title: G392E_on_rep3

status: Public on Apr 20 2013

city: Cambridge

first: Timothy

last: Newton

address: Addenbrooke's Hospital

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Hybridization was carried out following the beadchip manufacturer's instructions (Illumina)

scan_protocol: Illumina iScan  with iScan Control Software 1.3.10+

data_processing: Raw data were pre-processed using R software (http://www.r-project.org) and the bioconductor (http://www.bioconductor.org) package lumi (Du et al., 2008).  Probes were removed from the data set where the Illimuna detection p-value was greater than 0.01.  The data were then transformed using the variance stabilisation transformation algorithm (VST) and normalised using the quantile normalisation method.  Differentially expressed genes for each condition (wild-type neuroserpin ‘on’ versus wild-type neuroserpin ‘off’, G392E neuroserpin ‘on’ versus G392E neuroserpin ‘off and Δ neuroserpin ‘on’ versus Δ neuroserpin ‘off’’) were identified by fitting linear models with the bioconductor R package limma (Smyth, 2004).  To account for multiple hypotheses testing, p-values were adjusted using the Benjamini & Hochberg False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995).  In order to assess the gene expression profiles at a pathway level, Gene Set Enrichment analysis (Subramanian et al., 2005) was performed on the normalised gene expression values for each group. Gene Set Enrichment analysis uses a priori defined gene sets to determine pathway differences between two phenotypic states.  Gene expression data is therefore evaluated at the pathway level rather than the single gene. Gene Set Enrichment analysis first ranks the genes according to their relative difference in gene expression.  The ranked list is then compared to gene sets (pathways) and an enrichment score (ES) is calculated for each gene.  When a gene is present in the gene set of interest, the running enrichment score is increased.  If the gene is absent the running enrichment score is decreased.  The enrichment statistic is the maximum deviation of the running enrichment score from zero.  Statistical significance is assessed by performing a permutation test procedure.  To account for the differences in gene set size, a normalised enrichment score (NES) is calculated.  Estimated significance levels are also adjusted for multiple hypothesis testing.  False Discovery Rate (FDR) is the estimated probability that a gene set with a given enrichment statistic represents a false-positive finding.  A total of 639 pathways (gene sets) were analysed from Kyoto Encyclopedia of Genes and Genomes, Reactome, and BioCarta databases (http://www.genome.jp/kegg/pathway.html, http://www.reactome.org/ and http://www.biocarta.com/genes/index.asp respectively). Gene sets containing less than 15 and greater than 500 genes were filtered out, along with gene sets containing no genes from the input data set.

source_name: G392E, 2 ug/ml doxycycline

label_protocol: Sample was labelled with biotin as part of the Ambion Total Prep kit (Ambion, UK) protocol.

growth_protocol: 250,000 Cells per well were grown in six well plates for 72 hours.  The cells were cultured in DMEM supplemented with 10% v/v Tet-free approved FBS (Clontech), 200 µg/ml Geneticin and 100 µg/ml Hygromycin B (both selective antibiotics from Invitrogen, Paisley, UK), at 37°C and 5% v/v CO2 in a humidified incubator.

extract_protocol: Cells were collected by trypsinisation and pelleted at 700 g for 10 min at 4⁰C.  RNA was isolated with Tri Reagent (Sigma).  RNA amplification was performed using Ambion Total Prep kit (Ambion, UK)

treatment_protocol: Neuroserpin expression was induced in 'on' samples with 2 ug/ml doxycycline 48 hours before collection.  'off' samples remained untreated.

tag: cell type

value: HeLa

tag: genotype/variation

value: Transfected with G392E Neuroserpin


title: G392E_on_rep2

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens


title: G392E_off_rep2

source_name: G392E, no doxycycline


title: G392E_off_rep3


title: G392E_on_rep1


title: Rv3286c OE by ATc 100 ng Atc 18 Hours TFOE_9544_3286c

status: Public on Feb 19 2013

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

country: USA

institute: Seattle Biomedical Research Institute

description:
TFOE_9544_3286c
Rv3286c OE by ATc
18
Hours
100
ng

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization with the 'affy' package for R.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: TFOE experiments done at indicated concentration of anhydrotetracycline.  Hypoxic experiments conducted as described previously (Rustad et al., 2008)

tag: experiment

tag: time

value: 18 Hours

tag: dose

value: 100 ng Atc

tag: treatment

value: Rv3286c OE by ATc


title: Colon_control_repl3

status: Public on Mar 11 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat (control) diet , replicate 3

hyb_protocol: Hybridization, washing and scanning of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

organism: Mus musculus

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

extract_protocol: Total RNA was prepared from colonic scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice were fed a low fat control diet for 2 weeks. After this adaptation period, mice were stratified according to their body weight and allocated to the control diet group (n=5, low fat diet) or inulin diet group (n=6, low fat diet with 10% w/w corn starch replaced by inulin). After 10 days of dietary intervention, mice were fasted overnight and subsequently provided with 1 g of experimental diet. After 4 hours, mice were anesthetized using isoflurane and sacrificed by cervical dislocation. Colon was removed, mucosal scrapings were collected, snap-frozen in liquid nitrogen and stored at −80°C (scrapings).

tag: strain/background

tag: gender

value: male

tag: age

value: 12 weeks

tag: tissue

value: colonic mucosal scrapings


title: Rv3334 OE by ATc 100 ng Atc 18 Hours TFOE_9642_3334

description:
TFOE_9642_3334
Rv3334 OE by ATc
18
Hours
100
ng

tag: replicate

value: A

value: Rv3334 OE by ATc


title: G392E_off_rep1


title: Colon_inulin_repl5

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 5


title: Rv0324 OE by ATc 100 ng Atc 18 Hours TFOE_8699_0324

description:
TFOE_8699_0324
Rv0324 OE by ATc
18
Hours
100
ng

value: Rv0324 OE by ATc


title: Rv3223c OE by ATc 100 ng Atc 18 Hours TFOE_9004_3223c

description:
TFOE_9004_3223c
Rv3223c OE by ATc
18
Hours
100
ng

value: Rv3223c OE by ATc


title: Rv0465c OE by ATc 100 ng Atc 18 Hours TFOE_8951_0465c_c

description:
TFOE_8951_0465c_c
Rv0465c OE by ATc
18
Hours
100
ng

value: C

value: Rv0465c OE by ATc


title: Rv3830c OE by ATc 100 ng Atc 18 Hours TFOE_9939_3830c

description:
TFOE_9939_3830c
Rv3830c OE by ATc
18
Hours
100
ng

value: Rv3830c OE by ATc


title: Rv3133c OE by ATc 100 ng Atc 18 Hours TFOE_9652_3133c_A

description:
TFOE_9652_3133c_A
Rv3133c OE by ATc
18
Hours
100
ng

value: Rv3133c OE by ATc


title: Rv2506 OE by ATc 100 ng Atc 18 Hours TFOE_8765_2506

description:
TFOE_8765_2506
Rv2506 OE by ATc
18
Hours
100
ng

value: Rv2506 OE by ATc


title: Colon_control_repl1

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat (control) diet , replicate 1


title: Colon_inulin_repl6

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 6


title: Rv0353 OE by Atc 100 ng Atc 18 Hours TFOE_9336_0353

description:
TFOE_9336_0353
Rv0353 OE by Atc
18
Hours
100
ng

value: Rv0353 OE by Atc


title: Colon_control_repl4

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat (control) diet , replicate 4


title: Rv2069 OE by Atc 100 ng Atc 18 Hours TFOE_9229_2069

description:
TFOE_9229_2069
Rv2069 OE by Atc
18
Hours
100
ng

value: Rv2069 OE by Atc


title: Colon_control_repl5

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat (control) diet , replicate 5


title: Rv1909c OE by ATc 100 ng Atc 18 Hours TFOE_9243_1909c

description:
TFOE_9243_1909c
Rv1909c OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv1909c OE by ATc


title: Colon_inulin_repl4

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 4


title: Colon_inulin_repl3

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 3


title: Rv3855 OE by ATc 100 ng Atc 18 Hours TFOE_9032_3855

description:
TFOE_9032_3855
Rv3855 OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv3855 OE by ATc


title: Rv0602c OE by ATc 100 ng Atc 18 Hours TFOE_8883_0602c

description:
TFOE_8883_0602c
Rv0602c OE by ATc
18
Hours
100
ng

value: Rv0602c OE by ATc


title: Colon_inulin_repl2

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 2

value: male

value: 12 weeks

value: colonic mucosal scrapings


title: Colon_inulin_repl1

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat diet supplemented with 10% (w/w) inulin (at the expense of corn starch), replicate 1


title: Colon_control_repl2

description: scraped-off epithelial cells of mouse colon, after 10 days on a low fat (control) diet , replicate 2


title: Rv0981 OE by ATc 100 ng Atc 18 Hours TFOE_8486_0981_b

description:
TFOE_8486_0981_b
Rv0981 OE by ATc
18
Hours
100
ng

value: B

value: Rv0981 OE by ATc


title: Rv2374c OE by ATc 100 ng Atc 18 Hours TFOE_9916_2374c

description:
TFOE_9916_2374c
Rv2374c OE by ATc
18
Hours
100
ng

value: A

value: Rv2374c OE by ATc


title: Rv3849 OE by ATc 100 ng Atc 18 Hours TFOE_8192_3849

description:
TFOE_8192_3849
Rv3849 OE by ATc
18
Hours
100
ng

value: Rv3849 OE by ATc


title: Rv2703 OE by ATc 100 ng Atc 18 Hours TFOE_9973_2703

description:
TFOE_9973_2703
Rv2703 OE by ATc
18
Hours
100
ng

value: Rv2703 OE by ATc


title: Rv1473A OE by ATc 100 ng Atc 18 Hours TFOE_7293_1473A

description:
TFOE_7293_1473A
Rv1473A OE by ATc
18
Hours
100
ng

value: Rv1473A OE by ATc


title: Rv3133c OE by ATc 100 ng Atc 18 Hours TFOE_7016_3133c_C

description:
TFOE_7016_3133c_C
Rv3133c OE by ATc
18
Hours
100
ng

value: C

value: Rv3133c OE by ATc


title: Rv3840 OE by ATc 100 ng Atc 18 Hours TFOE_7414_3840

description:
TFOE_7414_3840
Rv3840 OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv3840 OE by ATc


title: Rv0465c-b OE by ATc 100 ng Atc 18 Hours TFOE_7861_0465c_b

description:
TFOE_7861_0465c_b
Rv0465c-b OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv0465c-b OE by ATc


title: Rv1332 OE by ATc 100 ng Atc 18 Hours TFOE_7099_1332

description:
TFOE_7099_1332
Rv1332 OE by ATc
18
Hours
100
ng

value: Rv1332 OE by ATc


title: Rv3249c OE by ATc 100 ng Atc 18 Hours TFOE_8008_3249c

description:
TFOE_8008_3249c
Rv3249c OE by ATc
18
Hours
100
ng

value: Rv3249c OE by ATc


title: Rv3160c OE by ATc 100 ng Atc 18 Hours TFOE_7537_3160c

description:
TFOE_7537_3160c
Rv3160c OE by ATc
18
Hours
100
ng

value: Rv3160c OE by ATc


title: Rv2034 OE by ATc 100 ng Atc 18 Hours TFOE_7000_2034

description:
TFOE_7000_2034
Rv2034 OE by ATc
18
Hours
100
ng

value: Rv2034 OE by ATc


title: Rv0586 OE by ATc 100 ng Atc 18 Hours TFOE_6778_0586

description:
TFOE_6778_0586
Rv0586 OE by ATc
18
Hours
100
ng

value: Rv0586 OE by ATc


title: Rv2324 OE by ATc 100 ng Atc 18 Hours TFOE_7476_2324

description:
TFOE_7476_2324
Rv2324 OE by ATc
18
Hours
100
ng

value: B

value: Rv2324 OE by ATc


title: Rv1674c OE by ATc 100 ng Atc 18 Hours TFOE_7826_1674c

description:
TFOE_7826_1674c
Rv1674c OE by ATc
18
Hours
100
ng

value: Rv1674c OE by ATc


title: Rv1846c OE by ATc 100 ng Atc 18 Hours TFOE_6565_1846c

description:
TFOE_6565_1846c
Rv1846c OE by ATc
18
Hours
100
ng

value: Rv1846c OE by ATc


title: Rv1560 OE by ATc 100 ng Atc 18 Hours TFOE_7581_1560

description:
TFOE_7581_1560
Rv1560 OE by ATc
18
Hours
100
ng

value: Rv1560 OE by ATc


title: Rv1773c OE by ATc 100 ng Atc 18 Hours TFOE_7984_1773c

description:
TFOE_7984_1773c
Rv1773c OE by ATc
18
Hours
100
ng

value: Rv1773c OE by ATc


title: Rv2034 OE by ATc 100 ng Atc 18 Hours TFOE_6378_2034

description:
TFOE_6378_2034
Rv2034 OE by ATc
18
Hours
100
ng

value: A


title: Rv1255c OE by ATc 100 ng Atc 18 Hours TFOE_8005_1255c

description:
TFOE_8005_1255c
Rv1255c OE by ATc
18
Hours
100
ng

value: Rv1255c OE by ATc


title: Rv3183 OE by ATc 100 ng Atc 18 Hours TFOE_6841_3183

description:
TFOE_6841_3183
Rv3183 OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv3183 OE by ATc


title: Rv0827c OE by ATc 100 ng Atc 18 Hours TFOE_7662_0827c_A

description:
TFOE_7662_0827c_A
Rv0827c OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv0827c OE by ATc


title: Rv3405c OE by ATc 100 ng Atc 18 Hours TFOE_6644_3405c

description:
TFOE_6644_3405c
Rv3405c OE by ATc
18
Hours
100
ng

value: Rv3405c OE by ATc


title: Rv2258c OE by ATc 100 ng Atc 18 Hours TFOE_6543_2258c

description:
TFOE_6543_2258c
Rv2258c OE by ATc
18
Hours
100
ng

value: Rv2258c OE by ATc


title: Rv3862c OE by ATc 100 ng Atc 18 Hours TFOE_6830_3862c

description:
TFOE_6830_3862c
Rv3862c OE by ATc
18
Hours
100
ng

value: Rv3862c OE by ATc


title: Rv0324 OE by ATc 100 ng Atc 18 Hours TFOE_6147_0324

description:
TFOE_6147_0324
Rv0324 OE by ATc
18
Hours
100
ng

value: Rv0324 OE by ATc


title: Rv2642 OE by ATc 100 ng Atc 18 Hours TFOE_6112_2642

description:
TFOE_6112_2642
Rv2642 OE by ATc
18
Hours
100
ng

value: Rv2642 OE by ATc


title: Rv1152 OE by ATc 100 ng Atc 18 Hours TFOE_6301_1152_B

description:
TFOE_6301_1152_B
Rv1152 OE by ATc
18
Hours
100
ng

value: C

value: Rv1152 OE by ATc


title: Rv2478c OE by Atc 100 ng Atc 18 Hours TFOE_6098_2478c

description:
TFOE_6098_2478c
Rv2478c OE by Atc
18
Hours
100
ng

value: Rv2478c OE by Atc


title: Rv1353c OE by Atc 100 ng Atc 18 Hours TFOE_5958_1353c

description:
TFOE_5958_1353c
Rv1353c OE by Atc
18
Hours
100
ng

value: Rv1353c OE by Atc


title: Rv3291c OE by ATc 100 ng Atc 18 Hours TFOE_6107_3291c

description:
TFOE_6107_3291c
Rv3291c OE by ATc
18
Hours
100
ng

value: Rv3291c OE by ATc


title: Rv1460 OE by ATc 100 ng Atc 18 Hours TFOE_4497_1460

description:
TFOE_4497_1460
Rv1460 OE by ATc
18
Hours
100
ng

value: Rv1460 OE by ATc


title: Rv3249c OE by ATc 100 ng Atc 18 Hours TFOE_5586_3249c

description:
TFOE_5586_3249c
Rv3249c OE by ATc
18
Hours
100
ng

value: A

value: Rv3249c OE by ATc


title: Rv3167c OE by ATc 100 ng Atc 18 Hours TFOE_5913_3167c

description:
TFOE_5913_3167c
Rv3167c OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv3167c OE by ATc


title: Rv3295 OE by ATc 100 ng Atc 18 Hours TFOE_5343_3295

description:
TFOE_5343_3295
Rv3295 OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv3295 OE by ATc


title: Rv0623 OE by ATc 100 ng Atc 18 Hours TFOE_5381_0623

description:
TFOE_5381_0623
Rv0623 OE by ATc
18
Hours
100
ng

value: Rv0623 OE by ATc


title: Rv1423 OE by ATc 100 ng Atc 18 Hours TFOE_5292_1423

description:
TFOE_5292_1423
Rv1423 OE by ATc
18
Hours
100
ng

value: Rv1423 OE by ATc


title: Rv3597c OE by ATc 100 ng Atc 18 Hours TFOE_5338_3597c

description:
TFOE_5338_3597c
Rv3597c OE by ATc
18
Hours
100
ng

value: Rv3597c OE by ATc


title: Rv0818 OE by Atc 100 ng Atc 18 Hours TFOE_6079_0818

description:
TFOE_6079_0818
Rv0818 OE by Atc
18
Hours
100
ng

value: Rv0818 OE by Atc


title: Rv3301c OE by ATc 100 ng Atc 18 Hours TFOE_4398_3301c

description:
TFOE_4398_3301c
Rv3301c OE by ATc
18
Hours
100
ng

value: Rv3301c OE by ATc


title: Rv2359 OE by ATc 100 ng Atc 18 Hours TFOE_4270_2359

description:
TFOE_4270_2359
Rv2359 OE by ATc
18
Hours
100
ng

value: C

value: Rv2359 OE by ATc


title: Rv0330c OE by Atc 100 ng Atc 18 Hours TFOE_4688_0330c

description:
TFOE_4688_0330c
Rv0330c OE by Atc
18
Hours
100
ng

value: Rv0330c OE by Atc


title: Rv2017 OE by Atc 100 ng Atc 18 Hours TFOE_5219_2017

description:
TFOE_5219_2017
Rv2017 OE by Atc
18
Hours
100
ng

value: Rv2017 OE by Atc


title: Rv1267c OE by ATc 100 ng Atc 18 Hours TFOE_5216_1267c

description:
TFOE_5216_1267c
Rv1267c OE by ATc
18
Hours
100
ng

value: Rv1267c OE by ATc


title: Rv3219 OE by ATc 100 ng Atc 18 Hours TFOE_4681_3219

description:
TFOE_4681_3219
Rv3219 OE by ATc
18
Hours
100
ng

value: Rv3219 OE by ATc


title: Rv2324 OE by ATc 100 ng Atc 18 Hours TFOE_5002_2324

description:
TFOE_5002_2324
Rv2324 OE by ATc
18
Hours
100
ng

value: A

value: Rv2324 OE by ATc


title: Rv3124 OE by ATc 100 ng Atc 18 Hours TFOE_4863_3124

description:
TFOE_4863_3124
Rv3124 OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv3124 OE by ATc


title: Rv1189 OE by ATc 100 ng Atc 18 Hours TFOE_5112_1189

description:
TFOE_5112_1189
Rv1189 OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv1189 OE by ATc


title: Rv2258c OE by Atc 100 ng Atc 18 Hours TFOE_5114_2258c

description:
TFOE_5114_2258c
Rv2258c OE by Atc
18
Hours
100
ng

value: Rv2258c OE by Atc


title: Rv3133c OE by ATc 100 ng Atc 18 Hours TFOE_4265_3133c_B

description:
TFOE_4265_3133c_B
Rv3133c OE by ATc
18
Hours
100
ng

value: B

value: Rv3133c OE by ATc


title: Rv1994c OE by ATc 100 ng Atc 18 Hours TFOE_4221_1994c

description:
TFOE_4221_1994c
Rv1994c OE by ATc
18
Hours
100
ng

value: Rv1994c OE by ATc


title: Rv3143 OE by ATc 100 ng Atc 18 Hours TFOE_3883_3143

description:
TFOE_3883_3143
Rv3143 OE by ATc
18
Hours
100
ng

value: Rv3143 OE by ATc


title: Rv3060c OE by ATc 100 ng Atc 18 Hours TFOE_5383_3060c

description:
TFOE_5383_3060c
Rv3060c OE by ATc
18
Hours
100
ng

value: Rv3060c OE by ATc


title: Rv3246c OE by ATc 100 ng Atc 18 Hours TFOE_5371_3246c

description:
TFOE_5371_3246c
Rv3246c OE by ATc
18
Hours
100
ng

value: Rv3246c OE by ATc


title: Rv3583c OE by ATc 100 ng Atc 18 Hours TFOE_4577_3583c

description:
TFOE_4577_3583c
Rv3583c OE by ATc
18
Hours
100
ng

value: Rv3583c OE by ATc


title: Rv0324 OE by ATc 100 ng Atc 18 Hours TFOE_3809_0324

description:
TFOE_3809_0324
Rv0324 OE by ATc
18
Hours
100
ng

value: C

value: Rv0324 OE by ATc


title: Rv1027c OE by ATc 100 ng Atc 18 Hours TFOE_3781_1027c 1

description:
TFOE_3781_1027c 1
Rv1027c OE by ATc
18
Hours
100
ng

value: Rv1027c OE by ATc


title: Rv3574 OE by ATc 100 ng Atc 18 Hours TFOE_4186_3574_B

description:
TFOE_4186_3574_B
Rv3574 OE by ATc
18
Hours
100
ng

value: Rv3574 OE by ATc


title: Rv3133c OE by ATc 1 ng Atc 18 Hours TFOE_3722_3133c__1.0

description:
TFOE_3722_3133c__1.0
Rv3133c OE by ATc
18
Hours
1
ng

value: Rv3133c-Atc dilution

value: 1 ng Atc


title: Rv1221 OE by ATc 100 ng Atc 18 Hours TFOE_3680_1221

description:
TFOE_3680_1221
Rv1221 OE by ATc
18
Hours
100
ng

value: A

value: 18 Hours

value: Rv1221 OE by ATc


title: Rv0681 OE by ATc 100 ng Atc 18 Hours TFOE_3679_0681

description:
TFOE_3679_0681
Rv0681 OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv0681 OE by ATc


title: Rv1176c OE by ATc 100 ng Atc 18 Hours TFOE_4001_1176c

description:
TFOE_4001_1176c
Rv1176c OE by ATc
18
Hours
100
ng

value: Rv1176c OE by ATc


title: Rv3597c OE by ATc 100 ng Atc 18 Hours TFOE_3373_3597c

description:
TFOE_3373_3597c
Rv3597c OE by ATc
18
Hours
100
ng

value: B

value: Rv3597c OE by ATc


title: Rv1359 OE by ATc 100 ng Atc 18 Hours TFOE_3603_1359

description:
TFOE_3603_1359
Rv1359 OE by ATc
18
Hours
100
ng

value: Rv1359 OE by ATc


title: Rv3574 OE by ATc 100 ng Atc 18 Hours TFOE_3005_3574_A

description:
TFOE_3005_3574_A
Rv3574 OE by ATc
18
Hours
100
ng


title: Rv1719 OE by ATc 100 ng Atc 18 Hours TFOE_3497_1719

description:
TFOE_3497_1719
Rv1719 OE by ATc
18
Hours
100
ng

value: Rv1719 OE by ATc


title: Rv1395 OE by ATc 100 ng Atc 18 Hours TFOE_3534_1395

description:
TFOE_3534_1395
Rv1395 OE by ATc
18
Hours
100
ng

value: Rv1395 OE by ATc


title: Rv0452 OE by ATc 100 ng Atc 18 Hours TFOE_2520_0452

description:
TFOE_2520_0452
Rv0452 OE by ATc
18
Hours
100
ng

value: Rv0452 OE by ATc


title: Rv1985b2 OE by ATc 100 ng Atc 18 Hours TFOE_2686_1985b2

description:
TFOE_2686_1985b2
Rv1985b2 OE by ATc
18
Hours
100
ng

value: Rv1985b2 OE by ATc


title: Rv1556 OE by ATc 100 ng Atc 18 Hours TFOE_2914_1556

description:
TFOE_2914_1556
Rv1556 OE by ATc
18
Hours
100
ng

value: Rv1556 OE by ATc


title: Rv2887 OE by ATc 100 ng Atc 18 Hours TFOE_2591_2887

description:
TFOE_2591_2887
Rv2887 OE by ATc
18
Hours
100
ng

value: Rv2887 OE by ATc


title: Rv2989 OE by ATc 100 ng Atc 18 Hours TFOE_3550_2989

description:
TFOE_3550_2989
Rv2989 OE by ATc
18
Hours
100
ng

value: Rv2989 OE by ATc


title: Rv0653c OE by ATc 100 ng Atc 18 Hours TFOE_3642_0653c

description:
TFOE_3642_0653c
Rv0653c OE by ATc
18
Hours
100
ng

value: Rv0653c OE by ATc


title: Rv3066 OE by ATc 100 ng Atc 18 Hours TFOE_2629_3066

description:
TFOE_2629_3066
Rv3066 OE by ATc
18
Hours
100
ng

value: A

value: Rv3066 OE by ATc


title: Rv0465c-a OE by ATc 100 ng Atc 18 Hours TFOE_2670_0465c_a

description:
TFOE_2670_0465c_a
Rv0465c-a OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv0465c-a OE by ATc


title: Rv1657 OE by ATc 100 ng Atc 18 Hours TFOE_2216_1657

description:
TFOE_2216_1657
Rv1657 OE by ATc
18
Hours
100
ng

value: 100 ng Atc

value: Rv1657 OE by ATc


title: Rv3260c OE by ATc 100 ng Atc 18 Hours TFOE_2104_3260c

description:
TFOE_2104_3260c
Rv3260c OE by ATc
18
Hours
100
ng

value: Rv3260c OE by ATc


title: Rv1287 OE by ATc 100 ng Atc 18 Hours TFOE_1741_1287

description:
TFOE_1741_1287
Rv1287 OE by ATc
18
Hours
100
ng

value: B

value: Rv1287 OE by ATc


title: Rv2640c OE by Atc 100 ng Atc 18 Hours TFOE_1608_2640c

description:
TFOE_1608_2640c
Rv2640c OE by Atc
18
Hours
100
ng

value: Rv2640c OE by Atc


title: Rv1186c OE by Atc 100 ng Atc 18 Hours TFOE_1808_1186c

description:
TFOE_1808_1186c
Rv1186c OE by Atc
18
Hours
100
ng

value: Rv1186c OE by Atc


title: Rv2175c OE by Atc 100 ng Atc 18 Hours TFOE_1515_2175c

description:
TFOE_1515_2175c
Rv2175c OE by Atc
18
Hours
100
ng

value: Rv2175c OE by Atc


title: Rv1152 OE by ATc 100 ng Atc 18 Hours TFOE_1474_1152

description:
TFOE_1474_1152
Rv1152 OE by ATc
18
Hours
100
ng

value: Rv1152 OE by ATc


title: Rv2621c OE by ATc 100 ng Atc 18 Hours TFOE_1371_2621c

description:
TFOE_1371_2621c
Rv2621c OE by ATc
18
Hours
100
ng

value: Rv2621c OE by ATc


title: genomic DNA from cerebellum_6057825115_R02C01_Cohort 3A

status: Public on Jan 24 2013

type: genomic

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

institute: King's College London

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2011.1 used to generate the raw intensity file (unmethylated and methylated signal intensities).
Data used in the development of the R wateRmelon package for analysis of Illumina Infinium450 Human Methylation data.
The GenomeStudio v2011.1-computed Average Betas (normalized) is betaqn_geo_all cohorts.csv.
Thirteen other wateRmelon-generated normalized beta matrices include:
danen_geo_all cohorts.csv
danes_geo_all cohorts.csv
danet_geo_all cohorts.csv
daten1_geo_all cohorts.csv
daten2_geo_all cohorts.csv
fuks_geo_all cohorts.csv
nanes_geo_all cohorts.csv
nanet_geo_all cohorts.csv
nasen_geo_all cohorts.csv
naten_geo_all cohorts.csv
swan_geo_all cohorts.csv
tost_geo_all cohorts.csv
dasen_geo_all cohorts.csv

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from post-mortem brain or blood samples using phenol-chloroform protocol according to standard instructions

tag: subjectid

tag: barcode

tag: lunnonetal

value: FALSE

tag: Sex

tag: source tissue

value: cerebellum


title: genomic DNA from cerebellum_6057825115_R06C01_Cohort 3A


title: Erythroid TAL1

status: Public on Jan 28 2013

type: SRA

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: Raw data (fastq, SRA) is missing for this TAL1 chIP-seq dataset

library_source: genomic

data_processing:
Basecalls were performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the hg18 genome assembly using elandv2.
The eland extended format alignments were converted to bed format using the elandextended2bed.py script.
Peaks were called against the total input sample using macs version 1.4.0rc2 with default parameters.
Quality scores in the fastq files were converted from Illumina1.3 to sanger using the fq_all2std.pl script.
Genome_build: hg18
Supplementary_files_format_and_content: The macs peaks.bed output files have a fifth field that is -10*log10(pvalue)

source_name: R3/R4 Erythroid cells

growth_protocol: Human CD34+-selected stem and progenitor cells were obtained from the Yale Center for Excellence in Molecular Hematology. To obtain primary human erythroid cells, CD34+ cells were cultured and selected as described.(Panzenbock, B., Bartunek, P., Mapara, M. Y., and Zenke, M. (1998) Blood 92, 3658-3668. Migliaccio, A. R., Migliaccio, G., Di Baldassarre, A., and Eddleman, K. (2002) Bone Marrow Transplant 30, 75-80) Briefly, Human CD34-selected stem and progenitor cells were cultured  for 9 to 14 days in StemSpan SF expansion medium which contains human transferrin (200 ng/ml) and insulin (10 ng/ml) (StemSpan 09650) and was supplemented with estradiol (1 micromolar), dexamethasone (1 micromolar),  Flt3 ligand (100 ng/ml), stem cell factor (100 ng/ml), interleukin-3 (50 ng/ml), interleukin-6 (20 ng/ml), insulin-like growth factor 1 (50 ng/ml), and erythropoietin (3 U/ml). FACS analysis was used to analyze cellular expression of CD71 (transferrin receptor) and CD235a (glycophorin A). These cells represent the R3/R4 cell population of nucleated erythroid cells defined by Zhang et al.(Zhang, J., Socolovsky, M., Gross, A. W., and Lodish, H. F. (2003) Blood 102, 3938-3946)

extract_protocol: Approximately 500ng of ChIP DNA was run on a 1.5% agarose gel to size select ChIP DNA in the 200-300-bp range. The size-selected ChIP DNA was purified using a gel extraction kit (Qiagen) and processed for sequencing as per manufacturer's protocol. Briefly, size-selected ChIP DNA was end repaired using an End-IT DNA end repair kit (ER0720; Epicenter), followed by addition of an adenine base at the 3′ end by Klenow reaction and Solexa adaptor ligation. The modified DNA was then PCR amplified with one initial heating step of 98°C for 30 s, followed by 15 cycles of amplification with a melting temperature of 98°C for 30 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 5 min was performed. Amplified ChIP DNA was then size selected on a 1.5% agarose gel, purified by using a gel extraction kit (Qiagen), and subjected to deep sequencing.

treatment_protocol: ChIP assays were performed as previously described with minor variations (Steiner, L. A., Maksimova, Y., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., and Gallagher, P. G. (2009) Mol Cell Biol). 1 × 107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by Dounce homogenization. Cross-linked nuclei were isolated, followed by sonication with a Covaris S2 shearing device (duty cycle 10%, intensity 5, 15 minutes), to obtain chromatin-containing DNA fragments with an average size of ~200-400bp. For each ChIP, 20 µg of antibody or the appropriate control IgG species was used. Samples were immunoprecipitated with antibodies against GATA1 (sc-265; Santa Cruz), NF-E2 (sc-22827; Santa Cruz), KLF1 (ab2483; Abcam), SCL/Tal1 (sc-12984; Santa Cruz), P300 (sc-585; Santa Cruz) and nonspecific rabbit IgG (sc-2091; Santa Cruz). The antigen-antibody complex was captured on protein G beads, washed four times with radioimmunoprecipitation assay buffer, and then washed with phosphate-buffered saline. The DNA-protein complex was eluted from the protein G beads with 1% sodium dodecyl sulfate at 65°C, and cross-linking of DNA-protein adducts was reversed by 4 hours of incubation at 65°C. After proteinase K and RNase digestion of the reverse-cross-linked sample, DNA was cleaned with the QIAquick PCR Purification Kit (Qiagen) according to manufacturer instructions.

tag: cell

value: R3/R4 Erythroid cells

tag: chip antibody


title: genomic DNA from cerebellum_6057825128_R05C01_Cohort 3A


title: Rv2242 OE by Atc 100 ng Atc 18 Hours TFOE_1260_2242

description:
TFOE_1260_2242
Rv2242 OE by Atc
18
Hours
100
ng

value: Rv2242 OE by Atc


title: Rv2250c OE by Atc 100 ng Atc 18 Hours TFOE_1288_2250c

description:
TFOE_1288_2250c
Rv2250c OE by Atc
18
Hours
100
ng

value: Rv2250c OE by Atc


title: Rv3765c OE by ATc 100 ng Atc 18 Hours TFOE_1156_3765c

description:
TFOE_1156_3765c
Rv3765c OE by ATc
18
Hours
100
ng

value: 18 Hours

value: Rv3765c OE by ATc


title: Rv2711 OE by ATc 100 ng Atc 18 Hours TFOE_0700_2711

description:
TFOE_0700_2711
Rv2711 OE by ATc
18
Hours
100
ng

value: A

value: 100 ng Atc

value: Rv2711 OE by ATc


title: genomic DNA from cerebellum_6057825128_R01C02_Cohort 3A


title: genomic DNA from cerebellum_6057825128_R03C01_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R04C02_Cohort 3A


title: Rv3681c OE by ATc 100 ng Atc 18 Hours TFOE_2092_3681c

description:
TFOE_2092_3681c
Rv3681c OE by ATc
18
Hours
100
ng

value: Rv3681c OE by ATc


title: genomic DNA from cerebellum_6057825128_R05C02_Cohort 3A


title: Rv0737 OE by ATc 100 ng Atc 18 Hours TFOE_1168_0737

description:
TFOE_1168_0737
Rv0737 OE by ATc
18
Hours
100
ng

value: Rv0737 OE by ATc


title: genomic DNA from cerebellum_6057825115_R06C02_Cohort 3A


title: genomic DNA from cerebellum_6057825128_R01C01_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R02C02_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R05C02_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R01C02_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R03C02_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R05C01_Cohort 3A


title: genomic DNA from cerebellum_6057825115_R03C01_Cohort 3A


title: genomic DNA from cerebellum_6057825128_R03C02_Cohort 3A


title: Rv1626 OE by ATc 100 ng Atc 18 Hours TFOE_0383_1626

description:
TFOE_0383_1626
Rv1626 OE by ATc
18
Hours
100
ng

value: Rv1626 OE by ATc


title: genomic DNA from cerebellum_6057825115_R04C01_Cohort 3A


title: Rv2021c OE by ATc 100 ng Atc 18 Hours TFOE_0658_2021c

description:
TFOE_0658_2021c
Rv2021c OE by ATc
18
Hours
100
ng

value: Rv2021c OE by ATc


title: genomic DNA from frontal cortex_6055432012_R04C01_Cohort2B

value: frontal cortex


title: genomic DNA from cerebellum_6057825115_R01C01_Cohort 3A


title: genomic DNA from entorhinal cortex_7796806029_R04C01_Cohort 1BC

value: entorhinal cortex


title: genomic DNA from frontal cortex_7796806029_R01C02_Cohort 1BC

value: TRUE

value: FEMALE

value: C


title: genomic DNA from frontal cortex_7796806029_R03C01_Cohort 1BC

value: MALE

value: AD


title: genomic DNA from entorhinal cortex_7796806002_R06C02_Cohort 1BC

value: E


title: genomic DNA from frontal cortex_7796806002_R05C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R03C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R05C02_Cohort 1BC

value: Exclude


title: genomic DNA from entorhinal cortex_7796806029_R06C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806002_R04C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806002_R05C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R01C01_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806002_R04C01_Cohort 1BC

value: F

value: superior temporal gyrus


title: genomic DNA from entorhinal cortex_7796806002_R02C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806002_R03C02_Cohort 1BC

value: A


title: genomic DNA from frontal cortex_7796806002_R01C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806002_R02C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806002_R01C01_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R06C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R06C01_Cohort 1BC


title: Rv0757 OE by ATc 100 ng Atc 18 Hours TFOE_2546_0757

description:
TFOE_2546_0757
Rv0757 OE by ATc
18
Hours
100
ng

value: 18 Hours

value: 100 ng Atc

value: Rv0757 OE by ATc


title: genomic DNA from frontal cortex_7796806016_R06C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R02C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806029_R04C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806029_R02C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R05C02_Cohort 1BC


title: genomic DNA from frontal cortex_7796806002_R06C01_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R05C01_Cohort 1BC


title: Rv0472c OE by Atc 100 ng Atc 18 Hours TFOE_8690_0472c

description:
TFOE_8690_0472c
Rv0472c OE by Atc
18
Hours
100
ng

value: Rv0472c OE by Atc


title: genomic DNA from entorhinal cortex_7796806016_R04C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R03C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806016_R03C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R01C01_Cohort 1BC


title: genomic DNA from frontal cortex_7796806016_R01C02_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R06C02_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R02C01_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R06C01_Cohort 1BC


title: genomic DNA from entorhinal cortex_7796806016_R04C01_Cohort 1BC


title: Rv2282c OE by Atc 100 ng Atc 18 Hours TFOE_8575_2282c

description:
TFOE_8575_2282c
Rv2282c OE by Atc
18
Hours
100
ng

value: Rv2282c OE by Atc


title: genomic DNA from frontal cortex_7796806016_R02C02_Cohort 1BC

value: frontal cortex


title: genomic DNA from frontal cortex_7786923107_R04C02_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R05C01_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R01C02_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R02C02_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R03C02_Cohort 1BC


title: genomic DNA from frontal cortex_7786923107_R03C01_Cohort 1BC


title: genomic DNA from entorhinal cortex_7786923107_R05C02_Cohort 1BC

value: entorhinal cortex


title: genomic DNA from frontal cortex_7786923107_R02C01_Cohort 1BC

value: TRUE


title: genomic DNA from cerebellum_7786923063_R06C02_Cohort 1AD

value: H

value: cerebellum


title: genomic DNA from cerebellum_7786923063_R05C02_Cohort 1AD

value: FEMALE


title: genomic DNA from superior temporal gyrus_7786923063_R05C01_Cohort 1AD

value: AD


title: Rv1956 OE by ATc 100 ng Atc 18 Hours TFOE_2915_1956

description:
TFOE_2915_1956
Rv1956 OE by ATc
18
Hours
100
ng

value: Rv1956 OE by ATc


title: genomic DNA from superior temporal gyrus_7786923063_R04C02_Cohort 1AD

value: MALE


title: genomic DNA from cerebellum_7786923063_R04C01_Cohort 1AD

value: Exclude


title: genomic DNA from superior temporal gyrus_7786923063_R03C02_Cohort 1AD

value: F

value: C

value: superior temporal gyrus


title: genomic DNA from cerebellum_7786923063_R03C01_Cohort 1AD


title: genomic DNA from entorhinal cortex_7786923107_R04C01_Cohort 1BC

value: E


title: genomic DNA from superior temporal gyrus_7786923063_R01C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923063_R01C01_Cohort 1AD


title: genomic DNA from cerebellum_7786923063_R06C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R06C01_Cohort 1AD


title: genomic DNA from entorhinal cortex_7786923107_R01C01_Cohort 1BC


title: genomic DNA from superior temporal gyrus_7786923063_R02C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806038_R05C01_Cohort 1AD


title: genomic DNA from cerebellum_7796806038_R06C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R04C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R04C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R03C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R06C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R01C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R01C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7786923046_R06C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806038_R03C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7786923046_R04C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7786923046_R02C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R05C01_Cohort 1AD


title: genomic DNA from cerebellum_7796806038_R02C01_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R05C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806038_R02C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923063_R02C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7786923046_R03C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R03C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R06C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R02C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R05C02_Cohort 1AD


title: genomic DNA from cerebellum_7786923046_R01C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806038_R05C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806022_R04C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806022_R05C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R03C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7786923046_R01C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R04C01_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R03C01_Cohort 1AD


title: genomic DNA from cerebellum_7796806022_R01C02_Cohort 1AD


title: genomic DNA from superior temporal gyrus_7796806022_R02C01_Cohort 1AD


title: genomic DNA from cerebellum_7796806022_R01C01_Cohort 1AD


title: genomic DNA from whole blood_7512560117_R05C01_Cohort 1E

value: FALSE

value: whole blood


title: genomic DNA from whole blood_7512560117_R05C02_Cohort 1E

value: blood


title: genomic DNA from whole blood_7512560117_R06C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R04C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R04C01_Cohort 1E


title: genomic DNA from whole blood_7512560117_R06C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R06C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R06C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R01C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R02C01_Cohort 1E


title: genomic DNA from whole blood_7512560117_R01C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R05C02_Cohort 1E


title: genomic DNA from whole blood_7512560157_R04C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R03C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R03C02_Cohort 1E


title: genomic DNA from whole blood_7512560157_R05C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R02C02_Cohort 1E


title: genomic DNA from whole blood_7512560157_R04C01_Cohort 1E


title: genomic DNA from whole blood_7512560157_R03C01_Cohort 1E


title: genomic DNA from whole blood_7512560117_R02C02_Cohort 1E


title: genomic DNA from superior temporal gyrus_7796806022_R02C02_Cohort 1AD


title: genomic DNA from cerebellum_7796806022_R06C01_Cohort 1AD


title: genomic DNA from whole blood_7512560157_R01C02_Cohort 1E


title: genomic DNA from whole blood_7512560157_R01C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R06C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R05C02_Cohort 1E


title: genomic DNA from whole blood_7512560157_R02C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R05C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R04C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R03C02_Cohort 1E


title: genomic DNA from whole blood_7512560088_R03C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R02C02_Cohort 1E


title: genomic DNA from whole blood_7512560117_R03C02_Cohort 1E


title: genomic DNA from whole blood_7512560088_R02C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R01C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R05C02_Cohort 1E


title: genomic DNA from whole blood_7512560088_R01C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R06C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R04C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R04C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R03C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R03C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R06C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R02C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R01C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R05C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R06C02_Cohort 1E


title: genomic DNA from whole blood_7512551028_R02C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R06C01_Cohort 1E


title: genomic DNA from whole blood_7796806113_R06C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R05C01_Cohort 1E


title: genomic DNA from whole blood_7796806113_R04C01_Cohort 1E


title: genomic DNA from whole blood_7512551028_R01C01_Cohort 1E


title: genomic DNA from whole blood_7796806113_R03C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R04C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R03C01_Cohort 1E


title: genomic DNA from whole blood_7512560088_R04C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R02C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R02C01_Cohort 1E


title: genomic DNA from whole blood_7796806113_R01C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R01C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R06C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R06C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R05C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R05C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R04C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R03C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R04C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R02C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R03C01_Cohort 1E


title: genomic DNA from whole blood_7796814007_R02C02_Cohort 1E


title: genomic DNA from whole blood_7796806113_R05C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R06C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R01C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R03C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R04C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R05C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R06C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R03C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R02C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R04C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R01C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R01C01_Cohort 1E


title: genomic DNA from whole blood_7796806143_R05C02_Cohort 1E


title: genomic DNA from whole blood_7796806143_R02C02_Cohort 1E


title: genomic DNA from whole blood_7796806142_R06C01_Cohort 1E


title: genomic DNA from whole blood_7796806142_R05C02_Cohort 1E


title: genomic DNA from whole blood_7796806142_R04C02_Cohort 1E


title: genomic DNA from whole blood_7796806142_R04C01_Cohort 1E


title: genomic DNA from whole blood_7796806142_R05C01_Cohort 1E


title: genomic DNA from whole blood_7796806142_R06C02_Cohort 1E


title: genomic DNA from whole blood_7796814007_R01C01_Cohort 1E


title: genomic DNA from whole blood_7796806142_R02C02_Cohort 1E


title: genomic DNA from whole blood_7796806142_R03C01_Cohort 1E


title: genomic DNA from whole blood_7796806142_R02C01_Cohort 1E


title: genomic DNA from superior temporal gyrus_6042316061_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R06C02_Cohort 1D


title: genomic DNA from whole blood_7796806142_R01C02_Cohort 1E


title: genomic DNA from superior temporal gyrus_6042316061_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R05C02_Cohort 1D


title: genomic DNA from whole blood_7796806142_R03C02_Cohort 1E


title: genomic DNA from superior temporal gyrus_6042316053_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316061_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316053_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316050_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316036_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R05C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316103_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R01C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R01C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R06C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R06C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316063_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R04C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R03C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R05C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R02C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R03C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316065_R04C01_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R02C02_Cohort 1D


title: genomic DNA from superior temporal gyrus_6042316054_R05C02_Cohort 1D


title: genomic DNA from entorhinal cortex_6929718138_R04C02_Cohort 1C


title: genomic DNA from superior temporal gyrus_6042316054_R01C01_Cohort 1D


title: genomic DNA from entorhinal cortex_6929718138_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R03C02_Cohort 1C


title: genomic DNA from superior temporal gyrus_6042316054_R01C02_Cohort 1D


title: genomic DNA from entorhinal cortex_6929718138_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718136_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718138_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929718123_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6929726046_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568118_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568087_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R01C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R06C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R02C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R05C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R03C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R04C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568084_R04C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R03C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R02C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R01C02_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R06C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R05C01_Cohort 1C


title: genomic DNA from entorhinal cortex_6969568082_R02C01_Cohort 1C


title: genomic DNA from frontal cortex_6042316099_R06C02_Cohort 1B

value: A

value: frontal cortex


title: genomic DNA from frontal cortex_6042316099_R04C02_Cohort 1B

value: TRUE


title: genomic DNA from frontal cortex_6042316099_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R03C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316099_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R06C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316094_R04C02_Cohort 1B


title: genomic DNA from entorhinal cortex_6969568082_R03C01_Cohort 1C

value: entorhinal cortex


title: genomic DNA from frontal cortex_6042316069_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R05C02_Cohort 1B


title: genomic DNA from entorhinal cortex_6969568082_R04C01_Cohort 1C


title: genomic DNA from frontal cortex_6042316069_R03C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316069_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R06C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R06C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R03C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316121_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R06C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316066_R03C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R06C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R03C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R01C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R01C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R06C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R04C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316048_R02C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316110_R05C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R04C01_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R03C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R05C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R02C02_Cohort 1B


title: genomic DNA from frontal cortex_6042316035_R01C01_Cohort 1B


title: genomic DNA from cerebellum_6057825018_R06C02_Cohort 1Aii

value: cerebellum


title: genomic DNA from cerebellum_6057825018_R06C01_Cohort 1Aii


title: genomic DNA from frontal cortex_6042316110_R02C01_Cohort 1B


title: genomic DNA from cerebellum_6057825018_R04C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R05C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R04C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R03C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R02C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R05C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R03C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R02C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R01C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825018_R01C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R05C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R06C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R06C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R05C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R04C02_Cohort 1Aii


title: genomic DNA from frontal cortex_6042316035_R05C01_Cohort 1B

value: FEMALE


title: genomic DNA from cerebellum_6057825017_R02C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R04C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R03C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R02C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R01C02_Cohort 1Aii


title: genomic DNA from frontal cortex_6042316035_R03C01_Cohort 1B

value: AD


title: genomic DNA from cerebellum_6057825017_R03C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R06C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825017_R01C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R06C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R04C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R05C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R05C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R04C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R03C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R02C02_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R02C01_Cohort 1Aii


title: genomic DNA from cerebellum_6057825014_R01C02_Cohort 1Aii


title: genomic DNA from cerebellum_6042316127_R06C02_Cohort 1Ai

value: H


title: genomic DNA from cerebellum_6042316127_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R02C01_Cohort 1Ai

value: MALE


title: genomic DNA from cerebellum_6042316127_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R01C02_Cohort 1Ai

value: Exclude


title: genomic DNA from cerebellum_6042316113_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R03C01_Cohort 1Aii


title: genomic DNA from cerebellum_6042316113_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R01C01_Cohort 1Aii


title: genomic DNA from cerebellum_6042316107_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316127_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316107_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6042316113_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6042316085_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825018_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R06C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R06C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R04C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R03C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R04C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R03C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825017_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R05C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R02C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R01C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R02C02_Cohort 1Ai


title: genomic DNA from cerebellum_6057825008_R01C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R05C01_Cohort 1Ai


title: genomic DNA from cerebellum_6057825014_R02C02_Cohort 1Ai


title: HEK293T cell culture,transfected,biological rep 6

status: Public on Nov 21 2012

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 6_24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell line


title: HEK293T cell culture,untransfected,biological rep 1

source_name: HEK293T human embryonic epithelial kidney cell culture,untransfected,biological rep 1_24h


title: Human in vivo, occupational exposure nickel, subject 5

status: Public on Aug 28 2012

city: Tuxedo

first: Adriana

last: Arita

address: 57 Old Forge Road

institute: New York University

hyb_protocol: Samples were hybridized to a GeneChip Human Gene 1.0 ST Array (Affymetrix) that contains 28,869 well annotated genes.

scan_protocol: Hybridization and scanning of the arrays was performed using a standard procedure

data_processing: Gene expression analyses were performed using R. Gene expression data were imported and normalized in batches using the Affymetrix package and robust multichip average (RMA) [Affy package v.1.30.0. in R v.2.13.2 GUI 1.42 Leopard build 32-bit]. Samples were then batch normalized and log-transformed using an empirical Bayes approach with the R package COMBAT [VA 3.0.2 in R 2.14.0 GUI 1.42 Leopard build 32-bit]. Significance of gene expression changes between the exposed and referent populations was assessed using a gene-wise linear model approach with LIMMA, which utilizes an empirical Bayes approach to generate moderated t-statistics by taking into account the standard errors and estimated log-fold changes.

source_name: Human PBMC_occupational exposure nickel

label_protocol: cRNA probes were synthesized and labeled using GeneChip Whole Transcript Terminal Labeling Expression Kit (Affymetrix).

extract_protocol: 50 mL of blood was collected from each subject by venipuncture by a local registered nurse. PBMC were isolated from blood using a standard Ficoll-Gradient procedure. PBMCs were frozen Trizol at -80C. Total RNA was extracted from each sample according to the TRIzol (Invitrogen) manufacturer's protocol

tag: subject group

value: nickel refinery workers

tag: exposure to nickel

value: occupational

tag: cell type

value: peripheral blood mononuclear cells

tag: batch


title: Human in vivo, occupational exposure nickel, subject 4


title: Human in vivo, occupational exposure nickel, subject 6


title: Human in vivo, occupational exposure nickel, subject 2


title: Human in vivo, occupational exposure nickel, subject 7


title: Human in vivo, occupational exposure nickel, subject 3


title: HEK293T cell culture,transfected,biological rep 5

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 5_24h


title: HEK293T cell culture,untransfected,biological rep 3

source_name: HEK293T human embryonic epithelial kidney cell culture,untransfected,biological rep 3_24h


title: Human in vivo, occupational exposure nickel, subject 1


title: HEK293T cell culture,transfected,biological rep 4

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 4_24h


title: Human in vivo, occupational exposure nickel, subject 8


title: Myotubes after 2 days in differentiating medium - Replicate 3

status: Public on Jul 05 2012

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: For microarray analysis, 100ng of total RNA was amplified and hybridized to the Mouse Gene 1.0 ST array.

scan_protocol: According to the standard Affymetrix protocol using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was RMA normalized from CEL file data per replicate set using GenePattern software from the Broad Institute.

source_name: Myotubes 2 days in differentiating medium

label_protocol: According to the Affymetrix protocol.

growth_protocol: HAMS's F10 + 20% FBS + bFGF(4ng/ml) for the specified time (0h, 2d, 5d).

extract_protocol: Total RNA was isolated in triplicates from mouse primary myoblasts and myotubes in growth and differentiation, respectively, using the RNeasy mini kit (Qiagen). The purity of RNA was analyzed by Bioanalyzer (Agilent Technologies, Santa Clara CA). All samples showed RNI > 9.0 and were used for subsequent labeling and hybridization.

tag: strain

value: Balb/c

tag: genotype

value: wild type

tag: tissue of origin

value: skeletal muscle

value: myotubes

tag: time

value: 2 days


title: Cycling myoblasts - Replicate 3

source_name: Cycling myoblasts

value: myoblasts

value: 0 hr

tag: replicate


title: Myotubes after 2 days in differentiating medium - Replicate 1


title: HEK293T cell culture, untransfected, biological rep 2

status: Public on Jun 03 2012

last: Martin

address: 32 Chase Hall

department: Biological Systems Engineering

description: 24 h gene profile of untransfected (GFP negative) HEK293T cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm.

data_processing: The data was analysed using R 2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: HEK293T human embryonic epithelial kidney cell culture, untransfected_24h

growth_protocol: HEK293T cells were grown in T75 in DMEM supplemented with 10% FBS, 1% Pen/Strep, 1% Sodium Pyruvate.

treatment_protocol: Cationic PEI polymer mixed with pEGFP-LUC to form polyplexes. Cells were treated with polyplexes 18 h after seeding and flow separated after another 24 h.

tag: cell population

value: untransfected


title: Myotubes after 5 days in differentiating medium - Replicate 3

source_name: Myotubes 5 days in differentiating medium

value: 5 days


title: Cycling myoblasts - Replicate 2


title: Myotubes after 5 days in differentiating medium - Replicate 2


title: HEK293T cell culture,untransfected,biological rep 2

source_name: HEK293T human embryonic epithelial kidney cell culture,untransfected,biological rep 2_24h


title: HEK293T cell culture, transfected, biological rep 3

description: 24 h gene profile of transfected (GFP positive) HEK293T cells.

source_name: HEK293T human embryonic epithelial kidney cell culture, transfected_24h

value: transfected


title: Myotubes after 5 days in differentiating medium - Replicate 1


title: Ei-2 non-infected control sample 15

status: Public on Jul 04 2012

city: Valencia

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

country: Spain

institute: CSIC-UPV

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
Babelomics 4.2 (http://babelomics.bioinfo.cipf.es)
Series supplementary file contains Limma normalized signal intensity

organism: Arabidopsis thaliana

source_name: non-infected

label_protocol: standard Agilent protocol

growth_protocol: plants were mantained in a BSL-2 greenhouse at 16:8h light:dark and 24:20 day:night temperature until sample collection on 21 days post infection.

extract_protocol: Quiagen, RNasyPlant Mini kit manufacturer protocol

treatment_protocol: Plants infected with TEV strain previosly adapted to A.thaliana ssp. Ler and non-infected plants as a control

tag: ecotype

tag: tissue

value: whole organism

tag: infection

value: non-infected


title: Myotubes after 2 days in differentiating medium - Replicate 2


title: Ler-0 infected replicate 9 sample 14

source_name: infected

value: Tobacco etch potyvirus


title: WCEpos_ChIPSeq

status: Public on Aug 24 2011

first: Bill

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: WCE control

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 (July 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed using the Young Lab Analysis tool (described in PMID: 19884255)

source_name: fetal liver cells

growth_protocol: Primary fetal liver cells were isolated from E14.5 C57Bl6 pregnant mice and homogenized.  Using anti-Ter119 magnetic beads, the positive and negative fractions were separated for each samole (for each cell type listed above).  Fresh cells were fixed with 1% formaldehyde and then quenched with 2.5M glycine.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: None, cells were isolated in-vivo and fixed immediately

value: fetal liver erythroid Ter119+ cells

tag: passages

value: primary cells

tag: gender

value: female


title: Cycling myoblasts - Replicate 1


title: HEK293T cell culture, transfected, biological rep 2


title: HEK293T cell culture, untransfected, biological rep 3


title: HEK293T cell culture, untransfected, biological rep 1


title: HEK293T cell culture,transfected,biological rep 3

status: Public on Oct 05 2011

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 3_24h


title: HEK293T cell culture, transfected, biological rep 1


title: HEK293T cell culture,transfected,biological rep 2

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 2_24h


title: HEK293T cell culture,transfected,biological rep 1

source_name: HEK293T human embryonic epithelial kidney cell culture,transfected,biological rep 1_24h


title: 070427A-244k

status: Public on Jul 19 2011

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: cancer-adjacent normal tissue

extract_protocol: Qiagen RNeasy Kit.

value: cancer-adjacent normal tissue

tag: patient id

tag: active or "inactive"

value: negative

tag: age at diagnosis (year)

tag: menopause status

value: Post

tag: histopathology

value: Invasive

tag: breast cancer subtype (pam50)

value: Basal-like

tag: er status

tag: hormone treated

value: no

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: 071054B-244K

data_processing: Data for both channels were Lowess-normalized using the UNC microarray database, and then the log(2) ratio was taken.

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

extract_protocol: Total RNA isolated by stratagene

source_name: breast tumor

extract_protocol: Qiagen Rneasy Kit

tag: tissue

value: Tumor

tag: age at diagnosis

value: LumA

tag: tumor stage (t)

tag: overall survival (months)


title: 071054A-244k

tag: sample type

tag: composition

tag: patient id

value: Pre

value: Lum A

value: positive

value: yes

value: positve


title: 070804A-244K


title: 071567B-244K

tag: menopause status


title: 071567A-244K


title: 070804B-244K

tag: histopathology


title: 060708A-244K

tag: active or "inactive"

tag: age at diagnosis (year)

tag: breast cancer subtype (pam50)

value: Normal-like


title: 050364B-244K

value: Basal

tag: er status

tag: hormone treated

tag: her2 status


title: 061398B-244K

value: reference

tag: tumor grade

tag: overall survival event (dead=1, alive=0)


title: 990428A-244K

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: tissue


title: 061398A-244K

value: cancer-adjacent normal tissue

tag: tumor size (cm)

tag: overall survival (month)


title: 990428B-244K

tag: age at diagnosis

tag: tumor stage (t)

tag: overall survival (months)


title: 070726A-244K

tag: sample type

tag: composition


title: 050521B-244K

tag: menopause status

tag: histopathology


title: 060545B-244K

value: LumB


title: 060952B-244K


title: 071340B-244K


title: 060952A-244K

tag: patient id

tag: active or "inactive"

value: negative

tag: age at diagnosis (year)

value: unknown


title: 060545A-244K


title: 050618B-244K

value: breast tumor


title: 071340A-244k

value: Invasive

tag: breast cancer subtype (pam50)

tag: er status

tag: hormone treated


title: 050521A-244K


title: 050364A-244K


title: 060708B-244K


title: 060117A-244K


title: 050618A-244K


title: 060117B-244K

value: Tumor

tag: her2 status

tag: tumor grade

tag: overall survival event (dead=1, alive=0)


title: 070726B-244K

tag: tissue


title: 050362B-244K

tag: age at diagnosis


title: 050113B-244K

tag: tumor stage (t)


title: 050259A-244K

value: Post

value: Basal-like

value: no

tag: tumor size (cm)

tag: overall survival (month)


title: 050362A-244k

tag: sample type

tag: composition

value: Pre


title: 050113A-244k

tag: menopause status

tag: histopathology

value: Lum A

value: positive

value: yes


title: 050088B-244K

tag: overall survival (months)


title: 050005B-244K


title: 050259B-244K

value: Basal


title: 040095B-244K

value: reference


title: 050088A-244K

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: 050005A-244K

value: cancer-adjacent normal tissue

tag: patient id

tag: active or "inactive"

tag: age at diagnosis (year)

value: Her 2

value: positve


title: 050093B-244K

tag: breast cancer subtype (pam50)

value: LumB

tag: er status

tag: hormone treated


title: 040593B-244K

tag: her2 status

tag: tumor grade

tag: overall survival event (dead=1, alive=0)


title: 040593A-244k

tag: tissue

value: negative

value: Normal-like


title: 020300B-244K

value: breast tumor


title: UNC99-0456A-244K


title: 040095A-244K


title: 020300A-244K

value: Post

value: Invasive

value: unknown

tag: tumor size (cm)


title: 050093A-244K


title: UNC99-0543A-244K


title: UNC00-0164A-244K


title: UNC00-0164B-244K


title: UNC99-0543B-244K


title: UNC99-0339A-244K


title: UNC99-0363B-244K


title: UNC99-0216A-244K


title: UNC99-0456B-244K


title: UNC99-0363A-244K


title: UNC99-0182A-244K


title: UNC99-0306B-244K7ug


title: UNC99-0364A-244K


title: UNC99-0216B-244K


title: UNC99-0364B-244K


title: UNC99-0281A-244K


title: UNC99-0339B-244K


title: 07-0427B-244k


title: UNC99-0306B-244K10ug


title: UNC99-0182B-244K10ug


title: UNC99-0306A-244K


title: UNC99-0158A-244K


title: UNC99-0158B-244K7ug


title: UNC99-0182B-244K7ug


title: 07-0475B-244k


title: UNC99-0281B-244K


title: 07-0342B-244k


title: UNC99-0141A-244K


title: UNC99-0158B-244K10ug


title: UNC99-0141B-244K


title: 06-1413A-244k


title: 07-0342A-244k


title: 07-0021A-244k


title: UNC98-2049A-244K


title: 07-0158A-244k


title: UNC98-0107B-244K10ug


title: 06-1413B-244k


title: 06-1381A-244k


title: 06-1381B-244k


title: 06-1291B-244k


title: UNC04-0550B-244K


title: UNC98-2048A-244K


title: UNC98-0107B-244K7ug


title: 06-1291A-244k


title: UNC98-2048B-244K


title: UNC04-0547B-244K


title: 06-1067B-244k


title: UNC061381A

description: UNC061381A replicate


title: UNC061291A

description: UNC061291A replicate


title: UNC070475A


title: FoldChanges05, MA__1000252324310002, OdT_KE0TPA_Cy5_KE0Ctrl_Cy3_1.4

status: Public on Apr 12 2011

city: Berlin

first: Ulf

middle: Andersson

last: Ørom

address: Ihnestrasse 63-73

department: OWL

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: 05_MA_1000252324310002_OdT_KE0TPA_Cy5_KE0Ctrl_Cy3_1.4.gpr

hyb_protocol: Agilent hybridization protocol.

scan_protocol: Agilent scanner.

data_processing: Extracted raw data were normalized using the limma package (Smyth 2004) developed within the Bioconductor project in the R statistical programming environment. Raw data was background corrected using the normexp method (Ritchie et al. 2007). The two channels were balanced by global lowess normalization, followed by scaling across arrays (Yang et al. 2002). Differential expression analysis was performed using SAM (Significance Analysis of Microarrays, Tusher et al. 2001).

source_name: Primary human keratinocytes isolated from newborn human foreskin, TPA

label_protocol: Cy3/Cy5 Agilent label protocol.

growth_protocol: Primary human keratinocytes were grown in complete KSFM from Invitrogen.

extract_protocol: Total RNA was extracted with TRIzol according to the manufacturer's recommendations.

treatment_protocol: Cells were left untreated or differentiated with 25 ng/ml TPA.

tag: gender

value: male

value: newborn foreskin

tag: cell type

value: primary keratinocytes

tag: treatment

value: TPA

source_name: Primary human keratinocytes isolated from newborn human foreskin, control


title: UNC04-0547A-244K

tag: sample type

tag: composition


title: UNC98-0107A-244K


title: FoldChanges07, MA__3000252324310002, OdT_KG0TPA_Cy5_KG0Ctrl_Cy3_3.4

description: 07_MA_3000252324310002_OdT_KG0TPA_Cy5_KG0Ctrl_Cy3_3.4.gpr


title: UNC060121A


title: FoldChanges08, MA__4000252324310002, OdT_KG0Ctrl_Cy5_KG0TPA_Cy3_4.4_DS

description: 08_MA_4000252324310002_OdT_KG0Ctrl_Cy5_KG0TPA_Cy3_4.4.gpr


title: 06-0678B-244k


title: FoldChanges03, MA__3000252324310001, OdT_KD0TPA_Cy5_KD0Ctrl_Cy3_3.4

description: 03_MA_3000252324310001_OdT_KD0TPA_Cy5_KD0Ctrl_Cy3_3.4.gpr


title: 06-0694B-244k


title: UNC04-0115B-244K10ug


title: FoldChanges06, MA__2000252324310002, OdT_KE0Ctrl_Cy5_KE0TPA_Cy3_2.4_DS

description: 06_MA_2000252324310002_OdT_KE0Ctrl_Cy5_KE0TPA_Cy3_2.4.gpr


title: FoldChanges01, MA__1000252324310001, OdT_KK1TPA_Cy5_KK1Ctrl_Cy3_1.4

description: 01_MA_1000252324310001_OdT_KK1TPA_Cy5_KK1Ctrl_Cy3_1.4.gpr


title: 06-0694A-244k


title: UNC02-0575B-244K7ug


title: C, rep 2

hyb_protocol: Standard protocol.

scan_protocol: Standard protocol.

data_processing: Data were normalized.

source_name: A549, control

label_protocol: Standard protocol.

growth_protocol: Cultured in DMEM, 10% FCS.

extract_protocol: RNA extracted with TRIzol.

treatment_protocol: A549 cells were transfected with Snai1 siRNA, ncRNA-a7 siRNa, or control.

tag: cell line

value: control siRNA


title: C, rep 1


title: ncRNA-a7, rep 1

source_name: A549, ncRNA-a7 knockdown

value: ncRNA-a7 siRNA


title: UNC04-0115A-244K

value: reference

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: Snai1, rep 1

source_name: A549, Snai1 knockdown

value: Snai1 siRNA


title: Snai1, rep 2


title: ncRNA-a7, rep 2


title: UNC03-0477B-244K


title: UNC03-0477A-244K

value: cancer-adjacent normal tissue


title: 07-0021B-244k


title: UNC02-0575B-244K10ug


title: Ovarian cancer_sample 68

status: Public on Jul 11 2010

city: boston

first: panagiotis

last: konstantinopoulos

address: 330 brookline av

department: hem/onc

institute: bidmc

description: 121401 HGU95Av2 SC R6

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: RMA

source_name: Ovarian cancer

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates

extract_protocol: RNA was isolated using the trizol protocol

tag: overall survival (months)

tag: overall survival (censored)

value: 1 [event (death)]

tag: dfs

tag: dfs(censored)

tag: histology

value: PS

tag: age

tag: Stage

tag: grade

tag: debulking (1=optimal)


title: Ovarian cancer_sample 66

description: 091803 HU95AV2 TL 15D9

value: 0 [censored]


title: Ovarian cancer_sample 67

description: 121401 HGU95Av2 SC R5


title: UNC02-0575A-244K

tag: tissue


title: Ovarian cancer_sample 69

description: 121401 HGU95Av2 SC R7


title: Ovarian cancer_sample 62

description: 091301 HGU95Av2 SC H2


title: Ovarian cancer_sample 64

description: 091803 HU95AV2 TL 15D6

value: E


title: Ovarian cancer_sample 70

description: 121401 HGU95Av2 SC R8

value: C


title: Ovarian cancer_sample 28


title: Ovarian cancer_sample 22


title: Ovarian cancer_sample 24