title: Sample247_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample252_Control

status: Public on Oct 21 2015

type: genomic

city: Baltimore

first: Andrew

last: Jaffe

state: MD

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

country: USA

institute: Lieber Institute for Brain Development

description: Human DLPFC DNA methylation sample

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
idat files were read in using the minfi Bioconductor package and processed using the preprocessQuantile approach
GEO_procData.csv: the resulting Illumina "Beta" matrix (proportion methylation) after stratified quantile normalization.
GEO_rawData.csv: Unmethylated and methylated signal intensities
suppTable9_meQTLs_allPairs.csv: all significant SNP-CpG pairs for meQTLs with FDR < 0.01, with corresponding annotation.

molecule: genomic DNA

organism: Homo sapiens

source_name: DLPFC

label_protocol: Following manufacturer's protocol

extract_protocol: Genomic DNA was extracted from 100 mg of pulverized dorsolateral prefrontal cortex (DLPFC) tissue with the phenol-chloroform method.

treatment_protocol: Bisulfite conversion of 600 ng genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: FALSE

tag: sex (clinical gender)

value: M

tag: race

value: AA

tag: group

value: Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample255_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: lung_K458

type: RNA

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

label: biotin

molecule: total RNA

source_name: lung adenocarcinoma

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: gender

value: WHITE

value: Non Spanish/Hispanic

value: Ever

value: Dead

tag: Stage

value: WT


title: lung_K264


title: atypical adenomatous hyperplasia_29

city: Shanghai

first: Lu

last: Shaohua

address: No. 180 Feng Lin Road

department: Department of Pathology

country: China

institute: Zhongshan Hospital

description: laser capture microdissection(LCM)-selected cells

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 9 (Agilent technologies, Santa Clara, CA, US).

source_name: lung atypical adenomatous hyperplasia tissue,29

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA of the frozen tissue sections was extracted using mirVanamiRNA isolation kit according to the manufacturer`s instructions (Applied Biosystems, Foster City, CA). The concentration was quantified by NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Waltham, MA). The quality control of RNA was performed by a 2100 Bioanalyzer using the RNA 6000 Pico LabChip kit (Agilent Technologies, Santa Clara, CA). The quality was measured using RNA integrity number (RIN). A RNA sample was discarded if the RIN score was less than 5.0.

treatment_protocol: The target cell populations (~200,000 cells)were selected and captured using ultraviolet laser cutting following the manufacturer’s recommended protocol. Additionally, haematoxylin eosin(H&E)-stained sections were prepared for each tissue to guide the area of interest for LCM.

value: female


title: Sample246_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: CAUC

value: Schizo

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample244_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

tag: group

tag: age (in years)


title: lung_K144

value: F

value: Alive

value: Mut


title: Sample243_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: adenocarcinoma_29

source_name: lung adenocarcinoma tissue,29


title: lung_K415

value: BLACK


title: Sample242_Schizo

description: Human DLPFC DNA methylation sample

value: FALSE

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: normal_29

source_name: lung adjacent normal tissue,29

tag: gender


title: Sample241_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample245_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

value: M

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample240_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

tag: group


title: Sample239_Control

description: Human DLPFC DNA methylation sample

value: AA

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample238_Control

description: Human DLPFC DNA methylation sample

value: Control

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K162

tag: Stage


title: Sample237_Control

description: Human DLPFC DNA methylation sample

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K301

tag: gender


title: Sample236_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

value: TRUE


title: Sample235_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: adenocarcinoma_27

source_name: lung adenocarcinoma tissue,27


title: adenocarcinoma_28

source_name: lung adenocarcinoma tissue,28


title: Sample234_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: adenocarcinoma_26

source_name: lung adenocarcinoma tissue,26

value: male


title: Sample233_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample232_Control

description: Human DLPFC DNA methylation sample

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: normal_28

source_name: lung adjacent normal tissue,28

tag: gender


title: normal_26

source_name: lung adjacent normal tissue,26


title: Sample230_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)


title: adenocarcinoma_25

source_name: lung adenocarcinoma tissue,25


title: Sample229_Schizo

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample228_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K072

value: WHITE

value: Non Spanish/Hispanic

tag: Stage


title: bronchioloalveolar carcinoma_23

source_name: lung bronchioloalveolar carcinoma tissue,23


title: lung_K086

value: Ever

value: Dead


title: lung_K346

value: WT


title: lung_K117

value: Missing


title: lung_K442


title: Sample231_Schizo

description: Human DLPFC DNA methylation sample

value: CAUC

value: Schizo

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: lung_K376


title: adenocarcinoma_22

source_name: lung adenocarcinoma tissue,22

value: female


title: Sample226_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample225_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K464

tag: gender

value: F

tag: race

value: Alive

value: Mut


title: lung_K466


title: Sample224_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

value: FALSE

tag: sex (clinical gender)

value: M

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample222_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample221_Control

description: Human DLPFC DNA methylation sample

value: AA

value: Control

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample220_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample223_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: squamous cell carcinoma_42

source_name: lung squamous cell carcinoma tissue,42

tag: gender

value: male


title: normal_22

source_name: lung adjacent normal tissue,22


title: normal_25

source_name: lung adjacent normal tissue,25


title: adenocarcinoma_20

source_name: lung adenocarcinoma tissue,20


title: normal_21

source_name: lung adjacent normal tissue,21


title: Sample227_Control

description: Human DLPFC DNA methylation sample

source_name: DLPFC

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample219_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample218_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: adenocarcinoma_21

source_name: lung adenocarcinoma tissue,21


title: Sample216_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample214_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample215_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: adenocarcinoma_1

source_name: lung adenocarcinoma tissue,1

tag: gender


title: Sample212_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample210_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample209_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: normal_1

source_name: lung adjacent normal tissue,1


title: Sample211_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: adenocarcinoma_19

source_name: lung adenocarcinoma tissue,19


title: normal_19

source_name: lung adjacent normal tissue,19


title: Sample208_Schizo

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: lung_K043

source_name: lung adenocarcinoma

value: WHITE

value: Non Spanish/Hispanic

tag: Stage


title: lung_K090

tag: gender

value: Ever

value: Dead

value: SpliceSite


title: lung_K275

value: Missing

value: WT


title: lung_K219


title: Sample217_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K323

tag: race


title: Sample206_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: normal_20

source_name: lung adjacent normal tissue,20


title: lung_K379


title: Sample205_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: atypical adenomatous hyperplasia_18

source_name: lung atypical adenomatous hyperplasia tissue,18

value: female


title: lung_K130


title: Sample213_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: adenocarcinoma_18

source_name: lung adenocarcinoma tissue,18

tag: gender


title: Sample204_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: CAUC

value: Schizo

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample203_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample202_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample201_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample207_Control

description: Human DLPFC DNA methylation sample

value: F

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: adenocarcinoma_17

source_name: lung adenocarcinoma tissue,17


title: Sample200_Control

description: Human DLPFC DNA methylation sample

value: FALSE

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: normal_18

source_name: lung adjacent normal tissue,18

tag: gender


title: Sample198_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: M

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample199_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

value: AA

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K465

value: BLACK

value: Alive

tag: Stage


title: Sample197_Schizo

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

value: TRUE


title: lung_K215

value: WHITE

value: Never

value: Mut


title: normal_17

source_name: lung adjacent normal tissue,17


title: Sample195_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample196_Schizo

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: adenocarcinoma_16

source_name: lung adenocarcinoma tissue,16

tag: gender


title: Sample194_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: Control

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample193_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K325

value: Non Spanish/Hispanic

tag: Stage


title: lung_K372

value: Ever


title: lung_K059

value: Dead

value: WT


title: lung_K013


title: lung_K199

value: Missing


title: Sample192_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: lung_K004


title: normal_16

source_name: lung adjacent normal tissue,16

value: female


title: Sample191_Control

description: Human DLPFC DNA methylation sample

value: F

value: CAUC

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K014

tag: gender

value: Spanish/Hispanic


title: Sample190_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

value: FALSE

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: normal_15

source_name: lung adjacent normal tissue,15


title: lung_K191


title: Sample189_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

value: M

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: adenocarcinoma_15

source_name: lung adenocarcinoma tissue,15


title: Sample187_Control

description: Human DLPFC DNA methylation sample

source_name: DLPFC

tag: race

tag: group

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample186_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: adenocarcinoma_14

source_name: lung adenocarcinoma tissue,14


title: Sample185_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: normal_14

source_name: lung adjacent normal tissue,14

tag: gender


title: Sample184_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

value: AA

value: Schizo

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: adenocarcinoma_13

source_name: lung adenocarcinoma tissue,13


title: Sample183_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample182_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample181_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample188_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)


title: Sample180_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample179_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample177_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: normal_12

source_name: lung adjacent normal tissue,12

tag: gender

value: male


title: adenocarcinoma_12

source_name: lung adenocarcinoma tissue,12


title: lung_K133

source_name: lung adenocarcinoma

value: WHITE

tag: Stage

value: Mut


title: Sample176_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

value: Control

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: adenocarcinoma_11

source_name: lung adenocarcinoma tissue,11


title: lung_K231

tag: race

value: Non Spanish/Hispanic

value: Ever

value: Alive


title: lung_K270

value: WT


title: lung_K289


title: lung_K137

value: OTHER

value: Dead


title: lung_K176

value: F


title: normal_11

source_name: lung adjacent normal tissue,11


title: Sample174_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample175_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample172_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample173_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

value: CAUC

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample170_Control

description: Human DLPFC DNA methylation sample

value: FALSE

tag: sex (clinical gender)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K121

tag: gender

value: M

tag: race

tag: Stage


title: Sample178_Control

description: Human DLPFC DNA methylation sample

value: AA

tag: group

tag: age (in years)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample171_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: normal_13

source_name: lung adjacent normal tissue,13

value: female


title: lung_K371

value: Missing


title: lung_K395

value: SpliceSite


title: Sample168_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

value: TRUE


title: adenocarcinoma_10

source_name: lung adenocarcinoma tissue,10

value: male


title: Sample167_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

value: Control

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample165_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample166_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)


title: Sample163_Control

description: Human DLPFC DNA methylation sample

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample162_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample169_Schizo

description: Human DLPFC DNA methylation sample

value: Schizo

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample161_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample160_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample164_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample159_Control

description: Human DLPFC DNA methylation sample

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K295

tag: gender

tag: race

value: WHITE

value: Non Spanish/Hispanic

value: Ever

tag: Stage

value: Mut


title: lung_K085

value: Dead

value: WT


title: lung_K322

value: F

value: Alive


title: lung_K463


title: Sample158_Control

description: Human DLPFC DNA methylation sample

value: FALSE

value: CAUC

tag: group

tag: age (in years)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample155_Control

description: Human DLPFC DNA methylation sample

value: M

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample156_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample154_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample157_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample152_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)


title: lung_K293

tag: gender

value: Missing

tag: Stage


title: Sample153_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample151_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K106


title: Sample149_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample150_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample148_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)


title: Sample147_Control

description: Human DLPFC DNA methylation sample

value: AA

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample146_Control

description: Human DLPFC DNA methylation sample

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample144_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample145_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample143_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: Sample142_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K036

tag: gender

tag: race

tag: Stage


title: Sample141_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K033


title: lung_K080


title: lung_K168


title: Sample138_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample137_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample136_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K290

tag: gender

tag: race

tag: Stage


title: lung_K413

value: Never


title: lung_K200


title: lung_K350


title: Sample139_Control

description: Human DLPFC DNA methylation sample

tag: group

value: Control

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K467


title: Sample135_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K365


title: Sample134_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample131_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample132_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K344

tag: gender

tag: Stage


title: lung_K065


title: Sample133_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample140_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K181


title: Sample130_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample129_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample128_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample127_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample126_Control

description: Human DLPFC DNA methylation sample

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K131

tag: gender

tag: Stage


title: Sample125_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K409

value: Spanish/Hispanic


title: Sample123_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample124_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample122_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample119_Control

description: Human DLPFC DNA methylation sample

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample120_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample118_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample116_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: lung_K339

tag: gender

value: WHITE

tag: Stage


title: lung_K366

value: Non Spanish/Hispanic


title: Sample121_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample112_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: lung_K356


title: Sample114_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K367

value: Ever


title: lung_K310

value: OTHER

value: Mut


title: lung_K122

value: WT


title: Sample110_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K108

tag: gender

value: F

tag: Stage


title: Sample109_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: sex (clinical gender)


title: lung_K128

tag: race

value: Alive


title: lung_K234

value: Dead


title: Sample113_Control

description: Human DLPFC DNA methylation sample

value: FALSE

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K089


title: lung_K012


title: Sample108_Control

description: Human DLPFC DNA methylation sample

value: CAUC

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample107_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample106_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample117_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: M


title: lung_K172

tag: gender

tag: race

value: Missing

tag: Stage


title: Sample105_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

value: AA

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample115_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

value: TRUE

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample104_Control

description: Human DLPFC DNA methylation sample

value: Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample101_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample102_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race


title: Sample100_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group


title: Sample97_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample103_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample98_Control

description: Human DLPFC DNA methylation sample

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample96_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample95_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample94_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample93_Control

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample92_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race


title: lung_K060

tag: gender

tag: Stage


title: lung_K095


title: lung_K433

value: Spanish/Hispanic


title: lung_K155

value: WHITE


title: Sample90_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample99_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample87_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample89_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample88_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race


title: Sample86_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group


title: Sample84_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample83_Control

description: Human DLPFC DNA methylation sample

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K329

tag: gender

value: BLACK

value: Non Spanish/Hispanic

tag: Stage


title: lung_K446

value: Ever


title: lung_K358

value: Mut


title: lung_K284

value: WT


title: lung_K229

value: F


title: lung_K440

value: Alive


title: Sample82_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample91_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample81_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K420

value: Never


title: Sample85_Control

description: Human DLPFC DNA methylation sample

value: FALSE

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample78_Control

description: Human DLPFC DNA methylation sample

value: CAUC

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample79_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample80_Control

description: Human DLPFC DNA methylation sample

value: M

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample77_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample73_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample76_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race


title: Sample75_Control

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K237

tag: gender

tag: Stage


title: Sample74_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample72_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample71_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample69_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality control)

tag: race

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample70_Control

description: Human DLPFC DNA methylation sample

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample68_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group


title: Sample67_Control

description: Human DLPFC DNA methylation sample

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample66_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample65_Control

description:
Human DLPFC DNA methylation sample
The negative ages refer to fetal/pre-birth samples

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K018

tag: gender

value: Missing

tag: Stage


title: lung_K328


title: Sample64_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

value: AA

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: lung_K227

tag: race

value: SpliceSite


title: Sample62_Control

tag: dropsample (whether to remove the sample for failing quality control)

value: Control

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

value: TRUE

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample61_Control

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K246

value: WHITE

value: Dead


title: Sample63_Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)


title: lung_K093

tag: gender

value: Non Spanish/Hispanic

tag: Stage


title: Sample60_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: lung_K426

tag: race


title: lung_K390

value: Ever


title: lung_K186

value: Mut


title: Sample59_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample58_Control

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K092

value: WT


title: lung_K306

value: F


title: Sample55_Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample57_Control

tag: brnum (brain number, indicates unique subjects)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample53_Control

tag: plate (processing plate)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: lung_K220

tag: gender

tag: race

tag: Stage


title: Sample52_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: lung_K064

value: BLACK

value: Alive


title: lung_K457


title: Sample56_Control

value: FALSE

tag: sex (clinical gender)

tag: group

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample51_Control

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample48_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample49_Control

tag: race

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)


title: Sample47_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample54_Control

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample44_Control

tag: sex (clinical gender)

tag: group


title: Sample46_Control

value: CAUC

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample50_Control

value: M

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: lung_K142

tag: gender

tag: Stage


title: Sample41_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K416

tag: race


title: Sample43_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K338

value: Spanish/Hispanic


title: lung_K361


title: Sample111_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample42_Control

value: AA

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample40_Control

tag: brnum (brain number, indicates unique subjects)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)


title: Sample45_Control

tag: plate (processing plate)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample39_Control

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K049

tag: gender

value: Missing

tag: Stage


title: lung_K364


title: Sample38_Control

tag: dropsample (whether to remove the sample for failing quality control)

value: Control

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K171


title: Sample36_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: Sample35_Control

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

value: TRUE

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample37_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample34_Control

tag: race

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample33_Control

tag: dropsample (whether to remove the sample for failing quality control)

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample32_Control

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample30_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample31_Control

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)


title: lung_K146

tag: gender

value: WHITE

tag: Stage


title: Sample29_Control

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K388

value: Dead


title: lung_K450

value: Non Spanish/Hispanic


title: lung_K205

value: Ever


title: lung_K079


title: PNET M15

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description: Gene expression data from pediatric PNET

hyb_protocol: Affymetrix hybridization kit was used including fragmentation according to Affymetrix's protocol. Hybridization was done on Affymetrix U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: The arrays were scanned using the Affymetrix Genechip scanner

data_processing: Data were summarized using MAS5 in R using the Affy package, followed by variance stabilization normalization using the vsn package

source_name: pediatric brain tumor

label_protocol: 8ul 125ng/ul was used as input for the Affymetrix in vitro one cycle kit, followed by IVT labelling (Affymetrix)

growth_protocol: Fresh-frozen tumor samples collected at Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands between 1990 and 2004. Before RNA extraction, 4-um cryosections were prepared from the same tissue blocks and stained with hematoxylin and eosin to confirm tumor histology.

extract_protocol: RNA was isolated by homogenizing tissue samples in Trizol reagent using a tissue homogenizer. Total RNA was isolated according to the manufacturer's instructions.

tag: type

value: primitive neuroectodermal tumor

tag: subtype

tag: tissue

value: primary


title: lung_K258

value: F

tag: race

value: WT

value: Mut


title: lung_K345

value: Alive


title: lung_K262

value: Never


title: Sample25_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: FALSE

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample19_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample24_Control

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample27_Control

tag: brnum (brain number, indicates unique subjects)

tag: race


title: lung_K266

tag: gender

tag: Stage


title: Sample23_Control

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample17_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample18_Control

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample28_Control

tag: group

tag: age (in years)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample21_Control

tag: brnum (brain number, indicates unique subjects)

value: M

tag: race


title: Sample16_Control

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

value: AA


title: Sample20_Control

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)


title: Sample15_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)


title: Sample14_Control

tag: predictedsex (sex predicted by sex chromosome probes)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: Sample22_Control

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)


title: Sample13_Control

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample11_Control

tag: group

tag: age (in years)


title: lung_K035

tag: gender

tag: Stage


title: PNET M113

tag: type

tag: subtype

tag: tissue


title: lung_K399

tag: race


title: Sample9_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: Sample10_Control

tag: sex (clinical gender)

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_es (composition estimates for embryonic stem cells (escs)

tag: comp_npc (composition estimates for neural progenitor cells (npcs)

tag: comp_neun_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K447

tag: gender

tag: Stage


title: lung_K432

tag: race


title: lung_K224


title: lung_K047


title: PNET M117

tag: type

tag: subtype

tag: tissue


title: Sample26_Control

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: dropsample (whether to remove the sample for failing quality control)

tag: group

tag: age (in years)

tag: negativecontrolpc1 (negative control principal component 1 for batch correction)

tag: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: lung_K249

value: Missing


title: lung_K174


title: Sample12_Control

tag: sex (clinical gender)

value: Control

tag: negativecontrolpc2 (negative control principal component 2 for batch correction)

tag: negativecontrolpc3 (negative control principal component 3 for batch correction)

tag: negativecontrolpc4 (negative control principal component 4 for batch correction)

tag: predictedsex (sex predicted by sex chromosome probes)

tag: bestqc (best sample to use when more than 1 array were run on the same subject/brnum)

tag: comp_da_neuron (composition estimates for dopamine neurons derived from escs)


title: lung_K120

tag: gender

tag: race

tag: Stage


title: PNET M105

tag: type

tag: subtype

tag: tissue


title: lung_K304


title: lung_K331


title: PNET M103


title: lung_K027


title: medulloblastoma M1

description: Gene expression data from pediatric medulloblastoma

value: medulloblastoma

value: with radiological visible leptomeningeal metastases

value: relapse


title: lung_K102

value: WHITE

value: Non Spanish/Hispanic


title: ependymoma E8

description: Gene expression data from pediatric ependymoma

value: ependymoma

value: anaplastic


title: lung_K417

value: Ever

value: Dead


title: lung_K141

value: F

value: WT


title: lung_K020

value: Alive


title: ependymoma E4

value: primary


title: ependymoma E6

value: cellular


title: ependymoma E2


title: ependymoma E3B


title: medulloblastoma M104

value: without radiological visible leptomeningeal metastases


title: lung_K211

value: M


title: ependymoma E3A


title: ependymoma E109


title: lung_K326

value: Mut


title: lung_K430


title: lung_K317

value: Missing


title: ependymoma E110


title: lung_K125


title: lung_K094

value: Never


title: lung_K203


title: ependymoma E108


title: lung_K307


title: lung_K135


title: ependymoblastoma E104

description: Gene expression data from pediatric ependymoblastoma

value: ependymoblastoma


title: ependymoma E107


title: hESC.conventional_wa09_rep45_450k

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner settings.

data_processing: 450k data were normalized using the subset-quantile within array normalization (SWAN) method (Maksimovic, Gordon et al. 2012).

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using a DNeasy kit (Qiagen) according to the manufacturer’s recommendations.

tag: derivation type


title: lung_K163

value: WHITE


title: hESC.conventional_wa09_rep46_450k


title: hESC.conventional_wa09_rep40_450k


title: hESC.conventional_wa09_rep32_450k


title: hESC.conventional_wa09_rep42_450k


title: hESC.conventional_wa09_rep44_450k


title: hESC.conventional_wa09_rep41_450k


title: ependymoma E1


title: hESC.conventional_wa09_rep38_450k


title: ependymoma E102


title: hESC.conventional_wa09_rep34_450k


title: hESC.conventional_wa09_rep33_450k


title: hESC.conventional_wa09_rep31_450k


title: ependymoma E101


title: hESC.conventional_wa07_rep29_450k


title: hESC.conventional_wa09_rep37_450k


title: lung_K076

value: Non Spanish/Hispanic


title: hESC.conventional_wa07_rep30_450k


title: lung_K436

value: UNKNOWN


title: hESC.conventional_wa09_rep36_450k


title: hESC.conventional_sivf050_rep26_450k


title: hESC.conventional_wa09_rep39_450k


title: hESC.conventional_wa07_rep27_450k


title: hESC.conventional_wa09_rep35_450k


title: itcc0611

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix, Santa Clara, CA)

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: Neuroblastoma tumor

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

value: tissue:Neuroblastoma tumor

tag: myn amp

value: no

tag: inss-stage


title: lung_K214

value: Ever


title: lung_K369


title: lung_K348

value: Dead


title: hESC.conventional_wa09_rep43_450k


title: hESC.conventional_sivf024_rep23_450k


title: itcc0607


title: hESC.conventional_sivf043_rep25_450k


title: hESC.conventional_wa07_rep28_450k


title: hESC.conventional_shhes2_rep21_450k


title: hESC.conventional_miz6_rep20_450k


title: hESC.conventional_lis25.fap_rep16_450k


title: hESC.conventional_sivf002_rep22_450k


title: itcc0602


title: itcc0608


title: lung_K341

value: WT

value: SpliceSite


title: lung_K209

value: F

value: Alive


title: lung_K273


title: itcc0604

value: yes


title: itcc0601


title: hESC.conventional_sivf025_rep24_450k


title: lung_K223


title: lung_K252

value: M


title: itcc0600


title: itcc0596


title: itcc0609


title: lung_K385


title: lung_K274

value: Mut


title: hESC.conventional_lis12.dm1_rep14_450k


title: itcc0595


title: hESC.conventional_lis25.fap_rep17_450k


title: lung_K315


title: lung_K184


title: lung_K150


title: hESC.conventional_mel1_rep18_450k


title: itcc0593


title: itcc0592


title: itcc0594


title: hESC.conventional_lis04.twist1_rep13_450k


title: hESC.conventional_hes2_rep9_450k


title: lung_K023


title: hESC.conventional_hues9_rep11_450k


title: itcc0591


title: lung_K017


title: hESC.conventional_fes22_rep8_450k


title: hESC.conventional_lis12.dm1_rep15_450k


title: hESC.conventional_hes4_rep10_450k


title: hESC.conventional_cyt49_rep3_450k


title: itcc0558


title: hESC.conventional_cyt49_rep7_450k


title: itcc0589


title: hESC.conventional_mel4_rep19_450k


title: hESC.conventional_cm6_rep1_450k


title: hESC.blastomere_ucsfb7_rep3_450k


title: hESC.conventional_cyt49_rep4_450k


title: hESC.conventional_cyt49_rep6_450k


title: itcc0557


title: lung_K318


title: itcc0590


title: itcc0555


title: hESC.conventional_csc14_rep2_450k


title: lung_K251


title: hESC.conventional_cyt49_rep5_450k


title: itcc0588


title: itcc0556


title: hESC.blastomere_ucsfb6_rep2_450k


title: lung_K353


title: lung_K386


title: itcc0552


title: itcc0551


title: itcc0550


title: lung_K197


title: lung_K037


title: hESC.conventional_lis04.twist1_rep12_450k


title: itcc0549


title: hESC.blastomere_ucsfb5_rep1_450k


title: lung_K111


title: lung_K105


title: lung_K096

value: Missing


title: lung_K370


title: itcc0546


title: lung_K336


title: itcc0542


title: itcc0545


title: itcc0538


title: itcc0536


title: lung_K357


title: lung_K250

value: BLACK

value: Never


title: itcc0537


title: itcc0533


title: lung_K075

value: WHITE


title: lung_K164

value: Non Spanish/Hispanic


title: lung_K115


title: lung_K100


title: itcc0541


title: lung_K452


title: lung_K312


title: hESC.conventional_wa09_rep224_HT12v3

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v3 Expression BeadChips (Illumina, Inc.).

data_processing: In GenomeStudio, probes were filtered for those detected at p<0.01 in at least 1 sample and exported for normalization in R using robust spline normalization (RSN).

label_protocol: 200 ng RNA per sample was amplified using the Total PrepTM RNA Amplification Kit (Illumina, Inc.) according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted from snap-frozen sample pellets (Ambion mirVana Kit, Life Technologies, Inc.) according to the manufacturer’s protocol. RNA quantity (QubitTM RNA BR Assay Kits, Life Technologies, Inc.) and quality (RNA6000 Nano Kit and Bioanalyzer 2100, Agilent) was determined to be optimal for each sample prior to further processing.


title: hESC.conventional_wa09_rep227_HT12v3


title: lung_K410


title: lung_K009


title: hESC.conventional_wa09_rep228_HT12v3


title: itcc0544


title: hESC.conventional_wa09_rep223_HT12v3


title: hESC.conventional_wa09_rep226_HT12v3


title: lung_K424


title: lung_K165


title: hESC.conventional_wa09_rep225_HT12v3


title: lung_K052


title: lung_K280


title: lung_K335


title: lung_K208


title: hESC.conventional_wa09_rep218_HT12v3


title: hESC.conventional_wa09_rep219_HT12v3


title: lung_K292


title: hESC.conventional_wa09_rep222_HT12v3


title: lung_K429


title: hESC.conventional_wa09_rep216_HT12v3


title: hESC.conventional_wa09_rep217_HT12v3


title: hESC.conventional_wa09_rep221_HT12v3


title: lung_K383


title: hESC.conventional_wa09_rep213_HT12v3


title: hESC.conventional_wa09_rep215_HT12v3


title: hESC.conventional_wa09_rep220_HT12v3


title: lung_K057


title: lung_K278


title: lung_K138


title: lung_K055


title: hESC.conventional_wa09_rep211_HT12v3


title: hESC.conventional_wa09_rep214_HT12v3


title: hESC.conventional_wa09_rep209_HT12v3


title: hESC.conventional_wa09_rep212_HT12v3


title: lung_K126


title: lung_K169


title: lung_K167


title: lung_K098


title: hESC.conventional_wa09_rep208_HT12v3


title: lung_K177


title: lung_K377


title: lung_K384


title: hESC.conventional_wa09_rep207_HT12v3


title: lung_K407


title: hESC.conventional_wa09_rep205_HT12v3


title: lung_K222


title: lung_K201


title: hESC.conventional_wa07_rep201_HT12v3


title: hESC.conventional_wa09_rep206_HT12v3


title: hESC.conventional_wa07_rep204_HT12v3


title: lung_K029


title: lung_K019


title: lung_K261


title: hESC.conventional_wa07_rep198_HT12v3


title: lung_K161


title: lung_K124


title: hESC.conventional_wa07_rep202_HT12v3


title: hESC.conventional_wa07_rep200_HT12v3


title: hESC.conventional_wa07_rep197_HT12v3


title: lung_K437


title: hESC.conventional_wa07_rep199_HT12v3


title: lung_K046


title: Flag leaves of line 51 Replicate 2

city: Beijing

first: Congming

last: Lu

state: Beijing

address: Haidian Xiangshan Nanxincun 20#

department: The Key Laboratory of Photobiology, CAS

institute: Institute of Botany, CAS

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression Microarray（4x44K） for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Oryza sativa

source_name: Transgenic Line 51 Flag Leaves

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The wild-type rice (Oryza sativa L.) was the japonica variety, Zhonghua 11. The wild-type and transgenic plants were grown in a field station in Beijing, China, from May through October, 2012.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

tag: genotype/variation

value: line 51 (transgenic)

value: flag leaves

tag: development stage

value: 10th day after fertilization


title: Flag leaves of line 51 Replicate 3


title: hESC.conventional_wa01_rep196_HT12v3


title: Flag leaves of WT Replicate 3

source_name: Zhonghua 11 Flag Leaves

value: Zhonghua 11 (wild type)


title: Flag leaves of line 51 Replicate 1


title: lung_K178

value: Ever


title: lung_K157

value: Dead

value: WT


title: lung_K016

value: F


title: Flag leaves of WT Replicate 2


title: hESC.conventional_wa01_rep194_HT12v3


title: hESC.conventional_wa01_rep195_HT12v3


title: lung_K183


title: hESC.conventional_wa07_rep203_HT12v3


title: hESC.conventional_wa01_rep193_HT12v3


title: hESC.conventional_wa01_rep192_HT12v3


title: Developing seeds of line 51 Replicate 3

source_name: Transgenic Line 51 Developing seeds

value: developing seeds


title: lung_K414

value: Spanish/Hispanic

value: Alive


title: lung_K182

value: Mut


title: lung_K003

value: Missing


title: lung_K418

value: M


title: hESC.conventional_uc06_rep191_HT12v3


title: lung_K445


title: Developing seeds of WT Replicate 3

source_name: Zhonghua 11 Developing seeds


title: lung_K088


title: hESC.conventional_uc06_rep190_HT12v3


title: lung_K268


title: hESC.conventional_uc06_rep189_HT12v3


title: Developing seeds of line 51 Replicate 2


title: Developing seeds of WT Replicate 2


title: Developing seeds of line 51 Replicate 1


title: mcc-negctrl-rep2

city: Toronto

first: Victor

last: Tron

state: ON

address: 30 Bond St.,Rm 2-040b CC Wing

department: Laboratory Medicine and Pathobiology

country: Canada

institute: St. Michael's Hospital, University of Toronto

description: Negative control in MCC26 cell line (replicate 2)

hyb_protocol: cRNA was subsequently fragmented at 60°C for 30 minutes and hybridized to Agilent Human 4X44K whole genome microarrays in a rotating oven at 65°C for 17 hours

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-105-Dec08 and Grid: 014850_D-F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Merkel carcinoma from human skin

label_protocol: For each sample, 500 ng total RNA was mixed with the Agilent One-Color Spike-in RNA control, with the resulting mixture amplified and labeled using the Agilent One color, Quick Amp Labeling kit to generate Cy3-labelled cRNA

growth_protocol: MCC26 were grown in RPMI medium 1640 (Hyclone, Logan, UT) supplemented with 15% fetal bovine serum (Hyclone) at 37°C in a humidified atmosphere with 5% CO2

extract_protocol: Total RNA from MCC26 cells was isolated 72 hours post-transfection using the miRNeasy Mini kit (Qiagen).

treatment_protocol: Cells were transfected for 72 hours with mirVana miR-375 or neg cntrl miRNA mimics using lipofectamine 2000.

tag: cell line

tag: transfection

value: negative control

value: Skin


title: Developing seeds of WT Replicate 1


title: hESC.conventional_wa09_rep210_HT12v3


title: hESC.conventional_uc06_rep185_HT12v3


title: mcc-negctrl-rep1

description: Negative control in MCC26 cell line (replicate 1)


title: hESC.conventional_uc06_rep187_HT12v3


title: hESC.conventional_uc06_rep186_HT12v3


title: hESC.conventional_uc06_rep188_HT12v3


title: Flag leaves of WT Replicate 1


title: lung_K058

value: WHITE

value: Non Spanish/Hispanic


title: lung_K159

value: Never


title: mcc-mir375overexp-rep1

description: Overexpressed miR375 in MCC26 cell line (replicate 1)


title: lung_K363


title: hESC.conventional_uc06_rep184_HT12v3


title: lung_K298


title: mcc-mir375overexp-rep2

description: Overexpressed miR375 in MCC26 cell line (replicate 2)


title: hESC.conventional_uc06_rep183_HT12v3


title: lung_K321


title: hESC.conventional_uc06_rep182_HT12v3


title: hESC.conventional_sivf048_rep178_HT12v3


title: hESC.conventional_wa09_rep79_HT12v4

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.).


title: lung_K238


title: lung_K368


title: hESC.conventional_sivf043_rep174_HT12v3


title: lung_K303


title: hESC.conventional_wa09_rep75_HT12v4


title: lung_K154


title: lung_K170


title: hESC.conventional_sivf047_rep177_HT12v3


title: hESC.conventional_sivf049_rep179_HT12v3


title: hESC.conventional_wa09_rep76_HT12v4


title: hESC.conventional_wa09_rep81_HT12v4


title: hESC.conventional_sivf050_rep180_HT12v3


title: hESC.conventional_sivf045_rep175_HT12v3


title: hESC.conventional_wa09_rep82_HT12v4


title: lung_K398

value: BLACK


title: hESC.conventional_wa09_rep78_HT12v4


title: lung_K221


title: hESC.conventional_wa09_rep80_HT12v4


title: hESC.conventional_sivf046_rep176_HT12v3


title: hESC.conventional_wa09_rep77_HT12v4


title: hESC.conventional_wa09_rep73_HT12v4


title: lung_K039


title: hESC.conventional_uc06_rep181_HT12v3


title: hESC.conventional_wa09_rep74_HT12v4


title: hESC.conventional_sivf043_rep173_HT12v3


title: lung_K242


title: hESC.conventional_sivf029_rep169_HT12v3


title: hESC.conventional_wa09_rep72_HT12v4


title: hESC.conventional_wa09_rep70_HT12v4


title: lung_K140

value: THAI


title: hESC.conventional_wa09_rep71_HT12v4


title: lung_K099

value: Ever


title: lung_K281


title: hESC.conventional_sivf042_rep172_HT12v3


title: hESC.conventional_wa09_rep67_HT12v4


title: hESC.conventional_sivf041_rep171_HT12v3


title: hESC.conventional_sivf025_rep165_HT12v3


title: lung_K109


title: hESC.conventional_sivf028_rep168_HT12v3


title: lung_K441


title: lung_K309


title: hESC.conventional_sivf027_rep167_HT12v3


title: hESC.conventional_sivf026_rep166_HT12v3


title: lung_K351


title: hESC.conventional_wa09_rep69_HT12v4


title: hESC.conventional_wa09_rep68_HT12v4


title: hESC.conventional_wa09_rep65_HT12v4


title: hESC.conventional_sivf025_rep164_HT12v3


title: lung_K025


title: hESC.conventional_wa09_rep64_HT12v4


title: hESC.conventional_wa09_rep63_HT12v4


title: lung_K010

value: Dead


title: hESC.conventional_wa09_rep62_HT12v4


title: hESC.conventional_wa09_rep66_HT12v4


title: lung_K143

value: WT


title: lung_K235

value: F


title: hESC.conventional_sivf023_rep161_HT12v3


title: hESC.conventional_sivf024_rep162_HT12v3


title: hESC.conventional_sivf024_rep163_HT12v3


title: hESC.conventional_wa09_rep59_HT12v4


title: hESC.conventional_wa09_rep60_HT12v4


title: lung_K243


title: hESC.conventional_wa09_rep61_HT12v4


title: hESC.conventional_sivf023_rep159_HT12v3


title: lung_K123


title: lung_K253


title: hESC.conventional_sivf023_rep160_HT12v3


title: hESC.conventional_sivf022_rep157_HT12v3


title: hESC.conventional_wa09_rep58_HT12v4


title: lung_K045


title: hESC.conventional_sivf022_rep156_HT12v3


title: hESC.conventional_wa09_rep55_HT12v4