title: Sciatic nerve Pool N.2 KO

city: Genova

first: Anna

middle: Margherita

last: Corradi

address: Viale Benedetto XV 3

department: Dimes

institute: University of Genova

description: Gene expression data from P2 wt and Ebf2-/- sciatic nerves at P2.

hyb_protocol: 5.5 μg of fragmented and labeled cDNA target was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array at 45°C for 17 h on a GeneChip Hybridization Oven 640 (Affymetrix)

scan_protocol: Hybridized arrays were washed and stained on a gene Chip Fluidics Station 450 and finally scanned on a Gene Chip Scanner 3000 7G (Affymetrix), generating an intensity file (*.CEL) for each array

data_processing: Normalization with RMA algorithm followed by non specific filtering, performed removing: 1) non annotated and duplicated probes 2) low variance probes using interquartile function (IQR) with a 0.5 cutoff (Bourgon et al., PNAS 2010, 107;9546-9551)

source_name: P2 Ebf2-/- mouse sciatic nerves

label_protocol: cDNA was fragmented and end-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: We set up Ebf2 het X Ebf2 het crosses. Births were monitored and pups were genotyped at P1, sciatic nerves were excised at P2.

extract_protocol: RNeasy Micro kit (Qiagen, Italy) RNA quality was checked by digital electrophoresis on Experion platform (Bio-Rad USA) and quantified by Nanodrop ND1000 (Celbio, Italy)

treatment_protocol: Sciatic nerves were excised and pooled according to genotype

value: C57Bl6N background

value: sciatic nerves

value: Ebf2-/- knock out

tag: age

value: 2 days postnatal (P2)


title: 003+IFNg+TNFa

status: Public on Dec 21 2016

type: RNA

city: Copenhagen

first: Tina

last: Jehs

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Gene expression data from primary choroidal melanocyte culture (donor 003) stimulated with IFNγ+TNFα

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing: The data was analyzed with the Expression Console

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: choroidal melanocytes

label_protocol: Biotinylated cRNA was prepared according to the strandard Affymetrix one-cycle protocol from RNA (Expression Analysis Technical Manual 2001, Affymetrix)

growth_protocol: Choroidal melanocyte were used at an early passage which did not exceed p+4. 100,000 cells were plated into 6-well plates and grown for 14-21 d in FIC medium which is F12 medium (Gibco) supplemented with 10% FCS (Seralab, West Sussex, UK), 2 mM glutamine (Gibco), 20 ng/ml basic fibroblast growth factor (Gibco), 0.1 mM isobutylmethylxanthine (Sigma), 10 ng/ml cholera toxin (Sigma) and 50 µg/ml gentamicin (Gibco). The culture medium was then changed to the serum-free Melanocyte Growth Medium M2 (PromoCell, Heidelberg, Germany) and the cells cultured for another 12-25 d, at which time they became highly pigmented and developed a three-dimensional structure.

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

treatment_protocol: The cells were stimulated for 48 h at 37 °C and 5% CO2 with 1.5 ml of supernatant from activated T-cells and 1.5 ml of fresh M2 medium, or 27 ng/ml IFN-γ and 10 ng/ml recombinant TNF-α (both from R&D Systems, Minneapolis, MN) in a total volume of 3 ml.

tag: donor

tag: cell type

value: choroidal melanocytes


title: 007 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 007) unstimulated

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark


title: BEC_bLN_D3_3

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

hyb_protocol: Performed using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

scan_protocol: Performed using GeneChip Scanner 7G (Affymetrix), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

data_processing: Probe intensities were background corrected, normalized and summarized at the probe-set level by the RMA algorithm using the aroma.affymetrix package in R.

label: Biotin

organism: Mus musculus

source_name: brachial lymph nodes, HSV, 3 days p.i.

label_protocol: Performed using Encore Biotin module (Nugen), at Molecular Genomics Core Facility, Peter MacCallum Cancer Centre, Australia.

extract_protocol: Briefly, brachial draining lymph nodes were digested with collagenase D (Roche) and DNase (Sigma), followed by further incubation with Dispase (Roche).

treatment_protocol: HSV infection

tag: strain

tag: Sex

value: female

tag: tissue

value: Brachial draining lymph node

tag: phenotype

value: BEC

tag: infection

value: HSV, 3 days p.i.


title: Sciatic nerve Pool N.11 WT

country: Italy

source_name: P2 wt mouse sciatic nerves

tag: genotype

value: Ebf2+/+ wild type


title: BEC_bLN_Naive_4

source_name: brachial lymph nodes, naïve

value: naïve


title: Sciatic nerve Pool N.9 WT


title: Sciatic nerve Pool N.4 KO


title: BEC_bLN_Naive_1


title: 003 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 003) unstimulated


title: 003+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 003) stimulated with supernatant from activated T cells


title: Sciatic nerve Pool N.1 WT


title: BEC_bLN_D3_2


title: 015+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 015) stimulated with IFNγ+TNFα


title: BEC_bLN_Naive_3


title: BEC_bLN_Naive_2


title: 001+T cell supern.

description: Gene expression data from primary choroidal melanocyte culture (donor 001) stimulated with supernatant from activated T cells


title: L-1236-siNT-Seq2-Rep3

city: Berlin

first: Claus

last: Scheidereit

address: Robert Roessle Str. 10

department: Signal Transduction in Tumor Cells

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

hyb_protocol: Biotinylated cDNAs were hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays according to the Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).

scan_protocol: Scanning was performed according to the Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).

data_processing: For each experimental group, canonical or non-canonical, the data was normalized separately using RMA with background correction and quantile normalization as implemented in the Bioconductor library oligo. Finally the data was log2 transformed.

source_name: Hodgkin Lymphoma Cell Line

label_protocol: Microarray experiments were carried out following Ambion (Ambion, AMB), and Affymetrix (Affymetrix Inc, Santa Clara, CA) protocols. Briefly, 100 ng total RNA from each sample was reverse transcribed to cDNA, which was further amplified by in vitro transcription. Single stranded cDNA was then fragmented and labeled with biotin.

growth_protocol: Cells were cultivated in 90% RPMI 1640 (Gibco) + 10% heat inactivated FBS.

extract_protocol: Following RNAi treatment, total RNA from L-1236 cells was prepared accordingly to manufacturer’s protocol (RNeasy Kit; QIAGEN, Hilden, Germany). RNA quality was assessed by 260/280 and 260/230 ratios, as well as by RNA Integrity Number (RIN) using a Eukaryote total RNA nano chip in an Agilent 2100 Bioanalyser (Agilent Technologies). Only RNA samples with 260/280 and 260/230 ratios higher than 1.8, and a RIN higher than 8.5, were used for preparation of microarray samples.

treatment_protocol: Chemically synthesized Accell siRNAs (Dharmacon) were passively transfected into L-1236 cells using Accell delivery media (Dharmacon) and 1% heat inactivated, according to the manufacturer’s instructions. Cells were treated with 500 nM siRNAs for two days, followed by one day of normal cultivation conditions (10% FBS).

tag: cell line

value: Hodgkin lymphoma cell-line L1236

tag: treatment

tag: scan date


title: 001+IFNg+TNFa

description: Gene expression data from primary choroidal melanocyte culture (donor 001) stimulated with IFNγ+TNFα


title: Q1021A_blood

type: genomic

city: Hong Kong

first: Brian

last: Chung

state: Hong Kong

address: 102 Pokfulam Road

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina protocol using iScan

data_processing:
Data were processed by Genome Studio Methylation Module V1.9.0 under default setting. Data matrix contains unmethylated (signal A) and methylated (signal B) signal intensities were provided (Intensities.txt).
Average Beta values are provided in the *txt file linked to each sample.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina labeling protocol

growth_protocol: EDTA-blood in 4oC refrigerator before DNA extraction

extract_protocol: DNA was extracted from whole blood using FlexiGene DNA Kit according to the manufacturer’s protocol (Qiagen). DNA samples were then bisulfite converted using the EpiTect Bisulfite Kit according to the manufacturer’s protocol (Qiagen)

tag: subject status

value: Systemic Lupus Erythematosus (SLE) patient

tag: gender

tag: ethnic background

value: chinese

value: blood


title: Q0982A_blood


title: Q0435A_blood


title: Q0377A_blood


title: Q0246A_blood


title: L-1236-siNFKB2-Seq1-Rep2


title: L-1236-siNT-Seq1-Rep3


title: Q0245A_blood


title: L-1236-siNT-Seq2-Rep2


title: L-1236-siNFKB2-Seq1-Rep3


title: L-1236-siNFKB2-Seq2-Rep2


title: Q0237A_blood


title: L-1236-siNFKB2-Seq2-Rep3


title: Q0200A_blood


title: Q0118A_blood


title: Q0104A_blood


title: 001 unstimulated

description: Gene expression data from primary choroidal melanocyte culture (donor 001) unstimulated


title: L-1236-siNFKB2-Seq2-Rep1


title: L-1236-siNT-Seq1-Rep2


title: L-1236-siNT-Seq2-Rep1


title: Q0065A_blood


title: Q0024A_blood


title: Cntrl-09

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1803_032_A9_m01_AK_200213_(Mouse430_2)

hyb_protocol: Resulting targets, fragmented and labeled RNA, were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 in an Affymetrix fluidic station 450

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing: Quality assessment and preprocessing of the microarrays was done in R version 2.15.1 by utilizing the Bioconductor packages affyPLM version 1.32.0 and GCRMA version 2.28.0 respectively

source_name: amygdala of a control mouse

label_protocol: 500 ng of RNA per sample were processed to generate biotinylated hybridization targets using the Affymetrix GeneChip 3′ IVT Express kit and the Affymetrix GeneChip hybridization, wash, and stain kit

extract_protocol: 2 h following extinction training, mice were euthanized using a saturated carbon dioxide chamber and the amygdala were dissected, shock frozen in liquid nitrogen, and stored at −80 °C. Total RNA was purified from tissue using the Qiagen RNeasy Lipid Tissue Kit according to manufacturer's protocol, including the optional on-column DNase I digestion (RNase free DNase Set, Qiagen).

tag: diet

value: Ctrl

value: male

value: 8-10 weeks

tag: protocol

value: fear extinction training

value: amygdala


title: ZnR-10

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1804_032_A10_m01_AK_200213_(Mouse430_2)

source_name: amygdala of Zn dieted mouse

value: ZnR

tag: age


title: L-1236-siNT-Seq1-Rep1


title: ICN_LSK_reconst_wk37

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

country: USA

institute: Johns Hopkins University School of Medicine

hyb_protocol: Described in manuscript

scan_protocol: Described in manuscript

data_processing: R/Bioconductor, probeset summarization with justRMA (no normalization),

source_name: ICN

label_protocol: Described in manuscript

growth_protocol: Described in manuscript

extract_protocol: Described in manuscript

treatment_protocol: Described in manuscript

value: Donor-derived ES-HSC


title: M7_S1_ZnR

description:
mRNA extracts from pre-frontal cortex cells of a Zn dieted mouse
2126_032_M7_S1_ZnR_Ext_m01_AK210818_(Mouse430_2).CEL.gz

extract_protocol: 2 h following extinction training, mice were euthanized using a saturated carbon dioxide chamber and the mPFC (both hemispheres) were dissected, shock frozen in liquid nitrogen, and stored at −80 °C. Total RNA was purified from tissue using the Qiagen RNeasy Lipid Tissue Kit according to manufacturer's protocol, including the optional on-column DNase I digestion (RNase free DNase Set, Qiagen).

value: PFC (both hemispheres)


title: Cntrl-11

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1805_032_A11_m01_AK_200213_(Mouse430_2)


title: M5_S1_Ctl

description:
mRNA extracts from pre-frontal cortex cells of a control mouse
2125_032_M5_S1_Ctl_Ext_m01_AK210817_(Mouse430_2).CEL.gz


title: M9_S1_Ctl

description:
mRNA extracts from pre-frontal cortex cells of a control mouse
2127_032_M9_S1_Ctl_Ext_m01_AK210819_(Mouse430_2).CEL.gz


title: ICN_LSK_reconst_wk18


title: M3_S1_ZnR

description:
mRNA extracts from pre-frontal cortex cells of a Zn dieted mouse
2123_032_M3_S1_ZnR_Ext_m01_AK210815_(Mouse430_2).CEL.gz

source_name: pre-frontal cortex cells of Zn dieted mouse


title: BFC828_blood

value: healthy control

value: female


title: ICN_DL1_2

value: ES-HSC


title: ICN_DL1_1


title: M11_S1_ZnR

description:
mRNA extracts from pre-frontal cortex cells of a Zn dieted mouse
2129_032_M11_S1_ZnR_Ext_m01_AK210821_(Mouse430_2).CEL.gz


title: BFC815_blood


title: Cdx4_DL1_4


title: Cdx4_DL1_3


title: ZnR-03

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1799_032_A3_m01_AK_200213_(Mouse430_2)


title: BFC778_blood


title: M1_S1_Ctl

description:
mRNA extracts from pre-frontal cortex cells of a control mouse
@52002900951100052016423263428030.CEL.gz


title: ZnR-07

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1802_032_A7_m01_AK_200213_(Mouse430_2)


title: Cdx4_DL1_1


title: AV_DL1_invitro_LSK_2


title: Cdx4_DL1_2


title: BFC649_blood


title: AV_DL1_invitro_LSK_1


title: ICN_OP9_1


title: ICN_OP9_2


title: Cdx4_OP9_5


title: BFC2232_blood


title: BFC2376_blood


title: Perinatal control 4 [979]

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

country: France

institute: INRA

hyb_protocol: Microarrays were hybridized at 42°C for 17-18h in a NimbleGen hybridization system (transcriptomic platform POPS, IPS2, INRA, France) and washed using a wash buffer kit (Roche-NimbleGen) according to the manufacturer’s instructions. The hybridization lay-out incorporated technical dye-swaps for every sample.

scan_protocol: Fluorescent signals were scanned at 532 nm and 635 nm using an Innoscan 900 scanner (Innopsys) at a 3 μm resolution. Raw data files containing the Cy3 and Cy5 signal quantifications for each probe were generated using Nimblescan 2.6 software (Roche-NimbleGen).

data_processing: Probes with signal enrichment in the MeDIP sample (“enriched probes”) were identified using the ChIPmix R package [Martin-Magniette ML, Mary-Huard T, Berard C, Robin S: ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics 2008, 24:i181-186] as follows. Hybridization data were normalized as described previously using an ANOVA model [Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V: Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 2007, 3:e86]. Data were averaged on the dye-swap to remove dye biases. For each probe, the local CpG percentage was then computed within a 400 bp genomic window centred on the probe position. Finally, ChIPmix was run on the normalized data, with three classes of probes analysed independently: low CpG class (CpGs<1%), intermediate CpG class (1%≤CpGs<4%) and high CpG class (CpGs≥4%).

organism: Bos taurus

source_name: MeDIP DNA from individual #979

label_protocol: After purification with the QIAquick PCR purification kit (Qiagen), 1 μg amplified samples were labelled with Cy3 and Cy5 in two separate reactions using a dual-colour DNA labelling kit (Roche-NimbleGen). For each sample, 15 μg labelled MeDIP and 15 μg labelled input were then assembled in both combinations (Cy3-input with Cy5-MeDIP or Cy5-input with Cy3-MeDIP), dried and resuspended in hybridization reagents (hybridization kit, Roche-NimbleGen)

extract_protocol: DNA extraction from the liver samples, MeDIP and quality controls by PCR were performed as described in [Kiefer H: Genome-Wide Analysis of Methylation in Bovine Clones by Methylated DNA Immunoprecipitation (MeDIP). Methods Mol Biol 2015, 1222:267-280]. In order to prevent any technical biases, the products of 9-10 independent MeDIP experiments were pooled for each animal. 100 ng of this material, as well as 100 ng input DNA, were then subjected to moderate genome amplification (10 cycles; GenomePlex complete WGA kit, Sigma).

tag: Stage

value: Perinatal period

tag: reproductive technology

value: Artificial insemination

source_name: Input DNA from individual #979


title: BFC504_blood


title: Cdx4_OP9_2

tag: cell type


title: Cdx4_OP9_4


title: AV_OP9_2


title: Perinatal clone 7 [828]

source_name: MeDIP DNA from individual #828

value: Nuclear transfert

source_name: Input DNA from individual #828


title: Perinatal control 3 [972]

source_name: MeDIP DNA from individual #972

source_name: Input DNA from individual #972


title: Adult clone 7 [512]

source_name: MeDIP DNA from individual #512

value: Adulthood

source_name: Input DNA from individual #512


title: Perinatal control 2 [964]

source_name: MeDIP DNA from individual #964

source_name: Input DNA from individual #964


title: Cdx4_OP9_1


title: AV_OP9_1


title: B6_LSK_reconst_3

value: Donor-derived HSC


title: Adult control 7 [5538]

source_name: MeDIP DNA from individual #5538

source_name: Input DNA from individual #5538


title: Perinatal control 1 [955]

source_name: MeDIP DNA from individual #955

source_name: Input DNA from individual #955


title: B6_LSK_reconst_1


title: BFC138_blood

value: chinese

value: blood


title: B6_LSK_reconst_2


title: B6_BM_LSK_2

value: Bone marrow HSC


title: Adult clone 6 [477]

source_name: MeDIP DNA from individual #477

source_name: Input DNA from individual #477


title: L-1236-siNFKB2-Seq1-Rep1

source_name: Hodgkin Lymphoma Cell Line

value: Hodgkin lymphoma cell-line L1236


title: B6_BM_LSK_4


title: BFC2217_blood


title: B6_BM_LSK_3


title: Cdx4_OP9_3


title: Adult clone 4 [447]

source_name: MeDIP DNA from individual #447

source_name: Input DNA from individual #447


title: Adult clone 5 [468]

source_name: MeDIP DNA from individual #468

source_name: Input DNA from individual #468


title: B6_BM_LSK_1


title: Cntrl-01

description:
Gene expression data from amygdala cells preapred from 8-10 weeks old male S1 mice
1798_032_A1_m01_AK_200213_(Mouse430_2)

source_name: amygdala of a control mouse

value: Ctrl

tag: strain

value: male

value: 8-10 weeks

value: fear extinction training


title: BFC1381_blood

tag: tissue


title: Adult control 6 [460]

source_name: MeDIP DNA from individual #460

source_name: Input DNA from individual #460


title: Adult control 8 [578]

source_name: MeDIP DNA from individual #578

source_name: Input DNA from individual #578


title: Adult clone 2 [437]

source_name: MeDIP DNA from individual #437

source_name: Input DNA from individual #437


title: Perinatal clone 6 [411]

source_name: MeDIP DNA from individual #411

source_name: Input DNA from individual #411


title: Adult clone 3 [439]

source_name: MeDIP DNA from individual #439

source_name: Input DNA from individual #439


title: Adult control 4 [428]

source_name: MeDIP DNA from individual #428

source_name: Input DNA from individual #428


title: Adult control 5 [449]

source_name: MeDIP DNA from individual #449

source_name: Input DNA from individual #449


title: MPNST8

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

institute: Paris Descartes University

description: MPNST DNA from Patient 8

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Tumor and constitutional DNAs were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours. The sandwiched slides were hybridized for 24 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).

data_processing: Log2 ratios were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s CGH Analytics v3.5 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.

source_name: MPNST

label_protocol: 500 ng of genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions. tumor and constitutional DNA were labeled with Cy5-dUTP and Cy3-dUTP, respectively

extract_protocol:
High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from tumors and wholeblood leukocytes, respectively
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.

value: NF1-associated human MPNST

source_name: pooled normal DNA

value: control


title: MPNST7

description: MPNST DNA from Patient 7


title: Perinatal clone 4 [3304]

source_name: MeDIP DNA from individual #3304

source_name: Input DNA from individual #3304


title: Perinatal clone 5 [406]

source_name: MeDIP DNA from individual #406

source_name: Input DNA from individual #406


title: MB3_SIL

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Exon expression data from Human. MBNL1 3,  silenced

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were processed from  oneChannel Graphical User Interface v1.4.5.   The filtering procedure and statistical evaluations were performed with oneChannelGUI graphical interface package to Bioconductor tools.

source_name: MBNL1 3,  silenced

label_protocol: standard Affymetrix protocol

growth_protocol: CELF1 (GeneBank Acc. No.: NM_006560) and MBNL1 (Acc. No.: NM_021038) genes were silenced by transfection with the oligonucleotides CELF1sense (5´-GUUACGACAAUCCUGUUUCdTdT-3´), CELF1antisense (5´-GAAACAGGAUUGUCGUAACdTdT-3´), MBNL1sense (5´- CACUGGAAGUAUGUAGAGAdTdT-3´), MBNL1antisense (5´- UCUCUACAUACUUCCAGUGdTdT-3´). These sequences specifically target in the human CELF1 exon 2 and MBNL1 exon 14, which are exons common to every splice variant described for both genes. HeLa cells (ECACC No 93021013) (http://www.hpacultures.org.uk/collections/ecacc.jsp) were seeded in six-well plates (200,000 cells per well) and transfected by triplicate with 25-100 nM of the CELF1 or MBNL1 oligonucleotides using the NTER Nanoparticle siRNA Transfection System (Sigma), following the manufacturer´s protocol, and incubated for 48 or 72 h at 37 ºC. Control cells were treated in the same conditions but without oligonucleotides. These experiments were performed three times (replicates). After the indicated times, cells were harvested and triplicates of each replicate were pulled and resuspended in 1 ml PBS and 50 µl were used for immunoblotting assays. The rest of the cells were pelleted and maintained at -20 ºC until RNA extraction.   For overexpression assays CDS sequences of CELF1 (GeneBank Acc. No.: NM_006560) and MBNL1 (Acc. No.: NM_021038) were PCR amplified from commercial human brain cDNA (R1234035-50, BioChain Institute Inc.), using the following oligonucleotides for CELF1:  NheI-CELF1Fwd (5´-cccgctagcATGaacggcaccctgg-3´), ApaI-CELF1Rev (5´-ggggggcccTCAgtagggcttgc-3´), and for MBNL1: NheI-MBNL1Fwd (5´-cccgctagcATGgctgttagtgtcac-3´) and ApaI-MBNL1 Rev (5´-ggggggcccCTAcatctgggtaac-3´). PCR cycle conditions were: 95°C for 5 min, 35 cycles at 95°C for 30 s, 55ºC for 30 s, 72ºC for 1.5 min and a final extension step at 72°C for 10 min. PCR products were purified in agarose gels, and inserted into pcDNA3.1/Zeo(-) plasmid by digestion with NheI and ApaI restriction enzymes to obtain the final pCELF1_pcDNA and pMBNL1_pcDNA constructs.    For transfection experiments, HeLa cells were cultured in six-well plates the day before transfection (200,000 cells per well). The following day 2 µg of the pCELF1-pcDNA or pMBNL1-pcDNA constructs were transfected in triplicate using Trans-IT Reagent according to the manufacturer's protocol. The empty vector pcDNA3.1/Zeo(-) was used to transfect control cells. After 48 h cells were harvested and prepared to immunoblot analyses, as described above, and the rest of the cells were pelleted and maintained at -20 ºC until RNA extraction.

extract_protocol: Total RNA was isolated from MBNL1 or CELF1 silenced or over-expressed HeLa cells pellets described above using the SV Total RNA Isolation System (Promega), according to the manufacturer’s instructions. Two hundred nanograms of total RNA and 0.5 µg oligo (dT)15 (Promega) were used to perform single-stranded cDNA by reverse transcription (RT) with the Improm II Reverse Transcription System (Promega), in a final volume of 20 µl.

treatment_protocol: not applicable

value: HeLA

tag: sample type

value: MBNL1,  silenced


title: CT3_SIL

description: Exon expression data from Human. Control 3, silenced

source_name: Control 3, silenced

value: Control, silenced


title: Root at mock T3, Technical rep1

city: NEW DELHI

first: DEVENDRA

middle: KUMAR

last: CHOUDHARY

state: DELHI

address: PUSA CAMPUS

department: PLANT PATHOLOGY

country: India

institute: INDIAN AGRICULTURAL RESEARCH INSTITUTE

description: Gene expression data from twenty six day old plant mock inoculated

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip ATH1-121501. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the agilent microarray scanner laser.

data_processing: The data were analyzed with genespring 12.6 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 plants mock inoculated

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

growth_protocol: Sterilized seeds were placed on Murashige and Skoog medium (Murashige and Skoog, 1962) and seeds were arranged in line at two third of Petri plate and transferred to growth chamber, after 48 hours of cold treatment at 4°C. The Growth conditions were 22/20˚C (day/night) temperature, 24 hours light period and 40 % relative humidity.

treatment_protocol: Seeds were sterilized 500 µl (0.1% SDS) + 500 µl (0.1% HgCl2) and five seed was placed on MS plate in a line and allowed for air drying, At twenty one day 10^8 & 10^9 cfu/ml dilution of bacterial suspension (5µl per seed) were spot inoculated on Root and sterile water were mock inoculated too. Different plants were used for different dilution, and mock inoculation.

value: Whole plants

value: twenty six day


title: CUG3_SIL

description: Exon expression data from Human. CUG 3, silenced

source_name: CUG 3, silenced

value: CUG, silenced


title: Root at mock T3, Technical rep2


title: MPNST5

description: MPNST DNA from Patient 5


title: CUG1_SIL

description: Exon expression data from Human. CUG 1, silenced

source_name: CUG 1, silenced


title: MPNST3

description: MPNST DNA from Patient 3


title: MPNST2

description: MPNST DNA from Patient 2


title: Root at 10^9 cfu/ml T1, Technical rep2

description: Gene expression data from twenty six day old plant inoculated with Rs 10^9 cfu/ml

source_name: Arabidopsis Col-0 plants inouculated with Ralstonia solanacearum race 4


title: CUG2_SIL

description: Exon expression data from Human. CUG 2, silenced

source_name: CUG 2, silenced


title: MB2_SIL

description: Exon expression data from Human. MBNL1 2,  silenced

source_name: MBNL1 2,  silenced


title: MB1_SIL

description: Exon expression data from Human. MBNL1 1,  silenced

source_name: MBNL1 1,  silenced


title: Root at 10^9 cfu/ml T1, Technical rep1


title: CT1_SIL

description: Exon expression data from Human. Control 1, silenced

source_name: Control 1, silenced


title: MB2_OV

description: Exon expression data from Human. MBNL1 2,  over-expression

source_name: MBNL1 2,  over-expression

value: MBNL1,  over-expression


title: MPNST1

description: MPNST DNA from Patient 1

source_name: MPNST


title: MB1_OV

description: Exon expression data from Human. MBNL1 1,  over-expression

source_name: MBNL1 1,  over-expression


title: MB3_OV

description: Exon expression data from Human. MBNL1 3,  over-expression

source_name: MBNL1 3,  over-expression


title: Root at 10^8 cfu/ml T0, Technical rep1

description: Gene expression data from twenty six day old plant inoculated with Rs 10^8 cfu/ml


title: CUG3_OV

description: Exon expression data from Human. CUG 3, over-expression

source_name: CUG 3, over-expression

value: CUG, over-expression


title: CT2_SIL

description: Exon expression data from Human. Control 2, silenced

source_name: Control 2, silenced


title: CML-DCs2_IM2.5microM

city: Bunkyo-City

first: Masashi

last: Miyauchi

state: Tokyo

address: 7-3-1 Hongo

department: Department of Hematology and Oncology

country: Japan

institute: Graduate School of Medicine,  The University of Tokyo

description: Gene expression after 6hr in 2.5microM imatinib-treated human hematopoietic differentiated cells from CML iPSC

hyb_protocol: 2.0 ug of Cy3-labelled cDNA  was  hybridized to SurePrint G3 Human GE 8x60K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven by usisg Gene Expression Hybridization Kit (Agilent).  After hybridization, microarrays were washed at room temperature with Gene Expression Wash Pack (Agilent) according manumacturer's protocol, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner (G2600D).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DCs from CML-iPSCs Pt1_2 Imatinib_6hr

label_protocol: The amplification and  the preperation of Cyanine-3 (Cy3) labeled cDNA was performed using the Ovation Pico WTA System V2 (NuGEN), according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using RNAeasy reagents (QIAGEN) following the manufacturer's recommendations.  The protocol includes hematopoietic-differentiated cells and an on-column DNase digestion. . RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Pre-HPCs and DCs from iPSCs were cultured in the α-MEM containing 20% FCS supplemented with 100 ng/mL SCF, 10 ng/mL TPO, 100 ng/mL FL3L, 10 ng/mL IL3, and 100 ng/mL IL6 in the presence or the absence of imitinib.  The cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.

value: hematopoietic-differentiated cells

tag: source tissue disease state

value: chronic myelogenous leukemia (CML)


title: Perinatal clone 2 [3302]

source_name: MeDIP DNA from individual #3302

value: Perinatal period

value: Nuclear transfert

source_name: Input DNA from individual #3302


title: CML-DCs3_IM2.5microM

source_name: DCCs from CML-iPSCs Pt2 Imatinib_6hr


title: Perinatal clone 3 [3303]

source_name: MeDIP DNA from individual #3303

source_name: Input DNA from individual #3303


title: Adult clone 1 [248]

source_name: MeDIP DNA from individual #248

value: Adulthood

source_name: Input DNA from individual #248


title: Root at 10^8 cfu/ml T0, Technical rep2

source_name: Arabidopsis Col-0 plants inouculated with Ralstonia solanacearum race 4

tag: genotype


title: Adult control 1 [2]

source_name: MeDIP DNA from individual #2

value: Artificial insemination

source_name: Input DNA from individual #2


title: Adult control 2 [229]

source_name: MeDIP DNA from individual #229

source_name: Input DNA from individual #229


title: CUG2_OV

description: Exon expression data from Human. CUG 2, over-expression

source_name: CUG 2, over-expression

tag: cell line


title: CT3_OV

description: Exon expression data from Human. Control 3, over-expression

source_name: Control 3, over-expression

value: Control, over-expression


title: CML-DCs1_IM2.5microM

source_name: DCs from CML-iPSCs Pt1_1 Imatinib_6hr


title: CML-DCs3_DMSO

description: Gene expression after 6hr in DMSO-treated human hematopoietic differentiated cells from CML iPSC

source_name: DCs from CML-iPSCs Pt2 DMSO_6hr


title: CML-DCs2_DMSO

source_name: DCs from CML-iPSCs Pt1_2 DMSO_6hr


title: Perinatal clone 1 [2263]

source_name: MeDIP DNA from individual #2263

source_name: Input DNA from individual #2263


title: MPNST6

description: MPNST DNA from Patient 6

source_name: MPNST

value: NF1-associated human MPNST

source_name: pooled normal DNA


title: CML-pre-HPCs2_IM2.5microM

description: Gene expression after 6hr in 2.5microM imatinib-treated pre-HPC from CML iPSC

source_name: pre-HPCs from CML-iPSCs Pt1_2 Imatinib_6hr

value: pre-hematopoietic progenitor cells (pre-HPCs)


title: CT2_OV

description: Exon expression data from Human. Control 2, over-expression

source_name: Control 2, over-expression

value: HeLA


title: Nrf1KO_2

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description: Gene expression in the liver from Nrf1 flox/flox::Cyp1a1 mouse treated with 3MC, replicate 2.

hyb_protocol: Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner.

data_processing: The data were normalized by 75th percentile shift and baseline transformation to median, and filtered by flag, using GeneSpring GX software (Silicon Genetics).

source_name: Nrf1flox/flox::Cyp1a1-Cre, 3MC, Liver

label_protocol: RNA samples were labeled with Cy3 using the Quick Amp Labeling kit (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from mouse liver using RNeasy spin column (Qiagen).

treatment_protocol: Nrf1flox/flox::CYP1A1-Cre and Nrf1flox/flox mice were subcutaneously injected with 40 mg/kg body weight of 3MC (Nrf1 CKO and control, respectively). Livers were obtained 2 weeks after the 3MC injection.

tag: strain/background

tag: genotype/variation

value: liver

tag: treatment


title: CML-pre-HPCs3_IM2.5microM

source_name: pre-HPCs from CML-iPSCs Pt2 Imatinib_6hr


title: Adult control 3 [2353]

source_name: MeDIP DNA from individual #2353

source_name: Input DNA from individual #2353


title: CT1_OV

description: Exon expression data from Human. Control 1, over-expression

source_name: Control 1, over-expression


title: CML-DCs1_DMSO

source_name: DCs from CML-iPSCs Pt1_1 DMSO_6hr


title: Nrf1KO_3

description: Gene expression in the liver from Nrf1 flox/flox::Cyp1a1 mouse treated with 3MC, replicate3.


title: Nrf1F/F::Cyp1a1-Cre_CornOil

description: Gene expression in the liver from Nrf1 flox/flox::Cyp1a1 mouse treated with corn oil.

source_name: Nrf1flox/flox::Cyp1a1-Cre, Corn oil, Liver

value: corn oil


title: Nrf1KO_1

description: Gene expression in the liver from Nrf1 flox/flox::Cyp1a1 mouse treated with 3MC, replicate1.


title: Control_2

description: Gene expression in the liver from Nrf1 flox/flox mouse treated with 3MC, replicate2.

source_name: Nrf1flox/flox, 3MC, Liver


title: CML-pre-HPCs3_DMSO

description: Gene expression after 6hr in DMSO treated pre-HPC from CML iPSC

source_name: pre-HPCs from CML-iPSCs Pt2 DMSO_6hr


title: CML-pre-HPCs1_IM2.5microM

source_name: pre-HPCs from CML-iPSCs Pt1_1 Imatinib_6hr


title: Control_1

description: Gene expression in the liver from Nrf1 flox/flox mouse treated with 3MC, replicate1.


title: Normal-pre-HPCs2_DMSO

description: Gene expression after 6hr in DMSO treated pre-HPC from normal iPSC

source_name: pre-HPCs from Normal-iPSCs H_2 DMSO_6hr

value: normal


title: Normal-pre-HPCs2_IM2.5microM

description: Gene expression after 6hr in 2.5microM imatinib-treated pre-HPC from normal iPSC

source_name: pre-HPCs from Normal-iPSCs H_2 Imatinib_6hr


title: CUG1_OV

description: Exon expression data from Human. CUG 1, over-expression

source_name: CUG 1, over-expression


title: CML-pre-HPCs2_DMSO

source_name: pre-HPCs from CML-iPSCs Pt1_2 DMSO_6hr


title: Normal-pre-HPCs3_IM2.5microM

source_name: pre-HPCs from Normal-iPSCs Pt2 Imatinib_6hr


title: Control_3

description: Gene expression in the liver from Nrf1 flox/flox mouse treated with 3MC, replicate3.


title: CML-pre-HPCs1_DMSO

source_name: pre-HPCs from CML-iPSCs Pt1_1 DMSO_6hr


title: Normal-pre-HPCs1_IM2.5microM

source_name: pre-HPCs from Normal-iPSCs H_1 Imatinib_6hr


title: Normal-pre-HPCs3_DMSO

source_name: pre-HPCs from Normal-iPSCs Pt2 DMSO_6hr


title: S3 M Af PRP

status: Public on Dec 20 2016

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

institute: University Hospital of Würzburg

description: Macrophage + A. fumigatus germ tubes + PRP

hyb_protocol: Standard Affymetrix GeneTitan Hyb protocol

scan_protocol: Standard Affymetrix GeneTitan Scan protocol

data_processing: RMA normalisation

label_protocol: Standard 3´-Assay Labeling for Affymetrix Plates

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from leucocyte concentrate blood of healthy donors (Univeristy Hospital Würzburg, transfusion medicine, Germany) by Ficoll-Hypaque density gradient centrifugation (Biochrom AG, Berlin, Germany). Human monocytes were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany).  A. fumigatus was cultivated on beer mesh plates at 37°C. After 3 days, conidia were detached by adding sterile water and singularized by a 40 µm cell strainer. Swelling and germination was achieved by incubation in RPMI 1640 medium with refocabin at room temperature and 37°C, respectively. Germ tubes  were inactivated by incubation in 100% Ethanol for 45°min.

extract_protocol: Qiagen RNA-Isolation Kit (miRNeasy Mini)

treatment_protocol: Differentiation of monocytes into immature DCs or macrophages was achieved by cultivating cells in RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) with 10% fetal calf serum (FCS, Sigma-Aldrich, Taufkirchen, Germany)  and 100 mg/ml Refobacin (Merck, Darmstadt, Germany) supplemented with either 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (Leukine, Novartis, Basel, Switzerland) and 10 ng/ml interleukin-4 (Miltenyi Biotec, Germany) or 500iU/ml macrophage colony-stimulating factor (AL Immunotools, Germany). Cultures were fed with fresh medium and cytokines every other day. After culturing for 6 days at 37°C and 5% CO2, DCs and macrophages were stimulated with 1 x 10^6 Aspergillus fumigatus germ tubes, PRP (1:30) and the combination of both stimuli.

value: macrophage


title: S3 M Af

description: Macrophage + A. fumigatus germ tubes

source_name: Macrophage + A. fumigatus germ tubes


title: S3 M PRP

description: Macrophage + PRP

source_name: Macrophage + PRP


title: S3 DC Af

description: DC + A. fumigatus germ tubes

source_name: DC + A. fumigatus germ tubes

value: dendritic cell


title: S1 M Control

description: Macrophage negative control

source_name: Macrophage negative control


title: S1 M Af PRP

source_name: Macrophage + A. fumigatus germ tubes + PRP


title: S3 DC Af PRP

description: DC + A. fumigatus germ tubes + PRP

source_name: DC + A. fumigatus germ tubes + PRP


title: S2 M Af PRP


title: S2 M Control

description: Macrophage negative control


title: S1 DC Af PRP

description: DC + A. fumigatus germ tubes + PRP


title: S3 DC Control

description: DC negative control

source_name: DC negative control


title: S2 DC Control

description: DC negative control


title: S2 M PRP

description: Macrophage + PRP


title: Nrf1F/F_CornOil

description: Gene expression in the liver from Nrf1 flox/flox mouse treated with corn oil.

source_name: Nrf1flox/flox, Corn oil, Liver


title: S2 DC Af

description: DC + A. fumigatus germ tubes


title: S1 M PRP

description: Macrophage + PRP


title: S1 M Af

description: Macrophage + A. fumigatus germ tubes


title: S2 DC Af PRP

description: DC + A. fumigatus germ tubes + PRP


title: S1 DC Af

description: DC + A. fumigatus germ tubes


title: S3 M Control

description: Macrophage negative control


title: S3 DC PRP

description: DC + PRP

source_name: DC + PRP


title: S2 DC PRP

description: DC + PRP


title: Normal-pre-HPCs1_DMSO

source_name: pre-HPCs from Normal-iPSCs H_1 DMSO_6hr


title: S2 M Af

description: Macrophage + A. fumigatus germ tubes


title: S1 DC Control

description: DC negative control


title: DLPFC_Male_BipolarDisorder_r_UMichigan_109961

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

hyb_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures.

data_processing:
A fully-cited description of the preprocessing can be found in the supplementary section of Li 2013 PNAS 110: 9950-9955:    Microarray experiments were performed in separate experimental cohorts, ranging from five to eight cohorts depending on the brain region.  Each cohort contained a mixture of cases and controls, with most RNA samples analyzed in duplicate at two laboratories (some analyzed in three laboratories).  The generation of probe-level intensity data (i.e., the CEL files) relied on standard Affymetrix library files and further processed using a custom annotation file (see below).      While most cohorts were analyzed on Affymetrix U133A platform, several of the latest cohorts were analyzed on the newer, U133Plus-v2 platform, which contains all U133A probe sets as a subset.  We extracted the U133A subset of the data for these samples and combined them with data for those analyzed on the U133A platform.  We applied RMA (Robust Multi-array Analysis) to summarize probe set expression levels, using the web interface at http://arrayanalysis.mbni.med.umich.edu.  RMA output, in the form of logged (base 2) expression levels, was generated using the custom ENTREZ12.1 Chip Definition Files (CDF), which defined probe sets for 11,912 ENTREZ transcripts and 68 control probe sets (http://nmg-r.bioinformatics.nl/Packages_for_R2.12.html).  The reason for using our custom-defined CDF files rather than the probe annotation provided by Affymetrix was to re-map all probes to the latest human genome build available, and to annotate probes according to one of the most detailed gene models.  The RMA results in this study thus represented 11,912 transcripts defined by ENTREZ in 03/2010 and are covered by probes on the U133A microarrays.  All downstream analyses were performed in R, using contributed packages available in early 2010.      To gain an overview of sample heterogeneity, we calculated sample-sample similarities for each region using pairwise Pearson's correlation coefficients (r), and calculated the average r of each sample to all other samples of the same region.  We chose the threshold of average r = 0.85 to define and remove outlier microarrays.  The outliers could result from either technical or biological differences. We removed additional microarrays corresponding to data produced at one laboratory for one cohort due to low average r and poor match with the duplicate microarrays from the second laboratory (denoted “batch 15” in the GEO metadata).     Although the RMA method has normalized probe intensity distributions across microarrays, the resulting probe set summaries still showed between-cohort, between microarray type (U133A versus U133 Plus v2), and between-laboratory variations, thus requiring further normalization.  For each brain region, we quantile-normalized the probe set values, and used pairwise correlation coefficients to define recognizable batches, which usually coincides with naturally occurring sample groups (>15 samples) according to cohorts or chip types.  The 68 negative control probe sets on the microarray platform, representing spiked-in non-human transcripts, show nearly identical batch effects as using all probes (not shown), indicating that most of the batch variation is due to technical differences in reagents and instruments rather than due to biological differences between samples in different batches.   To adjust for batch effects, we median-centered the expression levels of each transcript within each batch, and confirmed, by using the correlation matrices, that the batch-effects were removed after the adjustment.     We compared the result of this simple correction with the alternative, Bayesian batch-correction approach implemented in combat, and did not see meaningful differences in performance in terms of duplicate-sample concordance (results not shown).  While this is contrary to the published comparison results showing that combat is a better algorithm for dealing with batch effects, its advantage is probably blunted in our dataset because (1) we have larger sample sizes per batch (typically >15) than what was tested in the published comparisons, and we used median centering rather than mean-centering.  The latter is susceptible to the influence of outlier values, yet was used in earlier comparisons with combat.  We note that combat has decreased the scale of variation for most transcripts (as a consequence of improving the group variance estimation) and resulted in under-reporting of fold-changes between sample groups.  We therefore opted to maintain the use of the median-centering approach in this study.  After per-batch median-centering, we quantile-normalized the resulting values, and averaged the replicate microarrays for the same samples, yielding a dataset for unique subjects for each region.
Microarray experiments were performed in separate experimental cohorts, ranging from five to eight cohorts depending on the brain region.  Each cohort contained a mixture of cases and controls, with most RNA samples analyzed in duplicate at two laboratories (some analyzed in three laboratories).  The generation of probe-level intensity data (i.e., the CEL files) relied on standard Affymetrix library files and further processed using a custom annotation file (see below).
While most cohorts were analyzed on Affymetrix U133A platform, several of the latest cohorts were analyzed on the newer, U133Plus-v2 platform, which contains all U133A probe sets as a subset.  We extracted the U133A subset of the data for these samples and combined them with data for those analyzed on the U133A platform.  We applied RMA (Robust Multi-array Analysis) to summarize probe set expression levels, using the web interface at http://arrayanalysis.mbni.med.umich.edu.  RMA output, in the form of logged (base 2) expression levels, was generated using the custom ENTREZ12.1 Chip Definition Files (CDF), which defined probe sets for 11,912 ENTREZ transcripts and 68 control probe sets (http://nmg-r.bioinformatics.nl/Packages_for_R2.12.html).  The reason for using our custom-defined CDF files rather than the probe annotation provided by Affymetrix was to re-map all probes to the latest human genome build available, and to annotate probes according to one of the most detailed gene models.  The RMA results in this study thus represented 11,912 transcripts defined by ENTREZ in 03/2010 and are covered by probes on the U133A microarrays.  All downstream analyses were performed in R, using contributed packages available in early 2010.
To gain an overview of sample heterogeneity, we calculated sample-sample similarities for each region using pairwise Pearson's correlation coefficients (r), and calculated the average r of each sample to all other samples of the same region.  We chose the threshold of average r = 0.85 to define and remove outlier microarrays.  The outliers could result from either technical or biological differences. We removed additional microarrays corresponding to data produced at one laboratory for one cohort due to low average r and poor match with the duplicate microarrays from the second laboratory (denoted “batch 15” in the GEO metadata).
Although the RMA method has normalized probe intensity distributions across microarrays, the resulting probe set summaries still showed between-cohort, between microarray type (U133A versus U133 Plus v2), and between-laboratory variations, thus requiring further normalization.  For each brain region, we quantile-normalized the probe set values, and used pairwise correlation coefficients to define recognizable batches, which usually coincides with naturally occurring sample groups (>15 samples) according to cohorts or chip types.  The 68 negative control probe sets on the microarray platform, representing spiked-in non-human transcripts, show nearly identical batch effects as using all probes (not shown), indicating that most of the batch variation is due to technical differences in reagents

extract_protocol: Coronal slices of the brain were rapidly frozen on pre-cooled (to −120°C) aluminum plates, and stored at −80°C. Dorsolateral prefrontal cortex samples (area 9 plus 46) were trimmed to include an approximately equal  ratio  of  gray  and  white  matter,  the  latter  being  restricted  to  a  region  approximately  the  same  thickness  as layer VI of the cortex. Samples were taken from the left side. Following tissue dissection, total RNA was isolated by using TRIzol reagents (Invitrogen, Carlsbad, CA, USA), and shipped to the three research groups that collaborate on this project (University of California, Irvine; University of California, Davis; University of Michigan). For details, see (Evans 2003 Neurobiol Dis 14:240-250, Vawter 2003 Neuropsychopharm 29: 373-384, Li 2004 Biol Psychiatry 55:346-352, Li 2013 PNAS 110: 9950-9955).

tag: cohort

value: Dep Cohort 1

tag: site of processing

tag: diagnosis

value: Bipolar Disorder

tag: subject id

tag: agonal factor

tag: tissue ph (cerebellum)

tag: gender

value: M

tag: race

value: Caucasian

tag: post-mortem interval

tag: suicide (1=yes)

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Female_Control_UMichigan_109991

label_protocol: Sample labeling and hybridization followed the exact Affymetrix procedures.

value: Schiz Cohort 1

value: Control

value: F

tag: age

tag: tissue


title: DLPFC_Male_BipolarDisorder_UMichigan_109961


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_109899

value: Dep Cohort 4

value: Major Depressive Disorder


title: DLPFC_Male_Control_UMichigan_109422


title: DLPFC_Male_BipolarDisorder_r_UMichigan_108923


title: S1 DC PRP

description: DC + PRP

tag: cell type


title: DLPFC_Male_Control_UMichigan_109779

value: Asian


title: DLPFC_Female_Control_UMichigan_108858

value: Dep Cohort 3


title: DLPFC_Female_Schizophrenia_UMichigan_108583

value: Schizophrenia

value: Hispanic


title: DLPFC_Male_Control_UMichigan_108396


title: DLPFC_Female_Control_UMichigan_108634


title: DLPFC_Female_BipolarDisorder_UMichigan_109377


title: DLPFC_Male_BipolarDisorder_UMichigan_108107

value: Other


title: DLPFC_Male_Control_UMichigan_108632


title: DLPFC_Male_Control_UMichigan_108759


title: DLPFC_Male_Control_UMichigan_109170


title: DLPFC_Male_BipolarDisorder_UMichigan_108923


title: DLPFC_Male_BipolarDisorder_UMichigan_107610


title: DLPFC_Male_Control_UMichigan_108925

value: African American


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_107683

value: Dep Cohort 2


title: DLPFC_Male_MajorDepressiveDisorder_r_UMichigan_107727

value: Dep Cohort 1


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_107727


title: DLPFC_Male_BipolarDisorder_UMichigan_107366

value: Bipolar Disorder


title: DLPFC_Female_BipolarDisorder_UMichigan_107706


title: DLPFC_Female_Control_UMichigan_107886


title: DLPFC_Male_BipolarDisorder_r_UMichigan_108107

value: M


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_109430

value: Caucasian


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_107185

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Female_Control_UMichigan_107199


title: DLPFC_Male_BipolarDisorder_r_UMichigan_107366


title: DLPFC_Male_Control_UMichigan_107084


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_106917


title: DLPFC_Male_BipolarDisorder_UMichigan_106851


title: DLPFC_Male_Control_UMichigan_106742


title: DLPFC_Male_Schizophrenia_UMichigan_106495

value: Schiz Cohort 1


title: DLPFC_Male_MajorDepressiveDisorder_r_UMichigan_107185


title: DLPFC_Female_BipolarDisorder_UMichigan_106664


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_106256


title: DLPFC_Male_Control_UMichigan_106293

value: Control


title: DLPFC_Male_Control_UMichigan_106679


title: DLPFC_Female_MajorDepressiveDisorder_r_UMichigan_106355

value: F


title: DLPFC_Male_Control_r_UMichigan_106742


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_107061


title: DLPFC_Male_Control_UMichigan_106229


title: DLPFC_Female_MajorDepressiveDisorder_UMichigan_106149


title: DLPFC_Female_Control_UMichigan_107131

value: Dep Cohort 4


title: DLPFC_Male_Control_UMichigan_105952


title: DLPFC_Male_Control_UMichigan_105928


title: DLPFC_Female_MajorDepressiveDisorder_UMichigan_106355

value: Major Depressive Disorder


title: DLPFC_Female_BipolarDisorder_UMichigan_105867


title: DLPFC_Female_Control_UMichigan_105976

value: Asian


title: DLPFC_Male_Control_UMichigan_106589


title: DLPFC_Female_MajorDepressiveDisorder_UMichigan_105643


title: DLPFC_Male_BipolarDisorder_UMichigan_105621


title: DLPFC_Male_Control_r_UMichigan_105928


title: DLPFC_Male_Control_UMichigan_105476


title: DLPFC_Female_Control_UMichigan_105141


title: DLPFC_Female_Control_r_UMichigan_105141


title: DLPFC_Male_Control_UMichigan_105669

value: Dep Cohort 3


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_105506


title: DLPFC_Male_Control_UMichigan_105262


title: DLPFC_Female_MajorDepressiveDisorder_UMichigan_105080


title: DLPFC_Male_BipolarDisorder_UMichigan_107029


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_104851


title: DLPFC_Female_BipolarDisorder_UMichigan_104767


title: DLPFC_Female_BipolarDisorder_UMichigan_104808


title: DLPFC_Female_BipolarDisorder_r_UMichigan_104808


title: DLPFC_Female_Control_UMichigan_104659


title: DLPFC_Male_Schizophrenia_UMichigan_104655

value: Schizophrenia


title: DLPFC_Male_BipolarDisorder_UMichigan_104184


title: DLPFC_Male_BipolarDisorder_UMichigan_104097


title: DLPFC_Male_Schizophrenia_UMichigan_104259


title: DLPFC_Male_Schizophrenia_UMichigan_103311


title: DLPFC_Male_Control_UMichigan_103984


title: DLPFC_Male_Control_UMichigan_103262


title: DLPFC_Male_Control_UMichigan_103068


title: DLPFC_Female_Schizophrenia_UMichigan_103037


title: DLPFC_Male_Control_UMichigan_103998


title: DLPFC_Male_Control_r_UMichigan_103998


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_102513


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_103091


title: DLPFC_Female_Control_UMichigan_102785


title: DLPFC_Male_Control_UMichigan_102475


title: DLPFC_Male_Control_UMichigan_102440


title: DLPFC_Male_Control_UMichigan_104126


title: DLPFC_Female_MajorDepressiveDisorder_UMichigan_102432


title: DLPFC_Male_Control_r_UMichigan_108925


title: DLPFC_Male_Schizophrenia_UMichigan_102118


title: DLPFC_Male_Control_UMichigan_101923


title: DLPFC_Female_Control_UMichigan_102212


title: DLPFC_Male_Control_r_UMichigan_101811


title: DLPFC_Male_Control_UMichigan_101811


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_102636


title: DLPFC_Male_Control_r_UMichigan_102475


title: DLPFC_Female_Control_UMichigan_102422


title: DLPFC_Female_Control_UMichigan_102420


title: DLPFC_Male_Control_UMichigan_102539


title: DLPFC_Male_BipolarDisorder_UMichigan_101690


title: DLPFC_Male_MajorDepressiveDisorder_r_UMichigan_101739


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_101739


title: DLPFC_Male_Control_UMichigan_105676


title: DLPFC_Female_Control_UMichigan_101283


title: DLPFC_Male_Control_UMichigan_101488


title: DLPFC_Female_Control_UMichigan_101309


title: DLPFC_Male_Control_UMichigan_101244


title: DLPFC_Male_Control_UCIrvine_109422


title: DLPFC_Male_BipolarDisorder_r_UMichigan_101690


title: DLPFC_Female_Control_UCIrvine_107886


title: DLPFC_Male_Control_UCIrvine_109779


title: DLPFC_Female_Schizophrenia_UMichigan_101657

value: Hispanic


title: DLPFC_Male_Schizophrenia_UMichigan_101078


title: DLPFC_Female_Control_UCIrvine_109991


title: DLPFC_Male_Control_UCIrvine_106589


title: DLPFC_Male_Control_UMichigan_101431


title: DLPFC_Female_Schizophrenia_UCIrvine_108583


title: DLPFC_Male_Schizophrenia_UCIrvine_106495


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_101597


title: DLPFC_Male_Schizophrenia_UCIrvine_104259


title: DLPFC_Male_Schizophrenia_UCIrvine_103311

value: Other


title: DLPFC_Male_Control_UCIrvine_104126


title: Input_2

city: Warsaw

first: Rafal

last: Archacki

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

description:
fraction: nuclear DNA
sonicated chromatin

hyb_protocol: Labeled DNA was hybridized to Arabidopsis Agronomics microarray (Rehrauer et al., 2010) using a GeneChip Hybridization Wash and Stain Kit according to the manufacturer’s recommendations (Affymetrix).

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 3000. The signals were recorded and processed using Affymetrix® GeneChip® Command Console® Software (AGCC).

data_processing:
ChIP-chip microarray probe signals were extracted using Affymetrix APT-cel software.
The resulting bed files were generated by the Affymetrix APT-cel software. SGR files contain the normalized probe intensities. Signals for both strands were merged for each replicate and then transformed to TAIR10 coordinates. The signal was normalized separately for each of the two biological replicates and the average of the replicates for each probe was used. Log2 (IP/Input) was computed for every probe and the significant regions were then called by finding regions of length > 40 probes with enrichment > 1.5 (log2 enrichment >0.58), excluding at most 3 faulty probes. The BED file on the series record contains the significantly enriched regions.

source_name: Arabidopsis WT, none

label_protocol: Four µg of DNA was used for fragmentation and labeling according to Affymetrix chromatin immunoprecipitation assay protocol (P/N 702238 Rev.4) using a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Chromatin was isolated from 3-week-old seedlings of wild-type Arabidopsis (Col-0 ecotype) grown in soil under long-day conditions. Aerial parts of plants were harvested and rinsed in water.

extract_protocol: Samples were diluted 10-fold with ChIP Dilution Buffer (1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors (Roche). For immunoprecipitation, Anti-BRM antibody [Archacki et al., 2009) was bound to Dynabeads Protein A (Invitrogen) and incubated overnight with aliquotes of diluted chromatin (100 µg of DNA). Beads were washed with Low Salt, High Salt and LiCl, and TE buffer as described (Gendrel et al., 2005). Immune complexes were eluted by adding 500 µl of Elution Buffer (1% SDS, 0.1 M NaHCO3) to the pelleted beads. Cross-links were reversed by addition of 40 ul 2.5 M NaCl and incubation at 65°C overnight. DNA was purified with a PCR purification kit (Qiagen) and subjected to two rounds of amplification using a WGA2 GenomePlex Complete whole genome amplification kit (Sigma-Aldrich), according to the manufacturer’s protocol.

treatment_protocol: Plant tissue was crosslinked in 1% formaldehyde in 1xPBS buffer under vaccume (2x 10 min.). After incubation in 0.125 M glycine for 5 min, plant tissues were washed twice with 1× PBS. Nuclear extracts were prepared as described by Gendrel et al. (2005) and sonicated using Bioruptor sonicator (Diagenode). The extracts were then centrifuged for 5 minutes, 4°C at 10,000 × g and the supernatants were used for immunoprecipitation.

value: aerial parts of plant

tag: ecotype

value: sonicated chromatin

tag: antibody

value: 3-weeks old


title: DLPFC_Male_Schizophrenia_UCIrvine_102118


title: DLPFC_Male_Control_UCIrvine_102440


title: DLPFC_Female_Control_UCIrvine_102212


title: Input_1


title: DLPFC_Female_Schizophrenia_UCIrvine_103037


title: DLPFC_Female_Schizophrenia_UCIrvine_101657


title: DLPFC_Male_Control_UCIrvine_106229


title: DLPFC_Female_BipolarDisorder_UCDavis_109533

value: Dep Cohort 2

value: Bipolar Disorder


title: DLPFC_Male_Schizophrenia_UCIrvine_101078

value: M

value: Caucasian


title: DLPFC_Male_Schizophrenia_UCIrvine_104655

value: Schiz Cohort 1

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_109430


title: DLPFC_Male_Control_UCDavis_109779

value: Control


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_109899

value: Dep Cohort 4


title: DLPFC_Female_Control_UCDavis_109092

value: F


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_109923

value: Major Depressive Disorder


title: DLPFC_Male_BipolarDisorder_UCDavis_109961

value: Dep Cohort 1


title: DLPFC_Male_Control_UCDavis_109170


title: DLPFC_Female_Control_UCDavis_109991


title: DLPFC_Male_Control_UCDavis_108925

value: African American


title: DLPFC_Female_BipolarDisorder_UCDavis_109377

value: Dep Cohort 3


title: DLPFC_Male_Control_UCDavis_109422


title: DLPFC_Male_BipolarDisorder_UCDavis_108923


title: DLPFC_Female_Control_UCDavis_108858


title: BRM_ChIP_1

description:
fraction: nuclear DNA
sonicated chromatin, anti-BRM

source_name: Arabidopsis WT, anti-BRM

value: sonicated chromatin, anti-BRM

value: anti-BRM


title: BRM_ChIP_2

description:
fraction: nuclear DNA
sonicated chromatin anti-BRM

value: aerial parts of plant


title: brm-1_repl3

description: gene expression data from Arabidopsis plants grown under long-days conditions

hyb_protocol: 5.5 μg of cRNA was hybridized with an Agronomics array (Rehrauer et al., 2010) using a GeneChip Hybridization Wash and Stain Kit, according to the manufacturer’s recommendations (Affymetrix).

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Probe intensities for strand-specific signals were extracted using Affymetrix apt-cel software. Probe positions were transformed to the TAIR10 genome assembly. The signal was normalized separately for each of the three biological replicates and the average of the replicates for each probe was used for gene expression measurements. The .sgr files contain normalized signals for each probe.

source_name: 3-week old seedlings

label_protocol: 100 ng of RNA was used for cDNA synthesis with an Ambion WT Expression Kit. Fragmentation and labeling was done using a GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer`s protocol.

growth_protocol: RNA was isolated from 3-week-old seedlings of wild-type Arabidopsis (Col-0 ecotype) grown in soil under long-day conditions. Aerial parts of plants were harvested.

extract_protocol: Total RNA was extracted using RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol, followed by treatment with TURBO DNase (Ambion) and RiboMinus™ Plant Kit (Invitrogen) to reduce the rRNA fraction.

treatment_protocol: Plant material was harvested, frozen in liquid nitrogen and ground into powder

value: aerial parts of soil-grown plants

tag: genotype

value: 3-weeks old


title: brm-1_repl2


title: brm-1_repl1


title: wt_repl3

value: WT


title: wt_repl1


title: wt_repl2


title: DLPFC_Female_Control_UCDavis_108634


title: DLPFC_Male_Control_UCDavis_108632

value: M


title: DLPFC_Male_Control_UCDavis_108396

value: Caucasian


title: DLPFC_Female_Schizophrenia_UCDavis_108583

value: Schiz Cohort 1

value: Schizophrenia

value: Hispanic


title: DLPFC_Female_Control_UCDavis_107886

value: Control

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Male_BipolarDisorder_UCDavis_107610

value: Bipolar Disorder


title: DLPFC_Female_Control_UCDavis_107199

value: Dep Cohort 4

value: F


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_107683

value: Dep Cohort 2

value: Major Depressive Disorder


title: DLPFC_Male_Control_UCDavis_108493

value: Asian


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_107061


title: DLPFC_Female_Control_UCDavis_108021


title: DLPFC_Male_Control_UCDavis_107084


title: DLPFC_Female_BipolarDisorder_UCDavis_107706


title: DLPFC_Male_BipolarDisorder_UCDavis_108107

value: Other


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_107727

value: Dep Cohort 1


title: DLPFC_Female_Control_UCDavis_108030


title: DLPFC_Male_Control_UCDavis_107032


title: DLPFC_Male_MajorDepressiveDisorder_UMichigan_109923


title: DLPFC_Male_BipolarDisorder_UCDavis_107366


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_107185


title: DLPFC_Female_Control_UCDavis_107131


title: DLPFC_Male_BipolarDisorder_UCDavis_107029

value: Dep Cohort 3


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_106917


title: DLPFC_Male_Control_UCDavis_106589


title: DLPFC_Male_Control_UCDavis_106742


title: DLPFC_Male_Control_UCDavis_106679


title: DLPFC_Female_BipolarDisorder_UCDavis_106664


title: DLPFC_Female_BipolarDisorder_UCDavis_106692


title: DLPFC_Male_Schizophrenia_UCDavis_106495


title: DLPFC_Female_MajorDepressiveDisorder_UCDavis_106355


title: DLPFC_Male_Control_UCDavis_106293


title: DLPFC_Male_BipolarDisorder_UCDavis_106851


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_106256


title: DLPFC_Male_Control_r_p_UCDavis_106229


title: DLPFC_Female_Control_UCDavis_105976


title: DLPFC_Male_Control_UCDavis_105952


title: DLPFC_Male_Control_UCDavis_105928


title: DLPFC_Male_Control_UCDavis_105669


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_104851


title: DLPFC_Female_BipolarDisorder_UCDavis_105867


title: DLPFC_Female_MajorDepressiveDisorder_UCDavis_105080


title: DLPFC_Male_Control_UCDavis_105676


title: DLPFC_Female_Control_UCDavis_105141


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_105506


title: DLPFC_Male_Control_UCDavis_106229


title: DLPFC_Male_Control_UCDavis_105476


title: DLPFC_Female_Control_UCDavis_104659


title: DLPFC_Female_BipolarDisorder_UCDavis_104767


title: DLPFC_Female_BipolarDisorder_UCDavis_104808


title: DLPFC_Male_BipolarDisorder_UCDavis_105621


title: DLPFC_Female_MajorDepressiveDisorder_UCDavis_106149


title: DLPFC_Female_MajorDepressiveDisorder_UCDavis_105643


title: DLPFC_Male_Schizophrenia_UCDavis_104655


title: DLPFC_Male_Control_UCDavis_105262


title: DLPFC_Male_Schizophrenia_UCDavis_104259


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_103091


title: DLPFC_Male_Control_UCDavis_104126


title: DLPFC_Male_BipolarDisorder_UCDavis_104097


title: DLPFC_Male_Schizophrenia_UCDavis_103311


title: DLPFC_Male_BipolarDisorder_UCDavis_104184


title: DLPFC_Male_Control_UCDavis_103998


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_102636


title: DLPFC_Female_Schizophrenia_UCDavis_103037


title: DLPFC_Male_Control_UCDavis_103068


title: DLPFC_Male_Control_UCDavis_103262


title: DLPFC_Male_Control_UCDavis_103984


title: DLPFC_Female_Control_UCDavis_102785


title: DLPFC_Male_Control_UCDavis_102539


title: DLPFC_Male_Control_UCDavis_102475


title: DLPFC_Male_Control_UCDavis_102440


title: DLPFC_Female_Control_UCDavis_102422


title: DLPFC_Female_Control_UCDavis_102420


title: DLPFC_Female_Control_UCDavis_102212


title: DLPFC_Female_MajorDepressiveDisorder_UCDavis_102432


title: DLPFC_Female_Control_UCDavis_101956


title: DLPFC_Male_Control_UCDavis_101811


title: DLPFC_Male_Control_UCDavis_101923


title: DLPFC_Female_Control_UCDavis_102038


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_102513


title: DLPFC_Male_Control_UCDavis_108759


title: DLPFC_Male_BipolarDisorder_UCDavis_101690


title: DLPFC_Female_Control_UCDavis_101309


title: DLPFC_Male_Schizophrenia_UCDavis_102118


title: DLPFC_Male_Control_UCDavis_101736


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_101739


title: DLPFC_Female_Control_UCDavis_101283


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_101674


title: DLPFC_Male_Control_UCDavis_101488


title: wild type group_23

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: For each sample a hybridization cocktail was created that includes a total of 2.5 micrograms of fragmented cDNA. Probe arrays were filled with hybridization cocktail and placed in a GeneChip® Hybridization Oven 640 (Affymetrix) for 18 hours. Arrays were then washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G. All files including .dat, .cel, and .chp files were created by the scanning and analysis software, the Genechip Operating Software (Affymetrix).

data_processing:
Use RMA to normalize all arrays (samples) for a project. Average means of samples in the same group, i.e. TRAF6 transgenic mice versus wild type groups. Create interpretations to compare TRAF6 transgenic mice versus wild type groups. Filter raw data to remove entities (genes) not being expressed. The processed data set was used for gene set enrichment analysis and gene ontology.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: LSK wild type group_23

label_protocol: Assays from NuGEN were used to create biotin-labeled cDNA target. Specifically the WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) was used to prepare target cDNA.  Then the WT-Ovation Exon Module v1.0 (NuGEN) was used to create sense-strand cDNA targets. Finally the FL-Ovation cDNA Biotin Module V2 (NuGEN) chemically fragmented and labeled the sense-strand cDNA targets.

growth_protocol: Bone marrow cells were harvested from TRAF6 transgenic mice and wild type control littermates. Hematopoietic stem and progenitor cell enriched population (Lineage negative, Sca-1 positive and c-Kit positive) was fractionated with flow cytometry, followd by RNA extraction.

extract_protocol: Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

treatment_protocol: The mice haven't received any treatment at the time of bone marrow harvest.

tag: strain

value: FVB

tag: genotype/variation

value: wild type

value: bone marrow

value: adult


title: TRAF6 transgenic group_03

source_name: LSK TRAF6 transgenic group_03

value: TRAF6 transgenic


title: DLPFC_Female_Schizophrenia_UCDavis_101657

tag: cohort

value: Schiz Cohort 1

tag: site of processing

value: Schizophrenia

value: Hispanic


title: DLPFC_Male_Control_UCDavis_101244

tag: diagnosis

value: Control

tag: subject id

value: M

value: Caucasian

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Male_Control_UCDavis_101431

value: Dep Cohort 4

tag: agonal factor

tag: tissue ph (cerebellum)


title: DLPFC_Male_Schizophrenia_UCDavis_101078

tag: gender

tag: race


title: DLPFC_Male_MajorDepressiveDisorder_UCDavis_101597

value: Major Depressive Disorder

tag: post-mortem interval

tag: suicide (1=yes)


title: wild type group_21

source_name: LSK wild type group_21

tag: tissue

tag: age


title: TRAF6 transgenic group_05

source_name: LSK TRAF6 transgenic group_05


title: TRAF6 transgenic group_04

source_name: LSK TRAF6 transgenic group_04


title: wild type group_24

source_name: LSK wild type group_24


title: wild type group_22

source_name: LSK wild type group_22


title: POLR2A [9702496158_R03C02]

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Illumina scanner

data_processing:
We first processed raw intensity files (*.idat) and obtained ratio between Illumina methylated probe intensity and total probe intensities (beta-values) using the champ R package. Then, we assessed the quality of the methylation samples and probes. We removed sites containing missing values. The probes targeting a CpG with a SNP were also removed from analysis. Probes targeting the X and Y chromosomes were excluded. The sites having at least 50 % samples with detection p-value > 0.05 are removed. The detection p-value is calculated using the reported background signal levels of both the methylated and unmethylated channels. After preprocessing the raw data, we performed beta mixture quantile normalization (BMIQ), a normalization correction for the technical differences between the Type I and Type II array designs 28. The DNA methylation score for each probe is described as the ratio of intensities between methylated and unmethylated alleles: M/(M+U). Finally batch effect is corrected using combat algorithm in champ R package.
Unmethylated and methylated signal intensities

source_name: meningioma

label_protocol: Standard Illumina Protocol

growth_protocol: Samples were excised during neurosugical procedures and frozen in OCT for later use. H&E slides were prepared for each sample to confirm tumor histology and assess tissue density.

extract_protocol: 10 to 15 frozen sections of each tumor block or dura sample were collected for each experiment. DNA was extracted using the Allprep DNA/RNA Mini Kit (Qiagen, 80004).

treatment_protocol: All samples are untreated, primary specimens from brain tumor patients.

tag: tissue id

tag: tissue type

value: meningioma

tag: mutation subtype

tag: grade

tag: batch


title: NF2/Chr22/SMARCB1 [9702496158_R02C02]


title: NF2/Chr22 [9702496158_R04C02]


title: TRAF7/PIK3 [200109350018_R01C01]


title: POLR2A [9702496158_R05C01]


title: TRAF7/PIK3 [200109350018_R02C01]


title: TRAF7/PIK3 [200109350018_R04C01]


title: Hedgehog [9702496158_R06C01]

value: Hedgehog


title: NF2/Chr22 [9702496158_R02C01]


title: NF2/Chr22 [9702496158_R04C01]


title: Hedgehog [9702496149_R06C02]


title: NF2/Chr22 [6969568085_R04C01]


title: POLR2A [9702496149_R04C02]


title: NF2/Chr22 [9702496149_R05C02]


title: NF2/Chr22 [6969568085_R06C02]


title: Hedgehog [9702496149_R02C01]


title: TRAF7/PIK3 [9702496149_R03C02]


title: NF2/Chr22 [6969568085_R05C02]


title: NF2/Chr22 [6969568085_R02C02]


title: NF2/Chr22/SMARCB1 [6969568085_R01C02]


title: NF2/Chr22 [9702496149_R01C01]


title: NF2/Chr22 [6969568085_R03C02]


title: Hedgehog [9702496149_R02C02]


title: NF2/Chr22 [6969568085_R05C01]


title: NF2/Chr22/SMARCB1 [9702496149_R05C01]


title: TRAF7/PIK3 [9702496149_R01C02]


title: NF2/Chr22 [6969568085_R03C01]


title: NF2/Chr22 [6969568085_R06C01]


title: POLR2A [9702496149_R03C01]


title: POLR2A [6969568085_R02C01]


title: NF2/Chr22 [6969568012_R04C02]


title: TRAF7/KLF4 [6969568012_R02C02]


title: NF2/Chr22 [6969568012_R03C02]


title: NF2/Chr22 [6969568012_R05C02]


title: NF2/Chr22 [6969568012_R05C01]


title: NF2/Chr22 [6969568012_R04C01]


title: NF2/Chr22 [6969568012_R03C01]


title: NF2/Chr22 [6969568012_R06C02]


title: Hedgehog [6969568012_R01C02]


title: 889_W3::3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from WT MEFs

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: WT MEFs

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Grow in DMEM medium containing 10% FBS, 25 mM Glucose, and 4 mM Glutamine

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: No special treatment

tag: cell line

value: WT MEFs

value: female


title: 889_W2::2

description: Gene expression from WT MEFs


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_109833

tag: cohort

value: Dep Cohort 5

tag: site of processing


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_109436

value: Dep Cohort 6

tag: diagnosis

tag: subject id


title: TRAF7/PIK3 [6969568093_R06C02]


title: DLPFC_Male_Control_p_UMichigan_109882

tag: agonal factor

tag: tissue ph (cerebellum)


title: 889_W10::5

description: Gene expression from WT MEFs

tag: gender


title: DLPFC_Male_Schizophrenia_p_UMichigan_109371

value: Schiz Cohort 2

tag: race

tag: post-mortem interval


title: 889_W1::1

description: Gene expression from WT MEFs


title: NF2/Chr22 [6969568093_R02C02]


title: NF2/Chr22 [6969568093_R02C01]


title: 889_K7::5

description: Gene expression from SIRT1 homozygous MEFs

source_name: SIRT1 Homozygous MEFs

value: SIRT1 KO MEFs


title: TRAF7/KLF4 [6969568093_R03C01]


title: TRAF7/PIK3 [6969568038_R02C01]


title: TRAF7/KLF4 [6969568038_R04C02]


title: NF2/Chr22 [6969568093_R05C01]


title: Hedgehog [6969568093_R06C01]


title: Control [6969568038_R06C02]


title: NF2/Chr22 [6969568093_R01C01]


title: TRAF7 [6969568093_R04C01]


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_109257

tag: suicide (1=yes)

tag: tissue


title: TRAF7/KLF4 [6969568012_R01C01]

tag: tissue id


title: 889_K3::3


title: NF2/Chr22 [6969568038_R01C02]

tag: tissue type


title: Control [6969568038_R06C01]

tag: mutation subtype


title: Control [6969568038_R05C01]

tag: grade


title: TRAF7 [6969568038_R04C01]

tag: batch


title: NF2/Chr22/SMARCB1 [6969568093_R01C02]


title: NF2/Chr22 [6969568038_R03C02]


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_109120

tag: age


title: TRAF7/PIK3 [6969568038_R02C02]


title: TRAF7 [6969568038_R05C02]


title: DLPFC_Female_Control_p_UMichigan_109103

tag: cohort

value: F


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_109248

tag: site of processing


title: DLPFC_Male_Control_p_UMichigan_108778

tag: diagnosis


title: DLPFC_Male_Control_p_UMichigan_108425

tag: subject id


title: DLPFC_Male_BipolarDisorder_p_UMichigan_108454

value: Bipolar Disorder

tag: agonal factor


title: DLPFC_Female_MajorDepressiveDisorder_p_UMichigan_108700

tag: tissue ph (cerebellum)


title: DLPFC_Male_Control_p_UMichigan_108291

tag: gender


title: 889_H3::3

description: Gene expression from SIRT1 heterozygous MEFs

source_name: SIRT1 Heterozygous MEFs

tag: cell line

value: SIRT1 Het MEFs


title: 889_HOct::4


title: 889_H8::5


title: 889_K2::2


title: DLPFC_Male_BipolarDisorder_p_UMichigan_108104

tag: race

tag: post-mortem interval


title: Trp53-null mammary tumor developed in mouse TB208

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse TB208 (K8-CreER;Trp53L/L) injected with tamoxifen

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute
Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Wild-type or Trp53-null mammary epithelial cells were sorted from female mice with the indicated genotypes; Trp53-null mammary tumors were collected from Trp53L/L female mice after Ad-K8-Cre injection or from K8-CreER;Trp53L/L female mice after tamoxifen injection.

extract_protocol: RNeasy kit (Qiagen, #73504) was used on sorted mammary epithelial cells or mammary tumors according to manufacturer's protocol

treatment_protocol: Wild-type or Trp53-null mammary epithelial cells were obtained from female mice with the indicated genotypes 4-weeks after induction of K8-CreER activity by tamoxifen; Trp53-null mammary tumors were obtained from Trp53L/L females 6-7 months after intraductal injection of Ad-K8-Cre adenovirus or from K8-CreER;Trp53L/L female mice 6-7 months after tamoxifen injection.

tag: strain

tag: cell type

value: Trp53-null mammary tumor


title: 889_H2::2


title: DLPFC_Male_Control_p_UMichigan_108022

value: Control

value: M

value: African American

tag: suicide (1=yes)

tag: tissue


title: TRAF7/KLF4 [6969568038_R01C01]

tag: tissue id

tag: tissue type

tag: mutation subtype

tag: grade


title: DLPFC_Male_Control_p_UMichigan_108017

tag: cohort

tag: site of processing

value: Caucasian

tag: age

value: Dorsolateral Prefrontal Cortex


title: Trp53-null mammary tumor developed in mouse TB239

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse TB239 (K8-CreER;Trp53L/L) injected with tamoxifen


title: Trp53-null mammary tumor developed in mouse E9

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E9 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: Trp53-null mammary tumor developed in mouse E7

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E7 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: Trp53-null mammary tumor developed in mouse E8

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E8 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: Trp53-null mammary tumor developed in mouse TB209

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse TB209 (K8-CreER;Trp53L/L) injected with tamoxifen


title: DLPFC_Female_MajorDepressiveDisorder_p_UMichigan_107845

tag: diagnosis

value: Major Depressive Disorder

tag: subject id

tag: agonal factor


title: Trp53-null mammary tumor developed in mouse E5

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E5 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

tag: gender


title: DLPFC_Male_Control_p_UMichigan_107309

tag: tissue ph (cerebellum)

tag: race


title: DLPFC_Male_Control_p_UMichigan_106798

tag: post-mortem interval


title: DLPFC_Male_Control_p_UMichigan_108066


title: DLPFC_Male_Control_p_UMichigan_106966


title: Trp53-null mammary tumor developed in mouse E4

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E4 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus

tag: strain

tag: cell type


title: 889_KOct::4

tag: cell line


title: Trp53-null mammary tumor developed in mouse E2

description: Gene expression data for a Trp53-null mammary tumor developed in female mouse E2 (Trp53L/L;Rosa26-Stop-YFP) injected with Ad-K8-Cre adenovirus


title: DLPFC_Male_Schizophrenia_p_UMichigan_106564

value: Schizophrenia

tag: suicide (1=yes)

tag: tissue


title: DLPFC_Male_Schizophrenia_p_UMichigan_106725


title: DLPFC_Male_Control_p_UMichigan_106276


title: DLPFC_Male_Schizophrenia_p_UMichigan_106753


title: DLPFC_Male_Schizophrenia_p_UMichigan_106082

value: Asian


title: Trp53-null YFP+ K8+ luminal mammary epithelial cells from TC213

description: Gene expression data for Trp53-null YFP-marked K8+ luminal cells sorted from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC213 4-weeks after tamoxifen induction

source_name: Trp53-null YFP-marked K8+ luminal cells from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC213

value: female

value: Trp53-null YFP-marked K8+ luminal cells


title: Trp53-null YFP+ K8+ luminal mammary epithelial cells from TC258

description: Gene expression data for Trp53-null YFP-marked K8+ luminal cells sorted from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC258 4-weeks after tamoxifen induction

source_name: Trp53-null YFP-marked K8+ luminal cells from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC258


title: Normal YFP+ K8+ luminal mammary epithelial cells from TC143

description: Gene expression data for normal YFP-marked K8+ luminal cells sorted from K8-CreER;Rosa26-Stop-YFP female TC143 4-weeks after tamoxifen induction

source_name: Normal YFP-marked K8+ luminal cells from K8-CreER;Rosa26-Stop-YFP female TC143

value: Normal YFP-marked K8+ luminal cells


title: DLPFC_Female_Control_p_UMichigan_106172

value: Dep Cohort 5


title: Trp53-null YFP+ K8+ luminal mammary epithelial cells from TC201

description: Gene expression data for Trp53-null YFP-marked K8+ luminal cells sorted from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC201 4-weeks after tamoxifen induction

source_name: Trp53-null YFP-marked K8+ luminal cells from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC201


title: DLPFC_Male_Control_p_UMichigan_106051


title: Normal YFP+ K8+ luminal mammary epithelial cells from TC189

description: Gene expression data for normal YFP-marked K8+ luminal cells sorted from K8-CreER;Rosa26-Stop-YFP female TC189 4-weeks after tamoxifen induction

source_name: Normal YFP-marked K8+ luminal cells from K8-CreER;Rosa26-Stop-YFP female TC189


title: DLPFC_Male_Control_p_UMichigan_106049


title: DLPFC_Female_Control_p_UMichigan_105725

value: Schiz Cohort 2


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_105947


title: DLPFC_Male_Control_p_UMichigan_105589

value: Dep Cohort 6


title: DLPFC_Female_BipolarDisorder_p_UMichigan_105687

value: Bipolar Disorder

value: F


title: DLPFC_Male_BipolarDisorder_p_UMichigan_105544


title: DLPFC_Female_Schizophrenia_p_UMichigan_104344


title: DLPFC_Female_MajorDepressiveDisorder_p_UMichigan_104630


title: Normal YFP+ K8+ luminal mammary epithelial cells from TC190

description: Gene expression data for normal YFP-marked K8+ luminal cells sorted from K8-CreER;Rosa26-Stop-YFP female TC190 4-weeks after tamoxifen induction

source_name: Normal YFP-marked K8+ luminal cells from K8-CreER;Rosa26-Stop-YFP female TC190


title: Trp53-null YFP+ K8+ luminal mammary epithelial cells from TC204

description: Gene expression data for Trp53-null YFP-marked K8+ luminal cells sorted from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC204 4-weeks after tamoxifen induction

source_name: Trp53-null YFP-marked K8+ luminal cells from K8-CreER;Trp53L/L;Rosa26-Stop-YFP female TC204


title: SW620-CD133+_2_

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: Cells were cultured in RMPI medium plus 10% FBS

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


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_104349


title: DLPFC_Male_Schizophrenia_p_UMichigan_104049


title: SW620-CD133+_1_


title: SW620-5FU-R_2_


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_103625


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_103917


title: DLPFC_Male_Control_p_UMichigan_103610


title: DLPFC_Male_Control_p_UMichigan_103166


title: DLPFC_Female_BipolarDisorder_p_UMichigan_103211


title: DLPFC_Male_Control_p_UMichigan_102854


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_104521


title: SW620-5FU-R_1_


title: DLPFC_Female_Schizophrenia_p_UMichigan_103620


title: LS411N-5FU-R+VA 0nM_1_

source_name: LS411N-5FU-R+VA 0nM


title: LS411N-CD133+_2_


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_102482


title: DLPFC_Male_Control_p_UMichigan_102579


title: LS411N-5FU-R+VA 0nM_2_


title: LS411N-CD133+_1_


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_102362


title: DLPFC_Male_Control_p_UMichigan_102194


title: DLPFC_Male_Control_p_UMichigan_102349


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_102608


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_101850


title: DLPFC_Male_Schizophrenia_p_UMichigan_102317


title: DLPFC_Male_Schizophrenia_p_UMichigan_102218


title: DLPFC_Female_BipolarDisorder_p_UMichigan_101677


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_101276


title: DLPFC_Male_Control_p_UMichigan_101108


title: DLPFC_Female_BipolarDisorder_p_UMichigan_101101


title: DLPFC_Male_Schizophrenia_p_UMichigan_101421


title: DLPFC_Female_Schizophrenia_p_UMichigan_101057


title: DLPFC_Male_Control_p_UCDavis_109779

value: Schiz Cohort 1


title: DLPFC_Male_MajorDepressiveDisorder_p_UMichigan_101032


title: DLPFC_Male_Control_p_UMichigan_101407

value: Control


title: DLPFC_Male_Control_p_UCDavis_109882

value: M


title: DLPFC_Male_Schizophrenia_p_UCDavis_109371


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_109248


title: DLPFC_Male_Control_r_p_UCDavis_109779


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_109257


title: DLPFC_Male_Control_p_UMichigan_101091


title: DLPFC_Female_Schizophrenia_p_UMichigan_101618


title: DLPFC_Male_Control_p_UCDavis_108425


title: DLPFC_Male_BipolarDisorder_p_UCDavis_108104


title: DLPFC_Male_BipolarDisorder_p_UCDavis_108454


title: DLPFC_Female_Control_p_UCDavis_109103


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_109833


title: DLPFC_Male_Control_p_UCDavis_107309


title: DLPFC_Male_Control_p_UCDavis_108017


title: DLPFC_Female_MajorDepressiveDisorder_p_UCDavis_107845


title: DLPFC_Male_Schizophrenia_p_UCDavis_106753


title: DLPFC_Male_Control_p_UCDavis_106798


title: DLPFC_Female_MajorDepressiveDisorder_p_UCDavis_108700


title: DLPFC_Male_Schizophrenia_p_UCDavis_106725


title: DLPFC_Male_Control_p_UCDavis_108066


title: DLPFC_Male_Control_p_UMichigan_102623


title: DLPFC_Male_Control_p_UCDavis_106966


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_105947


title: DLPFC_Male_Control_p_UCDavis_106589


title: DLPFC_Female_Control_p_UCDavis_105725


title: DLPFC_Male_Schizophrenia_p_UCDavis_106564


title: DLPFC_Male_Control_p_UCDavis_106229


title: DLPFC_Male_Schizophrenia_r_p_UCDavis_104259


title: DLPFC_Female_BipolarDisorder_p_UCDavis_105687


title: DLPFC_Male_Control_r_p_UCDavis_106589


title: DLPFC_Male_Schizophrenia_p_UCDavis_104259


title: DLPFC_Male_Control_p_UCDavis_106049


title: DLPFC_Male_BipolarDisorder_p_UCDavis_105544


title: DLPFC_Male_Control_p_UCDavis_106051


title: DLPFC_Male_Control_r_p_UCDavis_104126


title: DLPFC_Female_Schizophrenia_p_UCDavis_104344


title: DLPFC_Male_Control_p_UCDavis_103610


title: DLPFC_Male_Control_p_UCDavis_104126


title: DLPFC_Male_Control_p_UCDavis_103166


title: DLPFC_Male_Control_p_UCDavis_102854


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_103625


title: DLPFC_Female_Control_p_UCDavis_106172


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_104349


title: DLPFC_Male_Schizophrenia_p_UCDavis_103311

value: Other


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_102362

value: Caucasian


title: DLPFC_Male_Control_p_UCDavis_102623

value: Dorsolateral Prefrontal Cortex


title: DLPFC_Male_MajorDepressiveDisorder_p_UCDavis_102482

value: Major Depressive Disorder


title: DLPFC_Male_Schizophrenia_p_UCDavis_102317

value: Schizophrenia


title: DLPFC_Male_Schizophrenia_r_p_UCDavis_103311


title: DLPFC_Male_Schizophrenia_p_UCDavis_102218


title: DLPFC_Male_Control_p_UCDavis_101772


title: OCRL knock down cells, biological replicate3

city: Napoli

first: Giovanna

last: De Leo

address: via Castellino 111

institute: Tigem

description: Gene expression data from OCRL-siRNA treated renal cells

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip human U133A Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: OCRL-siRNA treated renal cells

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: HK2 cells were grown in complete DMEM F12 1:1 supplemented with ITS (insulin transferrin and selenium)

extract_protocol: Total RNAs from control and knock down cells in three independent experiments were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: HK2 cells were seeded and at 30% of confluence were siRNA treated (non targeting siRNA used as control and OCRL-siRNA)  for 96h using Dharmafect 4 as transfection reagents to achieve high-efficiency of silencing

value: kidney


title: CTR, biological replicate 3

description: Gene expression data from non targeting-siRNA treated renal cells

source_name: non targeting-siRNA treated renal cells


title: OCRL knock down cells, biological replicate2


title: OCRL knock down cells, biological replicate1


title: DLPFC_Male_Schizophrenia_r_p_UCDavis_102118


title: DLPFC_Male_Schizophrenia_p_UCDavis_102118


title: DLPFC_Female_Schizophrenia_p_UCDavis_101618


title: CTR, biological replicate 1


title: CTR, biological replicate 2


title: human embryonic stem cell line HUES1, biological replicate2

city: Ioannina

first: Carol

last: Murphy

address: Panepistimioupoli

department: Biomedical reseach

country: Greece

institute: FORTH-IMBB

description: gene expression data of human embryonic stem cell (control cell line)

hyb_protocol: Following fragmentation and labeling (5.5ug of ssDNA was fragmented) (Affymetrix, #900671), 2.3 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: The data were analyzed using GeneSpring12.6 (Affymetrix Expression experiment type; Exon analysis type, RMA16 summarization algorithm)

source_name: gene expression data in standard growth medium

label_protocol: Biotinylated cDNA was synthesized from 150ng of total RNA (was converted to cRNA then to ssDNA, using 10ug of cRNA for ssDNA synthesis) using Ambion WT Expression kit (#4491974)

growth_protocol: hiPS and HUES lines were grown on matrigel coating and mTeSR medium. HEFs fibroblasts growth medium was ATCC basal medium, suplemented with 10%FBS and 1%pen/step

extract_protocol: total RNA extraction was performed using Macherey-Nagel nucleospin RNA extraction kit (#740955.50) according to the manufacturer's instructions.

value: embryonic stem cell line


title: DLPFC_Male_Control_p_UCDavis_102194


title: human embryonic stem cell line HUES1, biological replicate1

treatment_protocol: hiPS and HUES lines were grown on matrigel coating and mTeSR medium. HEFs fibroblasts growth medium was ATCC basal medium, suplemented with 10%FBS and 1%pen/step


title: human fibroblasts, biological replicate1

description: gene expression data of human epidermal fibroblasts (before reprogramming)

value: epidermal fibroblast cell line


title: DLPFC_Female_BipolarDisorder_p_UCDavis_101677


title: DLPFC_Male_Control_p_UCDavis_101108


title: DLPFC_Male_Control_p_UCDavis_101091


title: human fibroblasts, biological replicate2


title: hiPS line 3, biological replicate 1

description: gene expression data of human induced pluripotent line3

value: fully reprogrammed cell line


title: DLPFC_Male_Control_p_UCDavis_101407

value: Dep Cohort 5


title: hiPS line 2, biological replicate 2

description: gene expression data of human induced pluripotent line2


title: hiPS line 1, biological replicate 2

description: gene expression data of human induced pluripotent line1