title: Wild-type_rep1

city: Fayetteville

first: Andy

last: Pereira

state: Arkansas

address: 115 Plant Science Building

department: Crop, Soil and Environmental Sciences

institute: University of Arkansas

hyb_protocol: 4 µg RNA samples were hybridized to the Affymetrix Rice Genome Array. Hybridization was done using the GeneChip Hybridization, Wash, and Stain kit. The cocktail included 12.5 μg aRNA, control oligo B2, 20x hyb controls of bioB, bioC, bioD, and cre, 2X hyb mix, and DMSO. The hybe mix is heated at 99C for 5 min, 45C for 5 min, and then hybridized for 16h at 45C.

scan_protocol: Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).

data_processing: Raw data were background corrected, normalized and summarized according to the custom CDF (GPL11322) using RMA (Irizarry et al., 2003). The custom CDF was built by uniquely mapping 442,810 probe sequences to 35,161 rice gene-based probe sets.

organism: Oryza sativa Japonica Group

source_name: Plant tissue from WT control lines

label_protocol: Following second-strand synthesis, in vitro transcription was performed using the GeneChip® IVT Labeling Kit.

growth_protocol: HYR and WT (wild-type) Nipponbare plants were grown side by side to the late vegetative stage under well-watered/semi-flooded conditions for 4 weeks. Plants were grown in environmentally controlled growth chambers maintained at 28 C±1 day and 25 C±1 night temperature, 65% relative humidity with a daily photoperiodic cycle of 14h light and 10h dark.

extract_protocol: Total RNA was isolated from plant tissue using the RNeasy plant kit (Qiagen, USA), quantity/quality measured by the Agilent 2100 Bioanalyzer (Agilent Technolgies, USA), and 4 µg RNA used to generate first-strand cDNA with a T7-Oligo(dT) primer.

treatment_protocol: The rice HYR (HIGHER YIELD RICE) gene (Loc_Os03g02650) was used to make an overexpression construct that was transformed into rice to produce HYR overexpression lines. HYR lines and WT lines were grown in pots with soil in the greenhouse and given stress at the vegetative V4 stage of growth (Counce, 2000). Drought stress treatment was given by stopping watering and allowing the plants to reach leaf rolling stage due to drought stress perception. At this stage the leaf relative water content was measured and plant leaf samples were taken from control (well-watered) and drought stress (leaf rolling) treatments.

tag: cultivar

value: Nipponbare

value: leaf tissue

value: 1 month old

tag: line

value: WT control


title: HYR_rep1

status: Public on Aug 30 2014

type: RNA

country: USA

label: biotin

molecule: total RNA

source_name: Plant tissue from HYR lines

tag: tissue

tag: age

value: HYR-expression


title: ctrl-1

city: Heidelberg

first: Manuel

last: Roehrich

state: Baden-Württemberg

address: INF 280

department: Molecular Radiation Oncology

country: Germany

institute: DKFZ Heidelberg

description: mRNA expression human glioblastoma stem cell like cells  6 h after treatment (untreated)

hyb_protocol: 500 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (GPL 10332) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20060807).

data_processing: Data was quantile normalized with ChipSkipper Table Butler and SUMO software (http://angiogenesis.dkfz.de/oncoexpress/software/index.htm).

organism: Homo sapiens

source_name: NMA 23_untreated_6 hrs

label_protocol: 500 ng of total RNA were labeled with Cyanin-3 using the Agilent Low RNA Input Linear Amplification Kit following the detailed protocol described in the user´s manual.

growth_protocol: NMA-23 cells were maintained in their undifferentiated state using Neurobasal Media supplemented with epidermal growth factor and basic fibroblast growth factor (each at 10 μg/500 mL media), sodium pyruvate, glutamine, B27 supplement, non-essential amino acids and penicillin/ streptomycin (Gibco, Grand Island, NY). NMA 23 cells were maintained at 37C in a humidified incubator with 5% CO2

extract_protocol: 6 h after treatment exposures, CSLCs cells were solubilized and homogenized in TRIzol (Invitrogen, Carlsbad, CA). Total RNA was isolated according to the manufacturer´s instruction and purity and integrity of the RNA was assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: NMA-23 were treated with FG-3019 (30 μg/ml)  and/or irradiated with 4 Gy with 6 MV X-rays (Mevatron, Siemens, Erlangen, Germany) at a dose rate of 2,5 Gy/min. Then, the cultures were incubated for 6 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: cell type

value: glioblastoma stem cell like cells

tag: treated with

value: none for 6h (untreated control)


title: 6-1 (Parg A-1)

city: Logan

first: Ralph

middle: G

last: Meyer

state: UT

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

hyb_protocol: standard Affymetrix methods

scan_protocol: standard Affymetrix methods

data_processing: Gene expression profiles of individual embryos were generated by hybridization of the amplified cDNA to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).  Gene expression data, as well as tiling microarray data (see below), were analyzed using Partek® Genomics SuiteTM software. Copyright, Partek Inc., St. Louis, MO.  Raw intensities were subjected to background correction, quantile normalization, log2 transformation and probe set summarization with the RMA (Robust Multichip Average) method.

organism: Mus musculus

source_name: 2-cell embryo

label_protocol: standard Affymetrix methods

growth_protocol: Natural mating

extract_protocol: RNA from individual embryos was isolated and amplified using the WT-Ovation One-Direct RNA Amplification kit (NuGen Technologies)

treatment_protocol: Genetic disruption of the Parg gene (Parg(110)-/-) in sires, wt mothers, embryos are heterozygous for deletion of exons 2 and 3 (Parg(110)-/+)

tag: father

tag: developmental stage

value: 2-cell embryo

tag: genotype

tag: background strain

value: 129SVE (=129S6/SvEvTac, Taconic)


title: HYR_rep2


title: WT_1-1

value: Wild-type


title: 6-2 (Parg A-2)


title: WT_3-1


title: PJ34-MTM13-1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

source_name: 2-cell embryo, sire PJ34 treated

label_protocol: standard Affymetrix protocol

treatment_protocol: Wildtype males with identical genetic background were daily injected with PJ34 (or saline as controls) for 6 weeks, then naturally mated with untreated wildtype females and 2-cell embryos were harvested.

value: MTM13 (PJ34 B)

tag: strain


title: PJ34-MTM14-2

value: MTM14 (PJ34 C)


title: WT_3-3


title: PJ34-MTM13-3


title: PJ34-MTM14-1


title: Wild-type_rep2


title: PJ34-MTM11-1

value: MTM11 (PJ34 A)


title: PJ34-MTM13-4


title: WT_1-3


title: PJ34-MTM11-2


title: WT_1-2


title: Genom2 Input PJ34

type: genomic

description:
Wtgenomic
Input control: whole sperm DNA sheared
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

data_processing: Mnase sensitive sperm DNA was analyzed and mapped to the mm8 genome by hybridization of the amplified genomic DNA fragments to GeneChip Mouse Promoter 1.0R tiling arrays (Affymetrix). Individual sperm samples, no sample DNA pooling, using fragmented genomic sperm DNA for input subtraction.  Tiling microarray data were analyzed using Partek® Genomics SuiteTM software (Partek Inc., St. Louis, MO).  Raw intensities were subjected to background correction, quantile normalization, log2 transformation and probe set summarization with the RMA (Robust Multichip Average) method.  A second data set was generated by combining array data from all Parg(110)-/- samples compared to the pooled wild-type data set ("Other" files above).  Genomic regions affected by differential histone association gene promoter regions were identified by their differential association with the soluble mononucleosomal fraction in Parg(110)-/- compared to wild-type control mice.

molecule: genomic DNA

source_name: Wild-type sheared whole sperm genomic DNA

growth_protocol: Mononuclease-sensitive fractions from sperm of individual mice (wild-type or wild-type PJ34-treated) were isolated using a swim-up technique with purification steps to eliminate all potentially contaminating somatic cells. Genomic controls for input subtraction were generated by complete DNA isolation from sperm (wild-type or wild-type PJ34-treated) followed by random fragmentation.

extract_protocol: Genomic DNA was isolated by limited Mnase digest, gel-purified and amplified using the Genomeplex Complete Whole Genome amplification (WGA2) kit (Sigma).

treatment_protocol: Wild-type mice (strain 129SVE (=129S6/SvEvTac, Taconic) or wild-type with continuous pharmacologic disruption of poly(ADP-ribose) metabolism using the PARP1/PARP2  inhibitor PJ34 in sires.

value: sperm

tag: treatment


title: R200#11

city: Okayama

first: Shinya

last: Satoh

address: 2-5-1 Shikata-cho Kita-ku

country: Japan

institute: Okayama University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0  Array. GeneChips were hybridized, washed and stained by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

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

source_name: RBV resistant

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA by using GeneChip 3' IVT Express kit (Affymetrix).

growth_protocol: Cells were grown in 5% CO2 incubator at 37C

extract_protocol: Total RNA was extracted by using RNeasy Mini kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Cells were lysed in RLT solution (Qiagen) for RNA extrction.

value: hepatoma

tag: rbv-sensitivity status

value: resistant


title: PJ34-MTM11-3


title: Genom3 Input PJ34


title: Control-B-3

source_name: 2-cell embryo, saline treated control

value: B - untreated control


title: Control-D-3

value: D - untreated control


title: Control-D-2


title: 2CW Input 2CW


title: R200#8


title: 2CV Input 2CV


title: Genom1 Input PJ34


title: PJ34 C MTM14

description:
MTM14
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

source_name: PJ34 treated males, sperm Mnase fraction


title: R200#1


title: OL8(3.5Y)

source_name: RBV sensitive

value: sensitive


title: PJ34 B MTM13

description:
MTM13
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: Control-B-1


title: Control-B-2


title: PJ34-MTM11-4


title: WTNuc control WT7

description:
WT7
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

source_name: Wild-type sperm Mnase fraction


title: Control-A-2

value: A - untreated control


title: PJ34 D MTM12

description:
MTM12
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: 2CT Input 2CT


title: Control-D-1


title: PJ34 A MTM11

description:
MTM11
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: 6-3 (Parg A-3)


title: ATAF1-IOE-5h mature leaf +EST

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

description: Gene expression data from ATAF1-IOE, 5 h after estradiol treatment

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: MAS 5.0

organism: Arabidopsis thaliana

source_name: Arabidopsis ATAF1-IOE mature leaves treated with EST (10 µM)

growth_protocol: The two-week-old Arabidopsis seedlings were carefully transferred from plates to pots in a growth chamber with a 16-h day (120 μmol m-2 s-1) and a day/night temperature of 22/16°C and 60/75% RH. The plants were allowed to grow for 2 weeks.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: After two weeks, seedlings were transferred to half-strength liquid MS medium containing 10 μM β-estradiol (treatment) or 0.1% ethanol (mock) for 5 h.  Subsequently, seedlings were harvested at 1 h, 2 h and 5 h after estradiol addition. In the case of mature leaves, after 2 weeks of growth in soil, opposing leaves of a whorl were excised and incubated in half-strength liquid MS medium containing 10 μM estradiol (treatment) or 0.1% ethanol (mock) for 5 h.

value: Mature leaves

value: ATAF1-IOE (Col-0)

value: four-week-old

value: estradiol

tag: time

value: 5 h


title: ATAF1-IOE-5h mature leaf +Mock

description: Gene expression data from ATAF1-IOE, 5 h after mock treatment

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

source_name: Arabidopsis ATAF1-IOE mature leaves treated with ethanol (0.1%)

value: mock


title: ATAF1-IOE-2h seedling +Mock

description: Gene expression data from ATAF1-IOE, 2 h after mock treatment

source_name: Arabidopsis ATAF1-IOE Seedlings treated with ethanol (0.1%)

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

growth_protocol: Seeds were surface-sterilized for 1 min in 70% ethanol and then in sterilisation solution (20% sodium hypochlorite) for 30 min. After sterilization, the seeds were sown on half-strength MS medium (Murashige and Skoog, 1962), supplemented with 1% (w/v) sucrose and hygromycin, and solidified with 0.7% (w/v) phytoagar. After imbibition, the seeds were stratified at 4°C for 3 days. The seeds were germinated at 22°C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime. The two-week-old Arabidopsis seedlings were carefully removed from plates and subjected to EST or mock treatments for 1 h, 2 h and 5 h.

value: Whole seedlings

value: two-week-old

value: 2 h


title: ATAF1-IOE-5h seedling +EST

source_name: Arabidopsis ATAF1-IOE Seedlings treated with EST (10 µM)


title: ATAF1-IOE-5h seedling +Mock


title: ATAF1-IOE-2h seedling +EST

description: Gene expression data from ATAF1-IOE, 2 h after estradiol treatment


title: Wilms Tumour ICH-3061

city: London

first: Richard

middle: Dafydd

last: Williams

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: UCL Institute of Child Health

hyb_protocol: Tumour and reference cDNA were co-hybridized to the Breakthrough Breast Cancer Research Centre 17k 2.1.2 cDNA microarray, using the protocol described by Hegde et al. (2000) Biotechniques 29: 548–562.

scan_protocol: Arrays were scanned on an Axon GenePix 4000A instrument (Molecular Devices, Sunnyvale, CA, USA). PMT gain was used to balance the intensities in the two channels to detect most of the features without saturation of intensity. Images were processed with the manufacturer’s software.

data_processing: Data were filtered and normalized using BRB ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html). Probes were excluded from further analysis if fewer then 70% of the data points were flagged by the GenePix software as high quality features across the data set, leaving a filtered set of 15437 probes. Lowess intensity dependent normalization within print-tip groups was applied to adjust for differences in dye labelled intensities, and local background subtraction was applied. The array probes were annotated and genes assigned with a custom Perl script.

source_name: Wilms Tumour ICH-3061

label_protocol: mRNA was amplified from total RNA using the MessageAmp II system (Ambion, Austin, TX). Cyanine-5 (tumour) or cyanine-3 (reference) labelled cDNA was prepared from 5 micrograms of amplified RNA by random-primed reverse transcription in the presence of an aminoallyl-labelled nucleotide, followed by covalent coupling to the cyanine dye ester, as described by Hegde et al. (2000) Biotechniques 29: 548–562.

extract_protocol: Tumour samples were pulverised at liquid nitrogen temperatures in a Sartorius Mikro-Dismembrator. RNA was extracted from this material with Trizol reagent (Life Technologies) according to the manufacturer's instructions. Two rounds of extraction were performed.

value: Wilms tumour

tag: Sex

value: Male

tag: Stage

value: III

tag: relapse (months)

value: N/E

tag: death (months)

tag: copy number aberrations

tag: tp53 copy number

value: Loss

tag: tp53 sequence

value: normal

tag: overall tp53 status

value: aberrant

source_name: Stratagene Universal Human Reference RNA

value: Pooled various


title: Wilms Tumour ICH-3062

source_name: Wilms Tumour ICH-3062

tag: tissue

value: Female

value: IV

value: Normal


title: Wilms Tumour ICH-3143

source_name: Wilms Tumour ICH-3143

value: I

value: mutant


title: WTNuc control WT5

description:
WT5
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

value: sperm


title: Wilms Tumour ICH-3060

source_name: Wilms Tumour ICH-3060


title: ATAF1-IOE-1h seedling +EST

description: Gene expression data from ATAF1-IOE, 1 h after estradiol treatment

value: Whole seedlings

value: ATAF1-IOE (Col-0)

tag: age

value: estradiol

value: 1 h


title: WTNuc control WT6

description:
WT6
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: WTNuc control WT4

description:
WT4
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: ATAF1-IOE-1h seedling +Mock

description: Gene expression data from ATAF1-IOE, 1 h after mock treatment

value: two-week-old

value: mock


title: WTNuc control WT3

description:
WT3
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: WTNuc control WT1

description:
WT1
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: Wilms Tumour ICH-3057

source_name: Wilms Tumour ICH-3057

value: Wilms tumour

value: N/E


title: Wilms Tumour ICH-3056

source_name: Wilms Tumour ICH-3056

value: Male

value: Loss


title: Wilms Tumour ICH-3058

source_name: Wilms Tumour ICH-3058

value: normal

value: Pooled various


title: Tumour sample ICH-3062

hyb_protocol: Test (Cy-5) and reference (Cy-3) DNA were combined with 100ug human Cot1 DNA (Invitrogen # 15279-011) and co-precipitated for 1-2 hours at –20C with 1/10 volume sodium acetate and 2.5 volumes of ice cold 100% ethanol. The precipitated DNA was centrifuged at 13000rpm for 30 minutes and washed with 70% ethanol and left to dry in the dark. Pellets were resuspended in 60 microlitres of hybridisation buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 2mg yeast tRNA), denatured at 75C for 5 minutes, and pre-annealed for 30 minutes at 37C. Slides were blocked in 10% BSA/ 50% formamide solution at 42C for 45 minutes. The labelled DNA was applied to the slide under a glass coverslip and hybridised overnight at 42C. Slides were washed with 2X SSC, 0.1% SDS for 15 minutes at 45C, followed by 2X SSC, 50% formamide for 15 minutes at 45C, then with 2X SSC, 0.1% SDS for a further 30 minutes at 45C, and finally for 15 minutes in 0.2X SSC at room temperature on a rocker. Slides were centrifuged to dry in a slide rack at 1200rpm for 2 minutes and stored in a slide box covered in foil at room temperature. [Adapted from A. Grigoriadis, ArrayExpress P-MEXP-7388].

scan_protocol: Arrays were scanned on an Axon GenePix 4000B instrument (Molecular Devices, Sunnyvale, CA, USA). PMT gain was used to balance the intensities in the two channels to detect most of the features without saturation of intensity. Images were processed with the manufacturer’s software.

data_processing: The 32k data set was processed with a custom S-PLUS script. Intensity data from each channel were read without background subtraction, discarding features flagged as bad by the GenePix software. Log2 ratios were calculated and loess normalisation applied within print-tip groups, and again across the entire array to remove spatial and intensity-dependent signal biases. Clone positions were mapped to the UCSC hg18/NCBI 36 human genome assembly using data supplied by CHORI (http://bacpac.chori.org/pHumanMinSet.htm) and the UCSC LiftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver). 10% of clones with consistent low intensity, commonly flagged values or with the greatest deviation from a running median of 3 clones (i.e., those with the greatest deviation from their overlapping contiguous neighbours) were removed as outliers. The filtered data set of 29,308 clones was finally normalised by estimating the consistent median absolute deviation from a running median of 201 clones across all the arrays in the study, applying a least trimmed squared robust linear fit, and normalising each array to this consistent estimate of bias using loess regression.

label_protocol: 1 microgram of tumour or control DNA was labelled with the BioPrime system according  to the manufacturer's instructions

extract_protocol: DNA was extracted by the SDS-proteinase K method, followed by phenol-chloroform extraction and ethanol precipitation.

value: Female

value: IV

source_name: Unrelated normal blood

value: normal blood

tag: gender

value: female


title: Tumour sample ICH-3061

value: III

value: aberrant


title: Tumour sample ICH-3143

value: I

value: mutant


title: WTNuc control MTM3

description:
MTM3
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

value: sperm


title: WTNuc control MTM2

description:
MTM2
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm


title: PJ34-MTM13-2

source_name: 2-cell embryo, sire PJ34 treated

tag: developmental stage

value: 2-cell embryo

tag: father

value: MTM13 (PJ34 B)

value: 129SVE (=129S6/SvEvTac, Taconic)


title: Wilms Tumour ICH-3055

source_name: Wilms Tumour ICH-3055

value: Wilms tumour

value: II

value: N/E

value: Normal


title: WTNuc control MTM1

description:
MTM1
nucleosomal genomic DNA
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

tag: strain


title: Tumour sample ICH-3060

value: Male

value: Loss

value: normal


title: Wilms Tumour ICH-3053

source_name: Wilms Tumour ICH-3053

value: Pooled various


title: Wilms Tumour ICH-3052

source_name: Wilms Tumour ICH-3052


title: Tumour sample ICH-3056

value: IV

value: normal blood

value: female


title: Tumour sample ICH-3058

value: Female


title: Wilms Tumour ICH-3050

source_name: Wilms Tumour ICH-3050

value: I


title: 4AB

description:
D23genomic
Input control: whole sperm DNA sheared
whole sperm genomic DNA input control

source_name: Parg(110)-/- sheared whole sperm genomic DNA

growth_protocol: Mononuclease-sensitive fractions from sperm of individual mice (wild-type or Parg(110)-/-) were isolated using a swim-up technique with purification steps to eliminate all potentially contaminating somatic cells. Genomic controls for input subtraction were generated by complete DNA isolation from sperm (wild-type or Parg(110)-/-) followed by random fragmentation.

treatment_protocol: Wild-type (129SVE (=129S6/SvEvTac, Taconic) or genetic disruption of the Parg gene (Parg(110)-/-, identical genetic background, 129S6/SvEvTac, Taconic) in sires.

value: sperm

tag: genotype


title: Tumour sample ICH-3055


title: Wilms Tumour ICH-3047

source_name: Wilms Tumour ICH-3047

value: III

value: mutant

value: aberrant


title: Tumour sample ICH-3053

value: Wilms tumour


title: BTIC73 meC

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description:
MeDIP-chip B73 cells methylated DNA (meC) antibody antibody
32419902

hyb_protocol: According to NimbleGen standard guidelines for HD2 arrays

scan_protocol: Scanned on an Axon 4000B scanner using standard protocols; scanning performed by NimbleGen.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: MeDIP DNA from B73 cells

growth_protocol: The GBM BTSCs and fNSC neurospheres were maintained and expanded in serum-free NS media (NeuroCult NS-A media, StemCell Technologies, Cat:05751) supplemented with EGF (20 ng/mL, Peprotech, Cat:AF-100-15), FGF (20 ng/mL, R&D Systems, Cat:233-FB) and heparin sulfate (2 μg/mL, StemCell Technologies, Cat:07980). BTSC and fNSC neurospheres were passaged when the sphere reached an adequate size (200 ~ 400 microns). For cell passaging, the neurospheres were dissociated into single cells by treating with Accumax (Innovative Cell Technologies, #AM105) for 10 min at 37 °C and gently triturating using P200 pipettes (Gilson). Cells were then counted and replated. When necessary, cells were fed weekly by adding the supplementary factors listed above (FGF 20 ng/mL, EGF 20 ng/mL, heparin 2 μg /mL).

extract_protocol: BTIC and fNSC spheres were grown to be approximately 200 to 400 microns in size, cells were collected and dissociated using 300μL to 1.0mL Accumax enzyme and triturated to produce a single cell suspension. At this point, protocol follows standard Farnham lab protocol for ChIP-chip with small modifications. 5 x 10^6 cells were used per ChIP reaction. Formaldehyde was added in culture media to induce crosslinking at a final concentration of 1.0% for 15 minutes at room temperature on a rocking bench. Reaction was quenched using final glycine concentration of 0.125M with a 5 minute incubation, cells were washed with standard phosphate-buffered saline (PBS). After wash and collection, cells were resuspended in 1.0mL of Cell Lysis Buffer (CLB) containing protease inhibitors PMSF (10 μL/mL), aprotinin (1 μL/mL) and leupeptin (1 μL/mL) and incubated for 30-60 min on ice. Cells were dounced and nuclei collected, followed by resuspension in Nuclei Lysis Buffer (NLB) containing the same protease inhibitors as for the CLB. Chromatin was sonicated using a Bioruptor (Diagenode, Belgium) at maximum power; set for 30 seconds ON followed by 1 minutes OFF for 5 to 18 pulses, or 15 seconds ON followed by 30 seconds OFF for 10 to 20 pulses. Blocked StaphA cells were used to pre-clear chromatin, then antibody added with 12-18 hour incubation at 4C. After removal of StaphA cells, crosslinks were removed by resuspension of chromatin in 5M NaCl and heating at 67C for 12-18 hours. 1μL DNase-free RNase was then added for an incubation of 15 minutes at 37°C. Finally,  1μL Proteinase K was added for an incubation of 15 minutes at 67°C. Chromatin was purified using a QiaQuick column and eluted into water. Input DNA was prepared beginning with the precleared chromatin; crosslinks were reversed (using 5M NaCl and DNAase-free RNAase and Proteinase K as above) and purified into water using a QiaQuick column. DNA was amplified using WGA2 amplification kit from Sigma following manufacturer's protocol.

treatment_protocol: These cells are an established cell line obtained from the Weiss and Cairncross laboratories, University of Calgary

tag: cell line

tag: cell type

value: brain tumor stem cells (BTSCs)

tag: chip antibody

value: methylated DNA (meC) antibody

tag: chip antibody vendor

value: Eurogentec

tag: chip antibody cat. #

source_name: Input DNA from B73 cells

value: none, input DNA


title: 4AA


title: 4AC


title: Wilms Tumour ICH-3045

source_name: Wilms Tumour ICH-3045

tag: Sex

tag: Stage

tag: relapse (months)

value: N/E

tag: death (months)

value: Normal

source_name: Stratagene Universal Human Reference RNA


title: Tumour sample ICH-3052

value: Male

tag: copy number aberrations

tag: tp53 copy number

value: Loss

tag: tp53 sequence

tag: overall tp53 status


title: 2CW

description:
Wtgenomic
Input control: whole sperm DNA sheared
whole sperm genomic DNA input control

source_name: Wild-type sheared whole sperm genomic DNA

tag: tissue

value: Wild-type


title: Wilms Tumour ICH-3044

source_name: Wilms Tumour ICH-3044

value: Pooled various


title: Wilms Tumour ICH-3048

source_name: Wilms Tumour ICH-3048

value: Female


title: 2CV


title: BTIC12 meC

description:
MeDIP-chip B12 cells methylated DNA (meC) antibody antibody
32089502

source_name: MeDIP DNA from B12 cells

label_protocol: According to NimbleGen standard guidelines for HD2 arrays

source_name: Input DNA from B12 cells


title: BTIC73 H3K9me3

description:
ChIP-chip B73 cells Anti-Histone H3 (tri methyl K9) antibody antibody
32006902

source_name: H3K9me3 ChIP DNA from B73 cells

value: Abcam


title: Tumour sample ICH-3048

source_name: Unrelated normal blood

value: normal blood

tag: gender

value: female


title: fNSC H3K4me3

description:
ChIP-chip fNSC cells H3K4me3 polyclonal antibody antibody
32007202

source_name: H3K4me3 ChIP DNA from fNSC cells

value: fNSC

value: fetal neural stem cells (fNSCs)

value: H3K4me3 polyclonal antibody

value: Diagenode

source_name: Input DNA from fNSC cells


title: Wilms Tumour ICH-3043

source_name: Wilms Tumour ICH-3043

value: Wilms tumour

value: III

value: normal

value: aberrant


title: 2CT

value: sperm

tag: strain


title: BTIC12 H3K9me3

description:
ChIP-chip B12 cells Anti-Histone H3 (tri methyl K9) antibody antibody
32038502

source_name: H3K9me3 ChIP DNA from B12 cells

value: brain tumor stem cells (BTSCs)

value: none, input DNA


title: BTIC48 H3K9me3

description:
ChIP-chip B48 cells Anti-Histone H3 (tri methyl K9) antibody antibody
33969802

source_name: H3K9me3 ChIP DNA from B48 cells

source_name: Input DNA from B48 cells


title: BTIC25 meC

description:
MeDIP-chip B25 cells methylated DNA (meC) antibody antibody
33975202

source_name: MeDIP DNA from B25 cells

value: methylated DNA (meC) antibody

value: Eurogentec

source_name: Input DNA from B25 cells


title: BTIC48 H3K4me3

description:
ChIP-chip B48 cells H3K4me3 polyclonal antibody antibody
33975802

source_name: H3K4me3 ChIP DNA from B48 cells


title: BTIC25 H3K9me3

description:
ChIP-chip B25 cells Anti-Histone H3 (tri methyl K9) antibody antibody
33963302

source_name: H3K9me3 ChIP DNA from B25 cells


title: WT7

description:
WTNuc
nucleosomal genomic DNA,
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

source_name: Wild-type sperm Mnase fraction

tag: genotype

value: Wild-type


title: Wilms Tumour ICH-3041

source_name: Wilms Tumour ICH-3041

value: Female

value: N/E

value: Loss

value: mutant

source_name: Stratagene Universal Human Reference RNA

value: Pooled various


title: Tumour sample ICH-3047

source_name: Wilms Tumour ICH-3047

value: normal blood

value: female


title: Wilms Tumour ICH-3039

source_name: Wilms Tumour ICH-3039

value: Wilms tumour

value: IV

value: Normal


title: 120min EGF+DEX treated MCF10A cells rep 1

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

data_processing: Plier + lowess

label_protocol: According to Affymetrix manual

growth_protocol: MCF10A cells were grown in DME:F12 medium (Gibco BRL, Grand Island, NY) supplemented with 10 μg/ml insulin, 0.1 μg/ml cholera toxin, 0.5 μg/ml hydrocortisone, 5% heat-inactivated horse serum (Gibco BRL) and 10 ng/ml EGF, as previously described (Katz, Amit et al. 2007).

extract_protocol: RNA was isolated using the PerfectPure RNA Cultured Cell Kit (5 Prime, Hamburg, Germany) including DNAse 1 digestion.

treatment_protocol: Cells were stimulated in DMEM/F12 phenol free medium (Invitrogen) with EGF (10 ng/ml), Dex (100 nM).

tag: cell line

tag: time(minutes)

tag: treatment

value: EGF+DEX


title: Tumour sample ICH-3050

source_name: Wilms Tumour ICH-3050

value: I

value: normal


title: Tumour sample ICH-3045

source_name: Wilms Tumour ICH-3045

source_name: Unrelated normal blood


title: WT6

value: sperm


title: 240min EGF+DEX treated MCF10A cells rep 1


title: WT5


title: fNSC H3K27me3

description:
ChIP-chip fNSC cells Anti-trimethyl-Histone H3 (Lys27) Antibody antibody
32038802

source_name: H3K27me3 ChIP DNA from fNSC cells

value: fNSC

tag: cell type

value: fetal neural stem cells (fNSCs)

tag: chip antibody

tag: chip antibody vendor

value: Upstate

source_name: Input DNA from fNSC cells

value: none, input DNA


title: Wilms Tumour ICH-3033

source_name: Wilms Tumour ICH-3033

tag: Sex

value: Female

tag: Stage

value: N/E


title: Wilms Tumour ICH-3036

source_name: Wilms Tumour ICH-3036

value: II

tag: relapse (months)

tag: death (months)

value: Loss

value: mutant

value: aberrant


title: WT3

value: Wild-type


title: Tumour sample ICH-3044

source_name: Wilms Tumour ICH-3044

value: Wilms tumour

value: Male

tag: copy number aberrations

tag: tp53 copy number

value: normal blood

value: female


title: fNSC H3K9me3

description:
ChIP-chip fNSC cells Anti-Histone H3 (tri methyl K9) antibody antibody
32251702

source_name: H3K9me3 ChIP DNA from fNSC cells

value: Abcam

tag: chip antibody cat. #


title: Wilms Tumour ICH-2557

source_name: Wilms Tumour ICH-2557

tag: tissue

value: III

tag: tp53 sequence

tag: overall tp53 status

value: Pooled various


title: Wilms Tumour ICH-2967

source_name: Wilms Tumour ICH-2967


title: Tumour sample ICH-3043

source_name: Wilms Tumour ICH-3043

value: normal

tag: gender


title: fNSC meC

description:
MeDIP-chip fNSC cells methylated DNA (meC) antibody antibody
32111102_01

source_name: MeDIP DNA from fNSC cells

tag: cell line

value: fNSC

value: fetal neural stem cells (fNSCs)

value: methylated DNA (meC) antibody

value: Eurogentec


title: WT4

source_name: Wild-type sperm Mnase fraction

value: sperm

tag: strain

tag: genotype


title: BTIC12 H3K4me3

description:
ChIP-chip B12 cells H3K4me3 polyclonal antibody antibody
32095902

source_name: H3K4me3 ChIP DNA from B12 cells

tag: cell type

value: brain tumor stem cells (BTSCs)

value: H3K4me3 polyclonal antibody

value: Diagenode

source_name: Input DNA from B12 cells

value: none, input DNA


title: BTIC48 meC

description:
MeDIP-chip B48 cells methylated DNA (meC) antibody antibody
33969502

source_name: MeDIP DNA from B48 cells

tag: chip antibody

source_name: Input DNA from B48 cells


title: 60min EGF+DEX treated MCF10A cells rep 2

tag: time(minutes)

tag: treatment

value: EGF+DEX


title: BTIC73 H3K4me3

description:
ChIP-chip B73 cells H3K4me3 polyclonal antibody antibody
32118102

source_name: H3K4me3 ChIP DNA from B73 cells

tag: chip antibody vendor

source_name: Input DNA from B73 cells


title: BTIC73 H3K27me3

description:
ChIP-chip B73 cells Anti-trimethyl-Histone H3 (Lys27) Antibody antibody
33967202

source_name: H3K27me3 ChIP DNA from B73 cells

value: Upstate


title: 40min EGF+DEX treated MCF10A cells rep 2


title: BTIC25 H3K4me3

description:
ChIP-chip B25 cells H3K4me3 polyclonal antibody antibody
33970102

source_name: H3K4me3 ChIP DNA from B25 cells

source_name: Input DNA from B25 cells


title: WT1

value: Wild-type


title: MTM3


title: MTM2


title: Wilms Tumour ICH-2220

source_name: Wilms Tumour ICH-2220

value: Wilms tumour

tag: Sex

value: Female

tag: Stage

tag: relapse (months)

value: N/E

value: Normal

source_name: Stratagene Universal Human Reference RNA


title: Tumour sample ICH-3036

source_name: Wilms Tumour ICH-3036

value: II

tag: death (months)

tag: copy number aberrations

tag: tp53 copy number

value: Loss

value: mutant

value: aberrant

source_name: Unrelated normal blood

value: normal blood

value: female


title: Tumour sample ICH-3033

source_name: Wilms Tumour ICH-3033

tag: tissue

value: IV

tag: tp53 sequence

value: normal


title: D23m8

description:
D23Nuc
nucleosomal genomic DNA,
nucleosomal sperm DNA extracted after limited Mnase digestion of sperm

source_name: Parg(110)-/- sperm Mnase fraction

value: sperm


title: Wilms Tumour ICH-1149

source_name: Wilms Tumour ICH-1149

value: III

tag: overall tp53 status

value: Pooled various


title: 40min EGF+DEX treated MCF10A cells rep 1

tag: cell line

value: EGF+DEX


title: 20min EGF+DEX treated MCF10A cells rep 2


title: Tumour sample ICH-3041

source_name: Wilms Tumour ICH-3041

tag: gender


title: MTM1

source_name: Wild-type sperm Mnase fraction

tag: strain

tag: genotype

value: Wild-type


title: Tumour sample ICH-3039

source_name: Wilms Tumour ICH-3039

value: Wilms tumour


title: Tumour sample ICH-2557

source_name: Wilms Tumour ICH-2557

value: Female


title: Wilms Tumour ICH-1144

source_name: Wilms Tumour ICH-1144

value: N/E


title: 60min EGF+DEX treated MCF10A cells rep 1


title: Wilms Tumour ICH-1146

source_name: Wilms Tumour ICH-1146

value: Normal


title: D23m7


title: Tumour sample ICH-1149


title: 20min EGF+DEX treated MCF10A cells rep 1


title: BTIC25 H3K27me3

description:
ChIP-chip B25 cells Anti-trimethyl-Histone H3 (Lys27) Antibody antibody
38297402

source_name: H3K27me3 ChIP DNA from B25 cells

tag: cell type

value: brain tumor stem cells (BTSCs)

tag: chip antibody

value: Upstate

tag: chip antibody cat. #

value: none, input DNA


title: BTIC12 H3K27me3

description:
ChIP-chip B12 cells Anti-trimethyl-Histone H3 (Lys27) Antibody antibody
33975502

source_name: H3K27me3 ChIP DNA from B12 cells

tag: chip antibody vendor

source_name: Input DNA from B12 cells


title: Wilms Tumour ICH-1145

source_name: Wilms Tumour ICH-1145

tag: Sex

value: mutant

value: aberrant


title: BTIC48 H3K27me3

description:
ChIP-chip B48 cells Anti-trimethyl-Histone H3 (Lys27) Antibody antibody
38904402

source_name: H3K27me3 ChIP DNA from B48 cells

source_name: Input DNA from B48 cells


title: Tumour sample ICH-1146

tag: Stage

value: normal blood

value: female


title: Tumour sample ICH-1144

tag: relapse (months)

value: Loss


title: 240min DEX treated MCF10A cells rep 1

tag: time(minutes)

tag: treatment

value: DEX


title: 120min DEX treated MCF10A cells rep 1


title: D23m5

value: sperm


title: D23m6


title: D23m2


title: D23m4


title: D23m3


title: Wilms Tumour ICH-1143

source_name: Wilms Tumour ICH-1143

value: III

tag: death (months)

tag: copy number aberrations

tag: tp53 copy number

value: normal

source_name: Stratagene Universal Human Reference RNA

value: Pooled various


title: Wilms Tumour ICH-1136

source_name: Wilms Tumour ICH-1136

tag: tissue

value: Wilms tumour

value: I

tag: tp53 sequence

tag: overall tp53 status


title: 60min DEX treated MCF10A cells rep 2

tag: cell line


title: Wilms Tumour ICH-1142

source_name: Wilms Tumour ICH-1142

value: Female

value: II

value: N/E


title: Wilms Tumour ICH-1137

source_name: Wilms Tumour ICH-1137

value: Male

value: Normal


title: Tumour sample ICH-1140

source_name: Wilms Tumour ICH-1140

source_name: Unrelated normal blood

tag: gender


title: Tumour sample ICH-1143


title: Wilms Tumour ICH-1138

source_name: Wilms Tumour ICH-1138


title: MTM8 (Parg C)

source_name: Parg(110)-/- sperm Mnase fraction

tag: strain

tag: genotype


title: Tumour sample ICH-1142

value: mutant


title: Tumour sample ICH-1138


title: MTM6 (Parg A)


title: Tumour sample ICH-1136

value: aberrant


title: 60min DEX treated MCF10A cells rep 1


title: Wilms Tumour ICH-1135

source_name: Wilms Tumour ICH-1135


title: 40min DEX treated MCF10A cells rep 2


title: MTM7 (Parg B)


title: Wilms Tumour ICH-1134

source_name: Wilms Tumour ICH-1134


title: Tumour sample ICH-1134

value: normal blood


title: 240min EGF treated MCF10A cells rep 1

value: EGF


title: Wilms Tumour ICH-1133

source_name: Wilms Tumour ICH-1133

value: Loss


title: 20min DEX treated MCF10A cells rep 2

value: DEX


title: 035/09_white matter

status: Public on Aug 29 2014

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

institute: UCL Institute of Neurology

description: This entry supercedes previous accession: GSM1135831

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using Affymetrix Power Tools 1.14.3. Arrays were pre-processed using RMA quantile normalization with background correction. Gene level summary signals were generated by calculating the Winsorized mean (10% and 90%) of all probe sets annotated to a transcript.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: Core_adapted_from_netaffyx31
Transcript assignments are based on genome build hg19
Core exons only are included in this analysis

source_name: post-mortem brain tissue, individual ID 035/09, white matter

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal labelling kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, UK). cDNA synthesis and amplification were performed using the Ambion┬«WT Expression Kit (Ambion, UK).

treatment_protocol: Not applicable.

tag: individual id

tag: brain region

value: white matter

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

tag: Cause of death

value: Suspension by ligature

tag: age at death (in years)

tag: post-mortem interval (in hours)

tag: ancestry

value: European

tag: brain ph

tag: rin


title: 025/05_white matter

description: This entry supercedes previous accession: GSM1135808

source_name: post-mortem brain tissue, individual ID 025/05, white matter

tag: Sex


title: 036/08_white matter

description: This entry supercedes previous accession: GSM1135794

source_name: post-mortem brain tissue, individual ID 036/08, white matter


title: 40min DEX treated MCF10A cells rep 1

tag: time(minutes)

tag: treatment


title: Tumour sample ICH-1135

tag: tissue

value: Wilms tumour

tag: Stage

value: I

tag: relapse (months)

tag: death (months)

tag: copy number aberrations

tag: tp53 copy number

tag: tp53 sequence

tag: overall tp53 status

value: female


title: Tumour sample ICH-1133

value: Female

value: N/E

tag: gender


title: Tumour sample ICH-1137

value: Male

value: II

value: Normal

value: normal


title: Wilms Tumour ICH-1140

value: Pooled various


title: 023/08_white matter

description: This entry supercedes previous accession: GSM1135801

source_name: post-mortem brain tissue, individual ID 023/08, white matter

tag: individual id

tag: brain region

tag: disease status

tag: brain bank

tag: Cause of death

tag: age at death (in years)


title: 034/06_white matter

description: This entry supercedes previous accession: GSM1135826

source_name: post-mortem brain tissue, individual ID 034/06, white matter

tag: Sex

tag: post-mortem interval (in hours)

tag: ancestry

tag: brain ph

tag: rin


title: 021/08_white matter

description: This entry supercedes previous accession: GSM1135776

source_name: post-mortem brain tissue, individual ID 021/08, white matter


title: 036/08_thalamus

description: This entry supercedes previous accession: GSM1136009

source_name: post-mortem brain tissue, individual ID 036/08, thalamus

value: thalamus


title: 20min DEX treated MCF10A cells rep 1

tag: cell line

tag: time(minutes)

tag: treatment

value: DEX


title: 120min EGF treated MCF10A cells rep 1

value: EGF


title: 001/06_white matter

description: This entry supercedes previous accession: GSM1135785

source_name: post-mortem brain tissue, individual ID 001/06, white matter

value: white matter

value: neurologically and neuropathologically normal


title: 021/08_thalamus

description: This entry supercedes previous accession: GSM1136033

source_name: post-mortem brain tissue, individual ID 021/08, thalamus

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

value: Suspension by ligature


title: 001/06_thalamus

description: This entry supercedes previous accession: GSM1136046

source_name: post-mortem brain tissue, individual ID 001/06, thalamus

value: European


title: 035/09_thalamus

description: This entry supercedes previous accession: GSM1135997

source_name: post-mortem brain tissue, individual ID 035/09, thalamus


title: 60min EGF treated MCF10A cells rep 2


title: 40min EGF treated MCF10A cells rep 1


title: 025/05_thalamus

description: This entry supercedes previous accession: GSM1136047

source_name: post-mortem brain tissue, individual ID 025/05, thalamus


title: 023/08_thalamus

description: This entry supercedes previous accession: GSM1136030

source_name: post-mortem brain tissue, individual ID 023/08, thalamus


title: 023/08_substantia nigra

description: This entry supercedes previous accession: GSM1135132

source_name: post-mortem brain tissue, individual ID 023/08, substantia nigra

value: substantia nigra


title: 40min EGF treated MCF10A cells rep 2


title: 036/08_substantia nigra

description: This entry supercedes previous accession: GSM1135139

source_name: post-mortem brain tissue, individual ID 036/08, substantia nigra


title: 023/08_temporal cortex

description: This entry supercedes previous accession: GSM1135902

source_name: post-mortem brain tissue, individual ID 023/08, temporal cortex

value: temporal cortex


title: 60min EGF treated MCF10A cells rep 1


title: 025/05_substantia nigra

description: This entry supercedes previous accession: GSM1135166

source_name: post-mortem brain tissue, individual ID 025/05, substantia nigra


title: 021/08_temporal cortex

description: This entry supercedes previous accession: GSM1135913

source_name: post-mortem brain tissue, individual ID 021/08, temporal cortex


title: 035/09_temporal cortex

description: This entry supercedes previous accession: GSM1135899

source_name: post-mortem brain tissue, individual ID 035/09, temporal cortex


title: 20min EGF treated MCF10A cells rep 2


title: 021/08_substantia nigra

description: This entry supercedes previous accession: GSM1135146

source_name: post-mortem brain tissue, individual ID 021/08, substantia nigra


title: 036/08_temporal cortex

description: This entry supercedes previous accession: GSM1135896

source_name: post-mortem brain tissue, individual ID 036/08, temporal cortex

value: Female


title: 001/06_substantia nigra

description: This entry supercedes previous accession: GSM1135874

source_name: post-mortem brain tissue, individual ID 001/06, substantia nigra


title: 021/08_putamen

description: This entry supercedes previous accession: GSM1135710

source_name: post-mortem brain tissue, individual ID 021/08, putamen

value: putamen


title: 035/09_substantia nigra

description: This entry supercedes previous accession: GSM1135169

source_name: post-mortem brain tissue, individual ID 035/09, substantia nigra

value: Male


title: 034/06_putamen

description: This entry supercedes previous accession: GSM1135733

source_name: post-mortem brain tissue, individual ID 034/06, putamen


title: untreated MCF10A cells rep 1

value: untreated


title: 035/09_putamen

description: This entry supercedes previous accession: GSM1135731

source_name: post-mortem brain tissue, individual ID 035/09, putamen


title: 025/05_putamen

description: This entry supercedes previous accession: GSM1135708

source_name: post-mortem brain tissue, individual ID 025/05, putamen


title: untreated MCF10A cells rep 2


title: 001/06_putamen

description: This entry supercedes previous accession: GSM1135712

source_name: post-mortem brain tissue, individual ID 001/06, putamen


title: 023/08_occipital cortex

description: This entry supercedes previous accession: GSM1135601

source_name: post-mortem brain tissue, individual ID 023/08, occipital cortex

value: occipital cortex


title: 20min EGF treated MCF10A cells rep 1


title: 021/08_occipital cortex

description: This entry supercedes previous accession: GSM1135620

source_name: post-mortem brain tissue, individual ID 021/08, occipital cortex


title: 001/06_occipital cortex

description: This entry supercedes previous accession: GSM1135575

source_name: post-mortem brain tissue, individual ID 001/06, occipital cortex


title: 034/06_occipital cortex

description: This entry supercedes previous accession: GSM1135652

source_name: post-mortem brain tissue, individual ID 034/06, occipital cortex


title: 036/08_putamen

description: This entry supercedes previous accession: GSM1135700

source_name: post-mortem brain tissue, individual ID 036/08, putamen


title: 025/05_occipital cortex

description: This entry supercedes previous accession: GSM1135572

source_name: post-mortem brain tissue, individual ID 025/05, occipital cortex


title: 035/09_occipital cortex

description: This entry supercedes previous accession: GSM1135644

source_name: post-mortem brain tissue, individual ID 035/09, occipital cortex


title: 021/08_medulla

description: This entry supercedes previous accession: GSM1135488

source_name: post-mortem brain tissue, individual ID 021/08, medulla

value: medulla


title: 021/08_hippocampus

description: This entry supercedes previous accession: GSM1135416

source_name: post-mortem brain tissue, individual ID 021/08, hippocampus

value: hippocampus


title: 036/08_medulla

description: This entry supercedes previous accession: GSM1135523

source_name: post-mortem brain tissue, individual ID 036/08, medulla


title: 034/06_hippocampus

description: This entry supercedes previous accession: GSM1135441

source_name: post-mortem brain tissue, individual ID 034/06, hippocampus


title: 023/08_medulla

description: This entry supercedes previous accession: GSM1135526

source_name: post-mortem brain tissue, individual ID 023/08, medulla


title: 035/09_medulla

description: This entry supercedes previous accession: GSM1135539

source_name: post-mortem brain tissue, individual ID 035/09, medulla


title: 023/08_hippocampus

description: This entry supercedes previous accession: GSM1135402

source_name: post-mortem brain tissue, individual ID 023/08, hippocampus


title: 035/09_hippocampus

description: This entry supercedes previous accession: GSM1135445

source_name: post-mortem brain tissue, individual ID 035/09, hippocampus


title: 023/08_putamen

description: This entry supercedes previous accession: GSM1135687

source_name: post-mortem brain tissue, individual ID 023/08, putamen


title: 025/05_medulla

description: This entry supercedes previous accession: GSM1135506

source_name: post-mortem brain tissue, individual ID 025/05, medulla


title: 025/05_hippocampus

description: This entry supercedes previous accession: GSM1135419

source_name: post-mortem brain tissue, individual ID 025/05, hippocampus


title: 036/08_hippocampus

description: This entry supercedes previous accession: GSM1135426

source_name: post-mortem brain tissue, individual ID 036/08, hippocampus


title: 001/06_hippocampus

description: This entry supercedes previous accession: GSM1135429

source_name: post-mortem brain tissue, individual ID 001/06, hippocampus


title: 036/08_frontal cortex

description: This entry supercedes previous accession: GSM1135295

source_name: post-mortem brain tissue, individual ID 036/08, frontal cortex

value: frontal cortex


title: 023/08_frontal cortex

description: This entry supercedes previous accession: GSM1135301

source_name: post-mortem brain tissue, individual ID 023/08, frontal cortex


title: 034/06_frontal cortex

description: This entry supercedes previous accession: GSM1135361

source_name: post-mortem brain tissue, individual ID 034/06, frontal cortex


title: 001/06_frontal cortex

description: This entry supercedes previous accession: GSM1135292

source_name: post-mortem brain tissue, individual ID 001/06, frontal cortex


title: 035/09_frontal cortex

description: This entry supercedes previous accession: GSM1135359

source_name: post-mortem brain tissue, individual ID 035/09, frontal cortex


title: 025/05_frontal cortex

description: This entry supercedes previous accession: GSM1135333

source_name: post-mortem brain tissue, individual ID 025/05, frontal cortex


title: 95_03_white matter

source_name: post-mortem brain tissue, individual ID 95_03, white matter

value: Sun Health Research Institute

value: Respiratory failure


title: 07_73_white matter

source_name: post-mortem brain tissue, individual ID 07_73, white matter

value: white matter


title: 021/08_frontal cortex

description: This entry supercedes previous accession: GSM1135323

source_name: post-mortem brain tissue, individual ID 021/08, frontal cortex

value: neurologically and neuropathologically normal


title: 07_37_white matter

source_name: post-mortem brain tissue, individual ID 07_37, white matter


title: 001/06_medulla

description: This entry supercedes previous accession: GSM1135512

source_name: post-mortem brain tissue, individual ID 001/06, medulla

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh


title: 07_73_thalamus

source_name: post-mortem brain tissue, individual ID 07_73, thalamus

value: thalamus


title: 036/08_white matter

source_name: post-mortem brain tissue, individual ID 036/08, white matter

value: Suspension by ligature

value: European


title: 07_37_thalamus

source_name: post-mortem brain tissue, individual ID 07_37, thalamus


title: 95_03_temporal cortex

source_name: post-mortem brain tissue, individual ID 95_03, temporal cortex

value: temporal cortex


title: 023/08_white matter

source_name: post-mortem brain tissue, individual ID 023/08, white matter

value: Female


title: 035/09_thalamus

source_name: post-mortem brain tissue, individual ID 035/09, thalamus


title: 034/06_white matter

source_name: post-mortem brain tissue, individual ID 034/06, white matter


title: 07_37_temporal cortex

source_name: post-mortem brain tissue, individual ID 07_37, temporal cortex


title: 001/06_white matter

source_name: post-mortem brain tissue, individual ID 001/06, white matter


title: 95_03_thalamus

source_name: post-mortem brain tissue, individual ID 95_03, thalamus


title: 07_37_substantia nigra

source_name: post-mortem brain tissue, individual ID 07_37, substantia nigra

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title: 036/08_thalamus

source_name: post-mortem brain tissue, individual ID 036/08, thalamus


title: 021/08_white matter

source_name: post-mortem brain tissue, individual ID 021/08, white matter

value: Male


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source_name: post-mortem brain tissue, individual ID 07_73, substantia nigra


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source_name: post-mortem brain tissue, individual ID 035/09, white matter


title: 001/06_thalamus

source_name: post-mortem brain tissue, individual ID 001/06, thalamus


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title: 021/08_thalamus

source_name: post-mortem brain tissue, individual ID 021/08, thalamus


title: 07_73_temporal cortex

source_name: post-mortem brain tissue, individual ID 07_73, temporal cortex


title: 07_37_putamen

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value: putamen


title: 023/08_temporal cortex

source_name: post-mortem brain tissue, individual ID 023/08, temporal cortex


title: 023/08_thalamus

source_name: post-mortem brain tissue, individual ID 023/08, thalamus


title: 07_73_putamen

source_name: post-mortem brain tissue, individual ID 07_73, putamen


title: 07_73_occipital cortex

source_name: post-mortem brain tissue, individual ID 07_73, occipital cortex

value: occipital cortex


title: 035/09_temporal cortex

source_name: post-mortem brain tissue, individual ID 035/09, temporal cortex


title: 07_37_occipital cortex

source_name: post-mortem brain tissue, individual ID 07_37, occipital cortex


title: 036/08_temporal cortex

source_name: post-mortem brain tissue, individual ID 036/08, temporal cortex


title: 07_73_medulla

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source_name: post-mortem brain tissue, individual ID 035/09, substantia nigra


title: 025/05_thalamus

source_name: post-mortem brain tissue, individual ID 025/05, thalamus


title: 025/05_white matter

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title: 023/08_substantia nigra

source_name: post-mortem brain tissue, individual ID 023/08, substantia nigra


title: 95_03_occipital cortex

source_name: post-mortem brain tissue, individual ID 95_03, occipital cortex


title: 036/08_occipital cortex

description: This entry supercedes previous accession: GSM1135625

source_name: post-mortem brain tissue, individual ID 036/08, occipital cortex


title: 95_03_medulla

source_name: post-mortem brain tissue, individual ID 95_03, medulla


title: 036/08_substantia nigra

source_name: post-mortem brain tissue, individual ID 036/08, substantia nigra


title: 07_37_medulla

source_name: post-mortem brain tissue, individual ID 07_37, medulla


title: 95_03_frontal cortex

source_name: post-mortem brain tissue, individual ID 95_03, frontal cortex


title: 07_73_hippocampus

source_name: post-mortem brain tissue, individual ID 07_73, hippocampus

value: hippocampus


title: 07_37_frontal cortex

source_name: post-mortem brain tissue, individual ID 07_37, frontal cortex

value: frontal cortex


title: 07_73_frontal cortex

source_name: post-mortem brain tissue, individual ID 07_73, frontal cortex

value: Sun Health Research Institute


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source_name: post-mortem brain tissue, individual ID 021/08, substantia nigra


title: 025/05_substantia nigra

source_name: post-mortem brain tissue, individual ID 025/05, substantia nigra


title: 035/09_putamen

source_name: post-mortem brain tissue, individual ID 035/09, putamen


title: 034/06_putamen

source_name: post-mortem brain tissue, individual ID 034/06, putamen


title: 023/08_putamen

source_name: post-mortem brain tissue, individual ID 023/08, putamen


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source_name: post-mortem brain tissue, individual ID 001/06, substantia nigra


title: 029/09_white matter

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source_name: post-mortem brain tissue, individual ID 029/09, white matter

value: Road traffic accident


title: 025/05_putamen

source_name: post-mortem brain tissue, individual ID 025/05, putamen


title: 012/09_white matter

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source_name: post-mortem brain tissue, individual ID 012/09, white matter

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source_name: post-mortem brain tissue, individual ID 006/09, white matter

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title: 007/09_white matter

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source_name: post-mortem brain tissue, individual ID 007/09, white matter

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh


title: 021/08_putamen

source_name: post-mortem brain tissue, individual ID 021/08, putamen


title: 001/06_putamen

source_name: post-mortem brain tissue, individual ID 001/06, putamen


title: 036/08_occipital cortex

source_name: post-mortem brain tissue, individual ID 036/08, occipital cortex


title: 007/09_thalamus

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source_name: post-mortem brain tissue, individual ID 007/09, thalamus

value: thalamus


title: 001/06_occipital cortex

source_name: post-mortem brain tissue, individual ID 001/06, occipital cortex

value: Suspension by ligature


title: 006/09_thalamus

description: This entry supercedes previous accession: GSM1136014

source_name: post-mortem brain tissue, individual ID 006/09, thalamus

value: European


title: 034/06_occipital cortex

source_name: post-mortem brain tissue, individual ID 034/06, occipital cortex


title: 012/09_thalamus

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source_name: post-mortem brain tissue, individual ID 012/09, thalamus


title: 036/08_putamen

source_name: post-mortem brain tissue, individual ID 036/08, putamen


title: 023/08_occipital cortex

source_name: post-mortem brain tissue, individual ID 023/08, occipital cortex


title: 029/09_temporal cortex

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source_name: post-mortem brain tissue, individual ID 029/09, temporal cortex

value: temporal cortex


title: 029/09_thalamus

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source_name: post-mortem brain tissue, individual ID 029/09, thalamus


title: 025/05_occipital cortex

source_name: post-mortem brain tissue, individual ID 025/05, occipital cortex


title: 025/05_medulla

source_name: post-mortem brain tissue, individual ID 025/05, medulla


title: 035/09_occipital cortex

source_name: post-mortem brain tissue, individual ID 035/09, occipital cortex


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source_name: post-mortem brain tissue, individual ID 021/08, occipital cortex


title: 021/08_temporal cortex

source_name: post-mortem brain tissue, individual ID 021/08, temporal cortex


title: 012/09_temporal cortex

description: This entry supercedes previous accession: GSM1135886

source_name: post-mortem brain tissue, individual ID 012/09, temporal cortex


title: 021/08_medulla

source_name: post-mortem brain tissue, individual ID 021/08, medulla


title: 036/08_medulla

source_name: post-mortem brain tissue, individual ID 036/08, medulla

value: Female


title: 007/09_temporal cortex

description: This entry supercedes previous accession: GSM1135903

source_name: post-mortem brain tissue, individual ID 007/09, temporal cortex


title: 023/08_medulla

source_name: post-mortem brain tissue, individual ID 023/08, medulla


title: 012/09_substantia nigra

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source_name: post-mortem brain tissue, individual ID 012/09, substantia nigra

value: substantia nigra


title: 006/09_substantia nigra

description: This entry supercedes previous accession: GSM1135131

source_name: post-mortem brain tissue, individual ID 006/09, substantia nigra

value: Male


title: 012/09_putamen

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source_name: post-mortem brain tissue, individual ID 012/09, putamen

value: putamen


title: 035/09_medulla

source_name: post-mortem brain tissue, individual ID 035/09, medulla


title: 021/08_hippocampus

source_name: post-mortem brain tissue, individual ID 021/08, hippocampus


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source_name: post-mortem brain tissue, individual ID 006/09, occipital cortex

value: occipital cortex


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source_name: post-mortem brain tissue, individual ID 007/09, occipital cortex


title: 006/09_putamen

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source_name: post-mortem brain tissue, individual ID 006/09, putamen


title: 007/09_putamen

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source_name: post-mortem brain tissue, individual ID 007/09, putamen


title: 001/06_medulla

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source_name: post-mortem brain tissue, individual ID 029/09, substantia nigra


title: 025/05_hippocampus

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value: hippocampus


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source_name: post-mortem brain tissue, individual ID 035/09, hippocampus


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source_name: post-mortem brain tissue, individual ID 034/06, hippocampus


title: 029/09_putamen

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source_name: post-mortem brain tissue, individual ID 029/09, putamen


title: 029/09_occipital cortex

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source_name: post-mortem brain tissue, individual ID 029/09, occipital cortex


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source_name: post-mortem brain tissue, individual ID 012/09, occipital cortex


title: 023/08_hippocampus

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source_name: post-mortem brain tissue, individual ID 036/08, hippocampus


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source_name: post-mortem brain tissue, individual ID 007/09, medulla


title: 036/08_frontal cortex

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value: frontal cortex


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source_name: post-mortem brain tissue, individual ID 034/06, frontal cortex


title: 025/05_frontal cortex

source_name: post-mortem brain tissue, individual ID 025/05, frontal cortex


title: 006/09_temporal cortex

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source_name: post-mortem brain tissue, individual ID 006/09, temporal cortex


title: 021/08_frontal cortex

source_name: post-mortem brain tissue, individual ID 021/08, frontal cortex


title: 035/09_frontal cortex

source_name: post-mortem brain tissue, individual ID 035/09, frontal cortex


title: 006/09_medulla

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source_name: post-mortem brain tissue, individual ID 006/09, medulla


title: 029/09_medulla

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source_name: post-mortem brain tissue, individual ID 029/09, medulla


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source_name: post-mortem brain tissue, individual ID 007/09, hippocampus


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source_name: post-mortem brain tissue, individual ID 012/09, hippocampus


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source_name: post-mortem brain tissue, individual ID 012/09, frontal cortex


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source_name: post-mortem brain tissue, individual ID 007/09, frontal cortex


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source_name: post-mortem brain tissue, individual ID 029/09, frontal cortex


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title: 006/09_frontal cortex

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source_name: post-mortem brain tissue, individual ID 006/09, frontal cortex

value: Road traffic accident


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source_name: post-mortem brain tissue, individual ID 023/08, frontal cortex


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source_name: post-mortem brain tissue, individual ID 029/09, hippocampus


title: 006/09_hippocampus

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source_name: post-mortem brain tissue, individual ID 006/09, hippocampus


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title: 95_03_white matter

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value: white matter

value: Sun Health Research Institute

value: Respiratory failure


title: 08_55_white matter

source_name: post-mortem brain tissue, individual ID 08_55, white matter

value: neurologically and neuropathologically normal

value: renal failure


title: 001/06_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 001/06, cerebellar cortex

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

value: Suspension by ligature

value: European


title: 00_38_white matter

source_name: post-mortem brain tissue, individual ID 00_38, white matter

value: Female


title: 07_73_white matter

source_name: post-mortem brain tissue, individual ID 07_73, white matter


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source_name: post-mortem brain tissue, individual ID 07_37, white matter

value: Male


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source_name: post-mortem brain tissue, individual ID 036/08, cerebellar cortex


title: 06_02_thalamus

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title: 01_37_white matter

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title: 06_02_white matter

source_name: post-mortem brain tissue, individual ID 06_02, white matter


title: 08_55_thalamus

source_name: post-mortem brain tissue, individual ID 08_55, thalamus


title: 012/09_medulla

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source_name: post-mortem brain tissue, individual ID 012/09, medulla


title: 07_73_temporal cortex

source_name: post-mortem brain tissue, individual ID 07_73, temporal cortex

value: temporal cortex


title: 07_37_temporal cortex

source_name: post-mortem brain tissue, individual ID 07_37, temporal cortex


title: 95_03_thalamus

source_name: post-mortem brain tissue, individual ID 95_03, thalamus


title: 07_37_substantia nigra

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title: 08_55_temporal cortex

source_name: post-mortem brain tissue, individual ID 08_55, temporal cortex


title: 95_03_temporal cortex

source_name: post-mortem brain tissue, individual ID 95_03, temporal cortex


title: 95_03_substantia nigra

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title: 07_73_thalamus

source_name: post-mortem brain tissue, individual ID 07_73, thalamus


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title: 01_37_temporal cortex

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title: 07_37_putamen

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value: putamen


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title: 07_73_occipital cortex

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source_name: post-mortem brain tissue, individual ID 07_37, occipital cortex


title: 00_38_putamen

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title: 06_02_temporal cortex

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title: 01_37_putamen

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title: 95_03_occipital cortex

source_name: post-mortem brain tissue, individual ID 95_03, occipital cortex


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title: 07_73_medulla

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title: 07_73_hippocampus

source_name: post-mortem brain tissue, individual ID 07_73, hippocampus

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title: 06_02_occipital cortex

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title: 07_37_frontal cortex

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value: frontal cortex


title: 08_55_substantia nigra

source_name: post-mortem brain tissue, individual ID 08_55, substantia nigra

value: Sun Health Research Institute


title: 07_73_frontal cortex

source_name: post-mortem brain tissue, individual ID 07_73, frontal cortex

value: Respiratory failure


title: 08_55_putamen

source_name: post-mortem brain tissue, individual ID 08_55, putamen

value: neurologically and neuropathologically normal


title: 00_38_occipital cortex

source_name: post-mortem brain tissue, individual ID 00_38, occipital cortex

value: renal failure


title: 08_55_occipital cortex

source_name: post-mortem brain tissue, individual ID 08_55, occipital cortex


title: 95_03_medulla

source_name: post-mortem brain tissue, individual ID 95_03, medulla


title: 07_37_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 07_37, cerebellar cortex

value: cerebellar cortex


title: 95_03_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 95_03, cerebellar cortex


title: 07_37_medulla

source_name: post-mortem brain tissue, individual ID 07_37, medulla


title: 06_02_putamen

source_name: post-mortem brain tissue, individual ID 06_02, putamen


title: 01_37_occipital cortex

source_name: post-mortem brain tissue, individual ID 01_37, occipital cortex


title: 012/09_white matter

source_name: post-mortem brain tissue, individual ID 012/09, white matter

value: white matter

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

value: Road traffic accident


title: 06_02_medulla

source_name: post-mortem brain tissue, individual ID 06_02, medulla

value: Male

value: European


title: 95_03_frontal cortex

source_name: post-mortem brain tissue, individual ID 95_03, frontal cortex

value: Female


title: 006/09_white matter

source_name: post-mortem brain tissue, individual ID 006/09, white matter


title: 07_73_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 07_73, cerebellar cortex


title: 08_55_medulla

source_name: post-mortem brain tissue, individual ID 08_55, medulla


title: 00_38_medulla

source_name: post-mortem brain tissue, individual ID 00_38, medulla


title: 007/09_white matter

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title: 029/09_white matter

source_name: post-mortem brain tissue, individual ID 029/09, white matter


title: 01_37_medulla

source_name: post-mortem brain tissue, individual ID 01_37, medulla


title: 06_02_hippocampus

source_name: post-mortem brain tissue, individual ID 06_02, hippocampus


title: 01_37_hippocampus

source_name: post-mortem brain tissue, individual ID 01_37, hippocampus


title: 08_55_hippocampus

source_name: post-mortem brain tissue, individual ID 08_55, hippocampus


title: 07_73_putamen

source_name: post-mortem brain tissue, individual ID 07_73, putamen


title: 012/09_thalamus

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value: thalamus


title: 007/09_thalamus

source_name: post-mortem brain tissue, individual ID 007/09, thalamus


title: 029/09_temporal cortex

source_name: post-mortem brain tissue, individual ID 029/09, temporal cortex

value: temporal cortex


title: 06_02_frontal cortex

source_name: post-mortem brain tissue, individual ID 06_02, frontal cortex


title: 029/09_thalamus

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title: 006/09_thalamus

source_name: post-mortem brain tissue, individual ID 006/09, thalamus


title: 01_37_frontal cortex

source_name: post-mortem brain tissue, individual ID 01_37, frontal cortex


title: 018/09_white matter

description: This entry supercedes previous accession: GSM1135772

source_name: post-mortem brain tissue, individual ID 018/09, white matter

value: Ruptured aortic aneurysm


title: 018/06_white matter

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source_name: post-mortem brain tissue, individual ID 018/06, white matter


title: 08_55_frontal cortex

source_name: post-mortem brain tissue, individual ID 08_55, frontal cortex


title: 032/08_white matter

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source_name: post-mortem brain tissue, individual ID 032/08, white matter


title: 00_38_hippocampus

source_name: post-mortem brain tissue, individual ID 00_38, hippocampus


title: 012/09_temporal cortex

source_name: post-mortem brain tissue, individual ID 012/09, temporal cortex


title: 006/09_temporal cortex

source_name: post-mortem brain tissue, individual ID 006/09, temporal cortex


title: 014/08_white matter

description: This entry supercedes previous accession: GSM1135827

source_name: post-mortem brain tissue, individual ID 014/08, white matter


title: 00_38_frontal cortex

source_name: post-mortem brain tissue, individual ID 00_38, frontal cortex


title: 006/09_substantia nigra

source_name: post-mortem brain tissue, individual ID 006/09, substantia nigra

value: substantia nigra


title: 028/08_white matter

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source_name: post-mortem brain tissue, individual ID 028/08, white matter


title: 029/09_substantia nigra

source_name: post-mortem brain tissue, individual ID 029/09, substantia nigra


title: 006/09_putamen

source_name: post-mortem brain tissue, individual ID 006/09, putamen

value: putamen


title: 007/09_putamen

source_name: post-mortem brain tissue, individual ID 007/09, putamen


title: 012/09_medulla

source_name: post-mortem brain tissue, individual ID 012/09, medulla

value: medulla


title: 005/09_white matter

description: This entry supercedes previous accession: GSM1135812

source_name: post-mortem brain tissue, individual ID 005/09, white matter


title: 006/09_occipital cortex

source_name: post-mortem brain tissue, individual ID 006/09, occipital cortex

value: occipital cortex


title: 029/09_putamen

source_name: post-mortem brain tissue, individual ID 029/09, putamen


title: 012/09_putamen

source_name: post-mortem brain tissue, individual ID 012/09, putamen


title: 018/09_thalamus

description: This entry supercedes previous accession: GSM1136013

source_name: post-mortem brain tissue, individual ID 018/09, thalamus


title: 012/09_substantia nigra

source_name: post-mortem brain tissue, individual ID 012/09, substantia nigra


title: 007/09_temporal cortex

source_name: post-mortem brain tissue, individual ID 007/09, temporal cortex


title: 032/08_thalamus

description: This entry supercedes previous accession: GSM1136034

source_name: post-mortem brain tissue, individual ID 032/08, thalamus


title: 007/09_occipital cortex

source_name: post-mortem brain tissue, individual ID 007/09, occipital cortex


title: 012/09_occipital cortex

source_name: post-mortem brain tissue, individual ID 012/09, occipital cortex


title: 018/06_temporal cortex

description: This entry supercedes previous accession: GSM1135917

source_name: post-mortem brain tissue, individual ID 018/06, temporal cortex


title: 028/08_thalamus

description: This entry supercedes previous accession: GSM1136020

source_name: post-mortem brain tissue, individual ID 028/08, thalamus


title: 005/09_thalamus

description: This entry supercedes previous accession: GSM1136000

source_name: post-mortem brain tissue, individual ID 005/09, thalamus


title: 029/09_occipital cortex

source_name: post-mortem brain tissue, individual ID 029/09, occipital cortex


title: 007/09_medulla

source_name: post-mortem brain tissue, individual ID 007/09, medulla


title: 018/09_temporal cortex

description: This entry supercedes previous accession: GSM1135935

source_name: post-mortem brain tissue, individual ID 018/09, temporal cortex


title: 028/08_temporal cortex

description: This entry supercedes previous accession: GSM1135920

source_name: post-mortem brain tissue, individual ID 028/08, temporal cortex


title: 018/06_thalamus

description: This entry supercedes previous accession: GSM1136037

source_name: post-mortem brain tissue, individual ID 018/06, thalamus


title: 014/08_temporal cortex

description: This entry supercedes previous accession: GSM1135936

source_name: post-mortem brain tissue, individual ID 014/08, temporal cortex


title: 032/08_temporal cortex

description: This entry supercedes previous accession: GSM1135959

source_name: post-mortem brain tissue, individual ID 032/08, temporal cortex


title: 007/09_hippocampus

source_name: post-mortem brain tissue, individual ID 007/09, hippocampus

value: hippocampus


title: 014/08_thalamus

description: This entry supercedes previous accession: GSM1135991

source_name: post-mortem brain tissue, individual ID 014/08, thalamus

value: neurologically and neuropathologically normal


title: 005/09_temporal cortex

description: This entry supercedes previous accession: GSM1135918

source_name: post-mortem brain tissue, individual ID 005/09, temporal cortex


title: 029/09_medulla

source_name: post-mortem brain tissue, individual ID 029/09, medulla


title: 006/09_medulla

source_name: post-mortem brain tissue, individual ID 006/09, medulla


title: 006/09_hippocampus

source_name: post-mortem brain tissue, individual ID 006/09, hippocampus


title: 012/09_hippocampus

source_name: post-mortem brain tissue, individual ID 012/09, hippocampus


title: 029/09_hippocampus

source_name: post-mortem brain tissue, individual ID 029/09, hippocampus


title: 012/09_frontal cortex

source_name: post-mortem brain tissue, individual ID 012/09, frontal cortex

value: frontal cortex


title: 007/09_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 007/09, cerebellar cortex

value: cerebellar cortex


title: 029/09_frontal cortex

source_name: post-mortem brain tissue, individual ID 029/09, frontal cortex


title: 005/09_substantia nigra

description: This entry supercedes previous accession: GSM1135143

source_name: post-mortem brain tissue, individual ID 005/09, substantia nigra


title: 018/09_substantia nigra

description: This entry supercedes previous accession: GSM1135133

source_name: post-mortem brain tissue, individual ID 018/09, substantia nigra


title: 018/09_putamen

description: This entry supercedes previous accession: GSM1135713

source_name: post-mortem brain tissue, individual ID 018/09, putamen


title: 018/06_substantia nigra

description: This entry supercedes previous accession: GSM1135163

source_name: post-mortem brain tissue, individual ID 018/06, substantia nigra


title: 032/08_substantia nigra

description: This entry supercedes previous accession: GSM1135157

source_name: post-mortem brain tissue, individual ID 032/08, substantia nigra


title: 007/09_frontal cortex

source_name: post-mortem brain tissue, individual ID 007/09, frontal cortex


title: 006/09_frontal cortex

source_name: post-mortem brain tissue, individual ID 006/09, frontal cortex


title: 028/08_putamen

description: This entry supercedes previous accession: GSM1135738

source_name: post-mortem brain tissue, individual ID 028/08, putamen


title: 006/09_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 006/09, cerebellar cortex


title: 012/09_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 012/09, cerebellar cortex


title: 029/09_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 029/09, cerebellar cortex


title: 018/06_putamen

description: This entry supercedes previous accession: GSM1135722

source_name: post-mortem brain tissue, individual ID 018/06, putamen


title: 08_55_white matter

source_name: post-mortem brain tissue, individual ID 08_55, white matter

value: white matter

value: Sun Health Research Institute

value: renal failure


title: 06_02_white matter

source_name: post-mortem brain tissue, individual ID 06_02, white matter

value: Male


title: 01_37_white matter

source_name: post-mortem brain tissue, individual ID 01_37, white matter

value: European


title: 00_38_white matter

source_name: post-mortem brain tissue, individual ID 00_38, white matter

value: Female


title: 06_02_thalamus

source_name: post-mortem brain tissue, individual ID 06_02, thalamus

value: thalamus


title: 014/08_putamen

description: This entry supercedes previous accession: GSM1135758

source_name: post-mortem brain tissue, individual ID 014/08, putamen

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh


title: 005/09_putamen

description: This entry supercedes previous accession: GSM1135692

source_name: post-mortem brain tissue, individual ID 005/09, putamen

value: Ruptured aortic aneurysm


title: 032/08_putamen

description: This entry supercedes previous accession: GSM1135682

source_name: post-mortem brain tissue, individual ID 032/08, putamen


title: 018/06_occipital cortex

description: This entry supercedes previous accession: GSM1135573

source_name: post-mortem brain tissue, individual ID 018/06, occipital cortex


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description: This entry supercedes previous accession: GSM1135649

source_name: post-mortem brain tissue, individual ID 014/08, occipital cortex


title: 028/08_occipital cortex

description: This entry supercedes previous accession: GSM1135656

source_name: post-mortem brain tissue, individual ID 028/08, occipital cortex


title: 032/08_occipital cortex

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source_name: post-mortem brain tissue, individual ID 032/08, occipital cortex


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description: This entry supercedes previous accession: GSM1135612

source_name: post-mortem brain tissue, individual ID 018/09, occipital cortex


title: 005/09_occipital cortex

description: This entry supercedes previous accession: GSM1135619

source_name: post-mortem brain tissue, individual ID 005/09, occipital cortex


title: 08_55_thalamus

source_name: post-mortem brain tissue, individual ID 08_55, thalamus


title: 06_02_temporal cortex

source_name: post-mortem brain tissue, individual ID 06_02, temporal cortex

value: temporal cortex


title: 028/08_medulla

description: This entry supercedes previous accession: GSM1135534

source_name: post-mortem brain tissue, individual ID 028/08, medulla


title: 00_38_temporal cortex

source_name: post-mortem brain tissue, individual ID 00_38, temporal cortex


title: 014/08_medulla

description: This entry supercedes previous accession: GSM1135551

source_name: post-mortem brain tissue, individual ID 014/08, medulla


title: 06_02_substantia nigra

source_name: post-mortem brain tissue, individual ID 06_02, substantia nigra

value: substantia nigra


title: 08_55_temporal cortex

source_name: post-mortem brain tissue, individual ID 08_55, temporal cortex


title: 01_37_temporal cortex

source_name: post-mortem brain tissue, individual ID 01_37, temporal cortex


title: 01_37_substantia nigra

source_name: post-mortem brain tissue, individual ID 01_37, substantia nigra


title: 08_55_substantia nigra

source_name: post-mortem brain tissue, individual ID 08_55, substantia nigra


title: 01_37_putamen

source_name: post-mortem brain tissue, individual ID 01_37, putamen

value: putamen


title: 032/08_medulla

description: This entry supercedes previous accession: GSM1135509

source_name: post-mortem brain tissue, individual ID 032/08, medulla

value: medulla


title: 018/09_medulla

description: This entry supercedes previous accession: GSM1135531

source_name: post-mortem brain tissue, individual ID 018/09, medulla


title: 018/06_medulla

description: This entry supercedes previous accession: GSM1135483

source_name: post-mortem brain tissue, individual ID 018/06, medulla


title: 08_55_putamen

source_name: post-mortem brain tissue, individual ID 08_55, putamen


title: 00_38_substantia nigra

source_name: post-mortem brain tissue, individual ID 00_38, substantia nigra


title: 028/08_hippocampus

description: This entry supercedes previous accession: GSM1135450

source_name: post-mortem brain tissue, individual ID 028/08, hippocampus

value: hippocampus


title: 018/09_hippocampus

description: This entry supercedes previous accession: GSM1135386

source_name: post-mortem brain tissue, individual ID 018/09, hippocampus

value: neurologically and neuropathologically normal


title: 00_38_thalamus

source_name: post-mortem brain tissue, individual ID 00_38, thalamus


title: 005/09_medulla

description: This entry supercedes previous accession: GSM1135505

source_name: post-mortem brain tissue, individual ID 005/09, medulla


title: 018/06_hippocampus

description: This entry supercedes previous accession: GSM1135415

source_name: post-mortem brain tissue, individual ID 018/06, hippocampus


title: 00_38_putamen

source_name: post-mortem brain tissue, individual ID 00_38, putamen


title: 005/09_hippocampus

description: This entry supercedes previous accession: GSM1135385

source_name: post-mortem brain tissue, individual ID 005/09, hippocampus


title: 032/08_hippocampus

description: This entry supercedes previous accession: GSM1135394

source_name: post-mortem brain tissue, individual ID 032/08, hippocampus


title: 00_38_occipital cortex

source_name: post-mortem brain tissue, individual ID 00_38, occipital cortex

value: occipital cortex


title: 018/06_frontal cortex

description: This entry supercedes previous accession: GSM1135297

source_name: post-mortem brain tissue, individual ID 018/06, frontal cortex

value: frontal cortex


title: 06_02_putamen

source_name: post-mortem brain tissue, individual ID 06_02, putamen


title: 014/08_hippocampus

description: This entry supercedes previous accession: GSM1135455

source_name: post-mortem brain tissue, individual ID 014/08, hippocampus


title: 08_55_occipital cortex

source_name: post-mortem brain tissue, individual ID 08_55, occipital cortex


title: 01_37_occipital cortex

source_name: post-mortem brain tissue, individual ID 01_37, occipital cortex


title: 00_38_medulla

source_name: post-mortem brain tissue, individual ID 00_38, medulla


title: 032/08_frontal cortex

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source_name: post-mortem brain tissue, individual ID 032/08, frontal cortex


title: 005/09_frontal cortex

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source_name: post-mortem brain tissue, individual ID 005/09, frontal cortex


title: 018/09_frontal cortex

description: This entry supercedes previous accession: GSM1135330

source_name: post-mortem brain tissue, individual ID 018/09, frontal cortex


title: 01_37_hippocampus

source_name: post-mortem brain tissue, individual ID 01_37, hippocampus


title: 08_55_medulla

source_name: post-mortem brain tissue, individual ID 08_55, medulla


title: 06_02_medulla

source_name: post-mortem brain tissue, individual ID 06_02, medulla


title: 01_37_medulla

source_name: post-mortem brain tissue, individual ID 01_37, medulla


title: 028/08_frontal cortex

description: This entry supercedes previous accession: GSM1135342

source_name: post-mortem brain tissue, individual ID 028/08, frontal cortex


title: 06_02_occipital cortex

source_name: post-mortem brain tissue, individual ID 06_02, occipital cortex


title: 00_38_hippocampus

source_name: post-mortem brain tissue, individual ID 00_38, hippocampus


title: 08_55_hippocampus

source_name: post-mortem brain tissue, individual ID 08_55, hippocampus


title: 00_38_frontal cortex

source_name: post-mortem brain tissue, individual ID 00_38, frontal cortex


title: 014/08_frontal cortex

description: This entry supercedes previous accession: GSM1135354

source_name: post-mortem brain tissue, individual ID 014/08, frontal cortex


title: 033/08_white matter

description: This entry supercedes previous accession: GSM1135814

source_name: post-mortem brain tissue, individual ID 033/08, white matter

value: white matter

value: pulmonary embolism


title: 06_02_hippocampus

source_name: post-mortem brain tissue, individual ID 06_02, hippocampus

value: Sun Health Research Institute

value: renal failure


title: 022/08_white matter

description: This entry supercedes previous accession: GSM1135836

source_name: post-mortem brain tissue, individual ID 022/08, white matter

value: European


title: 08_55_frontal cortex

source_name: post-mortem brain tissue, individual ID 08_55, frontal cortex

value: Male


title: 06_02_frontal cortex

source_name: post-mortem brain tissue, individual ID 06_02, frontal cortex


title: 01_37_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 01_37, cerebellar cortex

value: cerebellar cortex

value: Female


title: 028/08_white matter

source_name: post-mortem brain tissue, individual ID 028/08, white matter

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

value: Ruptured aortic aneurysm


title: 06_02_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 06_02, cerebellar cortex


title: 024/10_white matter

description: This entry supercedes previous accession: GSM1135786

source_name: post-mortem brain tissue, individual ID 024/10, white matter


title: 018/06_white matter

source_name: post-mortem brain tissue, individual ID 018/06, white matter


title: 012/10_white matter

description: This entry supercedes previous accession: GSM1135859

source_name: post-mortem brain tissue, individual ID 012/10, white matter


title: 018/09_white matter

source_name: post-mortem brain tissue, individual ID 018/09, white matter


title: 01_37_frontal cortex

source_name: post-mortem brain tissue, individual ID 01_37, frontal cortex


title: 08_55_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 08_55, cerebellar cortex


title: 033/08_thalamus

description: This entry supercedes previous accession: GSM1135999

source_name: post-mortem brain tissue, individual ID 033/08, thalamus

value: thalamus


title: 00_38_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 00_38, cerebellar cortex


title: 014/08_white matter

source_name: post-mortem brain tissue, individual ID 014/08, white matter


title: 034/08_thalamus

description: This entry supercedes previous accession: GSM1136038

source_name: post-mortem brain tissue, individual ID 034/08, thalamus


title: 021/05_white matter

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source_name: post-mortem brain tissue, individual ID 021/05, white matter


title: 021/05_thalamus

description: This entry supercedes previous accession: GSM1136045

source_name: post-mortem brain tissue, individual ID 021/05, thalamus


title: 022/08_thalamus

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source_name: post-mortem brain tissue, individual ID 022/08, thalamus


title: 012/10_thalamus

description: This entry supercedes previous accession: GSM1136051

source_name: post-mortem brain tissue, individual ID 012/10, thalamus


title: 024/10_thalamus

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source_name: post-mortem brain tissue, individual ID 024/10, thalamus


title: 032/08_thalamus

source_name: post-mortem brain tissue, individual ID 032/08, thalamus


title: 014/08_thalamus

source_name: post-mortem brain tissue, individual ID 014/08, thalamus


title: 028/08_thalamus

source_name: post-mortem brain tissue, individual ID 028/08, thalamus


title: 034/08_temporal cortex

description: This entry supercedes previous accession: GSM1135924

source_name: post-mortem brain tissue, individual ID 034/08, temporal cortex

value: temporal cortex


title: 022/08_temporal cortex

description: This entry supercedes previous accession: GSM1135927

source_name: post-mortem brain tissue, individual ID 022/08, temporal cortex


title: 018/09_thalamus

source_name: post-mortem brain tissue, individual ID 018/09, thalamus


title: 033/08_substantia nigra

description: This entry supercedes previous accession: GSM1135158

source_name: post-mortem brain tissue, individual ID 033/08, substantia nigra

value: substantia nigra


title: 005/09_thalamus

source_name: post-mortem brain tissue, individual ID 005/09, thalamus


title: 033/08_temporal cortex

description: This entry supercedes previous accession: GSM1135948

source_name: post-mortem brain tissue, individual ID 033/08, temporal cortex


title: 018/06_thalamus

source_name: post-mortem brain tissue, individual ID 018/06, thalamus


title: 005/09_white matter

source_name: post-mortem brain tissue, individual ID 005/09, white matter


title: 028/08_temporal cortex

source_name: post-mortem brain tissue, individual ID 028/08, temporal cortex


title: 032/08_white matter

source_name: post-mortem brain tissue, individual ID 032/08, white matter


title: 012/10_temporal cortex

description: This entry supercedes previous accession: GSM1135963

source_name: post-mortem brain tissue, individual ID 012/10, temporal cortex


title: 022/08_substantia nigra

description: This entry supercedes previous accession: GSM1135171

source_name: post-mortem brain tissue, individual ID 022/08, substantia nigra


title: 024/10_substantia nigra

description: This entry supercedes previous accession: GSM1135182

source_name: post-mortem brain tissue, individual ID 024/10, substantia nigra