title: Sample603_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample610_Schizo

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

value: F

tag: race

value: AA

tag: group

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: 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)

value: TRUE

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)

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: Sample609_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)

value: M

value: CAUC

value: Control


title: Sample607_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample604_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample593_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample591_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample589_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)


title: Sample600_Schizo

description: Human DLPFC DNA methylation sample

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: Sample587_Schizo

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: Sample601_Schizo

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: Sample594_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample595_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample588_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample582_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample592_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample590_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: Sample579_Schizo

description: Human DLPFC DNA methylation sample

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: Sample577_Schizo

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: Sample581_Schizo

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: Sample578_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample568_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample580_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample566_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample567_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample575_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)


title: Sample586_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)

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


title: Sample573_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: Sample572_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: Sample584_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample576_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample565_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample563_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample570_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample574_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)


title: Sample583_Schizo

description: Human DLPFC DNA methylation sample

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: Sample559_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: Sample569_Schizo

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: Sample558_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample571_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample554_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample585_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample552_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample564_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: Sample553_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)

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


title: Sample551_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: Sample545_Schizo

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: Sample549_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample561_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample544_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample547_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: FXRKO-PCLS DMSO 5

status: Public on Oct 22 2015

type: RNA

city: Wageningen

first: Ewa

last: Szalowska

address: Akkermaalsbos 2

country: Netherlands

institute: RIKILT-Wageningen UR

description: Gene expression data from precision cut liver slices prepared from livers of FXR knockout mice treated with DMSO for 24h.

hyb_protocol: Per sample, 7.5ug cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 ug /ul on the Affymetrix HT Mouse genome 430 PM array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, USA) using the Affymetrix HWS kit for Gene Titan, absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software.

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software. The data Quality Control was performed in the program Affymetrix Expression Console v 1.1 (Affymetrix, Santa Clara, CA, USA) software to determine if all parameters were within quality specifications. The Probe Logarithmic Intensity Error Estimation (PLIER) algorithm method was used for probe summarisation. Non-normalized data in a form of the Cell Intensity File (*.CEL) were re-annotated (mogene11st_Mm_ENTREZG) and the data were RMA normalized.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotin- labelled cRNA was generated from high-quality total RNA with the Affymetrix 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng total RNA.

growth_protocol: 12-weeks old male C57BL/6 mice and 12-weeks old FXRKO mice on a C57BL/6 mice background were bred at the animal facility of University Medical Centre Groningen (UMCG), the Netherlands. After arrival to the animal facility of Wageningen University, animals were kept for 2 weeks at a housing temperature of 22°C and at a relative humidity of 30–70%. The lighting cycle was 12-h light and 12-h dark. At the age of 24 weeks animals were sacrificed by an overdose of isoflurane. The treatment protocol was approved by the Ethical Committee for Animal Experiments of Wageningen University.  Immediately after the animals were killed, the liver was perfused with PBS and placed in ice-cold Krebs–Henseleit buffer (KHB) (pH 7.4, supplemented with 11 mM glucose). Liver tissue was transported to the laboratory within approximately 30 min and cylindrical liver cores were produced using a surgical biopsy punch with diameter of 5 mm (KAI, SynErgo Europe, Romania). Liver cores were placed in a Krumdieck tissue slicer (Alabama Research and Development, Munford, AL, USA) filled with ice-cold KHB aerated with carbogen and supplemented with 11 mM glucose. Slices with a diameter of 5 mm, a thickness of 0.2 mm and a weight of approximately 6 mg were prepared. Immediately after preparation, slices were transferred into culture plates filled with pre-warmed (37⁰C) WEM supplemented with pen/strep. Three liver slices were pre-cultured in one well of the 6-well plate filled with 4 ml of WEM for one hour with continuous agitation (70 rpm). Incubations were performed in an oxygen controlled incubator (Galaxy 48 R, New Brunswick, Nijmegen, the Netherlands) at 80% of oxygen, 5% CO2, and the remaining gas volume was filled up to 95% with N2. After one hour of pre-incubation, media were removed and replaced with fresh media containing test compounds or appropriate solvents. After incubations, samples were snap-frozen in liquid nitrogen and stored in -80 °C for further analysis.

extract_protocol: RNA was extracted from three slices using the RNeasy Tissue Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Precision cut liver slices (PCLS) obtained from livers of wild type (WT) and farnesoid X receptor knockout (FXRKO) mice were exposed for 24 hours to 40uM of CyclosporinA (CsA).

tag: background strain

tag: genotype/variation

value: FXR knockout


title: Sample541_Schizo

description: Human DLPFC DNA methylation sample

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)


title: Sample539_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)

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: Sample550_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)

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: Sample556_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

tag: race

tag: group


title: Sample560_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample542_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample562_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)


title: Sample543_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)

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


title: Sample537_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: Sample555_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample548_Schizo

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: Sample546_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample540_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample557_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample538_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample536_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)


title: Sample533_Schizo

description: Human DLPFC DNA methylation sample

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: Sample532_Schizo

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: Sample531_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample529_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: Sample535_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample526_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample524_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample525_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample519_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: Sample521_Schizo

description: Human DLPFC DNA methylation sample

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: Sample516_Schizo

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: Sample514_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample517_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: Sample513_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample527_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample515_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample512_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample523_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)


title: Sample534_Schizo

description: Human DLPFC DNA methylation sample

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: Sample507_Schizo

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: Sample518_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample511_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: Sample520_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample528_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample506_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample508_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample509_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: Sample505_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)

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


title: Sample501_Schizo

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: Sample522_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample499_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: Sample496_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample494_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample510_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample502_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample504_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: Sample503_Schizo

description: Human DLPFC DNA methylation sample

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: Sample491_Schizo

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: Sample489_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample483_Schizo

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: Sample497_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample495_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample485_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample481_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample482_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)


title: Sample480_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)

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


title: Sample490_Schizo

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: Sample498_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample639_Schizo

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: Sample477_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample492_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample488_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample487_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample493_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)


title: Sample476_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)

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


title: Sample484_Schizo

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: Sample473_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample472_Schizo

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: Sample500_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample478_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample475_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample467_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample474_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: Sample479_Schizo

description: Human DLPFC DNA methylation sample

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: Sample463_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: Sample530_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample461_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: Sample486_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample468_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample458_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample460_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample470_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: Sample471_Schizo

description: Human DLPFC DNA methylation sample

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: Sample456_Schizo

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: Sample452_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample462_Schizo

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: Sample464_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample457_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample451_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample453_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample466_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: Sample459_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)

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


title: Sample450_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: Sample455_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample454_Schizo

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: Sample445_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample438_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample436_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample447_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample446_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)


title: Sample469_Schizo

description: Human DLPFC DNA methylation sample

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: Sample449_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: Sample448_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample465_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: Sample444_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample432_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample430_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample443_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample442_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)


title: Sample431_Schizo

description: Human DLPFC DNA methylation sample

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: Sample441_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: Sample435_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample429_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: Sample428_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample426_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample422_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample423_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample439_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)


title: Sample421_Schizo

description: Human DLPFC DNA methylation sample

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: Sample434_Schizo

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: Sample437_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample420_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: Sample440_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample433_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample418_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample419_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample425_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: Sample414_Schizo

description: Human DLPFC DNA methylation sample

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: Sample424_Schizo

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: Sample408_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample427_Schizo

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: Sample407_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample409_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample415_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample416_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample406_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: Sample417_Schizo

description: Human DLPFC DNA methylation sample

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: Sample403_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: Sample413_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample412_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: Sample393_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample396_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample402_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample395_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample399_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)


title: Sample398_Schizo

description: Human DLPFC DNA methylation sample

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: Sample400_Schizo

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: Sample404_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample392_Schizo

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: Sample394_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample410_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample391_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample389_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample401_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: Sample390_Schizo

description: Human DLPFC DNA methylation sample

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: Sample411_Schizo

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: Sample397_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample405_Schizo

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: Sample388_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: Sample385_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample384_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample386_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample383_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)


title: Sample381_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)

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


title: Sample379_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: Sample387_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample378_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: Sample382_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)


title: atypical adenomatous hyperplasia_9

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,9

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.

tag: gender

value: female


title: adenocarcinoma_9

source_name: lung adenocarcinoma tissue,9


title: adenocarcinoma_94

source_name: lung adenocarcinoma tissue,94

value: male


title: adenocarcinoma_91

source_name: lung adenocarcinoma tissue,91


title: squamous cell carcinoma_89

source_name: lung squamous cell carcinoma tissue,89


title: adenocarcinoma_86

source_name: lung adenocarcinoma tissue,86


title: small cell lung carcinoma_96

source_name: small cell lung carcinoma tissue,96


title: small cell lung carcinoma_95

source_name: small cell lung carcinoma tissue,95


title: squamous cell carcinoma_90

source_name: lung squamous cell carcinoma tissue,90


title: small cell lung carcinoma_97

source_name: small cell lung carcinoma tissue,97


title: normal_9

source_name: lung adjacent normal tissue,9


title: adenocarcinoma_93

source_name: lung adenocarcinoma tissue,93


title: bronchioloalveolar carcinoma_92

source_name: lung bronchioloalveolar carcinoma tissue,92


title: squamous cell carcinoma_82

source_name: lung squamous cell carcinoma tissue,82


title: small cell lung carcinoma_85

source_name: small cell lung carcinoma tissue,85


title: squamous cell carcinoma_88

source_name: lung squamous cell carcinoma tissue,88


title: Sample377_Schizo

description: Human DLPFC DNA methylation sample

source_name: DLPFC

tag: race

tag: group

tag: age (in years)


title: squamous cell carcinoma_83

source_name: lung squamous cell carcinoma tissue,83


title: squamous cell carcinoma_84

source_name: lung squamous cell carcinoma tissue,84


title: Sample380_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)


title: squamous cell carcinoma_80

source_name: lung squamous cell carcinoma tissue,80


title: squamous cell carcinoma_81

source_name: lung squamous cell carcinoma tissue,81


title: Sample373_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)


title: squamous cell carcinoma_79

source_name: lung squamous cell carcinoma tissue,79


title: Sample374_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)

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


title: Sample372_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)

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


title: Sample367_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: plate (processing plate)

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


title: Sample369_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group


title: Sample371_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: Sample376_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample375_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)


title: Sample368_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)

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


title: Sample364_Schizo

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: Sample365_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)


title: Sample370_Schizo

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: small cell lung carcinoma_77

source_name: small cell lung carcinoma tissue,77

tag: gender


title: small cell lung carcinoma_76

source_name: small cell lung carcinoma tissue,76


title: Sample366_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

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


title: small cell lung carcinoma_75

source_name: small cell lung carcinoma tissue,75


title: Sample361_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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


title: bronchioloalveolar carcinoma_70

source_name: lung bronchioloalveolar carcinoma tissue,70


title: small cell lung carcinoma_71

source_name: small cell lung carcinoma tissue,71


title: Sample362_Schizo

description: Human DLPFC DNA methylation sample

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: Sample363_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: small cell lung carcinoma_73

source_name: small cell lung carcinoma tissue,73


title: Sample360_Schizo

description: Human DLPFC DNA methylation sample

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

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

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


title: adenocarcinoma_69

source_name: lung adenocarcinoma tissue,69


title: bronchioloalveolar carcinoma_6

source_name: lung bronchioloalveolar carcinoma tissue,6


title: normal_70

source_name: lung adjacent normal tissue,70


title: adenocarcinoma_74

source_name: lung adenocarcinoma tissue,74


title: squamous cell carcinoma_78

source_name: lung squamous cell carcinoma tissue,78


title: Sample359_Control

description: Human DLPFC DNA methylation sample

source_name: DLPFC

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)

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


title: Sample358_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race


title: Sample356_Control

description: Human DLPFC DNA methylation sample

tag: group

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


title: Sample354_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: small cell lung carcinoma_67

source_name: small cell lung carcinoma tissue,67

tag: gender


title: normal_69

source_name: lung adjacent normal tissue,69


title: squamous cell carcinoma_68

source_name: lung squamous cell carcinoma tissue,68


title: normal_68

source_name: lung adjacent normal tissue,68


title: Sample357_Schizo

description: Human DLPFC DNA methylation sample

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: Sample355_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: small cell lung carcinoma_65

source_name: small cell lung carcinoma tissue,65


title: squamous cell carcinoma_64

source_name: lung squamous cell carcinoma tissue,64


title: squamous cell carcinoma_66

source_name: lung squamous cell carcinoma tissue,66


title: normal_66

source_name: lung adjacent normal tissue,66


title: Sample351_Control

description: Human DLPFC DNA methylation sample

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

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

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


title: Sample350_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)

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


title: Sample352_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

tag: group


title: adenocarcinoma_61

source_name: lung adenocarcinoma tissue,61


title: normal_64

source_name: lung adjacent normal tissue,64


title: Sample347_Schizo

description: Human DLPFC DNA methylation sample

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: Sample348_Control

description: Human DLPFC DNA methylation sample

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

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


title: normal_61

source_name: lung adjacent normal tissue,61

tag: gender


title: squamous cell carcinoma_59

source_name: lung squamous cell carcinoma tissue,59


title: normal_5

source_name: lung adjacent normal tissue,5


title: adenocarcinoma_5

source_name: lung adenocarcinoma tissue,5


title: Sample346_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: normal_60

source_name: lung adjacent normal tissue,60


title: normal_59

source_name: lung adjacent normal tissue,59


title: Sample353_Schizo

description: Human DLPFC DNA methylation sample

source_name: DLPFC

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

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

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


title: Sample345_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)

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


title: Sample342_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

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


title: Sample344_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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


title: Sample349_Control

description: Human DLPFC DNA methylation sample

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: Sample341_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: Sample343_Schizo

description: Human DLPFC DNA methylation sample

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

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


title: Sample340_Schizo

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: Sample339_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)


title: squamous cell carcinoma_58

source_name: lung squamous cell carcinoma tissue,58

tag: gender


title: squamous cell carcinoma_60

source_name: lung squamous cell carcinoma tissue,60


title: Sample337_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

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


title: Sample335_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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


title: normal_57

source_name: lung adjacent normal tissue,57


title: Sample338_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)


title: squamous cell carcinoma_57

source_name: lung squamous cell carcinoma tissue,57


title: normal_56

source_name: lung adjacent normal tissue,56


title: Sample331_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: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample330_Schizo

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality 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: squamous cell carcinoma_56

source_name: lung squamous cell carcinoma tissue,56


title: squamous cell carcinoma_55

source_name: lung squamous cell carcinoma tissue,55


title: Sample329_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)

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


title: Sample332_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race


title: Sample333_Control

description: Human DLPFC DNA methylation sample

tag: group

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


title: Sample328_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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


title: adenocarcinoma_53

source_name: lung adenocarcinoma tissue,53

tag: gender


title: normal_52

source_name: lung adjacent normal tissue,52


title: small cell lung carcinoma_52

source_name: small cell lung carcinoma tissue,52


title: Sample327_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)


title: Sample336_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: comp_neun_neg(composition estimates for adult cortex-derived non-neuronal cells)


title: Sample334_Control

description: Human DLPFC DNA methylation sample

tag: dropsample (whether to remove the sample for failing quality 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: Sample325_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: sex (clinical gender)

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


title: adenocarcinoma_51

source_name: lung adenocarcinoma tissue,51


title: Sample324_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

tag: group


title: Sample323_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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: Sample321_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: Sample322_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: normal_51

source_name: lung adjacent normal tissue,51

tag: gender


title: Sample318_Control

description: Human DLPFC DNA methylation sample

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

tag: predictedsex (sex predicted by sex chromosome probes)

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


title: Sample317_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: adenocarcinoma_50

source_name: lung adenocarcinoma tissue,50


title: Sample316_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: sex (clinical gender)

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


title: Sample319_Schizo

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: age (in years)


title: Sample313_Control

description: Human DLPFC DNA methylation sample

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

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: Sample314_Control

description: Human DLPFC DNA methylation sample

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: normal_50

source_name: lung adjacent normal tissue,50

tag: gender


title: Sample312_Control

description: Human DLPFC DNA methylation sample

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

tag: predictedsex (sex predicted by sex chromosome probes)

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


title: bronchioloalveolar carcinoma_4

source_name: lung bronchioloalveolar carcinoma tissue,4


title: Sample326_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: Sample320_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: sex (clinical gender)

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


title: Sample311_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

tag: age (in years)


title: adenocarcinoma_47

source_name: lung adenocarcinoma tissue,47


title: adenocarcinoma_48

source_name: lung adenocarcinoma tissue,48


title: normal_49

source_name: lung adjacent normal tissue,49


title: Sample309_Schizo

description: Human DLPFC DNA methylation sample

source_name: DLPFC

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

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: Sample308_Schizo

description: Human DLPFC DNA methylation sample

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: Sample315_Schizo

description: Human DLPFC DNA methylation sample

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

tag: predictedsex (sex predicted by sex chromosome probes)


title: adenocarcinoma_49

source_name: lung adenocarcinoma tissue,49

tag: gender


title: Sample310_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: Sample307_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: sex (clinical gender)

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


title: Sample306_Control

description: Human DLPFC DNA methylation sample

tag: race

tag: group

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


title: Sample305_Schizo

description: Human DLPFC DNA methylation sample

tag: age (in years)

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

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


title: Sample304_Control

description: Human DLPFC DNA methylation sample

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

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

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


title: adenocarcinoma_46

source_name: lung adenocarcinoma tissue,46


title: normal_47

source_name: lung adjacent normal tissue,47


title: Sample303_Schizo

description: Human DLPFC DNA methylation sample

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

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

tag: predictedsex (sex predicted by sex chromosome probes)


title: normal_45

source_name: lung adjacent normal tissue,45

tag: gender


title: Sample301_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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_K265

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

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.

value: WHITE

value: Non Spanish/Hispanic

value: Missing

value: Dead

tag: Stage

value: Mut

value: WT


title: lung_K419

tag: race


title: lung_K207

value: Ever


title: lung_K461

value: Alive


title: Sample299_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

value: FALSE

tag: sex (clinical gender)

value: AA

tag: group

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


title: Sample297_Control

description: Human DLPFC DNA methylation sample

tag: age (in years)

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

value: TRUE

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

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


title: Sample300_Control

description: Human DLPFC DNA methylation sample

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

value: M

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

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

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


title: adenocarcinoma_44

source_name: lung adenocarcinoma tissue,44

tag: gender


title: Sample296_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

value: F

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: Sample298_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

tag: race

value: Schizo

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


title: lung_K311

tag: Stage


title: Sample302_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: group

value: Control

tag: age (in years)

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


title: normal_44

source_name: lung adjacent normal tissue,44

value: female


title: Sample293_Schizo

description: Human DLPFC DNA methylation sample

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

tag: negativecontrolpc1 (negative control principal component 1 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: lung_K103

tag: gender


title: lung_K230


title: lung_K153


title: Sample295_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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

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

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


title: lung_K448


title: squamous cell carcinoma_43

source_name: lung squamous cell carcinoma tissue,43

value: male


title: lung_K355

value: WHITE


title: bronchioloalveolar carcinoma_45

source_name: lung bronchioloalveolar carcinoma tissue,45


title: normal_43

source_name: lung adjacent normal tissue,43


title: Sample292_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

value: CAUC

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: Sample290_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

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


title: Sample294_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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


title: Sample288_Schizo

description: Human DLPFC DNA methylation sample

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

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

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


title: lung_K271

tag: gender

tag: Stage


title: lung_K360

value: Non Spanish/Hispanic


title: small cell lung carcinoma_41b

source_name: small cell lung carcinoma tissue,41b


title: Sample287_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: small cell lung carcinoma_41

source_name: small cell lung carcinoma tissue,41


title: small cell lung carcinoma_40

source_name: small cell lung carcinoma tissue,40


title: Sample286_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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: Sample291_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

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: Sample284_Control

description: Human DLPFC DNA methylation sample

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

tag: group

tag: age (in years)

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


title: Sample283_Control

description: Human DLPFC DNA methylation sample

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

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


title: lung_K340

tag: gender

tag: Stage


title: Sample282_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: lung_K434

value: Dead


title: lung_K044

value: Missing

value: Mut


title: Sample281_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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: squamous cell carcinoma_3

source_name: lung squamous cell carcinoma tissue,3


title: normal_40

source_name: lung adjacent normal tissue,40


title: lung_K198

tag: race

value: Ever

value: WT


title: Sample289_Control

description: Human DLPFC DNA methylation sample

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

value: FALSE

tag: sex (clinical gender)

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: Sample279_Control

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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

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


title: Sample278_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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


title: normal_3

source_name: lung adjacent normal tissue,3

tag: gender


title: Sample277_Schizo

description: Human DLPFC DNA methylation sample

source_name: DLPFC

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: Sample285_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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

tag: predictedsex (sex predicted by sex chromosome probes)


title: small cell lung carcinoma_39

source_name: small cell lung carcinoma tissue,39


title: lung_K116

tag: race

value: Alive

tag: Stage


title: Sample275_Control

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)

value: AA

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

value: TRUE

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


title: lung_K051

value: F


title: small cell lung carcinoma_38

source_name: small cell lung carcinoma tissue,38


title: normal_39

source_name: lung adjacent normal tissue,39


title: lung_K259


title: Sample273_Control

description: Human DLPFC DNA methylation sample

value: M

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: Sample272_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

value: Control

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

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


title: Sample274_Schizo

description: Human DLPFC DNA methylation sample

value: Schizo

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: Sample271_Schizo

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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

tag: predictedsex (sex predicted by sex chromosome probes)


title: lung_K332

tag: gender

tag: race

tag: Stage


title: lung_K286


title: lung_K263


title: lung_K283


title: Sample269_Schizo

description: Human DLPFC DNA methylation sample

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

tag: sex (clinical gender)

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

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


title: Sample270_Control

description: Human DLPFC DNA methylation sample

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: squamous cell carcinoma_37

source_name: lung squamous cell carcinoma tissue,37

value: male


title: Sample268_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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: Sample276_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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: squamous cell carcinoma_36

source_name: lung squamous cell carcinoma tissue,36

tag: gender


title: Sample266_Control

description: Human DLPFC DNA methylation sample

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

tag: race

tag: predictedsex (sex predicted by sex chromosome probes)


title: Sample264_Schizo

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

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

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


title: Sample265_Schizo

description: Human DLPFC DNA methylation sample

tag: group

tag: age (in years)

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


title: Sample263_Schizo

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

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

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


title: normal_35

source_name: lung adjacent normal tissue,35


title: Sample262_Schizo

description: Human DLPFC DNA methylation sample

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: lung_K443

source_name: lung adenocarcinoma

value: WHITE

tag: Stage


title: squamous cell carcinoma_34

source_name: lung squamous cell carcinoma tissue,34

tag: gender


title: normal_34

source_name: lung adjacent normal tissue,34


title: squamous cell carcinoma_35

source_name: lung squamous cell carcinoma tissue,35


title: squamous cell carcinoma_33

source_name: lung squamous cell carcinoma tissue,33


title: Sample261_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: negativecontrolpc4 (negative control principal component 4 for batch correction)

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


title: lung_K152

tag: race


title: Sample259_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

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_pos (composition estimates for adult cortex-derived neuronal cells)


title: lung_K294


title: Sample280_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

value: CAUC

tag: group

tag: age (in years)

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


title: Sample260_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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

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

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


title: Sample267_Control

description: Human DLPFC DNA methylation sample

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

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


title: Sample258_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: lung_K408

tag: gender

tag: race

value: Non Spanish/Hispanic

tag: Stage


title: lung_K225


title: Sample256_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

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: Sample257_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: group

tag: age (in years)

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


title: normal_33

source_name: lung adjacent normal tissue,33


title: Sample254_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

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

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

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


title: squamous cell carcinoma_32

source_name: lung squamous cell carcinoma tissue,32


title: Sample253_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: squamous cell carcinoma_31

source_name: lung squamous cell carcinoma tissue,31

tag: gender


title: squamous cell carcinoma_30

source_name: lung squamous cell carcinoma tissue,30


title: Sample251_Control

description: Human DLPFC DNA methylation sample

tag: sex (clinical gender)

tag: race

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


title: normal_2

source_name: lung adjacent normal tissue,2

value: female


title: Sample250_Schizo

description: Human DLPFC DNA methylation sample

source_name: DLPFC

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_K260

tag: Stage

value: SpliceSite


title: lung_K256

value: Dead

value: Mut


title: Sample249_Control

description: Human DLPFC DNA methylation sample

tag: brnum (brain number, indicates unique subjects)

tag: group

tag: age (in years)

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


title: lung_K396

value: Ever

value: WT


title: Sample248_Control

description: Human DLPFC DNA methylation sample

tag: plate (processing plate)

value: FALSE

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

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

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