title: evglu 3

city: New York

first: Ivan

last: Gusarov

address: 450E 29th street

department: Biochemistry

institute: NYU School of Medicine

data_processing:
basecalls performed by basespace (Illumina)
reads alignment, transcripts assembly and quantification and differential expression analysis were performed using tuxedo software suite (v2.1.1). Read were aligned to known transcriptome of WS220 C.elegans genome assembly (Ensembl) using tophat with the following paramters: --b2-sensitive, --no-novel junctions.
Transcripts assembly and quantification was performed by cufflinks with default parameters.
Differential expression analysis was performed by cuffdiff with default parameters.
Genome_build: Ensembl WS220
Supplementary_files_format_and_content: gene_exp.diff, genes.fpkm_tracking

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: worms were grown on NGM seeded with E.coli OP50 at 20oC

extract_protocol:
Worms were picked, washed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Glucose was mixed in the NGM media

tag: strain

value: one day old adults

tag: media

value: NGM+ 2%Glucose


title: lung_JF1_P28_rep5

status: Public on Jul 26 2017

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
JF1_P28_5
Gene expression data from lung_JF1_P28_rep5.

hyb_protocol: According to the Affymetrix expression protocol.

scan_protocol: According to the Affymetrix expression protocol (Scanner 3000 7G).

data_processing:
Expression Console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation).
mm9 (MGSCv37) is the genome build upon which transcript assignments are based.
'Extended' is the exon group used in the analysis.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Total lung tissue from JF1/MsJ mice at postnatal day 28

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix) without rRNA depletion.

growth_protocol: Mice were housed in specific pathogen-free conditions. Food and water were available ad libitum.

extract_protocol: RNeasy Mini Kit (#74104; Qiagen, Hilden, Germany).

treatment_protocol: No treatment.

tag: strain/background

tag: tissue

value: lung

tag: developmental stage

value: postnatal day 28

tag: gender

value: female


title: lung_JF1_P70_rep1

description:
JF1_P70_1
Gene expression data from lung_JF1_P70_rep1.

source_name: Total lung tissue from JF1/MsJ mice at postnatal day 70

value: postnatal day 70


title: CH1_Adrenal_9

type: genomic

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: DNA methylation data was functional normalized. Probes were discarded if they had a low bead count (< 3), high detection P value  (> 0.01), or  a low success rate (< 95%).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Adrenal

label_protocol: According to Illumina protocol

extract_protocol: Chlorophorm/isoamyl alcohol protocol

value: Adrenal

tag: age (weeks after last menstrual period)


title: lung_JF1_P70_rep3

description:
JF1_P70_3
Gene expression data from lung_JF1_P70_rep3.


title: ev 3

type: SRA

state: NY

country: USA

library_source: transcriptomic

tag: age

value: NGM


title: U-CH1 LIF

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description: Gene expression data from monolayer U-CH1 cell line grown with 100 ng /mL LIF for 3 weeks

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software

source_name: U-CH1 cells grown under 100 ng/mL Leukemia Inhibitory Factor

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

growth_protocol: Cells were cultured in culture flasks or well plates coated with 0.1% gelatin (SIGMA-ALDRICH cat. no. G1890-100G), (IMDM/RPMI (4:1) containing 10% fetal bovine serum and 1% antibiotics)

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

treatment_protocol: 100 ng/mL human recombinant LIF in medium has been administered to cell lines except control groups for 3 weeks.

tag: cell line


title: ev 1


title: ev 2


title: CJ1_HeartV_9

source_name: HeartV

value: HeartV


title: lung_JF1_P28_rep4

description:
JF1_P28_4
Gene expression data from lung_JF1_P28_rep4.


title: lung_JF1_P28_rep3

description:
JF1_P28_3
Gene expression data from lung_JF1_P28_rep3.


title: lung_JF1_P28_rep2

description:
JF1_P28_2
Gene expression data from lung_JF1_P28_rep2.


title: CJ1_HeartA_9

source_name: HeartA

value: HeartA


title: CJ1_Placenta_9

source_name: Placenta

value: Placenta


title: lung_JF1_P28_rep1

description:
JF1_P28_1
Gene expression data from lung_JF1_P28_rep1.


title: lung_JF1_E18_rep4

description:
JF1_E18_4
Gene expression data from lung_JF1_E18_rep4.

source_name: Total lung tissue from JF1/MsJ mice at embryonic day 18

value: embryonic day 18

value: not determined


title: CJ1_Intestine_9

source_name: Intestine

value: Intestine


title: lung_JF1_E18_rep5

description:
JF1_E18_5
Gene expression data from lung_JF1_E18_rep5.


title: CJ1_Pancreas_9

source_name: Pancreas

value: Pancreas


title: lung_JF1_E18_rep1

description:
JF1_E18_1
Gene expression data from lung_JF1_E18_rep1.


title: CJ1_Tongue_9

source_name: Tongue

value: Tongue


title: lung_JF1_E18_rep2

description:
JF1_E18_2
Gene expression data from lung_JF1_E18_rep2.


title: CJ1_Stomach_9

source_name: Stomach

value: Stomach


title: lung_C3H_P70_rep4

description:
C3H_P70_4
Gene expression data from lung_C3H_P70_rep4.

source_name: Total lung tissue from C3H/HeJ mice at postnatal day 70


title: CJ1_Eye_9

source_name: Eye

value: Eye


title: lung_C3H_P28_rep4

description:
C3H_P28_4
Gene expression data from lung_C3H_P28_rep4.

source_name: Total lung tissue from C3H/HeJ mice at postnatal day 28


title: lung_C3H_P70_rep2

description:
C3H_P70_2
Gene expression data from lung_C3H_P70_rep2.


title: lung_C3H_P70_rep5

description:
C3H_P70_5
Gene expression data from lung_C3H_P70_rep5.


title: lung_C3H_P28_rep5

description:
C3H_P28_5
Gene expression data from lung_C3H_P28_rep5.


title: lung_C3H_P70_rep1

description:
C3H_P70_1
Gene expression data from lung_C3H_P70_rep1.


title: lung_C3H_P28_rep3

description:
C3H_P28_3
Gene expression data from lung_C3H_P28_rep3.


title: lung_C3H_P70_rep3

description:
C3H_P70_3
Gene expression data from lung_C3H_P70_rep3.


title: CJ1_Adrenal_9


title: CJ1_Spinalcord_9

source_name: Spinal Cord

value: Spinal Cord


title: lung_JF1_E18_rep3

description:
JF1_E18_3
Gene expression data from lung_JF1_E18_rep3.

value: lung


title: lung_C3H_E18_rep5

description:
C3H_E18_5
Gene expression data from lung_C3H_E18_rep5.

source_name: Total lung tissue from C3H/HeJ mice at embryonic day 18


title: lung_C3H_P28_rep1

description:
C3H_P28_1
Gene expression data from lung_C3H_P28_rep1.

value: postnatal day 28


title: lung_C3H_E18_rep4

description:
C3H_E18_4
Gene expression data from lung_C3H_E18_rep4.


title: lung_C3H_P28_rep2

description:
C3H_P28_2
Gene expression data from lung_C3H_P28_rep2.

value: female


title: CJ1_Amnion_9

source_name: Amnion

value: Amnion


title: CJ1_Gonad_9

source_name: Gonad

value: Gonad


title: lung_C3H_E18_rep1

description:
C3H_E18_1
Gene expression data from lung_C3H_E18_rep1.


title: lung_C3H_E18_rep3

description:
C3H_E18_3
Gene expression data from lung_C3H_E18_rep3.


title: lung_C3H_E18_rep2

description:
C3H_E18_2
Gene expression data from lung_C3H_E18_rep2.


title: Clonal 3D7 strain_3D7_clone2_6A_R

status: Public on Jul 25 2017

type: mixed

city: Singapore

first: Archana

middle: P

last: Gupta

address: 60 Nanyang Drive

department: School Of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Hybridizations were performed on the Agilent hybridization system  for 20 h

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria)

data_processing: Data was processed using Limma Package of R (Edwards, D. (2003). Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics 19, 825-833). . Briefly, lowess normalization was applied to all spots on each array followed by quantile normalization between arrays. Spots with flag >0 and median foreground intensity >1.5-fold median background intensity for either channel were included.  The normalized log2 ratio of Cy5 versus Cy3 channel was used to present the fold change.

organism: Plasmodium falciparum

source_name: RNA from 3D7 clone2 at ring stage

label_protocol: Labeling  carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.

extract_protocol: RNA extraction was carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.

treatment_protocol: P. falciparum cells were sorbitol synchronized and grown up to 10-15% parasetemia in 2% hematocrit. Wild type cells were  harvested either directly  for RNA extraction or after drug treatment. Transfected  cells were grown in media supplemented with Blasticidin

tag: Stage

value: ring

source_name: 3D7 reference pool_amplified genomic DNA

tag: control type

value: Reference pool consisting of RNA from 6 time points across 3D7 parental strain


title: Clonal 3D7 strain_3D7_clone4_2B_S

source_name: RNA from 3D7 clone4 at schizont stage

value: schizont


title: Clonal 3D7 strain_3D7_clone1_9A_R

source_name: RNA from 3D7 clone1 at ring stage


title: Clonal 3D7 strain_3D7_clone1_9A_T

source_name: RNA from 3D7 clone1 at trophozoite stage

value: trophozoite


title: Clonal 3D7 strain_3D7_clone4_2B_T

source_name: RNA from 3D7 clone4 at trophozoite stage


title: Clonal 3D7 strain_3D7_clone3_8B_R

source_name: RNA from 3D7 clone3 at ring stage


title: Clonal 3D7 strain_3D7_clone1_9A_S

source_name: RNA from 3D7 clone1 at schizont stage


title: Clonal 3D7 strain_3D7_clone4_2B_R

source_name: RNA from 3D7 clone4 at ring stage


title: Clonal 3D7 strain_3D7_clone2_6A_T

source_name: RNA from 3D7 clone2 at trophozoite stage


title: Clonal 3D7 strain_3D7_clone2_6A_S

source_name: RNA from 3D7 clone2 at schizont stage


title: Clonal 3D7 strain_3D7_clone3_8B_S

source_name: RNA from 3D7 clone3 at schizont stage


title: Wild type 3D7_TSA_6h/2h_replicate2

source_name: RNA from 6h TSA treatment and subsequent wash off for 2h at trophozoite stage_replicate 2


title: Wild type 3D7_TSA_6h/0h_replicate3

source_name: RNA from 6h TSA treatment at trophozoite stage_replicate 3


title: Wild type 3D7_TSA_6h/4h_replicate2

source_name: RNA from 6h TSA treatment and subsequent wash off for 4h at trophozoite stage_replicate 2


title: Wild type 3D7_TSA_6h/4h_replicate1

source_name: RNA from 6h TSA treatment and subsequent wash off for 4h at trophozoite stage_replicate 1


title: Clonal 3D7 strain_3D7_clone3_8B_T

source_name: RNA from 3D7 clone3 at trophozoite stage


title: Wild type 3D7_TSA_6h/0.5h_replicate1

source_name: RNA from 6h TSA treatment and subsequent wash off for 0.5h at trophozoite stage_replicate 1


title: Wild type 3D7_TSA_6h/0h_replicate2

source_name: RNA from 6h TSA treatment at trophozoite stage_replicate 2

source_name: 3D7 reference pool_amplified genomic DNA


title: Wild type 3D7_TSA_6h/2h_replicate1

source_name: RNA from 6h TSA treatment and subsequent wash off for 2h at trophozoite stage_replicate 1


title: Wild type 3D7_DMSO_6h/4h_replicate2

source_name: RNA from 6h DMSO treatment and subsequent wash off for 4h at trophozoite stage_replicate 2


title: Wild type 3D7_TSA_6h/0h_replicate1

source_name: RNA from 6h TSA treatment at trophozoite stage_replicate 1


title: Wild type 3D7_TSA_6h/0.5h_replicate2

source_name: RNA from 6h TSA treatment and subsequent wash off for 0.5h at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/0.5h_replicate2

source_name: RNA from 6h DMSO treatment and subsequent wash off for 0.5h at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/0.5h_replicate1

source_name: RNA from 6h DMSO treatment and subsequent wash off for 0.5h at trophozoite stage_replicate 1


title: Wild type 3D7_DMSO_6h/0h_replicate2

source_name: RNA from 6h DMSO treatment at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/2h_replicate1

source_name: RNA from 6h DMSO treatment and subsequent wash off for 2h at trophozoite stage_replicate 1


title: Wild type 3D7_DMSO_6h/2h_replicate2

source_name: RNA from 6h DMSO treatment and subsequent wash off for 2h at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/4h_replicate1

source_name: RNA from 6h DMSO treatment and subsequent wash off for 4h at trophozoite stage_replicate 1


title: Wild type 3D7_DMSO_6h/0h_replicate3

source_name: RNA from 6h DMSO treatment at trophozoite stage_replicate 3


title: Transfected 3D7_H4ac4R_S3_replicate3

source_name: RNA from schizont stage_replicate3 grown at blasticidin 10µg/ml

tag: transfection construct


title: Wild type 3D7_DMSO_6h/0h_replicate1

source_name: RNA from 6h DMSO treatment at trophozoite stage_replicate 1


title: evglu 2

source_name: whole body

value: one day old adults

value: NGM+ 2%Glucose


title: Transfected 3D7_H4K5R_S3_replicate3


title: Transfected 3D7_H4K5R_S2_replicate2

source_name: RNA from schizont stage_replicate2 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4ac4R_S1_replicate1

source_name: RNA from schizont stage_replicate1 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4K16R_S3_replicate3

source_name: 3D7 reference pool_amplified genomic DNA


title: Transfected 3D7_H4K16R_S2_replicate2


title: Transfected 3D7_H4ac4R_T1_replicate1

source_name: RNA from trophozoite stage_replicate1 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4K12R_S2_replicate2


title: Transfected 3D7_H4K16R_S1_replicate1


title: Transfected 3D7_H4K12R_S1_replicate1


title: Transfected 3D7_H4K5R_S1_replicate1


title: Transfected 3D7_H4K12R_S3_replicate3


title: Transfected 3D7_H4ac4R_T2_replicate2

source_name: RNA from trophozoite stage_replicate2 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4-HA_S2_replicate2


title: Transfected 3D7_H4-HA_S1_replicate1


title: Transfected 3D7_H4ac4R_S2_replicate2


title: Transfected 3D7_H4-HA_S3_replicate3


title: Transfected 3D7_H4K8R_S1_replicate1


title: Transfected 3D7_H4K8R_S3_replicate3


title: Transfected 3D7_H4K5R_T3_replicate3

source_name: RNA from trophozoite stage_replicate3 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4K12R_T1_replicate1


title: Transfected 3D7_H4K5R_T1_replicate1


title: Transfected 3D7_H4K12R_T3_replicate3


title: Transfected 3D7_H4ac4R_T3_replicate3


title: Transfected 3D7_H4K16R_T2_replicate2


title: Transfected 3D7_H4K8R_T3_replicate3


title: Transfected 3D7_H4K16R_T1_replicate1


title: Transfected 3D7_H4K12R_T2_replicate2


title: Transfected 3D7_H4K5R_T2_replicate2


title: Transfected 3D7_H4-HA_T2_replicate2


title: Transfected 3D7_H4K8R_T1_replicate1


title: Transfected 3D7_H4-HA_T1_replicate1


title: Transfected 3D7_H4ac4R_R3_replicate3

source_name: RNA from ring stage_replicate3 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4-HA_T3_replicate3


title: Transfected 3D7_H4K5R_R2_replicate2

source_name: RNA from ring stage_replicate2 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4ac4R_R2_replicate2


title: Transfected 3D7_H4K16R_R3_replicate3


title: Transfected 3D7_H4K12R_R2_replicate2


title: Transfected 3D7_H4K12R_R1_replicate1

source_name: RNA from ring stage_replicate1 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4K5R_R3_replicate3


title: Transfected 3D7_H4K8R_R3_replicate3


title: Transfected 3D7_H4K16R_T3_replicate3


title: Transfected 3D7_H4ac4R_R1_replicate1


title: Transfected 3D7_H4K16R_R1_replicate1


title: Transfected 3D7_H4K5R_R1_replicate1


title: Transfected 3D7_H4K8R_T2_replicate2


title: Transfected 3D7_H4K8R_R2_replicate2


title: Transfected 3D7_H4K12R_R3_replicate3


title: Transfected 3D7_H4-HA_R2_replicate2


title: Transfected 3D7_H4-HA_R1_replicate1


title: Transfected 3D7_H4K8R_R1_replicate1


title: Transfected 3D7_H4K8R_Schizonts_B2.5

source_name: RNA from schizont stage grown at blasticidin 2.5µg/ml


title: Transfected 3D7_H4-HA_R3_replicate3


title: Transfected 3D7_H4-HA_time point 2

source_name: RNA from time point 2 (16 hpi) grown at blasticidin 10ug/ml

tag: time point (hpi)


title: Transfected 3D7_H4-HA_time point 3

source_name: RNA from time point 3 (24 hpi) grown at blasticidin 10ug/ml


title: Transfected 3D7_H4-HA_time point 4

source_name: RNA from time point 4 (32 hpi) grown at blasticidin 10µg/ml


title: Transfected 3D7_HA_time point 5

source_name: RNA from time point 5 (40 hpi) grown at blasticidin 10ug/ml

value: HA


title: Transfected 3D7_H4-HA_time point 1

source_name: RNA from time point 1 (8 hpi) grown at blasticidin 10ug/ml


title: Transfected 3D7_HA_time point 4

source_name: RNA from time point 4 (32 hpi) grown at blasticidin 10ug/ml


title: Transfected 3D7_H4-HA_time point 5

source_name: RNA from time point 5 (40 hpi) grown at blasticidin 10µg/ml


title: Transfected 3D7_HA_time point 3


title: Transfected 3D7_H4K16R_R2_replicate2


title: Transfected 3D7_HA_time point 1


title: Wild type 3D7_ChIP with anti-H4K8ac antibody_S

hyb_protocol: Hybridizations were performed on the Agilent hybridization system  for 24 h

source_name: amplified ChIP DNA using anti H4K8ac antibody at schizont stage

extract_protocol: Chromatin-immuno precipitation was carried out as described in Gupta, A.P., Chin, W.H., Zhu, L., Mok, S., Luah, Y.H., Lim, E.H., and Bozdech, Z. (2013). Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum. PLoS pathogens 9, e1003170.

treatment_protocol: P. falciparum cells were sorbitol synchronized and grown upto 10-15% parasetemia in 2% hematocrit. Wild type cells were  harvested after formaldehyde cross linking either directly  or after drug treatment. Transfected  cells were grown in media supplemented with Blasticidin.

tag: antibody

source_name: amplified input pool

value: amplified input consisting of sonicated genomic DNA pooled from 3d7 ring, trophozoite and schizont stages


title: Wild type 3D7_ChIP with anti-H4K8ac antibody_R

source_name: amplified ChIP DNA using anti H4K8ac antibody at ring stage


title: Wild type 3D7_TSA_6h/2h_ChIP with anti-H4K8ac antibody_rep2

source_name: amplified ChIP DNA using anti H4K8ac antibody from TSA treatment and subsequent wash off at trophozoite stage_replicate 2

value: amplified input consisting of sonicated genomic DNA from 6h DMSO treatment


title: Wild type 3D7_TSA_6h/2h_ChIP with anti-H4K8ac antibody_rep1

source_name: amplified ChIP DNA using anti H4K8ac antibody from TSA treatment and subsequent wash off at trophozoite stage_replicate 1


title: Transfected 3D7_HA_time point 2

source_name: 3D7 reference pool_amplified genomic DNA


title: Wild type 3D7_TSA_6h/0.5h_ChIP with anti-H4K8ac antibody_rep2


title: Wild type 3D7_ChIP with anti-H4K8ac antibody_T

source_name: amplified ChIP DNA using anti H4K8ac antibody at trophozoite stage


title: Control Sample, Biological Replicate 3

city: Chapel Hill

first: Scott

last: Hutton

state: NC

address: 115 Mason Farm Rd. Rm 8131

department: Neuroscience Center

institute: University of North Carolina

description: Gene Expression Data from P17 striatum of control mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: Gene Chips were scanned using Affymetrix GeneChip Scanner 3000 7G Plus Targeted Genotyping System with Autoloader

data_processing: Data was analyzed using Affymetrix Transcriptome Analysis Console 3 using default settings. RMA normalization.

source_name: P17 striatal tissue, Mapk3(Erk1)-/-; Mapk1(Erk2)Floxed/Floxed mouse

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

growth_protocol: Striatal punches were extracted from control and mutant mice at postnatal day 17

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) followed by mRNA extraction using an RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: Mice were cervically dislocated and the brain removed and placed in ice-cold 1x PBS. 1mm coronal sections were made using a chilled acrylix brain matrix. 1mm diameter punches were then taken from dorsal striatum and flash frozen using liquid nitrogen

value: Postnatal day 17

tag: Sex

value: male

tag: genotype

value: striatum


title: Control Sample, Biological Replicate 1


title: Mutant Sample, Biological Replicate 3

description: Gene Expression Data from P17 striatum of ERK knockout mice

source_name: P17 striatal tissue, Drd2Cre;Mapk3(Erk1)-/-; Mapk1(Erk2)Floxed/Floxed mouse


title: Wild type 3D7_TSA_6h/4h_ChIP with anti-H4K8ac antibody_rep2


title: Wild type 3D7_TSA_6h/4h_ChIP with anti-H4K8ac antibody_rep1


title: Wild type 3D7_TSA_6h/0.5h_ChIP with anti-H4K8ac antibody_rep1


title: Wild type 3D7_TSA_6h/0h_ChIP with anti-H4K8ac antibody_rep3

source_name: amplified ChIP DNA using anti H4K8ac antibody from TSA treatment at trophozoite stage_replicate 3


title: Mutant Sample, Biological Replicate 2


title: Control Sample, Biological Replicate 2


title: Mutant Sample, Biological Replicate 1


title: Wild type 3D7_TSA_6h/0h_ChIP with anti-H4K8ac antibody_rep2

source_name: amplified ChIP DNA using anti H4K8ac antibody from TSA treatment at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/0.5h_ChIP with anti-H4K8ac antibody_rep2

source_name: amplified ChIP DNA using anti H4K8ac antibody from DMSO treatment and subsequent wash off at trophozoite stage_replicate 2


title: Wild type 3D7_DMSO_6h/2h_ChIP with anti-H4K8ac antibody_rep1

source_name: amplified ChIP DNA using anti H4K8ac antibody from DMSO treatment and subsequent wash off at trophozoite stage_replicate 1


title: Wild type 3D7_TSA_6h/0h_ChIP with anti-H4K8ac antibody_rep1

source_name: amplified ChIP DNA using anti H4K8ac antibody from TSA treatment at trophozoite stage_replicate 1


title: Wild type 3D7_DMSO_6h/4h_ChIP with anti-H4K8ac antibody_rep2


title: Wild type 3D7_DMSO_6h/4h_ChIP with anti-H4K8ac antibody_rep1


title: Wild type 3D7_DMSO_6h/0.5h_ChIP with anti-H4K8ac antibody_rep1


title: Wild type 3D7_DMSO_6h/0h_ChIP with anti-H4K8ac antibody_rep3

source_name: amplified ChIP DNA using anti H4K8ac antibody from DMSO treatment at trophozoite stage_replicate 3


title: Wild type 3D7_DMSO_6h/2h_ChIP with anti-H4K8ac antibody_rep2


title: Wild type 3D7_DMSO_6h/0h_ChIP with anti-H4K8ac antibody_rep2

source_name: amplified ChIP DNA using anti H4K8ac antibody from DMSO treatment at trophozoite stage_replicate 2


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep3_S

source_name: amplified ChIP DNA using anti-HA antibody at schizont stage_replicate 3

value: anti-HA

value: amplified input consisting of sonicated genomic DNA from transfectant with empty vector control


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep2_T

source_name: amplified ChIP DNA using anti-HA antibody at trophozoite stage_replicate 2


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep2_S

source_name: amplified ChIP DNA using anti-HA antibody at schizont stage_replicate 2

source_name: amplified input pool


title: Wild type 3D7_DMSO_6h/0h_ChIP with anti-H4K8ac antibody_rep1

source_name: amplified ChIP DNA using anti H4K8ac antibody from DMSO treatment at trophozoite stage_replicate 1


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep3_T

source_name: amplified ChIP DNA using anti-HA antibody at trophozoite stage_replicate 3


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep1_S

source_name: amplified ChIP DNA using anti-HA antibody at schizont stage_replicate 1


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep1_T

source_name: amplified ChIP DNA using anti-HA antibody at trophozoite stage_replicate 1


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep3_R

source_name: amplified ChIP DNA using anti-HA antibody at ring stage_replicate 3


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep2_R

source_name: amplified ChIP DNA using anti-HA antibody at ring stage_replicate 2


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep3_S


title: Transfected 3D7_H4K8R_ChIP with anti-HA antibody_rep1_R

source_name: amplified ChIP DNA using anti-HA antibody at ring stage_replicate 1


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep2_S


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep1_S


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep1_T


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep3_R


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep2_R


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep3_T


title: Transfected 3D7_H4-HA_Schizonts_B2.5

source_name: RNA from schizont stage grown at blasticidin 2.5µg/ml

source_name: 3D7 reference pool_amplified genomic DNA


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep1_R


title: Transfected 3D7_H4K8R_S2_replicate2

source_name: RNA from schizont stage_replicate2 grown at blasticidin 10µg/ml


title: Transfected 3D7_H4-HA_ChIP with anti-HA antibody_rep2_T


title: CRC1063_Xenopatients [200055410116_B]

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized by Bioconductor (3.0) lumi pipeline with loess normalization

source_name: Colorectal Cancer

label_protocol: Synthesis of cDNA and biotinylated cRNA were performed using the Illumina Total-Prep RNA Amplification Kit (Ambion, Austin, TX, USA, cat. no. IL1791), according to the manufacturer’s protocol, for which hybridization was carried out on Illumina HumanHT-12 V4 arrays

growth_protocol: PDX were collected upon surgical resection and stored in liquid nitrogen, XenoSphere were grown in standard stem cells medium

extract_protocol: RNA was extracted using the Trizol Plus purification Kit (Invitrogen, Frederick, MD, USA, cat. no.12183555), according to the manufacturer’s protocol. Quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cryostatic section of the frozen specimens were cut for RNA extraction

tag: treatment

value: Standard growth medium

tag: sample of origin

value: Xenopatient


title: CRC0705_Xenopatients [200055410078_H]


title: CRC1157_Xenopatients [200055410116_H]


title: CRC0578_Xenopatients [200055410078_C]


title: CRC1083_Xenopatients [200055410116_E]


title: CRC1182_Xenopatients [200055410116_I]


title: CRC1157_Xenopatients [200055410116_G]


title: CRC0729_Xenopatients [200055410078_I]


title: CRC0578_Xenopatients [200055410078_D]


title: CRC1257_Xenopatients [200055410116_L]


title: CRC0544_Xenopatients [200055410078_B]


title: CRC0151_Xenopatients [5688887009_J]


title: CRC1083_Xenopatients [200055410116_D]


title: CRC0705_Xenopatients [200055410078_G]


title: CRC0772_Xenopatients [200055410078_K]


title: CRC0687_Xenopatients [200055410078_E]


title: CRC0772_Xenopatients [200055410078_L]


title: CRC0574_Xenopatients [9967501037_G]


title: CRC0687_Xenopatients [200055410078_F]


title: CRC0729_Xenopatients [200055410078_J]


title: CRC1139_Xenopatients [200055410116_F]


title: CRC1182_Xenopatients [200055410116_J]


title: CRC1078_Xenopatients [200055410116_C]


title: CRC0059_Xenopatients [5557641029_D]


title: CRC0574_Xenopatients [9967501037_H]


title: CRC1257_Xenopatients [200055410116_K]


title: CRC0059_Xenopatients [5557641029_C]


title: CRC1063_Xenopatients [200055410116_A]


title: CRC0544_Xenopatients [200055410078_A]


title: CRC0179_Xenopatients [5753677155_F]


title: CRC0059_Xenopatients [5753677162_E]


title: CRC0261_Xenopatients [6898368007_H]


title: CRC0179_Xenopatients [5753677155_E]


title: CRC0254_Xenopatients [5753685002_I]


title: CRC0254_Xenopatients [5753685002_J]


title: CRC0202_Xenopatients [6898368007_J]


title: CRC0078_Xenopatients [6898368009_L]


title: CRC0327_Xenopatients [9023874083_C]


title: CRC0030_Xenopatients [7927520027_J]


title: CRC0030_Xenopatients [7927520027_I]


title: CRC0261_Xenopatients [6898368007_G]


title: CRC0081_Xenopatients [7196780028_F]


title: CRC0078_Xenopatients [6898368009_K]


title: CRC0264_Xenopatients [8803828035_H]


title: CRC0104_Xenopatients [7196780056_B]


title: CRC0394_Xenopatients [9031292020_C]


title: CRC1257_XenoSphere [9992580043_K]

value: Xenosphere


title: CRC0080_Xenopatients [7196780098_E]


title: CRC0202_Xenopatients [6898368007_I]


title: CRC1182_XenoSphere [9992580043_L]


title: CRC0104_Xenopatients [7196780056_A]


title: CRC0202_XenoSphere [9992580043_I]


title: CRC0394_XenoSphere [9992580043_H]


title: CRC0327_Xenopatients [9023874083_D]


title: CRC0081_Xenopatients [7196780028_E]


title: CRC0264_Xenopatients [8803828035_G]


title: CRC0394_Xenopatients [9031292020_D]


title: CRC0059_Xenopatients [5753677162_F]


title: CRC0080_XenoSphere [9992580043_G]


title: CRC0080_Xenopatients [7196780098_F]


title: CRC0574_XenoSphere [9992580043_B]


title: CRC0772_XenoSphere [9992580043_F]


title: CRC0151_XenoSphere [9992580065_H]


title: CRC0705_XenoSphere [9992580065_D]


title: CRC1139_XenoSphere [9992580065_B]


title: CRC0578Xa_XenoSphere_NGR1 [9444360044_L]


title: CRC0578Xb_XenoSphere [9992580043_A]


title: CRC0081_XenoSphere [9992580065_E]


title: CRC1083_XenoSphere [9992580065_F]


title: CRC0687_XenoSphere [9992580065_L]


title: CRC1157_XenoSphere [9992580065_K]


title: CRC0729_XenoSphere [9992580043_C]


title: CRC1063_XenoSphere [9992580043_E]


title: CRC0030_XenoSphere [9992580065_G]


title: logarithmic ParB+++, biological rep2

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: Gene expression data from logarithmic phase of growth of PAO1161 (pKGB8.62.2 araBADp-parB) + 0.02% ara.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45 degrees Cent. on GeneChip P. aeruginosa Genome Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray gene expression data was analyzed using Partek Genomics Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using GeneChip Robust Multiarray Averaging (GC RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAO1161 (pKGB8.62.2 araBADp-parB) L broth + 0.02% ara in logarithmic phase of growth

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, (Affymetrix).

growth_protocol: Cells of P. aeruginosa PAO1161 were taken from a deep-frozen stock, spread on L-agar plates and grown overnight at 37oC. Plasmids pKGB8.02 or pKGB8.62 were introduced into PAO1161 by transformation to obtain PAO1161 (pKGB8.02 araBADp) and PAO1161 (pKGB8.62.2 araBADp-parB) strains. 150 μg ml-1 chloramphenicol was used to select transformants on L-agar plates. Bacteria from single colonies were then used to inoculate L broth liquid cultures and grown overnight with shaking at 37oC. For selection of plasmids in liquid cultures of P. aeruginosa PAO1161, 75 μg ml-1 chloramphenicol was used. To induce the expression from the araBAD promoter, arabinose was added to 0.02% to cultures of PAO1161 with pKGB8.0.2 or pKGB8.62.2. Independent overnight cultures for each strain were diluted 1:100 into fresh L broth supplemented with chloramphenicol and arabinose, if necessary, and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from exponential-phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol: Biological replicates of total RNA were isolated from each strain using an RNeasy mini-kit with on-column DNase digestion (Qiagen) according to the manufacturer's instructions followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.

treatment_protocol: Liquid culture in L broth at 37oC with shaking.

tag: genotype/variation

value: pKGB8.62.2 araBADp-parB

tag: induction

value: arabinose

tag: growth phase

value: logarithmic


title: CRC0179_XenoSphere [9992580043_D]


title: logarithmic ParB+++, biological rep1

tag: strain/background


title: logarithmic ParB+++, biological rep3


title: logarithmic ParB+, biological rep3

description: Gene expression data from logarithmic phase of growth of PAO1161 (pKGB8.62.2 araBADp-parB).

source_name: Pseudomonas aeruginosa PAO1161 (pKGB8.62.2 araBADp-parB) L broth in logarithmic phase of growth


title: CRC0254_XenoSphere_NGR1 [9444360044_F]


title: CRC0264_XenoSphere_NGR1 [9444360044_H]


title: CRC1078_XenoSphere [9992580065_C]


title: logarithmic EV, biological rep3

description: Gene expression data from logarithmic phase of growth of PAO1161 (pKGB8.02 araBADp) + 0.02% ara.

source_name: Pseudomonas aeruginosa PAO1161 (pKGB8.02 araBADp) L broth + 0.02% ara in logarithmic phase of growth

value: pKGB8.02 araBADp


title: logarithmic ParB+, biological rep2


title: logarithmic EV, biological rep1


title: CRC0104_XenoSphere [9992580065_I]


title: CRC0327_XenoSphere [9444360044_I]


title: logarithmic ParB+, biological rep1


title: CRC0544_XenoSphere [9992580065_A]


title: CRC0254_XenoSphere [9444360044_E]


title: CRC0327_XenoSphere_NGR1 [9444360044_J]


title: CRC0264_XenoSphere [9444360044_G]


title: CRC0261_XenoSphere [9992580065_J]


title: CRC0078_XenoSphere_NGR1 [9444360044_D]


title: CRC0578Xa_XenoSphere [9444360044_K]


title: logarithmic WT, biological rep1

description: Gene expression data from logarithmic phase of growth of PAO1161.

source_name: Pseudomonas aeruginosa PAO1161 in logarithmic phase of growth

value: WT


title: logarithmic WT, biological rep2


title: CRC0059_XenoSphere_NGR1 [9444360044_B]


title: CRC0059_XenoSphere [9444360044_A]


title: CRC0078_XenoSphere [9444360044_C]


title: logarithmic EV, biological rep2


title: Jmjd1c RNAi-3#-1, biological rep1

status: Public on Jul 24 2017

city: Shanghai

first: Ying

last: Jin

state: Shanghai

address: Room 1334 ,Block A, Life Science Research Building, 320 Yueyang Road

country: China

institute: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Gene expression data from ESCs transfected with shJmjd1c#3 (Jmjd1c RNAi-3#)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the the Affymetrix Scanner3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Jmjd1c KD ESCs

growth_protocol: J1 ESCs and KD ESCs were cultured on gelatin-coated plates in standard ESC medium consisting of DMEM (Dulbecco’s modified Eagle’s medium) (Gibico) supplemented with 15% fetal bovine serum (Gibico), 2 mM Glutamax (Gibico), 0.1% b-mercaptoethanol (Sigma), 1 mM MEM pyruvate sodium (Gibico), 0.1 mM MEM nonessential amino acid (Gibico), 1% Penicillin/Streptomycin (Hyclone), and 1000 U/ml recombinant leukemia inhibitory factor (Millipore).

treatment_protocol: ESCs were washed twice with PBS buffer, tryipsinized and washed twice with PBS, and placed on ice in the Trizol solution (Invitrogen).

tag: strain

tag: cell type

value: ESCs

value: Jmjd1c knockdown

tag: transfection


title: Jmjd1c RNAi-4#-2, biological rep2

description: Gene expression data from ESCs transfected with shJmjd1c#4 (Jmjd1c RNAi-4#)


title: Jmjd1c RNAi-3#-2, biological rep2


title: NCi#-2, biological rep2

description: Gene expression data from ESCs transfected with shNT (NCi)

source_name: Control ESCs

value: wild type


title: NCi#-1, biological rep1


title: Jmjd1c RNAi-4#-1, biological rep1


title: large cell MALT lymphoma 26

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

description: Hybridized to HG U133 2.0 plus array

hyb_protocol: 2µg of total RNA were used for the One-Cycle target labeling assay, further processed and hybridized to the GeneChip® Human Genome U133 Plus 2.0 array from Affymetrix according to manufacturer’s instructions.

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

data_processing: Statistical analyses were carried out using R (v. 2.14.1) (R-Development-Core-Team, 2010). Arrays have been normalized using Robust Multichip Average (RMA, affy package) (Gautier et al., 2004).

source_name: large cell MALT lymphoma 26

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Total RNA was extracted using the PicoPureTM RNA isolation kit (Arcturus) according to manufacturer’s instructions. Quality was assured with the RNA 6000 Nano Asay kit on the 2100 Bioanalyzer (Agilent).

tag: tissue

value: lung


title: large cell MALT lymphoma 21

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 21

value: stomach


title: large cell MALT lymphoma 27

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 27


title: large cell MALT lymphoma 24

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 24


title: large cell MALT lymphoma 16

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 16


title: large cell component composite MALT lymphoma 9

description: Hybridized to HG U133 2.0 plus array


title: large cell component composite MALT lymphoma 12

description: Hybridized to HG U133 2.0 plus array


title: large cell MALT lymphoma 28

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 28


title: large cell MALT lymphoma 23

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 23


title: large cell MALT lymphoma 25

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 25


title: large cell component composite MALT lymphoma 8_87

description: Hybridized to HG U133 2.0 plus array


title: large cell MALT lymphoma 22

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 22


title: large cell component composite MALT lymphoma 11

description: Hybridized to HG U133 2.0 plus array


title: large cell MALT lymphoma 17

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 17


title: large cell component composite MALT lymphoma 14

description: Hybridized to HG U133 2.0 plus array


title: large cell MALT lymphoma 19

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 19


title: small cell MALT lymphoma 8

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 8

value: large intestine


title: large cell component composite MALT lymphoma 13

description: Hybridized to HG U133 2.0 plus array

value: small intestine


title: large cell component composite MALT lymphoma 8_85

description: Hybridized to HG U133 2.0 plus array


title: small cell MALT lymphoma 6

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 6


title: large cell MALT lymphoma 18

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 18


title: small cell MALT lymphoma 5

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 5


title: small cell MALT lymphoma 4

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 4


title: small cell MALT lymphoma 2

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 2


title: small cell MALT lymphoma 1

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 1


title: large cell component composite MALT lymphoma 10

description: Hybridized to HG U133 2.0 plus array


title: small cell MALT lymphoma 7

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 7


title: small cell MALT lymphoma 3

description: Hybridized to HG U133 2.0 plus array

source_name: small cell MALT lymphoma 3


title: large cell component composite MALT lymphoma 15

description: Hybridized to HG U133 2.0 plus array


title: large cell MALT lymphoma 20

description: Hybridized to HG U133 2.0 plus array

source_name: large cell MALT lymphoma 20

value: illeocoecum


title: follicular lymphoma 2

description: Hybridized to HG U133 2.0 plus array

source_name: follicular lymphoma 2


title: follicular lymphoma 1

description: Hybridized to HG U133 2.0 plus array

source_name: follicular lymphoma 1


title: Bur-0_control_replicate 1

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from root of plants grown hydroponically for 6 weeks in 1/10 Hoaglands solution.

hyb_protocol: Fragmented aRNA was hybridized to an Arabidopsis GeneChip microarray (Zhu et al., 2001) at the „Zentum für medizinische Grundlagenforschung der Martin-Luther-Universität“ in Halle.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to analyze the hybridized microarray, applying an Affymetrix GeneChip Operating Software (GCOS)

data_processing: Program R (version 3.0.0) (‘The R Project for Statistical Computing’) and the Bioconductor packages (Gentleman et al., 2004) were used for data normalization implementing the robust multi-chip average (RMA) method, pre-processing, and quality control.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana root mature plant in vegetative state

label_protocol: Biotinylated cRNA was prepared using the GeneChip® 3’ IVT Express Kit from Affymetrix following the intructions of the manufacturer.

growth_protocol: Plants were grown in a hydroponic culture in a modified, 1/10 Hoagland medium (87.1 µM (NH4)2HPO4, 200 µM MgSO4, 400 µM Ca(NO3)2, 600 µM KNO3, 5 µM Fe-HBED, 4.63 µM H3BO3, 0.032 µM CuSO4, 0.915 µM MnCl2, 0.077 µM ZnSO4, 0.011 µM MoO3; pH 5.7).  The plants were cultivated in climate chambers at short day conditions of 8 h light (200µE)/ 16 h dark with 22 °C during the light period and 20 °C during the dark period.

extract_protocol: Root material was frozen in liquid nitrogen upon harvesting and ground with mortar and pestil. Total RNA was extreacted by Trizol according to the manufacturers instructions and further purified using the RNAeasy Kit from Quiagen, following the instruction of the manufacturer.

treatment_protocol: After 5 weeks of growth plants were treated with 1µM CdCl2 or grown at control conditions for one week before harvesting root material.

tag: accession

value: control

value: root


title: Bur-0_Cd-stress_replicate 1

description: Gene expression data from root of plants grown hydroponically for 6 weeks in 1/10 Hoaglands solution containing 1µM CdCl2.

value: Cadmium


title: Bur-0_control_replicate 2


title: Bur-0_Cd-stress_replicate 2


title: Col-0_control_replicate 1


title: Col-0_Cd-stress_replicate 2


title: Col-0_Cd-stress_replicate 1


title: Col-0_control_replicate 2


title: yedL_2

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: Deletion of yedL decreases type three secretion of Escherichia coli O157:H7 TUV93-0. The transcriptional profile and wild type and mutant bacteria grown under type three secretion inducing conditions were compared.

hyb_protocol: Prior to hybridization, the slides were treated with the background-reducing Pronto! Pre-Soak System (Corning Life Sciences). The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42 °C and washed twice in 0.1_SSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5_ SSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1_ SSC, 0.1% SDS for 1 min and twice in 0.1_ SSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800_g. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 _l of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5_ SSC (1_ SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 _g of poly(A), and 1_Denhardt’s solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C. After hybridization was complete, the slides were washed in 2_SSC, 0.1% SDS at 42 °C for 2 min in 0.1_SSC, 0.1% SDS for 2 min at room temperature, and finally twice in 0.1_ SSC for 2 min at room temperature. The microarray slides were dried by centrifugation for 5 min at 800g.

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: Genespring GX 7.3.  Raw signals are Lowess normalized, thresholded, log transformed ratios. Then normalized by summarization, thresholding, log transformation, ratio (difference) and baseline transformation. Lowess paramters: smoothing coefficient 0.2

organism: Escherichia coli

source_name: TUV93-0 delta yedL

label_protocol:
20 ug total RNA was converted to Cy3-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy5 NHS-dye esters to the amino-allyl-labelled
cDNAs.

growth_protocol: Sample was grown shaking at 37oC in MEM-HEPES to OD600 = 0.8

extract_protocol: An RNeasy minikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd).

treatment_protocol: 15 ml of culture was mixed with 30 ml of RNAprotect bacterial reagent (QIAGEN Ltd).

value: Escherichia coli O157:H7 TUV93-0 delta yedL

tag: media

value: MEM-HEPES supplemented with 0.1% glucose and 250nM Fe(NO3)2

label_protocol:
20 ug total RNA was converted to Cy3-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy3 NHS-dye esters to the amino-allyl-labelled
cDNAs

value: Escherichia coli O157:H7 TUV93-0


title: yhaO_2

description: Deletion of yhaO decreases type three secretion of Escherichia coli O157:H7 TUV93-0. The transcriptional profile and wild type and mutant bacteria grown under type three secretion inducing conditions were compared.

source_name: TUV93-0 delta yhaO

label_protocol:
20 ug total RNA was converted to Cy3-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy3 NHS-dye esters to the amino-allyl-labelled
cDNAs.

value: Escherichia coli O157:H7 TUV93-0 delta yhaO

tag: od

value: MEM-HEPES supplemented with 0.1% glucose and 250 nM Fe(NO3)2


title: yhaO_1

description: Deletion of yhaO decreases type three secretion of Escherichia coli O157:H7 TUV93-0. The transcriptional profile and wild type and mutant bacteria grown under thype three secretion inducing conditions were compared.

label_protocol:
20 ug total RNA was converted to Cy5-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy5 NHS-dye esters to the amino-allyl-labelled
cDNAs.

growth_protocol: Sample was grown shaking at 37oC in MEM-HEPES to an OD of 0.8

value: MEM-HEPES


title: yhaO_3

value: Media:MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2


title: yedL_3

description: Deletion of yedL decreases type three secretion of Escherichia coli O157:H7 TUV93-0. The transcriptional profile and wild type and mutant bacteria grown under thype three secretion inducing conditions were compared.

source_name: TUV93-0 delta yedL_3


title: yedL_1

value: MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2


title: 18A

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing: Idat files were loaded into R and analyzed with R/Bioconductor packages

label: Cy5 and Cy3

source_name: normal

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using standard procedures. Bisulfite conversion was performed on 600 ng of DNA by EZ DNA Methylation kit (Zymo Research Corp., Irvine, CA, USA) according to manufacturer’s instructions and modified DNA was eluted in 16 µl of water.

tag: asbestos exposed

value: yes

tag: average pack-years of cigarette-smoking (py; one py = one year of smoking 20 cigarettes/day)

tag: age (years)

tag: gender

value: male


title: 19A


title: 22A


title: 15A


title: 26A


title: 23A


title: 28A


title: 3A

value: no


title: 11A


title: 7A


title: 6A


title: 20A


title: 27A


title: 2A


title: 10A


title: 17A


title: 21A


title: 5A


title: 24A


title: 25A


title: 16A


title: 14A


title: 1A


title: 12A


title: 13A


title: 9A


title: D2A1-m2 subline of BALB/c-derived D2A1 cell line_2

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

description:
replicate 2
D2A1-m2.2

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data were filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples in the dataset probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation (VST) and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization. Then, was batch-corrected using the function (ComBat) in the R package (sva).

source_name: D2A1-m2 subclone of BALB/c-derived D2A1 cell line

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

extract_protocol: mRNA from i) D2A1, ii) D2A1-m1, and iii) D2A1-m2 cell lines was extracted with RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions, and was assessed for concentration and quality using a SpectroStar (BMG Labtech) and a Bioanalyser (Agilent Technologies).

tag: cell line

value: D2A1-m2 subclone

tag: batch


title: 26T

source_name: tumor


title: 8A


title: 16T


title: 4A


title: parental D2A1 cells_1

description:
replicate 1
D2A1.1

source_name: parental D2A1 cells


title: D2A1-m2 subline of BALB/c-derived D2A1 cell line_1

description:
replicate 1
D2A1-m2.1


title: parental D2A1 cells_2

description:
replicate 2
D2A1.2


title: D2A1-m2 subline of BALB/c-derived D2A1 cell line_3

description:
replicate 3
D2A1-m2.3


title: D2A1-m1 subline of BALB/c-derived D2A1 cell line_1

description:
replicate 1
D2A1-m1.1

source_name: D2A1-m1 subclone of BALB/c-derived D2A1 cell line

value: D2A1-m1 subclone


title: D2A1-m1 subline of BALB/c-derived D2A1 cell line_2

description:
replicate 2
D2A1-m1.2


title: 24T


title: parental D2A1 cells_3

description:
replicate 3
D2A1.3


title: 17T


title: 25T


title: 21T


title: 15T


title: 11T


title: 20T


title: 2T


title: 23T


title: 22T


title: OVSAHO parental1

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

institute: CRO Aviano

description: Constitutive microRNA profile of EOC cells.

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Dynamic Range of Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Epithelial Ovarian Carcinoma cells no treated

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

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from MCL cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: not applicable

value: ovarian cell line

tag: histotype

value: serous


title: TOV-112D  MI-res2

source_name: Epithelial Ovarian Carcinoma cells treated with platinum

value: endometrioid


title: TOV-112D  MI-res1


title: 10T


title: OVSAHO parental2


title: MDAH parental1


title: MDAH parental2


title: TOV-112D parental1


title: TOV-112D parental2


title: 27T


title: 18T


title: MDAH  MI-res1


title: OVSAHO  MI-res2


title: OVSAHO  MI-res1


title: MDAH  MI-res2


title: 19T


title: 28T


title: 3T


title: 9T


title: 6T


title: 12T


title: 14T


title: 5T


title: 8T


title: I100

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

source_name: Burkitt Lymphoma

growth_protocol: Burkitt lymphomas cell lines were obtained by the IARC biobank

extract_protocol: After trypsinization, cells were pelleted and resuspended in lysis buffer (1% SDS, 0.1M NaCl, 0.1M EDTA, 0.05M Tris pH8) with Proteinase K (500ug/ml) and incubated for 2 hours at 55°C. DNA was saturated with NaCl (6M), precipitated with isopropanol, and cleaned with 70% ethanol. Extracted DNA was finally resuspended in water.

treatment_protocol: All cell lines were culture in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin G, 100 mg/ml streptomycin, 2 mM L-glutamine, and 1 mM sodium pyruvate

value: Burkitt Lymphoma cell line I100

tag: ebv status

value: Pos


title: 29N

source_name: control


title: BL116

value: Burkitt Lymphoma cell line BL116


title: B65

value: Burkitt Lymphoma cell line B65


title: BL41

value: Burkitt Lymphoma cell line BL41

value: Neg


title: 13T


title: BL56

value: Burkitt Lymphoma cell line BL56


title: BL60

value: Burkitt Lymphoma cell line BL60


title: BL135

value: Burkitt Lymphoma cell line BL135


title: 34N

value: unknown


title: 1T

value: male


title: BL70

value: Burkitt Lymphoma cell line BL70


title: 33N


title: 30N

value: yes


title: 7T

value: no


title: BL53

value: Burkitt Lymphoma cell line BL53


title: 4T


title: BL110

value: Burkitt Lymphoma cell line BL110


title: 32N


title: BL103

value: Burkitt Lymphoma cell line BL103


title: BL112

value: Burkitt Lymphoma cell line BL112


title: 4H11IL12-MYE-2

first: Oladapo

last: Yeku

address: 1275 York Avenue, Box 242

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: nCounter XT CodeSet Gene Expression Assays, July-2016.

scan_protocol: Data Collection is carried out in the nCounter® Digital Analyzer. At the highest standard data resolution, 555–1155 fields of view (FOV) are  collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts.  Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV)  format.

data_processing: nCounter® Expression Data Analysis Guide-MAN-C0011-03, using nSolver Analysis Software v2.5.

label: Nanostring oligonucleotide probe

label_protocol: Biotinylated cRNA were prepared according to the standard Nanostring protocol from 2 ug total RNA.

growth_protocol: RPMI media in 37 degree and 5% CO2 incubator

extract_protocol: Total RNA was extracted with Ambion RNA extraction kit

value: TAMs (recovered from armored IL-12 secreting CAR T cells)


title: grapevine hairy root line, transgenic for GFP,sample 77,biological replicate 1

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

description: Gene expression data from grapevine hairy roots transformed with GFP (control)

hyb_protocol: Labelled cRNA (10µg) was fragmented and quality control checked using the Bioanalyser 2100. If the quality control was correct, then fragmented cRNA were hybridized to the GrapeGen chip. Hybridization was performed for 16 h at 45ºC.

scan_protocol: Chips were scanned using the GeneChip® Scanner 3000, Scanning Software: GCOS (GeneChip Operating Software)

data_processing: The data was analyzed inside the R statistical language (R version 3.2.1 ). Microarray data were normalized using the robust multi-array average (RMA) procedure provided by the R package affy (version 1.48.0).

organism: Vitis vinifera

source_name: grapevine hairy roots; genotype: GFP

label_protocol: Total RNA was quality controlled using the Agilent Bioanalyser 2100 using the NanoChip protocol. Biotinylated cRNA were prepared from 5 micrograms of total RNA according to the standard Affymetrix protocol.

growth_protocol: Using the Agrobacterium rhizogenes strain ATCC 15834, transgenic MYBF1 or GFP-GUS expressing grapevine hairy roots were produced by induction of hairy root growth from leaves from in vitro–grown Chardonnay plants. After transformation and induction, transgenic hairy roots were routinely kept on Hairy root (HR) medium and transferred to fresh medium after four weeks.

extract_protocol: RNA of VviMYBF1 and GFP transgenic grapevine hairy roots was isolated following the protocol of the EURx GeneMATRIX Universal RNA purification kit (Roboklon). Prior to RT reactions, RNA samples were heated to 65°C for 10 min and immediately placed on ice to destroy secondary structures. Synthesis of cDNA was performed with SuperScriptTM III First-Strand Biosynthesis System (Invitrogen, catalaog no. 18080-051) according to the instructions in the manual for RT using oligo dT primers.

treatment_protocol: For microarray analysis, selected hairy root lines were transferred to fresh HR medium. Two weeks after transfer hairy roots from all VviMYBF1 and GFP lines were harvested at the same time during the day by placing the hairy root material into individual 15ml Falcon tubes, rapidly shock freezing the tubes in liquid nitrogen and subsequently storing them at -80°C. The whole material was then grinded to a fine powder under liquid nitrogen and aliquoted for downstream analysis.

tag: genotype

value: GFP

tag: cultivar

value: Chardonnay


title: 4H11IL12-CAR-3

value: armored IL-12 secreting CAR T cells


title: 4H11IL12-MYE-1


title: grapevine hairy root line, transgenic for VviMYBF1,sample 62,biological replicate 4

description: Gene expression data from grapevine hairy roots transformed with VviMYBF1

source_name: grapevine hairy roots; genotype: VviMYBF1


title: 31N


title: grapevine hairy root line, transgenic for VviMYBF1,sample 32,biological replicate 1


title: grapevine hairy root line, transgenic for GFP,sample 97,biological replicate 3


title: 373

value: Burkitt Lymphoma cell line 373

value: Pos


title: 4H11IL12-CAR-2


title: I176B

value: Burkitt Lymphoma cell line I176B


title: BL79

value: Burkitt Lymphoma cell line BL79


title: 4H11IL12-CAR-1


title: TOV-112D parental2

description: Constitutive Gene expression of EOC cells.

value: ovarian cell line

value: endometrioid


title: 4H11IL12-MYE-3


title: grapevine hairy root line, transgenic for GFP,sample 83,biological replicate 2


title: TOV-112D parental1


title: grapevine hairy root line, transgenic for VviMYBF1,sample 33,biological replicate 2


title: BL2

value: Burkitt Lymphoma cell line BL2

value: Neg


title: BL104

value: Burkitt Lymphoma cell line BL104


title: BL58

value: Burkitt Lymphoma cell line BL58


title: 4H11-MYE-2

value: TAMs (recovered from second generation CAR T cells)


title: 4H11-MYE-3


title: ∆13RAP2.12_rosette_rep2

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

institute: Scuola Superiore Sant'Anna

description: transgenic

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: R/Bioconductor, RMA algorithm

source_name: Arabidopsis thaliana, 4-w rosette

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were sown in 7-cm diameter pots containing moisted Arabidopsis soil. The seeds were stratified at 4°C in the dark for 2 days and then the pots were moved in a growth chamber at netral photoperiodic conditions (12h light 12 h darkness) with 18°C in the night and 22°C in the day.

extract_protocol: Total RNA was extracted from whole 4-week old plants using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis Genome GeneChip arrays.

treatment_protocol: Rosettes were harvested 10h after the beginning of the light phase

tag: ecotype

tag: genotype/variation

tag: age

value: 4 weeks old

value: rosette


title: 4H11-MYE-1

city: New York

tag: cell type


title: BL102

value: Burkitt Lymphoma cell line BL102


title: 4H11-CAR-2

value: second-generation CAR T cells


title: Col-0_rosette_rep2

description: wild-type

value: wild-type

tag: tissue


title: 4H11-CAR-1


title: MDAH parental2


title: OVSAHO parental2

value: serous


title: OVSAHO parental1


title: MDAH  MI-res1


title: Col-0_rosette_rep1

description: wild-type


title: MDAH parental1


title: MDAH  MI-res2


title: TOV-112D  MI-res1


title: OVSAHO  MI-res1


title: 902-CR-L3-R2

status: Public on Jul 23 2017

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

institute: University of Pittsburgh

description:
pair 17, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 17, layer L3, diagnosis Control, replicate R2

hyb_protocol: cDNA was synthesized and amplified using the Ovation Pico WTA System

scan_protocol: loaded on an Affymetrix GeneChip® HT HG-U133+ PM Array Plate

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

source_name: dorsolateral prefrontal cortex

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Tissue sections (12 μm) containing DLPFC area 9 were cut on a cryostat, mounted on glass polyethylene naphthalate membrane slides (Leica Microsystems, Bannockburn, IL) which were blinded as to diagnosis, and stained with thionin for Nissl substance.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for all 72 subjects on the basis of medical records and structured diagnostic interviews conducted with the decedent’s family members.

value: dorsolateral prefrontal cortex

value: pyramidal neuron cell

tag: dsm-iv diagnoses

value: Unaffected Comparison


title: 1086-CR-L5-R2

description:
pair 2, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 2, layer L5, diagnosis Control, replicate R2


title: 1105-SZ-L5-R1

description:
pair 5, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 5, layer L5, diagnosis Schiz, replicate R1

value: Schizoaffective disorder


title: 1092-CR-L5-R1

description:
pair 3, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 3, layer L5, diagnosis Control, replicate R1


title: OVSAHO  MI-res2

value: ovarian cell line


title: 1263-SZ-L3-R1

description:
pair 7, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 7, layer L3, diagnosis Schiz, replicate R1

value: Undifferentiated schizophrenia; ADR


title: TOV-112D  MI-res2

value: endometrioid


title: 1086-CR-L3-R1

description:
pair 2, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 2, layer L3, diagnosis Control, replicate R1


title: 1284-CR-L3-R2

description:
pair 6, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 6, layer L3, diagnosis Control, replicate R2


title: 1189-SZ-L3-R1

description:
pair 13, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 13, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; AAR


title: 1178-SZ-L3-R1

description:
pair 3, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 3, layer L3, diagnosis Schiz, replicate R1


title: 1361-SZ-L3-R1

description:
pair 17, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 17, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ODC


title: 1361-SZ-L5-R2

description:
pair 17, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 17, layer L5, diagnosis Schiz, replicate R2


title: 1189-SZ-L5-R2

description:
pair 13, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 13, layer L5, diagnosis Schiz, replicate R2


title: 1336-CR-L5-R1

description:
pair 4, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 4, layer L5, diagnosis Control, replicate R1


title: 970-CR-L5-R1

description:
pair 8, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 8, layer L5, diagnosis Control, replicate R1


title: 1105-SZ-L3-R1

description:
pair 5, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 5, layer L3, diagnosis Schiz, replicate R1


title: 1092-CR-L3-R1

description:
pair 3, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 3, layer L3, diagnosis Control, replicate R1


title: 1307-CR-L5-R1

description:
pair 12, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 12, layer L5, diagnosis Control, replicate R1


title: 1263-SZ-L5-R1

description:
pair 7, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 7, layer L5, diagnosis Schiz, replicate R1


title: 902-CR-L5-R1

description:
pair 17, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 17, layer L5, diagnosis Control, replicate R1


title: 1307-CR-L3-R2

description:
pair 12, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 12, layer L3, diagnosis Control, replicate R2


title: 1178-SZ-L5-R1

description:
pair 3, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 3, layer L5, diagnosis Schiz, replicate R1


title: 1361-SZ-L3-R2

description:
pair 17, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 17, layer L3, diagnosis Schiz, replicate R2


title: 1336-CR-L3-R1

description:
pair 4, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 4, layer L3, diagnosis Control, replicate R1


title: 1189-SZ-L5-R1

description:
pair 13, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 13, layer L5, diagnosis Schiz, replicate R1


title: 1263-SZ-L3-R2

description:
pair 7, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 7, layer L3, diagnosis Schiz, replicate R2


title: 1105-SZ-L5-R2

description:
pair 5, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 5, layer L5, diagnosis Schiz, replicate R2


title: 1307-CR-L5-R2

description:
pair 12, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 12, layer L5, diagnosis Control, replicate R2


title: 1284-CR-L5-R1

description:
pair 6, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 6, layer L5, diagnosis Control, replicate R1


title: 1086-CR-L3-R2

description:
pair 2, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 2, layer L3, diagnosis Control, replicate R2


title: 1284-CR-L3-R1

description:
pair 6, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 6, layer L3, diagnosis Control, replicate R1


title: 970-CR-L5-R2

description:
pair 8, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 8, layer L5, diagnosis Control, replicate R2


title: 970-CR-L3-R1

description:
pair 8, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 8, layer L3, diagnosis Control, replicate R1


title: 1189-SZ-L3-R2

description:
pair 13, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 13, layer L3, diagnosis Schiz, replicate R2


title: 1092-CR-L3-R2

description:
pair 3, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 3, layer L3, diagnosis Control, replicate R2


title: 1178-SZ-L5-R2

description:
pair 3, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 3, layer L5, diagnosis Schiz, replicate R2


title: grapevine hairy root line, transgenic for VviMYBF1,sample 34,biological replicate 3

description: Gene expression data from grapevine hairy roots transformed with VviMYBF1

value: Chardonnay


title: 1105-SZ-L3-R2

description:
pair 5, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 5, layer L3, diagnosis Schiz, replicate R2


title: 902-CR-L5-R2

description:
pair 17, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 17, layer L5, diagnosis Control, replicate R2


title: 970-CR-L3-R2

description:
pair 8, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 8, layer L3, diagnosis Control, replicate R2


title: 1361-SZ-L5-R1

description:
pair 17, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 17, layer L5, diagnosis Schiz, replicate R1


title: 1336-CR-L5-R2

description:
pair 4, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 4, layer L5, diagnosis Control, replicate R2


title: 1307-CR-L3-R1

description:
pair 12, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 12, layer L3, diagnosis Control, replicate R1


title: 1092-CR-L5-R2

description:
pair 3, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 3, layer L5, diagnosis Control, replicate R2


title: 1336-CR-L3-R2

description:
pair 4, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 4, layer L3, diagnosis Control, replicate R2


title: 1263-SZ-L5-R2

description:
pair 7, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 7, layer L5, diagnosis Schiz, replicate R2


title: 902-CR-L3-R1

description:
pair 17, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 17, layer L3, diagnosis Control, replicate R1


title: 1284-CR-L5-R2

description:
pair 6, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 6, layer L5, diagnosis Control, replicate R2


title: 1391-CR-L5-R2

description:
pair 13, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 13, layer L5, diagnosis Control, replicate R2


title: 1178-SZ-L3-R2

description:
pair 3, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 3, layer L3, diagnosis Schiz, replicate R2


title: 1247-CR-L5-R2

description:
pair 9, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 9, layer L5, diagnosis Control, replicate R2


title: 1326-CR-L5-R1

description:
pair 16, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 16, layer L5, diagnosis Control, replicate R1


title: 1240-SZ-L3-R1

description:
pair 9, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 9, layer L3, diagnosis Schiz, replicate R1


title: 1314-SZ-L3-R1

description:
pair 16, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 16, layer L3, diagnosis Schiz, replicate R1

value: Undifferentiated schizophrenia


title: 1099-CR-L3-R1

description:
pair 11, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 11, layer L3, diagnosis Control, replicate R1


title: 1173-SZ-L5-R1

description:
pair 4, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 4, layer L5, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia; ADR


title: 10025-SZ-L5-R1

description:
pair 2, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 2, layer L5, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia; OAR


title: 1222-SZ-L3-R2

description:
pair 8, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 8, layer L3, diagnosis Schiz, replicate R2

value: Undifferentiated schizophrenia; AAC


title: 1326-CR-L3-R2

description:
pair 16, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 16, layer L3, diagnosis Control, replicate R2


title: 1240-SZ-L5-R2

description:
pair 9, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 9, layer L5, diagnosis Schiz, replicate R2


title: 1282-CR-L5-R2

description:
pair 14, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 14, layer L5, diagnosis Control, replicate R2


title: ∆13RAP2.12_rosette_rep1

description: transgenic

value: 4 weeks old

value: rosette


title: 1314-SZ-L5-R2

description:
pair 16, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 16, layer L5, diagnosis Schiz, replicate R2


title: 10023-SZ-L5-R1

description:
pair 11, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 11, layer L5, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia


title: 1247-CR-L5-R1

description:
pair 9, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 9, layer L5, diagnosis Control, replicate R1

value: dorsolateral prefrontal cortex


title: 1222-SZ-L5-R1

description:
pair 8, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 8, layer L5, diagnosis Schiz, replicate R1

value: pyramidal neuron cell


title: 1173-SZ-L5-R2

description:
pair 4, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 4, layer L5, diagnosis Schiz, replicate R2


title: 1391-CR-L3-R1

description:
pair 13, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 13, layer L3, diagnosis Control, replicate R1

value: Unaffected Comparison


title: 1099-CR-L3-R2

description:
pair 11, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 11, layer L3, diagnosis Control, replicate R2


title: 10023-SZ-L3-R1

description:
pair 11, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 11, layer L3, diagnosis Schiz, replicate R1


title: 10025-SZ-L3-R2

description:
pair 2, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 2, layer L3, diagnosis Schiz, replicate R2


title: 1099-CR-L5-R1

description:
pair 11, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 11, layer L5, diagnosis Control, replicate R1


title: 1282-CR-L3-R1

description:
pair 14, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 14, layer L3, diagnosis Control, replicate R1


title: 1240-SZ-L5-R1

description:
pair 9, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 9, layer L5, diagnosis Schiz, replicate R1


title: 1326-CR-L5-R2

description:
pair 16, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 16, layer L5, diagnosis Control, replicate R2


title: 1173-SZ-L3-R2

description:
pair 4, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 4, layer L3, diagnosis Schiz, replicate R2


title: 1314-SZ-L3-R2

description:
pair 16, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 16, layer L3, diagnosis Schiz, replicate R2


title: 10025-SZ-L3-R1

description:
pair 2, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 2, layer L3, diagnosis Schiz, replicate R1


title: 1247-CR-L3-R2

description:
pair 9, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 9, layer L3, diagnosis Control, replicate R2


title: 1391-CR-L5-R1

description:
pair 13, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 13, layer L5, diagnosis Control, replicate R1


title: 1282-CR-L3-R2

description:
pair 14, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 14, layer L3, diagnosis Control, replicate R2


title: 1247-CR-L3-R1

description:
pair 9, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 9, layer L3, diagnosis Control, replicate R1


title: 10023-SZ-L3-R2

description:
pair 11, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 11, layer L3, diagnosis Schiz, replicate R2


title: 1391-CR-L3-R2

description:
pair 13, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 13, layer L3, diagnosis Control, replicate R2


title: 1240-SZ-L3-R2

description:
pair 9, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 9, layer L3, diagnosis Schiz, replicate R2


title: 1314-SZ-L5-R1

description:
pair 16, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 16, layer L5, diagnosis Schiz, replicate R1


title: 10023-SZ-L5-R2

description:
pair 11, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 11, layer L5, diagnosis Schiz, replicate R2


title: 1159-CR-L5-R1

description:
pair 15, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 15, layer L5, diagnosis Control, replicate R1


title: 10025-SZ-L5-R2

description:
pair 2, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 2, layer L5, diagnosis Schiz, replicate R2


title: 10024-SZ-L5-R2

description:
pair 12, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 12, layer L5, diagnosis Schiz, replicate R2

value: Paranoid schizophrenia


title: 1211-SZ-L3-R1

description:
pair 14, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 14, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder


title: 1222-SZ-L3-R1

description:
pair 8, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 8, layer L3, diagnosis Schiz, replicate R1


title: 10020-SZ-L3-R2

description:
pair 10, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 10, layer L3, diagnosis Schiz, replicate R2

value: Paranoid schizophrenia; AAC; OAC


title: 1326-CR-L3-R1

description:
pair 16, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 16, layer L3, diagnosis Control, replicate R1


title: 1047-CR-L5-R2

description:
pair 1, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 1, layer L5, diagnosis Control, replicate R2


title: 1099-CR-L5-R2

description:
pair 11, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 11, layer L5, diagnosis Control, replicate R2


title: 1222-SZ-L5-R2

description:
pair 8, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 8, layer L5, diagnosis Schiz, replicate R2


title: 1173-SZ-L3-R1

description:
pair 4, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 4, layer L3, diagnosis Schiz, replicate R1


title: 10024-SZ-L3-R1

description:
pair 12, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 12, layer L3, diagnosis Schiz, replicate R1


title: 10020-SZ-L5-R2

description:
pair 10, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 10, layer L5, diagnosis Schiz, replicate R2


title: 1159-CR-L3-R1

description:
pair 15, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 15, layer L3, diagnosis Control, replicate R1


title: 1159-CR-L3-R2

description:
pair 15, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 15, layer L3, diagnosis Control, replicate R2


title: 10020-SZ-L3-R1

description:
pair 10, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 10, layer L3, diagnosis Schiz, replicate R1


title: 10024-SZ-L5-R1

description:
pair 12, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 12, layer L5, diagnosis Schiz, replicate R1


title: 1159-CR-L5-R2

description:
pair 15, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 15, layer L5, diagnosis Control, replicate R2


title: 1211-SZ-L5-R1

description:
pair 14, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 14, layer L5, diagnosis Schiz, replicate R1


title: 1047-CR-L5-R1

description:
pair 1, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 1, layer L5, diagnosis Control, replicate R1


title: 1047-CR-L3-R2

description:
pair 1, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 1, layer L3, diagnosis Control, replicate R2


title: 1211-SZ-L5-R2

description:
pair 14, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 14, layer L5, diagnosis Schiz, replicate R2


title: 10024-SZ-L3-R2

description:
pair 12, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 12, layer L3, diagnosis Schiz, replicate R2


title: 10020-SZ-L5-R1

description:
pair 10, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 10, layer L5, diagnosis Schiz, replicate R1


title: 1282-CR-L5-R1

description:
pair 14, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 14, layer L5, diagnosis Control, replicate R1


title: 1086-CR-L5-R1

description:
pair 2, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 2, layer L5, diagnosis Control, replicate R1


title: 1122-CR-L5-R2

description:
pair 5, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 5, layer L5, diagnosis Control, replicate R2


title: 1211-SZ-L3-R2

description:
pair 14, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 14, layer L3, diagnosis Schiz, replicate R2


title: 1191-CR-L3-R1

description:
pair 7, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 7, layer L3, diagnosis Control, replicate R1


title: 1209-SZ-L3-R2

description:
pair 1, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 1, layer L3, diagnosis Schiz, replicate R2


title: 930-SZ-L5-R1

description:
pair 35, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 35, layer L5, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia; ADR; OAR


title: 1296-SZ-L3-R1

description:
pair 15, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 15, layer L3, diagnosis Schiz, replicate R1


title: 1122-CR-L3-R1

description:
pair 5, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 5, layer L3, diagnosis Control, replicate R1


title: 1188-SZ-L5-R2

description:
pair 6, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 6, layer L5, diagnosis Schiz, replicate R2

value: Undifferentiated schizophrenia; AAR; OAR


title: 604-CR-L5-R1

description:
pair 21, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 21, layer L5, diagnosis Control, replicate R1


title: 1191-CR-L5-R2

description:
pair 7, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 7, layer L5, diagnosis Control, replicate R2


title: 1122-CR-L5-R1

description:
pair 5, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 5, layer L5, diagnosis Control, replicate R1


title: 1188-SZ-L3-R1

description:
pair 6, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 6, layer L3, diagnosis Schiz, replicate R1


title: 987-CR-L3-R1

description:
pair 34, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 34, layer L3, diagnosis Control, replicate R1


title: 1324-CR-L3-R2

description:
pair 10, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 10, layer L3, diagnosis Control, replicate R2


title: 656-SZ-L3-R1

description:
pair 31, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 31, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ADC


title: 1191-CR-L5-R1

description:
pair 7, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 7, layer L5, diagnosis Control, replicate R1


title: 852-CR-L3-R1

description:
pair 33, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 33, layer L3, diagnosis Control, replicate R1


title: 1296-SZ-L5-R1

description:
pair 15, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 15, layer L5, diagnosis Schiz, replicate R1


title: 1296-SZ-L5-R2

description:
pair 15, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 15, layer L5, diagnosis Schiz, replicate R2


title: 1324-CR-L5-R2

description:
pair 10, layer L5, diagnosis Control, replicate R2
Gene expression data for pair 10, layer L5, diagnosis Control, replicate R2


title: 822-CR-L5-R1

description:
pair 26, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 26, layer L5, diagnosis Control, replicate R1


title: 1324-CR-L5-R1

description:
pair 10, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 10, layer L5, diagnosis Control, replicate R1


title: 1296-SZ-L3-R2

description:
pair 15, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 15, layer L3, diagnosis Schiz, replicate R2


title: 1188-SZ-L3-R2

description:
pair 6, layer L3, diagnosis Schiz, replicate R2
Gene expression data for pair 6, layer L3, diagnosis Schiz, replicate R2


title: 1188-SZ-L5-R1

description:
pair 6, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 6, layer L5, diagnosis Schiz, replicate R1


title: 1122-CR-L3-R2

description:
pair 5, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 5, layer L3, diagnosis Control, replicate R2


title: 634-CR-L3-R1

description:
pair 32, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 32, layer L3, diagnosis Control, replicate R1


title: 1191-CR-L3-R2

description:
pair 7, layer L3, diagnosis Control, replicate R2
Gene expression data for pair 7, layer L3, diagnosis Control, replicate R2


title: 806-CR-L3-R1

description:
pair 25, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 25, layer L3, diagnosis Control, replicate R1


title: 1324-CR-L3-R1

description:
pair 10, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 10, layer L3, diagnosis Control, replicate R1


title: 739-CR-L3-R1

description:
pair 36, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 36, layer L3, diagnosis Control, replicate R1


title: 722-SZ-L5-R1

description:
pair 32, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 32, layer L5, diagnosis Schiz, replicate R1

value: Chronic undifferentiated schizophrenia; ODR; OAR


title: 566-SZ-L5-R1

description:
pair 20, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 20, layer L5, diagnosis Schiz, replicate R1

value: Chronic undifferentiated schizophrenia; AAR


title: 1322-CR-L3-R1

description:
pair 20, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 20, layer L3, diagnosis Control, replicate R1


title: 787-SZ-L5-R1

description:
pair 26, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 26, layer L5, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ODC


title: 988-CR-L5-R1

description:
pair 30, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 30, layer L5, diagnosis Control, replicate R1


title: 781-SZ-L3-R1

description:
pair 33, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 33, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ADR


title: 700-CR-L3-R1

description:
pair 29, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 29, layer L3, diagnosis Control, replicate R1


title: 1322-CR-L5-R1

description:
pair 20, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 20, layer L5, diagnosis Control, replicate R1


title: 871-CR-L5-R1

description:
pair 28, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 28, layer L5, diagnosis Control, replicate R1


title: 739-CR-L5-R1

description:
pair 36, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 36, layer L5, diagnosis Control, replicate R1


title: 829-SZ-L3-R1

description:
pair 27, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 27, layer L3, diagnosis Schiz, replicate R1

value: Schizoaffective disorder; ADC; OAR


title: 604-CR-L3-R1

description:
pair 21, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 21, layer L3, diagnosis Control, replicate R1


title: 625-SZ-L5-R1

description:
pair 23, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 23, layer L5, diagnosis Schiz, replicate R1

value: Chronic disorganized schizophrenia; AAC


title: 878-SZ-L3-R1

description:
pair 28, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 28, layer L3, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia; ADC


title: 539-SZ-L3-R1

description:
pair 29, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 29, layer L3, diagnosis Schiz, replicate R1


title: 933-SZ-L3-R1

description:
pair 36, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 36, layer L3, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia


title: 857-CR-L3-R1

description:
pair 35, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 35, layer L3, diagnosis Control, replicate R1

value: dorsolateral prefrontal cortex


title: 802-SZ-L3-R1

description:
pair 34, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 34, layer L3, diagnosis Schiz, replicate R1

value: pyramidal neuron cell

value: Schizoaffective disorder; ADC; ODR


title: 640-SZ-L3-R1

description:
pair 24, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 24, layer L3, diagnosis Schiz, replicate R1

value: Chronic paranoid schizophrenia


title: 551-CR-L3-R1

description:
pair 23, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 23, layer L3, diagnosis Control, replicate R1

value: Unaffected Comparison


title: 592-CR-L3-R1

description:
pair 18, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 18, layer L3, diagnosis Control, replicate R1


title: 567-CR-L5-R1

description:
pair 19, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 19, layer L5, diagnosis Control, replicate R1


title: 987-CR-L5-R1

description:
pair 34, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 34, layer L5, diagnosis Control, replicate R1


title: 806-CR-L5-R1

description:
pair 25, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 25, layer L5, diagnosis Control, replicate R1


title: 621-SZ-L3-R1

description:
pair 30, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 30, layer L3, diagnosis Schiz, replicate R1

value: Chronic undifferentiated schizophrenia


title: 1047-CR-L3-R1

description:
pair 1, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 1, layer L3, diagnosis Control, replicate R1


title: 533-SZ-L5-R1

description:
pair 18, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 18, layer L5, diagnosis Schiz, replicate R1


title: 930-SZ-L3-R1

description:
pair 35, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 35, layer L3, diagnosis Schiz, replicate R1

value: Disorganized schizophrenia; ADR; OAR


title: 625-SZ-L3-R1

description:
pair 23, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 23, layer L3, diagnosis Schiz, replicate R1


title: 822-CR-L3-R1

description:
pair 26, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 26, layer L3, diagnosis Control, replicate R1


title: 988-CR-L3-R1

description:
pair 30, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 30, layer L3, diagnosis Control, replicate R1


title: 686-CR-L3-R1

description:
pair 31, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 31, layer L3, diagnosis Control, replicate R1


title: 1209-SZ-L5-R2

description:
pair 1, layer L5, diagnosis Schiz, replicate R2
Gene expression data for pair 1, layer L5, diagnosis Schiz, replicate R2

value: Schizoaffective disorder


title: 852-CR-L5-R1

description:
pair 33, layer L5, diagnosis Control, replicate R1
Gene expression data for pair 33, layer L5, diagnosis Control, replicate R1


title: 665-SZ-L3-R1

description:
pair 25, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 25, layer L3, diagnosis Schiz, replicate R1

value: Chronic paranoid schizophrenia; ADC


title: 587-SZ-L5-R1

description:
pair 22, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 22, layer L5, diagnosis Schiz, replicate R1


title: 640-SZ-L5-R1

description:
pair 24, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 24, layer L5, diagnosis Schiz, replicate R1


title: 566-SZ-L3-R1

description:
pair 20, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 20, layer L3, diagnosis Schiz, replicate R1


title: 587-SZ-L3-R1

description:
pair 22, layer L3, diagnosis Schiz, replicate R1
Gene expression data for pair 22, layer L3, diagnosis Schiz, replicate R1


title: 829-SZ-L5-R1

description:
pair 27, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 27, layer L5, diagnosis Schiz, replicate R1


title: 539-SZ-L5-R1

description:
pair 29, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 29, layer L5, diagnosis Schiz, replicate R1


title: 581-SZ-L5-R1

description:
pair 21, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 21, layer L5, diagnosis Schiz, replicate R1

value: Chronic paranoid schizophrenia; ADC; OAC


title: 681-CR-L3-R1

description:
pair 24, layer L3, diagnosis Control, replicate R1
Gene expression data for pair 24, layer L3, diagnosis Control, replicate R1


title: 665-SZ-L5-R1

description:
pair 25, layer L5, diagnosis Schiz, replicate R1
Gene expression data for pair 25, layer L5, diagnosis Schiz, replicate R1