title: CD14+CD16++ monocytes, SIV infection at necropsy with AIDS, biological rep 2

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 118 post-SIV infection

source_name: peripheral blood monocytes, CD14+CD16++, at necropsy with AIDS


title: CD14+CD16++ monocytes, before SIV infection, biological rep 1

status: Public on May 10 2017

type: RNA

city: Chestnut Hill

first: Kenneth

middle: C

last: Williams

state: MA

address: 140 Commonwealth Ave

department: Biology

country: USA

institute: Boston College

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, pre-SIV infection

hyb_protocol: 20 ug of fragmented cRNA was hybridized with a preequilibrated Affymetrix GeneChip Rhesus Macaque Genome Array at 45°C for 16 hours

scan_protocol: GeneChips were scanned in an HP ChipScanner

data_processing: The data were analyzed with Partek Express Genomics Suite software. The data were normalized by using a robust multi-chip average (RMA) algorithm.

label: biotin

molecule: total RNA

organism: Macaca mulatta

source_name: peripheral blood monocytes, CD14+CD16++, pre-SIV infection

label_protocol: Biotinylated cRNA was prepared using the BioArray High Yield RNA Transcript Labeling kit from Enzo Diagnostics according to the manufacturer's instructions

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) according to the manufacturer’s instructions

treatment_protocol: Mononuclear cells were isolated from 10mL EDTA treated whole blood by density gradient centrifugation over Ficoll-Hypaque and stained for 15 minutes with anti-CD14-PacificBlue, anti-CD16-PE, anti-HLA-DR-PerCP-Cy-5.5, anti-CD3-FITC, and anti-CD20-APC in PBS containing 2% FBS. Monocytes were isolated by forward and side scatter characteristics and HLA-DR+CD3-CD20-CD14+ expression and sorted by FACS into subpopulations by CD14 and CD16 expression. Sorted monocytes were washed in PBS and vacuum pelleted.

tag: animal number

tag: stage of siv infection

value: pre-SIV infection

tag: cell type

value: sorted CD14+CD16++ peripheral blood monocytes


title: CD14++CD16+ monocytes, before SIV infection, biological rep 4

description: Gene expression data from sorted CD14++CD16+ rhesus macaque peripheral blood monocytes, pre-SIV infection

source_name: peripheral blood monocytes, CD14++CD16+, pre-SIV infection

value: sorted CD14++CD16+ peripheral blood monocytes


title: CD14++CD16+ monocytes, day 26 post-SIV infection, biological rep 2

description: Gene expression data from sorted CD14++CD16+ rhesus macaque peripheral blood monocytes, day 26 post-SIV infection

source_name: peripheral blood monocytes, CD14++CD16+, day 26 post-SIV infection

value: day 26 post-SIV infection


title: CD14++CD16+ monocytes, SIV infection at necropsy with AIDS, biological rep 3

description: Gene expression data from sorted CD14++CD16+ rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 75 post-SIV infection

source_name: peripheral blood monocytes, CD14++CD16+, at necropsy with AIDS


title: CD14++CD16+ monocytes, before SIV infection, biological rep 3


title: CD14+CD16++ monocytes, SIV infection at necropsy with AIDS, biological rep 1

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 91 post-SIV infection


title: CD14++CD16- monocytes, day 26 post-SIV infection, biological rep 1

description: Gene expression data from sorted CD14++CD16- rhesus macaque peripheral blood monocytes, day 26 post-SIV infection

source_name: peripheral blood monocytes, CD14++CD16-, day 26 post-SIV infection

value: sorted CD14++CD16- peripheral blood monocytes


title: CD14++CD16+ monocytes, before SIV infection, biological rep 1


title: CD14++CD16+ monocytes, SIV infection at necropsy with AIDS, biological rep 2

description: Gene expression data from sorted CD14++CD16+ rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 118 post-SIV infection


title: CD14++CD16- monocytes, day 26 post-SIV infection, biological rep 4


title: CD14++CD16- monocytes, before SIV infection, biological rep 4

description: Gene expression data from sorted CD14++CD16- rhesus macaque peripheral blood monocytes, pre-SIV infection

source_name: peripheral blood monocytes, CD14++CD16-, pre-SIV infection


title: CD14++CD16+ monocytes, day 26 post-SIV infection, biological rep 3


title: CD14++CD16+ monocytes, SIV infection at necropsy with AIDS, biological rep 1

description: Gene expression data from sorted CD14++CD16+ rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 91 post-SIV infection


title: CD14++CD16- monocytes, SIV infection at necropsy with AIDS, biological rep 2

description: Gene expression data from sorted CD14++CD16- rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 118 post-SIV infection

source_name: peripheral blood monocytes, CD14++CD16-, at necropsy with AIDS


title: CD14++CD16+ monocytes, day 26 post-SIV infection, biological rep 1


title: CD14++CD16- monocytes, before SIV infection, biological rep 1


title: CD14++CD16+ monocytes, before SIV infection, biological rep 2


title: CD14++CD16- monocytes, day 26 post-SIV infection, biological rep 2


title: CD14++CD16+ monocytes, day 26 post-SIV infection, biological rep 4


title: CD14++CD16- monocytes, SIV infection at necropsy with AIDS, biological rep 1

description: Gene expression data from sorted CD14++CD16- rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 91 post-SIV infection


title: CD14++CD16- monocytes, SIV infection at necropsy with AIDS, biological rep 3

description: Gene expression data from sorted CD14++CD16- rhesus macaque peripheral blood monocytes, at necropsy with AIDS day 75 post-SIV infection


title: CD14++CD16- monocytes, before SIV infection, biological rep 3


title: CD14+CD16++ monocytes, day 26 post-SIV infection, biological rep 3

description: Gene expression data from sorted CD14+CD16++ rhesus macaque peripheral blood monocytes, day 26 post-SIV infection

source_name: peripheral blood monocytes, CD14+CD16++, day 26 post-SIV infection


title: CD14++CD16- monocytes, day 26 post-SIV infection, biological rep 3


title: CD14++CD16- monocytes, before SIV infection, biological rep 2


title: metM-Wnt (lung) Replicate 2

city: Chapel ill

first: Stephen

middle: D

last: Hursting

state: NC

address: 135 Dauer Drive

institute: University of North Carolina at Chapel Hill

description: NIH 3T3 cells, control

hyb_protocol: Sample and Reference RNA were co-hybridized to an Agilent Mouse Oligo Microarray (GPL11383)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and normalization.

organism: Mus musculus

source_name: metM-Wnt mammary tumor cells

label_protocol: 0.5 µg was reverse trascribed, amplified and labelled using the Low Input Quick Amp labeling kit, according to manufacturer's instructions

growth_protocol: Cells were grown to 75% confluency in RPMI supplemented with 10% FBS, 2mM Glutamine and 100u/ml penicillin/streptomycin

extract_protocol: Total RNA was extracted using Rneasy Mini Kit according to manufacturer's conditions

tag: cell line

value: metM-Wnt (lung)

tag: age

tag: tissue

value: lung metastasis

tag: strain

source_name: NIH3T3 cells

value: NIH/Swiss

value: unknown

value: embryonic fibroblasts


title: miRNA_986_S10nM_1

status: Public on May 09 2017

city: Lille

first: Odile

last: Poulain-Godefroy

address: 1, rue du Pr Calmette

department: Center for Infection and Immunity of Lille (CIIL)

country: France

institute: Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10nM of bisphenol S

hyb_protocol: For mRNA samples, a total of 600 ng of cRNA was fragmented and hybridized overnight at 65 °C. The purified labeled miRNAs were prepared with 10 × Blocking Agent and 2 × Hi-RPM hybridization buffer and incubated with the array in hybridization chambers (Agilent) for 20 hours at 55 °C. The slides were then washed as described in the protocol. The efficiency of the hybridization procedure was verified with the Agilent miRNA Spike-in Kit.

scan_protocol: Microarrays were run on a SureScan microarray scanner (Agilent Technologies). Raw data were acquired with Feature Extraction Software (ver. 10.7.3.1). Calculation of the total gene signal for each miRNA replicated probe subtracted background signals.

data_processing: After a preliminary between-array normalization, unexpressed probes were filtered out according to detection pvalues. Expression values were normalized with housekeeping genes for mRNA and estimated using a linear model to take into account the probe affinity over the 30 probes characterizing each one of the miRNA. All analyses were performed using R (packages Limma and AgiMicroRna).

organism: Homo sapiens

source_name: miRNA, patient 986, bisphenol S 10nM, replicate 1

label_protocol: 100 ng of total RNA per sample were dephosphorylated by incubation with a calf intestinal phosphatase at 37 °C for 30 min and denatured with 100% DMSO at 100 °C for 7 min. They were then labeled with Cyanine 3-pCp at 16°C for 2 hours, with a T4 ligase. Micro Bio-Spin 6 chromatography columns (Bio-Rad Laboratories, Hercules, CA) were used to purify the labeled RNA. The efficiency of the labeling procedure was verified with the Agilent miRNA Spike-in Kit.

growth_protocol: Primary human white subcutaneous pre-adipocytes were cultured in PBM-2 medium. Confluent pre-adipocytes were induced to differentiate with PBM-2 medium supplemented with insulin, dexamethasone, IBMX and indomethacin (all supplied by Lonza) for ten days according to the instructions of the manufacturer.

extract_protocol: Specific kits (Kit Small & Large RNA; Macherey Nagel) were used to extract all species of RNAs. The RNA concentration was determined by absorbance at 260 nm (A260), and the purity was estimated by determining the A260/A230 ratio with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). RNA Integrity Number (RIN) was assessed with a Bioanalyzer (Agilent). This kit allowed the extraction of small and large RNAs with no degradation (RIN>9).

treatment_protocol: They were induced to differentiate into adipocytes with either vehicle (DMSO) or the selected chemical (BPA, BPF, BPS) at 10nM or 10µM.

tag: patient id

value: Adipocyte

tag: treatment

value: BPS

tag: concentration


title: miRNA_348_S10nM_2

source_name: miRNA, patient 348, bisphenol S 10nM, replicate 2


title: miRNA_986_S10nM_2

source_name: miRNA, patient 986, bisphenol S 10nM, replicate 2


title: 2 (suppression of LRH-1 in HepG2)

city: Shenzhen

first: Xiao

last: Lijia

address: Xinhu road 1333

country: China

institute: Shenzhen Hospital of Southern Medical University

description: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 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 v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 2 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: HepG2 with suppression of LRH-1 expression

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HepG2 is cultured in conventional media according to the original suppliers’ instructions.

treatment_protocol: LRH-1 exression in HepG2 is supprssed by TALENs in treatment group

value: liver cancer cell line HepG2

tag: genotype/variation


title: miRNA_899_S10nM_2

source_name: miRNA, patient 899, bisphenol S 10nM, replicate 3


title: miRNA_348_S10nM_1

source_name: miRNA, patient 348, bisphenol S 10nM, replicate 1


title: miRNA_899_S10μM_2

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10μM of bisphenol S

source_name: miRNA, patient 899, bisphenol S 10μM, replicate 2


title: metM-Wnt (liver) Replicate 1

description: NIH 3T3 cells, control

value: metM-Wnt (liver)

value: liver metastasis


title: miRNA_899_S10μM_1

source_name: miRNA, patient 899, bisphenol S 10μM, replicate 1


title: metM-Wnt (lung) Replicate 1

description: NIH 3T3 cells, control


title: miRNA_986_S10μM_1

source_name: miRNA, patient 986, bisphenol S 10μM, replicate 1


title: miRNA_348_S10μM_2

source_name: miRNA, patient 348, bisphenol S 10μM, replicate 2


title: M-Wnt Replicate 1

description: NIH 3T3 cells, control

source_name: M-Wnt mammary tumor cells

value: M-Wnt

value: mammary tumor


title: 1 (HepG2)

source_name: HepG2 parental

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: control


title: M-Wnt Replicate 3

description: NIH 3T3 cells, control


title: miRNA_348_F10nM_2

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10nM of bisphenol F

source_name: miRNA, patient 348, bisphenol F 10nM, replicate 2

value: BPF


title: miRNA_348_F10nM_1

source_name: miRNA, patient 348, bisphenol F 10nM, replicate 1


title: miRNA_986_F10μM_2

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10μM of bisphenol F

source_name: miRNA, patient 986, bisphenol F 10μM, replicate 2


title: miRNA_899_S10nM_1

source_name: miRNA, patient 899, bisphenol S 10nM, replicate 2


title: miRNA_986_F10nM_1

source_name: miRNA, patient 986, bisphenol F 10nM, replicate 1


title: miRNA_899_F10nM_2

source_name: miRNA, patient 899, bisphenol F 10nM, replicate 2


title: M-Wnt Replicate 2

description: NIH 3T3 cells, control

source_name: NIH3T3 cells


title: miRNA_899_F10μM_2

source_name: miRNA, patient 899, bisphenol F 10μM, replicate 2


title: miRNA_348_S10μM_1

source_name: miRNA, patient 348, bisphenol S 10μM, replicate 1


title: miRNA_986_F10μM_1

source_name: miRNA, patient 986, bisphenol F 10μM, replicate 1


title: miRNA_899_F10nM_1

source_name: miRNA, patient 899, bisphenol F 10nM, replicate 1


title: miRNA_986_S10μM_2

source_name: miRNA, patient 986, bisphenol S 10μM, replicate 2


title: metM-Wnt (lung) Replicate 3

description: NIH 3T3 cells, control

source_name: metM-Wnt mammary tumor cells


title: miRNA_899_F10μM_1

source_name: miRNA, patient 899, bisphenol F 10μM, replicate 1


title: miRNA_348_F10μM_1

source_name: miRNA, patient 348, bisphenol F 10μM, replicate 1


title: miRNA_986_A10nM_2

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10nM of bisphenol A

source_name: miRNA, patient 986, bisphenol A 10nM, replicate 2

value: BPA


title: miRNA_348_A10nM_1

source_name: miRNA, patient 348, bisphenol A 10nM, replicate 1


title: miRNA_899_A10nM_1

source_name: miRNA, patient 899, bisphenol A 10nM, replicate 2


title: miRNA_348_F10μM_2

source_name: miRNA, patient 348, bisphenol F 10μM, replicate 2


title: miRNA_986_A10nM_1

source_name: miRNA, patient 986, bisphenol A 10nM, replicate 1


title: miRNA_899_A10μM_2

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation with 10μM of bisphenol A

source_name: miRNA, patient 899, bisphenol A 10μM, replicate 2


title: miRNA_899_A10μM_1

source_name: miRNA, patient 899, bisphenol A 10μM, replicate 1


title: miRNA_986_A10μM_2

source_name: miRNA, patient 986, bisphenol A 10μM, replicate 2


title: miRNA_899_A10nM_2

source_name: miRNA, patient 899, bisphenol A 10nM, replicate 3


title: miRNA_348_A10nM_2

source_name: miRNA, patient 348, bisphenol A 10nM, replicate 3


title: miRNA_986_A10μM_1

source_name: miRNA, patient 986, bisphenol A 10μM, replicate 1


title: miRNA_986_Df_3

description: miRNA profiling of human primary adipocytes after 10 days of diffentiation

source_name: miRNA, patient 986, adipocyte, replicate 3


title: miRNA_986_Df_1

source_name: miRNA, patient 986, adipocyte, replicate 1


title: miRNA_348_A10μM_1

source_name: miRNA, patient 348, bisphenol A 10μM, replicate 1


title: miRNA_986_Df_4

source_name: miRNA, patient 986, adipocyte, replicate 4


title: miRNA_899_Df_5

source_name: miRNA, patient 899, adipocyte, replicate 6


title: miRNA_986_Df_2

source_name: miRNA, patient 986, adipocyte, replicate 2


title: miRNA_348_Df_5

source_name: miRNA, patient 348, adipocyte, replicate 6


title: miRNA_899_Df_1

source_name: miRNA, patient 899, adipocyte, replicate 1


title: miRNA_899_Df_2

source_name: miRNA, patient 899, adipocyte, replicate 2


title: miRNA_348_A10μM_2

source_name: miRNA, patient 348, bisphenol A 10μM, replicate 2


title: miRNA_899_Df_4

source_name: miRNA, patient 899, adipocyte, replicate 5


title: miRNA_899_Df_3

source_name: miRNA, patient 899, adipocyte, replicate 3


title: miRNA_348_Df_2

source_name: miRNA, patient 348, adipocyte, replicate 2


title: miRNA_348_Df_3

source_name: miRNA, patient 348, adipocyte, replicate 3


title: miRNA_348_Df_4

source_name: miRNA, patient 348, adipocyte, replicate 5


title: miRNA_986_NDf_4

source_name: miRNA, patient 986, pre-adipocyte, replicate 5

value: Pre-adipocyte


title: miRNA_986_NDf_3

description: miRNA profiling of human primary white subcutaneous pre-adipocytes

source_name: miRNA, patient 986, pre-adipocyte, replicate 4


title: miRNA_986_NDf_1

source_name: miRNA, patient 986, pre-adipocyte, replicate 2


title: miRNA_986_NDf_2

source_name: miRNA, patient 986, pre-adipocyte, replicate 3


title: miRNA_348_Df_1

source_name: miRNA, patient 348, adipocyte, replicate 1


title: miRNA_348_NDf_4

source_name: miRNA, patient 348, pre-adipocyte, replicate 6


title: miRNA_348_NDf_5

source_name: miRNA, patient 348, pre-adipocyte, replicate 7


title: miRNA_348_NDf_3

source_name: miRNA, patient 348, pre-adipocyte, replicate 5


title: miRNA_348_NDf_1

source_name: miRNA, patient 348, pre-adipocyte, replicate 2


title: miRNA_899_NDf_2

source_name: miRNA, patient 899, pre-adipocyte, replicate 2


title: miRNA_348_NDf_2

source_name: miRNA, patient 348, pre-adipocyte, replicate 3


title: miRNA_899_NDf_5

source_name: miRNA, patient 899, pre-adipocyte, replicate 6


title: mRNA_986_S10nM_2

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10nM of bisphenol S

source_name: mRNA, patient 986, bisphenol S 10nM, replicate 2


title: mRNA_986_S10μM_2

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10μM of bisphenol S

source_name: mRNA, patient 986, bisphenol S 10μM, replicate 2


title: mRNA_899_S10μM_1

source_name: mRNA, patient 899, bisphenol S 10μM, replicate 1


title: mRNA_348_S10μM_1

source_name: mRNA, patient 348, bisphenol S 10μM, replicate 1


title: mRNA_986_F10nM_1

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10nM of bisphenol F

source_name: mRNA, patient 986, bisphenol F 10nM, replicate 1


title: mRNA_348_S10μM_2

source_name: mRNA, patient 348, bisphenol S 10μM, replicate 2


title: mRNA_348_S10nM_1

source_name: mRNA, patient 348, bisphenol S 10nM, replicate 1


title: mRNA_899_S10μM_2

source_name: mRNA, patient 899, bisphenol S 10μM, replicate 2


title: mRNA_899_S10nM_2

source_name: mRNA, patient 899, bisphenol S 10nM, replicate 2


title: mRNA_348_S10nM_2

source_name: mRNA, patient 348, bisphenol S 10nM, replicate 2


title: mRNA_986_S10μM_1

source_name: mRNA, patient 986, bisphenol S 10μM, replicate 1


title: mRNA_899_S10nM_1

source_name: mRNA, patient 899, bisphenol S 10nM, replicate 1


title: mRNA_986_F10nM_2

source_name: mRNA, patient 986, bisphenol F 10nM, replicate 2


title: mRNA_986_S10nM_1

source_name: mRNA, patient 986, bisphenol S 10nM, replicate 1


title: miRNA_899_NDf_1

source_name: miRNA, patient 899, pre-adipocyte, replicate 1


title: mRNA_899_F10nM_2

source_name: mRNA, patient 899, bisphenol F 10nM, replicate 2


title: mRNA_348_F10nM_1

source_name: mRNA, patient 348, bisphenol F 10nM, replicate 1


title: mRNA_348_F10nM_2

source_name: mRNA, patient 348, bisphenol F 10nM, replicate 2


title: mRNA_986_F10μM_2

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10μM of bisphenol F

source_name: mRNA, patient 986, bisphenol F 10μM, replicate 2


title: mRNA_348_F10μM_2

source_name: mRNA, patient 348, bisphenol F 10μM, replicate 2


title: mRNA_899_F10μM_2

source_name: mRNA, patient 899, bisphenol F 10μM, replicate 2


title: mRNA_986_A10nM_2

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10nM of bisphenol A

source_name: mRNA, patient 986, bisphenol A 10nM, replicate 2


title: mRNA_348_F10μM_1

source_name: mRNA, patient 348, bisphenol F 10μM, replicate 1


title: mRNA_899_F10μM_1

source_name: mRNA, patient 899, bisphenol F 10μM, replicate 1


title: mRNA_899_F10nM_1

source_name: mRNA, patient 899, bisphenol F 10nM, replicate 1


title: mRNA_899_A10nM_2

source_name: mRNA, patient 899, bisphenol A 10nM, replicate 2


title: mRNA_348_A10nM_1

source_name: mRNA, patient 348, bisphenol A 10nM, replicate 1


title: mRNA_986_Df_1

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation

source_name: mRNA, patient 986, adipocyte, replicate 1


title: metM-Wnt (liver) Replicate 2

description: NIH 3T3 cells, control

source_name: metM-Wnt mammary tumor cells

source_name: NIH3T3 cells


title: mRNA_899_A10nM_1

source_name: mRNA, patient 899, bisphenol A 10nM, replicate 1


title: mRNA_348_A10nM_2

source_name: mRNA, patient 348, bisphenol A 10nM, replicate 2


title: mRNA_986_F10μM_1

source_name: mRNA, patient 986, bisphenol F 10μM, replicate 1


title: mRNA_986_Df_4

source_name: mRNA, patient 986, adipocyte, replicate 4


title: mRNA_899_A10μM_2

description: mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10μM of bisphenol A

source_name: mRNA, patient 899, bisphenol A 10μM, replicate 2


title: mRNA_986_Df_2

source_name: mRNA, patient 986, adipocyte, replicate 2


title: mRNA_986_Df_3

source_name: mRNA, patient 986, adipocyte, replicate 3


title: mRNA_986_A10μM_1

source_name: mRNA, patient 986, bisphenol A 10μM, replicate 1


title: mRNA_986_A10μM_2

source_name: mRNA, patient 986, bisphenol A 10μM, replicate 2


title: mRNA_986_A10nM_1

source_name: mRNA, patient 986, bisphenol A 10nM, replicate 1


title: mRNA_899_Df_2

source_name: mRNA, patient 899, adipocyte, replicate 2


title: mRNA_986_NDf_4

description: mRNA profiling of human primary white subcutaneous pre-adipocytes

source_name: mRNA, patient 986, pre-adipocyte, replicate 4


title: mRNA_348_A10μM_1

source_name: mRNA, patient 348, bisphenol A 10μM, replicate 1


title: mRNA_348_Df_4

source_name: mRNA, patient 348, adipocyte, replicate 4


title: mRNA_986_NDf_3

source_name: mRNA, patient 986, pre-adipocyte, replicate 3


title: mRNA_899_A10μM_1

source_name: mRNA, patient 899, bisphenol A 10μM, replicate 1


title: mRNA_899_Df_1

source_name: mRNA, patient 899, adipocyte, replicate 1


title: mRNA_348_A10μM_2

source_name: mRNA, patient 348, bisphenol A 10μM, replicate 2


title: mRNA_348_Df_3

source_name: mRNA, patient 348, adipocyte, replicate 3


title: mRNA_348_Df_1

source_name: mRNA, patient 348, adipocyte, replicate 1


title: mRNA_899_Df_3

source_name: mRNA, patient 899, adipocyte, replicate 3


title: mRNA_986_NDf_2

source_name: mRNA, patient 986, pre-adipocyte, replicate 2


title: mRNA_986_NDf_1

source_name: mRNA, patient 986, pre-adipocyte, replicate 1


title: mRNA_899_NDf_3

source_name: mRNA, patient 899, pre-adipocyte, replicate 3


title: mRNA_899_NDf_2

source_name: mRNA, patient 899, pre-adipocyte, replicate 2


title: mRNA_899_NDf_4

source_name: mRNA, patient 899, pre-adipocyte, replicate 4


title: mRNA_348_NDf_1

source_name: mRNA, patient 348, pre-adipocyte, replicate 1


title: mRNA_348_Df_2

source_name: mRNA, patient 348, adipocyte, replicate 2


title: mRNA_348_NDf_3

source_name: mRNA, patient 348, pre-adipocyte, replicate 3


title: mRNA_348_NDf_2

source_name: mRNA, patient 348, pre-adipocyte, replicate 2


title: mRNA_348_NDf_4

source_name: mRNA, patient 348, pre-adipocyte, replicate 4


title: CRISPR screen

status: Public on May 06 2017

type: SRA

city: Philadelphia

first: Jian

last: Huang

state: PA

address: 3500 N Broad St

department: 9Department of Pathology and Laboratory Medicine

institute: Temple University

description: sgRNA library screen

library_source: genomic

data_processing:
Fastqc was used for raw data quality control.
Cutadapt was used to remove adaptors and unsed primer sequence.
Bowtie was used for gRNA mapping to GeCKO library purchased from Addgene (#1000000048)
Number of unique gRNAs mapped to the same gene and total gRNA number mapped to given gene were extracted from mapping sam files using customized perl script.
The enrichment score were calculated by (sgRNA number from the reads) / (sgRNA number in the library) X log2(average abundance).

molecule: genomic DNA

growth_protocol: MV4-11 cells were maintained in RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
After treatment with AC220,genomic DNA was extracted with DNeasy Blood & Tissue Kit from Qiagen (69504)
sgRNAs were amplified and appended with Illumina adaptors.
DNA-Seq

treatment_protocol: MV4-11 cells were treated with AC220 at 3nM for 14 days.

tag: sample type

value: CRISPR screen


title: mRNA_899_Df_4

source_name: mRNA, patient 899, adipocyte, replicate 4


title: mRNA_899_NDf_1

source_name: mRNA, patient 899, pre-adipocyte, replicate 1


title: Undifferentiated C6 glioma

city: Seoul

first: Jinsoo

last: Oh

address: Yonsei-ro, Shinchon-dong, Seodaemoon-gu

department: Neurosurgery

country: South Korea

institute: Yonsei University

description: Gene expression data from undifferentiated C6 glioma

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

organism: Rattus norvegicus

source_name: Undifferentiated C6 glioma

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: cells were cultured in DMEM containing 10% FBS and P/S.

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

treatment_protocol: Cells were treated with CHIR99021 (20uM) and forskolin (100uM) for 35 days

value: glioma


title: small molecule induced C6 glioma (SMiN)

description: Gene expression data from C6 glioma treated with CHIR99021 and forskolin for 35 days

label: biotin-labeled with TdT (terminal deoxynucleotidyl transferase)

source_name: C6 glioma treated with small molecule (CHIR99021, forskolin) for 35 days


title: DRG_miRNA_rep3

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

hyb_protocol: 600 ng of Cy3-labelled 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 GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K microarray (G4853A) for 17 hours at 65°C at 10 rpm in a rotating Agilent hybridization oven.  After hybridization, the microarray slide was washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) 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 image was analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DRG, miR-17-92 AAV, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop 1000 spectrophotometer.

extract_protocol: Total RNA was prepared using RNAiso Plus (Takara Bio, Shiga, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop 1000 spectrophotometer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Rat received AAV vector injection into the L5 DRG under deep anesthesia 7 days befor sacrifice.

value: Sprague-Dawley

value: L5 dorsal root ganglion (DRG)

tag: gender

value: male

value: 7 weeks


title: DRG_CNT_rep4

source_name: DRG, control AAV, replicate 4


title: DRG_miRNA_rep1

source_name: DRG, miR-17-92 AAV, replicate 1


title: DRG_miRNA_rep2

source_name: DRG, miR-17-92 AAV, replicate 2


title: DRG_CNT_rep3

source_name: DRG, control AAV, replicate 3


title: DRG_CNT_rep2

source_name: DRG, control AAV, replicate 2


title: sample 1

city: Chongqing

first: Li

last: Zhonghu

address: No. 30 Gaotanyan Street, Shapingba District,

institute: Hepatobiliary Surgery Institute

description: RNA from exosomes of pancreatic cancer cell medium was purified

hyb_protocol: 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. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

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 1 out of 2 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.

source_name: exosomes of Hs767t

label_protocol: 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).

growth_protocol: pancreatic cancer cells (hs766t and hs766t-l2) were cultured with RPMI-1640 medium (Gibco, USA) supplemented with 10% exosome-depleted fetal bovine serum (FBS) .

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis


title: miRNA_899_NDf_4

source_name: miRNA, patient 899, pre-adipocyte, replicate 5


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 6

city: Lucknow

first: Sudeep

last: Kumar

state: Uttar Pradesh

address: Raebareli Road

department: Cardiology

country: India

institute: Sanjay Gandhi Post Graduate Institute of Medical Sciences

description: Gene expression data from coronary artery disease patient, Triple vessels disease, gensini score for lesion 50-60.

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

scan_protocol: Gene Chips were scanned using the Affymetrix Scanner30007G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console Software.

source_name: Peripheral Venous whole Blood, Fasting

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (User Guide, Gene Chip 3'IVT PLUS Reagent Kit, Affymetrix P/N 703210 Rev 2).

tag: diagnosis

value: coronary artery disease (CAD), triple vessel

value: Whole blood

value: Mean Age 55.0±8.8 Years


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 5


title: miRNA_899_NDf_3

source_name: miRNA, patient 899, pre-adipocyte, replicate 3


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 2


title: DRG_CNT_rep1

source_name: DRG, control AAV, replicate 1


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 1


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 6

description: Gene expression data from coronary artery disease patient, Single vessel disease, Left anterior descending artery, gensini score for lesion 20-30.

value: coronary artery disease (CAD), single vessel

value: Mean Age 56.1±8.5 Years


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 3


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 5


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 4


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 2


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 3


title: Coronary Artery Disease free control rep 6

description: Gene expression data from coronary artery disease free patients

value: atypical angina with normal coronary angiogram (control)

value: Mean Age 52.0±7.4 Years


title: Coronary Artery Disease patirnts, Single Vessels Disease rep 1


title: Coronary Artery Disease free control rep 3


title: Coronary Artery Disease patirnts, triple Vessels Disease rep 4


title: DRG_miRNA_rep4

source_name: DRG, miR-17-92 AAV, replicate 4


title: Coronary Artery Disease free control rep 4


title: Coronary Artery Disease free control rep 2


title: Coronary Artery Disease free control rep 5


title: Coronary Artery Disease free control rep 1


title: sample 2

source_name: exosomes of Hs766t-L2


title: Aged heads at 25 days old, rep3

status: Public on May 05 2017

city: Obu

first: Koichi

middle: M

last: Iijima

state: Aichi

address: 7-430 Morioka-cho

department: Alzheimer's Disease Research

institute: National Center for Geriatrics and Gerontology

description: Gene expression data from aged fly heads.

hyb_protocol: Biotin-labeled amplified RNA was fragmented and hybridized onto the microarrays (GeneChip Drosophila Genome 2.0) according to the Affymetrix protocol.

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

data_processing: The raw data were normalized with the RMA method in R statistical environment 2.12.2 and analyzed with Bioconductor and Limma.

organism: Drosophila melanogaster

source_name: Adult heads at 25 days old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol 2.0.

growth_protocol: Flies were raised and maintained at 25°C under 12hr light/dark condition.

treatment_protocol: Flies were quickly frozen in liquid nitrogen and heads were collected on dry ice.

tag: strain/background

value: W*

value: head

value: 25 days


title: Young heads at 2 days old, rep1

description: Gene expression data from young fly heads.

source_name: Adult heads at 2 days old

value: 2 days


title: nT-Th2 2

status: Public on May 04 2017

city: Manchester

first: Victoria

middle: S

last: Pelly

state: Manchester

address: Wilmslow road

country: United Kingdom

institute: Cancer Research UK, Manchester Cancer Research Centre

hyb_protocol: Labelled cDNA was hybridised to an Affymetric GeneChip® mouse Genome 430A 2.0 microarray using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) and ran on the 450 Affymetrix GeneChip Fluidics Station (Affymetrix)

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

data_processing: Microarray data was analysed using the GeneSpring software (Agilent). Samples were summarized and normalized using the Affymetrix MicroArray Suite 5 method (MAS5)

source_name: nT-IL-4gfp+ biological replicate 2

label_protocol: Samples were amplified using the Ovation® Pico WTA system (version 2) (NuGEN) and labelled with the Encore Biotin Module (NuGEN)

extract_protocol: RNA samples were extracted using RNAeasy purification kit (Qiagen)


title: Young heads at 2 days old, rep2


title: HpTR - Th2 3

source_name: HpTR-IL-4gfp+ biological replicate 3


title: Aged heads at 25 days old, rep2


title: Young heads at 2 days old, rep3


title: HpTR - Th2 2

source_name: HpTR-IL-4gfp+ biological replicate 2


title: Naïve T cell 3

source_name: Naive T cell biological replicate 3

value: Naive T cell


title: H. poly Treg 3

source_name: HpTR biological replicate 3

value: HpTR


title: HpTR - Th2 1

source_name: HpTR-IL-4gfp+ biological replicate 1


title: nT-Th2 1

source_name: nT-IL-4gfp+ biological replicate 1


title: Aged heads at 25 days old, rep1


title: H. poly Treg 1

source_name: HpTR biological replicate 1


title: H. poly Treg 2

source_name: HpTR biological replicate 2


title: nT-Th2 3

source_name: nT-IL-4gfp+ biological replicate 3


title: Naïve T cell 2

source_name: Naive T cell biological replicate 2


title: Prostate-specific Pten and Pml double knockout dorsolateral prostate tumor, biological rep3

city: Boston

first: Ming

last: Chen

address: 330 Brookline Ave

department: Medicine and Pathology

institute: Beth Isreal Deaconess Medical Center/Harvard Medical School

hyb_protocol: Two hundred nanograms of total RNA was hybridized to Affymetrix Mouse Gene 2.1 ST arrays by the Beth Israel Deaconess Medical Center Genomics and Proteomics Core according to the manufacturer's instructions.

scan_protocol: Affymetrix protocol

data_processing: The obtained raw intensity .cel files were normalzied by robust multichip analysis (Bioconductor release 3.1) and differential expression was determined using the limma Bioconductor Package by fitting a linear model.

source_name: Prostate-specific Pten and Pml double knockout dorsolateral prostate tumor at 12 weeks of age

label_protocol: Affymetrix protocol

growth_protocol: Dorsolateral prostates from the three genotpes of mice were isolated and immediately sliced and placed into QIAzol.

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

value: a mixed C57BL/6 (80%) × 129S1/SvImJ(20%) background

value: dorsolateral prostate tumor


title: Prostate-specific Pten knockout dorsolateral prostate tumor, biological rep2

source_name: Prostate-specific Pten knockout dorsolateral prostate tumor at 12 weeks of age


title: Prostate-specific Pten knockout dorsolateral prostate tumor, biological rep3


title: Prostate-specific Pten and Pml double knockout dorsolateral prostate tumor, biological rep1


title: Wild type dorsolateral prostate, biological rep1

source_name: Wild type dorsolateral prostate at 12 weeks of age

value: dorsolateral prostate


title: Wild type dorsolateral prostate, biological rep2


title: Prostate-specific Pten and Pml double knockout dorsolateral prostate tumor, biological rep2


title: Naïve T cell 1

source_name: Naive T cell biological replicate 1


title: Wild type dorsolateral prostate, biological rep3


title: Prostate-specific Pten knockout dorsolateral prostate tumor, biological rep1


title: EndoC-βH1 20mM glucose + Forskolin, biological rep1

city: Paris

first: Latif

last: Rachdi

address: 123 bvd Port-Royal

institute: Institut Cochin - Bat. Cassini

description: Gene expression data from EndoC-βH1 treated with 20mM glucose + Forskolin

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

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

data_processing: The data were analyzed with R Bioconductor packages using RMA as normalization method

source_name: 20mM glucose + Forskolin

label_protocol: Total RNA is reverse transcribed following the GeneChip™ WT PLUS Reagent Kit (applied biosystems). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).   After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.

extract_protocol: RNeasy Micro kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: beta cells


title: EndoC-βH1 20mM glucose, biological rep2

description: Gene expression data from EndoC-βH1 treated with 20mM glucose

source_name: 20mM glucose


title: EndoC-βH1 20mM glucose, biological rep3


title: EndoC-βH1 0,5mM glucose, biological rep3

description: Gene expression data from EndoC-βH1 treated with 0,5mM glucose

source_name: 0,5mM glucose


title: EndoC-βH1 20mM glucose + Forskolin, biological rep3


title: EndoC-βH1 0,5mM glucose, biological rep2


title: EndoC-βH1 20mM glucose + Forskolin, biological rep2


title: TotalRNA_CM_Rep3

status: Public on May 03 2017

city: Clayton

first: Alex

last: Hodge

state: VIC

address: 246 Clayton Road

department: Gastroenterology and Hepatology Unit

country: Australia

institute: Monash Health

description: Gene expression of LPCs after CM

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1xAgilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression hybridisation buffer was added and 40ul of sample hybridised for 17 hours at 65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 8x60k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid:028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Liver Progenitor Cells, CM, Replicate 3

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: LPC total RNA was isolated according to the manufacturer’s instructions using the Qiagen RNeasy mini kit (Qiagen Pty Ltd, Hilden, Germany). Following elution, RNA concentration was determined using the Nanodrop ND-100 spectrophotometer (Thermo Scientific, Waltham, MA, USA). Total RNA was analysed using the Agilent SurePrint G3 Mouse Gene Expression 8 x 60K G4852A (028005) slide.

value: Bipotential Murine Embryonic Liver cell line (BMEL)

tag: media

value: CM


title: EndoC-βH1 0,5mM glucose, biological rep1


title: EndoC-βH1 20mM glucose, biological rep1


title: TotalRNA_DIFF_Rep2

description: Gene expression of LPCs after DIFF media

source_name: Liver Progenitor Cells, DIFF, Replicate 1

value: DIFF media


title: TotalRNA_DIFF_Rep1


title: TotalRNA_CM_Rep1

description: Gene expression of LPCs after CM

source_name: Liver Progenitor Cells, CM, Replicate 1


title: TotalRNA_CM_Rep2

description: Gene expression of LPCs after CM

source_name: Liver Progenitor Cells, CM, Replicate 2


title: TotalRNA_NoRX_Rep3

description: Gene expression of LPCs after NoRX media

source_name: Liver Progenitor Cells, NoRX, Replicate 3

value: NoRX media


title: TotalRNA_NoRX_Rep2

source_name: Liver Progenitor Cells, NoRX, Replicate 2


title: 18207 - S1-23L.2

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

hyb_protocol: Standard affymetrix hybridization protocol.

scan_protocol: The microarrays were scanned with the use of Affymetrix GeneChip 7G 3000 Scanner.

data_processing: quantile normalized

source_name: Knee cartilage

label_protocol: Biotinylated cDNA was prepared through NuGEN Ovation Pico WTA Amplification System.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: tibial plateau cartilage

value: osteoarthritis (OA)

tag: age (years)

tag: Sex

value: Male

tag: bmi (kg/m2)

tag: side

value: Right


title: TotalRNA_NoRX_Rep1

source_name: Liver Progenitor Cells, NoRX, Replicate 1

tag: cell line


title: 17743 - S1-15L

value: Female

value: Left


title: 17744 - S1-16L


title: 17752 - S1-24L


title: 17750 - S1-22L


title: 17747 - S1-19L


title: 17746 - S1-18L


title: 17739 - S1-11L


title: 17748 - S1-20L


title: 17736 - S1-8L


title: 17741 - S1-13L


title: 17740 - S1-12L


title: 17745 - S1-17L


title: 17754 - S1-26L


title: 17738 - S1-10L


title: 17753 - S1-25L


title: 17749 - S1-21L


title: 17742 - S1-14L


title: 17755 - S1-27L


title: 17732 - S1-27M


title: 17735 - S1-6L


title: 17730 - S1-25M


title: 17731 - S1-26M


title: 17726 - S1-21M


title: 17733 - S1-2L


title: 17729 - S1-24M


title: 17734 - S1-3L


title: 17737 - S1-9L


title: 17727 - S1-22M


title: 17720 - S1-15M


title: 17724 - S1-19M


title: 17722 - S1-17M


title: 18206 - S1-14M.2


title: 17714 - S1-9M


title: 17716 - S1-11M


title: 17713 - S1-8M


title: 17710 - S1-2M


title: 17728 - S1-23M


title: 17725 - S1-20M


title: 17723 - S1-18M


title: 17721 - S1-16M


title: 17715 - S1-10M


title: PCOS woman, biological rep2

city: Los Angeles

first: Daniel

last: Dumesic

state: CA

address: 10833 Le Conte Ave, CHS 22-222

department: Ob/Gyn

institute: UCLA

description: PCOS woman

hyb_protocol: Hybridization was performed using Affymetrix GeneChip Hybridization Wash and Stain kit.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.full.mps

source_name: subcutaneous adipose tissue from fat biopsy

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Approximately 0.5-1g of freshly isolated SC adipose was obtained through a 1 cm lower abdominal incision and was washed with DMEM and then digested at 37°C in DMEM containing 0.075% collagenase for 45-60 min on a shaker. Adipocytes (floating cells) were separated from pellets by centrifugation (800×g, 10 min). Pellets containing stromal-vascular fraction were resuspended in DMEM/5% fetal calf serum (FCS), filtered through 150-mm mesh and washed with DMEM/10% FCS. Cells were plated in 60 mm dishes containing DMEM/10% FCS, 0.05 U/ml penicillin, 0.05 mg/ml streptomycin, 1.25 mg/ml fungizone and cultured at 37°C for 1-2 weeks until cells reached confluency

extract_protocol: Total cellular RNA was isolated from 2 x 10 cm dishes of SC abdominal ASCs using RNeasy mini kit (Qiagen, Carlsbad, CA) according to the manufacturer’s protocol.

treatment_protocol: not applicable

tag: age

value: adipose tissue

tag: genotype

value: not applicable


title: PCOS woman, biological rep4

description: PCOS woman

tag: tissue


title: 17717 - S1-12M


title: PCOS woman, biological rep3

description: PCOS woman


title: 17711 - S1-3M


title: 17718 - S1-13M


title: normoandrogenic woman, biological rep3

description: NL woman


title: normoandrogenic woman, biological rep2

description: NL woman


title: PCOS woman, biological rep1

description: PCOS woman


title: normoandrogenic woman, biological rep4

description: NL woman


title: Stassi_Day 7

city: Davis

first: Heather

last: Knych

state: California

address: 620 W.  Health Sciencse Drive

department: CAHFS

institute: University of California Davis

description: Gene expression data from horse synovial fluid Day7 after administration of  8 mg of  isoflupredone acetate into the right antebrachiocarpal joint; Day 7 time point

hyb_protocol: Following fragmentation 10ug of cRNA were hypridized for 16 hr at 45C on Equus caballus Gene 1.0 ST Array [transcript (gene) version] represents the equine gene 1.ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console.  Data visualization and filtering was performed in Transcriptome Analysis console version 3.0

organism: Equus caballus

source_name: Horse received 8 mg of  isoflupredone acetate into the right antebrachiocarpal join; sample collected at Day 7

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

extract_protocol: RNA Extraction and Quality Assessment: RNA was isolated by adding 200µl of synovial fluid to 1 ml of QIAzol lysis reagenth.  The sample was vortexed, passed through a 20-gauge needle attached to a sterile syringe and subjected to chloroform extraction and centrifugation.  RNA was purified using an miRNeasy® Mini kith and the integrity assessed using an Experion Automated Electrophoresis Systemi.  RNA samples with a RIN ≥ 8 and a 260/280 and 260/230 ratios between 1.7 and 2.1 were used (Denisov et al 2008) (Fleige et al 2006)

treatment_protocol: Six of the horses received 8 mg of Isoflupredone acetate (IPA).  Immediately prior to drug administration, the area over the right antebrachiocarpal joint was scrubbed with betadine solutionc and 70% isopropyl alcohol, the joint flexed and a total dose of 8 mg of IPA (Predef® 2X)d  administered aseptically into the right joint.  The IPA dose chosen for this study was based upon a published survey of the most commonly used dose by equine practitioners [Ferris, D.J, 2009].

tag: tag

value: Synovial fluid Day 7


title: Sadie_Day 7


title: Enrique_Baseline

description: Gene expression data from horse synovial fluid before administration of  8 mg of  isoflupredone acetate into the right antebrachiocarpal joint; baseline time point

source_name: Horse before receiving 8 mg of  isoflupredone acetate into the right antebrachiocarpal joint; baseline

value: Synovial fluid baseline


title: Sadie_24 hr

description: Gene expression data from horse synovial fluid 24hours after administration of  8 mg of  isoflupredone acetate into the right antebrachiocarpal joint; 24 hours time point

source_name: Horse received 8 mg of  isoflupredone acetate into the right antebrachiocarpal join; sample collected at 24 Hour

value: Synovial fluid 24 Hour


title: Emma1_24 hr


title: Emma1_Baseline


title: Simon_Baseline


title: Stassi_24 hr


title: normoandrogenic woman, biological rep1

description: NL woman


title: Emma1_Day 7


title: Enrique_Day 7


title: Bekrhala_24 hr


title: Bekrhala_Day 7


title: Sadie_Baseline


title: Simon_Day 7


title: 17712 - S1-6M


title: Stassi_Baseline


title: Bekrhala_Baseline


title: TUMOR LIVER 17

status: Public on May 02 2017

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

description: miRNA expression data from FFPE Tumor Liver

hyb_protocol: Labeled RNA was hybridized to an Affymetrix miRNA v.3 microarray using and Affymetrix hybridziation oven 640 for 16 hours at 48 degrees with a rotation speed of 60 RPM. Arrays were then washed and stained using a Gene Chip Fluidics 450 Station.

scan_protocol: Signal intensity was measured on the Affymetrix GeneChip Scanner 3000 with the 7G Upgrade

data_processing: Individual array data (.cel files) were uploaded to Partek Genomics Suite 6.5. Normalization was conducted on 42 arrays in a single set using RMA Background and Quantile Normalization sub-routine. Specifically, .cel files were imported into Partek using the RMA importing method. Background was corrected on the Perfect Match values and Quantile Normalizaiton conducted across all arrays. Signal intensities were log2 transformed and probe set values summarized using Median Polish Summarization method. Following importation and normalization, all non-human miRNA probe intensity data were removed from the data set and were not included in downstream analysis.

label: Biotin

source_name: FFPE Tumor Liver

label_protocol: RNA was labeled using Affymetrix FlashTaq Biotin HSR labeling kit and protocol

extract_protocol: RNA was isolated from the FFPE primary colon tumor and liver metastases patient slides using the Rneasy FFPE Kit (Qiagne catalog # 73504) according to manufactuer's protocols.

treatment_protocol: Tumor tissues were formalin fixed and paraffin embedded and then archived. All sample were from  patients with a colorectal diagnosis and registered in the colorectal tumor registry in conjuntion with the OHSU Knight Cancer Institute biorepository.

tag: disease state

value: Tumor

value: Liver


title: TUMOR LIVER 7


title: TUMOR LIVER 6


title: TUMOR LIVER 9


title: TUMOR LIVER 16


title: TUMOR LIVER 14


title: TUMOR LIVER 2


title: TUMOR LIVER 4


title: TUMOR LIVER 3


title: TUMOR LIVER 5


title: Enrique_24 hr


title: TUMOR LIVER 13

value: Unknown


title: TUMOR LIVER 10


title: TUMOR LIVER 12


title: TUMOR COLON 3

description: miRNA expression data from FFPE Tumor Colon

source_name: FFPE Tumor Colon

value: Colon


title: TUMOR COLON 5


title: TUMOR COLON 13


title: TUMOR COLON 7


title: TUMOR COLON 14


title: TUMOR COLON 12


title: TUMOR COLON 10


title: TUMOR LIVER 1


title: TUMOR COLON 6


title: TUMOR COLON 16


title: TUMOR COLON 4


title: NORMAL LIVER 10

description: miRNA expression data from FFPE Normal Liver

source_name: FFPE Normal Liver

value: Normal


title: NORMAL LIVER 2


title: NORMAL LIVER 4


title: NORMAL COLON 4

description: miRNA expression data from FFPE Normal Colon

source_name: FFPE Normal Colon


title: NORMAL LIVER 7


title: TUMOR COLON 17


title: NORMAL LIVER 3


title: NORMAL COLON 5


title: NORMAL COLON 3


title: TUMOR COLON 2


title: NORMAL COLON 2


title: NORMAL COLON 7


title: NORMAL LIVER 1


title: TUMOR COLON 9


title: TUMOR COLON 1


title: NORMAL COLON 10


title: NORMAL LIVER 5


title: NORMAL COLON 1


title: Acute vehicle control treatment in UVA608 rep1

city: Charlottesville

first: Edik

middle: Matthew

last: Blais

state: Virginia

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

description:
biological replicate 1
Gene expression of a human pancreatic tumor orthotopically implanted and grown in a mouse

hyb_protocol: Hybridized to arrays at 45°C for 16 hours

scan_protocol: Affymetrix GeneChip system performed by University of Virginia Core Biomolecular Analysis Facility, which is supported by the University Of Virginia School Of Medicine. Laser GeneArray scanner was used for measuring amounts of bound probes

data_processing: Transcriptomics analyses were performed in the R/Bioconductor programming environment.  Raw gene expression data files (.CEL) were preprocessed using robust multi-array averaging (RMA) as implemented in the oligo package [PMID:20688976], medianpolish summarization for probesets as annotated in the hugene10sttranscriptcluster.db package (version 8.3.1), and quantiles normalization between arrays.

source_name: Acute vehicle control treatment in UVA608 PDAC PDX tumors, biological rep1

label_protocol: Biotin labelled according to the standard Affymetrix protocol

extract_protocol: All protect (Qiagen) was used to preserve RNA in all tissue samples. TissueLyzer LT (Qiagen) was used to homogenize tissue. RNA was extracted using the Allprep kit (Qiagen).

tag: host organism

value: Athymic nude mouse

tag: xenograft generation

value: Mouse Passage #10 (F10)

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

tag: treatment summary

value: Control

tag: trametinib active dosing

value: No active treatment with trametinib

tag: lapatinib active dosing

tag: trametinib prior dosing

value: No prior treatment with trametinib

tag: lapatinib prior dosing

value: No prior exposure to lapatinib

tag: trametinib duration

value: No trametinib exposure

tag: lapatinib duration

value: No lapatinib exposure

tag: sample batch

tag: patient biopsy site

tag: patient cancer type

value: Pancreatic adenocarcinoma

tag: patient tumor stage

value: Metastatic

tag: patient tumor differentiation

value: Well-Mod

tag: patient tumor grade

value: High Grade

tag: patient tumor stromal content

value: Low


title: Acute vehicle control treatment in UVA608 rep2

description:
biological replicate 2
Gene expression of a human pancreatic tumor orthotopically implanted and grown in a mouse

source_name: Acute vehicle control treatment in UVA608 PDAC PDX tumors, biological rep2

tag: host organism

tag: xenograft generation

tag: xenograft tissue

value: Liver


title: Acute trametinib plus lapatinib treatment in UVA608 rep1

source_name: Acute trametinib plus lapatinib treatment in UVA608 PDAC PDX tumors, biological rep1

tag: xenograft biopsy site

tag: treatment condition

tag: treatment summary

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

value: Acute trametinib treatment (24 hours) prior to sample collection

value: Acute lapatinib treatment (24 hours) prior to sample collection


title: Acute trametinib alone treatment in UVA608 rep3

description:
biological replicate 3
Gene expression of a human pancreatic tumor orthotopically implanted and grown in a mouse

source_name: Acute trametinib alone treatment in UVA608 PDAC PDX tumors, biological rep3

value: Athymic nude mouse

value: Mouse Passage #10 (F10)

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

value: T (1 day)

tag: trametinib active dosing

tag: lapatinib active dosing

tag: trametinib prior dosing


title: Acute lapatinib alone treatment in UVA608 rep3

source_name: Acute lapatinib alone treatment in UVA608 PDAC PDX tumors, biological rep3

value: L (1 day)

value: No active treatment with trametinib

value: No prior treatment with trametinib

tag: lapatinib prior dosing

value: No prior exposure to lapatinib

tag: trametinib duration

value: No trametinib exposure

tag: lapatinib duration


title: Acute lapatinib alone treatment in UVA608 rep1

source_name: Acute lapatinib alone treatment in UVA608 PDAC PDX tumors, biological rep1

tag: sample batch

tag: patient biopsy site

tag: patient cancer type

value: Pancreatic adenocarcinoma

value: Metastatic

value: Well-Mod

value: High Grade

value: Low


title: Acute trametinib plus lapatinib treatment in UVA608 rep3

source_name: Acute trametinib plus lapatinib treatment in UVA608 PDAC PDX tumors, biological rep3

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

value: Acute trametinib treatment (24 hours) prior to sample collection

value: Liver

tag: patient tumor stage

tag: patient tumor differentiation

tag: patient tumor grade


title: Acute lapatinib alone treatment in UVA608 rep2

source_name: Acute lapatinib alone treatment in UVA608 PDAC PDX tumors, biological rep2

tag: host organism

value: Athymic nude mouse

tag: xenograft generation

value: Mouse Passage #10 (F10)

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

value: Acute lapatinib treatment (24 hours) prior to sample collection

tag: patient tumor stromal content


title: Acute trametinib alone treatment in UVA608 rep1

source_name: Acute trametinib alone treatment in UVA608 PDAC PDX tumors, biological rep1

tag: xenograft tissue

tag: xenograft biopsy site

tag: treatment condition

value: T (1 day)

value: No active treatment with trametinib

value: No prior treatment with trametinib

value: No prior exposure to lapatinib

value: No lapatinib exposure


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 rep1

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 PDAC PDX tumors, biological rep1

value: Mouse Passage #13 (F13)

tag: treatment summary

tag: trametinib active dosing

value: 0.3 mg/kg trametinib given orally twice per day

tag: lapatinib active dosing

value: Chronic trametinib treatment (5 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained prior to sample collection

value: Pancreatic adenocarcinoma

value: Metastatic

value: Well-Mod

value: High Grade


title: Simon_24 hr

tag: tag

value: Synovial fluid 24 Hour


title: Acute vehicle control treatment in UVA608 rep3

source_name: Acute vehicle control treatment in UVA608 PDAC PDX tumors, biological rep3

value: Athymic nude mouse

value: Mouse Passage #11 (F11)

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Control

tag: trametinib prior dosing

tag: lapatinib prior dosing

tag: trametinib duration

value: No trametinib exposure

tag: lapatinib duration

value: Liver

value: Low


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 rep2

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep2

value: Mouse pancreas

value: No active treatment with trametinib

value: 65 mg/kg lapatinib given orally twice per day

value: Chronic trametinib treatment (4 xenograft generations) discontinued prior to sample collection

value: Chronic lapatinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: sample batch

tag: patient biopsy site

tag: patient cancer type

tag: patient tumor stage


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 rep2

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 PDAC PDX tumors, biological rep2

tag: host organism

tag: xenograft generation

value: Mouse Passage #13 (F13)

value: 0.3 mg/kg trametinib given orally twice per day

value: Chronic trametinib treatment (5 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained prior to sample collection

value: Pancreatic adenocarcinoma

tag: patient tumor differentiation

tag: patient tumor grade


title: Acute trametinib plus lapatinib treatment in UVA608 rep2

source_name: Acute trametinib plus lapatinib treatment in UVA608 PDAC PDX tumors, biological rep2

value: Athymic nude mouse

value: Mouse Passage #10 (F10)

tag: xenograft tissue

tag: xenograft biopsy site

tag: treatment condition

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: No prior treatment with trametinib

value: No prior exposure to lapatinib

value: Acute trametinib treatment (24 hours) prior to sample collection

value: Acute lapatinib treatment (24 hours) prior to sample collection

value: Metastatic

value: Well-Mod

value: High Grade

tag: patient tumor stromal content


title: Acute trametinib alone treatment in UVA608 rep2

source_name: Acute trametinib alone treatment in UVA608 PDAC PDX tumors, biological rep2

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

tag: treatment summary

value: T (1 day)

tag: trametinib active dosing

tag: lapatinib active dosing

value: No active treatment with trametinib

value: No lapatinib exposure

value: Liver

value: Low


title: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 rep1

source_name: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep1

value: Athymic nude mouse

value: Mouse Passage #13 (F13)

value: 1 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

tag: trametinib prior dosing

tag: lapatinib prior dosing

tag: trametinib duration

value: Chronic trametinib treatment (5 xenograft generations) sustained and escalated prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained and escalated prior to sample collection

value: Pancreatic adenocarcinoma


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 rep1

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep1

value: 0.3 mg/kg trametinib given orally twice per day

value: Chronic trametinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: lapatinib duration

value: Chronic lapatinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: sample batch

tag: patient biopsy site

value: Metastatic


title: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 rep3

source_name: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep3

tag: host organism

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

tag: patient cancer type

tag: patient tumor stage

value: Well-Mod

value: High Grade


title: Chronic trametinib plus lapatinib treatment sustained for 3 xenograft generations in UVA608 rep1

source_name: Chronic trametinib plus lapatinib treatment sustained for 3 xenograft generations in UVA608 PDAC PDX tumors, biological rep1

tag: xenograft generation

value: Mouse Passage #10 (F10)

value: Chronic trametinib treatment (3 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (3 xenograft generations) sustained prior to sample collection

value: Liver

tag: patient tumor differentiation

tag: patient tumor grade


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 rep3

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep3

value: Athymic nude mouse

value: Mouse Passage #13 (F13)

tag: xenograft tissue

tag: xenograft biopsy site

tag: treatment condition

value: No active treatment with trametinib

value: Low


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 rep3

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA608 PDAC PDX tumors, biological rep3

tag: treatment summary

tag: trametinib active dosing

value: 65 mg/kg lapatinib given orally twice per day

value: Chronic trametinib treatment (5 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained prior to sample collection

value: Pancreatic adenocarcinoma

tag: patient tumor stromal content


title: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 rep2

source_name: Chronic trametinib plus lapatinib treatment escalated after 4 xenograft generations in UVA608 PDAC PDX tumors, biological rep2

value: 1 mg/kg trametinib given orally twice per day

tag: lapatinib active dosing

tag: trametinib prior dosing

tag: lapatinib prior dosing

value: Chronic trametinib treatment (5 xenograft generations) sustained and escalated prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained and escalated prior to sample collection

value: Metastatic


title: Acute lapatinib alone treatment in UVA366 rep3

source_name: Acute lapatinib alone treatment in UVA366 PDAC PDX tumors, biological rep3

value: Mouse Passage #8 (F8)

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

value: L (1 day)

value: No prior treatment with trametinib

value: No prior exposure to lapatinib

tag: trametinib duration

value: No trametinib exposure

tag: lapatinib duration

value: Acute lapatinib treatment (24 hours) prior to sample collection

tag: sample batch

value: Poor

value: High Grade


title: Acute trametinib plus lapatinib treatment in UVA366 rep3

source_name: Acute trametinib plus lapatinib treatment in UVA366 PDAC PDX tumors, biological rep3

tag: host organism

value: Athymic nude mouse

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

value: Acute trametinib treatment (24 hours) prior to sample collection

tag: patient biopsy site

value: Liver

tag: patient cancer type

value: Low


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 rep2

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 PDAC PDX tumors, biological rep2

tag: xenograft generation

value: Mouse Passage #10 (F10)

value: 0.3 mg/kg trametinib given orally twice per day

value: Chronic trametinib treatment (5 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained prior to sample collection

value: Pancreatic adenocarcinoma

tag: patient tumor stage

value: Metastatic

tag: patient tumor differentiation


title: Z(-) cell_technical rep1 and rep2

city: Tainan

first: Nan-Shan

last: Chang

address: 1 University Road

department: Molecular Medicine

country: Taiwan

institute: National Cheng Kung University

description: ZM_H001, ZM_H002

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (Wash I 42 ℃ 5 min; Wash II 42 ℃, 5 mins, 25 ℃ 5 mins; Wash III rinse 20 times).

scan_protocol: The arrays were scanned by Agilent G2505C scanner (laser power 100% PMT 30%; resolution: 10uM) and quantify the fluorescence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors from the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% median scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparison (Ranking and hypothesis testing).

source_name: spleen Z(-) cells

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Spleen cells were isolated and subjected to sorting immediately. No cell culture was involved.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: No treatment of spleen cells was involved.

tag: strain/background

value: NOD-SCID

tag: age

value: 6-8 weeks

tag: tissue

value: spleen

tag: cell type


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 rep3

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 PDAC PDX tumors, biological rep3

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

tag: treatment summary

tag: trametinib active dosing

value: Poor

tag: patient tumor grade

value: High Grade

tag: patient tumor stromal content


title: Acute vehicle control treatment in UVA366 rep1

source_name: Acute vehicle control treatment in UVA366 PDAC PDX tumors, biological rep1

tag: host organism

value: Athymic nude mouse

value: Mouse Passage #8 (F8)

value: Control

value: No active treatment with trametinib

tag: lapatinib active dosing

tag: trametinib prior dosing

value: No prior treatment with trametinib

tag: lapatinib prior dosing

value: No prior exposure to lapatinib

tag: trametinib duration

value: No trametinib exposure

tag: lapatinib duration

value: No lapatinib exposure

tag: sample batch


title: Acute lapatinib alone treatment in UVA366 rep2

source_name: Acute lapatinib alone treatment in UVA366 PDAC PDX tumors, biological rep2

tag: xenograft generation

value: L (1 day)

value: 65 mg/kg lapatinib given orally twice per day

value: Acute lapatinib treatment (24 hours) prior to sample collection

tag: patient biopsy site

value: Liver

tag: patient cancer type

value: Pancreatic adenocarcinoma

tag: patient tumor stage

tag: patient tumor differentiation

value: Low


title: Acute trametinib plus lapatinib treatment in UVA366 rep2

source_name: Acute trametinib plus lapatinib treatment in UVA366 PDAC PDX tumors, biological rep2

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: Acute trametinib treatment (24 hours) prior to sample collection

value: Metastatic


title: Acute trametinib alone treatment in UVA366 rep3

source_name: Acute trametinib alone treatment in UVA366 PDAC PDX tumors, biological rep3

value: Athymic nude mouse

value: Mouse Passage #8 (F8)

tag: treatment summary

value: T (1 day)

tag: trametinib active dosing

value: No active treatment with trametinib

value: Poor

tag: patient tumor grade

value: High Grade


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 rep1

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 PDAC PDX tumors, biological rep1

tag: host organism

value: Mouse Passage #10 (F10)

tag: lapatinib active dosing

value: 0.3 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

value: Chronic trametinib treatment (4 xenograft generations) discontinued prior to sample collection

value: Chronic lapatinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: patient tumor stromal content


title: Acute vehicle control treatment in UVA366 rep2

source_name: Acute vehicle control treatment in UVA366 PDAC PDX tumors, biological rep2

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Control

tag: trametinib prior dosing

value: No prior treatment with trametinib

tag: lapatinib prior dosing

value: No prior exposure to lapatinib

tag: trametinib duration

value: No trametinib exposure

value: No lapatinib exposure

value: Liver

value: Pancreatic adenocarcinoma

value: Low


title: Acute trametinib plus lapatinib treatment in UVA366 rep1

source_name: Acute trametinib plus lapatinib treatment in UVA366 PDAC PDX tumors, biological rep1

value: Athymic nude mouse

tag: xenograft generation

value: Mouse Passage #8 (F8)

value: Mouse pancreas

value: T+L (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: Acute trametinib treatment (24 hours) prior to sample collection

tag: lapatinib duration

value: Acute lapatinib treatment (24 hours) prior to sample collection

tag: sample batch

value: Metastatic


title: Acute trametinib alone treatment in UVA366 rep1

source_name: Acute trametinib alone treatment in UVA366 PDAC PDX tumors, biological rep1

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: T (1 day)

value: No active treatment with trametinib

tag: patient biopsy site

tag: patient cancer type

tag: patient tumor stage

value: Poor

value: High Grade


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 rep2

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 PDAC PDX tumors, biological rep2

value: Mouse Passage #10 (F10)

tag: xenograft tissue

tag: xenograft biopsy site

value: 0.3 mg/kg trametinib given orally twice per day

value: 65 mg/kg lapatinib given orally twice per day

value: Chronic trametinib treatment (4 xenograft generations) discontinued prior to sample collection

value: Chronic lapatinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: patient tumor differentiation


title: Acute vehicle control treatment in UVA366 rep3

source_name: Acute vehicle control treatment in UVA366 PDAC PDX tumors, biological rep3

value: Athymic nude mouse

value: Mouse Passage #8 (F8)

tag: treatment condition

tag: treatment summary

value: Control

tag: trametinib active dosing

value: No prior treatment with trametinib

value: No prior exposure to lapatinib

value: No trametinib exposure

value: No lapatinib exposure

value: Liver

value: Pancreatic adenocarcinoma

value: Low


title: Acute lapatinib alone treatment in UVA366 rep1

source_name: Acute lapatinib alone treatment in UVA366 PDAC PDX tumors, biological rep1

tag: host organism

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

value: Mouse pancreas

value: L (1 day)

value: No active treatment with trametinib

tag: lapatinib active dosing

value: Acute lapatinib treatment (24 hours) prior to sample collection

value: Metastatic

value: Poor

tag: patient tumor grade


title: Chronic trametinib alone treatment sustained for 3 xenograft generations in UVA608 rep1

source_name: Chronic trametinib alone treatment sustained for 3 xenograft generations in UVA608 PDAC PDX tumors, biological rep1

value: Athymic nude mouse

value: Mouse Passage #10 (F10)

value: 0.3 mg/kg trametinib given orally twice per day

tag: trametinib prior dosing

tag: lapatinib prior dosing

value: Chronic trametinib treatment (3 xenograft generations) sustained prior to sample collection

value: Well-Mod

value: High Grade

tag: patient tumor stromal content


title: Acute trametinib alone treatment in UVA366 rep2

source_name: Acute trametinib alone treatment in UVA366 PDAC PDX tumors, biological rep2

tag: xenograft generation

value: Mouse Passage #8 (F8)

value: T (1 day)

value: 3 mg/kg trametinib given orally twice per day

value: No prior treatment with trametinib

value: No prior exposure to lapatinib

tag: trametinib duration

value: Acute trametinib treatment (24 hours) prior to sample collection

tag: lapatinib duration

value: No lapatinib exposure


title: Z(+) cell_technical rep1 and rep2

description: ZP_H003, ZP_H004

source_name: spleen Z(+) cells

tag: strain/background

value: NOD-SCID

tag: age

value: 6-8 weeks

tag: tissue

value: spleen

tag: cell type


title: HGBL,NOS (Case 10)

type: genomic

city: Warsaw

first: Beata

last: Grygalewicz

address: 15B Wawelska str

country: Poland

institute: Cancer Center and Institute of Oncology

hyb_protocol: 16ul of labelled DNA, 2ul Cot-1(1mg/ml), 4,5ul Agilent 10xBlockin Agent , 22,5ul Agilent 2xHiRPM Hybridization Buffer, denaturation at 94°C for 3 min, incubation at 37°C for 30 min, samples were applied to microarray, enclosed in MaiTai assembly, hybridization for 48h at 65°C. After hybridiazation slides were washed sequential

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Lowess normalized, background substracted data obtained from log2 of processed Red signal/processed Green signal.CytoSure Interpret software 020022 (OGT) was used.

source_name: biopsy paraffin

label_protocol: CytoSure Genomic DNA labelling Kit: 600ug of total DNA (18ul) was mixed with 10ul random primers and 10ul Reaction Buffer, denatured at 99°C for 20 min, mixed with 10ul Cy3-dCTP or Cy5-dCTP and 1ul Klenow, labelling at 37°C for 2h, incubation at 65°C for 10min, purification  on columns, combined labelled tumor and control DNA, dried down and  resuspended in 16ul of water

extract_protocol: Total DNA extracted from biopsy matrial using QIAmp DNA Blood Mini Kit Qiagen following manufacturer's instructions

tag: gender

value: Male

value: tumor material from stomach lymph node, bigger 11q duplication with terminal deletion

source_name: normal lymph node paraffin

value: normal lymph node


title: Chronic trametinib alone treatment sustained for 3 xenograft generations in UVA366 rep1

source_name: Chronic trametinib alone treatment sustained for 3 xenograft generations in UVA366 PDAC PDX tumors, biological rep1

value: Athymic nude mouse

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

value: 0.3 mg/kg trametinib given orally twice per day

value: No active treatment with trametinib

tag: sample batch

tag: patient biopsy site

value: Liver

tag: patient cancer type

value: Pancreatic adenocarcinoma

tag: patient tumor stage

value: Metastatic

tag: patient tumor differentiation

value: Poor

value: Low


title: BL (Case 9)

source_name: biopsy fresh

value: tumor material from tonsil,smaller 11q duplication with internal multiplication and terminal deletion

source_name: normal blood fresh

value: normal blood fresh


title: B-1a_WT_biologicalrep4

city: Copenhagen

first: Jeremy

middle: A

last: Daniel

address: Blegdamsvej 3b

country: Denmark

institute: NNF Center for Protein Research, University of Copenhagen

hyb_protocol: cDNA synthesis, labeling, and hybridization with GeneChip Mouse Gene 2.0 ST Array according to the manufacturer standard protocol available at www.affymetrix.com.

scan_protocol: Arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images applying protocol recommended by the manufacturer.

data_processing: Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC, Affymetrix).  Raw intensity .CEL files were preprocessed by quantile normalization, and gene summaries were extracted via robust multi-array average (RMA). The probe level data (CEL files) were transformed into expression measure using R version 3.2.2 (http://cran.at.r-project.org).

source_name: FACS sorted B-1a cells from PerC of 5-week-old WT mice

label_protocol: Phycoerythrin conjugated streptavidin using the Affymetrix Fluidics Station 450.

growth_protocol: Mice were sacrificed and peritoneal lavage was immediately performed using 20ml PBS supplemented with 5% FBS.  Cells were counted and stained with FACS antibodies and sorted on an BD FACSAria III Cell Sorter.

extract_protocol: Total RNA was extracted using RNeasy Plus Micro kit (Qiagen) and RNA quality was assessed using an Agilent Bioanalyzer with RIN numbers > 8.

tag: organ

value: peritoneal cavity

tag: developmental stage

value: 5 weeks


title: BL (Case 11)

value: Male

value: tumor material from abdominal lymph nodes, bigger 11q duplication with internal multiplication and terminal deletion


title: BLL,11q (Case 6)

value: tumor material from cervical lymph node, bigger 11q dupilcation with internal multiplication without terminal deletion


title: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 rep1

source_name: Chronic trametinib plus lapatinib treatment sustained for 5 xenograft generations in UVA366 PDAC PDX tumors, biological rep1

tag: host organism

value: Athymic nude mouse

tag: xenograft generation

value: Mouse Passage #10 (F10)

tag: treatment summary

tag: trametinib active dosing

tag: lapatinib active dosing

value: 65 mg/kg lapatinib given orally twice per day

tag: trametinib prior dosing

tag: lapatinib prior dosing

tag: trametinib duration

value: Chronic trametinib treatment (5 xenograft generations) sustained prior to sample collection

value: Chronic lapatinib treatment (5 xenograft generations) sustained prior to sample collection

tag: patient tumor grade

value: High Grade

tag: patient tumor stromal content


title: B-1a_WT_biologicalrep3

tag: cell type


title: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 rep3

source_name: Chronic trametinib plus lapatinib treatment discontinued after 4 xenograft generations in UVA366 PDAC PDX tumors, biological rep3

tag: xenograft tissue

value: Human pancreatic tumor explant grown orthotopically on mouse pancreas

tag: xenograft biopsy site

value: Mouse pancreas

tag: treatment condition

value: No active treatment with trametinib

value: 0.3 mg/kg trametinib given orally twice per day

value: Chronic trametinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: lapatinib duration

value: Chronic lapatinib treatment (4 xenograft generations) discontinued prior to sample collection

tag: sample batch

tag: patient biopsy site

value: Liver

value: Pancreatic adenocarcinoma


title: BL (Case 8)

tag: gender

value: Male

tag: tissue

value: tumor material from cervical lymph node, bigger 11q dupilcation with terminal deletion

value: normal blood fresh


title: BLL,11q (Case 5)

value: tumor material from abdominal lymph nodes, smaller 11q duplication with internal multiplication and terminal deletion


title: B-1a_WT_biologicalrep1

tag: organ

value: peritoneal cavity

tag: developmental stage

value: 5 weeks


title: sediment_New River Estuary_Channel Marker 15_NC_winter

city: Gulf Breeze

first: Jessica

middle: Anne

last: Lisa

state: FL

address: 1 Sabine Island Drive

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: DNA extracted from sediments used to create 2 targets to run on duplicate arrays

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 65°C and washed (Jayakumar et al. 2013).

scan_protocol: Microarrays were washed and scanned on a GenePix 4000A scanner (Agilent Technologies, Palo Alto CA). Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices).

data_processing:
Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the nirS probe set (normalized fluorescence ratio; FRN); values below 1% were excluded from further analyses (listed as zero in the array data matrix).

organism: synthetic construct

source_name: Universal Internal Standard complement (20-mer DNA oligo)

label_protocol: Hybridization targets were prepared as described by Jayakumar et al. (2013) using 50 ng of genomic DNA from each sediment sample. Genomic DNA was digested with HinF1 and labeled by amino-allyl-dUTP (Ambion, now Life Technologies, www.lifetechnologies. com) incorporation during a random priming labeling reaction using the Klenow polymerase and random octamers (Invitrogen).

extract_protocol: Sediment DNA was extracted using PowerSoil DNA Kit (Mo-Bio Laboratories) following the manufacturer's protocol with slight modifications, as in Lisa et al. (2014).

tag: sample type

value: 20-mer complement to universal internal standard

organism: uncultured bacterium

source_name: PCR product for estuarine metagenome

tag: location

value: New River Estuary Site M15

tag: season

value: winter

tag: depth

value: surface sediments


title: lmrB-2,S. mutans lmrB mutant

city: Guangzhou

first: Jia

last: Liu

state: Guangzhou

address: 74 Zhong Shan Er Road,

institute: Sun Yat Sen University

description: Gene expression of S. mutans lmrB mutant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Streptococcus mutans UA159

source_name: S.mutans lmrB mutant, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Streptococcus mutans UA159 were grown at 37°C under anaerobic conditions (90% N2, 5% CO2, 5% H2) in BHI broth (Difco, Sparks, MD, USA).

extract_protocol: RNA samples from the wild-type and the lmrB mutant were extracted as follows: cells were grown to mid-logarithmic phase (OD600=0.5) and collected by centrifugation. The obtained S. mutans cells were suspended in lysis buffer (30 mM Tris-HCl, 1 mM EDTA, 20 mg/mL lysozyme, [pH8.0]) and incubated at 37oC with gentle agitation for 30min. Total RNA was purified using RNeasy Mini kits (Qiagen) according to the manufacturer’s instructions.The obtained RNA from each sample was quantified using the NanoDrop ND-2000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: strain

tag: genotype

value: lmrB mutant


title: BLL,11q (Case 2)

value: tumor material from tonsil, bigger 11q duplication with terminal deletion


title: sediment_New River Estuary_Channel Marker 47_NC_winter

value: New River Estuary Site M47


title: BLL,11q (Case 3)


title: sediment_New River Estuary_Channel Marker 31_NC_winter

value: New River Estuary Site M31


title: BLL,11q (Case 4)


title: B-1a_WT_biologicalrep2

tag: cell type


title: lmrB-1,S. mutans lmrB mutant

source_name: S.mutans lmrB mutant, replicate 1


title: B-1a_KO_biologicalrep2

source_name: FACS sorted B-1a cells from PerC of 5-week-old KO mice


title: B-1a_KO_biologicalrep4


title: HGBL,NOS (Case 7)

value: tumor material from stomach,intestine,abdominal lymph nodes, bigger 11q duplication with terminal deletion


title: B-1a_KO_biologicalrep3


title: sediment_New River Estuary_Channel Marker 15_NC_summer

value: summer


title: sediment_New River Estuary_Jacksonville_NC_summer

value: New River Estuary Site JAX


title: B-1a_KO_biologicalrep1


title: BLL,11q (Case 1)

value: Male


title: WT-2, S. mutans

description: Gene expression of S. mutans WT cells

source_name: S.mutans wild type, replicate 2

value: wild type


title: sediment_New River Estuary_Jacksonville_NC_winter


title: sediment_New River Estuary_Channel Marker 31_NC_summer


title: sediment_New River Estuary_Channel Marker 47_NC_summer


title: MDA-MB-231-NC,rep2

status: Public on May 01 2017

city: Beijing

first: Jie

last: Wu

address: #5, dongdan 3, dongcheng district

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science

description: Gene expression data from MDA-MB-231 cells stably expressing negative control.

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cells, stably expressing negative control

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

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) and supplemented with 10% fetal bovine serum (Hyclone).

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

treatment_protocol: MDA-MB-231 cells stably expressing CTCF and negative control were established using lentivector-based overexpression system.Then cells were washed 3 times with PBS and lysed with Trizol

tag: cell line

tag: expression

value: negative control


title: WT-1, S. mutans

description: Gene expression of S. mutans WT cells

source_name: S.mutans wild type, replicate 1


title: MDA-MB-231-CTCF,rep2

description: Gene expression data from MDA-MB-231 cells stably expressing CTCF.

source_name: cells, stably expressing CTCF

value: stably expressing CTCF