were purchased from Jackson Laboratories (Bar Harbor, ME). All procedures were performed in accordance with the Institutional Animal Care and Use Committee Protocols of the Mount Sinai School of Medicine. Mouse HSCs were isolated from WT and IL-15RKO mice using an established method with modifications. Briefly, the mouse liver was perfused in situ with pronase and collagenase, followed by Percoll (GE) density gradient centrifugation. HSC cultures were maintained in Dulbecco's Modified Eagle Medium with 20% Fetal Bovine Serum.

tag: strain

value: stellate cell

tag: genotype/variation

value: control


title: AML patient sample number 201 set2 plate 2

description:
Sample name: 201_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 198 set2 plate 2

description:
Sample name: 198_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 205 set2 plate 2

description:
Sample name: 205_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: control3

scan_protocol: Refer to the Illumina beadarray Assay System Manual

source_name: mouse, stellate cell, control,3


title: AML patient sample number 196 set2 plate 2

description:
Sample name: 196_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 195 set2 plate 2

description:
Sample name: 195_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: IL15RaKO1

source_name: mouse, stellate cell, IL15Ra-knockout,1

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: KO_4

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, and Behavior

institute: University of California Davis

hyb_protocol: Equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-ket arrays (Agilent). Hybridizations were performed for 14 hours, according to manufacturer's protocol (Agilent).

scan_protocol: Arrays were scannd using Agilent microarray scanner (Agilent, G2505B) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent) using default parameters (protocol GE1-107, grid 014868_D_F_20080627).

data_processing: Datasets were normalized using the quantile normalization method (Bolstad et al. 2003). Hybridization performance was assessed by Agilent Feature Extraction v10.1 (Agilent).

source_name: Medial ganglionic eminence

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplificant kits following the manufacturer's protocol (Agilent). Labeled cRNA was assessed using the Nanodrop ND-100.

extract_protocol: Total RNA was isolated from micro-dissected tissue using the RNeasy Mini Kit (Qiagen). RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer.

tag: genotype

tag: age

value: embryonic day 13.5

value: Medial ganglionic eminence


title: AML patient sample number 206 set2 plate 2

description:
Sample name: 206_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: KO_1


title: WT_2


title: WT_4


title: AML patient sample number 199 set2 plate 2

description:
Sample name: 199_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 203 set2 plate 2

description:
Sample name: 203_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: KO_2


title: AML patient sample number 194 set2 plate 2

description:
Sample name: 194_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 202 set2 plate 2

description:
Sample name: 202_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 197 set2 plate 2

description:
Sample name: 197_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: WT_1


title: AML patient sample number 193 set2 plate 2

description:
Sample name: 193_serie2_2
thawed samples of cells from acute myeloid leukemia patients

value: blood


title: AML patient sample number 192 set2 plate 2

description:
Sample name: 192_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 191 set2 plate 2

description:
Sample name: 191_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: WT_3


title: AML patient sample number 189 set2 plate 2

description:
Sample name: 189_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 186 set2 plate 2

description:
Sample name: 186_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 187 set2 plate 2

description:
Sample name: 187_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 188 set2 plate 2

description:
Sample name: 188_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 185 set2 plate 2

description:
Sample name: 185_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 181 set2 plate 2

description:
Sample name: 181_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 182 set2 plate 2

description:
Sample name: 182_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 180 set2 plate 2

description:
Sample name: 180_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 183 set2 plate 2

description:
Sample name: 183_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 184 set2 plate 2

description:
Sample name: 184_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 190 set2 plate 2

description:
Sample name: 190_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 178 set2 plate 2

description:
Sample name: 178_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 177 set2 plate 2

description:
Sample name: 177_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 174 set2 plate 2

description:
Sample name: 174_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 179 set2 plate 2

description:
Sample name: 179_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 176 set2 plate 2

description:
Sample name: 176_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 175 set2 plate 2

description:
Sample name: 175_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 173 set2 plate 2

description:
Sample name: 173_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 171 set2 plate 2

description:
Sample name: 171_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 172 set2 plate 2

description:
Sample name: 172_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: KO_3


title: AML patient sample number 169 set2 plate 2

description:
Sample name: 169_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 166 set2 plate 1

description:
Sample name: 166_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 167 set2 plate 1

description:
Sample name: 167_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 163 set2 plate 1

description:
Sample name: 163_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 162 set2 plate 1

description:
Sample name: 162_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 168 set2 plate 1

description:
Sample name: 168_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 165 set2 plate 1

description:
Sample name: 165_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 159 set2 plate 1

description:
Sample name: 159_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 160 set2 plate 1

description:
Sample name: 160_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 158 set2 plate 1

description:
Sample name: 158_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 170 set2 plate 2

description:
Sample name: 170_serie2_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 154 set2 plate 1

description:
Sample name: 154_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 153 set2 plate 1

description:
Sample name: 153_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 155 set2 plate 1

description:
Sample name: 155_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 156 set2 plate 1

description:
Sample name: 156_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 164 set2 plate 1

description:
Sample name: 164_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 152 set2 plate 1

description:
Sample name: 152_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 149 set2 plate 1

description:
Sample name: 149_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 151 set2 plate 1

description:
Sample name: 151_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 150 set2 plate 1

description:
Sample name: 150_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 145 set2 plate 1

description:
Sample name: 145_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 157 set2 plate 1

description:
Sample name: 157_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 141 set2 plate 1

description:
Sample name: 141_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 161 set2 plate 1

description:
Sample name: 161_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 146 set2 plate 1

description:
Sample name: 146_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 144 set2 plate 1

description:
Sample name: 144_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 148 set2 plate 1

description:
Sample name: 148_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 147 set2 plate 1

description:
Sample name: 147_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 139 set2 plate 1

description:
Sample name: 139_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 137 set2 plate 1

description:
Sample name: 137_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 138 set2 plate 1

description:
Sample name: 138_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 135 set2 plate 1

description:
Sample name: 135_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 136 set2 plate 1

description:
Sample name: 136_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML12_PBS_replicate_3

status: Public on Sep 22 2016

city: Durham

first: Matthew

last: Hirschey

state: NC

address: 300 N. Duke Street

department: Department of Medicine

institute: Duke University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina expression microarray data underwent a strict quality control evaluation using the lumi Bioconductor package from the R statistical programming environment.  Raw data underwent a variance stabilizing transformation followed by robust spline normalization to eliminate systematic differences across the arrays.

label: biotin

source_name: AML12 cells, treated 24h

label_protocol: Standard Illumina labeling protocol

growth_protocol: AML12 immortalized hepatocytes (ATCC) were plated at 350,000 cells per well in 6-well plates and allowed seed overnight.

extract_protocol: Cells were washed with PBS, lysed with Bio-Rad Aurum RNA lysis buffer and frozen at -80°C. RNA was collected using the Bio-Rad Aurum mini kit.

treatment_protocol: The following day cells were treated with PBS, 1 mM, 2 mM or 5 mM octanoate for 24 hours added to complete DMEM media with 10% FBS.

tag: agent

value: PBS

value: AML12 cells, immortalized mouse hepatocytes


title: AML patient sample number 143 set2 plate 1

description:
Sample name: 143_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 142 set2 plate 1

description:
Sample name: 142_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 134 set2 plate 1

description:
Sample name: 134_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 132 set2 plate 1

description:
Sample name: 132_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 131 set2 plate 1

description:
Sample name: 131_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 140 set2 plate 1

description:
Sample name: 140_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 133 set2 plate 1

description:
Sample name: 133_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 128 set2 plate 1

description:
Sample name: 128_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 126 set1 plate 3

description:
Sample name: 126_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 124 set1 plate 3

description:
Sample name: 124_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 127 set1 plate 3

description:
Sample name: 127_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 121 set1 plate 3

description:
Sample name: 121_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 125 set1 plate 3

description:
Sample name: 125_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 120 set1 plate 3

description:
Sample name: 120_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 130 set2 plate 1

description:
Sample name: 130_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 122 set1 plate 3

description:
Sample name: 122_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 116 set1 plate 3

description:
Sample name: 116_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 123 set1 plate 3

description:
Sample name: 123_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 114 set1 plate 3

description:
Sample name: 114_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 119 set1 plate 3

description:
Sample name: 119_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 118 set1 plate 3

description:
Sample name: 118_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 112 set1 plate 3

description:
Sample name: 112_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 111 set1 plate 3

description:
Sample name: 111_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 110 set1 plate 3

description:
Sample name: 110_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 113 set1 plate 3

description:
Sample name: 113_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 129 set2 plate 1

description:
Sample name: 129_serie2_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 107 set1 plate 3

description:
Sample name: 107_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 108 set1 plate 3

description:
Sample name: 108_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 109 set1 plate 3

description:
Sample name: 109_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 105 set1 plate 3

description:
Sample name: 105_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 103 set1 plate 3

description:
Sample name: 103_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 104 set1 plate 3

description:
Sample name: 104_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 102 set1 plate 3

description:
Sample name: 102_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: COUPTF2_unstim_2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description:
experiment 2
5796618055_E

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: fetal liver

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre Nano Total-Amp kit

growth_protocol: Pregnant CD1 strain mice at day 14.5 in gestation were obtained from Charles River. Single cell suspensions prepared from dissected fetal livers were purified over Ficoll-paque (GE Healthcare), residual erythrocytes were lysed by ammonium chloride treatment, and c-kit (CD117) positive cells were immuno-purified by positive section over magnetic columns (Miltenyi Biotech). 2 x10^5 c-kit+ cells were retrovirally transduced with 500ul of retroviral supernatant by centrifugation at 3200xg for 2hours at 20°C.  To produce retrovirus, TLX and COUPTF2 coding sequence were PCR amplified from the MGC sport6 vector using a forward primer that incorporated a BglII restriction site and flag-tag, and a reverse primer that incorporated an XhoI site. PCR products were digested and cloned into a murine stem cell virus (MSCV)-based retroviral expression vector containing a puromycin selection cassette and an internal ribosomal entry site (IRES) driving GFP expression and sequence verified (Mayr and Bartel, 2009). Retrovirus was produced by calcium phosphate transfection of HEK293T cells with 15 ug each of retroviral expression vector and pCL-eco packaging vector (Naviaux et al., 1996). Media was changed 6 hours after transfection, and supernatants containing virus were collected 24 and 30 hours later.

extract_protocol: RNA was isolated using the RNeasy Plus kit (Qiagen) and quality was assessed by Bioanalyzer (Agilent)

treatment_protocol: Retroviral supernatant was removed and cells were plated in a single well of 6-well plate in 2 ml lineage commitment media prepared in Iscove’s Modified Dulbecco’s Media (IMDM) containing: 10% platelet-depleted serum; 10% protein free hybridoma media; Glutamax; penicillin/streptomycin; stem cell factor (SCF, 100 ng/ml); methyl thiogalactoside (MTG, 400 uM, Sigma Aldrich); interleukin-6 (IL-6, 10 ng/ml); thrombopoietin (TPO, 5 ng/ml); human erythropoietin (EPO, 2 U/ml); interleukin-3 (IL-3, 1 ng/ml); interleukin-11 (IL-11, 5 ng/ml); granulocyte/monocyte- colony stimulating factor (GM-CSF, 3 ng/ml); monocyte-colony stimulating factor (M-CSF, 5 ng/ml).  These cultures were either left 'unstimulated' or interferon-gamma (IFN-γ, 20 ng/ml) was included in the lineage commitment media.  Unless otherwise noted, all media supplements were from Gibco, and recombinant cytokine and growth factors were murine and were obtained from Peprotech. After two days in culture, 2 ml fresh lineage media and puromycin (2 ug/ml) were added to cultures. One day 5 of culture, cells were recovered, analyzed by flow cytometry for lineage markers, and CD11b+ cells were immuno-purified from cultures by positive section over magnetic columns (Miltenyi Biotech).

tag: retroviral transduction

value: COUPTF retrovirus

tag: stimulation

value: unstimulated


title: COUPTF2_unstim_1

description:
experiment 1
5796618055_D


title: TLX_unstim_3

description:
experiment 3
5796618055_C

value: TLX retrovirus


title: AML patient sample number 115 set1 plate 3

description:
Sample name: 115_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 101 set1 plate 3

description:
Sample name: 101_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: COUPTF2_unstim_3

description:
experiment 3
5796618055_F


title: AML patient sample number 117 set1 plate 3

description:
Sample name: 117_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 100 set1 plate 3

description:
Sample name: 100_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 098 set1 plate 3

description:
Sample name: 098_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: TLX_unstim_2

description:
experiment 2
5796618055_B


title: AML patient sample number 106 set1 plate 3

description:
Sample name: 106_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: 3OC6-HSL-treated Arabidopsis vs. Control Arabidopsis

city: Shijiazhuang

first: Qian

last: Zhao

address: 46th South Street of Friendship

country: China

institute: Biology Institute, Hebei Academy of Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (3×SSC, 0.2%SDS, 5×Denhart’s, 25%Formamid) were added, and samples were applied to microarrays overnight in 42℃. After hybridization, slides were washed sequential

scan_protocol: Scanned on  the LuxScan 10KA two-channel laser scanner (CapitalBio, Beijing, China). Images were quantified using the LuxScan 3.0 (CapitalBio, Beijing, China) software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Call = check status of probe (P = checked, M = unchecked, A = low reliability)

organism: Arabidopsis thaliana

source_name: 3OC6-HSL-treated Arabidopsis wild-type Col-0 seedling

label_protocol: The probes were prepared using the CapitalBio® cRNA amplified labeling kit (Capitalbio, Beijing, China) and fluorescently labeled with Cy5-dCTP and Cy3-dCTP (GE Healthcare).

growth_protocol: Seedlings germinated on MS agar plates for 10 days were transplanted into a sterile hydroponic system containing sterile Hoagland medium. After 7 days, seedlings were used for N-acyl-homoserine lactones (AHLs) treatments.

extract_protocol: Total RNA was extracted from treated and control plants using the RNAiso Plus reagent (TaKaRa, Dalian, China) and purified using the NucleoSpin® RNA clean-up kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions.

treatment_protocol: 17-day-old seedling roots were soaked in Hoagland medium with 1µM 3OC6-HSL. After 24h seedlings were harvested for RNA extraction.

tag: cultivar

value: seedling

value: 17 day

source_name: untreated Arabidopsis wild-type Col-0 seedling


title: P0-dLGN-KO 2

city: San Juan de Alicante

first: Guillermina

last: López-Bendito

state: Alicante

address: Av. Ramón y Cajal, s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias de Alicante CSIC & UMH

description: Gene expression data from P0 dLGN (Sema6A-/-)

hyb_protocol: Mouse Genome 430 2.0 Array following the standard affymetrix protocol.

scan_protocol: Arrays were scanned on a 7G Affymetrix GeneChip Scanner.

data_processing: RMA normalization

source_name: Thalamic sample from Sema6A KO

label_protocol: 20 ng of total RNA were used for target preparation using the Nugen Ovation RNA amplification Systme V2 kit. Fragmentation and Labeling following were performed with the Encore Biotin v1 Module of Nugen.

growth_protocol: Mutant mice maintained on a C57BL/6 background were housed in a pathogen free Animal House under controlled temperature and light cycle

extract_protocol: RNA was extracted from the collected tissue using the RNeasy Mini Kit (Qiagen), including a DNaseI step.

treatment_protocol: To collect tissue from the dLGN nuclei at neonatal stages, animals were sacrificed and their brain was dissected out in RNase-free conditions to prevent RNA degradation. Vibratome sections (200μm) were obtained and collected in ice-cold oxygenated aCSF (117mM NaCl, 4.7mM KCl, 1.2mM MgCl2, 2.5mM CaCl2, 1.2mM NaH2PO4, 25mM NaHCO3 and 0.45% D-glucose), and the thalamic nucleus was rapidly microdissected under a microscope. The tissue was maintained overnight at 4 ºC in RNA-Later (Sigma) and stored at -80 ºC for subsequent RNA extraction.

value: Sema6A KO

value: dLGN thalamic nucleus

tag: background strain


title: control_IFNg_2

description:
experiment 2
5796618027_E

value: control retrovirus

value: IFN-gamma


title: control_IFNg_3

description:
experiment 3
5796618027_F


title: AML patient sample number 096 set1 plate 3

description:
Sample name: 096_serie1_3
thawed samples of cells from acute myeloid leukemia patients

value: acute myeloid leukemia

value: leukemic cells

value: bone marrow


title: P0-dLGN-CTRL 3

description: Gene expression data from P0 dLGN (control)

source_name: Thalamic sample from Sema6A HET

value: Sema6A heterozygous


title: P0-dLGN-CTRL 1


title: P0-dLGN-CTRL 2


title: P0-dLGN-KO 1


title: control_IFNg_1

description:
experiment 1
5796618027_D


title: eWAT_MUT_CT19a

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

country: Germany

institute: University of Lübeck

hyb_protocol: 17 hours, 60 rpm, 45C

scan_protocol: GeneChip Scanner 3000

data_processing: Data were extracted from CEL files and normalized by RMA method using Expression Console (Affymetrix) software.

label: Biotin

source_name: Mediobasal hypothalamus

label_protocol: Labelling was with GeneChip WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen)

treatment_protocol: MUT mice carry a functional deletion of circadian clock function in the SCN pacemaker.  All mice were kept under LD conditions for two weeks and then released into DD. On the second day mice were killed at 6-h intervals starting at CT1 (27h after lights off) by cervical dislocation. eWAT samples were dissected and stored in RNAlater at 4°C ON and then at -20°C.

value: Syt10-Cre/Cre x Bmal1-flox/-

tag: time point


title: eWAT_MUT_CT13c

description: GeneChip WT Terminal Labeling Kit (Affymetrix)


title: TLX_unstim_1

description:
experiment 1
5796618055_A


title: AML patient sample number 097 set1 plate 3

description:
Sample name: 097_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 092 set1 plate 2

description:
Sample name: 092_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 093 set1 plate 2

description:
Sample name: 093_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_MUT_CT19b


title: control_unstim_3

description:
experiment 3
5796618027_C


title: AML patient sample number 090 set1 plate 2

description:
Sample name: 090_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 088 set1 plate 2

description:
Sample name: 088_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_MUT_CT13b


title: AML patient sample number 095 set1 plate 3

description:
Sample name: 095_serie1_3
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 087 set1 plate 2

description:
Sample name: 087_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: control_unstim_2

description:
experiment 2
5796618027_B


title: eWAT_MUT_CT13a


title: control_unstim_1

description:
experiment 1
5796618027_A


title: eWAT_MUT_CT19c


title: eWAT_MUT_CT7c


title: AML patient sample number 086 set1 plate 2

description:
Sample name: 086_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_MUT_CT1b


title: eWAT_MUT_CT1c


title: eWAT_CON_CT19c

value: Syt10-Cre/Cre x Bmal1-+/-


title: eWAT_MUT_CT7b


title: AML patient sample number 085 set1 plate 2

description:
Sample name: 085_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: ClassIII_rep_2

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description: ClassIII da neuron-2

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Drosophila Melanogaster Genome Oligo Microarrays 4 x 44K (table 3) using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies)

data_processing: The Agilent Feature Extraction Software (FES, v.10.5.1.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. GeneSpring (Agilent) was used to normalize and analyze raw dataset. The raw data was quantile normalized, and the values were thresholded to 1.

organism: Drosophila melanogaster

source_name: Class-III da neuron-Larval L3 Stage

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: The isolation and purification of C-III da neurons was performed as previously described (Iyer et al., 2009). Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the ppk-Gal4,UAS-mCD8::GFP,ppk-Gal80 driver were collected and washed several times in ddH20. The larvae were rinsed in RNAse away followed by ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate was incubated with magnetic beads coupled with rat anti-CD8 antibody (Invitrogen) for 60 minutes. Finally the C-III neurons attached to the magnetic beads were separated using a powerful magnetic field. The cells were washed 5 times, before lysing them in SuperAmp™ (Miltenyi Biotec) RNA lysis buffer followed by storage of the RNA at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

tag: strain background

value: Oregon-R

tag: developmental stage

value: Larval L3

value: Class-III da neuron


title: ClassIII_rep_1

description: ClassIII da neuron-1


title: eWAT_CON_CT19a


title: eWAT_CON_CT13b


title: AML patient sample number 082 set1 plate 2

description:
Sample name: 082_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_CON_CT13c


title: eWAT_MUT_CT1a


title: eWAT_CON_CT7c


title: AML patient sample number 080 set1 plate 2

description:
Sample name: 080_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 079 set1 plate 2

description:
Sample name: 079_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 081 set1 plate 2

description:
Sample name: 081_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_CON_CT7b


title: Reactive hyperplasia 3

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

molecule: genomic DNA

source_name: Lymph Node  neck

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

value: Reactive hyperplasia

tag: gender

value: Male

value: FFPE


title: Reactive hyperplasia 2

source_name: left submental Lymph Node

value: Female


title: AML patient sample number 071 set1 plate 2

description:
Sample name: 071_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 077 set1 plate 2

description:
Sample name: 077_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 078 set1 plate 2

description:
Sample name: 078_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 069 set1 plate 2

description:
Sample name: 069_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_CON_CT1a

description: GeneChip WT Terminal Labeling Kit (Affymetrix)


title: eWAT_MUT_CT7a


title: AML patient sample number 070 set1 plate 2

description:
Sample name: 070_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 068 set1 plate 2

description:
Sample name: 068_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 076 set1 plate 2

description:
Sample name: 076_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: eWAT_CON_CT19b


title: eWAT_CON_CT1b


title: AML patient sample number 066 set1 plate 2

description:
Sample name: 066_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 067 set1 plate 2

description:
Sample name: 067_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 074 set1 plate 2

description:
Sample name: 074_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 075 set1 plate 2

description:
Sample name: 075_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Thalamic E18.5 green cells, biological rep3

description: Tamoxifen, 4mg at E9

hyb_protocol: Following fragmentation and labelling of 5 μg of ssDNA (NuGen Encore Biotin Module, #4200-12), cDNA samples were hybridized for 16 hours at 45°C on Affymetrix Mouse Gene 2.0 ST Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Quality controls, including determination of expression background levels, were done with Affymetrix Expression Console using Affymetrix default analysis settings before data was transferred to GeneSpring 12.6 (Agilent) for further analysis ((Affymetrix Expression experiment type; Exon analysis type, RMA16 summarization algorithm).

source_name: E18.5 green

label_protocol: Biotinylated cDNA was synthesized from 10 ng of total RNA using the Nugen Ovation Pico WTA System V2 kit (catalogue # 3302-12).

growth_protocol: Mutant mice were kept on a c57/BL6 genetic background.

extract_protocol: FACS was used to isolate cells. RNeasy mini kit (Qiagen) was used for total RNA extractions.

treatment_protocol: Tamoxifen delivered to pregnant females at E9–E9.5.

value: Embryonic day 18.5

value: embryonic thalamus


title: Thalamic E14.5 red cells, biological rep2

description: Tamoxifen, 4mg at E9.5

source_name: E14.5 red

value: Embryonic day 14.5


title: Pediatric type Follicular Lymphoma 38

source_name: Submandibular Lymph Node

value: Pediatric type Follicular Lymphoma


title: Pediatric type Follicular Lymphoma 37

source_name: Left parotid Lymph Node


title: Thalamic E18.5 double labeled cells, biological rep1

description: Tamoxifen, 4mg at E9

source_name: E18.5 yellow


title: Thalamic E14.5 green cells, biological rep2

description: Tamoxifen, 4mg at E9.5

source_name: E14.5 green


title: AML patient sample number 065 set1 plate 2

description:
Sample name: 065_serie1_2
thawed samples of cells from acute myeloid leukemia patients

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse

value: acute myeloid leukemia


title: Thalamic E18.5 double labeled cells, biological rep2

description: Tamoxifen, 4mg at E9


title: Thalamic E14.5 red cells, biological rep3

description: Tamoxifen, 4mg at E9.5


title: eWAT_CON_CT13a


title: Thalamic E14.5 green cells, biological rep1

description: Tamoxifen, 4mg at E9.5


title: Thalamic E14.5 red cells, biological rep1

description: Tamoxifen, 4mg at E9.5


title: Thalamic E18.5 green cells, biological rep2

description: Tamoxifen, 4mg at E9


title: Thalamic E14.5 green cells, biological rep3

description: Tamoxifen, 4mg at E9.5


title: Pediatric type Follicular Lymphoma 36


title: eWAT_CON_CT1c


title: eWAT_CON_CT7a


title: Pediatric type Follicular Lymphoma 35

source_name: Left Lymph Node axillary


title: AML patient sample number 064 set1 plate 2

description:
Sample name: 064_serie1_2
thawed samples of cells from acute myeloid leukemia patients

value: leukemic cells


title: Pediatric type Follicular Lymphoma 34

source_name: Post auricular lump


title: AML patient sample number 063 set1 plate 2

description:
Sample name: 063_serie1_2
thawed samples of cells from acute myeloid leukemia patients

value: bone marrow


title: AML patient sample number 062 set1 plate 2

description:
Sample name: 062_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 33

description: Hybridized to Affymetrix OncoScan FFPE Assay

source_name: Lymph Node parotid gland


title: Pediatric type Follicular Lymphoma 32

source_name: Cervical Lymph Node


title: Pediatric type Follicular Lymphoma 31

source_name: Left cervical Lymph Node


title: Pediatric type Follicular Lymphoma 29

source_name: right maxillary sinus Lymph Node


title: AML patient sample number 061 set1 plate 2

description:
Sample name: 061_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 30

source_name: Inguinal Lymph Node


title: AML patient sample number 059 set1 plate 2

description:
Sample name: 059_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 28

source_name: Right cervical Lymph Node


title: AML patient sample number 060 set1 plate 2

description:
Sample name: 060_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 27

source_name: right prehyoidal Lymph Node


title: AML patient sample number 058 set1 plate 2

description:
Sample name: 058_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 26


title: AML patient sample number 055 set1 plate 2

description:
Sample name: 055_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 057 set1 plate 2

description:
Sample name: 057_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 056 set1 plate 2

description:
Sample name: 056_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 054 set1 plate 2

description:
Sample name: 054_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 053 set1 plate 2

description:
Sample name: 053_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Thalamic E18.5 double labeled cells, biological rep3

description: Tamoxifen, 4mg at E9


title: AML patient sample number 052 set1 plate 2

description:
Sample name: 052_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: Thalamic E18.5 red cells, biological rep1

description: Tamoxifen, 4mg at E9

source_name: E18.5 red


title: Pediatric type Follicular Lymphoma 24

source_name: Left elbow mass


title: Pediatric type Follicular Lymphoma 23


title: Thalamic E18.5 green cells, biological rep1

description: Tamoxifen, 4mg at E9

source_name: E18.5 green


title: Thalamic E18.5 red cells, biological rep2

description: Tamoxifen, 4mg at E9


title: siRNA-MEFV a1 Human myelomonocytic THP-1 cells

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description:
siRNA_a1
72 h with 1 μM mixture of four different Accell siRNAs against MEFV.

hyb_protocol: Fifteen micrograms of fragmented cRNA of each sample were hybridized to miRNA-3_0 chips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix).

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the Expression Console software version 1.3.1 from Affymetrix.

data_processing: Data were analyzed analogue to High Performance Chip Data Analysis (HPCDA). Therefore, RMA normalized or without RMA normalization exported Signals (latter normalized with 4 different methods or scaled only) from Expression Console were analyzed with Access databases (Microsoft) using the default filter parameters for decreased and increased gene lists (as described in Biesen et al., 2008; PubMed ID: 18383365) to obtain seven different lists of significant miRNAs from each normalization. All 5 chips of group 1 (scr-siRNA, Experiment group) were compared to all the 4 chips of group 2 (siRNA-MEFV, Baseline group; chip siRNA_a3_miRNA-3_0 did not meet the QC criteria and was skipped for HPCDA) in this direction and chips within each group were compared to each other in both directions (due to blinded analyses for the publication the siRNA-MEFV group is the Experiment group and scr-siRNA is the Baseline group; sign of FC and related data changes therefore). The following parameters of absolute and comparative analysis were included in the Access database for all seven differently normalized Signal data sets: Normalized expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A or Present, P), log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Decrease, D or No Change, NC). Additionally, t-tests of log10 Signals and SLRs were included in the database. For each present transcript, the significance of differential expression between the two groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 20 SLR values of Experiment group vs. Baseline group and 20 + 12 = 32 SLR values within both groups (the latter 32 giving a mean SLR value of zero; p-value had to be <= 3.84E-08) or more than 50% of calculated Change calls i.e. 11 or more of all 20 Change calls had to be in the same direction and not No Changed. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Finally, published list of 29 miRNAs was reduced with help of Gene List Significance Index (GLSI), HPCDA-Score and HPCDA-Volcano-Plot (c.f.: https://www.researchgate.net/publication/292152558_Selection_of_29_miRNAs_with_High_Performance_Chip_Data_Analysis_HPCDA_GenesWork_Fold_Change_HPCDA-Score_and_HPCDA-Volcano-Plot). Default filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site, check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each, were analyzed in BioRetis with all possible 3 vs. 3 chips comparisons (one direction).

source_name: Human myelomonocytic THP-1 cells, siRNA-MEFV

label_protocol: Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA).

growth_protocol: Human myelomonocytic THP-1 cells were grown in RPMI-1640 medium supplemented with 10% heat-inactivated FBS, penicillin (100 U/ml)/streptomycin (0.1 mg/ml) and 0.5 mM β-mercaptoethanol in 5% CO2 at 37 °C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and amount was checked with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: THP-1 cells were seeded at the density of 1.0E06 cells/ml and transiently transfected for 72 h with 1 μM mixture of four different Accell siRNAs (0.25 μM each) against MEFV (siRNA-MEFV; Thermo Fisher Scientific) using siRNA delivery medium supplemented with low serum medium (range 0-3% FCS) according to the manufacturer's instructions. The Accell siRNAs are lipophilic and are readily taken up by the THP-1 cells under low FCS conditions (up to 3%). Control cells were also incubated for 72 h with RPMI medium alone (mock-transfected cells) or siRNA delivery medium plus non-silencing control/scrambled siRNA (scr-siRNA). Three days after transfection, cell lysates from mock transfected, siRNA-MEFV and scr-siRNA samples were collected and used to assess MEFV mRNA knockdown levels.

tag: cell line

value: myelomonocytic cells

tag: treatment

value: siRNA-MEFV


title: siRNA-MEFV b2 Human myelomonocytic THP-1 cells

description:
siRNA_b2
72 h with 1 μM mixture of four different Accell siRNAs against MEFV.

tag: cell type


title: siRNA-MEFV a2 Human myelomonocytic THP-1 cells

description:
siRNA_a2
72 h with 1 μM mixture of four different Accell siRNAs against MEFV.


title: siRNA-MEFV a3 Human myelomonocytic THP-1 cells (not used for HPCDA, QC not passed)

description:
siRNA_a3 (not used for HPCDA, QC not passed).
72 h with 1 μM mixture of four different Accell siRNAs against MEFV.


title: Thalamic E18.5 red cells, biological rep3

description: Tamoxifen, 4mg at E9

tag: tissue


title: siRNA-MEFV b1 Human myelomonocytic THP-1 cells

description:
siRNA_b1
72 h with 1 μM mixture of four different Accell siRNAs against MEFV.


title: scr-siRNA b2 Human myelomonocytic THP-1 cells

description:
scr-siRNA_b2
siRNA delivery medium plus non-silencing control/scrambled siRNA.

source_name: Human myelomonocytic THP-1 cells, scr-siRNA

value: scr-siRNA


title: AML patient sample number 050 set1 plate 2

description:
Sample name: 050_serie1_2
thawed samples of cells from acute myeloid leukemia patients

tag: diagnosis


title: AML patient sample number 051 set1 plate 2

description:
Sample name: 051_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: scr-siRNA b1 Human myelomonocytic THP-1 cells

description:
scr-siRNA_b1
siRNA delivery medium plus non-silencing control/scrambled siRNA.


title: scr-siRNA a2 Human myelomonocytic THP-1 cells

description:
scr-siRNA_a2
siRNA delivery medium plus non-silencing control/scrambled siRNA.


title: Pediatric type Follicular Lymphoma 22

description: Hybridized to Affymetrix OncoScan FFPE Assay


title: Pediatric type Follicular Lymphoma 21

source_name: Left Intraparotid Lymph Node


title: Pediatric type Follicular Lymphoma 25

source_name: Right inguinal Lymph Node


title: Pediatric type Follicular Lymphoma 20

source_name: Occipital Lymph Node


title: AML patient sample number 049 set1 plate 2

description:
Sample name: 049_serie1_2
thawed samples of cells from acute myeloid leukemia patients

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse


title: AML patient sample number 048 set1 plate 2

description:
Sample name: 048_serie1_2
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 047 set1 plate 1

description:
Sample name: 047_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 19

source_name: right jugular


title: Pediatric type Follicular Lymphoma 18

source_name: right thign Lymph Node


title: scr-siRNA a3 Human myelomonocytic THP-1 cells

description:
scr-siRNA_a3
siRNA delivery medium plus non-silencing control/scrambled siRNA.


title: AML patient sample number 045 set1 plate 1

description:
Sample name: 045_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 17


title: AML patient sample number 046 set1 plate 1

description:
Sample name: 046_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 16

source_name: Axilary Lymph Node


title: Pediatric type Follicular Lymphoma 14

source_name: Left submandibular Lymph Node


title: Pediatric type Follicular Lymphoma 15

source_name: parotid Lymph Node neck


title: scr-siRNA a1 Human myelomonocytic THP-1 cells

description:
scr-siRNA_a1
siRNA delivery medium plus non-silencing control/scrambled siRNA.


city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 3µm

data_processing: Agilent Feature Extraction software version 11.0.1.1; GeneSpring GX software version 12.1

source_name: Reference sample: pool of spleen B cells from 5 Dock10 knockout mice samples before culture (Pre from 6 to 10)

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: Mice were euthanized by carbon dioxide; spleens were surgically excised and crushed through a 100 µm strainer; spleen B cells were negatively selected with the Pan B cell Isolation Kit, mouse (Miltenyi Biotec) following the manufacturer's instructions; five of the samples from each group, wt and ko, were cultured for 18 hr in RPMI-1640 medium supplemented with 10% fetal calf serum with nothing or with 10 ng/ml mouse recombinant IL-4.

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: 10 ng/ml mouse recombinant IL-4 (BD Biosciences) or nothing

tag: strain

tag: genotype/variation

value: KO

value: Pre

tag: sample

value: spleen B cell

value: 12 weeks

tag: reference composition

value: Spleen B cell pool of KO samples 6 to 10, before culture (Pre)

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 9 cultured with IL-4

tag: test composition

value: Spleen B cell KO IL-4 sample 9


tag: age

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 10 cultured with IL-4

value: Spleen B cell KO IL-4 sample 10


title: Pediatric type Follicular Lymphoma 13

source_name: Posterior auricular

value: Male

value: FFPE


title: AML patient sample number 043 set1 plate 1

description:
Sample name: 043_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 044 set1 plate 1

description:
Sample name: 044_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 040 set1 plate 1

description:
Sample name: 040_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 042 set1 plate 1

description:
Sample name: 042_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 041 set1 plate 1

description:
Sample name: 041_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 9

source_name: Cervical Lymph Node


source_name: Test sample: Spleen B cells from Dock10 knockout mouse 8 cultured with IL-4

value: Spleen B cell KO IL-4 sample 8


title: AML patient sample number 038 set1 plate 1

description:
Sample name: 038_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Pediatric type Follicular Lymphoma 8

source_name: Right cervical Lymph Node

value: Pediatric type Follicular Lymphoma


source_name: Test sample: Spleen B cells from Dock10 knockout mouse 6 cultured with IL-4

value: Spleen B cell KO IL-4 sample 6


title: Pediatric type Follicular Lymphoma 6

source_name: Submandibular Lymph Node


title: AML patient sample number 037 set1 plate 1

description:
Sample name: 037_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: acute myeloid leukemia

value: leukemic cells


source_name: Test sample: Spleen B cells from Dock10 knockout mouse 8 cultured with nothing

value: Ctrl

value: Spleen B cell KO Ctrl sample 8


source_name: Test sample: Spleen B cells from Dock10 knockout mouse 7 cultured with IL-4

value: Spleen B cell KO IL-4 sample 7


title: Pediatric type Follicular Lymphoma 4

source_name: Left cervical Lymph Node


value: KO

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 10 cultured with nothing

value: Spleen B cell KO Ctrl sample 10


value: Pre

value: spleen B cell

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 9 cultured with nothing

value: Spleen B cell KO Ctrl sample 9


value: 12 weeks

value: Spleen B cell pool of KO samples 6 to 10, before culture (Pre)

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 7 cultured with nothing

value: Spleen B cell KO Ctrl sample 7


title: Pediatric type Follicular Lymphoma 11

value: Male

value: FFPE


title: AML patient sample number 036 set1 plate 1

description:
Sample name: 036_serie1_1
thawed samples of cells from acute myeloid leukemia patients

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse

value: bone marrow


source_name: Test sample: Spleen B cells from Dock10 knockout mouse 6 cultured with nothing

value: Spleen B cell KO Ctrl sample 6


title: Dock10 knockout mouse 10 before culture

source_name: Reference sample: pool of spleen B cells from 5 Dock10 knockout mice samples before culture (Pre from 6 to 10)

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 10 before culture

value: Spleen B cell KO Pre sample 10


title: Dock10 knockout mouse 9 before culture

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 9 before culture

value: Spleen B cell KO Pre sample 9


title: Pediatric type Follicular Lymphoma 3

value: Pediatric type Follicular Lymphoma


title: AML patient sample number 039

description:
Sample name: 039_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: acute myeloid leukemia

value: leukemic cells


title: Dock10 knockout mouse 8 before culture

value: KO

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 8 before culture

value: Spleen B cell KO Pre sample 8


title: Dock10 knockout mouse 6 before culture

value: Pre

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 6 before culture

value: Spleen B cell KO Pre sample 6


title: AML patient sample number 034 set1 plate 1

description:
Sample name: 034_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Dock10 knockout mouse 5 before culture

value: spleen B cell

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 5 before culture

value: Spleen B cell KO Pre sample 5


title: Pediatric type Follicular Lymphoma 1

description: Hybridized to Affymetrix OncoScan FFPE Assay

source_name: Midline cervical Lymph Node


title: AML patient sample number 033 set1 plate 1

description:
Sample name: 033_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Dock10 knockout mouse 4 before culture

value: 12 weeks

value: Spleen B cell pool of KO samples 6 to 10, before culture (Pre)

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 4 before culture

value: Spleen B cell KO Pre sample 4


title: Dock10 knockout mouse 3 before culture

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 3 before culture

value: Spleen B cell KO Pre sample 3


title: AML patient sample number 029 set1 plate 1

description:
Sample name: 029_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: bone marrow


title: AML patient sample number 031 set1 plate 1

description:
Sample name: 031_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 030 set1 plate 1

description:
Sample name: 030_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 032 set1 plate 1

description:
Sample name: 032_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 035 set1 plate 1

description:
Sample name: 035_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 027 set1 plate 1

description:
Sample name: 027_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 028 set1 plate 1

description:
Sample name: 028_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Dock10 knockout mouse 7 before culture

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 7 before culture

value: Spleen B cell KO Pre sample 7


title: AML patient sample number 026 set1 plate 1

description:
Sample name: 026_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 025 set1 plate 1

description:
Sample name: 025_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 023 set1 plate 1

description:
Sample name: 023_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 024 set1 plate 1

description:
Sample name: 024_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Dock10 knockout mouse 2 before culture

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 2 before culture

value: Spleen B cell KO Pre sample 2


title: Wild-type mouse 8 cultured with IL-4

source_name: Test sample: Spleen B cells from wild-type mouse 8 cultured with IL-4

value: WT

value: Spleen B cell WT IL-4 sample 8


title: Wild-type mouse 7 cultured with IL-4

source_name: Test sample: Spleen B cells from wild-type mouse 7 cultured with IL-4

value: Spleen B cell WT IL-4 sample 7


title: Dock10 knockout mouse 1 before culture

source_name: Test sample: Spleen B cells from Dock10 knockout mouse 1 before culture

value: Spleen B cell KO Pre sample 1


title: Wild-type mouse 10 cultured with nothing

value: KO

source_name: Test sample: Spleen B cells from wild-type mouse 10 cultured with nothing

value: Ctrl

value: Spleen B cell WT Ctrl sample 10


title: Wild-type mouse 9 cultured with IL-4

value: Pre

source_name: Test sample: Spleen B cells from wild-type mouse 9 cultured with IL-4

value: Spleen B cell WT IL-4 sample 9


title: Pediatric type Follicular Lymphoma 2

source_name: Submental Lymph Node

value: Pediatric type Follicular Lymphoma

value: Male

value: FFPE


title: AML patient sample number 022 set1 plate 1

description:
Sample name: 022_serie1_1
thawed samples of cells from acute myeloid leukemia patients

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse

value: acute myeloid leukemia

value: leukemic cells


title: AML patient sample number 021 set1 plate 1

description:
Sample name: 021_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: bone marrow


title: AML patient sample number 020 set1 plate 1

description:
Sample name: 020_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 019 set1 plate 1

description:
Sample name: 019_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Wild-type mouse 6 cultured with IL-4

source_name: Reference sample: pool of spleen B cells from 5 Dock10 knockout mice samples before culture (Pre from 6 to 10)

value: spleen B cell

value: 12 weeks

value: Spleen B cell pool of KO samples 6 to 10, before culture (Pre)

source_name: Test sample: Spleen B cells from wild-type mouse 6 cultured with IL-4

value: Spleen B cell WT IL-4 sample 6


title: Wild-type mouse 10 cultured with IL-4

source_name: Test sample: Spleen B cells from wild-type mouse 10 cultured with IL-4

value: WT

value: Spleen B cell WT IL-4 sample 10


title: Wild-type mouse 9 cultured with nothing

value: KO

source_name: Test sample: Spleen B cells from wild-type mouse 9 cultured with nothing

value: Spleen B cell WT Ctrl sample 9


title: Wild-type mouse 7 cultured with nothing

source_name: Test sample: Spleen B cells from wild-type mouse 7 cultured with nothing

value: Ctrl

value: Spleen B cell WT Ctrl sample 7


title: Wild-type mouse 8 cultured with nothing

value: Pre

source_name: Test sample: Spleen B cells from wild-type mouse 8 cultured with nothing

value: Spleen B cell WT Ctrl sample 8


title: AML patient sample number 018 set1 plate 1

description:
Sample name: 018_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Wild-type mouse 6 cultured with nothing

source_name: Test sample: Spleen B cells from wild-type mouse 6 cultured with nothing

value: Spleen B cell WT Ctrl sample 6


title: Wild-type mouse 9 before culture

source_name: Test sample: Spleen B cells from wild-type mouse 9 before culture

value: Spleen B cell WT Pre sample 9


title: AML patient sample number 017 set1 plate 1

description:
Sample name: 017_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: acute myeloid leukemia


title: AML patient sample number 016 set1 plate 1

description:
Sample name: 016_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: leukemic cells


title: Wild-type mouse 10 before culture

source_name: Test sample: Spleen B cells from wild-type mouse 10 before culture

value: Spleen B cell WT Pre sample 10


title: AML patient sample number 014 set1 plate 1

description:
Sample name: 014_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: bone marrow


title: AML patient sample number 015 set1 plate 1

description:
Sample name: 015_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 013 set1 plate 1

description:
Sample name: 013_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Wild-type mouse 7 before culture

value: spleen B cell

value: 12 weeks

source_name: Test sample: Spleen B cells from wild-type mouse 7 before culture

value: Spleen B cell WT Pre sample 7


title: Wild-type mouse 8 before culture

value: Spleen B cell pool of KO samples 6 to 10, before culture (Pre)

source_name: Test sample: Spleen B cells from wild-type mouse 8 before culture

value: WT

value: Spleen B cell WT Pre sample 8


title: Wild-type mouse 4 before culture

value: KO

source_name: Test sample: Spleen B cells from wild-type mouse 4 before culture

value: Spleen B cell WT Pre sample 4


title: Wild-type mouse 5 before culture

source_name: Test sample: Spleen B cells from wild-type mouse 5 before culture

value: Spleen B cell WT Pre sample 5


title: AML patient sample number 012 set1 plate 1

description:
Sample name: 012_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 011 set1 plate 1

description:
Sample name: 011_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Wild-type mouse 2 before culture

value: Pre

source_name: Test sample: Spleen B cells from wild-type mouse 2 before culture

value: Spleen B cell WT Pre sample 2


title: Wild-type mouse 3 before culture

source_name: Test sample: Spleen B cells from wild-type mouse 3 before culture

value: Spleen B cell WT Pre sample 3


title: Wild-type mouse 1 before culture

source_name: Test sample: Spleen B cells from wild-type mouse 1 before culture

value: Spleen B cell WT Pre sample 1


title: AML patient sample number 009 set1 plate 1

description:
Sample name: 009_serie1_1
thawed samples of cells from acute myeloid leukemia patients

source_name: HIMIP collection (BB-0033-00060) of the Cancer Research Center of Toulouse

value: acute myeloid leukemia


title: AML patient sample number 008 set1 plate 1

description:
Sample name: 008_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: leukemic cells


title: Wild-type mouse 6 before culture

source_name: Reference sample: pool of spleen B cells from 5 Dock10 knockout mice samples before culture (Pre from 6 to 10)

source_name: Test sample: Spleen B cells from wild-type mouse 6 before culture

value: Spleen B cell WT Pre sample 6


title: AML patient sample number 007 set1 plate 1

description:
Sample name: 007_serie1_1
thawed samples of cells from acute myeloid leukemia patients

value: bone marrow


title: AML patient sample number 004  set1 plate 1

description:
Sample name: 004_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 005 set1 plate 1

description:
Sample name: 005_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 010 set1 plate 1

description:
Sample name: 010_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 002  set1 plate 1

description:
Sample name: 002_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 003  set1 plate 1

description:
Sample name: 003_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: AML patient sample number 006 set1 plate 1

description:
Sample name: 006_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Testis, Tumor

city: Pierre Bénite

first: Jeremie

middle: FC

last: Becker

address: Centre Hospitalier Lyon Sud, Bâtiment 3F

department: Medical diagnostic Discovery department

institute: bioMérieux

hyb_protocol: Hybridization was performed at 50 °C for 18 hours in the oven under constant stirring (60 rpm). Washing (protocol FS450-0001) and staining were carried out according to the protocol supplied by the manufacturer, using the GeneChip fluidic station 450 (Affymetrix).

scan_protocol: The arrays were scanned using GeneChip scanner 3000 7G (Affymetrix). The data were then processed with Affymetrix Genechip Command Console (version 3.2.3.1515)

data_processing: RMA

source_name: Testis tumoral

label_protocol: Purified dsDNA was fragmented and labeled with the Encore Biotin Module kit (Nugen).

extract_protocol: Guanidine thiocyanate based techniques

tag: tumor/normal

value: Tumor

tag: tissue/cell line

value: Tissue

tag: replicate


title: Cell line, EBJ14, technical rep2

source_name: EBJ14 primary human cell lines

value: Cell line


title: Cell line, OSCAR, technical rep1

source_name: OSCAR primary human cell lines


title: Cell line, EBJ14, technical rep1


title: AML patient sample number 001 set1 plate 1

description:
Sample name: 001_serie1_1
thawed samples of cells from acute myeloid leukemia patients


title: Colon, patient 204, Tumor

source_name: Colon tumor


title: Palapattu_016_UDP_MDV4

status: Public on Sep 20 2016

city: Houston

first: Akash

middle: Kumar

last: Kaushik

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Affymetrix Gene ST 2.1 . Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression analysis with values for each gene being calculated using robust multi-array average (RMA).

source_name: C4-2 cells after 96 hours of UDP-GlcNAc + MDV3100 treatment

label_protocol: Extracted RNA samples were send for microarray using Human Affymetrix Gene ST 2.1

growth_protocol: C42 cells were grown in grown in T-media with 10 % Fetal Bovine with  and 1% PenStrip

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

treatment_protocol: 100,000 cells/well in 24 well plate were grown and 15 mM UDP-N-acetylglucosamine or 10uM MDV 3100 alone or in combination were added to the cells for 96 hours

value: Prostate cancer


title: colon, patient 2, Normal

source_name: Colon normal

value: Normal


title: placenta

source_name: Placenta


title: Testis, Normal

source_name: Testis normal


title: Palapattu_013_UDP_MDV1


title: Palapattu_015_UDP_MDV3


title: Palapattu_012_MDV4

source_name: C4-2 cells after 96 hours of MDV3100 treatment


title: prostate, patient 10483, Tumor

source_name: Prostate tumoral


title: Palapattu_009_MDV1


title: Palapattu_010_MDV2


title: colon, patient 2, Tumor


title: Cell line, EBJ14, technical rep3


title: Cell line, OSCAR, technical rep2


title: Colon, patient 204, Normal


title: brainuniversel_TIS12CL4, technical rep3

source_name: Ambion Human Brain / Stratagene Universal RNA

value: Tissue/Cell line


title: Palapattu_008_UDP4

source_name: C4-2 cells after 96 hours of UDP-GlcNAc treatment


title: colon, patient 257, Tumor


title: Palapattu_011_MDV3


title: Palapattu_006_UDP2


title: Palapattu_014_UDP_MDV2


title: brainuniversel_TIS4CL12, technical rep2


title: colon, patient 257, Normal


title: Cell line, OSCAR, technical rep3


title: brainuniversel_TIS4CL12, technical rep3


title: Palapattu_003_PBS3

source_name: C4-2 cells after 96 hours of PBS treatment


title: Palapattu_007_UDP3


title: prostate, patient 10483, Normal

source_name: Prostate normal


title: brainuniversel_TIS12CL4, technical rep2


title: Palapattu_004_PBS4


title: Palapattu_005_UDP1


title: Palapattu_001_PBS1


title: Palapattu_002_PBS2


title: T387A-8

city: cleveland

first: Yuxin

last: Wang

state: OH

address: 9500 Euclid avenue

department: Cancer Biology

institute: cleveland clinic foundation

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

source_name: fibrosarcoma cell line

label_protocol: Standard Illumina protocol

growth_protocol: U6A cells were growed in DMEM medium with 5%FBS

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: U6A cells were treated with 100 IU/ml IFN-beta as indicated.

value: fibrosarcoma cell line

value: cells expressing T387A STAT2


title: T387A-24


title: T387A-4


title: Expo [344_2_1]

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

institute: ANSES

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 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 (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.log2-transformed and normalized (scaling and baseline transformation)

source_name: Expo

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary human keratinocytes, pooled and isolated from 3 neonatal foreskin circumcised patients, were maintained as advised by supplier (Invitrogen, Saint-Aubin, France). Briefly, cells were cultured onto collagen IV coated plates (Becton Dikinson Franklin Lakes, NJ), in supplemented Keratinocyte-SFM medium (Gibco, Carlsbad, CA) with antibiotics (Invitrogen, Saint-Aubin, France).

extract_protocol: RNA was prepared using the RNAeasy column purification (Qiagen, Hilden, Germany), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop technology, Cambridge, UK) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the overall RNA integrity numbers (RIN) were between 9.8 and 10.

treatment_protocol: For each exposure experiment, 250 000 cells per well within a 6-well collagen IV plate were used. Keratinocytes were exposed (Expo) and control cells (Sham) were cultured under the same athermic conditions, but the MMW generator switched off. Cells were exposed during 3 hours at 60.4 GHz, with an average IPD of 20 mW/cm². In order to determine the coexposure effect 20 mM of 2dG were used alone (Sham_2dG) or in cotreatment with 20 MW/cm² of MMW for 3 hours (Expo_2dG).

value: Primary culture Keratinocyte

tag: protocol

value: Expo


title: Sham_2dG [344_2_2]


title: Sham [344_1_4]

source_name: Sham

value: Sham


title: Sham_2dG [344_1_1]


title: Expo_2dG [344_2_4]


title: Expo [344_2_3]


title: universel_CL, technical rep3

source_name: Stratagene Universal RNA


title: universel_CL, technical rep2


title: Sham_2dG [343_1_2]


title: Expo [343_2_3]


title: universel_CL, technical rep1


title: brainuniversel_TIS12CL4, technical rep1


title: Expo_2dG [343_1_1]


title: Expo_2dG [343_1_4]


title: Expo [341_2_2]


title: Sham_2dG [343_1_3]


title: Expo_2dG [341_1_3]


title: Sham [341_2_3]


title: Sham [343_2_1]


title: brainuniversel_TIS4CL12, technical rep1


title: Sham [341_1_2]


title: WKY PBL CD8+ RT1B+ [WKY PBL RT1B+ CD8+_252827911789_S01_GE1_1100_Jul11_2_3_S7]

first: David

middle: S

last: Loose

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

hyb_protocol: 65C 16h in Agilent hybridization buffer

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Featutre Extractor v 11.0.1.1, BRB Array Tools v4.4b2; Matrix worksheet contains all probe data, log transformed , not filtered, and is quantile normalized.

organism: Rattus norvegicus

source_name: Peripheral Blood

label_protocol: Agilent one-color low-input

extract_protocol: PBMC were harvested through Ficoll gradiation. Kidneys were minced and digested for isolation of glomeruli. The glomeruli were digested to release immune cells. Both PBMC and glomerular immune cells were subjected to three step magnetic bead-based cell sorting. The isolated cells were immediately used for RNA isolation. Their purities were confirmed by flow cytometry. Total RNA from various cell populations were isolated with a kit (Qiagen, Valencia, CA, Cat. No. 74004) and checked for their quality.

treatment_protocol: Peripheral blood and kidneys were collected 30 to 35 days after immunization with an autoantigen to induce autoimmune glomerulonephritis when the animals were euthanised.

value: Wista Kyoto

value: Female

tag: cell sub-population

value: Peripheral blood leukocyte population with a phenotype of CD8+ MHC-II (RT1B)+

value: 15 weeks


title: WKY PBL CD8+ RT1B+ [WKY PBL RT1B+ CD8+_252827911789_S01_GE1_1100_Jul11_2_4_S8]

tag: gender


title: WKY PBL CD8+ RT1Blow [WKY PBL RT1B- CD8+_252827911789_S01_GE1_1100_Jul11_2_1_S5]

value: Peripheral blood leukocyte population with a phenotype of CD8+ MHC-II (RT1B)low


title: brain_TIS, technical rep3

source_name: Ambion Human Brain


title: WKY Glomeruli-infiltrating CD8+ RT1Blow [WKY GIL RT1B- CD8+_252827912358_S01_GE1_1100_Jul11_1_1_S9]

source_name: Glomeruli

value: Glomeruli-infiltrating leukocyte population with a phenotype of CD8+ MHC-II (RT1B)low


title: WKY Glomeruli-infiltrating CD8+ RT1Blow [WKY GIL RT1B- CD8+_252827912358_S01_GE1_1100_Jul11_1_2_S10]


title: WKY Glomeruli-infiltrating CD8+ RT1B+ [WKY GIL RT1B+ CD8+_252827912358_S01_GE1_1100_Jul11_1_3_S11]

value: Glomeruli-infiltrating leukocyte population with a phenotype of CD8+ MHC-II (RT1B)+


title: LEW PBL CD8+ RT1Blow [LEW PBL RT1B- CD8+_252827911789_S01_GE1_1100_Jul11_1_2_S2]

value: Lewis


title: CBA-hypothalamus-old-8

city: Omaha

first: Stephen

middle: John

last: Bonasera

state: Nebraska

address: 3028 Durham Research Center

department: Internal Medicine

institute: University of Nebraska Medical Center

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent)

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).

data_processing: Hybridization performance was assessed by Agilent's Feature Extraction 9.1. This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). This procedure was carried out using the Bioconductor package limma (http://www.bioconductor.org). No background subtraction was performed.

source_name: hypothalamus

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent).

extract_protocol: RNA was purified by well-established methods (RNAqueous and RNALater, Ambion, for tissue samples), and underwent extensive quality control to assure that only samples meeting stringent standards for purity and minimal degradation would be tested. We used a TissueLyser II (Qiagen, Valencia CA) and a Qiacube (Qiagen) for tissue sample dissociation and RNA purification to limit variability in yield and degradation. Samples were assayed for RNA concentration and purity (NanoDrop II, Thermo, Waltham MA) and degradation (BioAnalyzer 2100, Agilent Technologies). Samples with A260/A280 ratios less than 1.8 were unsuitable for analysis secondary to RNA contamination. Samples with larger 18S instead of 28S peaks were unsuitable for microarray analysis secondary to RNA degradation.

value: CBA

value: 21-23 mo old

tag: Sex

value: male


title: WKY Glomeruli-infiltrating MØ [WKY GIL PANT+_252827912358_S01_GE1_1100_Jul11_2_4_S16]


title: WKY Glomeruli-infiltrating MØ [WKY GIL PANT+_252827912358_S01_GE1_1100_Jul11_2_3_S15]


title: CBA-hypothalamus-old-5


title: LEW PBL CD8+ RT1Blow [LEW PBL RT1B- CD8+_252827911789_S01_GE1_1100_Jul11_1_1_S1]


title: CBA-hypothalamus-old-7


title: brain_TIS, technical rep1

value: Tissue


title: WKY PBL Pan T [WKY PBL PANT+_252827912358_S01_GE1_1100_Jul11_2_2_S14]

value: Peripheral blood pan T cell population


title: LEW PBL CD8+ RT1B+ [LEW PBL RT1B+ CD8+_252827911789_S01_GE1_1100_Jul11_1_3_S3]


title: WKY Glomeruli-infiltrating CD8+ RT1B+ [WKY GIL RT1B+ CD8+_252827912358_S01_GE1_1100_Jul11_1_4_S12]


title: LEW PBL CD8+ RT1B+ [LEW PBL RT1B+ CD8+_252827911789_S01_GE1_1100_Jul11_1_4_S4]


title: WKY PBL CD8+ RT1Blow [WKY PBL RT1B- CD8+_252827911789_S01_GE1_1100_Jul11_2_2_S6]


title: CBA-hypothalamus-old-6


title: CBA-hypothalamus-old-4


title: FFPE DS-48857

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

hyb_protocol: The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol, and then scanned using an Affymetrix GeneChip Scanner 3000.

scan_protocol: The arrays were then scanned using an Affymetrix GeneChip Scanner 3000. The acquisition and initial quantification of array images were conducted using the AGCC software (Affymetrix).

data_processing: The samples were normalized using the RMA method. After normalization, filtration of probes was performed for the data. Probes were retained if they had at least 1.5-fold change in either direction of the median expression level in at least 20% of the samples and if they had at most 50% missing values across the samples. The entire probe filtration process was implemented by the BRB-ArrayTools software.

label_protocol: Microarray targets were prepared using NuGEN WT-Ovation Formalin-Fixed Paraffin-Embedded RNA Amplification System and FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA, USA) and then hybridized to the Affymetrix GeneChip U133 Plus 2.0 Array (Affymetrix), all according to manufacturers' instructions.

extract_protocol: Total RNA was isolated using the QIAGEN kit according to the manufacturer's instructions

value: colon


title: brain_TIS, technical rep2


title: FFPE DS-60353


title: CBA-hypothalamus-old-3


title: WKY PBL Pan T [WKY PBL PANT+_252827912358_S01_GE1_1100_Jul11_2_1_S13]


title: FFPE DS-51803


title: FFPE DS-33635


title: FFPE DS-54783


title: FFPE DS-54363


title: CBA-hypothalamus-old-1


title: FFPE DS-60252


title: FFPE DS-51977


title: FFPE DS-51797


title: CBA-hypothalamus-old-2


title: CBA-hypothalamus-middle-5

value: 12-13 mo old


title: T387A-0

tag: cell line

value: fibrosarcoma cell line

value: cells expressing T387A STAT2


title: FFPE DS-49826


title: CBA-hypothalamus-middle-2


title: FFPE DS-48055


title: FFPE DS-48764


title: FFPE DS-44878


title: CBA-hypothalamus-middle-3


title: FFPE DS-50687


title: FFPE DS-53114


title: FFPE DS-51043


title: CBA-hypothalamus-middle-4


title: CBA-hypothalamus-middle-1


title: FFPE DS-52210


title: CBA-hypothalamus-young-5

value: 2-3 mo old


title: FFPE DS-58258


title: FFPE DS-53211


title: FFPE DS-49315


title: CBA-hypothalamus-young-6


title: FFPE DS-56293


title: FFPE DS-54051


title: FFPE DS-52681


title: FFPE DS-48893


title: FFPE DS-67980


title: CBA-hypothalamus-young-3


title: CBA-hypothalamus-young-7


title: FFPE DS-54129


title: CBA-hypothalamus-young-4


title: FFPE DS-51982


title: FFPE DS-56963


title: CBA-hypothalamus-young-2


title: CBA-hypothalamus-young-1


title: BALB-striatum-old-5

source_name: striatum

value: BALB


title: BALB-striatum-old-3


title: FFPE DS-56858


title: FFPE DS-52853


title: FFPE DS-56376


title: FFPE DS-48607


title: FFPE DS-56326


title: FFPE DS-53453


title: BALB-striatum-old-2


title: FFPE DS-54503


title: FFPE DS-50925


title: FFPE DS-53191


title: FFPE DS-52790


title: FFPE DS-49796


title: FFPE DS-54564


title: FFPE DS-51652


title: FFPE DS-58341


title: BALB-striatum-old-1


title: BALB-striatum-middle-5


title: FFPE DS-67955


title: BALB-striatum-old-4


title: FFPE DS-60296


title: BALB-striatum-middle-3


title: FFPE DS-40199


title: FFPE DS-47369


title: BALB-striatum-middle-4


title: BALB-striatum-middle-1


title: BALB-striatum-young-2


title: BALB-striatum-young-3


title: FFPE DS-52151


title: BALB-striatum-middle-2


title: FFPE DS-52320


title: FF DS-33635


title: FF DS-54363


title: FFPE DS-54041


title: FFPE DS-51997


title: BALB-striatum-young-1


title: BALB-frontalcortex-old-5

source_name: frontal cortex

value: 15-16 mo old

value: female


title: BALB-frontalcortex-old-8


title: FFPE DS-49639


title: FF DS-60353


title: FFPE DS-70294


title: FFPE DS-54589


title: FF DS-48764


title: FF DS-48857


title: FF DS-60252


title: FF DS-51977


title: FF DS-54783


title: FF DS-52151


title: FFPE DS-52838


title: BALB-frontalcortex-old-7


title: FF DS-51803


title: FF DS-48055


title: FF DS-51797


title: FF DS-44878


title: FF DS-53114


title: FF DS-50687


title: BALB-frontalcortex-old-3


title: FF DS-51043


title: BALB-frontalcortex-old-4


title: FF DS-49826


title: FF DS-49315


title: FF DS-52210


title: BALB-frontalcortex-old-2


title: BALB-frontalcortex-young-8


title: FF DS-52681


title: BALB-frontalcortex-young-7


title: BALB-frontalcortex-young-6


title: FF DS-58258


title: BALB-frontalcortex-old-6


title: FF DS-53211


title: FF DS-54051


title: FF DS-56293


title: BALB-frontalcortex-old-1


title: FF DS-54129


title: FF DS-67980


title: BALB-frontalcortex-young-5


title: BALB-frontalcortex-young-4


title: FF DS-51982


title: FF DS-56963


title: FF DS-67955


title: FF DS-56858


title: FF DS-48893


title: FF DS-54503


title: BALB-frontalcortex-young-3


title: BALB-frontalcortex-young-1


title: FF DS-50925


title: FF DS-40199


title: FF DS-49796


title: FF DS-53453


title: FF DS-54564


title: FF DS-53191


title: C57BL6-cerebellum-old-6

source_name: cerebellum


title: FF DS-56326


title: FF DS-52790


title: FF DS-52853


title: FF DS-60296


title: FF DS-56376


title: FF DS-58341


title: C57BL6-cerebellum-old-2


title: C57BL6-cerebellum-old-4


title: BALB-frontalcortex-young-2


title: FF DS-54041


title: FF DS-51652


title: FF DS-52320


title: C57BL6-cerebellum-old-3


title: FF DS-51997


title: FF DS-48607


title: C57BL6-cerebellum-middle-2


title: C57BL6-cerebellum-old-5


title: C57BL6-cerebellum-old-1


title: FF DS-70294


title: FF DS-47369


title: C57BL6-cerebellum-middle-1


title: FF DS-54589


title: C57BL6-cerebellum-young-4


title: FF DS-52838


title: FF DS-49639


title: BALB-cerebellum-old-2


title: BALB-cerebellum-old-1


title: BALB-cerebellum-old-4


title: C57BL6-cerebellum-young-3


title: BALB-cerebellum-old-3


title: BALB-cerebellum-middle-6


title: C57BL6-cerebellum-young-2


title: Blimp1-positive plasma cell rapamycin rep5

first: Brian

middle: Thomas

last: Gaudette

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G System.

data_processing:
Analysis was performed using the R statistical environment v3.x and the Bioconductor suite of packages including the oligo, pd.mogene.2.0.st and mogene20sttranscriptcluster.db.
Log2 RMA-normalized signal intensity unfiltered or variance filtered (IQR cutoff 0.5) max-mean selected for multiple probes.

source_name: bone marrow plasma cell, Blimp1 positive, rapamycin treated

label_protocol: Samples were biotinylated using an Affymetrix labeling kit.

extract_protocol: FACS-sorted B220-negative Blimp1-positive bone marrow plasma cells were collected into Trizol reagent, and RNA was isolated.

treatment_protocol: B6.BLIMP1 +/GFP mice were treated with rapamycin, or untreated.

tag: strain/background

value: B6.BLIMP1 +/GFP

tag: cell type

tag: treatment

value: rapamycin


title: BALB-cerebellum-middle-3

tag: strain


title: Blimp1-positive plasma cell rapamycin rep3

value: B220-negative Blimp1-positive bone marrow plasma cell


title: Blimp1-positive plasma cell rapamycin rep4


title: Blimp1-positive plasma cell untreated rep2

source_name: bone marrow plasma cell, Blimp1 positive, untreated

value: untreated


title: Blimp1-positive plasma cell rapamycin rep1


title: Blimp1-positive plasma cell untreated rep1


title: BALB-cerebellum-middle-4


title: BALB-cerebellum-middle-1


title: BALB-cerebellum-middle-5


title: Blimp1-positive plasma cell untreated rep3


title: BALB-cerebellum-middle-2