title: EBV positive PTCL-U case#3

city: Seoul

first: Sang Yun

last: Ha

state: Seoul

address: Ilwondong Kangnamgu

department: Pathology

country: South Korea

institute: Samsung Medical center

description:
Raw data file: EXPRE_EBV_PTCL3.txt
EBV positive PTCL-U case#3
Agilent 8x60K(02800)
Tumor-3

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

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

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

source_name: EBV positive PTCL-U case#3

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

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

value: EBV positive PTCL-U


title: RDv6-CD4

status: Public on Feb 01 2012

type: RNA

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

country: USA

institute: Duke University

description: dominance ranks : 1 = high, 5 = low

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization and variance stabilization using the lumi package in R. Probes were filtered from the full set of HT-12 probes based on the following criteria: 1) probes must have mapped (via blat) uniquely to the rhesus macaque genome (rheMac2) at 80% or greater identity; 2) probes must not have overlapped annotated segmental duplicates >1 kb in rhesus macaque; 3) probes must have exhibited evidence of detectable signal in at least one array sample (p < 0.001) compared to Illumina control probes.

label: biotin

molecule: total RNA

organism: Macaca mulatta

source_name: helper T cells_rank 4

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

extract_protocol: RNA was extracted with the Qiagen RNEasy kit, including DNase I treatment, in accordance with the manufacturer's protocol. Quality control was performed with the Agilent Bioanalyzer.

tag: dominance rank

tag: age

value: adult

tag: gender

value: female

tag: tissue source

value: peripheral blood mononuclear cells

tag: cell type

value: helper T cells


title: RDv6-CD8

description: dominance ranks : 1 = high, 5 = low

source_name: cytotoxic T cells_rank 4

value: cytotoxic T cells


title: AA_e8_5

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

description: Sample name: 40

data_processing: quantile normalized and variance transformed using LUMI package in R

organism: Homo sapiens

source_name: PBMCs

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

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: population

value: African-American

tag: treatment

value: vehicle (EtOH)

tag: in vitro lymphocyte gc sensitivity (lgs - %inhibition by dex)

tag: duration of treatment (hours)

value: male

tag: age (years)


title: EA_e24_6

description: Sample name: 42

value: European-American


title: EA_e8_6

description: Sample name: 44


title: AA_e24_6

description: Sample name: 46


title: AA_e8_6

description: Sample name: 48


title: AA_d24_6

description: Sample name: 45

value: dexamethasone


title: EA_d8_5

description: Sample name: 35


title: EA_d24_5

description: Sample name: 33


title: AA_d24_4

description: Sample name: 25


title: AA_d8_4

description: Sample name: 27


title: EA_d24_4

description: Sample name: 29


title: EA_d8_4

description: Sample name: 31


title: AA_e24_4

description: Sample name: 26


title: EA_e24_4

description: Sample name: 30


title: EA_e24_3

description: Sample name: 24


title: AA_e8_4

description: Sample name: 28


title: EA_e8_4

description: Sample name: 32


title: EA_e24_5

description: Sample name: 34


title: EA_e8_5

description: Sample name: 36


title: AA_d8_5

description: Sample name: 39


title: AA_e24_5

description: Sample name: 38


title: AA_d8_6

description: Sample name: 47


title: AA_d24_5

description: Sample name: 37


title: EA_d24_6

description: Sample name: 41


title: EA_d24_3

description: Sample name: 23


title: AA_d24_3

description: Sample name: 19


title: EA_d8_3

description: Sample name: 21


title: EA_d8_6

description: Sample name: 43


title: EA_e24_2

description: Sample name: 12


title: AA_e24_2

description: Sample name: 16


title: AA_e8_2

description: Sample name: 14


title: EA_e8_2

description: Sample name: 10


title: AA_e8_3

description: Sample name: 18


title: RZr2.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RZr2.1-1

tag: Sex

tag: tissue


title: AA_e24_3

description: Sample name: 20


title: AA_d8_3

description: Sample name: 17


title: EA_e8_3

description: Sample name: 22


title: EA_e24_1

description: Sample name: 8


title: RZt5.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RZt5.1-2


title: RZr2.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RZr2.1-2


title: RZp6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RZp6.1-1


title: RZt5.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RZt5.1-1


title: AA_d24_1

description: Sample name: 3


title: EA_d24_2

description: Sample name: 11


title: EA_e8_1

description: Sample name: 6


title: AA_d24_2

description: Sample name: 15


title: AA_d8_2

description: Sample name: 13


title: AA_d8_1

description: Sample name: 1


title: EA_d24_1

description: Sample name: 7


title: RZp6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RZp6.1-2


title: AA_e8_1

description: Sample name: 2


title: EA_d8_2

description: Sample name: 9


title: EA_d8_1

description: Sample name: 5


title: AA_e24_1

description: Sample name: 4


title: RZk6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RZk6.1-1


title: RZd7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RZd7.1-2


title: RZk6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RZk6.1-2


title: RWu4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RWu4.1-2


title: RWe7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RWe7.1-2


title: NOD mouse pancreatic lymph node rep3

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v3 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

organism: Mus musculus

source_name: NOD mouse CD4+ high/ CD62low /CD44 high T cells sorted from pancreatic lymph nodes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA using MessageAmp™ II aRNA Kit from Ambion

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

tag: genotype

value: NOD (Taconic line 6359)

tag: disease state

value: diabetes susceptible


title: RZd7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RZd7.1-1


title: RYn5.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RYn5.1-2


title: Idd9 mouse pancreatic lymph node rep3

source_name: Idd9 mouse CD4+ high/ CD62low /CD44 high T cells sorted from pancreatic lymph nodes

value: NOD.B10 Idd9 congenic (Taconic line 905)

value: diabetes protected


title: NOD mouse pancreatic lymph node rep1


title: RYh4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RYh4.1-2


title: RYn5.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RYn5.1-1


title: RYh4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RYh4.1-1


title: NOD mouse pancreatic lymph node rep2


title: RWe7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RWe7.1-1


title: RVi4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RVi4.1-2


title: RVh5.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RVh5.1-2


title: Idd9 mouse pancreatic lymph node rep2


title: Idd9 mouse pancreatic lymph node rep1


title: RWb7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RWb7.1-1


title: RWb7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RWb7.1-2


title: RVi4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RVi4.1-1


title: CA3 of Hippocampus_Stressed_Vinclozolin_biological rep3

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: CA3 of the hippocampus from 120 days old F3-generation Vinclozolin lineage rat stressed at PND 23-43

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 450.

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

data_processing:
The data for each of the four studied brain areas (BLA, CRTX, CA1, and CA3) were pre-processed and analyzed as a separate group (4 groups, 12 chips per group) with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) in August-October, 2010, using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.
Logarithm of  signal values, base 2, pre-processed with RMA, GC-content adjusted algorithm - each of the 4 bran areas separately. Scan  date batch effect was removed if applicable.

organism: Rattus norvegicus

source_name: CA3 of the hippocampus from F3-generation Vinclozolin lineage stressed rat brain

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003].  Male rats of the F3 generation of Vinclozolin and Control lineages were selected out of litters from untreated F2 generation.  One animal from each lineage (Control and Vinclozolin) were pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the study.

extract_protocol: RNA was isolated from tissue homogenates in 800 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.  100 ul Trizol homogenates from 4 randomly chosen individuals within the same tissue/treatment group were pooled together for one RNA sample (one microarray biological replica).   Samples from the same set of 4 dyads were pooled for one Vinclozolin or Control replica for all 4 brain areas, stressed or non-stressed.  For microarray analysis, 3 biological replicas were prepared as above for each brain area/treatment group.

treatment_protocol: Half of the F3-Vinclozolin/Control rats dyads were randomly chosen to be administered a chronic stress treatment. This stress paradigm entails 6 hours of daily restraint stress for 21 consecutive days (PND 23-43) in an apparatus consisted of a 25.4 square cm metal wire mesh folded in half and bound with a plastic mould.  After the initial 21 days of stressing, all animals were left in the housing room constantly and were only removed for handling, weighing, and behavioural testing on scheduled days.  All rats were sacrificed at age of 4 months (PND 120) and certain brain areas samples were collected as 2 mm tissue punches and put into Trizol™ reagent (Invitrogen, USA).

tag: rna prep date

tag: scan date

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

value: Male

value: CA3 of the hippocampus

tag: developmental stage

value: Rat brain  at day PND 120


title: RWb7.1 replicate 3

description:
dominance ranks : 1 = high,  5 = low
RWb7.1-3

value: female

tag: age

value: adult

tag: dominance rank


title: CA3 of Hippocampus_Stressed_Vinclozolin_biological rep2

tag: gender


title: CA3 of Hippocampus_Non-Stressed_Vinclozolin_biological rep2

description: CA3 of the hippocampus from 120 days old F3-generation Vinclozolin lineage non-stressed rat brain

source_name: CA3 of the hippocampus from F3-generation Vinclozolin lineage non-stressed rat brain


title: CA3 of Hippocampus_Stressed_Vinclozolin_biological rep1


title: CA3 of Hippocampus_Non-Stressed_Vinclozolin_biological rep3


title: RTr4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RTr4.1-2

value: peripheral blood mononuclear cells


title: RTr4.1 replicate 3

description:
dominance ranks : 1 = high,  5 = low
RTr4.1-3


title: RTv6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RTv6.1-2


title: CA3 of Hippocampus_Stressed_Control_biological rep3

description: CA3 of the hippocampus from 120 days old F3-generation control (vehicle) lineage rat stressed at PND 23-43

source_name: CA3 of the hippocampus from F3-generation control lineage (vehicle) stressed rat brain


title: RRu6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RRu6.1-2


title: RUo4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RUo4.1-1


title: RTr4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RTr4.1-1


title: CA3 of Hippocampus_Stressed_Control_biological rep2


title: CA3 of Hippocampus_Non-Stressed_Control_biological rep1

description: CA3 of the hippocampus from 120 days old F3-generation control (vehicle) lineage non-stressed rat brain

source_name: CA3 of the hippocampus from F3-generation control lineage (vehicle) non-stressed rat brain


title: RUo4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RUo4.1-2


title: CA1 of Hippocampus_Stressed_Vinclozolin_biological rep1

description: CA1 of the hippocampus from 120 days old F3-generation Vinclozolin lineage rat stressed at PND 23-43

source_name: CA1 of the hippocampus from F3-generation Vinclozolin lineage stressed rat brain

value: CA1 of the hippocampus


title: RTv6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RTv6.1-1


title: RRb7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RRb7.1-2


title: RRa7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RRa7.1-2


title: RVg5.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RVg5.1-1


title: RVh5.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RVh5.1-1


title: CA1 of Hippocampus_Stressed_Vinclozolin_biological rep2


title: CA3 of Hippocampus_Stressed_Control_biological rep1


title: CA3 of Hippocampus_Non-Stressed_Control_biological rep2


title: CA3 of Hippocampus_Non-Stressed_Control_biological rep3


title: RRb7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RRb7.1-1


title: RWu4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RWu4.1-1


title: RVg5.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RVg5.1-2


title: RRu6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RRu6.1-1


title: RQq4.2 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RQq4.2-2


title: CA1 of Hippocampus_Stressed_Control_biological rep2

description: CA1 of the hippocampus from 120 days old F3-generation control (vehicle) lineage rat stressed at PND 23-43

source_name: CA1 of the hippocampus from F3-generation control lineage (vehicle) stressed rat brain


title: CA3 of Hippocampus_Non-Stressed_Vinclozolin_biological rep1

description: CA3 of the hippocampus from 120 days old F3-generation Vinclozolin lineage non-stressed rat brain


title: CA1 of Hippocampus_Stressed_Control_biological rep1


title: CA1 of Hippocampus_Non-Stressed_Vinclozolin_biological rep3

description: CA1 of the hippocampus from 120 days old F3-generation Vinclozolin lineage non-stressed rat brain

source_name: CA1 of the hippocampus from F3-generation Vinclozolin lineage non-stressed rat brain


title: CA1 of Hippocampus_Stressed_Vinclozolin_biological rep3


title: RRa7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RRa7.1-1


title: CA1 of Hippocampus_Non-Stressed_Vinclozolin_biological rep1


title: CA1 of Hippocampus_Non-Stressed_Vinclozolin_biological rep2


title: CA1 of Hippocampus_Stressed_Control_biological rep3


title: ROy4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
ROy4.1-2


title: CA1 of Hippocampus_Non-Stressed_Control_biological rep1

description: CA1 of the hippocampus from 120 days old F3-generation control (vehicle) lineage non-stressed rat brain

source_name: CA1 of the hippocampus from F3-generation control lineage (vehicle) non-stressed rat brain


title: ROh4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
ROh4.1-1


title: RQq4.2 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RQq4.2-1


title: ROh4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
ROh4.1-2


title: BL2_OHT_treat_vs_nontreat

type: genomic

city: Kyoto

first: Tasuku

last: Honjo

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Kyoto University

hyb_protocol: Samples were hybridised to GeneChip Human Promoter 1.0R Arrays (16 hours at 45°C) and stained using the GeneChip Hybridization, Wash and Stain Kit, following manufacturers instructions (all Affymetrix).

scan_protocol: Slides were scanned on an Affymetrix GeneChip scanner.

data_processing:
CisGenome was used to generate BAR and COD files. Quantile normalization was applied prior to analysis, and a moving average (MA) statistic was computed for each probe based on a half-window size of 250 bp or 5 probes. Peaks were discarded if they contained less than five probes or were less than 150 base pairs in width. Peaks that were separated by less than 200 base pairs or 5 probes were merged. All probe sequences were mapped to the hg19 genome asembly.
results file descriptions: fc.bar and ma.bar are generated by CisGenome. fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average (MA) statistic for each probe. The AID_break_MA3_all.cod file contains breakage sites with MA>3.0. AID_break_MA3_all_annot.txt has details of gene loci neighbouring these sites.

molecule: genomic DNA

source_name: biotin linker-enriched DNA from BL2 cells after OHT treatment

label_protocol: DNA was labeled according to the Affymetrix sample preparation protocol.

growth_protocol: BL2 Burkitt’s lymphoma cell line was cultured in RPMI medium 1640 containing 10% FCS, 100 μM NEAA, 1 mM sodium pyruvate, 100 units/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: The biotin-labeled DNA break assay was performed as described previously (Doi et al., 2009) with slight modifications. After nuclear permeabilization, cells were washed with cold PBS and re-suspended in 1x T4 DNA polymerase buffer. Blunting was performed using T4 DNA Polymerase (Takara). After washing with cold PBS, 4 μl of T4 DNA Ligase (Takara) and 13.4 μl of an annealed biotinylated P1 linker were added, and the cells were incubated overnight at 16 °C. Genomic DNA was purified by phenol:chloroform extraction.

treatment_protocol: 4-hydroxytamoxifen (4-OHT) was added to a concentration of 1 μM.

tag: cell line

value: BL2 cells

value: OHT treatment

source_name: biotin linker-enriched DNA from control BL2 cells (no OHT treatment)


title: Primary and Secondary Motor Cortex_Stressed_Vinclozolin_biological rep3

description: Primary and secondary motor cortex from 120 days old F3-generation Vinclozolin lineage rat stressed at PND 23-43

source_name: Primary and secondary motor cortex from F3-generation Vinclozolin lineage stressed rat brain

value: Primary and secondary motor cortex


title: RNu7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RNu7.1-1


title: RNf6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RNf6.1-2


title: CA1 of Hippocampus_Non-Stressed_Control_biological rep2


title: CA1 of Hippocampus_Non-Stressed_Control_biological rep3


title: ROb6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
ROb6.1-2


title: ROb6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
ROb6.1-1


title: RNu7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RNu7.1-2


title: RNf6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RNf6.1-1


title: ROy4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
ROy4.1-1


title: Primary and Secondary Motor Cortex_Non-Stressed_Vinclozolin_biological rep3

description: Primary and secondary motor cortex from 120 days old F3-generation Vinclozolin lineage non-stressed rat brain

source_name: Primary and secondary motor cortex from F3-generation Vinclozolin lineage non-stressed rat brain


title: Primary and Secondary Motor Cortex_Stressed_Control_biological rep2

description: Primary and secondary motor cortex from 120 days old F3-generation control (vehicle) lineage rat stressed at PND 23-43

source_name: Primary and secondary motor cortex from F3-generation control lineage (vehicle) stressed rat brain


title: Primary and Secondary Motor Cortex_Non-Stressed_Vinclozolin_biological rep2


title: RMu3.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RMu3.1-1


title: RNf4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RNf4.1-2


title: RMu3.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RMu3.1-2


title: Primary and Secondary Motor Cortex_Stressed_Vinclozolin_biological rep1


title: Primary and Secondary Motor Cortex_Stressed_Control_biological rep1


title: Primary and Secondary Motor Cortex_Stressed_Vinclozolin_biological rep2


title: Primary and Secondary Motor Cortex_Stressed_Control_biological rep3


title: Primary and Secondary Motor Cortex_Non-Stressed_Control_biological rep3

description: Primary and secondary motor cortex from 120 days old F3-generation control (vehicle) lineage non-stressed rat brain

source_name: Primary and secondary motor cortex from F3-generation control lineage (vehicle) non-stressed rat brain


title: Primary and Secondary Motor Cortex_Non-Stressed_Vinclozolin_biological rep1


title: RMg5.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RMg5.1-2


title: Primary and Secondary Motor Cortex_Non-Stressed_Control_biological rep2


title: RMf4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RMf4.1-1


title: RMg3.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RMg3.1-2


title: Basolateral Amygdala_Stressed_Vinclozolin_biological rep2

description: Basolateral amygdala from 120 days old F3-generation Vinclozolin lineage rat stressed at PND 23-43

source_name: Basolateral amygdala from F3-generation Vinclozolin lineage stressed rat brain

value: Basolateral amygdala


title: RNf4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RNf4.1-1


title: RMg5.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RMg5.1-1


title: RJc6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RJc6.1-2


title: Basolateral Amygdala_Stressed_Vinclozolin_biological rep3


title: RMg3.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RMg3.1-1


title: RMf4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RMf4.1-2


title: RJc6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RJc6.1-1


title: Basolateral Amygdala_Stressed_Control_biological rep2

description: Basolateral amygdala from 120 days old F3-generation control (vehicle) lineage rat stressed at PND 23-43

source_name: Basolateral amygdala from F3-generation control lineage (vehicle) stressed rat brain


title: Basolateral Amygdala_Stressed_Control_biological rep3


title: Basolateral Amygdala_Stressed_Control_biological rep1


title: Basolateral Amygdala_Non-Stressed_Vinclozolin_biological rep1

description: Basolateral amygdala from 120 days old F3-generation Vinclozolin lineage non-stressed rat brain

source_name: Basolateral amygdala from F3-generation Vinclozolin lineage non-stressed rat brain


title: RIp7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RIp7.1-2


title: Primary and Secondary Motor Cortex_Non-Stressed_Control_biological rep1


title: RIz6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RIz6.1-1


title: Basolateral Amygdala_Stressed_Vinclozolin_biological rep1


title: RIz6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RIz6.1-2


title: Basolateral Amygdala_Non-Stressed_Vinclozolin_biological rep2


title: Basolateral Amygdala_Non-Stressed_Control_biological rep3

description: Basolateral amygdala from 120 days old F3-generation control (vehicle) lineage non-stressed rat brain

source_name: Basolateral amygdala from F3-generation control lineage (vehicle) non-stressed rat brain


title: RId7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RId7.1-2


title: RId7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RId7.1-1


title: LCL_LowCount_Female_24

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

hyb_protocol: Samples were hybridized overnight at 58°C and processed using a SciGene Little Dipper Processor.

scan_protocol: Chips were scanned using an iScan reader and intensity values were extracted and compiled using BeadArray software.

data_processing:
Intensity values were log-transformed and quantile normalized using the 'lumi' package in R.  Two batch effects were regressed out.
See study for exact details of normalization procedure (includes log transformation, quantile normalization, and regressing out covariates)

label: Biotin

source_name: Lymphoblastoid cell line

label_protocol: The Illumina-specific TotalPrep Kit from Ambion was used to prepare amplified, biotinylated cRNA.

growth_protocol: Cells were grown at 37°C with 5% CO2 in RPMI-1640 (containing L-glutamine) supplemented with 20% FBS and 50 µg/ml gentamicin.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini extraction kit. RNA quality was assessed with Agilent Bioanalyzer.

value: Female

tag: lymphocyte count group

value: Low


title: Basolateral Amygdala_Non-Stressed_Vinclozolin_biological rep3


title: RIp7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RIp7.1-1


title: RHn6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RHn6.1-2


title: Basolateral Amygdala_Non-Stressed_Control_biological rep1


title: Basolateral Amygdala_Non-Stressed_Control_biological rep2


title: LCL_LowCount_Female_23


title: LCL_LowCount_Female_20


title: RHc4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RHc4.1-2


title: LCL_LowCount_Female_22


title: dose 100cGy, 24 hrs, replicate 2

city: davis

first: David

last: Rocke

state: ca

address: 1 shields ave

department: Biostatistics/Public health

institute: UC davis

description:
4578168062_H
dose 100cGy, 24 hrs, replicate 2

data_processing: Background subtraction using BeadStudio.  Quantile normalisation and variance stabilisation was done using LMGene in R.

source_name: skin plug

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

treatment_protocol: dose 0 cGy was control and dose 10 cGy and 100 cGy were irradiated cells

tag: model system

value: 3D skin model (reconstructed skin tissue)

tag: cell type(s)

value: keratinocytes and fibroblasts

tag: stress

value: X-ray ionising radiation

tag: dose

tag: time

value: 24 hrs


title: LCL_LowCount_Female_21


title: LCL_LowCount_Female_18


title: RHn6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RHn6.1-1

tag: Sex

tag: tissue


title: RHc4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RHc4.1-1


title: LCL_LowCount_Female_19


title: LCL_LowCount_Female_17


title: LCL_LowCount_Female_14


title: dose 100cGy, 24 hrs , replicate 1

description:
4578168062_G
dose 100cGy, 24 hrs , replicate 1


title: dose 100cGy, 8 hrs, replicate 2

description:
4578168062_F
dose 100cGy, 8 hrs, replicate 2

value: 8 hrs


title: dose 100cGy, 3 hrs, replicate 2

description:
4578168062_D
dose 100cGy, 3 hrs, replicate 2

value: 3 hrs


title: LCL_LowCount_Female_11


title: LCL_LowCount_Female_16


title: LCL_LowCount_Female_12


title: LCL_LowCount_Female_15


title: LCL_LowCount_Female_13


title: dose 100cGy, 3 hrs, replicate 1

description:
4578168062_C
dose 100cGy, 3 hrs, replicate 1


title: RGv6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RGv6.1-1


title: dose 100cGy, 8 hrs, replicate 1

description:
4578168062_E
dose 100cGy, 8 hrs, replicate 1


title: LCL_LowCount_Female_09


title: RGs6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RGs6.1-2


title: LCL_LowCount_Female_10


title: RGv6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RGv6.1-2


title: RFp8.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RFp8.1-2


title: RGs6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RGs6.1-1


description:
4578168062_B
dose 100cGy, 0 hrs (control), replicate 2

value: control

value: 0 hrs (control)


title: LCL_LowCount_Female_08


title: LCL_LowCount_Female_06


title: RFp8.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RFp8.1-1

value: female

value: adult


description:
4578168062_A
dose 100cGy, 0 hrs (control), replicate 1


title: LCL_LowCount_Female_07


title: LCL_LowCount_Female_05


title: dose 10cGy, 8 hrs, replicate 2

description:
4578168057_F
dose 10cGy, 8 hrs, replicate 2


title: LCL_LowCount_Female_04


title: LCL_LowCount_Female_03


title: LCL_LowCount_Female_02


title: RFc6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RFc6.1-1

value: peripheral blood mononuclear cells


title: dose 10cGy, 24 hrs, replicate 2

description:
4578168057_H
dose 10cGy, 24 hrs, replicate 2


title: LCL_LowCount_Female_01


title: dose 10cGy, 24 hrs , replicate 1

description:
4578168057_G
dose 10cGy, 24 hrs , replicate 1


title: LCL_LowCount_Male_24

value: Male


title: LCL_LowCount_Male_21


title: LCL_LowCount_Male_23


title: REm6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
REm6.1-2


title: LCL_LowCount_Male_22


title: LCL_LowCount_Male_19


title: dose 10cGy, 3 hrs, replicate 2

description:
4578168057_D
dose 10cGy, 3 hrs, replicate 2


title: dose 10cGy, 8 hrs, replicate 1

description:
4578168057_E
dose 10cGy, 8 hrs, replicate 1


title: REm6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
REm6.1-1


title: RDv6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RDv6.1-2


title: LCL_LowCount_Male_18


title: LCL_LowCount_Male_20


title: LCL_LowCount_Male_15


title: dose 10cGy, 3 hrs, replicate 1

description:
4578168057_C
dose 10cGy, 3 hrs, replicate 1


title: RDv6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RDv6.1-1


description:
4578168057_B
dose 10cGy, 0 hrs (control), replicate 2


description:
4578168057_A
dose 10cGy, 0 hrs (control), replicate 1


title: RDe3.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RDe3.1-2


title: LCL_LowCount_Male_16


title: LCL_LowCount_Male_17


description:
4578168056_H
dose 0 cGy (control), 24 hrs, replicate 2

value: 0 cGy (control)


title: LCL_LowCount_Male_13


title: LCL_LowCount_Male_11


title: LCL_LowCount_Male_09


description:
4578168056_G
dose 0 cGy (control), 24 hrs , replicate 1


title: LCL_LowCount_Male_10


title: RCv6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RCv6.1-2


title: RDe3.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RDe3.1-1


title: LCL_LowCount_Male_12


description:
4578168056_E
dose 0 cGy (control), 8 hrs, replicate 1


title: LCL_LowCount_Male_14


title: LCL_LowCount_Male_07


title: LCL_LowCount_Male_08


description:
4578168056_C
dose 0 cGy (control), 3 hrs, replicate 1


title: RCt4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RCt4.1-2


title: RCk4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RCk4.1-1


title: RCv6.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RCv6.1-1


title: LCL_LowCount_Male_04


description:
4578168056_F
dose 0 cGy (control), 8 hrs, replicate 2


title: RCt4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RCt4.1-1


title: LCL_LowCount_Male_05


title: RCk4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RCk4.1-2


description:
4578168056_A
dose 0 cGy (control), 0 hrs (control), replicate 1


title: LCL_LowCount_Male_02


title: LCL_LowCount_Male_06


title: LCL_LowCount_Male_03


title: LCL_LowCount_Male_01


title: LCL_HighCount_Female_24

value: High


description:
4578168056_D
dose 0 cGy (control), 3 hrs, replicate 2


title: LCL_HighCount_Female_23


title: LCL_HighCount_Female_22


title: RBm4.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RBm4.1-1


title: RBk7.1 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RBk7.1-1


title: LCL_HighCount_Female_20


title: RBk7.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RBk7.1-2


title: LCL_HighCount_Female_17


title: RBe5.2 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RBe5.2-2


title: LCL_HighCount_Female_19


title: RFc6.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RFc6.1-2


title: RBe5.2 replicate 1

description:
dominance ranks : 1 = high,  5 = low
RBe5.2-1


title: LCL_HighCount_Female_21


title: LCL_HighCount_Female_18


title: 28-2 high RFP sort 3 4/1

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: Biological replicate 3 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

hyb_protocol: Conducted by Exiquon per manufacturer's standard protocol.

data_processing: LOWESS normalized, background subtraction was Normexp with offset value 10 (Convolution model described by Ritchie ME, Bioinformatics (2007), Vol. 23 no. 20 2007, pages 2700–2707).

source_name: 28-2 cells, 5% highest LMP1-mRFP

growth_protocol: 28-2 cells were grown in RPMI-1640 and 10% fetal bovine serum (supplemented with penicillin and streptomycin).

extract_protocol: Total RNA was extracted using TRIzol reagent per manufacturer's protocol

treatment_protocol: There were no additional treatments applied to these cells.

tag: cell type

value: B-cell strain

tag: ebv-status

value: Positive

tag: expression level

value: High  LMP1-mRFP

source_name: 28-2 cells, unsorted pool


title: LCL_HighCount_Female_10

value: Female


title: LCL_HighCount_Female_16


title: Rat brain microvessels, rep2

city: Little Rock

first: Li

last: Cui

state: AR

department: Neurology

institute: UAMS

hyb_protocol: Two-color, Cy3- and Cy5-labeled aRNA was hybridized to rat Agilent microarrays (∼22,000 features, catalog number G410A) following the manufacturer’s protocol, except that 1.0 μg of probe was used instead of 0.75 μg. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was conducted at 60 °C for 17 h with equal amounts of the two labeled aRNAs. After hybridization, slides were washed sequentially. Two microarrays using four sample RNAs (microvessels from the cerebral cortex vs. microvessels from the infratentorial block) were included in the present study.

scan_protocol: ScanArray® Express from PerkinElmer Life Sciences for sample 9958; ScanAlyze for sample 9955.

data_processing: Using ScanArray software and ScanAlyze, the image data were converted into numerical data and stored in a text file. The text files were imported into GeneSpring software (version 11.5) for microarray analysis. GeneSpring was used to Lowess normalize the data.

source_name: cerebral cortex microvessels

label_protocol: RNA was labeled with Cy3 and Cy5.

growth_protocol: 344 rats were decapitated, and brains were harvested immediately on an ice-cooled metal platform.

extract_protocol: A kit from Qiagen was used to purify the RNA.

treatment_protocol: A filtration method was used to isolate brain microvessels (at 4 °C) as described with slight modification. Briefly, the cerebral cortex and infratentorial brain blocks were minced on an ice- cold aluminum plate, homogenized, and transferred to the interior of a 210 μmNytex bag submerged in ice-cold isotonic PBS buffer containing glucose and sucrose. The tissue then passed through the bag and was recollected by low speed centrifugation. The pellet was resuspended and filtered through an 80 μm nitrocellulose filter under a vacuum. RNA Isolation and Quantity and Quality Determination. The vessels collected on the filter were washed with ice-cold buffer and then lysed for RNA isolation.

tag: strain

value: male

value: cerebral cortex microvessels

source_name: infratentorial brain microvessels

value: infratentorial brain microvessels


title: LCL_HighCount_Female_09


title: 28-2 low RFP sort 3 4/1

description: Biological replicate 3 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

scan_protocol: Conducted by Exiquon per manufacturer's standard protocol.

source_name: 28-2 cells, 5% lowest LMP1-mRFP

value: Low  LMP1-mRFP


title: RBm4.1 replicate 2

description:
dominance ranks : 1 = high,  5 = low
RBm4.1-2


title: LCL_HighCount_Female_15


title: LCL_HighCount_Female_12


title: LCL_HighCount_Female_14


title: Rat brain microvessels, rep1

tag: developmental stage


title: LCL_HighCount_Female_11


description:
4578168056_B
dose 0 cGy (control), 0 hrs (control), replicate 2

value: 3D skin model (reconstructed skin tissue)

value: keratinocytes and fibroblasts


title: LCL_HighCount_Female_13


title: LCL_HighCount_Female_08


title: LCL_HighCount_Female_07


title: 28-2 high RFP sort 1 3/19

description: Biological replicate 1 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

label_protocol: Conducted by Exiquon per manufacturer's standard protocol.

value: control


title: 28-2 low RFP  sort 1 3/19

description: Biological replicate 1 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: 28-2 high RFP sort 2 3/26

description: Biological replicate 2 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: 28-2 low RFP  sort 2 3/26

description: Biological replicate 2 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: LCL_HighCount_Female_06


title: LCL_HighCount_Female_02


title: LCL_HighCount_Male_18


title: LCL_HighCount_Male_15


title: LCL_HighCount_Male_22


title: LCL_HighCount_Male_14


title: LCL_HighCount_Male_24


title: LCL_HighCount_Male_20


title: LCL_HighCount_Male_16


title: LCL_HighCount_Male_19


title: LCL_HighCount_Female_04


title: LCL_HighCount_Male_21


title: LCL_HighCount_Female_03


title: LCL_HighCount_Male_17


title: LCL_HighCount_Female_01


title: LCL_HighCount_Male_23


title: LCL_HighCount_Male_12


title: LCL_HighCount_Male_13


title: LCL_HighCount_Male_11


title: LCL_HighCount_Male_09


title: LCL_HighCount_Male_10


title: LCL_HighCount_Male_08


title: LCL_HighCount_Male_06


title: LCL_HighCount_Male_07


title: LCL_HighCount_Male_03


title: LCL_HighCount_Male_05


title: PDS4_2

city: Prague

first: Ondrej

last: Seda

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University in Prague

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Transcriptomic data: after evaluation of the hybridization, the quality control and the data normalization by robust multi-array analysis (RMA), the gene expression was compared between the PD.SHR4a and PD strains utilizing PARTEK Genomics Suite (Partek, Inc.).

source_name: PD.SHR4 rat liver

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The animals were sacrificed and  liver tissue was snap frozen in liquid nitrogen for further analyses of gene expression.

extract_protocol: We extracted total RNA from the liver of 4-month-old males of both strains using phenol-chloroform and purified with the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol. The quality of the total RNA was verified by the Agilent 2100 Bioanalyzer system.

value: liver

tag: diet

value: standard chow


title: LCL_HighCount_Male_01


title: LCL_HighCount_Male_04


title: Uterus R3.1

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

description: a pool of three uterus

hyb_protocol: Standard applied at the Genom'IC platform (Cochin Institute)

data_processing: RMA

source_name: uterus R3 IRCS

growth_protocol: Gestation obtained by crossing females B6 or R3 with males B6

extract_protocol: Trizol protocol

treatment_protocol: RNA purification from uterus and placenta dissected at 10.5 days post coitum

value: IRCS R3

value: uterus


title: LCL_HighCount_Male_02

value: Male


title: Uterus R3.2

description: a pool of three uterus

scan_protocol: Standard applied at the Genom'IC platform (Cochin Institute)


title: Uterus B6.2

description: a pool of three uterus

source_name: uterus B6


title: Placenta B6.2

description: a pool of three placentas

source_name: placenta B6

value: placenta


title: Uterus B6.1

description: a pool of three uterus


title: Placenta R3.2

description: a pool of three placentas

source_name: placenta R3 IRCS


title: Placenta B6.1

description: a pool of three placentas


title: 13358.s1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

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

department: Hematology and Medical Oncology

institute: Emory University

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

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

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

label: biotin nucleotide or dinitrophenyl labeled

source_name: leukocyte

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

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

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

value: leukocyte

tag: sample id

tag: sentrix id

tag: sentrix position

value: F

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: hv

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: white


title: Placenta R3.1

description: a pool of three placentas

tag: tissue


title: HG_CTL88

hyb_protocol: Followed the manufacturer's (Illumina) specifications

source_name: lymphoblast

tag: cell type

value: lymphoblast

tag: gender

value: D


title: 13381.s2

value: B

value: xm


title: Normal Breast Sample ATM_35

city: Cambridge

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

department: Department of Oncology

country: United Kingdom

institute: University of Cambridge

description:
A791-35.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The Affymetrix SNP 6.0 arrays data was pre-processed and analysed using the crlmm Bioconductor package (http://www.bioconductor.org/help/biocviews/release/bioc/html/crlmm.html) [Carvalho B, et al. Biostatistics 2007, 8:485-499] implemented in the R statistical programming language [Team RDC: R: A Language and Environment for Statistical Computing. 2010].

source_name: Human female breast tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from normal breast samples was extracted using a conventional SDS/proteinase K/phenol method

value: Human breast tissue

tag: disease status

value: healthy control

value: Female


title: 13340.s1

value: C

value: xx


title: sigS mutant_rep3

city: Tampa

first: Ronan

middle: Kevin

last: Carroll

address: 4202 E Fowler Ave

department: CMMB

institute: University of South Florida

hyb_protocol: Ten micrograms of amplified, labeled DNA was hybridized to Affymetrix S. Aureus Genome Arrays for 16 hours at 45° C according to the manufacturer's protocol.   The arrays were washed and stained using the ProkGE-WS2v3_450 fluidics script on the Affymetrix FS450 fluidics station.

scan_protocol: The arrays were scanned with an Affymetrix GCS 3000 7G Scanner.

data_processing: The .cel files were analyzed using the MAS5 algorithm in the Affymetrix Expression Console software.  The trimmed mean target intensity of each array was set to 500.

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

label_protocol: Fifty nangorams of total RNA was amplified with the Sigma Whole Transcriptome Amplifcation kit (WTA1) according to the manufacturer's protocol.  The resulting amplified DNA was fragmented with Dnase I and biotin-labeled with terminal deoxynucleotidyl Transferase, supplied by Affymetrix.

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol: Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free

treatment_protocol: 2.5 ml of bacterial culture was added to 2.5 ml of a 1:1 ethanol:acetone mixture and snap frozen.  Samples were stored at -80°C prior to RNA extraction

tag: strain

value: RN4220 sigS-


title: 13341.s1

value: K

value: asian


title: Normal Breast Sample ATM_37

description:
A791-37.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13300.s1

value: Male

value: L


title: 13324.s1

value: leukocyte

value: A


title: 13333.s1

value: I

value: white


title: Normal Breast Sample ATM_36

description:
A791-36.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: sigS mutant_rep2


title: 13301.s1


title: sigS mutant_rep1


title: Wild type_rep3


title: HG_CTL87

value: lymphoblast


title: Normal Breast Sample ATM_34

description:
A791-34.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13319.s1

value: hv

value: more-than-one-race


title: 13306.s1


title: Normal Breast Sample ATM_38

description:
A791-38.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue


title: Normal Breast Sample ATM_29

description:
A791-29.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: healthy control


title: Normal Breast Sample ATM_33

description:
A791-33.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Female


title: HG_CTL86

value: B


title: 13283.s1

value: lu


title: Wild type_rep2


title: Normal Breast Sample ATM_32

description:
A791-32.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13226.s2

value: kc

value: not-specified


title: 13254.s1

value: C

value: vn


title: Normal Breast Sample ATM_31

description:
A791-31.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Wild type_rep1


title: 13216.s1

value: Male


title: Normal Breast Sample ATM_28

description:
A791-28.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Normal Breast Sample ATM_30

description:
A791-30.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13187.s1

value: leukocyte

value: H

value: xm


title: Prostate cell line RCO.1-250K_Sty

city: Rochester

first: xiaoyang

last: ruan

state: MN

address: 200 1st Street

department: Health Science Research

institute: Mayo Clinic

description:
Hybridized to 250K_Sty
RCO.1-250ksty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G with AutoLoader.

data_processing: Genotype call was made by Affymetrix Power Tool (Linux, version 1.12.0) BRLMM algorithm. ROH was inferred by dChip (Version 2010/01) basic-HMM module, and PLINK (Version 1.07) ROH module. dChip ROH Call: L, R, and N; PLINK ROH Call: 0, 1 [dChip.txt, PLINK_coverted.txt, and PLINK_rawData.txt are provided as Series supplementary files.]

source_name: Prostate cell line

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

tag: tissue type

value: Prostate

tag: cell line


title: HG_CTL84

value: lymphoblast

tag: sample id

tag: sentrix id

value: L


title: 13196.s1

tag: sentrix position

tag: experiment

value: hv

value: white


title: 13195.s1

value: K

tag: group

tag: family

value: sb

value: more-than-one-race


title: HG_CTL85

value: A


title: 13193.s1

value: D

tag: distribution

tag: site


title: Prostate cell line DU_145 ATCC-250K_Sty

description:
Hybridized to 250K_Sty
DU_145 ATCC-250ksty

value: DU145 ATCC


title: Normal Breast Sample ATM_26

description:
A791-26.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue

value: healthy control

value: Female


title: Normal Breast Sample ATM_25

description:
A791-25.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13180.s1

value: leukocyte

value: Male

value: ox

tag: cpea dx

tag: age at collection (months)

value: asian


title: 13165.s1

value: B

value: vn

tag: ethnicity


title: Normal Breast Sample ATM_24

description:
A791-24.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: tissue


title: Renal pelvis cell line UO_31-250K_Sty

description:
Hybridized to 250K_Sty
UO_31-250ksty

source_name: Renal pelvis cell line

value: Renal pelvis


title: Normal Breast Sample ATM_27

description:
A791-27.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: gender


title: 13169.s1

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

tag: cell type

value: kc

value: white


title: Normal Breast Sample ATM_23

description:
A791-23.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: disease status


title: Renal pelvis cell line RXF-393-250K_Sty

description:
Hybridized to 250K_Sty
RXF_393-250ksty

tag: tissue type


title: Renal pelvis cell line SN12C-250K_Sty

description:
Hybridized to 250K_Sty
SN12C-250ksty

tag: cell line


title: 13144.s1

tag: sample id

value: oi


title: Normal Breast Sample ATM_22

description:
A791-22.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13174.s1

tag: sentrix id

value: C


title: Renal pelvis cell line CAKI-1-250K_Sty

description:
Hybridized to 250K_Sty
CAKI_1-250ksty

source_name: Metastasis_Renal pelvis cell line


title: Normal Breast Sample ATM_20

description:
A791-20.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Normal Breast Sample ATM_19

description:
A791-19.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: HG_CTL83

value: lymphoblast

tag: sentrix position

value: K


title: 13159.s1

value: F

tag: experiment


title: 13153.s1

value: G

tag: group


title: 13135.s1

value: A

tag: family

value: lu


title: 13290.s1

value: leukocyte

tag: distribution

value: african-amer


title: 13151.s1

value: Male

tag: site


title: 13111.s1

value: H

value: fl

tag: cpea dx

value: more-than-one-race


title: HG_CTL82

value: J


title: Normal Breast Sample ATM_21

description:
A791-21.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue

value: healthy control

value: Female


title: Renal pelvis cell line ACHN-250K_Sty

description:
Hybridized to 250K_Sty
ACHN-250ksty

value: Renal pelvis

value: ACHN


title: Renal pelvis cell line TK_10-250K_Sty

description:
Hybridized to 250K_Sty
TK_10-250ksty


title: Renal pelvis cell line A498-250K_Sty

description:
Hybridized to 250K_Sty
A498-250ksty


title: 13107.s1

value: D

tag: age at collection (months)

value: white


title: Normal Breast Sample ATM_18

description:
A791-18.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 13077.s1

value: K

tag: ethnicity


title: 13120.s1

value: E

value: oi


title: Normal Breast Sample ATM_17

description:
A791-17.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: tissue


title: 13038.s1

value: leukocyte

tag: gender

value: lu


title: Normal Breast Sample ATM_16

description:
A791-16.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Renal pelvis cell line 786_0-250K_Sty

description:
Hybridized to 250K_Sty
786_0-250ksty


title: 13041.s1

tag: cell type

value: Male

value: F


title: HG_CTL81

value: lymphoblast

value: I


title: Ovary cell line SK_OV_3-250K_Sty

description:
Hybridized to 250K_Sty
SK_OV_3-250ksty

source_name: Ascites_Ovary cell line

value: Ovary


title: 13050.s1

value: hv


title: Prostate cell line DU_145 DTP-250K_Sty

description:
Hybridized to 250K_Sty
DU_145 DTP-250ksty

value: Prostate

value: DU145 DTP


title: Normal Breast Sample ATM_15

description:
A791-15.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue

tag: disease status

value: healthy control

value: Female


title: 13018.s1

value: L

value: fl

value: white


title: 12984.s1

value: H

value: sb


title: 13001.s1

value: leukocyte

value: J

value: kc

value: more-than-one-race


title: Ovary cell line NCI_ADR_RES-250K_Sty

description:
Hybridized to 250K_Sty
NCI_ADR_RES-250ksty

source_name: Ovary cell line

tag: tissue type

value: NCI/ADR-RES


title: Normal Breast Sample ATM_13

description:
A791-13.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Prostate cell line PC_3-250K_Sty

description:
Hybridized to 250K_Sty
PC_3-250ksty

tag: cell line


title: HG_CTL80

value: lymphoblast

tag: sample id

value: Male

value: D


title: Normal Breast Sample ATM_12

description:
A791-12.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Ovary cell line OVCAR_8-250K_Sty

description:
Hybridized to 250K_Sty
OVCAR_8-250ksty

value: Ovary


title: 13034.s2

tag: sentrix id

value: K

value: hv


title: 12976.s1

tag: sentrix position

value: C


title: Ovary cell line OVCAR_5-250K_Sty

description:
Hybridized to 250K_Sty
OVCAR_5-250ksty


title: Normal Breast Sample ATM_11

description:
A791-11.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue

value: healthy control

value: Female


title: 12964.s1

tag: experiment

value: ox


title: 12970.s2

value: I

tag: group

value: xm

value: white


title: 12958.s1

value: leukocyte

value: H

tag: family

value: sb


title: 12967.s1

value: G

tag: distribution

value: fl


title: 12969.s1

value: Male

value: E

tag: site

value: asian


title: 12974.s1

value: pb

tag: cpea dx


title: 12955.s1

value: J

tag: age at collection (months)


title: Normal Breast Sample ATM_10

description:
A791-10.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue


title: Normal Breast Sample ATM_9

description:
A791-09.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: healthy control


title: Ovary cell line OVCAR_4-250K_Sty

description:
Hybridized to 250K_Sty
OVCAR_4-250ksty

value: Ovary


title: Ovary cell line IGROV1-250K_Sty

description:
Hybridized to 250K_Sty
IGROV1-250ksty


title: Ovary cell line OVCAR_3-250K_Sty

description:
Hybridized to 250K_Sty
OVCAR_3-250ksty


title: Ovary cell line OVCAR_3-250K_Sty.1

description:
Hybridized to 250K_Sty
OVCAR_3-250ksty


title: 12951.s1

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

value: D

value: hv

tag: ethnicity


title: HG_CTL78

value: lymphoblast

value: B


title: HG_CTL79

value: C


title: Normal Breast Sample ATM_8

description:
A791-08.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: tissue

value: Female


title: 12953.s1

value: leukocyte

tag: gender

value: A

value: xm

value: white


title: Normal Breast Sample ATM_4

description:
A791-04.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: Melanocyte cell line UACC-62-250K_Sty

description:
Hybridized to 250K_Sty
UACC_62-250ksty

source_name: Melanocyte cell line

value: Melanocyte


title: Normal Breast Sample ATM_7

description:
A791-07.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: 12940.s1

tag: cell type

value: Male

value: F

value: lu


title: 12938.s1

value: L

value: xx

value: more-than-one-race


title: Melanocyte cell line UACC-257-250K_Sty

description:
Hybridized to 250K_Sty
UACC_257-250ksty


title: 12930.s1

value: D

value: oi


title: 12950.s1

value: E

value: ox

value: asian


title: 12925.s2

value: B

value: hv


title: 12942.s1

value: leukocyte

value: I

value: sb


title: Melanocyte cell line SK_MEL-5-250K_Sty

description:
Hybridized to 250K_Sty
SK_MEL_5-250ksty

source_name: Metastasis_Melanocyte cell line

value: Melanocyte


title: Normal Breast Sample ATM_6

description:
A791-06.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

value: Human breast tissue

tag: disease status

value: healthy control

value: Female


title: HG_CTL77

value: lymphoblast

value: Male

value: A


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Male_3

city: St. Louis

first: Christina

middle: Marie

last: Ambrosi

state: MO

address: 1 Brookings Drive

department: Biomedical Engineering

institute: Washington University in St. Louis

description: NONISCHEMIC MALE EPI 3

data_processing: A relative quantification method (Livak and Schmittgen, 2001) based on the cycle at threshold (Ct) value was employed with GAPDH as an endogenous control and Nonfailing Male LV 2 as the calibrator sample.

label: Taqman

source_name: left ventricle, epicardium, nonischemic cardiomyopathy

label_protocol: Total RNA (1-2 μg) was first converted to cDNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).  Subsequent reactions were performed using 100 ng of cDNA loaded into each well of our custom-designed gene arrays mixed with Taqman Universal PCR Master Mix (Applied Biosystems).

extract_protocol: Total RNA was extracted from a total of 68 samples using the RNEasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.  RNA yield was measured using a Nanodrop 1000 (Thermo Scientific) and quality was assessed by verifying the presence of 18S and 28S bands as run on a 1% agarose gel.

treatment_protocol: Cardiac tissue preparations were preserved in RNAlater (Sigma-Aldrich, St. Louis, MO) and stored at -80 degrees Celsius until RNA extraction.

tag: tissue type

value: Left ventricular epicardium

tag: age

tag: disease state

value: Nonischemic cardiomyopathy


title: Melanocyte cell line MDA-N-250K_Sty

description:
Hybridized to 250K_Sty
MDA_N-250ksty

source_name: Pleural effusion_Melanocyte cell line

tag: cell line

value: MDA-N


title: Normal Breast Sample ATM_2

description:
A791-02.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Male_2

description: NONISCHEMIC MALE EPI 2


title: 12920.s1

tag: sample id

tag: sentrix id

tag: sentrix position

value: H

value: fl

value: white


title: 12923.s1

value: L

tag: experiment

tag: group

tag: family


title: 12905.s1

value: leukocyte

tag: distribution

tag: site

value: vn

tag: cpea dx


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Male_1

description: NONISCHEMIC MALE EPI 1


title: Melanocyte cell line SK_MEL-2-250K_Sty

description:
Hybridized to 250K_Sty
SK_MEL_2-250ksty


title: Melanocyte cell line SK_MEL-28-250K_Sty

description:
Hybridized to 250K_Sty
SK_MEL_28-250ksty


title: 12859.s1

value: J

value: oi

tag: age at collection (months)

tag: ethnicity


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Male_2

description: NONISCHEMIC MALE ENDO 2

source_name: left ventricle, endocardium, nonischemic cardiomyopathy

value: Left ventricular endocardium

tag: gender


title: HG_CTL76

tag: cell type

value: D


title: 12916.s1

value: B

value: pb


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Male_1

description: NONISCHEMIC MALE ENDO 1

tag: tissue type

value: Male


title: 12901.s1

value: A

value: xx

value: more-than-one-race


title: Melanocyte cell line MALME-3M-250K_Sty

description:
Hybridized to 250K_Sty
MALME_3M-250ksty

value: Melanocyte


title: 12857.s1

value: ox


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Male_3

description: NONISCHEMIC MALE ENDO 3

tag: age

value: Nonischemic cardiomyopathy


title: Normal Breast Sample ATM_14

description:
A791-14.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: tissue

value: Human breast tissue

tag: disease status

value: healthy control

value: Female


title: Melanocyte cell line M14-250K_Sty

description:
Hybridized to 250K_Sty
M14-250ksty

tag: cell line


title: 12865.s1

value: leukocyte

tag: sample id

tag: sentrix id

value: sb

value: white


title: 12853.s1

tag: sentrix position

value: F

tag: experiment

value: vn


title: 12902.s1

value: E

tag: group

tag: family


title: HG_CTL74

value: lymphoblast

value: B


title: Melanocyte cell line LOXIMVI-250K_Sty

description:
Hybridized to 250K_Sty
LOXIMVI-250ksty

value: LOXIMVI


title: 12851.s1

value: Male

value: K

tag: distribution

tag: site


title: Melanocyte cell line MDA-MB-435-250K_Sty

description:
Hybridized to 250K_Sty
MDA_MB_435-250ksty

value: Melanocyte


title: White blood cell line SR-250K_Sty

description:
Hybridized to 250K_Sty
SR-250ksty

source_name: White blood cell line

value: White blood cell

value: SR


title: HG_CTL75

value: C


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Female_2

description: NONISCHEMIC FEMALE EPI 2

value: Left ventricular epicardium

tag: disease state

value: Nonischemic cardiomyopathy


title: 12850.s1

value: leukocyte

value: kc

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: 12852.s1

tag: cell type

tag: gender

value: H

value: kr

value: white


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Female_1

description: NONISCHEMIC FEMALE EPI 1

tag: tissue type

value: Female

tag: age


title: LeftVentricularEpicardium_NonischemicCardiomyopathy_Female_3

description: NONISCHEMIC FEMALE EPI 3


title: White blood cell line RPMI_8226-250K_Sty

description:
Hybridized to 250K_Sty
RPMI_8226-250ksty

source_name: PB_White blood cell line

tag: cell line


title: 12794.s1

tag: sample id

value: lu


title: 12836.s1

tag: sentrix id

value: A

value: ox

value: more-than-one-race


title: Normal Breast Sample ATM_3

description:
A791-03.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

tag: tissue

value: Human breast tissue

tag: disease status

value: healthy control


title: White blood cell line MOLT_4-250K_Sty

description:
Hybridized to 250K_Sty
MOLT_4-250ksty

value: White blood cell


title: 12829.s1

value: Male

tag: sentrix position

value: I

tag: experiment

tag: group

value: fl


title: White blood cell line HL_60-250K_Sty

description:
Hybridized to 250K_Sty
HL_60-250ksty

source_name: PBL_White blood cell line


title: 12799.s1

source_name: leukocyte

value: J

tag: family

tag: distribution

tag: site


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Female_3

description: NONISCHEMIC FEMALE ENDO 3

value: Left ventricular endocardium

tag: disease state

value: Nonischemic cardiomyopathy


title: 12803.s1

value: leukocyte

value: E

value: oi

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: HG_CTL73

source_name: lymphoblast

tag: cell type

value: lymphoblast

tag: gender


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Female_2

description: NONISCHEMIC FEMALE ENDO 2

tag: tissue type

value: Female

tag: age


title: LeftVentricularEndocardium_NonischemicCardiomyopathy_Female_1

description: NONISCHEMIC FEMALE ENDO 1


title: White blood cell line K_562-250K_Sty

description:
Hybridized to 250K_Sty
K_562-250ksty

source_name: Pleural effusion_White blood cell line

tag: cell line


title: White blood cell line CCRF_CEM-250K_Sty

description:
Hybridized to 250K_Sty
CCRF_CEM-250ksty

value: CCRF-CEM


title: 12775.s1

tag: sample id

tag: sentrix id

value: K

value: white


title: LeftVentricularEpicardium_Nonfailing_Male_3

description: NONFAILING MALE EPI 3

source_name: left ventricle, epicardium, nonfailing

value: Left ventricular epicardium

value: Nonfailing


title: 12748.s1

tag: sentrix position

value: F

value: sb


title: 12739.s1

value: Male

value: I

tag: experiment

value: lu


title: 12743.s1

value: B

tag: group


title: HG_CTL72

value: L


title: LeftVentricularEpicardium_Nonfailing_Male_1

description: NONFAILING MALE EPI 1


title: LeftVentricularEpicardium_Nonfailing_Male_2

description: NONFAILING MALE EPI 2


title: Lung cell line NCI_H322M-250K_Sty

description:
Hybridized to 250K_Sty
NCI_H322M-250ksty

source_name: Lung cell line

value: Lung


title: 12817.s2

value: leukocyte

value: C

tag: family

value: vn


title: 12786.s1

value: A

tag: distribution

value: kr


title: 12676.s1

value: J

tag: site


title: Lung cell line NCI_H460-250K_Sty

description:
Hybridized to 250K_Sty
NCI_H460-250ksty

source_name: Pleural effusion_Lung cell line


title: 12735.s1

value: H

value: pb

value: white


title: Lung cell line NCI_H522-250K_Sty

description:
Hybridized to 250K_Sty
NCI_H522-250ksty


title: 12692.s1

value: ox


title: HG_CTL71

value: lymphoblast

value: K


title: Lung cell line NCI_H23-250K_Sty

description:
Hybridized to 250K_Sty
NCI_H23-250ksty


title: Normal Breast Sample ATM_1

description:
A791-01.CEL
Human female breast tissue hybridised onto Genome-Wide Human SNP Array 6.0

source_name: Human female breast tissue

tag: tissue

value: Human breast tissue

tag: disease status

value: healthy control

value: Female


title: LeftVentricularEndocardium_Nonfailing_Male_3

description: NONFAILING MALE ENDO 3

source_name: left ventricle, endocardium, nonfailing

value: Left ventricular endocardium

value: Male

tag: disease state

value: Nonfailing


title: LeftVentricularEndocardium_Nonfailing_Male_2

description: NONFAILING MALE ENDO 2


title: LeftVentricularEndocardium_Nonfailing_Male_1

description: NONFAILING MALE ENDO 1


title: LeftVentricularEpicardium_Nonfailing_Female_3

description: NONFAILING FEMALE EPI 3

value: Left ventricular epicardium


title: LeftVentricularEpicardium_Nonfailing_Female_1

description: NONFAILING FEMALE EPI 1


title: 12645.s1

value: leukocyte

value: F

value: fl

tag: cpea dx

tag: age at collection (months)

tag: ethnicity


title: LeftVentricularEndocardium_Nonfailing_Female_3

description: NONFAILING FEMALE ENDO 3

tag: tissue type

tag: gender


title: 12664.s1

tag: cell type

value: kr


title: HG_CTL70

tag: sample id

value: J


title: Lung cell line HOP_62-250K_Sty

description:
Hybridized to 250K_Sty
HOP_62-250ksty

value: Lung

tag: cell line


title: 12637.s1

tag: sentrix id

tag: sentrix position

value: E

value: white


title: 12573.s1

value: B

tag: experiment

tag: group


title: 12704.s2

value: C

tag: family

tag: distribution


title: 12605.s1

value: K

tag: site


title: 12592.s2

value: L

value: xm


title: Lung cell line NCI_H226-250K_Sty

description:
Hybridized to 250K_Sty
NCI_H226-250ksty


title: 12613.s1

value: ox


title: Lung cell line EKVX-250K_Sty

description:
Hybridized to 250K_Sty
EKVX-250ksty

value: EKVX


title: 12582.s1

value: Male

value: H

value: other


title: 12651.s1

value: leukocyte

value: D

value: vn


title: LeftVentricularEpicardium_Nonfailing_Female_2

description: NONFAILING FEMALE EPI 2

value: Left ventricular epicardium

value: Female

tag: age

value: Nonfailing


title: Colon cell line SW_620-250K_Sty

description:
Hybridized to 250K_Sty
SW_620-250ksty

source_name: Colon cell line

value: Colon


title: LeftVentricularEndocardium_Nonfailing_Female_2

description: NONFAILING FEMALE ENDO 2

value: Left ventricular endocardium

tag: disease state


title: Colon cell line HT29-250K_Sty

description:
Hybridized to 250K_Sty
HT29-250ksty

source_name: Primary_Colon cell line


title: Colon cell line KM12-250K_Sty

description:
Hybridized to 250K_Sty
KM12-250ksty


title: Lung cell line A549-250K_Sty

description:
Hybridized to 250K_Sty
A549-250ksty

value: Lung


title: HG_CTL68

value: lymphoblast


title: LeftVentricularEndocardium_Nonfailing_Female_1

description: NONFAILING FEMALE ENDO 1


title: Colon cell line HCT_15-250K_Sty

description:
Hybridized to 250K_Sty
HCT_15-250ksty


title: LeftVentricle_Nonfailing_Male_6

description: NONFAILING MALE LV 6

source_name: left ventricle, nonfailing

value: Left ventricle


title: HG_CTL69

value: I


title: Lung cell line HOP_92-250K_Sty

description:
Hybridized to 250K_Sty
HOP_92-250ksty


title: 12460.s1

value: F

value: ox

tag: cpea dx

value: white


title: 12548.s2

value: Male

value: B

value: oi

tag: age at collection (months)


title: LeftVentricle_Nonfailing_Male_5

description: NONFAILING MALE LV 5


title: LeftVentricle_Nonfailing_Male_4

description: NONFAILING MALE LV 4


title: Colon cell line HCT_116-250K_Sty

description:
Hybridized to 250K_Sty
HCT_116-250ksty


title: LeftVentricle_Nonfailing_Male_3

description: NONFAILING MALE LV 3


title: 12555.s2

value: leukocyte

value: K

value: sb

tag: ethnicity


title: 12512.s2

value: J


title: 12231.s2

value: pb


title: 12401.s1

value: E

value: hv


title: Colon cell line HCC_2998-250K_Sty

description:
Hybridized to 250K_Sty
HCC_2998-250ksty

tag: tissue type

value: Colon


title: HG_CTL67

value: lymphoblast

tag: gender

value: C


title: Colon cell line COLO205-250K_Sty

description:
Hybridized to 250K_Sty
COLO205-250ksty

source_name: Ascites_Colon cell line


title: 12325.s2

tag: cell type

value: I

value: xm


title: LeftVentricle_Nonfailing_Male_2

description: NONFAILING MALE LV 2

value: Left ventricle

value: Nonfailing


title: 12368.s1

tag: sample id

value: Male

value: G

value: white


title: 12334.s1

value: leukocyte

value: kr


title: 13364.s1


title: Central nervous system cell line U251-250K_Sty

description:
Hybridized to 250K_Sty
U251-250ksty

source_name: Central nervous system cell line

value: Central nervous system

tag: cell line


title: Central nervous system cell line SNB_75-250K_Sty

description:
Hybridized to 250K_Sty
SNB_75-250ksty


title: LeftAtrium_Nonfailing_Male_6

description: NONFAILING MALE LA 6

source_name: left atrium, nonfailing

value: Left atrium


title: 11905.s1

tag: sentrix id

value: K


title: HG_CTL66

tag: sentrix position

value: B


title: 12219.s2

tag: experiment

value: sb


title: Central nervous system cell line SNB_19-250K_Sty

description:
Hybridized to 250K_Sty
SNB_19-250ksty


title: LeftAtrium_Nonfailing_Male_5

description: NONFAILING MALE LA 5


title: LeftVentricle_Nonfailing_Male_1

description: NONFAILING MALE LV 1


title: 12116.s1

tag: group

value: lu

value: other


title: LeftAtrium_Nonfailing_Male_4

description: NONFAILING MALE LA 4


title: 11678.s1

value: H

tag: family

value: kc


title: LeftAtrium_Nonfailing_Male_3

description: NONFAILING MALE LA 3


title: 12076.s1

value: A

tag: distribution


title: Central nervous system cell line SF_295-250K_Sty

description:
Hybridized to 250K_Sty
SF_295-250ksty


title: Central nervous system cell line SF_539-250K_Sty

description:
Hybridized to 250K_Sty
SF_539-250ksty


title: 11838.s1

tag: site

value: xm


title: 11601.s1

value: I

value: hv


title: 12644.s1

value: Male

value: vn


title: HG_CTL65

value: lymphoblast


title: 11892.s2

value: leukocyte

value: C

value: white


title: 11671.s1

value: D

value: not-specified


title: Central nervous system cell line SF_268-250K_Sty

description:
Hybridized to 250K_Sty
SF_268-250ksty

value: Central nervous system


title: HG_CTL60

value: K


title: Breast cell line T47D-250K_Sty

description:
Hybridized to 250K_Sty
T47D-250ksty

source_name: Breast cell line

value: Breast


title: 12687.s1

value: F

value: oi


title: Breast cell line MDA_MB_231-250K_Sty

description:
Hybridized to 250K_Sty
MDA_MB_231-250ksty

source_name: Pleural effusion_Breast cell line


title: LeftVentricle_Nonfailing_Female_7

description: NONFAILING FEMALE LV 7

value: Left ventricle

value: Female

tag: age

value: Nonfailing


title: LeftAtrium_Nonfailing_Male_2

description: NONFAILING MALE LA 2

value: Left atrium

tag: disease state


title: LeftAtrium_Nonfailing_Male_1

description: NONFAILING MALE LA 1

value: Male


title: HG_CTL62

value: H


title: LeftVentricle_Nonfailing_Female_6

description: NONFAILING FEMALE LV 6


title: Breast cell line HS578T-250K_Sty

description:
Hybridized to 250K_Sty
HS578T-250ksty

source_name: Primary_Breast cell line


title: HG_CTL61

value: lymphoblast


title: LeftVentricle_Nonfailing_Female_5

description: NONFAILING FEMALE LV 5


title: 12113.s1.2

source_name: leukocyte

value: leukocyte

value: E

value: ox

tag: cpea dx


title: LeftVentricle_Nonfailing_Female_4

description: NONFAILING FEMALE LV 4


title: 12271.s1.2

value: D

value: kr

tag: age at collection (months)

value: white


title: Breast cell line MCF7-250K_Sty

description:
Hybridized to 250K_Sty
MCF7-250ksty


title: 12029.s1.2

value: J

value: xx

tag: ethnicity


title: 12552.s1.2

value: lu


title: 12115.s1.2

value: I

value: not-specified


title: Endosperm at 16DAF, biological rep1

city: Shanghai

first: Hong-Wei

last: Xue

state: Shanghai

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences

description: Endosperm were collected at 16 day after flowering

hyb_protocol: Affymetrix® GeneChip® Operating Software Version 1.0 was used for washing, staining, and scanning as described in the supplier’s protocol.

scan_protocol: Scanning procedures of the arrays were carried out using Affymetrix GeneChip Scanner 3000 as described in the Affymetrix technical manual.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: Rice Endosperm at 16 DAF

label_protocol: RNA was labeled for hybrid with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Rice (Oryza sativa, japonica cultivar Zhonghua 11), was cultivated at day/night temperatures (28/22 °C) in phytotron.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen) accordding to manufactures manual

treatment_protocol: All the meterials were collected quickly, and frozen in liquid nitrogen.

tag: tissue

value: Endosperm

tag: developmental stage

value: 16 day after flowering


title: Endosperm at 16DAF, biological rep2


title: Endosperm at 9DAF, biological rep2

description: Endosperm were collected at 9 day after flowering

source_name: Rice Endosperm at 9 DAF

value: 9 day after flowering


title: 12944.s1.2

tag: cell type

tag: gender

value: Male

value: B

value: xm


title: 12101.s1.2

value: leukocyte

tag: sample id


title: 12014.s1.2

tag: sentrix id

value: C


title: HG_CTL58

source_name: lymphoblast

value: lymphoblast

tag: sentrix position


title: HG_CTL59

tag: experiment


title: Endosperm at 9DAF, biological rep1


title: 12019.s1.2

value: A

tag: group

value: hv


title: LeftVentricle_Nonfailing_Female_1

description: NONFAILING FEMALE LV 1

tag: tissue type

value: Left ventricle

value: Female

value: Nonfailing


title: Endosperm at 3DAF, biological rep2

description: Endosperm were collected at 3 day after flowering

source_name: Rice Endosperm at 3 DAF

value: 3 day after flowering


title: Breast cell line BT_549-250K_Sty

description:
Hybridized to 250K_Sty
BT_549-250ksty

source_name: Metastasis_Breast cell line

value: Breast

tag: cell line


title: 11053.s1.2

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

value: J

tag: family

tag: distribution

tag: site

value: fl

value: white


title: LeftAtrium_Nonfailing_Female_7

description: NONFAILING FEMALE LA 7

value: Left atrium

tag: age

tag: disease state


title: Endosperm at 3DAF, biological rep1

value: Endosperm


title: LeftAtrium_Nonfailing_Female_6

description: NONFAILING FEMALE LA 6


title: HG_CTL57

value: Male


title: 11625.s1.2

value: xx

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: more-than-one-race


title: LeftAtrium_Nonfailing_Female_5

description: NONFAILING FEMALE LA 5


title: HG_CTL56

tag: cell type

value: L


title: LeftAtrium_Nonfailing_Female_2

description: NONFAILING FEMALE LA 2

tag: gender


title: LeftAtrium_Nonfailing_Female_4

description: NONFAILING FEMALE LA 4


title: Embryo at 9DAF, biological rep2

description: Embryo were collected at 9 day after flowering

source_name: Rice embryo at 9 DAF

tag: tissue

value: Embryo

tag: developmental stage

value: 9 day after flowering


title: Embryo at 12DAF, biological rep1

description: Embryo were collected at 12 day after flowering

source_name: Rice embryo at 12 DAF

value: 12 day after flowering


title: Embryo at 12DAF, biological rep2


title: 11167.s1.2

value: leukocyte

tag: sample id

tag: sentrix id

tag: sentrix position

value: F

value: kc

value: other


title: 13073.s1

tag: experiment

tag: group

value: hv


title: LeftAtrium_Nonfailing_Female_1

description: NONFAILING FEMALE LA 1

tag: tissue type

value: Female

value: Nonfailing


title: 13099.s1

value: G

tag: family

tag: distribution

value: white


title: 13154.s1

value: H

tag: site

value: lu


title: HG_CTL55

value: lymphoblast

value: Male

value: K


title: LeftVentricle_IschemicCardiomyopathy_Male_6

description: ISCHEMIC MALE LV 6

source_name: left ventricle, ischemic cardiomyopathy

value: Left ventricle

tag: age

tag: disease state

value: Ischemic cardiomyopathy


title: 13070.s1

value: xx

tag: cpea dx

tag: age at collection (months)


title: 13082.s1

tag: cell type

value: leukocyte

value: A

value: xm

tag: ethnicity


title: Embryo at 9DAF, biological rep1

tag: tissue

value: Embryo

value: 9 day after flowering


title: 13010.s1

tag: gender

value: I

value: more-than-one-race


title: Embryo at 3DAF, biological rep2

description: Embryo were collected at 3 day after flowering

source_name: Rice embryo at 3 DAF

tag: developmental stage

value: 3 day after flowering


title: 12996.s1

tag: sample id

tag: sentrix id

value: hv

value: white


title: 12780.s1

tag: sentrix position

value: H

tag: experiment


title: LeftVentricle_IschemicCardiomyopathy_Male_5

description: ISCHEMIC MALE LV 5

tag: tissue type


title: 13053.s1

value: B

tag: group

tag: family


title: Embryo at 3DAF, biological rep1


title: LeftVentricle_IschemicCardiomyopathy_Male_3

description: ISCHEMIC MALE LV 3

value: Male


title: LeftVentricle_IschemicCardiomyopathy_Male_4

description: ISCHEMIC MALE LV 4


title: Ovary, biological rep1

description: Ovaries were collected the day of flowering (0 DAF)

source_name: Rice ovary

value: Ovary

value: 0 day after flowering


title: HG_CTL54

value: lymphoblast

value: J


title: Ovary, biological rep2

description: Ovaries were collected the day of flowering (1 DAF)


title: 12772.s1

value: leukocyte

value: G

tag: distribution

tag: site

value: sb


title: LeftVentricle_Nonfailing_Female_2

description: NONFAILING FEMALE LV 2

source_name: left ventricle, nonfailing

value: Left ventricle

value: Female

tag: age

tag: disease state

value: Nonfailing


title: LeftVentricle_IschemicCardiomyopathy_Male_2

description: ISCHEMIC MALE LV 2

value: Ischemic cardiomyopathy


title: 12773.s1

value: F

value: xm

tag: cpea dx

tag: age at collection (months)


title: LeftVentricle_IschemicCardiomyopathy_Male_1

description: ISCHEMIC MALE LV 1


title: 12791.s1

tag: cell type

value: C

value: xx

tag: ethnicity

value: more-than-one-race


title: 12722.s1

tag: gender

value: Male

value: white


title: HG_CTL53

value: I


title: LeftAtrium_IschemicCardiomyopathy_Male_6

description: ISCHEMIC MALE LA 6

source_name: left atrium, ischemic cardiomyopathy

value: Left atrium


title: 12939.s1

value: E

value: hv

value: asian


title: 12784.s1

value: leukocyte

value: A

value: kr


title: LeftAtrium_IschemicCardiomyopathy_Male_5

description: ISCHEMIC MALE LA 5


title: LeftAtrium_IschemicCardiomyopathy_Male_4

description: ISCHEMIC MALE LA 4