title: liver_HC_HLD-3

tag: array ^sample

tag: diagnosis

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: nafld activity score

tag: waist (cm)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-8

status: Public on Nov 08 2016

type: RNA

city: Toronto

first: Johane

middle: P.

last: Allard

state: Ontario

address: 585 University Ave, 9-NU-973

department: Medicine

country: Canada

institute: University Health Network

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was checked for overall quality using R (v2.15.1) with the lumi Bioconductor package. Nine outliers (4 NASH, 5 SS), which fell below the threshold for one or more of the quality metrics  calculated with this package, were excluded from further analysis. The data were imported in GeneSpring v12.5 (Agilent) and normalized using a quantile normalization followed by a “per  probe” median centered normalization.

molecule: total RNA

organism: Homo sapiens

source_name: liver

label_protocol: 200 ng of RNA were labelled and amplified following Illumina Whole Genome Expression - DASL assay kit for partially degraded and FFPE derived RNA.

extract_protocol: Total RNA was extracted from liver biopsies using the mirVana miRNA Isolation kit (Life Technologies Corp., Carlsbad, CA, USA). RNA concentration and purity were assessed with a Thermo Scientific's NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

value: HC

tag: steatosis (%)

tag: ballooning (intensity)

tag: age (y)

tag: gender

value: male

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

value: no


title: liver_HC_HLD-1

tag: array ^sample

tag: diagnosis

tag: waist (cm)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-157

value: NASH

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

value: female

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)


title: liver_SS_CL-140

tag: array ^sample

value: SS

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_NASH_CL-160

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: waist (cm)

tag: ldl cholesterol (mmol/l)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-144

tag: array ^sample

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)


title: liver_NASH_CL-113

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: total cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_SS_CL-136

tag: array ^sample

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: waist (cm)

tag: ldl cholesterol (mmol/l)

tag: diabetes

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_SS_CL-145

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: gender


title: liver_HC_HLD-4

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_NASH_CL-111

tag: array ^sample

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes

value: yes

tag: liver arachidonic acid (% of total lipids)


title: liver_SS_CL-134

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: gender

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: ldl cholesterol (mmol/l)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-147

tag: array ^sample

tag: ballooning (intensity)

tag: nafld activity score

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_NASH_CL-152

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: age (y)

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)


title: liver_SS_CL-117

tag: array ^sample

tag: ballooning (intensity)

tag: nafld activity score

tag: gender

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: ldl cholesterol (mmol/l)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_HC_HLD-5

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_NASH_CL-116

tag: array ^sample

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)


title: liver_NASH_CL-128

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: gender

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: ldl cholesterol (mmol/l)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_SS_CL-114

tag: array ^sample

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_SS_CL-110

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: age (y)

tag: gender

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)


title: liver_NASH_CL-118

tag: array ^sample

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: ldl cholesterol (mmol/l)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-112

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: age (y)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_NASH_CL-103

tag: array ^sample

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: gender

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes

tag: liver arachidonic acid (% of total lipids)


title: liver_SS_CL-90

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: age (y)

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: ldl cholesterol (mmol/l)


title: liver_SS_CL-108

tag: array ^sample

tag: lobular inflammation (severity)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: liver_NASH_CL-98

tag: diagnosis

tag: steatosis (%)

tag: ballooning (intensity)

tag: nafld activity score

tag: gender

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: hemoglobin a1c

tag: diabetes


title: liver_SS_CL-100

tag: array ^sample

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: age (y)

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: ldl cholesterol (mmol/l)

tag: liver arachidonic acid (% of total lipids)


title: liver_SS_CL-92

tag: diagnosis

tag: steatosis (%)

tag: ballooning (intensity)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: fasting glucose (mmol/l)


title: liver_SS_CL-88

tag: nafld activity score

tag: gender

tag: waist (cm)

tag: hdl cholesterol (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: diabetes


title: liver_SS_CL-86

tag: array ^sample

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: age (y)

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: hemoglobin a1c


title: liver_SS_CL-95

tag: diagnosis

tag: steatosis (%)

tag: ballooning (intensity)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)


title: SAMPLE 6_SCD162-17-2-derived iPS cells_2

city: Hirakata

first: Keiko

last: Muguruma

address: 2-5-1 Shinmachi

department: Graduate School of Medicine

country: Japan

institute: Kansai Medical University

description: SAMPLE 6

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on the Agilent SureScan Microarray Scanner (G2600D) after washing with Agilent gene Expression Wash Buffers Pack .

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent). Normalized signal intensities were calculated using the scaling factor obtained from a trimmed average signal of the array after excluding the 2% of the probe sets with the highest and the lowest values.

source_name: case-derived iPS cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng Total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent:One-Colr) according to the manufacturer's instructions.

growth_protocol: Undifferentiated ES and iPS cells were cultured on feeder cells in maintenace media.

extract_protocol: Undifferentiated iPS and ES cells were collected, and RNA was extracted and purified using RNA mini kit (QIAGEN).

tag: cell type

value: pluripotent stem cells

tag: cell subtype

value: case-derived iPS cells


title: SAMPLE 10_Healthy control-derived iPS cells (201B7)_2

description: SAMPLE 10

source_name: control-derived iPS cells

value: control-derived iPS cells


title: liver_NASH_CL-97

tag: array ^sample

tag: nafld activity score

tag: gender

tag: waist (cm)

tag: fasting glucose (mmol/l)

tag: diabetes


title: liver_SS_CL-96

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: age (y)

tag: body mass index (kg/m2)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: hdl cholesterol (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance


title: liver_SS_CL-91

tag: diagnosis

tag: steatosis (%)

tag: ballooning (intensity)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)


title: SAMPLE 9_Healthy control-derived iPS cells (201B7)_1

description: SAMPLE 9

tag: cell type

tag: cell subtype


title: SAMPLE 3_Healthy control-derived iPS cells (HC-4)_1

description: SAMPLE 3


title: SAMPLE 5_SCD162-17-2-derived iPS cells_1

description: SAMPLE 5


title: Day35 Case-derived neural progenitor cells 3

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) and Subio Platform (ver. 1.19.4941, Subio Inc). gProcessedSignals were normalized to the 75th percentiles, and   transformed into log2 ratio against the average value of normalized intensities of 4 control iPSCs.

growth_protocol: hiPSCs were differentiated in three-dimenstional condition with SFEBq culture.

extract_protocol: iPSC-derived neural progenitors were collected on culture day35, and total RNA was extracted and purified using RNA mini kit (QIAGEN).

value: iPSC-derived neural progenitor

tag: sample source

value: spinocerebellar ataxia type 6 patient


title: liver_NASH_CL-87

tag: array ^sample

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: fasting glucose (mmol/l)

tag: hemoglobin a1c

tag: diabetes


title: SAMPLE 4_Healthy control-derived iPS cells (HC-4)_2

description: SAMPLE 4


title: SAMPLE 1_Embryonic stem cells

description: SAMPLE 1

source_name: ES cells

value: ES cells


title: SAMPLE 13_Normal human dermal fibroblasts

description: SAMPLE 13

source_name: dermal fibroblasts

value: somatic cells

value: dermal fibroblasts


title: SAMPLE 11_SCD166-2-14-derived iPS cells_1

description: SAMPLE 11


title: SAMPLE 8_SCD16-2E-derived iPS cells_2

description: SAMPLE 8


title: SAMPLE 12_SCD166-2-14-derived iPS cells_2

description: SAMPLE 12


title: Day35 Case-derived neural progenitor cells 4


title: SAMPLE 2_Embryonic stem cells

description: SAMPLE 2


title: Day35 Case-derived neural progenitor cells 2


title: SAMPLE 7_SCD16-2E-derived iPS cells_1

description: SAMPLE 7


title: liver_NASH_CL-106

tag: diagnosis

tag: steatosis (%)

tag: ballooning (intensity)

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: hdl cholesterol (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)


title: Day35 Control-derived neural progenitor cells 4

tag: cell type

tag: sample source

value: healthy control


title: Day35 Case-derived neural progenitor cells 1


title: Day35 Control-derived neural progenitor cells 3


title: Day35 Control-derived neural progenitor cells 1


title: PE04 Replicate A

city: Belfast

first: Jaine

last: Blayney

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queen's University

hyb_protocol: Samples were hybridised onto Ovarian Cancer Disease Specific Array™ in accordance with the NuGEN guidelines for hybridisation onto Affymetrix GeneChip arrays

scan_protocol: Arrays were scanned using the Affy Genechip® Scanner 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: The samples were processed with the R affy package using RMA with default settings.

label: biotin

source_name: PEO4 ovarian cells

label_protocol: The amplified single-stranded cDNA was fragmented and biotin labelled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies Inc).

growth_protocol: RPMI supplemented with 10%FCS and glutamine

extract_protocol: RNA was extracted using RNA STAT 60

value: ovarian cells

tag: cell line

tag: tumor site of origin

value: Ovarian

tag: histopathology

value: Poorly differentiated serous


title: PE04 Replicate C


title: PE04 Replicate B


title: TOV-21G Replicate C

source_name: TOV-21G ovarian cells

value: Clear Cell


title: PE01 Replicate B

source_name: PEO1 ovarian cells


title: TOV-112D Replicate A

source_name: TOV-112D ovarian cells

value: Endometrioid


title: TOV-112D Replicate B


title: OVCAR5 Replicate C

source_name: OVCAR5 ovarian cells

value: Well-differentiated adenocarcinoma


title: OVCAR5 Replicate B


title: IGR-OV1 Replicate A

source_name: IGR-OV1 ovarian cells

value: Endometroid with serous/clear cell


title: Day35 Control-derived neural progenitor cells 2


title: PE01 Replicate A


title: ES-2 Replicate C

source_name: ES-2 ovarian cells

value: Poorly differentiated clear cell


title: TOV-112D Replicate C


title: ES-2 Replicate B


title: OVCAR5 Replicate A


title: ES-2 Replicate A


title: SK-OV-3 Replicate B

source_name: SK-OV-3 ovarian cells


title: SK-OV-3 Replicate A


title: IGR-OV1 Replicate C


title: OVCAR8 Replicate C

source_name: OVCAR8 ovarian cells

value: Undifferentiated carcinoma


title: TOV-21G Replicate B


title: OVCAR8 Replicate B


title: IGR-OV1 Replicate B


title: PE01 Replicate C


title: SK-OV-3 Replicate C


title: TOV-21G Replicate A


title: OVCAR3 Replicate C

source_name: OVCAR3 ovarian cells

value: Poorly differentiated carcinoma


title: OVCAR8 Replicate A


title: NCI/ADR-RES Replicate C

source_name: NCI/ADR-RES ovarian cells

value: NCI/ADR-RES


title: UWB1.289

source_name: UWB1.289 ovarian cells

value: Serous


title: OVCAR4 Replicate C

source_name: OVCAR4 ovarian cells

value: Moderately differentiated carcinoma


title: OVCAR3 Replicate A


title: OV56 Replicate B

source_name: OV56 ovarian cells


title: NCI/ADR-RES Replicate B


title: NCI/ADR-RES Replicate A


title: COV318 Replicate A

source_name: COV318 ovarian cells


title: COV318 Replicate C


title: UWB1.289+BRCA1 Replicate B

source_name: UWB1.289+BRCA1 ovarian cells


title: OV56 Replicate C


title: SF767 cell_MBD3 KD_Rep_3

city: West Lafayette

first: Yi

last: Cui

state: Indiana

address: 1203 W. State Street

department: Agricultural and Biological Engineering

country: USA

institute: Purdue University

description: Gene expression in SF767 GBM cells with MBD3 knocked down

hyb_protocol: 0.6 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven (10x g).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028004_D_F_20140326) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human SF767 GBM cells, MBD3 KD, 72h, replicate 3

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

growth_protocol: Human GBM cell line SF767 was routinely cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% fetal bovine serum, 1% Pen Strep and 1% glutamate. After revival from liquid nitrogen, cells sub-cultured within 4 to 6 passages were used for knockdown and microarray experiments. The cultures were incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (QIAGEN), according to the manufacter's instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent Bioanalyzer.

treatment_protocol: Specific siRNAs targeting human MBD3 mRNA and scramble siRNA were obtained from Santa Cruz Biotechnology. Transfection was performed with the siRNA Reagent System (sc-45064). After 72 hours of incubation, the knockdown efficiency was determined by qRT-PCR, western blot, and immunofluorescence staining. From the results, a 70-75% of decrease in MBD3 trancription can be maintained up to 6 days after siRNA transfection, based on which microarray was performed.

tag: tissue

value: Brain glioblastoma cell line


title: SF767 cell_control_Rep_4

description: Gene expression in SF767 GBM cells

source_name: Human SF767 GBM cells, control sample, replicate 4


title: COV362 Replicate C

source_name: COV362 ovarian cells


title: SF767 cell_MBD3 KD_Rep_2

source_name: Human SF767 GBM cells, MBD3 KD, 72h, replicate 2


title: OVCAR3 Replicate B


title: COV362 Replicate B


title: UWB1.289+BRCA1 Replicate C


title: SF767 cell_MBD3 KD_Rep_4

source_name: Human SF767 GBM cells, MBD3 KD, 72h, replicate 4


title: OV56 Replicate A


title: UWB1.289+BRCA1 Replicate A


title: SF767 cell_MBD3 KD_Rep_1

source_name: Human SF767 GBM cells, MBD3 KD, 72h, replicate 1


title: COV318 Replicate B


title: COV362 Replicate A


title: SF767 cell_control_Rep_1

description: Gene expression in SF767 GBM cells

source_name: Human SF767 GBM cells, control sample, replicate 1


title: Glioma biopsy_WHO IV_Pat_3

description: Gene expression in human WHO grade IV glioma

source_name: Glioma biopsy, WHO Grade IV, patient 3

extract_protocol: RNA was prepared using the standard TRIzol reagent and protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent Bioanalyzer.

treatment_protocol: Glioma biopsy samples with characterized WHO grades were obtained from the Department of Neurosurgery in Xiangya Hospital of Central South University (Changsha, China). All patients received surgical resection to the extent feasible. After a pathologist confirmed the glioma grade according to the 2007 WHO Classification of Tumors of the Central Nervous System, the tumor RNA was immediately extracted from the surgically resected tissues.

value: Brain glioma

tag: tumor stage

value: WHO grade IV

tag: gender

value: male

tag: age


title: Glioma biopsy_WHO II_Pat_4

description: Gene expression in human WHO grade II glioma

source_name: Glioma biopsy, WHO Grade II, patient 4

value: WHO grade II


title: SF767 cell_control_Rep_3

description: Gene expression in SF767 GBM cells

source_name: Human SF767 GBM cells, control sample, replicate 3


title: Glioma biopsy_WHO IV_Pat_4

source_name: Glioma biopsy, WHO Grade IV, patient 4


title: COV504 Replicate C

source_name: COV504 ovarian cells

value: ovarian cells

value: Ovarian


title: Glioma biopsy_WHO II_Pat_3

source_name: Glioma biopsy, WHO Grade II, patient 3

value: female


title: SF767 cell_control_Rep_2

description: Gene expression in SF767 GBM cells

source_name: Human SF767 GBM cells, control sample, replicate 2


title: Clear Cell Epithelial Ovarian Cancer (R0171F487a)

hyb_protocol: Samples were hybridized onto Ovarian Cancer Disease Specific Array™ in accordance with the NuGEN guidelines for hybridization onto Affymetrix GeneChip arrays

source_name: Primary Tumor

value: CLEAR CELL

value: Epithelial Ovarian Cancer


title: Glioma biopsy_WHO IV_Pat_2

source_name: Glioma biopsy, WHO Grade IV, patient 2


title: COV504 Replicate B


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F485)

value: SEROUS LOW-GRADE


title: Mucinous Epithelial Ovarian Cancer (R0171F578)

value: MUCINOUS


title: Clear Cell Epithelial Ovarian Cancer (R0171F413)


title: Glioma biopsy_WHO IV_Pat_1

source_name: Glioma biopsy, WHO Grade IV, patient 1


title: COV504 Replicate A


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F397_h)


title: Glioma biopsy_WHO II_Pat_2

source_name: Glioma biopsy, WHO Grade II, patient 2


title: Clear Cell Epithelial Ovarian Cancer (R0171F532)


title: Mucinous Epithelial Ovarian Cancer (R0171F573)


title: Clear Cell Epithelial Ovarian Cancer (R0171F474)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F476)

value: SEROUS


title: Endometrioid Epithelial Ovarian Cancer (R0171F386)

value: ENDOMETRIOID


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F459)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F403)


title: OVCAR4 Replicate B

source_name: OVCAR4 ovarian cells


title: Tibetan30

type: genomic

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human 1M-duo chips

hyb_protocol: according to the manufacturer’s specifications

scan_protocol: chips were scanned using BeadArray instrument

data_processing: We used Genomestudio to call the genotypes of SNPs. We used EGT file provide by Illumina for SNP clustering.

molecule: genomic DNA

source_name: Tibetans

growth_protocol: Extraction of genomic DNA from cultured cells was performed using proteinase K and repeated phenol-chloroform extraction.

extract_protocol: genomic DNAs were extracted with DNA-extraction kits (Tiangen Biotech, Beijing, China)

treatment_protocol: immortalization of peripheral lymphocytes by the Epstein Barr virus  peripheral lymphocytes by the Epstein Barr virus

value: whole blood


title: Tibetan28

label_protocol: according to the manufacturer’s specifications


title: Tibetan29


title: Tibetan26


title: Tibetan27


title: Tibetan25


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F433)


title: Tibetan24


title: UCI3

city: Los Angeles

first: David

middle: Miguel

last: Padua

state: CA

department: Medicine-Division of Digestive Diseases

institute: UCLA

hyb_protocol: 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.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

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 v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 19 out of 26 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Volcano Plot filtering between two groups. Hierarchical Clustering was performed using the R software. GO analysis and Pathway analysis were performed in the standard enrichment computation method

source_name: Colon tissue

label_protocol: Sample labeling was 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 (Arraystar Flash RNA Labeling Kit, Arraystar). 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. 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.

extract_protocol: Total RNA was extracted using Trizol RNA extraction method

value: Male

tag: location

value: colon

tag: sample type

value: inactive ulcerative colitis


title: Tibetan23


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F344)


title: Endometrioid Epithelial Ovarian Cancer (R0171F377)


title: Tibetan22


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F303)


title: Clear Cell Epithelial Ovarian Cancer (R0171F353)


title: Mucinous Epithelial Ovarian Cancer (R0171F305a)


title: Mucinous Epithelial Ovarian Cancer (R0171F253)


title: Tibetan21


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F284)


title: Tibetan20


title: Tibetan18


title: Tibetan17


title: Tibetan19


title: Glioma biopsy_WHO II_Pat_1

source_name: Glioma biopsy, WHO Grade II, patient 1

value: Brain glioma


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F289)


title: UCA7

value: Female

value: active ulcerative colitis


title: Tibetan16


title: OVCAR4 Replicate A

value: Moderately differentiated carcinoma


title: UCI2


title: Tibetan15


title: UCA8


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F455)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F238)


title: UCI4


title: UCA6


title: UCI1


title: Tibetan14


title: UCA5


title: UCA2


title: UCA3


title: Tibetan12

value: male


title: Clear Cell Epithelial Ovarian Cancer (R0171F127)


title: Clear Cell Epithelial Ovarian Cancer (R0171F200)


title: Tibetan11


title: UCA4


title: Con5

value: control


title: Endometrioid Epithelial Ovarian Cancer (R0171F201a)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F202)


title: Con6


title: Mucinous Epithelial Ovarian Cancer (R0171F229)


title: Clear Cell Epithelial Ovarian Cancer (R0171F148)


title: Tibetan13


title: Endometrioid Epithelial Ovarian Cancer (R0171F145)


title: Endometrioid Epithelial Ovarian Cancer (R0171F151)


title: Clear Cell Epithelial Ovarian Cancer (R0171F133)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F129)


title: Clear Cell Epithelial Ovarian Cancer (R0171F106)


title: Endometrioid Epithelial Ovarian Cancer (R0171F088)


title: Con2


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F141)


title: Mucinous Epithelial Ovarian Cancer (R0171F098)


title: Con4


title: Tibetan9


title: Tibetan8


title: Tibetan6


title: Tibetan7


title: Tibetan10


title: Endometrioid Epithelial Ovarian Cancer (R0171F080)


title: Con7


title: Tibetan4


title: Tibetan3


title: Tibetan2


title: Tibetan1


title: UCA1


title: Con3


title: Mucinous Epithelial Ovarian Cancer (R0171F073)


title: Tibetan5


title: Clear Cell Epithelial Ovarian Cancer (R0171F065)


title: Con1


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F092)


title: Endometrioid Epithelial Ovarian Cancer (R0171F027)


title: Mucinous Epithelial Ovarian Cancer (R0171F041)


title: Serous Low-Grade Epithelial Ovarian Cancer (R0171F020)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F042)


title: Endometrioid Epithelial Ovarian Cancer (R0171F025)


title: High-Grade Serous Epithelial Ovarian Cancer (R0171F039)


title: Low-Grade Serous Epithelial Ovarian Cancer (R0171F057)


title: Mucinous Epithelial Ovarian Cancer (R0171F004a_h)


title: Clear Cell Epithelial Ovarian Cancer (R0171F018a)


title: atria CM7,rep7

status: Public on Nov 07 2016

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

description: Expression data from Homo sapiens atria

data_processing: The data was normalised using IlluminaGenomeStudio data analysis software

source_name: Atria from mitral regurgitation patient

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The atrial tissues were obtained during surgery in patients with mitral regurgitation. Atrial tissues of normal subjects were purchased from BioChain institute,Inc.

value: female

value: atria

tag: diagnosis

value: mitral regurgitation


title: atria CM5,rep5

description: Expression data from Homo sapiens atria


title: atria CM3,rep3

description: Expression data from Homo sapiens atria


title: atria CM6,rep6

description: Expression data from Homo sapiens atria


title: atria NC3,rep3

description: Expression data from Homo sapiens atria

source_name: Atria from normal control subject

value: normal (control)


title: atria CM1,rep1

description: Expression data from Homo sapiens atria


title: atria CM4,rep4

description: Expression data from Homo sapiens atria


title: atria CM2,rep2

description: Expression data from Homo sapiens atria


title: atria NC1,rep1

description: Expression data from Homo sapiens atria


title: atria NC2,rep2

description: Expression data from Homo sapiens atria


title: LYP9_Leaf_nutrient-deficient_3

city: Hefei

first: Longjiang

last: Gu

state: Anhui Province

address: 130 Changjiang West Avenue

department: School of Life Sciences

institute: Anhui Agricultural University

hyb_protocol: The biotin-labeled cRNA was then fragmented and hybridized to the GeneChip Rice Genome Array (Eukaryotic target preparation, Affymetrix) for 16 h, and then these arrays were washed, stained.

scan_protocol: Arrays were scanned using the Affymetrix Model 450 Fluidics station and Affymetrix Scanner 3000 using the manufacturer’s recommended protocols.

data_processing:
RMA expression value derived from software computeExprSet in affy packages
Raw datasets were initially quality checked by function ReadAffy in affy package from bioconductor sofeware, and then re-checked by RMAexpress software. After that, data were used for background adjustment and normalization by aff with rma method. Finally, expression level was calculated by computeExprSet funcion in affy packages.

label: Biotin

organism: Oryza sativa

label_protocol: Total RNA was used for reverse transcription of double-stranded complementary DNA (cDNA), which was then transcribed to complementary RNA (cRNA) and subsequently labeled with biotin.

growth_protocol: After germination, all seedlings were transplanted into mix nutrient soil (nutrient soil : vermiculite : fine sand = 1 : 1 :1) for 5 days, and then were transplanted in soil with about the same nutrition status.

extract_protocol: Total RNA of the 36 samples was extracted using Trizol reagent (Invitrogen, Grand Island, NY, USA) and purified by using a RNeasy Plant Mini kit (QIAGEN, 74204, Germany) according to the manufacturer’s protocol. RNA quality was assessed using agarose gel electrophoresis and further confirmed by measuring the A260/A280 ratio.

treatment_protocol: Then 15 seedlings of each variety were transplanted evenly in each of 12 sequare barrels, which were filled with raw soil containing limited natural organic nutrition. When the seedlings were 14 day-old, 10g urea and 10g compound fertilizer were applied to 6 of 12 sequare barrels. All seedlings were therefore classified as two groups, nutrient-sufficient group and nutrient-deficient group.

tag: cultivar

value: Leaf

tag: treatment

value: Nutrient-deficient


title: PA64s_Root_nutrient-deficient_1

value: Root


title: LYP9_Leaf_nutrient-deficient_1


title: PA64s_Root_nutrient-deficient_3


title: PA64s_Leaf_nutrient-deficient_3


title: PA64s_Root_nutrient-sufficient_2

value: Nutrient-sufficient


title: PA64s_Leaf_nutrient-sufficient_1


title: PA64s_Leaf_nutrient-sufficient_2


title: PA64s_Leaf_nutrient-deficient_1


title: LYP9_Leaf_nutrient-sufficient_2


title: PA64s_Root_nutrient-deficient_2


title: LYP9_Leaf_nutrient-sufficient_3


title: PA64s_Root_nutrient-sufficient_1


title: LYP9_Leaf_nutrient-deficient_2


title: LYP9_Root_nutrient-deficient_3


title: PA64s_Root_nutrient-sufficient_3


title: PA64s_Leaf_nutrient-sufficient_3


title: PA64s_Leaf_nutrient-deficient_2


title: 9311_Leaf_nutrient-deficient_3


title: LYP9_Root_nutrient-sufficient_2


title: LYP9_Root_nutrient-sufficient_3


title: LYP9_Root_nutrient-deficient_2


title: 9311_Leaf_nutrient-deficient_2


title: LYP9_Leaf_nutrient-sufficient_1


title: LYP9_Root_nutrient-sufficient_1


title: LYP9_Root_nutrient-deficient_1


title: patient 2, myeloid progenitor cells

city: Nijmegen

first: Niccolo

last: Mariani

address: Geert Grooteplein Zuid 8

country: Netherlands

institute: Radboudumc

description:
Test
SAMPLE 22

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions
For the normalization we used GAPDH
Target gene signals normalized to the average Ct value of four housekeeping gene measurements; 2^-deltaCt
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports MDS/control ratios.

label: SYBR Green

source_name: hematopoietic fraction from bone marrow CD13/33+

label_protocol: real-time PCR a 384 Microfluidic Card (Applied Biosystems) was employed according to manufacturer instructions. the expression of several genes implicated in erythroid differentiation (TFRC, GYPA, GYPB, GYPC, SPTB, SPTA1, EBP41, EBP42 and HBB) was determined to check whether these genes indeed showed highest expression in the CD71+ cell fraction. The erythroid genes were only used as controls and not included in subsequent statistical analyses.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: myeloid progenitor cells


title: donor 2, myeloid progenitor cells

description:
control
SAMPLE 25


title: patient 1, myeloid progenitor cells

description:
Test
SAMPLE 21


title: MH7A IL-1β-stimulated ex3

city: Bunkyo-ku

first: AKIMASA

last: SOMEYA

state: Tokyo

address: 2-1-1 Hongo

department: Department of Host Defense and Biochemical Research

institute: Juntendo University

description:
MH7A  Control 3-2
Gene expression data from IL-1β-stimulated MH7A

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
The data were analyzed with Affymetrix Expression Console using  Robust Multi-array Average (RMA) summarization method.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: IL-1β-stimulated MH7A

label_protocol: Biotinylated cRNA were prepared  using WT Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions from100 ng total RNA.

growth_protocol: Human synovial MH7A cells were maintained in RPMI-1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 µg/ml. streptomycin at 37°C in 5% CO2.

extract_protocol: Total RNA was purified using a QIA shredder (QIAGEN) and an RNeasy plus mini kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Cells (60-70% confluent) in 6-well plates were incubated in the presence or absence of 5 mM GlcN (Koyo Chemical, Japan) foｒ 2.5 hours, and then stimulated with  15 pg/ml IL-1β for 13h. In some experiments, cells were preincubated with 5 mM alloxan (O-GlcNAc transferase inhibitor) for 30 min, and then incubated with 2 mM alloxan and 5mM GlcN for 2.5 h, followed by stimulation with IL-1β. Thereafter, the cells were harvested, and total RNA was purified.

value: synovial cell line

tag: treatment group

value: IL-1β-stimulated MH7A


title: 9311_Leaf_nutrient-deficient_1


title: 9311_Leaf_nutrient-sufficient_3


title: MH7A IL-1β-stimulated Allo ex2

description:
MH7A Alloxan 2-5
Gene expression data from IL-1β-stimulated MH7A in the presence of alloxan

value: IL-1β-stimulated in the presence of alloxan


title: MH7A-nontreated ex2

description:
MH7A Resting 2-1
Gene expression data from non-treated MH7A cells

source_name: non-stimulated MH7A

value: non-stimulated


title: MH7A IL-1β-stimulated Allo ex3

description:
MH7A Alloxan 3-5
Gene expression data from IL-1β-stimulated MH7A in the presence of alloxan


title: donor 1, myeloid progenitor cells

description:
control
SAMPLE 24


title: MH7A IL-1β-stimulated GlcN ex2

description:
MH7A GlcN 2-3
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN

value: IL-1β-stimulated in the presence of GlcN


title: MH7A IL-1β-stimulated GlcN ex3

description:
MH7A GlcN 3-3
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN


title: 9311_Root_nutrient-deficient_1


title: MH7A IL-1β-stimulated GlcN and Allo ex3

description:
MH7A GlcN / Allo 3-4
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN and alloxan

value: IL-1β-stimulated in the presence of GlcN and alloxan


title: MH7A IL-1β-stimulated ex1

description:
MH7A  Control 1-2
Gene expression data from IL-1β-stimulated MH7A


title: 9311_Root_nutrient-deficient_3


title: MH7A IL-1β-stimulated Allo ex1

description:
MH7A Alloxan 1-5
Gene expression data from IL-1β-stimulated MH7A in the presence of alloxan


title: patient 3, myeloid progenitor cells

description:
Test
SAMPLE 23


title: 9311_Leaf_nutrient-sufficient_1


title: 9311_Leaf_nutrient-sufficient_2


title: donor 3, stem and progenitor cells

description:
control
SAMPLE 20

source_name: hematopoietic fraction from bone marrow CD71+

value: stem and progenitor cells


title: XYSHA460

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: SST-RMA values for gene and alt.splice derived from Gene Expression Console (Affymetrix, v 1.4.1)

hyb_protocol: All samples were hybridized to Affymetrix Mouse Transcriptome Assay 1.0 microarrays and scanned at the University of Kentucky College of Medicine Microarray Core Facility

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were analyzed with Gene Expression console (Affymetrix) using the RMA algorithm and resulting signal intensities for transcript-level data were transferred to flat files in Excel and associated with vendor-provided April 2015 annotation data.  Pre-statistical filtering retained unique, annotated probe sets with adequate signal intensity (signal intensity ≥ 4.2 on at least 4 arrays in the study). Filtered signal intensities were analyzed by two-way ANOVA to identify significant main effects of genotype (XX versus XY), surgery (Sham vs OVX), as well as interaction.  The False Discovery Rate (FDR) procedure was used to estimate the error of multiple testing.

organism: Mus musculus

source_name: abdominal aorta, sham operated XY female

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: At 8 weeks of age; XX (n = 10) and XY (n = 10) subjects underwent sham surgery or ovariectomy (OXV), yielding four treatment groups- XX Sham (n = 5); XX OVX (n = 5); XY Sham (n = 4); and XY OVX (n = 6). After two weeks of recovery, mice were fed the Western high fat diet for one week.

extract_protocol: Aortas were dissected under a dissecting microscope and placed in RNA later solution (Ambion, cat#AM7021).  Abdominal aortas (diaphragm to the ileac bifurcation) were used for RNA extraction. RNA was extracted using the Rneasy fibrous tissue mini kit (Qiagen, cat#74704), and the RNA concentration and quality was quantified by Agilent 2100 bioanalyzer using RNA 6000 Nano labchip kit (Agilent Technologies, Cat# 5067-151).  Harvested abdominal aortic RNA samples (n = 20) were of sufficient quantity and quality that did not differ significantly among treatment groups (Agilent Bioanalyzer RNA Integrity Number [RIN]: 9.51 ± 0.07 – p = 0.25; [RNA] (ng/ul): 39.5 ± 3.4 – p = 0.93; 28s:18s ratio: 2.83 ± 0.89 – p = 0.33-; all statistical tests by ANOVA)

treatment_protocol: All subjects were administered either a sham (SHA) or an ovariectomy (OVX) surgery

tag: surgery

value: sham

tag: sex chromosome complement

value: XY

tag: [rna] (ng/ ml)

tag: rin


title: 9311_Root_nutrient-sufficient_2


title: MH7A IL-1β-stimulated ex2

description:
MH7A  Control 2-2
Gene expression data from IL-1β-stimulated MH7A

tag: cell line

tag: cell type


title: MH7A-nontreated ex1

description:
MH7A Resting 1-1
Gene expression data from non-treated MH7A cells


title: MH7A IL-1β-stimulated GlcN and Allo ex2

description:
MH7A GlcN / Allo 2-4
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN and alloxan


title: donor 2, stem and progenitor cells

description:
control
SAMPLE 19


title: donor 1, stem and progenitor cells

description:
control
SAMPLE 18


title: XYSHA453


title: 9311_Root_nutrient-deficient_2


title: 9311_Root_nutrient-sufficient_3


title: MH7A IL-1β-stimulated GlcN and Allo ex1

description:
MH7A GlcN / Allo 1-4
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN and alloxan


title: 9311_Root_nutrient-sufficient_1


title: MH7A IL-1β-stimulated GlcN ex1

description:
MH7A GlcN 1-3
Gene expression data from IL-1β-stimulated MH7A in the presence of GlcN


title: MH7A-nontreated ex3

description:
MH7A Resting 3-1
Gene expression data from non-treated MH7A cells


title: XYSHA450


title: XYSHA498


title: patient 7, stem and progenitor cells

description:
Test
SAMPLE 17


title: XYOVX497

source_name: abdominal aorta, ovariectomized XY female

value: ovariectomy


title: patient 5, stem and progenitor cells

description:
Test
SAMPLE 15


title: donor 1, erythroid progenitor cells

description:
control
SAMPLE 8

value: erythroid progenitor cells


title: patient 6, stem and progenitor cells

description:
Test
SAMPLE 16


title: patient 7, erythroid progenitor cells

description:
Test
SAMPLE 7

source_name: hematopoietic fraction from bone marrow CD34+


title: XYOVX452


title: XYOVX442


title: patient 3, stem and progenitor cells

description:
Test
SAMPLE 13


title: XYOVX444


title: XXSHA459

source_name: abdominal aorta, sham operated XX female

value: XX


title: XYOVX443


title: XXSHA456


title: patient 5, erythroid progenitor cells

description:
Test
SAMPLE 5


title: patient 4, stem and progenitor cells

description:
Test
SAMPLE 14


title: donor 3, erythroid progenitor cells

description:
control
SAMPLE 10


title: XYOVX457


title: XXSHA496


title: patient 1, stem and progenitor cells

description:
Test
SAMPLE 11


title: patient 2, stem and progenitor cells

description:
Test
SAMPLE 12


title: patient 6, erythroid progenitor cells

description:
Test
SAMPLE 6


title: XXOVX499

source_name: abdominal aorta, ovariectamized XX female


title: patient 4, erythroid progenitor cells

description:
Test
SAMPLE 4


title: XXOVX476


title: XXOVX461


title: patient 2, erythroid progenitor cells

description:
Test
SAMPLE 2


title: XXOVX455


title: patient 3, erythroid progenitor cells

description:
Test
SAMPLE 3


title: XXOVX451


title: donor 2, erythroid progenitor cells

description:
control
SAMPLE 9


title: XXSHA475


title: XXSHA449


title: patient 1, erythroid precursor cells

description:
Test
SAMPLE 1

value: erythroid precursor cells


title: MPP_10_D10_3_R1

status: Public on Nov 06 2016

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Multipotent progenitor from peripheral blood

library_source: genomic

data_processing:
After de-multiplexing and adapter removal, we aligned reads using Bismark (parameters: -bowtie2; Bismark version: v0.12.2, Bowtie version: v2.2.9 )  to the human reference genome (GRCh38).
Duplicate reads were discarded and DNA methylation calls were extracted. Reads containing fewer than three cytosines outside a CpG context that have been converted to thymines were discarded, which effectively removes unconverted and contaminating DNA fragments.
Genome_build: hg38
Supplementary_files_format_and_content: DNA methylation calls in the format: chromosome coordinate number-of-methylated-reads number-of-total-reads

source_name: Multipotent progenitor

extract_protocol:
uWGBS (Farlik et al, Cell Reports, 2015)
uWGBS (Farlik et al, Cell Reports, 2015)

value: MPP

tag: donor number

tag: Sex

value: M

tag: age group

tag: cell number


title: MPP_10_D10_1_R1

tag: tissue


title: MPP_10_D10_5_R1


title: Mono_1000_D1_R1

description: Monocyte from peripheral blood

source_name: Monocyte

value: Mono


title: MPP_50_D9_2_R1


title: MPP_10_D10_2_R1


title: NK_1000_D2_R1

description: Natural killer cell from peripheral blood

source_name: Natural killer cell

value: NK

value: F


title: Neut_1000_D1_R1

description: Neutrophil from peripheral blood

source_name: Neutrophil

value: Neut


title: MPP_1000_D10_R1


title: MPP_10_D10_7_R1


title: MPP_50_D10_1_R1


title: Neut_1000_D2_R1

description: Neutrophil from peripheral blood


title: Mono_1000_D3_R1

description: Monocyte from peripheral blood


title: Neut_1000_D3_R1

description: Neutrophil from peripheral blood


title: MPP_10_D10_4_R1


title: MPP_50_D10_2_R1


title: MPP_10_D10_8_R1


title: NK_1000_D3_R1


title: MPP_10_D9_8_R1


title: MPP_10_D10_6_R1


title: Mono_1000_D2_R1

description: Monocyte from peripheral blood


title: MPP_50_D9_1_R1


title: MPP_10_D9_7_R1


title: MPP_10_D9_6_R1


title: MPP_10_D9_5_R1


title: macrophage-Ctrl siRNA

city: shang hai

first: Qian

address: xiangyin road 800

institute: Second military medical university

description: Ctrl

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: peritoneal macrophages_Control siRNA

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using QIAGEN kit following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: strain background

tag: gender

value: male

value: peritoneal macrophage

tag: transfected with

value: Control siRNA

tag: time point

value: 48hr after transfection


title: NK_1000_D1_R1


title: MPP_1000_D9_R1


title: MPP_10_D9_4_R1


title: macrophage-HDAC9 siRNA

source_name: peritoneal macrophages_HDAC9 siRNA

value: HDAC9 siRNA


title: MPP_10_D9_2_R1


title: MPP_10_D9_1_R1


title: MPP_10_D7_4_R1


title: MPP_10_D7_6_R1


title: MPP_10_D9_3_R1


title: MPP_10_D7_7_R1


title: MPP_10_D6_6_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D6_7_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D6_1_R1

description: Multipotent progenitor from cord blood


title: MPP_1000_D8_R1


title: MPP_50_D7_2_R1


title: MPP_10_D7_8_R1


title: MPP_10_D7_3_R1


title: MPP_50_D7_1_R1


title: MPP_10_D6_5_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D7_1_R1


title: MPP_10_D6_4_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D6_2_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D7_2_R1


title: MPP_50_D8_2_R1


title: MPP_10_D6_8_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D6_2_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D8_1_R1


title: MPP_10_D6_1_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D6_3_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D8_1_R1


title: MPP_1000_D6_R1

description: Multipotent progenitor from cord blood


title: MPP_1000_D7_R1


title: MPP_10_D5_6_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_7_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D5_1_R1

description: Multipotent progenitor from cord blood


title: MPP_1000_D5_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_8_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D5_2_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_3_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_22_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_1_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_4_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_3_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_4_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_23_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D4_2_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_7_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_6_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_4_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_6_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_3_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_8_R1

description: Multipotent progenitor from cord blood


title: MPP_50_D4_1_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_21_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_20_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_5_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_5_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_1_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D5_2_R1

description: Multipotent progenitor from cord blood


title: MPP_1000_D4_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_7_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_2_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_5_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_8_R1

description: Multipotent progenitor from cord blood


title: MPP_10_D4_2_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_17_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_19_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_15_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_14_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_13_R1

description: Multipotent progenitor from cord blood


title: MPP_1_D4_12_R1

description: Multipotent progenitor from cord blood


title: MPPbm_10_D2_6_R1

description: Multipotent progenitor from bone marrow


title: MPP_1_D4_11_R1

description: Multipotent progenitor from cord blood


title: MPPbm_10_D2_7_R1

description: Multipotent progenitor from bone marrow


title: MPPbm_1000_D2_R1

description: Multipotent progenitor from bone marrow


title: MPPbm_50_D2_2_R1

description: Multipotent progenitor from bone marrow


title: MPPbm_50_D2_1_R1

description: Multipotent progenitor from bone marrow


title: MPPbm_10_D2_2_R1

description: Multipotent progenitor from bone marrow


title: MPPbm_10_D2_4_R1

description: Multipotent progenitor from bone marrow


title: MLP3_10_D3_2_R1

description: Immature lymphoid progenitor 3 from peripheral blood

source_name: Immature lymphoid progenitor 3


title: MLP3_1000_D2_R2


title: MLP3_10_D2_8_R2


title: MLP3_10_D3_5_R1


title: MLP3_10_D2_7_R2


title: MPPbm_10_D2_5_R1

description: Multipotent progenitor from bone marrow


title: MLP3_50_D3_1_R1


title: MLP3_1000_D3_R1


title: MLP3_10_D3_3_R1


title: MLP3_10_D3_6_R1


title: MLP3_10_D3_4_R1


title: MLP3_10_D3_1_R1


title: MLP3_10_D3_8_R1


title: MLP3_10_D3_7_R1


title: MPPbm_10_D2_1_R1

description: Multipotent progenitor from bone marrow


title: MLP3_50_D2_1_R2


title: MLP3_50_D3_2_R1


title: MLP3_50_D2_2_R2


title: MPPbm_10_D2_8_R1

description: Multipotent progenitor from bone marrow


title: MLP3_10_D2_4_R2


title: MLP3_10_D2_3_R2


title: MLP3_10_D2_6_R2


title: MLP3_10_D2_5_R2


title: MLP3_10_D2_2_R2


title: MLP3_50_D1_2_R2


title: MLP3_1000_D1_R2


title: MLP3_10_D2_1_R2


title: MLP3_10_D1_6_R2


title: MLP3_10_D1_8_R2


title: MLP3_50_D1_1_R2


title: MLP3_10_D1_5_R2


title: MLP2_50_D2_1_R2

description: Immature lymphoid progenitor 2 from peripheral blood

source_name: Immature lymphoid progenitor 2


title: MLP2_10_D2_6_R2


title: MLP2_10_D2_7_R2


title: MLP2_10_D2_3_R2


title: MLP3_10_D1_7_R2


title: MLP2_10_D2_5_R2


title: MLP3_10_D1_1_R2


title: MLP2_10_D2_4_R2


title: MLP2_50_D2_2_R2


title: MLP3_10_D1_3_R2


title: MLP2_1000_D2_R2


title: MLP3_10_D1_2_R2


title: MLP2_10_D2_2_R2


title: MLP2_10_D2_1_R2


title: MLP2_10_D2_8_R2


title: MLP2_10_D1_8_R2


title: MLP2_50_D1_2_R2


title: MLP2_50_D1_1_R2


title: MLP2_10_D1_4_R2


title: MLP2_10_D1_5_R2


title: MLP2_10_D1_3_R2


title: MLP2_10_D1_7_R2


title: MLP2_1000_D3_R1


title: MLP2_10_D1_2_R2


title: MLP2_10_D1_1_R2


title: MLP2_50_D3_1_R1


title: MLP2_50_D3_2_R1


title: MLP1_1000_D1_R2

description: Immature lymphoid progenitor 1 from peripheral blood

source_name: Immature lymphoid progenitor 1


title: MLP1_50_D1_2_R2


title: MLP2_10_D3_8_R1


title: MLP2_10_D3_4_R1


title: MLP2_10_D3_5_R1


title: MLP2_10_D3_2_R1


title: MLP1_10_D1_7_R2


title: MLP2_10_D3_3_R1


title: MLP1_10_D1_8_R2


title: MLP1_10_D1_4_R2


title: MLP1_10_D1_2_R2


title: MLP1_50_D2_2_R2


title: MLP2_10_D1_6_R2


title: MLP1_10_D1_1_R2


title: MLP2_10_D3_6_R1


title: MLP1_50_D1_1_R2


title: MLP1_10_D1_6_R2


title: MLP2_10_D3_7_R1


title: MLP1_10_D1_5_R2


title: MLP1_10_D1_3_R2


title: MLP1_10_D2_3_R2


title: MLP1_10_D2_7_R2


title: MLP1_10_D2_2_R2


title: MLP1_10_D2_1_R2


title: MLP1_10_D2_5_R2


title: MLP1_10_D2_4_R2


title: MLP1_10_D2_8_R2


title: MLP1_50_D3_2_R1


title: MLP1_10_D3_7_R1


title: MLP1_10_D3_4_R1


title: MLP1_1000_D2_R2


title: MLP1_50_D3_1_R1


title: MLP1_10_D3_6_R1


title: MLP1_10_D3_5_R1


title: MLP0_50_D3_2_R1

description: Immature lymphoid progenitor 0 from peripheral blood

source_name: Immature lymphoid progenitor 0


title: MLP1_10_D3_8_R1


title: MLP0_1000_D3_R1


title: MLP1_10_D2_6_R2


title: MLP0_50_D3_1_R1


title: MLP0_10_D3_8_R1


title: MLP1_1000_D3_R1


title: MLP0_10_D3_7_R1


title: MLP1_10_D3_3_R1


title: MLP1_10_D3_2_R1


title: MLP0_10_D3_3_R1


title: MLP0_10_D3_5_R1


title: MLP0_10_D3_2_R1


title: MLP0_10_D3_6_R1


title: MLP1_10_D3_1_R1


title: MLP0_10_D2_5_R1


title: MLP0_1000_D2_R1


title: MLP0_10_D2_2_R1


title: MLP0_10_D3_4_R1


title: MLP0_10_D3_1_R1


title: MLP0_10_D2_8_R1


title: MLP0_10_D2_3_R1


title: MLP0_10_D2_6_R1


title: MLP0_10_D2_1_R1


title: MLP0_10_D2_7_R1


title: MLP0_50_D2_1_R1


title: MLP0_1000_D1_R1


title: MLP0_50_D1_1_R1


title: MLP0_10_D1_6_R1


title: MLP0_10_D1_7_R1


title: MLP0_50_D1_2_R1


title: MLP0_10_D1_8_R1


title: MLP0_10_D1_5_R1


title: MLP0_10_D1_3_R1


title: MLP0_1_D1_9_R1


title: MLP0_10_D1_1_R1


title: MLP0_10_D1_2_R1


title: MLP0_1_D1_8_R1


title: MLP0_1_D1_7_R1


title: MLP0_1_D1_5_R1


title: MLP0_1_D1_6_R1


title: MLP1_50_D2_1_R2


title: MLP0_1_D1_4_R1


title: MLP0_1_D1_3_R1


title: MLP0_1_D1_24_R1


title: MLP0_1_D1_23_R1


title: MLP0_1_D1_1_R1


title: MLP0_10_D2_4_R1


title: MLP0_1_D1_21_R1


title: MLP0_1_D1_20_R1


title: MLP0_1_D1_2_R1


title: MLP0_1_D1_18_R1


title: MLP0_1_D1_17_R1


title: MLP0_1_D1_19_R1


title: MLP0_1_D1_22_R1


title: MLP0_1_D1_15_R1


title: MLP0_1_D1_14_R1


title: MLP0_1_D1_16_R1


title: MLP0_1_D1_13_R1


title: MLP0_1_D1_11_R1


title: MLP0_1_D1_12_R1


title: MK_1_D3_8N_2_R1

description: Megakaryocyte from bone marrow

source_name: Megakaryocyte

value: MK


title: MLP0_1_D1_10_R1


title: MK_1_D3_4N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_32N_8_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_4N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_32N_6_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_32N_7_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_32N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_9_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_32N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_8_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_6_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_16N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_8N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_6_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_7_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_16N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_9_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_32N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_7_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_6_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D3_2N_7_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_4N_2_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_8N_2_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_8N_1_R1

description: Megakaryocyte from bone marrow


title: MLP0_50_D2_2_R1


title: MK_5_D1_4N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_4N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_8N_2_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_32N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_4N_1_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_2N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_8N_3_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_32N_1_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_16N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_8N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_4N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_8N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_4N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_8N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_4N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_32N_7_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_4N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D2_2N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_32N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_32N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_32N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_5_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_32N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_6_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_4_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_2N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_16N_4_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_16N_3_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_16N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_16N_2_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_1_R1

description: Megakaryocyte from bone marrow


title: MK_1_D1_2N_2_R1

description: Megakaryocyte from bone marrow


title: MK_5_D1_16N_2_R1

description: Megakaryocyte from bone marrow


title: MEP_50_D3_2_R1

description: Megakaryocyte erythrocyte progenitor from peripheral blood

source_name: Megakaryocyte erythrocyte progenitor

value: MEP


title: MEP_1000_D3_R1


title: MEP_50_D3_1_R1


title: MEP_10_D3_6_R1


title: MEP_10_D3_5_R1


title: MEP_10_D3_2_R1


title: MEP_50_D1_2_R1


title: MEP_10_D3_7_R1


title: MEP_10_D3_1_R1


title: MEP_10_D3_4_R1


title: MEP_1000_D1_R1


title: MEP_50_D1_1_R1


title: MEP_10_D1_8_R1


title: MEP_10_D1_2_R1


title: MEP_10_D1_3_R1


title: MEP_10_D1_5_R1


title: MEP_10_D1_7_R1


title: MEP_10_D1_6_R1


title: MEP_10_D1_4_R1


title: MEP_1000_D2_R2


title: MEP_50_D2_1_R2


title: MEP_10_D2_6_R2


title: MEP_10_D2_5_R2


title: MEP_10_D2_7_R2


title: MEP_10_D3_8_R1


title: MEP_10_D2_8_R2


title: MEP_10_D2_3_R2


title: MEP_10_D2_2_R2


title: MEP_10_D2_1_R2


title: HSC_50_D9_2_R1

description: Hematopoietic stem cell from peripheral blood

source_name: Hematopoietic stem cell

value: HSC


title: HSC_10_D9_7_R1


title: HSC_10_D9_6_R1


title: HSC_10_D9_2_R1


title: HSC_10_D9_4_R1


title: HSC_10_D7_8_R1


title: HSC_50_D7_1_R1


title: HSC_1000_D7_R1


title: HSC_50_D7_2_R1


title: MEP_10_D1_1_R1


title: HSC_10_D7_6_R1


title: HSC_10_D7_7_R1


title: HSC_10_D7_1_R1


title: HSC_10_D7_3_R1


title: MEP_50_D2_2_R2


title: HSC_1000_D10_R1


title: HSC_10_D7_2_R1


title: HSC_50_D10_2_R1


title: MEP_10_D2_4_R2


title: HSC_10_D10_7_R1


title: HSC_50_D10_1_R1


title: HSC_10_D10_3_R1


title: HSC_10_D10_2_R1


title: HSC_10_D10_1_R1


title: HSCfl_1000_D1_R1

description: Hematopoietic stem cell from fetal liver


title: HSCfl_50_D1_1_R1


title: HSC_50_D9_1_R1


title: HSC_10_D9_3_R1


title: HSCfl_10_D1_6_R1


title: HSCfl_10_D1_8_R1


title: HSCfl_10_D1_7_R1


title: HSC_10_D10_4_R1


title: HSCfl_10_D1_5_R1


title: HSCfl_10_D1_2_R1


title: HSCfl_50_D1_2_R1


title: HSCfl_50_D2_2_R1


title: HSCfl_50_D2_1_R1


title: HSCfl_10_D1_4_R1


title: HSCfl_10_D1_3_R1


title: HSC_50_D6_2_R1

description: Hematopoietic stem cell from cord blood


title: HSC_50_D6_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_5_R1

description: Hematopoietic stem cell from cord blood


title: HSCfl_10_D1_1_R1


title: HSC_10_D6_8_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_7_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1000_D6_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_4_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_3_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_6_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D6_2_R1

description: Hematopoietic stem cell from cord blood


title: HSC_50_D5_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1000_D5_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_8_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_7_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_6_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_5_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_4_R1

description: Hematopoietic stem cell from cord blood


title: HSC_50_D5_2_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_2_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_6_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_7_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_8_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_5_R1

description: Hematopoietic stem cell from cord blood


title: HSC_50_D4_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1000_D4_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_3_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_4_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_7_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D4_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_5_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_9_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_24_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_6_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_21_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_1_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_4_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_2_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_3_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_18_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_17_R1

description: Hematopoietic stem cell from cord blood


title: HSC_10_D5_3_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_16_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_15_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_14_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_13_R1

description: Hematopoietic stem cell from cord blood


title: HSC_1_D4_12_R1

description: Hematopoietic stem cell from cord blood


title: HSC_50_D4_2_R1

description: Hematopoietic stem cell from cord blood


title: HSCbm_1000_D1_R1

description: Hematopoietic stem cell from bone marrow


title: HSCbm_10_D1_7_R1


title: HSCbm_10_D1_6_R1


title: HSCbm_50_D1_2_R1


title: HSCbm_50_D1_1_R1


title: HSCbm_10_D1_8_R1


title: HSCbm_10_D1_5_R1


title: HSCbm_10_D1_4_R1


title: HSCbm_10_D1_3_R1


title: HSCbm_10_D1_1_R1


title: HSCbm_10_D1_2_R1


title: HSCbm_1000_D3_R1


title: HSCbm_50_D3_1_R1


title: HSCbm_10_D3_7_R1


title: HSCbm_10_D3_4_R1


title: HSCbm_10_D3_5_R1


title: HSCbm_50_D3_2_R1


title: HSCbm_10_D3_8_R1


title: HSCbm_10_D3_6_R1


title: HSCbm_10_D3_3_R1


title: GMP_50_D3_2_R1

description: Granulocyte macrophage progenitor from peripheral blood

source_name: Granulocyte macrophage progenitor

value: GMP


title: HSCbm_10_D3_1_R1


title: GMP_1000_D3_R1


title: GMP_10_D3_8_R1


title: HSC_1_D4_11_R1

description: Hematopoietic stem cell from cord blood


title: GMP_10_D3_7_R1


title: GMP_50_D3_1_R1


title: GMP_10_D3_5_R1


title: GMP_10_D3_4_R1


title: GMP_10_D3_1_R1


title: GMP_50_D2_2_R1


title: GMP_10_D3_2_R1


title: GMP_50_D2_1_R1


title: GMP_10_D2_8_R1


title: GMP_10_D2_7_R1


title: GMP_10_D2_4_R1


title: GMP_10_D2_1_R1


title: GMP_1000_D1_R1


title: GMP_10_D1_8_R1


title: GMP_50_D1_2_R1


title: GMP_50_D1_1_R1


title: GMP_10_D1_7_R1


title: GMP_10_D3_6_R1


title: GMP_10_D1_6_R1


title: GMP_10_D1_5_R1


title: GMP_10_D1_1_R1


title: GMP_10_D3_3_R1


title: GMP_1_D1_7_R1


title: GMP_10_D1_2_R1


title: GMP_10_D1_3_R1


title: GMP_1_D1_8_R1


title: GMP_1000_D2_R1


title: GMP_1_D1_4_R1


title: GMP_10_D1_4_R1


title: GMP_1_D1_6_R1


title: GMP_1_D1_9_R1


title: GMP_1_D1_22_R1


title: GMP_10_D2_2_R1


title: GMP_10_D2_3_R1


title: GMP_10_D2_6_R1


title: GMP_1_D1_2_R1


title: GMP_10_D2_5_R1


title: GMP_1_D1_20_R1


title: GMP_1_D1_18_R1


title: GMP_1_D1_1_R1


title: GMP_1_D1_16_R1


title: GMP_1_D1_15_R1


title: GMP_1_D1_19_R1


title: GMP_1_D1_14_R1


title: GMP_1_D1_13_R1


title: GMP_1_D1_24_R1


title: CMP_50_D3_2_R1

description: Common myeloid progenitor from peripheral blood

source_name: Common myeloid progenitor

value: CMP


title: GMP_1_D1_23_R1


title: GMP_1_D1_10_R1


title: CMP_1000_D3_R1


title: GMP_1_D1_12_R1


title: GMP_1_D1_5_R1


title: CMP_10_D3_7_R1


title: CMP_10_D3_6_R1


title: CMP_50_D3_1_R1


title: CMP_10_D3_8_R1


title: GMP_1_D1_21_R1


title: CMP_10_D3_4_R1


title: CMP_10_D3_1_R1


title: CMP_10_D3_3_R1


title: CMP_1000_D1_R2


title: CMP_50_D1_2_R2


title: CMP_50_D1_1_R2


title: CMP_10_D1_8_R2


title: GMP_1_D1_17_R1


title: CMP_10_D1_7_R2


title: CMP_10_D1_5_R2


title: CMP_10_D1_6_R2


title: CMP_10_D1_3_R2


title: CMP_10_D1_4_R2


title: CMP_10_D1_2_R2


title: CMP_10_D1_1_R2


title: CMP_1000_D2_R2


title: CMP_50_D2_2_R2


title: CMP_10_D2_8_R2


title: CMP_50_D2_1_R2


title: CMP_10_D2_6_R2


title: CMP_10_D2_7_R2


title: CMP_10_D3_2_R1


title: CMP_1_D2_7_R1


title: CMP_10_D2_5_R2


title: CMP_1_D2_9_R1


title: CMP_10_D3_5_R1


title: CMP_10_D2_4_R2


title: CMP_1_D2_5_R1


title: CMP_10_D2_2_R2


title: CMP_1_D2_2_R1


title: CMP_10_D2_3_R2


title: CMP_1_D2_23_R1


title: CMP_10_D2_1_R2


title: CMP_1_D2_8_R1


title: CMP_1_D2_6_R1


title: CMP_1_D2_3_R1


title: CMP_1_D2_4_R1


title: CMP_1_D2_21_R1


title: CMP_1_D2_20_R1


title: CMP_1_D2_18_R1


title: CMP_1_D2_1_R1


title: CMP_1_D2_14_R1


title: CMP_1_D2_12_R1


title: CMP_1_D2_11_R1


title: CMP_1_D2_15_R1


title: CLP_50_D3_2_R1

description: Common lymphoid progenitor from peripheral blood

source_name: Common lymphoid progenitor

value: CLP


title: CLP_50_D3_1_R1


title: CMP_1_D2_10_R1


title: CLP_1000_D3_R1


title: CLP_10_D3_8_R1


title: CLP_10_D3_7_R1


title: CMP_1_D2_13_R1


title: CLP_10_D3_6_R1


title: CLP_1000_D2_R1


title: CLP_10_D3_3_R1


title: CLP_10_D3_5_R1


title: CLP_10_D2_7_R1


title: CLP_50_D2_2_R1


title: CLP_10_D3_2_R1


title: CLP_10_D3_1_R1


title: CLP_50_D2_1_R1


title: CLP_10_D2_4_R1


title: CLP_10_D2_2_R1


title: CLP_10_D2_6_R1


title: CLP_10_D2_5_R1


title: CLP_10_D2_3_R1


title: CLP_10_D2_8_R1


title: CLP_10_D3_4_R1


title: CLP_10_D1_8_R2


title: CLP_10_D1_7_R2


title: CLP_10_D1_3_R2


title: CLP_10_D1_2_R2


title: CLP_10_D1_6_R2


title: CLP_10_D1_4_R2


title: CLP_10_D1_1_R2


title: CLP_1_D1_9_R1


title: CLP_10_D1_5_R2


title: CLP_1_D1_7_R1


title: CLP_1_D1_6_R1


title: CLP_50_D1_2_R2


title: CLP_1_D1_2_R1


title: CLP_1_D1_22_R1


title: CLP_1_D1_20_R1


title: CLP_1_D1_1_R1


title: CLP_1_D1_5_R1


title: CLP_1_D1_23_R1


title: CLP_1_D1_3_R1


title: CLP_1_D1_16_R1


title: CLP_1_D1_4_R1


title: CLP_1_D1_17_R1


title: CLP_50_D1_1_R2


title: CLP_1_D1_18_R1


title: CLP_1_D1_15_R1


title: CLP_1000_D1_R2


title: CLP_10_D2_1_R1


title: CLP_1_D1_13_R1


title: CLP_1_D1_19_R1


title: CD8_1000_D3_R1

description: CD8+ T cell from peripheral blood

source_name: CD8+ T cell


title: CD8_1000_D1_R1

description: CD8+ T cell from peripheral blood


title: CLP_1_D1_10_R1


title: CLP_1_D1_11_R1


title: CD4_1000_D3_R1

description: CD4+ T cell from peripheral blood

source_name: CD4+ T cell


title: CD4_1000_D2_R1

description: CD4+ T cell from peripheral blood


title: CD4_1000_D1_R1

description: CD4+ T cell from peripheral blood


title: CD8_1000_D2_R1

description: CD8+ T cell from peripheral blood


title: Bcell_1000_D1_R1

description: B cell from peripheral blood

source_name: B cell

value: Bcell


title: Bcell_1000_D3_R1

description: B cell from peripheral blood


title: CLP_1_D1_24_R1

value: M


title: RNA_D1_MLP3_100

library_source: transcriptomic

data_processing:
After de-multiplexing and adapter removal, we aligned reads using Bowtie v 1.1.1 (parameters: -q -p 6 -a -m 100 --minins 0 --maxins 5000 --fr --sam --chunkmbs 200) to the Ensembl cDNA reference. We used BitSeq (v 1.12.0) to quantify transcript levels.
Genome_build: hg38

molecule: polyA RNA

extract_protocol:
SMART-seq2
SMART-seq2


title: RNA_D1_MLP1_100


title: RNA_D1_HSCbm_100


title: RNA_D2_MLP1_100


title: RNA_D1_MPP_100

source_name: Multipotent progenitor

value: MPP


title: RNA_D1_MLP0_100


title: Bcell_1000_D2_R1

description: B cell from peripheral blood


title: RNA_D1_HSC_100


title: RNA_D2_CMP_100


title: RNA_D1_CLP_100


title: RNA_D1_GMP_100


title: RNA_D2_GMP_100


title: RNA_D1_MLP2_100


title: RNA_D2_MPP_100


title: CLP_1_D1_14_R1


title: KYSE520

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

hyb_protocol: According to manufacture’s instructions, labeled RNA was hybridized on the Human miRNA Oligo chip for 16 hour at 32˚C.

scan_protocol: A Human miRNA Oligo chip was scanned using ProScanArray (PerkinElmer).

data_processing: mean

label_protocol: According to manufacture’s instructions, 500 ng of total RNA was labeled with Hy5.

growth_protocol: KYSE cell lines were maintained in Ham’s F-12/RPMI 1640 (Invitrogen, San Diego, CA) containing 5% fetal bovine serum at 37 ˚C in a fully-humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted by the acid guanidinium thiocyanate-phenol-chloroform method.

value: human esophageal squamous cell carcinoma


title: KYSE960


title: KYSE890

hyb_protocol: According to manufacture’s instructions, labeled  RNA was hybridized on the Human miRNA Oligo chip for 16 hour at 32˚C.


title: KYSE450


title: A2780 cells infected with FAL-1 shRNA1

status: Public on Nov 05 2016

city: Philadelphia

first: Lin

state: PA

address: 3400 CIVIC CENTER BLVD BUILDING 421

institute: University of Pennsylvania

description: Gene expression data from FAL-1 shRNA1 cells

hyb_protocol: After fragmentation, 5.5 ug of cDNA was hybridized to a Affymetrix GeneChip® Human Gene 1.0 ST array for 16hr according to the manufacturer’s protocol.

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

data_processing: The data were analyzed using BRB-ArrayTools. The raw data were processed with the RMA algorithm.

source_name: Human ovarian cancer cell line

label_protocol: Total RNA was amplified and converted to cDNA using  WT Expression Kit (Ambion) according to the manufacturer’s instructions. The single stranded cDNA was fragmented and labeled using Affymetrix GeneChip® WT Terminal Labeling Kit according to the manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum

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

treatment_protocol: A2780 cells were transducted with ctrl shRNA, BMI1 shRNAs and FAL-1 shRNAs respectively. 96 hours later, cells were harvested for RNA extraction.

value: ovarian cancer cell line

tag: infection

value: FAL-1 shRNA1


title: A2780 cells infected with FAL-1 shRNA2

description: Gene expression data from FAL-1 shRNA2 cells

value: FAL-1 shRNA2


title: 360_PlaaG23V/G23V_Mutant

city: Edinburgh

first: Emma

middle: A

last: Hall

state: Midlothian

address: Western General Hospital, Crewe Road

department: University of Edinburgh

institute: MRC HGU, IGMM

description: RMA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: The hybridization was performed according to the GeneChip Whole Transcript (WT) Assay Manual

scan_protocol: The arrays were scanned using a GeneChip Scanner 3000 system (Affymetrix)

data_processing: The data were analysed using the Affymetrix Expression Console v.1.4.1

source_name: Caudal Brain PlaaG23V/G23V Mutant

label_protocol: The cDNA was labelled using the WT PLUS kit (Affymetrix) according to the GeneChip Whole Transcript (WT) Assay Manual

extract_protocol: Total RNA was extracted using Qiagen RNAeasy Lipid mini kits; including on-column DNAse digestion as per manufacter’s direction.

tag: genotype

value: Caudal brain (including cerebellum and hindbrain)

value: Male

tag: age of animal

value: 75 days


title: A2780 cells infected with FAL-1 Ctrl

description: Gene expression data from FAL-1 Ctrl cells

value: FAL-1 Ctrl


title: 363_PlaaG23V/G23V_Mutant

value: Female


title: patient no 382 tumor sample at III grade_ biological_rep1

city: Kraków

first: Paulina

last: Marona

state: Lesser

address: Gronostajowa 7

department: Department of General Biochemistry

country: Poland

institute: Jagiellonian University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on Affymetrix HuGene2.1 ST Array Strp. Arrays were washed and stained in the Affymetrix Gene Atlas Fluidics Station.

scan_protocol: Affymetric HuGene2.1 ST Array Strips were scanned using the GeneAtlas Imaging Station (S/N 91001280).

data_processing: The data were normalized with Expression Console Software 1.4.1 with RMA algorithm and analyse using Affymetrix Transcriptom Analysis Console (TAC) Software 3.1 with ANOVA one-way between subjects (unpaired)

source_name: human tumor sample in third stage of cancer

label_protocol: 100 ng of total RNA were used to synthesis and amplification of ss-cDNA, then samples were fragmented and labeled with biotin. Each step was performed according to Affymetrix GeneChip WT PLUS Reagent Kit Manual (2013 Affymetrix, P/N 703174 Rev. 2)

extract_protocol: total RNA was extracted using Eurx Universal RNA Purification Kit (EURx) according to manufacturer protocol. The quantity of ribosomal RNA and DNA contamination was examined using electrophoresis in 1% denaturing formaldehyde gel. Concentration of total RNA was assessed using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).

value: clear cell renal cell carcinoma

tag: Stage

value: third

value: male

tag: age


title: A2780 cells infected with BMI1 shRNA1

description: Gene expression data from BMI1 shRNA1 cells

value: BMI1 shRNA1


title: patient no 404 tumor sample at III grade_ biological_rep1

value: female


title: A2780 cells infected with BMI1 shRNA2

description: Gene expression data from BMI1 shRNA2 cells

value: BMI1 shRNA2


title: patient no 430_1 tumor sample at III grade_ biological_rep1


title: patient no 389 tumor sample at III grade_ biological_rep1


title: patient no 457 tumor sample at II grade_ biological_rep1

source_name: human tumor sample in second stage of cancer

value: second


title: 359_Plaa+/+_Wild_Type

source_name: Caudal Brain Plaa+/+ Wild Type

value: Plaa+/+


title: 362_Plaa+/+_Wild_Type


title: 262_PlaaG23V/G23V_Mutant

value: 81 days


title: A2780 cells infected with BMI1 Ctrl

description: Gene expression data from BMI1 Ctrl cells

value: ovarian cancer cell line

value: BMI1 Ctrl


title: patient no 452_3 tumor sample at IV grade_ biological_rep1

source_name: human tumor sample in fourth stage of cancer

value: fourth


title: patient no 455 tumor sample at II grade_ biological_rep1


title: patient no 399a tumor sample at II grade_ biological_rep1


title: patient no 465 tumor sample at I grade_ biological_rep1

source_name: human tumor sample in first stage of cancer

value: first


title: 261_Plaa+/+_Wild_Type

value: Caudal brain (including cerebellum and hindbrain)


title: patient no 228 tumor sample at IV grade_ biological_rep1


title: patient no 415 tumor sample at IV grade_ biological_rep1


title: patient no 453 tumor sample at I grade_ biological_rep1


title: patient no 397 tumor sample at I grade_ biological_rep1


title: patient no 398 tumor sample at IV grade_ biological_rep1


title: Primary DRG neurons subjected with 100μM MTR1B agonist 8-M-PDOT

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

description: Sample name = 3

hyb_protocol: 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 (Arraystar Flash RNA Labeling Kit, Arraystar). 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. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 x Blocking Agent and 1 μl of 25 x Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 x 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.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

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 using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 1 out of 4 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed lncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.
The 1, 2 and 3 groups represent the primary DRG neurons subjected with vehicle, 1mM melatonin and 100μM MTR1B agonist 8-M-PDOT, respectively. The ID_REFs represent the 35,923 lncRNAs and 24,881 coding transcripts that can be detected by our third-generation lncRNA microarray.

source_name: Primary DRG neurons, 8-M-PDOT

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.

growth_protocol: The neonatal mouse DRG neurons were isolated using the Felix methods (Gandini, M.A., A. Sandoval, and R. Felix, Whole-cell patch-clamp recordings of Ca2+ currents from isolated neonatal mouse dorsal root ganglion (DRG) neurons. Cold Spring Harb Protoc, 2014. 2014(4): p. 389-95.). The mice of 5-9d were decapitated using surgical scissors. Place the mice in a prone position and make a longitudinal incision with the mini dissecting scissors to expose cervical, thoracic, and lumbar regions of the vertebral column. A midline incision was made through the first vertebral arch and extend the cut along the vertebral column to expose the spinal cord. Using fine forceps, the spinal cord was carefully pulled away and DRGs were removed from the vertebral column. Firmly hold the DRGs with forceps and tug them gently. Place the DRGs into a 35 mm Petri dish containing 2ml of Advanced Dulbecco modified Eagle medium (DMEM). Transfer the DRGs to the dissociating medium solution and incubate for 40 min at 37˚C with 5% CO2 in air and at 80% relative humidity. Dissociate the cells using a fire-polished glass Pasteur pipette. Centrifuge the cell solution for 2min at 300r/min at room temperature. Discard the supernatant and add 1 ml of Advanced DMEM. Seed the cell suspension on coverslips coated with poly-L-lysine and add 1 ml of culture medium for DRG neurons. Incubate for at least 3h at 37˚C with 5% CO2 in air and at 80% relative humidity. These culture conditions should maintain neurons under optimal conditions for up to 7 d.

extract_protocol: Total RNA was extracted from each sample using TRIzol Reagent (Life Technologies, USA) according to the protocol from manufacturer. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).

treatment_protocol: The DRG neurons were cultivated for 5 days and the culture medium was renewed. The experimental agents of 1mM melatonin, 100μM melatonin membrane receptor 1B (MTR1B) agonist 8-M-PDOT or vehicle (1% ethanol of normal saline) were added into the medium directly for 24 h incubation.

tag: strain/background

value: normal primary dorsal root ganglia (DRG) neurons

tag: treatment

value: 100uM melatonin receptor 1B (MTR1B) agonist 8-M-PDOT


title: Primary DRG neurons subjected with vehicle (1% ethanol of normal saline)

description: Sample name = 1

source_name: Primary DRG neurons, vehicle

tag: cell type

value: vehicle (1% ethanol of normal saline)


title: E2

city: Galveston

first: Robin

last: Stephens

state: Texas

address: 301 University Blvd

department: Infectious Diseases

institute: UTMB

hyb_protocol: Cyanine-3 (Cy3)-labeled cDNA of the sample (0.6 µg) was hybridized onto Agilent SurePrint G3 Mouse Gene Expression Microarray (8x60K) using Agilent’s Gene Expression Hybridization Kit. Hybridization was performed for 17h, rotating at a speed of 10rpm at 65? in an Agilent hybridization oven.

scan_protocol: After hybridization, microarrays were washed for 1 minute at room temperature with Wash Buffer 1 and 1 minute at 37? with Wash buffer 2.  Microarrays were scanned with Agilent Microarray Scanner and the fluorescence intensities were quantified.

data_processing: Array Raw data files were loaded into R version 2.12.1 to process data analysis.

source_name: Splenic CD4 T cells

label_protocol: 0.1 µg of total RNA was amplified and labeled using Agilent's Low Input Quick Amp Labeling Kits. Dye incorporation and aRNA yield were checked using the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: B5 TCR Tg mice (BALB/cJ) were infected with Plasmodium chabaudi.

extract_protocol: RNA was isolated and processed according to Agilent Array protocol (PhalanxBio, Inc, San Diego, CA).

treatment_protocol: Splenic CD4 T cells from naive or infected B5 TCR Tg mice ( 5- to 12-wks-old) were enriched by EasySep biotin selection kit (Stemcell Technologies, Vancouver, BC, Canada) with a mixture of biotinylated anti-CD8a, B220 (RA3-6B2), CD11b (MI/70), CD11c (N418), F4/80 (BM8), and Ter119 (eBioscience). The negative fraction was then stained with anti-CD4-FITC, CD44-allophycocyanin-Cy7, CD127-PE, anti CD62L PE-TxRd and CD27 APC for the subsets. Cells were sorted on a FACS Aria with FACDiva software (BDbiosciences, San Diego, CA). Effector (CD44int-hi CD127neg) and memory (CD44hi CD127hi) subsets were sorted on d8 and d60 post-infection, respectively.

tag: strain

value: B5 TCR Tg mice (BALB/cJ)

tag: subset group

value: Early Effector (E, CD62Lhi CD27hi)

value: day 8 post P. chabaudi-infection


title: NE1

value: Naïve T cells (N, CD4+ CD44lo CD25-)

value: uninfected


title: TM2

value: Central Memory (TM, CD62Lhi CD27hi)


title: patient no 387 tumor sample at I grade_ biological_rep1

value: clear cell renal cell carcinoma

value: female


title: I2

value: Intermetiate Effector (I, CD62Llo CD27hi)


title: L2

value: Late Effector (L, CD62Llo CD27lo)


title: TL2

value: Effector memory Late (TL , CD62Llo CD27lo)


title: TE1

value: Effector memory Early (TE, CD62Llo CD27hi)


title: Primary DRG neurons subjected with 1mM melatonin

description: Sample name = 2

source_name: Primary DRG neurons, melatonin

value: 1mM melatonin


title: L1


title: NE2


title: TL1


title: I1


title: MG1363_Hexanol_5min_Rep1

status: Public on Nov 04 2016

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

department: DTU Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hydridzation according to Aglient Protocol. Aglient 8x15k custom microarray G2509F

scan_protocol: Aglient technologies scanner G2505C. Aglient’s Feature Extraction Software

data_processing: Quantile normalization

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: MG1363, Hexanol (2 mg/ml), 5 min, Biological Replica 1

label_protocol: Labbeling according to aglient protocol using random hexamer and Cy3

growth_protocol: Exponentially growing strains in SA medium with 1% glucose and 2 ug/ml lipoic acid. Alcohol stress (Ethanol 55 mg/ml, butanol 10mg/ml, or hexanol 2 mg/ml) were added following harvesting the references and the stressed cultures were harvested after 5 min and 60 min

extract_protocol: Cells were pelleted by centrifugation and washed in ice cold salin water (0.9% NaCl). RNA was extracted by the hot phenol method

treatment_protocol: Growth was stopped immidiately by transfer of 10 ml culture sample into a glass flask precolled on ice followed rapid swirling

value: Hexanol (2 mg/ml), 5 min


title: MG1363_Ref_Rep3

source_name: MG1363, Reference, Biological Replica 3

value: Reference


title: TE2


title: TM1


title: MG1363_Ref_Rep1

source_name: MG1363, Reference, Biological Replica 1


title: MG1363_Ref_Rep2

source_name: MG1363, Reference, Biological Replica 2


title: MG1363_Ethanol_60min_Rep1

source_name: MG1363, Ethanol (55 mg/ml), 60 min, Biological Replica 1

value: Ethanol (55 mg/ml), 60 min


title: MG1363_Ethanol_5min_Rep1

source_name: MG1363, Ethanol (55 mg/ml), 5 min, Biological Replica 1

value: Ethanol (55 mg/ml), 5 min


title: PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre), biological rep2

city: Ann arbor

first: Lei

last: Sun

state: MI

address: 109 Zina Pitcher Place, BSRB 4478

department: Pediatrics

institute: University of Michigan

description: gene expression data from PP2ACαfl/fl;lyM-Cre (myeloid specific knockout of PP2ACα exon1) bone marrow derived macrophages

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse ST 2.1 Array strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values

source_name: LPS-stimulated PP2ACα knockout BMDM (PP2ACαfl/fl;lyM-Cre)

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Bone marrow derived macrophages were cultured in RPMI medium supplemented with L-cell supernatant in vitro for 6 days

extract_protocol: RNA was isolated with Trizol method and purified with RNeasy Kit (Qiagen).

treatment_protocol: 100 ng/ml LPS for 2 hours

value: Bone marrow derived macrophages

value: PP2ACα knockout (PP2ACαfl/fl;lyM-Cre)