title: dez high-Zn, biological rep 2

city: Bochum

first: Scott

last: Sinclair

address: Universitaetstrasse 150

institute: Ruhr Universitaet Bochum

description: Gene expression from dark-grown seedlings

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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 100.

source_name: dez high-Zn

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

growth_protocol: Seeds were sterilised with chlorine gas, suspended in sterile water and plated on either control or high-Zn modified Hoaglands media. Seeds were exposed to light for 2-3 hours, then wrapped in two layers of aluminum foil and placed in a growth chamber for 7 days

extract_protocol: Qiagen QiaShredder Plant RNA extraction was performed according to manufacturer’s instructions

treatment_protocol: 7-day-old dark-grown seedlings were harvested directly off plates into liquid nitrogen at the end of the growth period in dim green light to minimise transcriptional responses to light during harvest

value: Whole dark-grown seedlings

value: dez

tag: age


title: HPC1 [9553572062_F]

status: Public on Nov 02 2017

type: RNA

city: London

first: Timothy

middle: Robert

last: Powell

address: 16 De Crespigny Park

department: SGDP Centre

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected, transformed (log2) and normalised (quantile) in Lumi (R package)

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Illumina TotalPrep kit amplification and labeling protocol

growth_protocol: The multipotent, human hippocampal progenitor cell line HPC0A07/03C (provided by ReNeuron, Surrey, UK) was used for all experiments. HPC03A/07 cells were grown in reduced modified media (RMM) consisting of Dulbecco’s Modified Eagle’s Media/ F12 (D6421, DMEM:F12, Invitrogen, UK) supplemented with 0.03% human albumin (Albunorm 20%, Octapharma, UK), 100 µg/ml human apo-transferrin (T1147, Sigma), 16.2 µg/ml human putrescine DiHCl (P5780, Sigma), 5 µg/ml human recombinant insulin (I9278, Sigma), 60ng/ml progesterone (P8783, Sigma), 2 mM L-glutamine (G7513, Sigma) and 40 ng/ml sodium selenite (S9133, Sigma). To maintain proliferation, 10 ng/ml human bFGF (EC100-18B, Peprotech), 20 ng/ml human EGF (AF100-15-500, Peprotech) and 100 nM 4-OHT (H7904, Sigma) were added. The cell culture media is free of any serum unless stated as a treatment in the experimental conditions. In addition, when serum is added, we also further supplement our media with 0.5mg/ml Penicillin Streptomycin (10,000 U/ml, 15140-122, Life Technologies).

extract_protocol: Trireagent (Sigma) following the standard protocol, with an additional ethanol precipitation step

treatment_protocol: Progenitor cells were plated on 6-well plates (Nunclon, Denmark) at a density of 30000 per well and cultured in the presence of EGF, bFGF and 4-OHT and treated with human serum during the initial proliferation phase for 48 hours and in the subsequent differentiation phase for 7 days or during the differentiation phase only.

tag: donor (sample)

tag: group

value: young

tag: Sex

value: male

tag: time point (hours)

tag: batch (array/biological replicate)


title: HPC1 [9534190119_F]

value: female


title: HPC1 [9553572062_E]


title: HPC1 [9553572062_C]

value: old


title: HPC1 [9534190119_D]


title: HPC1 [9553710057_L]

value: MediaO


title: HPC1 [9534190119_B]


title: HPC1 [9553572062_A]


title: HPC1 [9553572062_B]


title: dez high-Zn, biological rep 1

country: Germany

label: Biotin

organism: Arabidopsis thaliana

tag: tissue

tag: genotype


title: HPC1 [9553710057_F]


title: HPC1 [9553710057_J]

value: MediaY


title: HPC1 [9553710057_H]


title: HPC1 [9553710057_D]


title: dez control, biological rep 2

source_name: dez control


title: dez control, biological rep 1


title: Wild-type control, biological rep 2

source_name: Wild-type control

value: Wild-type


title: Wild-type high-Zn, biological rep 1

source_name: Wild-type high-Zn


title: HPC1 [9553710057_B]


title: HPC1 [9553710057_I]


title: HPC1 [9553710057_K]


title: HPC1 [9553710057_G]


title: HPC1 [9553710057_E]


title: HPC1 [9553710057_A]


title: Wild-type high-Zn, biological rep 2


title: HPC1 [9553710057_C]


title: Wild-type control, biological rep 1


title: 22_Breast_Adjacent_to_tumor_Normal [aCGH]

type: genomic

city: Toronto

first: Susan

last: Done

state: Ontario

address: 200 Elizabeth St. Rm 11E-228

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

description: Microdissected Normal Breast Epithelium

hyb_protocol: Hybridized using the aCGH Hybridization Kit on Agilent Human 244k arrays (Agilent Technologies, Mississauga, ON, Canada) as per manufacturer’s standard protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA).

data_processing: Microarray data were pre-processed: background corrected (offset = 16) and withinarray (loess) normalized using the limma package in R (for the data presented in the datamatrix). For the in-text results, the unprocessed data were imported into Agilent Genomic Workbench v7.0.4.0 (Agilent Technologies, Santa Clara, CA, USA) for subsequent analysis. Samples were normalized with Diploid Peak Centralization, GC corrected (Window size 2kb), and  analyzed using ADM-2 (threshold 6.0, and fuzzy zero).

molecule: genomic DNA

source_name: Breast Adjacent-to-tumor Epithelium

label_protocol: Arrays labelled using the Agilent Genomic DNA ULS Labelling Kit (Agilent Technologies, Mississauga, ON, Canada) as per manufacturer’s standard protocol.

extract_protocol: Snap frozen tissues were sectioned at 8 micron thickness using a microtome and lightly stained with hematoxylin.  Histological identification of tumour and normal ducts was confirmed by a pathologist.  Needle-microdissection was performed under a dissecting microscope for both tumour and ducts to ensure minimal stromal contamination of epithelial cells. DNA was extracted from microdissected tissue using the Qiagen Allprep RNA/DNA Micro Kit (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Fifteen patients undergoing mastectomy for biopsy-proven carcinoma were recruited at the Princess Margaret Cancer Center, University Health Network (Toronto, ON, Canada) from 2005 to 2008.  Inclusion criteria were defined as tumours at least 2cm in largest diameter as measured by imaging, and located at least 3cm from the nipple. During surgery, prior to removal of the breast, a ductoscopy procedure was performed using a 0.7mm mammary ductoscope (MF2-707, MD Fibertech Co, Japan). The duct leading to the tumour was identified by visual inspection and identification of the tumour. Methylene blue dye was injected to identify the involved duct for tissue sampling.  Immediately after the mastectomy procedure, tissue sampling was performed. Two samples were taken along the duct between the tumour and the nipple (previously dye stained) (T1 and T2) and one from the opposite duct within the same breast (as a normal control) (T3). A sample from the tumour was also obtained (T4). All tissues obtained were bisected, with one half snap frozen and the other half formalin-fixed and paraffin-embedded. Normal skin tissue was also obtained for control DNA.

tag: location

value: breast

source_name: Pooled lymph node tissue

tag: reference

value: Pooled lymph node tissue


title: 14_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor

source_name: Breast Tumor


title: 14_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium

source_name: Breast Normal Epithelium


title: 22_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 10_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 14_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 10_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium

source_name: Breast Normal Contraleteral Epithelium


title: 22_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 14_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 22_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 8b_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 6_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 4_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 6_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 10_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8b_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 8a_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 6_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 4_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 4_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: ccRCC_GW

status: Public on Nov 01 2017

city: GRONINGEN

first: Jun

last: Li

state: Netherlands

address: Esdoornlaan

department: Genetics

country: Netherlands

institute: University Medical Center Groningen

description:
Immortalized cell line ccRCC-GW
Sample name: SAMPLE 25

hyb_protocol: Each Cy-5 sample was mixed with the same amount of a cy3-labeled sample, which was non-relevant for this study, and hybridized at 65°C overnight on Agilent-050524 SurePrint G3 Custom Human 8x60K Microarrays.

scan_protocol: On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).

data_processing: Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 10.7.3.1. Data was analyzed by GeneSpring GX 12.5 software (Agilent Technologies). The data was subject to quantile normalization without base line transformation.

source_name: ccRCC-GW

label_protocol: First strand cDNA was synthesized from 50-100ng RNA, followed by cRNA amplification and labeling with Cy5 according to manufacturer's protocol (Agilent). Purification of Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.

growth_protocol: Primary proximal tubular epithelial cells (PTECs) were cultured in DMEM/F-12 GLUTMAX-1 (Sigma-Aldrich, St. Louis, MO, USA ) containing 10% FBS, 1% P/S (100 U/ml penicillin and 100 µg/ml streptomycin), 5μg/ml ITS (Sigma-Aldrich) and 5ng/ml EGF respectively. CcRCC derived cell lines were maintained in   RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100μg/ml streptomycin.

extract_protocol: Total RNA was isolated by using Gene JET RNA purification kit (Fermentas, Waltham, MA, USA) with the instruction offered by the manufacture.

treatment_protocol: Primary PTECs were transduced with PBRM1 shRNA (sh-PB1 and sh-PB2), and non-targeting shRNA (NT); PTECs without virus treatment were included as a control. Both PBRM1-WT and PBRM1-KD PTECs were transdused at high MOI and harvested at their early passages.

value: kidney

tag: cell type

value: immortalized cell line


title: 6_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 9_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 8a_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 2_Breast_Normal_Contralateral_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: ccRCC_6

description:
Immortalized cell line ccRCC-6
Sample name: SAMPLE 22


title: ccRCC_EW

description:
Immortalized cell line ccRCC-ER
Sample name: SAMPLE 23

source_name: ccRCC-EW


title: ccRCC_JF

description:
Immortalized cell line ccRCC-JF
Sample name: SAMPLE 27

source_name: ccRCC-JF


title: ccRCC_HS

description:
Immortalized cell line ccRCC-HS
Sample name: SAMPLE 26

source_name: ccRCC-HS


title: ccRCC_5

description:
Immortalized cell line ccRCC-5
Sample name: SAMPLE 21


title: ccRCC_FW

description:
Immortalized cell line ccRCC-FW
Sample name: SAMPLE 24

source_name: ccRCC-FW


title: 10_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Tumor [aCGH]

description: Microdissected Breast Tumor


title: 4_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: 2_Breast_Normal_Same_Duct [aCGH]

description: Microdissected Normal Breast Epithelium


title: PTECs_N3_sh PB2

description:
PBRM1-KD shRNA-PB2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate3
Sample name: SAMPLE 18

source_name: sh-PB2 treated PTECs

value: proximal tubular epithelial cells


title: PTECs_N2_sh2 SETD2

description:
SETD2-KD sh2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate2
Sample name: SAMPLE 11

source_name: SETD2-sh2 treated PTECs


title: PTECs_N3_sh PB1

description:
PBRM1-KD shRNA-PB1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate3
Sample name: SAMPLE 15

source_name: sh-PB1 treated PTECs


title: 2_Breast_Adjacent_to_tumor_Normal [aCGH]

description: Microdissected Normal Breast Epithelium


title: ccRCC_MF

description:
Immortalized cell line ccRCC-MF
Sample name: SAMPLE 28

source_name: ccRCC-MF


title: PTECs_N2_sh PB2

description:
PBRM1-KD shRNA-PB2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate2
Sample name: SAMPLE 17


title: PTECs_N1_sh PB2

description:
PBRM1-KD shRNA-PB2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 16


title: PTECs_N3_sh2 SETD2

description:
SETD2-KD sh2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate3
Sample name: SAMPLE 12


title: PTECs_N1_sh PB1

description:
PBRM1-KD shRNA-PB1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 13


title: PTECs_N2_sh PB1

description:
PBRM1-KD shRNA-PB1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate2
Sample name: SAMPLE 14


title: PTECs_N1_sh2 SETD2

description:
SETD2-KD sh2 treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 10


title: ccRCC_1

description:
Immortalized cell line ccRCC-1
Sample name: SAMPLE 19


title: ccRCC_4

description:
Immortalized cell line ccRCC-4
Sample name: SAMPLE 20


title: PTECs_N1_sh1 SETD2

description:
SETD2-KD sh1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 7

source_name: SETD2-sh1 treated PTECs


title: WT neutrophils SP rep3_miRNA

city: Chapel Hill

first: Claire

middle: M.

last: Doerschuk

state: NC

address: Marsico Hall 7205 CB#7248

department: Marsico Lung Institute

country: USA

institute: University of North Carolina at Chapel Hill

description: miR expression data from mouse lung neutrophils

hyb_protocol: Labeled RNA was hybridized to Agilent SurePrint G3 Mouse miRNA 8X60K arrays for 20 hours at 55°C and 20 RPM.  All reagents required for the labeling and hybridization steps were provided in Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456), and sample preparation and array processing were carried out according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on an Agilent Microarray scanner using the default settings for the array format (AgilentG3_miRNA for the 8x60K format).

data_processing: MicroRNA expression signals were extracted from microarray images using Agilent Feature Extraction (FE) software, and normalized using either LVSmiRNA or AgiMicroRna package from Bioconductor.  LVSmiRNA uses the least-variant set of miRs to normalize between the arrays (Calza, S., Valentini, D. & Pawitan, Y. BMC Bioinformatics 9, 140, doi:10.1186/1471-2105-9-140 (2008)), while AgiMicroRna uses RMA.  Data analyses were carried out on both LVS and RMA normalized log2 intensities in parallel.  Both LVS and RMA normalized values are available on the series record.

organism: Mus musculus

source_name: Lung neutrophils isolated from WT mice given S. pneumoniae

label_protocol: 100 ng of total RNA from each sample was labeled with Cyanine 3-pCp using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight. Neutrophils were isolated using MACS beads (Miltenyi, Auburn, CA) according to the manufacturer’s instructions. Briefly, single cell suspensions were prepared from dissected mouse lungs. The cells were washed with PBS containing 2 mM EDTA and 0.5% bovine serum albumin, and incubated with biotin-anti-Ly6G and magnetic beads coated with anti-biotin. The samples were passed through a column in a magnetic field, and cells bound to beads were collected for further analysis. Cells were kept at 4-8°C during staining and magnetic bead isolation.

value: Lung

value: neutrophils

value: Wild type (WT)

value: 6-12 weeks


title: PTECs_N3_NT

description:
NT-shRNA treated primary kidney proximl tubular epithelial cells at day 6  triplicate3
Sample name: SAMPLE 6

source_name: NT-shRNA treated PTECs


title: WT neutrophils SP rep2_miRNA


title: WT neutrophils PBS rep4_miRNA

source_name: Lung neutrophils isolated from WT mice given PBS


title: WT neutrophils SP rep1_miRNA


title: WT neutrophils SP rep4_miRNA


title: PTECs_N2_sh1 SETD2

description:
SETD2-KD sh1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate2
Sample name: SAMPLE 8


title: WT neutrophils PBS rep3_miRNA


title: WT neutrophils PBS rep2_miRNA


title: WT neutrophils PBS rep1_miRNA


title: H1_S2

type: SRA

city: Beijing

first: Tingting

address: 38 Xueyuan Rd

department: Medical informatics

country: China

institute: Peking University

library_source: genomic

data_processing:
The 50-bp sequencing reads were obtained from the Solid Genome Analyzer pipeline. Low-quality reads (with an average quality value below 8) were filtered, and the remaining reads were used for the mapping steps. We used the D. melanogaster reference sequence (assembly 2006) from UCSC for read mapping. The reads were mapped to the reference genome permitting at most 3 mismatches. Binding peaks were got by SICER. Reads located in peak regions were in wig format.
Genome Build:
H1_S2.bed: dm3
H1_S2_peak_step25.wig: dm3

organism: Drosophila melanogaster

growth_protocol: S2 cells were cultured at 25C in Schneider's Drosophila medium (GIBCO 11720) containing 10% fetal calf serum, 160 mg/ml penicillin and 250 mg/ml streptomycin.

extract_protocol: The ChIP-seq library weres constructed according to the manufacturer’s protocol (SOLiD Fragment Library Construction Kit, Invitrogen, #4401151). Briefly, the ChIP DNA (200-300 ng) was fragmented into 100-200-bp fragments by sonication, and then the DNA ends were repaired using T4 DNA polymerase (Invitrogen). Following ligation of a pair of SOLiD adaptors to the repaired ends, the ChIP DNA was amplified using adaptor-specific primers for 17 cycles, purified using a Qiagen MinElute PCR purification Kit (Qiagen #28004, 28006) and then separated by electrophoresis on a native 6% polyacrylamide gel. A fraction of the library in the size range of 140–200 bp (DNA ladder, Invitrogen #10821-015) was selected for SOLiD sequencing.

tag: cell line

tag: chip antibody


title: PTECs_N1_NT

description:
NT-shRNA treated primary kidney proximl tubular epithelial cells at day 6  triplicate1
Sample name: SAMPLE 4


title: HP1_Kc

data_processing:
The 50-bp sequencing reads were obtained from the Solid Genome Analyzer pipeline. Low-quality reads (with an average quality value below 8) were filtered, and the remaining reads were used for the mapping steps. We used the D. melanogaster reference sequence (assembly 2006) from UCSC for read mapping. The reads were mapped to the reference genome permitting at most 3 mismatches. Binding peaks were got by SICER. Reads located in peak regions were in wig format.
Genome Build:
HP1_Kc.bed: dm3
HP1_Kc_peak_step25.wig: dm3

source_name: Kc

value: Kc


title: PTECs_N3_CON

description:
non-treated primary kidney proximl tubular epithelial cells at day 6 triplicate3
Sample name: SAMPLE 3

source_name: control PTECs


title: PTECs_N2_CON

description:
non-treated primary kidney proximl tubular epithelial cells at day 6 triplicate2
Sample name: SAMPLE 2


title: H3K9me2 S2

data_processing: The 50-bp sequencing reads were obtained from the Solid Genome Analyzer pipeline. Low-quality reads (with an average quality value below 8) were filtered, and the remaining reads were used for the mapping steps. We used the D. melanogaster reference sequence (assembly 2006) from UCSC for read mapping. The reads were mapped to the reference genome permitting at most 3 mismatches. Binding peaks were got by SICER. Reads located in peak regions were in wig format.

source_name: H3K9me2 S2

growth_protocol: S2 cells were cultured at 25Â°C in Schneiderâs Drosophila medium (GIBCO 11720) containing 10% fetal calf serum, 160 mg/ml penicillin and 250 mg/ml streptomycin.

extract_protocol: The ChIP-seq library weres constructed according to the manufacturerâs protocol (SOLiD Fragment Library Construction Kit, Invitrogen, #4401151). Briefly, the ChIP DNA (200-300 ng) was fragmented into 100-200-bp fragments by sonication, and then the DNA ends were repaired using T4 DNA polymerase (Invitrogen). Following ligation of a pair of SOLiD adaptors to the repaired ends, the ChIP DNA was amplified using adaptor-specific primers for 17 cycles, purified using a Qiagen MinElute PCR purification Kit (Qiagen #28004, 28006) and then separated by electrophoresis on a native 6% polyacrylamide gel. A fraction of the library in the size range of 140â200 bp (DNA ladder, Invitrogen #10821-015) was selected for SOLiD sequencing.


title: HP1 S2

source_name: HP1 S2


title: H3K36me3 S2

source_name: H3K36me3 S2


title: H3K4me2 S2

source_name: H3K4me2 S2


title: H4K16Ac S2

source_name: H4K16Ac S2


title: Ad-Lkb1 verus WT BAT Replicate 2

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description: Total RNA of brown adipose tissue from littermates of  WT and Ad-Lkb1

hyb_protocol: 300 ng of cRNA from the control and test samples were combined and fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized on an Agilent SurePrint G3 mouse 8x60K microarray (028005) 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent SureScan Microarray scanner following manufacturer's protocol.

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Microarray analysis was completed with an ANOVA and a Tukey's post-hoc test when a significant ANOVA was observed. In addition, a mean absolute log2 expression ratio of at least 0.585 (50% increase or decrease in expression) must be satisfied.

source_name: whole brown adipose tissue Ad-Lkb1 10 week

label_protocol: Cy3 (WT) and Cy5 (Ad-LKB1) labeled cRNA was prepared using the Agilent LowInput QuickAmp Labeling Kit according to manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were all fed on regular chow diet

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: Male

value: Week 10

value: brown adipose tissue

tag: strain

source_name: whole brown adipose tissue wild type 10 week


title: PTECs_N1_CON

description:
non-treated primary kidney proximl tubular epithelial cells at day 6 triplicate1
Sample name: SAMPLE 1


title: Ad-Lkb1 verus WT BAT Replicate 3


title: Ad-Lkb1 verus WT BAT Replicate 1


title: ASC_Undifferentiated_rep2

city: Guangzhou

first: Guangxin

last: Huang

address: No.74 Zhongshan 2nd Road

institute: Sun Yat-sen University

description: Gene expression in undifferentiated human ASCs

hyb_protocol: 1 μg of each labeled cRNA (specific activity ≥9.0 pmol Cy3/μg cRNA) was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. After hybridization, microarrays were washed with Gene Expression Wash Buffer (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% for XDR High and 10% for XDR Low).

data_processing: The scanned images were analyzed with Feature Extraction Software v11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Adipose-derived stem cell, undifferentiated, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Arraystar Flash RNA Labeling Kit (Arraystar), followed by purification with RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Human ASCs purchased from Cyagen (Suzhou, China) were maintained in OriCellTM Human MSC Growth Medium containing 10% MSCs-Qualified Fetal Bovine Serum, 1% Penicillin-Streptomycin and 1% Glutamine (Cyagen, China) at 37 ºC, 5% CO2 condition.

extract_protocol: Total RNA from human ASCs was extracted using Trizol reagent (Invitrogen, USA) according to the instructions of the manufacturer. NanoDrop ND-1000 spectrophotometer was used for measuring RNA quantity and quality and agarose gel electrophoresis was used to examine RNA integrity.

treatment_protocol: When human ASCs cultured in standard growth medium reached 50-70% confluence, they were induced into osteoblasts for 14 days with OriCellTM human ASC Osteogenic Differentiation Medium (Cyagen, China) containing 10% Fetal Bovine Serum, 1% penicillin-streptomycin, 10mM L-glutamine, 50μM L-ascorbic acid, 10mM beta-glycerophosphate and 100nM dexamethasone.

value: Adipose-derived stem cell

tag: differentiation

value: undifferentiated


title: ASC_Osteogenesis_rep4

description: Gene expression after 14 days osteogenic induced human ASCs

source_name: Adipose-derived stem cell, osteogenic differentiated, replicate 4

value: osteogenic differentiated 14 days


title: ASC_Undifferentiated_rep4

source_name: Adipose-derived stem cell, undifferentiated, replicate 4


title: ASC_Osteogenesis_rep1

source_name: Adipose-derived stem cell, osteogenic differentiated, replicate 1


title: PTECs_N2_NT

description:
NT-shRNA treated primary kidney proximl tubular epithelial cells at day 6  triplicate2
Sample name: SAMPLE 5


title: ASC_Undifferentiated_rep3

source_name: Adipose-derived stem cell, undifferentiated, replicate 3


title: 424519A01_M3125_NO_exposed_rep1

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The normalized .calls files provided by NimbleGen (representing normalized gene expression values and accession numbers for each gene interrogated by the array) were imported into ArrayStar v.11 for comparative analysis.

organism: Fusarium verticillioides

source_name: M3125 NO-Exposed

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: F. verticillioides was inoculated (1x10^3 spores/mL) into 3 mL PDB buffered with 0.1 M sodium phosphate and incubated at 27C at 250 rpm.

extract_protocol: Harvested culture material was ground under liquid nitrogen.  RNA extraction and purification was performed using PureLink RNA Mini Kit.  TURBO Dnase was used for clean up.  RNA integrity was evaluated on an Agilent 2100 Bioanalyzer before sending to Roche Nimblegen for processing.

treatment_protocol: After three days of growth, 1.5 mM DETA NONOate was added to cultures.  Controls received a mock treatment.  Cultures were incubated for 30 minutes and then harvested for RNA extraction.

value: Wild-type M3125


title: ASC_Osteogenesis_rep2

source_name: Adipose-derived stem cell, osteogenic differentiated, replicate 2


title: 424526A01_M3125_NO_exposed_rep2


title: 424522A01_M3125_Control_rep2

source_name: M3125 Unexposed


title: 22RV1_HNF4Gsh2-Dox Replicate 2

city: New York

first: Shipra

last: Shukla

state: NY

address: 417 East 68th Street

institute: MSKCC

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina chip. The chip was incubated for about 18 hours at 58C.

scan_protocol: After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

data_processing:
The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Partek genomic suite.
Partek Genomic Suite was used to Log2 transform raw data followed by Quartile normalization.

label_protocol: ~500 ng of total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

growth_protocol: 22Rv1 sublines  are growing logarithmically in RPMI with 10% fetal bovine serum.

extract_protocol: RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

treatment_protocol: 22Rv1 sublines expressing doxycycline inducible hairpins against HNF4G (HNF4Gsh1 and HNF4Gsh2) and SCR control were treated with doxycycline  for three days after which cells were harvested for gene expression analysis.

value: Prostate Cancer cell line 22Rv1

tag: treatment


title: 22RV1_HNF4Gsh2- Replicate 1


title: 22RV1_HNF4Gsh2- Replicate 2


title: LNCaP_HNF4G- Replicate 2

hyb_protocol: The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina  chip. The chip was incubated for about 18 hours at 58C.

source_name: LNCaP Cells

growth_protocol: LNCaP cells are growing logarithmically in RPMI with 10% fetal bovine serum.

treatment_protocol: LNCaP cells were infected with retroviruses in triplicates for HNF4G and empty vector expression. After three days of infection cells were selcted with puromycin for 2 days and later on RNA was harvested for expression analysis.

value: Prostate Cancer cell line LNCaP

value: infected with retrovirus for HNF4G expression


title: 22RV1_HNF4Gsh1- Replicate 2


title: ASC_Undifferentiated_rep1

source_name: Adipose-derived stem cell, undifferentiated, replicate 1


title: LNCaP_Empty Vector- Replicate 3

value: control


title: 424523A01_M3125_Control_rep1


title: 22RV1_HNF4Gsh1-Dox Replicate 2


title: LNCaP_Empty Vector- Replicate 2


title: LNCaP_HNF4G- Replicate 3


title: 22RV1_HNF4Gsh1-Dox Replicate 1


title: LNCaP_HNF4G-Replicate 1


title: 22RV1_shScr-Dox Replicate 1

value: shScr-Dox


title: 22RV1_shScr Replicate 2

description: 22Rv1-shScr-Rep 2

value: shScr


title: 22RV1_shScr-Dox Replicate 2


title: 22RV1_HNF4Gsh1- Replicate 1


title: LNCaP_Empty Vector-Replicate 1


title: 22RV1_HNF4Gsh2-Dox Replicate 1


title: 22RV1_shScr Replicate 1


title: ASC_Osteogenesis_rep3

source_name: Adipose-derived stem cell, osteogenic differentiated, replicate 3


title: B2

city: GuangZhou

first: Shunwang

last: Cao

state: GuangDong

address: 1838 Guangzhoudadaobei road

department: Laboratory Medicine Center

institute: Nanfang Hospital, Southern Medical University,Guangzhou, China

description: gene expression of non-tumor tissue ajacent HCC tumor from Yonghua Tang

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Scanned on Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies).

source_name: Non-tumor tissues from patient whose name was Yonghua Tang

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Fresh HCC tissues and adjacent non-tumor tissues were collected and stores at from 3 patients who underwent initial hepatectomy and were diagnosed with HCC between October 2012 and February 2013 at the Nanfang Hospital of the Southern Medical University (Guangzhou, China).

extract_protocol: Total RNA extracted using Trizol(invitrigen) following manufacturer's instructions

value: male

tag: age

tag: source

value: Yonghua Tang

value: Non-tumor tissue adjacent HCC tumor


title: D2

description: gene expression of non-tumor tissue ajacent HCC tumor from Huachu He

source_name: Non-tumor tissues from patient whose name was Huachu He

value: Huachu He


title: RectalCancerTissue_patient25

first: Honglin

last: Guo

address: Panjiayuan Nanli 17#, Chaoyang Distinct

department: Department of Etiology and Carcinogenesis

institute: National Cancer Institute/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College

hyb_protocol: 0.72 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 30ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30ul of 2x Agilent GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Hmn GE 8×60K V2 Microarrays (G4851B) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute twice at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner Bundle (G4900DA) using one color scan setting for 8x60k array slides (Scan Area full agilent slide, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features with meidan raw signal less than 100 were excluded. Data were normalized by the median scale method using the R package limma.

source_name: Tumor tissue, rectal cancer patient

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

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, MD, USA). The RNA was quantified using an ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA), and its integrity was assessed using the RNA 6000 LabChip kit in combination with an Agilent 2100 Bioanalyzer (Agilent, CA, USA). An RNA with integrity number (RIN) greater than 7.0 was used in this study.

treatment_protocol: Malignant and matched normal tissues from each patient were snap-frozen in liquid nitrogen and stored at -80℃ for subsequent molecular analysis. The status of all tissue specimens was confirmed histologically. Clinicopathological information was obtained for all patients.

tag: patient status/id

value: rectal cancer patient 25

tag: tissue type

value: Tumor tissue


title: RectalCancerTissue_patient30

value: rectal cancer patient 30

value: female


title: A2

description: gene expression of non-tumor tissue ajacent HCC tumor from Guoqiang Luo

source_name: Non-tumor tissues from patient whose name was Guoqiang Luo

value: Guoqiang Luo


title: RectalCancerTissue_patient23

value: rectal cancer patient 23


title: A1

description: gene expression of HCC tumor from Guoqiang Luo

source_name: Tissues from patient whose name was Guoqiang Luo

value: HCC tumor


title: RectalCancerTissue_patient32

value: rectal cancer patient 32


title: RectalCancerTissue_patient31

value: rectal cancer patient 31


title: B1

description: gene expression of HCC tumor from Yonghua Tang

source_name: Tissues from patient whose name was Yonghua Tang


title: RectalCancerTissue_patient27

value: rectal cancer patient 27


title: RectalCancerTissue_patient29

value: rectal cancer patient 29


title: RectalCancerTissue_patient22

value: rectal cancer patient 22


title: D1

description: gene expression of HCC tumor from Huachu Tang

source_name: Tissues from patient whose name was Huachu He


title: RectalCancerTissue_patient20

value: rectal cancer patient 20


title: RectalCancerTissue_patient24

value: rectal cancer patient 24

value: male


title: RectalCancerTissue_patient21

value: rectal cancer patient 21


title: RectalCancerTissue_patient28

value: rectal cancer patient 28


title: RectalCancerTissue_patient18

value: rectal cancer patient 18


title: RectalCancerTissue_patient19

value: rectal cancer patient 19

value: Tumor tissue


title: RectalCancerTissue_patient26

value: rectal cancer patient 26

value: female


title: RectalCancerTissue_patient16

value: rectal cancer patient 16


title: RectalCancerTissue_patient15

value: rectal cancer patient 15


title: RectalCancerTissue_patient13

value: rectal cancer patient 13


title: RectalCancerTissue_patient17

value: rectal cancer patient 17


title: PTECs_N3_sh1 SETD2

description:
SETD2-KD sh1 treated primary kidney proximl tubular epithelial cells at day 6 triplicate3
Sample name: SAMPLE 9

source_name: SETD2-sh1 treated PTECs

value: kidney

value: proximal tubular epithelial cells


title: RectalCancerTissue_patient14

value: rectal cancer patient 14


title: RectalCancerTissue_patient12

value: rectal cancer patient 12


title: RectalCancerTissue_patient11

value: rectal cancer patient 11


title: RectalCancerTissue_patient10

value: rectal cancer patient 10

value: male


title: RectalCancerTissue_patient8

value: rectal cancer patient 8


title: RectalCancerTissue_patient5

value: rectal cancer patient 5


title: RectalCancerTissue_patient9

value: rectal cancer patient 9


title: RectalCancerTissue_patient1

value: rectal cancer patient 1

value: Tumor tissue


title: RectalCancerTissue_patient7

value: rectal cancer patient 7


title: RectalCancerTissue_patient2

value: rectal cancer patient 2

value: female


title: RectalCancerTissue_patient6

value: rectal cancer patient 6


title: AdjacentN_1cm_patient29

source_name: Adjacent normal tissue, 1 cm away from tumor, rectal cancer patient

value: rectal cancer patient 29

value: Adjacent normal tissue


title: AdjacentN_1cm_patient30

value: rectal cancer patient 30


title: AdjacentN_1cm_patient32

value: rectal cancer patient 32


title: AdjacentN_1cm_patient31

value: rectal cancer patient 31


title: AdjacentN_1cm_patient22

value: rectal cancer patient 22


title: AdjacentN_1cm_patient28

value: rectal cancer patient 28


title: AdjacentN_1cm_patient23

value: rectal cancer patient 23


title: AdjacentN_1cm_patient25

value: rectal cancer patient 25

value: male


title: shRanBP6 plus Dox rep3

city: Madrid

first: Massimo

last: Squatrito

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: Spanish National Research Center (CNIO)

description: Expression data from HEK293 RANBP6 shRNA cells

hyb_protocol: The biotin-labelled cDNA was fragmented, and processed to hybridization cocktail to be hybridized to the GeneChip Human Genome U133 Plus 2.0 arrays according to the Affymetrix GeneChip protocol

scan_protocol: Scanned using the Gene Chip Scanner 3000

data_processing: R/Bioconductor

source_name: HEK293 RANBP6 shRNA plus Dox

label_protocol: 500 ng of the RNA was reverse transcribed to double-stranded cDNA. The cDNA was used as a template for in vitro transcription with biotin-labelled uridine triphosphate at 37°C for 16 hours

growth_protocol: HEK-293T cells were grown in DMEM 10% FBS

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: HEK-293T cells expressing Doxycycline inducible RanBP6 hairpins were either treated with or without Doxycycline for 72 hours

value: Dox


title: AdjacentN_1cm_patient27

value: rectal cancer patient 27


title: shRanBP6 minus Dox rep3

source_name: HEK293 RANBP6 shRNA minus Dox

value: mock


title: AdjacentN_1cm_patient20

value: rectal cancer patient 20


title: RectalCancerTissue_patient4

value: rectal cancer patient 4

value: Tumor tissue


title: AdjacentN_1cm_patient26

value: rectal cancer patient 26

value: female


title: AdjacentN_1cm_patient21

value: rectal cancer patient 21

value: Adjacent normal tissue


title: AdjacentN_1cm_patient18

value: rectal cancer patient 18


title: AdjacentN_1cm_patient19

value: rectal cancer patient 19


title: RectalCancerTissue_patient3

value: rectal cancer patient 3


title: shRanBP6 minus Dox rep2


title: AdjacentN_1cm_patient24

value: rectal cancer patient 24


title: shRanBP6 plus Dox rep2


title: AdjacentN_1cm_patient17

value: rectal cancer patient 17


title: shRanBP6 plus Dox rep1


title: AdjacentN_1cm_patient16

value: rectal cancer patient 16


title: AdjacentN_1cm_patient14

value: rectal cancer patient 14

value: male


title: AdjacentN_1cm_patient13

value: rectal cancer patient 13


title: AdjacentN_1cm_patient10

value: rectal cancer patient 10


title: AdjacentN_1cm_patient12

value: rectal cancer patient 12


title: AdjacentN_1cm_patient5

value: rectal cancer patient 5


title: AdjacentN_1cm_patient9

value: rectal cancer patient 9


title: AdjacentN_1cm_patient6

value: rectal cancer patient 6


title: AdjacentN_1cm_patient8

value: rectal cancer patient 8

value: female


title: shRanBP6 minus Dox rep1

value: mock


title: AdjacentN_1cm_patient7

value: rectal cancer patient 7

value: Adjacent normal tissue


title: AdjacentN_1cm_patient15

value: rectal cancer patient 15


title: AdjacentN_1cm_patient4

value: rectal cancer patient 4


title: AdjacentN_1cm_patient2

value: rectal cancer patient 2


title: AdjacentN_1cm_patient3

value: rectal cancer patient 3


title: AdjacentN_5cm_patient31

source_name: Adjacent normal tissue, 5 cm away from tumor, rectal cancer patient

value: rectal cancer patient 31


title: AdjacentN_5cm_patient32

value: rectal cancer patient 32

value: male


title: AdjacentN_5cm_patient30

value: rectal cancer patient 30


title: AdjacentN_1cm_patient11

value: rectal cancer patient 11


title: AdjacentN_5cm_patient29

value: rectal cancer patient 29


title: AdjacentN_5cm_patient27

value: rectal cancer patient 27


title: AdjacentN_1cm_patient1

value: rectal cancer patient 1


title: AdjacentN_5cm_patient25

value: rectal cancer patient 25


title: AdjacentN_5cm_patient22

value: rectal cancer patient 22

value: female


title: AdjacentN_5cm_patient23

value: rectal cancer patient 23


title: AdjacentN_5cm_patient21

value: rectal cancer patient 21

value: Adjacent normal tissue


title: AdjacentN_5cm_patient28

value: rectal cancer patient 28


title: AdjacentN_5cm_patient26

value: rectal cancer patient 26


title: AdjacentN_5cm_patient24

value: rectal cancer patient 24


title: AdjacentN_5cm_patient18

value: rectal cancer patient 18


title: AdjacentN_5cm_patient15

value: rectal cancer patient 15


title: AdjacentN_5cm_patient17

value: rectal cancer patient 17

value: male


title: AdjacentN_5cm_patient19

value: rectal cancer patient 19


title: AdjacentN_5cm_patient14

value: rectal cancer patient 14


title: AdjacentN_5cm_patient9

value: rectal cancer patient 9


title: AdjacentN_5cm_patient13

value: rectal cancer patient 13


title: AdjacentN_5cm_patient10

value: rectal cancer patient 10


title: AdjacentN_5cm_patient16

value: rectal cancer patient 16


title: AdjacentN_5cm_patient11

value: rectal cancer patient 11

value: female


title: AdjacentN_5cm_patient20

value: rectal cancer patient 20


title: AdjacentN_5cm_patient12

value: rectal cancer patient 12

value: Adjacent normal tissue


title: AdjacentN_5cm_patient1

value: rectal cancer patient 1


title: AdjacentN_ProximalEnd_patient31

source_name: Adjacent normal tissue, as far as possible away from tumor, rectal cancer patient

value: rectal cancer patient31


title: AdjacentN_ProximalEnd_patient32

value: rectal cancer patient32


title: AdjacentN_5cm_patient2

value: rectal cancer patient 2


title: AdjacentN_5cm_patient7

value: rectal cancer patient 7


title: AdjacentN_5cm_patient8

value: rectal cancer patient 8


title: AdjacentN_ProximalEnd_patient30

value: rectal cancer patient30


title: AdjacentN_5cm_patient4

value: rectal cancer patient 4

value: male


title: AdjacentN_ProximalEnd_patient28

value: rectal cancer patient28


title: AdjacentN_5cm_patient5

value: rectal cancer patient 5


title: AdjacentN_5cm_patient6

value: rectal cancer patient 6


title: AdjacentN_ProximalEnd_patient29

value: rectal cancer patient29


title: AdjacentN_ProximalEnd_patient24

value: rectal cancer patient24


title: AdjacentN_ProximalEnd_patient26

value: rectal cancer patient26

value: female


title: AdjacentN_ProximalEnd_patient27

value: rectal cancer patient27

value: Adjacent normal tissue


title: AdjacentN_ProximalEnd_patient25

value: rectal cancer patient25


title: AdjacentN_5cm_patient3

value: rectal cancer patient 3


title: AdjacentN_ProximalEnd_patient21

value: rectal cancer patient21


title: AdjacentN_ProximalEnd_patient23

value: rectal cancer patient23


title: AdjacentN_ProximalEnd_patient22

value: rectal cancer patient22


title: AdjacentN_ProximalEnd_patient16

value: rectal cancer patient16


title: AdjacentN_ProximalEnd_patient20

value: rectal cancer patient20


title: AdjacentN_ProximalEnd_patient18

value: rectal cancer patient18


title: AdjacentN_ProximalEnd_patient17

value: rectal cancer patient17

value: male


title: AdjacentN_ProximalEnd_patient19

value: rectal cancer patient19


title: Ex-smoker 4 stimulated with TGF-β1

city: Groningen

first: Jennie

last: Ong

address: Hanzeplein 1

description: Primary parenchymal lung fibroblasts, ex-smoker, TGF-β1-stimulated

hyb_protocol: not provided.

scan_protocol: not provided.

data_processing: Robust Multi-array Average was performed using GeneSpring GX version 13.1.1 software for quantile normalization of the probe-level intensity measurements.

source_name: TGF-β1-stimulated primary parenchymal lung fibroblasts of an ex-smoking control subject

label_protocol: not provided.

growth_protocol: Primary lung fibroblasts were cultured with Ham's F12 containing 10% FCS. At passage 5, the fibroblasts were serum starved and subsequently stimulated with TGF-β1

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

treatment_protocol: After serum starving for 1 day, the fibroblasts were stimulated with 100 U/ml TGF-β1 for 24 hrs

value: lung parenchyma

value: parenchymal lung fibroblasts

tag: smoking status

value: Ex-smoker


title: Ex-smoker 6

description: Primary parenchymal lung fibroblasts, ex-smoker, untreated

source_name: Primary parenchymal lung fibroblasts of an ex-smoking control subject

growth_protocol: Primary lung fibroblasts were cultured with Ham's F12 containing 10% FCS. At passage 5, the fibroblasts were serum starved and subsequently stimulated with TGF-β

treatment_protocol: After serum starving for 1 day, the fibroblasts were stimulated with 100 U/ml TGF-β for 24 hrs


title: Ex-smoker 2


title: Ex-smoker 4


title: Ex-smoker 6 stimulated with TGF-β1


title: Ex-smoker 2 stimulated with TGF-β1


title: AdjacentN_ProximalEnd_patient13

value: rectal cancer patient13


title: AdjacentN_ProximalEnd_patient12

value: rectal cancer patient12

value: female


title: AdjacentN_ProximalEnd_patient14

value: rectal cancer patient14

value: Adjacent normal tissue


title: AdjacentN_ProximalEnd_patient9

value: rectal cancer patient9


title: Ex-smoker 1 stimulated with TGF-β1


title: AdjacentN_ProximalEnd_patient11

value: rectal cancer patient11


title: Current smoker 6 stimulated with TGF-β1

description: Primary parenchymal lung fibroblasts, current smoker, TGF-β1-stimulated

source_name: TGF-β1-stimulated primary parenchymal lung fibroblasts of a current smoking control subject

value: Current smoker


title: AdjacentN_ProximalEnd_patient10

value: rectal cancer patient10


title: Ex-smoker 1


title: AdjacentN_ProximalEnd_patient15

value: rectal cancer patient15


title: Current smoker 6

description: Primary parenchymal lung fibroblasts, current smoker, untreated

source_name: Primary parenchymal lung fibroblasts of a current smoking control subject


title: IP2 of primary parenchymal lung fibroblasts of control 1 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_1_4.txt
Primary parenchymal lung fibroblasts of control 1, stimulated with TGF-β1, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling

hyb_protocol: Dye-swap hybridizations were performed overnight using Gene Expression Hybridization Kit (Agilent Technologies)

scan_protocol: GE2_1200_Jun14 protocol was used for scanning the slide in the Agilent SureScan Microarray Scanner

data_processing: Feature Extraction software version 12.0.1.1 was used to extract information from probe features from our microarray scan data.

source_name: Primary parenchymal lung fibroblasts, IP2, Control 1, TGF-β1

label_protocol: RNA of the T and IP fraction (50-80 ng) was labeled with cyanine 3 (Cy3) and cyanine 5 (Cy5) using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer's protocol Version 6.9.1.

growth_protocol: Primary lung fibroblasts were cultured in complete Ham's F12 medium containing 10% FCS. At passage 5, 17-20 million cells were collected for the Ago2-IP experiment.

extract_protocol: The RNA in the Total (T) fraction and the immunoprecipitated (IP) fraction were isolated using miRNeasy Mini Kit and miRNeasy Micro Kit (both of Qiagen), respectively, according to manufacturer's protocol.

treatment_protocol: TGF-β1 stimulation: 24 hrs before the stimulation the cells were put in complete Ham's F12 medium containing 0.5% FCS. Afterwards, the lung fibroblasts were stimulated with 7.5 ng/ml TGF-β1 in complete Ham's F12 medium containing 0.5% FCS for 24 hrs. After the stimulation the cells were harvested for the Ago2-IP experiments.

value: Primary parenchymal lung fibroblasts


title: Current smoker 5 stimulated with TGF-β1


title: IP1 of primary parenchymal lung fibroblasts of control 2 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_2_3.txt
Primary parenchymal lung fibroblasts of control 2, stimulated with TGF-β1, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, IP1, Control 2, TGF-β1


title: AdjacentN_ProximalEnd_patient8

value: rectal cancer patient8


title: IP2 of primary parenchymal lung fibroblasts of control 2 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_2_4.txt
Primary parenchymal lung fibroblasts of control 2, stimulated with TGF-β1, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, IP2, Control 2, TGF-β1


title: Current smoker 5


title: T1 fraction of primary parenchymal lung fibroblasts of control 1 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_1_3.txt
Primary parenchymal lung fibroblasts of control 1, stimulated with TGF-β1, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, T1, Control 1, TGF-β1


title: T2 fraction of primary parenchymal lung fibroblasts of control 2 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_2_4.txt
Primary parenchymal lung fibroblasts of control 2, stimulated with TGF-β1, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, T2, Control 2, TGF-β1


title: IP1 of primary parenchymal lung fibroblasts of control 1 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_1_3.txt
Primary parenchymal lung fibroblasts of control 1, stimulated with TGF-β1, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, IP1, Control 1, TGF-β1


title: T1 fraction of primary parenchymal lung fibroblasts of control 2 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_2_3.txt
Primary parenchymal lung fibroblasts of control 2, stimulated with TGF-β1, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, T1, Control 2, TGF-β1


title: AdjacentN_ProximalEnd_patient7

value: rectal cancer patient7

value: male


title: AdjacentN_ProximalEnd_patient6

value: rectal cancer patient6


title: AdjacentN_ProximalEnd_patient5

value: rectal cancer patient5


title: Current smoker 4

value: lung parenchyma

value: parenchymal lung fibroblasts


title: T2 fraction of primary parenchymal lung fibroblasts of control 2

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_2_2.txt
Primary parenchymal lung fibroblasts of control 2, untreated, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling
T2 of control 2

source_name: Primary parenchymal lung fibroblasts, T2, Control 2

growth_protocol: Primary lung fibroblasts were cultured with Ham's F12 containing 10% FCS. At passage 5, 17-20 million cells were collected for the Ago2-IP experiment.


title: AdjacentN_ProximalEnd_patient4

value: rectal cancer patient4


title: Current smoker 2 stimulated with TGF-β1


title: Current smoker 2


title: T2 fraction of primary parenchymal lung fibroblasts of control 1 stimulated with TGF-β1

description:
US45102948_257236310965_S01_GE2_1200_Jun14_1_4.txt
Primary parenchymal lung fibroblasts of control 1, stimulated with TGF-β1, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling

source_name: Primary parenchymal lung fibroblasts, T2, Control 1, TGF-β1


title: Current smoker 4 stimulated with TGF-β1


title: IP1 of primary parenchymal lung fibroblasts of control 2

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_2_1.txt
Primary parenchymal lung fibroblasts of control 2, untreated, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling
IP1 of control 2

source_name: Primary parenchymal lung fibroblasts, IP1, Control 2


title: Current smoker 3


title: AdjacentN_ProximalEnd_patient2

value: rectal cancer patient2

value: female


title: T1 fraction of primary parenchymal lung fibroblasts of control 1

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_1_1.txt
Primary parenchymal lung fibroblasts of control 1, untreated, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling
T1 of control 1

source_name: Primary parenchymal lung fibroblasts, T1, Control 1


title: AdjacentN_ProximalEnd_patient3

value: rectal cancer patient3

value: Adjacent normal tissue


title: AdjacentN_ProximalEnd_patient1

value: rectal cancer patient1


title: T2 fraction of primary parenchymal lung fibroblasts of control 1

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_1_2.txt
Primary parenchymal lung fibroblasts of control 1, untreated, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling
T2 of control 1

source_name: Primary parenchymal lung fibroblasts, T2, Control 1


title: T1 fraction of primary parenchymal lung fibroblasts of control 2

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_2_1.txt
Primary parenchymal lung fibroblasts of control 2, untreated, harvested at passage 5, cRNA of T fraction after Ago2-IP was used for mRNA expression profiling
T1 of control 2

source_name: Primary parenchymal lung fibroblasts, T1, Control 2


title: Current smoker 3 stimulated with TGF-β1

value: Current smoker


title: IP2 of primary parenchymal lung fibroblasts of control 2

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_2_2.txt
Primary parenchymal lung fibroblasts of control 2, untreated, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling
IP2 of control 2

source_name: Primary parenchymal lung fibroblasts, IP2, Control 2


title: IP2 of primary parenchymal lung fibroblasts of control 1

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_1_2.txt
Primary parenchymal lung fibroblasts of control 1, untreated, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling
IP2 of control 1

source_name: Primary parenchymal lung fibroblasts, IP2, Control 1


title: IP1 of primary parenchymal lung fibroblasts of control 1

description:
raw data file: US45102948_257236310965_S01_GE2_1200_Jun14_1_1.txt
Primary parenchymal lung fibroblasts of control 1, untreated, harvested at passage 5, cRNA of IP fraction after Ago2-IP was used for mRNA expression profiling
IP1 of control 1

source_name: Primary parenchymal lung fibroblasts, IP1, Control 1


title: 2S199_M_CAU_Y_2_17

first: Jonathan

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

hyb_protocol: Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner.

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (v9.5.1.1 Agilent).The log expression ratios produced during the normalization step are provided.

source_name: Stratagene UHRR reference

label_protocol: 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

growth_protocol: Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw.  Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays.  The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD).  Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.

extract_protocol: RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).  RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions.  RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100.  RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.

tag: control type

value: pool of human cell line RNA

source_name: Whole blood, mononuclear cell extract

value: blood

value: mononuclear

value: M

tag: ancestry

value: CAU

value: Y

tag: cad class

tag: cxcl5 rank

tag: bmi

tag: diabetes

value: N

tag: hyperlipid

tag: hypertension

tag: batchid

value: B


title: 2S200_F_CAU_N_0_28

tag: tissue

tag: cell type

tag: gender

value: F


title: 2S195_M_CAU_Y_2_25


title: SD-RSA_11518

city: Hong Kong

first: Zirui

last: DONG

address: Shatin, N.T.

department: Dept. of Obstetrics and Gynaecology

institute: The Chinese University of Hong Kong

hyb_protocol: After clean up and QC check, Cy3 and Cy5 labeled DNA samples were mixed together with Cot-1 DNA, blocking agent and hybridization buffer using Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit according to manufacturer's protocol. Samples were hybridized on array for 24 hours at 65oC. After hybridization, slides were washed sequential

scan_protocol: Probe is designed based on hg19. Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction

source_name: Recurrent miscarriage couples

label_protocol: Procedure for DNA fragmentation and labelling: 300 ng of Genomic DNA samples were heat fragmented. The fragmented DNA samples were labeled with Cy5 and the corresponding fragmented reference controls were labeled Cy3 using Agilent SureTag DNA Labeling Kit.

growth_protocol: Uncultured samples of chorionic villus sampling, amniotic fluid,  placental tissue and blood were used for direct DNA extraction

extract_protocol: Genomic DNA extraction done by Qiagen DNeasy® Blood & Tissue Kit following manufacturer's instructions

treatment_protocol: Samples were untreated

tag: clinical indication

value: recurrent miscarriage couples

source_name: healthy Chinese adult

value: healthy


title: SD-RSA_21249


title: 2S191_M_CAU_Y_4_1


title: SD-RSA_11028


title: 2S194_F_CAU_N_1_58


title: 2S189_F_CAU_N_1_12

value: E


title: 2S187_F_AA_Y_2_66

value: AA


title: 15C0590


title: cells at week 3, replicate 2

city: hefei

first: YANG

last: WU

state: anhui

address: feixi

department: immunology

institute: USTC

description: no

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human EG 1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

source_name: cultured cells at week 3 from cord blood CD34 positive cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: We cultured cord blood CD34 positive cells with Flt3L,SCF,IL-15,IL21 and IGF-1, and then the cells differentiated into NK cells for five weeks.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: The cultured cells were counted and harvested each week. And we lysed the cells in TRIzol (Invitrogen) and freezed them in refrigerator (-80°C).

tag: developmental stage

value: pre-differntiated stage of NK cells


title: SD-RSA_22950


title: SD-RSA_22945


title: SD-RSA_11312


title: 2S186_M_CAU_Y_4_80


title: SD-RSA_22955


title: cells at week 2, replicate 2

description: no

source_name: cultured cells at week 2 from cord blood CD34 positive cells


title: SD-RSA_22996


title: 2S183_F_CAU_N_1_133


title: 2S184_M_AA_Y_3_18


title: cells at week 5, replicate 2

description: no

source_name: cultured cells at week 5 from cord blood CD34 positive cells

value: differentiated stage of NK cells


title: 2S188_M_CAU_Y_4_2


title: cells at week 4, replicate 2

description: no

source_name: cultured cells at week 4 from cord blood CD34 positive cells


title: cells at week 1, replicate 2

description: no

source_name: cultured cells at week 1 from cord blood CD34 positive cells


title: SD-RSA_22939


title: 2S182_F_CAU_N_0_129


title: SD-RSA_22566


title: cells at week 5, replicate 1

description: no


title: SD-RSA_12997


title: SD-RSA_12996


title: 2S178_F_AA_N_1_50


title: SD-RSA_12986


title: cells at week 2, replicate 1

description: no


title: 2S179_M_CAU_Y_4_8


title: cells at week 4, replicate 1

description: no


title: cells at week 1, replicate 1

description: no


title: SD-RSA_12959


title: cells at week 3, replicate 1

description: no


title: 2S175_F_AA_N_1_94


title: 2S172_M_CAU_Y_4_68

value: A


title: SD-RSA_21456


title: SD-RSA_12966


title: SD-RSA_21294


title: SD-RSA_12950


title: 2S171_M_CAU_Y_2_35


title: SD-RSA_21373


title: SD-RSA_12931


title: SD-RSA_12939


title: 2S176_M_AA_N_1_97


title: 2S173_M_AA_Y_4_11


title: 2S168_F_AA_N_0_62


title: 2S169_F_AA_N_0_38


title: 2S167_F_CAU_N_1_87


title: SD-RSA_22992


title: 2S165_M_AA_Y_4_23


title: SD-RSA_21400


title: SD-RSA_20733


title: SD-RSA_20749


title: SD-RSA_21871


title: 2S160_M_CAU_Y_2_76


title: 2S162_M_AA_Y_4_74


title: 2S177_M_CAU_Y_4_20


title: 2S181_M_CAU_Y_4_41


title: SD-RSA_21597


title: 2S156_F_CAU_Y_2_70


title: 2S159_F_CAU_Y_2_32


title: 2S163_M_CAU_Y_2_26


title: SD-RSA_10950


title: SD-RSA_20566


title: SD-RSA_22226


title: SD-RSA_10358


title: LPS activated bovine macrophages stimulated with FhWild-ES, replicate 2

city: Warsaw

first: Piotr

last: Bąska

state: Mazowieckie

address: Ciszewskiego 8

department: Department of Preclinical Sciences

country: Poland

institute: Warsaw University of Life Sciences WULS – SGGW

description: Technical replicate 2 of 4

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Bos taurus

source_name: BOMA, bovine macrophage cell  line

label_protocol: Quick Amp Labeling (Agilent Technologies) according to the manufacturer`s protocol

growth_protocol: The cells were cultivated in DMEM (with 5% FCS, 2 mM glutamine, 100 units/ml of penicillin, 100 µg/ml streptomycin)

extract_protocol: total RNA was extracted using RNA isolation kit (A&A Biotechnology)

treatment_protocol: Cells were ativated with LPS (8.9 µg/ml) and stimulated in quadruplicate with FhWey-ES (10 µg/ml for 26 hours) or FhWild-ES (10 µg/ml for 24 hours)

tag: cell line

value: BOMA

value: monocytes/ macrophages

tag: agent

source_name: BOMA, bovine macrophage cell  line stimulated with FhWild-ESP

value: FhWild-ES


title: LPS activated bovine macrophages stimulated with FhWild-ES, replicate 4

description: Technical replicate 4 of 4


title: 2S152_F_CAU_Y_2_10

value: pool of human cell line RNA

value: blood

value: mononuclear


title: LPS activated bovine macrophages stimulated with FhWild-ES, replicate 1

description: Technical replicate 1 of 4


title: LPS activated bovine macrophages stimulated with FhWey-ES, replicate 3

description: Technical replicate 3 of 4

source_name: BOMA, bovine macrophage cell  line stimulated with FhWey-ESP

value: FhWey-ES


title: 2S154_F_CAU_Y_4_9

value: CAU

value: Y


title: 2S157_M_AA_Y_3_78

value: M


title: SD-RSA_12313

value: recurrent miscarriage couples


title: 2S151_M_CAU_Y_4_5


title: 2S153_F_AA_Y_3_96

value: F

value: N


title: SD-RSA_10407

value: healthy


title: SD-RSA_12955


title: LPS activated bovine macrophages stimulated with FhWey-ES, replicate 4

description: Technical replicate 4 of 4


title: LPS activated bovine macrophages stimulated with FhWey-ES, replicate 2

description: Technical replicate 2 of 4


title: SD-RSA_11460


title: LPS activated bovine macrophages stimulated with FhWild-ES, replicate 3

description: Technical replicate 3 of 4


title: Embryonic Stem Cell CC9dunni replicate 2

city: Clayton

first: Justin

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

hyb_protocol: Labelled samples were combined with Cot-1 DNA, aCGH blocking agent and HI-RPM hybridisation buffer.  Prior to hybridisation samples were heated to 95oC / 3 minutes followed by incubation at 37oC / 30minutes.  Combined samples were hybridised for 40 hours at 67oC @ 20rpm in a rotating Agilent hybridisation oven.  After hybridisation, microarrays were washed 5 minutes at room temperature with Oligo aCGH wash buffer 1(Agilent) and 1 minute at 37oC with Oligo aCGH wash buffer 2(Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green/Red and 16 bit Tiff

data_processing: The scanned images were analysed with Agilent Feature Extraction Software v11.0.1.0

source_name: ESC CC9dunni_Input

label_protocol: 120-250ng of IP (Cy5) and 400ng Input (Cy3) genomic DNA was fluorescently labelled using the Agilent Sure Tag DNA labelling kit for 4hrs at 37oC.  Samples were column purified and yield and specific activity determined on the NanoDrop

growth_protocol: Mus musculus ES cells were cultured on feeder cells composed of mitomycin C-treated embryonic fibroblasts. All cell lines were cultured in ES cell media consisting of DMEM, 15% FBS, 2mM GlutaMax, 1% MEM nonessential amino acids, 0.5% penicillin-streptomycin, 0.1mM β-mercaptoethanol (all from Life Technologies) and 106 U ml-1 of ESGRO Leukemia inhibitory factor (LIF) (Millipore) under conditions of 37°C and 5% CO2. The cells were transferred to feeder-free conditions prior to experimental use.

extract_protocol: Total DNA was extracted from cells using the DNeasy Blood and Tissue Kit.  Immunoprecipitation of methylated DNA (MeDIP) was performed on 3 μg of sonicated DNA, which ranged between 200 to 1000 bp in size, was denatured at 95°C for 10 minutes and immunoprecipitated with 2 μg of  5-methylcytosine (5mC; Active Motif, USA) with 20 μl of Protein G Dynabeads (Invitrogen) in 500 μl of IP buffer (10mM Na-phosphate, pH 7.0, 140mM NaCl, 0.05% Triton X-100) at 4°C overnight. Samples were washed three times with 700 μl IP buffer and DNA was eluted using 250 μl of Proteinase K digestion buffer (5mM Tris, 1mM EDTA, pH8.0, 0.05% SDS) with 7 μl of 10mg/ml Proteinase K (Qiagen) at 50°C for 3 hours. The immunoprecipitated DNA was then purified using Qiagen PCR Purification Kit (Qiagen)

treatment_protocol: Prior to experimentation, cells were cultered for 48hrs in feeder cell free conditions

tag: mt haplotype

value: Mus terricolor

tag: source

value: ESC's derived from strain CC9.3.1 which originated from a 129SvEv-Gpi1c(129S6) embryo, but now harbouring divergent mitochondrial DNA

source_name: ESC CC9dunni_IP


title: Embryonic Stem Cell CC9dunni replicate 1


title: 2S149_M_AA_Y_2_34

tag: control type

tag: ancestry

value: AA

value: A


title: 2S148_F_CAU_Y_4_15

tag: cad class

tag: cxcl5 rank


title: LPS activated bovine macrophages stimulated with FhWey-ES, replicate 1

description: Technical replicate 1 of 4

value: BOMA

value: monocytes/ macrophages


title: Embryonic Stem Cell CC9dunni replicate 3


title: SD-RSA_10286


title: 2S145_F_CAU_Y_2_3

value: pool of human cell line RNA

tag: bmi

tag: diabetes


title: Embryonic Stem Cell CC9pahari replicate 3

source_name: ESC CC9pahari_Input

value: Mus pahari

source_name: ESC CC9pahari_IP


title: Embryonic Stem Cell CC9pahari replicate 2


title: 2S144_M_CAU_Y_2_71

value: blood

value: mononuclear

tag: hyperlipid

tag: hypertension


title: SD-RSA_10924

tag: tissue


title: 2S142_F_CAU_N_0_105

tag: cell type

value: CAU

tag: batchid


title: 2S141_M_AA_Y_3_44

tag: gender

value: Y


title: SD-RSA_11988

tag: clinical indication


title: Embryonic Stem Cell CC9spretus replicate 2

source_name: ESC CC9spretus_Input

value: Mus spretus

source_name: ESC CC9spretus_IP


title: 16BA0044

value: recurrent miscarriage couples


title: SD-RSA_11971


title: SD-RSA_11351


title: Embryonic Stem Cell CC9spretus replicate 3


title: SD-RSA_11446


title: 2S147_M_CAU_N_0_6

source_name: Stratagene UHRR reference

source_name: Whole blood, mononuclear cell extract

value: M


title: Embryonic Stem Cell CC9pahari replicate 1


title: 2S138_M_CAU_Y_2_4

value: N


title: 2S143_F_CAU_Y_4_16

value: F


title: Embryonic Stem Cell CC9mus replicate 3

source_name: ESC CC9mus_Input

value: Mus musculus

source_name: ESC CC9mus_IP


title: SD-RSA_10763

source_name: Recurrent miscarriage couples

source_name: healthy Chinese adult

value: healthy


title: 2S146_F_AA_Y_3_82

value: AA


title: 2S139_F_CAU_Y_2_65

value: A


title: Embryonic Stem Cell CC9spretus replicate 1

value: ESC's derived from strain CC9.3.1 which originated from a 129SvEv-Gpi1c(129S6) embryo, but now harbouring divergent mitochondrial DNA


title: Embryonic Stem Cell CC9mus replicate 2


title: SD-RSA_10796


title: SD-RSA_12787


title: 2S137_M_CAU_Y_4_14


title: SD-RSA_21189


title: high grade MEC 4

city: Amsterdam

first: Johannes

middle: Hendrikus

last: Muatse

address: Gustav Mahlerlaan 81

department: Department of Oral and Maxillofacial Surgery and Oral Pathology

institute: VU University medical center

hyb_protocol: Oligonucleotide arrayCGH was performed using the SurePrint G3 Human CGH Microarray Kit, containing 180880 in situ synthesized 60-mer oligonucleotides representing 169793 unique chromosomal locations evenly distributed over the genome (space ~17kb) and 4548 additional unique oligonucleotides, located at 238 of the Cancer Census genes (4x180K array, Agilent Technologies, Palo Alto, CA, USA). The exact array design can be found online in the Gene Expression Omnibus (GEO) GPL8687

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) according to the specifications of the used platform 4x180k. All data was processed with HG18.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction.

source_name: tumor

label_protocol: Equal amounts (500 ng) of DNA from MEC samples and from matching normal salivary gland tissue were labeled with cyanine 3’-dUTP (Cy3) and cyanine 5’-dUTP (Cy5) nucleotides (Enzo Life Sciences, Farmingdale, NY, USA). Free nucleotides were removed using the MinElute PCR Purification Kit (Qiagen).

extract_protocol: 6 sections of 10 μm were deparaffinized, macro-dissected and incubated with 1M sodium thiocyanate at 38°C, for 16 h, followed by a proteinase K treatment at 55°C for another 16 h. DNA was isolated using the QIAmp DNA micro-kit (Qiagen, Hilden, Germany). Purity and quantity of the DNA samples was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham, USA).

value: female

tag: age

source_name: normal salivary gland tissue


title: 2S133_F_AA_N_0_111

value: pool of human cell line RNA


title: 2S132_F_CAU_N_1_113


title: 2S134_M_CAU_Y_2_22


title: 2S130_F_CAU_Y_2_24


title: Embryonic Stem Cell CC9mus replicate 1


title: SD-RSA_10970


title: high grade MEC 3


title: SD-RSA_21164


title: 2S124_M_CAU_Y_3_31


title: intermediate grade MEC 6


title: 2S127_F_CAU_N_1_30


title: SD-RSA_22134


title: intermediate grade MEC 5

value: male


title: high grade MEC 2


title: intermediate grade MEC 4


title: 2S125_F_CAU_N_1_63

value: blood


title: intermediate grade MEC 3


title: intermediate grade MEC 2


title: high grade MEC 1


title: SD-RSA_21822


title: SD-RSA_11822


title: SD-RSA_11820


title: SD-RSA_10797


title: SD-RSA_12134


title: intermediate grade MEC 1


title: SD-RSA_20797


title: 2S118_M_CAU_N_1_119

value: mononuclear


title: 2S116_M_AA_Y_3_134


title: 2S121_M_CAU_Y_3_140

value: CAU


title: low grade MEC 16


title: 2S120_M_CAU_Y_3_88

value: Y


title: 2S119_M_CAU_N_1_136


title: 2S115_F_CAU_Y_2_121


title: SD-RSA_10504


title: SD-RSA_21359


title: low grade MEC 17


title: SD-RSA_20504


title: 2S114_F_AA_Y_3_107


title: low grade MEC 14


title: 2S112_M_CAU_Y_3_40


title: low grade MEC 15


title: low grade MEC 12


title: SD-RSA_10835


title: SD-RSA_11189


title: 2S111_M_CAU_Y_3_115


title: SD-RSA_11164


title: SD-RSA_11359


title: low grade MEC 11


title: low grade MEC 10


title: 2S110_M_CAU_Y_4_57


title: low grade MEC 13


title: SD-RSA_20835


title: SD-RSA_21820


title: 2S113_M_CAU_Y_3_49


title: low grade MEC 9


title: 2S109_M_CAU_Y_2_127


title: 2S108_M_CAU_Y_4_86


title: 2S105_F_CAU_N_1_48


title: SD-RSA_20970


title: 2S103_M_CAU_Y_4_95


title: SD-RSA_11182


title: SD-RSA_20580


title: low grade MEC 5


title: SD-RSA_21182


title: SD-RSA_20949


title: low grade MEC 6


title: SD-RSA_10580


title: 2S100_F_CAU_Y_2_118

value: E


title: 2S102_F_CAU_N_0_125


title: low grade MEC 8


title: low grade MEC 2


title: low grade MEC 3


title: 2S099_M_CAU_N_1_124


title: SD-RSA_10949

value: recurrent miscarriage couples


title: 2S101_F_CAU_N_1_110


title: SD-RSA_20763


title: low grade MEC 1


title: low grade MEC 4


title: SD-RSA_20668


title: low grade MEC 7


title: 2S098_M_CAU_N_1_102

value: M


title: SD-RSA_10668


title: 2S097_M_CAU_Y_4_90


title: SD-RSA_20404


title: 2S095_M_CAU_Y_4_51

value: N


title: 2S093_M_AA_N_1_117


title: SD-RSA_10404


title: SD-RSA_20796


title: 2S094_M_CAU_N_1_73


title: 2S090_M_CAU_Y_4_53


title: 2S089_M_CAU_Y_3_98


title: 2S087_M_CAU_Y_4_108


title: 2S088_M_CAU_Y_2_69


title: 2S080_F_CAU_Y_2_128

value: F

value: C


title: 2S083_M_CAU_Y_2_42


title: 2S082_F_AA_Y_4_19


title: 2S078_M_CAU_Y_3_132


title: KO DCs at 24h, biological replicate 1

city: Vienna

first: Klara

last: Soukup

address: Zimmermannplatz 10

department: Tumor Immunology

country: Austria

institute: St Anna Kinderkrebsforschung (Children's Cancer Research Institute)

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: splenic DCs from CD11cCre-MK2fl/fl mice 24h post-LPS activation

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: CD11c+ DCs were isolated from whole spleens of C57BL/6 WT and CD11cCre-MK2fl/fl mice via collagenase D (10 mg/mL) + DNase I (10 ug/mL) digestion and magnetic beads and cultured at 37 deg

extract_protocol: RNA extraction was performed using the QIAGEN RNeasy kit according to the manufacturer's instructions.

treatment_protocol: DCs were treated with 100 ng/mL LPS (E. coli O111:B4) in culture for 4 to 24 hours

tag: strain background

tag: genotype/variation

value: 14 weeks

value: splenic CD11c+ dendritic cells

tag: stimulated with

value: 100 ng/mL LPS

tag: time point

value: 24h post-LPS activation


title: 2S079_M_CAU_Y_3_36

tag: control type

tag: ancestry


title: KO DCs at 24h, biological replicate 2

value: female


title: 2S085_M_CAU_Y_3_29

value: pool of human cell line RNA

tag: cad class

tag: cxcl5 rank


title: KO DCs at 4h, biological replicate 2

source_name: splenic DCs from CD11cCre-MK2fl/fl mice 4h post-LPS activation

value: 4h post-LPS activation


title: WT DCs at 24h, biological replicate 1

source_name: splenic DCs from WT mice 24h post-LPS activation

value: wild type

value: male


title: 2S092_F_AA_Y_4_85

value: blood

value: mononuclear

value: AA

tag: bmi

tag: diabetes


title: KO DCs at 4h, biological replicate 1


title: WT DCs at 4h, biological replicate 2

source_name: splenic DCs from WT mice 4h post-LPS activation


title: WT DCs at 24h, biological replicate 2


title: 2S077_F_CAU_Y_2_79

value: CAU

value: Y

tag: hyperlipid

tag: hypertension


title: 2S076_M_CAU_Y_3_7

tag: tissue

tag: cell type

value: M


title: 2S075_F_AA_N_1_143

tag: gender

value: F

value: N

tag: batchid


title: WT DCs at 4h, biological replicate 1

tag: age

value: 14 weeks


title: KO DCs at 0h, biological replicate 2

source_name: splenic DCs from CD11cCre-MK2fl/fl mice before LPS activation

tag: strain background

value: splenic CD11c+ dendritic cells

value: before LPS activation


title: KO DCs at 0h, biological replicate 1

tag: genotype/variation


title: 2S072_M_CAU_N_0_54

value: C


title: 2S073_M_CAU_N_1_45


title: 2S074_F_CAU_N_0_83


title: WT DCs at 0h, biological replicate 2

source_name: splenic DCs from WT mice before LPS activation

value: female


title: 2S071_M_CAU_N_0_67

value: pool of human cell line RNA


title: 2S070_F_CAU_N_0_47


title: OB_AdvancedAD_R5

city: Pamplona

first: Enrique

last: Santamaría

state: Navarra

address: Irunlarrea, 3

institute: Navarrabiomed

description:
AD (A3B3C3)
AVANZADO_S19_BCN376_151217

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Human Gene 2.0 ST Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Olfactory bulb, advanced AD

label_protocol: The sense cDNA was prepared from 1 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit (PN902623). The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

growth_protocol: Not applicable.

extract_protocol: For olfactory bulb mRNA extraction, the Maxwell 16 simplyRNA kit (Promega) was used.

treatment_protocol: Not applicable.

tag: disease status

value: Advanced AD

value: Olfactory bulb

value: Male

value: 93 years


title: WT DCs at 0h, biological replicate 1

value: wild type

value: male

tag: time point


title: 2S173_M_AA_Y_4_11_genotype

hyb_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).

data_processing:
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings.
CHP files were imported into Partek Genomics Suite v6.6. Genotype Call (SNP call): AA, AB, BB, or NC (No Call).

extract_protocol: Blood was drawn early in the day from fasted subjects to minimize signals associated with nutritional and diurnal cycle and processed within fifteen minutes. Plasma samples were obtained and RNA and DNA recovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).

value: blood

value: mononuclear

value: AA


title: 2S069_M_CAU_N_1_84

tag: control type

value: M

value: CAU

value: Y


title: OB_AdvancedAD_R4

description:
AD (A3B3C3)
AVANZADO_S18_BCN369_151217

value: 86 years


title: 2S189_F_CAU_N_1_12_genotype

scan_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).

value: F

tag: ancestry

value: N


title: 2S188_M_CAU_Y_4_2_genotype

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).

tag: cad class


title: 2S169_F_AA_N_0_38_genotype

tag: cxcl5 rank


title: 2S199_M_CAU_Y_2_17_genotype

tag: bmi


title: 2S179_M_CAU_Y_4_8_genotype

tag: diabetes


title: 2S200_F_CAU_N_0_28_genotype

tag: hyperlipid


title: 2S067_F_AA_Y_4_142

tag: hypertension

value: D


title: 2S165_M_AA_Y_4_23_genotype

tag: tissue


title: OB_AdvancedAD_R2

description:
AD (A3B3C3)
AVANZADO_S16_BCN349_151214

value: 70 years


title: 2S065_F_AA_Y_4_61

value: pool of human cell line RNA

tag: cell type


title: 2S176_M_AA_N_1_97_genotype

tag: gender


title: 2S194_F_CAU_N_1_58_genotype


title: 2S066_F_CAU_Y_4_56

tag: batchid


title: 2S163_M_CAU_Y_2_26_genotype


title: OB_AdvancedAD_R3

description:
AD (A2B3C3)
AVANZADO_S17_BCN367_151214

value: Advanced AD

value: Olfactory bulb

tag: age

value: 89 years


title: OB_AdvancedAD_R1

description:
AD (A2B3C3)
AVANZADO_S15_BCN337_151214

value: Female

value: 77 years


title: 2S186_M_CAU_Y_4_80_genotype

value: blood


title: 2S154_F_CAU_Y_4_9_genotype

value: mononuclear


title: 2S177_M_CAU_Y_4_20_genotype


title: 2S061_M_CAU_N_1_99


title: 2S062_F_CAU_Y_2_122


title: 2S060_M_CAU_Y_4_93


title: OB_MiddleAD_R2

description:
AD (A2B2C2)
MEDIO_S12_BCN136_151214

source_name: Olfactory bulb, intermediate AD

value: Intermediate AD

value: 97 years


title: OB_MiddleAD_R1

description:
AD (A2B2C2)
MEDIO_S11_BCN0104_151214

value: Male

value: 85 years


title: 2S063_F_CAU_N_0_138

value: CAU

value: Y


title: 2S184_M_AA_Y_3_18_genotype

value: M

value: AA

value: N


title: OB_MiddleAD_R3

description:
AD (A2B2C1)
MEDIO_S13_BCN381_151214


title: 2S167_F_CAU_N_1_87_genotype

value: F


title: OB_MiddleAD_R4

description:
AD (A2B2C2)
MEDIO_S14_BCN222_151217

value: 86 years


title: 2S160_M_CAU_Y_2_76_genotype


title: OB_InitialAD_R5

description:
AD (A1B1C1)
INICIAL_S9_A120046_151217

source_name: Olfactory bulb, initial AD

value: Initial AD

value: Olfactory bulb

value: 72 years


title: 2S057_F_CAU_Y_2_89

source_name: Stratagene UHRR reference

value: pool of human cell line RNA

value: D


title: 2S054_F_CAU_N_1_33

source_name: Whole blood, mononuclear cell extract

value: blood

value: mononuclear


title: OB_InitialAD_R3

description:
AD (A2B1C1)
INICIAL_S7_BCN336_151214

value: 80 years


title: OB_InitialAD_R2

description:
AD (A2B1C1)
INICIAL_S6_BCN342_151214

value: Female


title: 2S056_F_CAU_Y_2_81


title: 2S053_F_CAU_Y_3_21


title: OB_InitialAD_R4

description:
AD (A1B1C1)
INICIAL_S8_BCN358_151214

value: 75 years


title: 2S152_F_CAU_Y_2_10_genotype

value: CAU


title: 2S148_F_CAU_Y_4_15_genotype

value: Y


title: 2S171_M_CAU_Y_2_35_genotype

value: M


title: 2S052_F_AA_N_0_137

value: AA


title: 2S058_F_CAU_Y_2_52

value: N


title: 2S147_M_CAU_N_0_6_genotype


title: 2S050_M_CAU_Y_4_103


title: OB_Control_R2

description:
No protein deposit + vascular disease
CONTROL_S2_BCN362_151214

source_name: Olfactory bulb, control

value: Control

value: Male

value: 103 years


title: OB_Control_R4

description:
PART ( Braak I)
CONTROL_S4_BCN387_151217

value: Olfactory bulb

value: 61 years


title: OB_Control_R3

description:
PART ( Braak I)
CONTROL_S3_BCN283_151214

value: 81 years


title: 2S153_F_AA_Y_3_96_genotype

value: F


title: 2S151_M_CAU_Y_4_5_genotype

value: blood


title: OB_Control_R1

description:
Thal 1 Cerad 1 no Tau deposit
CONTROL_S1_A1491_151214

value: 72 years


title: 2S146_F_AA_Y_3_82_genotype

value: mononuclear


title: 2S048_F_AA_N_0_141

value: pool of human cell line RNA

value: D


title: OB_InitialAD_R1

description:
AD (A2B1C2)
INICIAL_S10_A120067_151217

value: Initial AD

value: 88 years


title: 2S051_M_CAU_N_0_109

value: M

value: CAU

value: Y


title: 2S047_M_AA_Y_2_126

value: AA


title: 2S049_M_CAU_N_1_104

value: N


title: 2S145_F_CAU_Y_2_3_genotype


title: 2S046_M_CAU_Y_4_77


title: 2S142_F_CAU_N_0_105_genotype


title: 2S040_M_CAU_N_0_13


title: 2S044_F_AA_N_1_75


title: 2S144_M_CAU_Y_2_71_genotype


title: 2S042_F_CAU_N_1_131


title: 2S045_F_CAU_N_0_130


title: 2S039_M_CAU_Y_3_72


title: 2S037_F_CAU_Y_4_46


title: 2S143_F_CAU_Y_4_16_genotype


title: 2S035_F_AA_N_1_106

value: C


title: 2S141_M_AA_Y_3_44_genotype


title: 2S033_M_CAU_N_1_64


title: 2S137_M_CAU_Y_4_14_genotype


title: 2S132_F_CAU_N_1_113_genotype


title: 2S038_F_CAU_N_1_116


title: 2S133_F_AA_N_0_111_genotype


title: 2S029_M_CAU_Y_2_91


title: 2S138_M_CAU_Y_2_4_genotype


title: 2S130_F_CAU_Y_2_24_genotype


title: 2S031_M_CAU_Y_3_27


title: 2S026_F_CAU_Y_2_60


title: B. subtilis ccpA topA(S478P) mutant_exponential growth_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

hyb_protocol: 100 ng of Cy5-labeled cDNA and 100 ng of Cy3-labeled cDNAwere hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).
The normalization/ dye bias correction method as defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol GE2_105_Dec08) is: Linear and Lowess.  The normalization/ dye bias correction method is: Linear and Lowess.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D
(final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye,
GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis 168 mutant strains were grown under vigorous agitation at 37 °C in C minimal medium (Faires et al., 1999; PMID 10941796) supplemented with glucose (5 g/l) and potassium glutamate (8g/l).

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

treatment_protocol: Samples were taken at OD600 of 1.0.

value: pooled reference

tag: strain

source_name: ccpA topA mutant_exponential growth

tag: genotype

value: Bacillus subtilis ccpA topA(S478P) mutant


title: 2S023_F_AA_Y_3_101

city: Chapel Hill


title: B. subtilis ccpA topA(S478P) mutant_exponential growth_rep1


title: 2S025_F_CAU_N_1_100


title: B. subtilis ccpA topA(S478P) mutant_exponential growth_rep3


title: 2S134_M_CAU_Y_2_22_genotype


title: B. subtilis ccpA mutant_exponential growth_rep3

source_name: ccpA mutant_exponential growth

value: Bacillus subtilis ccpA mutant


title: 2S015_M_CAU_Y_4_37

value: E


title: 2S012_F_AA_Y_3_139

value: blood

value: F


title: NZO 3651

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

hyb_protocol: Fragmented cDNA samples were then hybridized to GeneChip Affymetrix GeneChip MOUSE GENE 430 2.0 (Affymetrix UK Ltd, Lahr, Germany).

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).  Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).  Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2010, Affymetrix). All synthesis steps were monitored with an RNA 6000 nano kit (Agilent, Taufkirchen, Germany) for quality control.

growth_protocol: Mice were bred and maintained in a regular 12h light/dark cycle under constant temperature and humidity (22°C ± 1°C, 50% ± 5% humidity) with unrestricted access to water and standart chow.

extract_protocol: Total RNA was extracted from 50-100 mg liver tissue with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).  Total RNA was extracted from 50-100 mg epidydimal adipose tissue and gastrocnemius muscle with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).  Total RNA was extracted from 50-100 mg liver tissue with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).

treatment_protocol: At 18 weeks of age male mice were sacrifced by CO2 asphyxation, liver was isolated and 100 mg aliquots were snap frozen in liquid nitrogen. Samples were stored at -80°C until processing.

value: male

value: 18 weeks

value: NZO

value: liver