title: 32148_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31908_H133_Plus_32148_3


title: 15

status: Public on Nov 17 2017

type: RNA

city: Malaga

first: Angela

last: Santonja

state: Malaga

address: Campus de teatinos s/n

department: Hospital Universitario Virgen de la Victoria

country: Spain

institute: Instituto de Investigación Biomédica de Málaga (IBIMA)

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient

hyb_protocol: Sample was hybridized to Affymetrix Human Transcriptome Array 2.0 array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were using the RMA algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from pretreatment biopsies of a triple negative breast cancer patient

label_protocol: 200ng of total RNA from each sample was amplified and labelled according to the Affymetrix SensationPlus FFPE protocol

extract_protocol: RNA was extracted with the RNeasy FFPE Kit (Qiagen) from 3-6 sections of 10µm formalin-fixed paraffin-embedded tumor tissue

tag: tissue

value: breast cancer

tag: treatment

value: Anthracyclines and/or taxanes + carboplatin

tag: pathological complete response

value: no


title: 32531_Placebo_Week_12

city: New Orleans

first: Tianhua

last: Niu

state: Louisiana

address: 1430 Tulane Avenue #8643

department: Biochemistry and Molecular Biology

country: USA

institute: Tulane University School of Medicine

description:
RNA expression data from whole blood sample
EA05064_31156_H133_Plus_32531_4

hyb_protocol: The labelled cRNAs were hybridized to the Affymetrix Human Genome U-133 Plus 2.0 (HG-U133plus2.0) arrays using standard Affymetrix hybridization, washing and staining kits according to the manufacturer's instructions by Expression Analysis Inc. (Durham, NC).

scan_protocol: GeneChips were scanned using standard Affymetrix GeneChip Scanner 3000 7G by Expression Analysis Inc. (Durham, NC).

data_processing: The data were analyzed with Bioconductor packages, such that data pre-processing and normalization were conducted by the Robust Multi-array Average (RMA) algorithm (Irizarry RA, et al., Nucleic Acids Res. 2003, PMID: 12582260).

label_protocol: Total RNAs were converted cDNAs and in vitro transcribed to biotin-labeled cRNAs according to the standard Affymetrix protocols by Expression Analysis Inc. (Durham, NC).

growth_protocol: This study was based on a previously published double-blind, multi-center, placebo-controlled, randomized, parallel-group study among 140 METH-dependent outpatients that were treated by either topiramate (N = 69) or placebo (N = 71) for 13 weeks (a dose titration phase: weeks 1-5; a maintenance phase: weeks 6-12; and a taper phase: week 13).

extract_protocol: Blood for RNA isolation were collected at approximately the same time of day for each individual at the three time points (i.e., baseline, Week 8, and Week 12) to control for potential circadian rhythm effects on expression. Total RNAs were extracted from the blood samples using the PAXgene Blood RNA Isolation Kit according to the manufacturer's instructions by Expression Analysis Inc. (Durham, NC).

treatment_protocol: Subjects meeting the eligibility criteria after a 14-day screening period and a baseline assessment were randomized into equivalent-size groups for oral treatment with TPM or placebo daily for 91 days (i.e., 13 weeks). There was a dose titration phase (Weeks 1-5) to a maximum tolerated dose of TPM not to exceed 200 mg/day, a maintenance phase (Weeks 6-12), and a taper phase (Week 13). To continue in the study, subjects had to maintain a minimum daily dose of 50 mg. Blood samples were collected on Day 1 (considered the baseline) and at the end of Weeks 8 and 12 from every participant who consented to participate in the genetics/expression study.

tag: individual id

tag: gender

value: Male

tag: age

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

value: Placebo

tag: time point

value: Week 12

value: whole blood


title: 32148_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31231_H133_Plus_32148_2

value: Female

value: Topiramate

value: Baseline


title: 32473_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_29694_H133_Plus_32473_2


title: 32568_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31076_H133_Plus_32568_3

value: Week 8


title: 16

value: Anthracyclines and/or taxanes

value: yes


title: 14


title: 32148_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_32726_H133_Plus_32148_4


title: 13


title: 11


title: 22334_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_37075_H133_Plus_22334_4


title: 12V


title: 22416_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_50629_H133_Plus_22416_4


title: 32531_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31155_H133_Plus_32531_3


title: 22416_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_39758_H133_Plus_22416_3


title: 10V


title: 22416_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_37453_H133_Plus_22416_2


title: 11V


title: 21949_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_35804_H133_Plus_21949_3


title: 21949_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_37074_H133_Plus_21949_4


title: 10


title: 9V


title: 7V


title: 22308_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_34548_H133_Plus_22308_2


title: 7A


title: 21165_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_35496_H133_Plus_21165_3


title: 21165_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_35825_N2_H133_Plus_21165_4


title: 8V


title: 22308_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_35796_H133_Plus_22308_3


title: 27V

description: Gene expression data from pretreatment biopsies of a triple negative breast cancer patient


title: 9


title: 22334_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_36358_H133_Plus_22334_3


title: 8


title: 21165_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_34311_H133_Plus_21165_2


title: 6V


title: 22308_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_36773_H133_Plus_22308_4


title: 10666_Placebo_Week_8

description:
RNA expression data from whole blood sample
EA05064_31832_H133_Plus_10666_3

value: Asian


title: 6


title: 10666_Placebo_Week_12

description:
RNA expression data from whole blood sample
EA05064_32219_H133_Plus_10666_4


title: 21126_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_33831_H133_Plus_21126_2


title: 10469_Topiramate_Baseline

description:
RNA expression data from whole blood sample
EA05064_31915_H133_Plus_10469_2

value: Unknown


title: 32789_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_32993_H133_Plus_32789_4

value: Hispanic


title: 5

value: breast cancer


title: 4

value: Anthracyclines and/or taxanes + carboplatin


title: 5V

value: no


title: 3


title: 4V


title: 10469_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_33508_H133_Plus_10469_3


title: 3V


title: 22A


title: 10265_Topiramate_Week_12

description:
RNA expression data from whole blood sample
EA05064_31736_H133_Plus_10265_4

value: Male

value: White


title: Huh751_Ctrl_c

city: Bethesda

first: T. Jake

last: Liang

state: MD

address: 9000 Rockville Pike, Bldg 10 Rm. 9B16

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institutes of Health

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 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: Data were analyzed using R/Bioconductor.  Data were normalized using the RMA method from the oligo package.

source_name: Huh7.5.1, Control, c

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: Cells were maintained in complete DMEM containing 10% FBS (Omega Scientific), 100 U/ml penicillin, and 100 μg/ml streptomycin at 37oC with 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen)

treatment_protocol: siRNAs (either siNDRG1 or siNT) were transfected into Huh7.5.1 cells at a 50 nM final concentration, using Oligofectamine (Invitrogen) in a 6-well plate.

tag: cell line

value: siNT (Control)


title: Huh751_NDRG1KD_c

source_name: Huh7.5.1, Knock Down, c

value: siNDRG1 (Knock Down)


title: Huh751_NDRG1KD_b

source_name: Huh7.5.1, Knock Down, b


title: 10265_Topiramate_Week_8

description:
RNA expression data from whole blood sample
EA05064_31476_H133_Plus_10265_3

value: Non-Hispanic

value: whole blood


title: 2V


title: Identification of miR-145-5p target genes in A549

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell type

value: lung cancer

tag: transfection

value: no transfection

source_name: miR-145-5p transfected cell line


title: Identification of miR-145-5p target genes in TE8

value: carcinoma

value: esophageal cancer


title: Identification of miR-145-3p target genes in A549

source_name: miR-145-3p transfected cell line


title: Redif_H9

status: Public on Nov 16 2017

type: genomic

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing:
DEVA (Nimblegen) software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias (limma package, R/Bioconductor) and early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
Processed data values: Log2 transformed early/late replication timing ratios quantile normalized and loess smoothed

molecule: genomic DNA

source_name: Early-replicating DNA

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: Human fibroblasts were maintained in DMEM containing 10% heat-inactivated FBS, 2 mM L-Glutamine, 1% penicillin and streptomycin (all from Invitrogen)

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

treatment_protocol: BrdU-labeled

tag: disease

value: Healthy

value: hESC-derived

source_name: Late-replicating DNA


title: iPSC_92yr

growth_protocol: Human ES cells and iPSCs were maintained on feeder-free culture on matrigel (BD Biosciences) with chemically defined mTeSR (Stemcell technologies) medium, as previously described (Ludwig et al., 2006).

value: iPSC 92 yrs


title: Redif_92yr

value: iPSC-derived


title: ESC_H9

value: Embryonic


title: iPSC_Fetal_R1

value: iPSC fetal


title: Identification of miR-145-3p target genes in TE8


title: Redif_Fetal_R2


title: Identification of miR-223-5p target genes in T24

value: bladder cancer

source_name: miR-223-5p transfected cell line


title: Huh751_Ctrl_b

source_name: Huh7.5.1, Control, b


title: Redif_Fetal_R1


title: Ctrl_0yr

value: Newborn


title: Ctrl_74yr

value: 74 yrs


title: 2

value: breast cancer

value: Anthracyclines and/or taxanes + carboplatin

value: no


title: Huh751_Ctrl_a

source_name: Huh7.5.1, Control, a

value: siNT (Control)


title: 1V

value: Anthracyclines and/or taxanes


title: Redif_74yr


title: iPSC_74yr

value: iPSC 74 yrs


title: Ctrl_96yr

value: 96 yrs


title: Differentially expressed genes by knocking down of PMM2_1 in A498

value: renal cancer

value: no transfection

source_name: si-PMM2-1 transfected cell line


title: HGPS_AG11513_8yr

value: Progeria

value: 8 yrs


title: PreS_Fetal

value: Healthy

value: Fetal


title: Identification of miR-223-3p target genes in T24

source_name: miR-223-3p transfected cell line


title: Huh751_NDRG1KD_a

source_name: Huh7.5.1, Knock Down, a

value: siNDRG1 (Knock Down)


title: PreS_74yr


title: Differentially expressed genes by knocking down of PMM2_2 in A498

source_name: si-PMM2-2 transfected cell line


title: Baf53a-cKO cells+Baf53a

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

description: Gene expression after rescued Baf53a.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Mouse Genome microarry 4x44K Ver. 2.0 (G2519F, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026655_D_F_20121126) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

organism: Mus musculus

source_name: Baf53a-expressing Baf53a-deficient ES cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 15% FBS DMEM + LIF + penicillin/streptomycin

extract_protocol: Total RNA was isolated using Sepasol-RNAⅠSuper G (Nakalai Tesuque, Japan) according to the manufacturer's instructions.

value: ES cells

tag: genotype/variation


title: Baf53a-cKO cells+Baf53b

description: Gene expression after rescued Baf53b.

source_name: Baf53b-expressing Baf53a-deficient ES cells


title: set2 T64

city: Liverpool

first: Violaine

last: See

address: Crown Street

department: Biochemistry

country: United Kingdom

institute: University of Liverpool

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 64h. It is the second of three  replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

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

growth_protocol: D283-MED were maintained in modified Eagle’s medium (MEM) with 10% FCS, 1% non-essential amino acid and 1% sodium pyruvate. Cells were typically cultured in 75cm2 tissue culture flasks (Corning, UK) and maintained in a growth condition of 37C, 5% CO2 in a humidified incubator (SAYO, Japan). For hypoxic conditions (1% O2) cells were manipulated and incubated in a hypoxic workstation (Don Whitley Scientific, UK)

extract_protocol: RNA extraction using Rneasy Plus (Qiagen, Germany) kit was identical to extraction using Rneasy kit as described earlier with the exception of one extra step. After homogenisation with QIAshredder (Qiagen), the homogenized lysate was transferred to a DNA Eliminator spin column, centrifuged for 3 seconds at 10,000rpm. The flow through was collected and used for RNA extraction following the ‘Spin Protocol’ as described in the manufacturer handbook. RNA was eluted with 30μl of RNase free water and the sample purity is quantified using spectrophotometry.


title: set3 T6

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 6h. It is the third of three  replicates used in this experiment, each from separate cultures.

treatment_protocol: For hypoxic conditions (1% O2) cells were manipulated and incubated in a hypoxic workstation (Don Whitley Scientific, UK)


title: set2 T0

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 21% O2 (control). It is the second of three  replicates used in this experiment, each from separate cultures.


title: set1 T96

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 96h. It is the first of three  replicates used in this experiment, each from separate cultures.


title: set1 T6

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 6h. It is the first of three  replicates used in this experiment, each from separate cultures.


title: IFN-g+RV16-4

city: Ann Arbor

first: Marc

last: Hershenson

state: MI

address: 1150 West Medical Center Drive

department: Pediatrics

institute: University of Michigan

description: gene expression data from Biological sample 4 for IFN-g+RV16

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 Plates, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: Data was analyzed using the oligo Bioconductor packages implemented in the R-statistical language version 3.3.0. RMA was used to fit normalized log2 transformed expression values

source_name: PBMC

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

growth_protocol: Isolated PBMCs were maintained at 37°C with 5% CO2 in RPMI 1640 medium (supplemented with 20% FCS and 1% pencillin-streptomycin), as described previously by Mor-vaknin et al.Mol Cell Biol, 2006. 26(24): p. 9484-96.

extract_protocol: QIAGEN RNeasy Mini Kit

treatment_protocol: PBMCs were cultured for 2 weeks and then polarized to an M1 phenotype by treating with 200 IU/ml IFN-y (R&D, Minneapolis, MN) or M2 phenotype by treating with 50 ng/ml IL-4 (R&D) for 24hrs.  The macrophages were then treated with sham or RV16 at multiplicity of infection of 10 for 24hrs.

tag: polarization state

value: M1 polarized


title: IFN-g+RV16-1

description: gene expression data from Biological sample 1 for IFN-g+RV16


title: set3 T64

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 64h. It is the third of three  replicates used in this experiment, each from separate cultures.


title: set3 T0

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 21% O2 (control). It is the third of three  replicates used in this experiment, each from separate cultures.


title: IFN-g+RV16-3

description: gene expression data from Biological sample 3 for IFN-g+RV16


title: IFN-g+sham-3

description: gene expression data from Biological sample 3 for IFN-g+sham

value: IFN-g+sham


title: IL4+RV16-4

description: gene expression data from Biological sample 4 for IL4+RV16

value: M2 polarized


title: IFN-g+sham-2

description: gene expression data from Biological sample 2 for IFN-g+sham


title: set2 T6

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 6h. It is the second of three  replicates used in this experiment, each from separate cultures.


title: set1 T64

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 64h. It is the first of three  replicates used in this experiment, each from separate cultures.


title: IFN-g+RV16-2

description: gene expression data from Biological sample 2 for IFN-g+RV16


title: IL4+sham-5

description: gene expression data from Biological sample 5 for IL4+sham


title: RV16-5

description: gene expression data from Biological sample 5 for RV16

value: unpolarized


title: set3 T96

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 96h. It is the third of three  replicates used in this experiment, each from separate cultures.


title: set2 T96

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 1% O2 for 96h. It is the second of three  replicates used in this experiment, each from separate cultures.


title: IFN-g+sham-1

description: gene expression data from Biological sample 1 for IFN-g+sham


title: sham-5

description: gene expression data from Biological sample 5 for sham

value: sham


title: set1 T0

description:
Cell Line D283 Med (ATCC® HTB-185™); Organism: Homo sapiens, human  /  Cell Type: Medulloblastoma  /  Tissue: brain/cerebellum; derived from metastatic site: peritoneum  /  Disease: medulloblastoma
This sample is D283-Med cells cultured at 21% O2 (control). It is the first of three  replicates used in this experiment, each from separate cultures.


title: 10666_Placebo_Baseline

description:
RNA expression data from whole blood sample
EA05064_30607_H133_Plus_10666_2

value: Male

value: Asian

value: Non-Hispanic

value: Placebo

value: Baseline

value: whole blood


title: RV16-4

description: gene expression data from Biological sample 4 for RV16


title: IL4+RV16-3

description: gene expression data from Biological sample 3 for IL4+RV16


title: IL4+RV16-5

description: gene expression data from Biological sample 5 for IL4+RV16


title: RV16-3

description: gene expression data from Biological sample 3 for RV16


title: IL4+sham-2

description: gene expression data from Biological sample 2 for IL4+sham


title: sham-3

description: gene expression data from Biological sample 3 for sham


title: sham-2

description: gene expression data from Biological sample 2 for sham


title: UMSCC1_NUP62i_rep1

description: Gene expression three days after siRNA transfection.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: UMSCC1, NUP62 knocked down cell, replicate 1

growth_protocol: 10% FBS DMEM + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Macherey-Nagel) according to the manufacturer's instructions.

value: head and neck squamous cell carcinoma cell line

tag: sirna transfection

value: NUP62 knockdown


title: IL4+sham-1

description: gene expression data from Biological sample 1 for IL4+sham


title: UMSCC1_NUP62i_rep2

source_name: UMSCC1, NUP62 knocked down cell, replicate 2


title: IL4+RV16-2

description: gene expression data from Biological sample 2 for IL4+RV16


title: UMSCC1_CTLi_rep1

source_name: UMSCC1, negative control cell, replicate 1

value: negative control


title: IL4+sham-3

description: gene expression data from Biological sample 3 for IL4+sham


title: sham-4

description: gene expression data from Biological sample 4 for sham


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep4

status: Public on Nov 15 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 4
Het_18M_13549

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary and quantile normalisation (Expression console v.1.3.0.187, Affymetrix)

organism: Rattus norvegicus

label_protocol: Ovation PicoSL WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

tag: strain

value: Sprague–Dawley white eye/Wistar–Kyoto

value: 18 months

tag: genotype

value: p27Kip1 (Cdknb1) mutant, heterozygous


title: RV16-1

description: gene expression data from Biological sample 1 for RV16

tag: treatment


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep3

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 3
Het_18M_192450

scan_protocol: According to the Affymetrix expression protocol


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep6

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 6
Het_18M_11676


title: P493-6_doxcycline treated_24 hours_rep1

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description:
total RNA (ncRNA and mRNA)
Gene expression after 24hr in doxcycline-treated P493-6 cell lines which carry the Myc tet-off system

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube: For 8*60K array Amount, cyanine 3-labeled, linearly amplified cRNA 0.6ug, 10X Blocking Agent 5ul, Nuclease-free water ×ul, 25X Fragmentation Buffer 1ul, Total volume 25ul. 4. Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA.  6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible.  10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. 12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14. Hand-tighten the clamp onto the chamber. 15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: 1. Assemble the slides into an slide holder.  2. Place assembled slide holders into scanner carousel. 3. Verify scan settings for one-color scans. Parameters: Scan region Scan Area (61 x 21.6 mm), Scan resolution (μm) 5, 5μm scanning mode Single Pass, eXtended Dynamic range (selected), Dye channel Green, Green PMT   XDR Hi 100%, XDR Lo 10%. 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing:
1. Open the Agilent Feature Extraction (FE) software. 2. Add the images (.tif) to be extracted to the FE Project. 3. Set FE Project Properties. 4. Check the Extraction Set Configuration. 5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6. Select Project > Start Extracting and export data to txt.
Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1. The GeneSpring GX v11.5.1 software package (Agilent Technologies) is used to produce the files LncRNA Expression Profiling Data.xls and mRNA Expression Profiling Data.xls (available on the series record).

source_name: P493-6, doxcycline treated, 24 hour, replicate 1

label_protocol: RNA was amplified and labeled with Cy3 by cDNA Master Mix and Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). And the cRNA was purified by RNeasy Mini Kit (Qiagen p/n 74104).

growth_protocol: P493-6 cells carrying a c-Myc tet-off system were cultured in RPMI medium 1640 containing 10% fetal bovine serum in a humidified incubator with 5% CO2.

extract_protocol: Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of P493-6 cells. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: P493-6 cells were seeded in 6-well plate and treated with doxcycline for 0 or 24 hours.


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep2

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 2
Het_18M_19676


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep1

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 1
Het_18M_711185


title: sham-1

description: gene expression data from Biological sample 1 for sham


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep4

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 4
Het_9M_13200

value: 9 months


title: Medullary_thyroid_carcinoma_Cdkn1b_het_18months_rep5

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 18 months, replicate 5
Het_18M_12931


title: P493-6_doxcycline treated_24 hours_rep2

source_name: P493-6, doxcycline treated, 24 hour, replicate 2


title: P493-6_doxcycline treated_0 hour_rep3

description:
total RNA (ncRNA and mRNA)
Gene expression after 0hr in doxcycline-treated P493-6 cell lines which carry the Myc tet-off system

source_name: P493-6, doxcycline treated, 0 hour, replicate 3


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep1

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 1
Het_9M_13830


title: P493-6_doxcycline treated_0 hour_rep2

source_name: P493-6, doxcycline treated, 0 hour, replicate 2


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep6

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 6
Het_9M_13198


title: IL4+RV16-1

description: gene expression data from Biological sample 1 for IL4+RV16


title: UMSCC1_CTLi_rep2

description: Gene expression three days after siRNA transfection.

source_name: UMSCC1, negative control cell, replicate 2


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep5

description:
Gene expression data from Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 5
Hom_9M_111631

value: p27Kip1 (Cdknb1) mutant, homozygous


title: P493-6_doxcycline treated_24 hours_rep3

source_name: P493-6, doxcycline treated, 24 hour, replicate 3


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep2

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 2
Het_9M_13202


title: P493-6_doxcycline treated_0 hour_rep1

source_name: P493-6, doxcycline treated, 0 hour, replicate 1


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep2

description:
Gene expression data from Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 2
Hom_9M_121792


title: G5F3Balb_c_Day_0_64

city: Woolloongabba

first: Ahmed

middle: Murtaza

last: Mehdi

state: QLD

address: 37 Kent Street

department: Diamantina Institute

country: Australia

institute: The University of Queensland

description: BALBc replicate 3 batch 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray data were initially extracted through Illumina GenomeStudio. We removed batch effects using the limma package in R. Raw data were normalized to the 50th percentile (per array) and each gene was normalized to its median expression across all arrays. Probes with Illumina detection values above 0.95 in all arrays were retained for analyses.

source_name: BALBc ileum sample rep 3

label_protocol: Not provided

extract_protocol: Total RNA was purified from terminal ileum of 8 naïve SKG and 3 naïve BALB/c mice using RNeasy kits (Qiagen). RNA from tissues selected for microarray (10 - 30mg, Bioanalyzer RNA Integrity Scores >6) was amplified using the TotalPrep RNA amplification kit (Ambion). Amplified RNA was hybrized to Illumina MouseRef-8 v2.0 Expression BeadChip arrays. Arrays were scanned on an Illumina iScan.

value: BALBc

tag: tissue

value: ileum

value: 8 - 12 weeks


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep6

description:
Gene expression data from Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 6
Hom_9M_111629


title: G1F6SKG_day_0_83

description: SKG replicate 8 batch 3

source_name: SKG ileum sample rep 8

value: SKG


title: G1F4SKG_day_0_81

description: SKG replicate 7 batch 3

source_name: SKG ileum sample rep 7


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep4

description:
Gene expression data from Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 4
Hom_9M_121790


title: IL4+sham-4

description: gene expression data from Biological sample 4 for IL4+sham

value: M2 polarized


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep3

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 3
Het_9M_13201


title: SKG_day_0_84

description: SKG replicate 2 batch 1

source_name: SKG ileum sample rep 2


title: Medullary_thyroid_carcinoma_Cdkn1b_het_9months_rep5

description:
Gene expression data from Medullary thyroid carcinoma of heterozygous Cdkn1b-mutant rat, age of 9 months, replicate 5
Het_9M_13199


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep3

description:
Gene expression data from Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 3
Hom_9M_121791


title: G1F1SKG_day_0_78

description: SKG replicate 4 batch 3

source_name: SKG ileum sample rep 4


title: Balb_c_Day_0_63

description: BALBc replicate 2 batch 2

source_name: BALBc ileum sample rep 2


title: Medullary_thyroid_carcinoma_Cdkn1b_hom_9months_rep1

description:
Gene expression data from medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months, replicate 1
Hom_9M_13351

source_name: Medullary thyroid carcinoma of homozygous Cdkn1b-mutant rat, age of 9 months


title: SKG_day_0_82

description: SKG replicate 3 batch 1

source_name: SKG ileum sample rep 3


title: SKG_day_0_85

description: SKG replicate 1 batch 1

source_name: SKG ileum sample rep 1


title: 30_(HuEx-1_0-st-v2)

city: Beijing

first: Yanqiong

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 15 non-responders) treated with TwHF.

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

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

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

source_name: At early stage of the disease

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

growth_protocol: peripheral blood extracted from RA patients' serum were stored at liquid nitrogen temperatures at once with protected with Rnasin inhibitors

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

treatment_protocol: peripheral blood mononuclear cells extracted from RA patients' serum were collected for further total RNA extraction

tag: response

value: Responder


title: 6_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 16 non-responders) treated with TwHF.

value: peripheral blood mononuclear cells extracted from RA patients' serum


title: Balb_c_Day_0_62

description: BALBc replicate 1 batch 2

source_name: BALBc ileum sample rep 1


title: 7_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 17 non-responders) treated with TwHF.


title: 25_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 14 non-responders) treated with TwHF.


title: 20_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 8 non-responders) treated with TwHF.

value: Non-responder


title: G1F3SKG_day_0_80

description: SKG replicate 6 batch 3

source_name: SKG ileum sample rep 6


title: 24_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 9 non-responders) treated with TwHF.


title: 17_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 12 non-responders) treated with TwHF.


title: G1F2SKG_day_0_79

description: SKG replicate 5 batch 3

source_name: SKG ileum sample rep 5


title: 19_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 7 non-responders) treated with TwHF.


title: 5_(miRNA-4_0)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 11 non-responders) treated with TwHF.

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip miRNA 4.0 array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450


title: 4_(miRNA-4_0)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 10 non-responders) treated with TwHF.


title: 17_(miRNA-4_0)


title: 22_(miRNA-4_0)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 13 non-responders) treated with TwHF.


title: NGP TFAP4 KD RNASeq [SD018]

type: SRA

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: SD018 raw data missing

library_source: transcriptomic

data_processing:
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated containing gene level read count values, gene FPKM and isoform FPKM values

source_name: NGP TFAP4 KD RNASeq

growth_protocol: NGP was maintained in RPMI-40 medium supplemented with 10% FBS and 1% penicillin/streptomycin (Invitrogen)

extract_protocol:
Total RNA was extracted using RNEASY mini kit (Qiagen).
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.
Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol:
1ug/ml Doxycycline adding into the medium to induce the shRNA
Lentiviral particles using shRNA (Dharmacon, V3THS_301154) against TFAP4.

value: NGP

tag: tissue source

value: bone marrow metastatic neuroblastoma

value: neuroblastoma cell line

value: Dox


title: 4_(HuEx-1_0-st-v2)


title: 25_(miRNA-4_0)


title: 19_(miRNA-4_0)


title: SKNDZ TFAP4 KD RNASeq [SD008]

description: SD008 raw data missing

source_name: SKNDZ TFAP4 KD RNASeq

growth_protocol: SKNDZ was maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin (Invitrogen).

value: SK-N-DZ

value: shRNA (Dharmacon, V3THS_301154) against TFAP4


title: 22_(HuEx-1_0-st-v2)


title: NGP TFAP4 KD RNASeq [SD012]

description: SD012 raw data missing


title: NGP Control RNASeq [SD011]

description: SD011 raw data missing

source_name: NGP Control RNASeq

treatment_protocol:
Control
Lentiviral particles using shRNA (Dharmacon, V3THS_301154) against TFAP4.

value: control

value: Control


title: 6_(miRNA-4_0)


title: 20_(miRNA-4_0)


title: 30_(miRNA-4_0)


title: PBS_3days

city: Stanford

first: Jayakar

middle: V.

last: Nayak

state: CA

address: 801 Welch Road

department: Otolaryngology

institute: Stanford University School of Medicine

hyb_protocol: The fragmented and labeled targets were hybridized to the Mouse gene 2.0 ST arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: pbs

label_protocol: Affymetrix WT Plus reagent kit was used to generate fragmented and biotin-labeled single stranded cDNA targets

extract_protocol: Total RNA was extracted using Nucleo Spin RNA (Macherey-Nagel, Duren, Germany) according to the manufacturer's instructions.

value: Nasal mucosa

tag: age

value: 4-6 weeks


title: NGP Control RNASeq [SD017]

description: SD017 raw data missing


title: SKNDZ TFAP4 KD RNASeq [SD0014]

description: SD014 raw data missing


title: 15_(HuEx-1_0-st-v2)

description: lncRNA and mRNA expression profiles in peripheral blood mononuclear cells obtained from a discovery cohort including 12 RA patients (6 responders and 6 non-responders) treated with TwHF.


title: DLBCL, GCB, Patient 8

city: Vienna

first: Wolfgang

middle: Michael

last: Bauer

address: Waehringerguertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

hyb_protocol: Hybridization mixture was prepared according to the Affymetrix protocol. Each sample was hybridized to a GeneChip PrimeView Human Gene Expression Array (Affymetrix). Arrays were washed and stained in a GeneChip Fluidics Station 450 .

scan_protocol: GeneChip Scanner 3000

data_processing: CEL files were generated from DAT files using GCOS software. To generate the log2 expression estimates, overall array intensity was normalized between arrays and the probe intensity of all probes in a probe set summarized to a single value using the Robust Multichip Average algorithm in Partek Genomics Suite 6.6

source_name: sorted tumor cells from a lymph node

label_protocol: biotin

extract_protocol: RNA was isolated using magnetic beads

treatment_protocol: FACS sorting

tag: origin

value: lymph node

tag: tumor cell

value: DLBCL, GCB


title: DLBCL, non-GCB, Patient 3

value: DLBCL, non-GCB


title: SKNDZ Control RNASeq [SD013]

description: SD013 raw data missing

source_name: SKNDZ Control RNASeq


title: DLBCL, GCB, Patient 7


title: IVLBCL tumor cells

source_name: sorted tumor cells from a skin biopsy

value: skin biopsy

value: IVLBCL


title: DLBCL, non-GCB, Patient 5


title: mirN1

status: Public on Nov 14 2017

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: microRNA expression data from healthy donor plasma cells

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Normal donor 1

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: diagnosis

value: healthy control

value: CD138+ plasma cells


title: 7_(miRNA-4_0)

value: Responder

value: peripheral blood mononuclear cells extracted from RA patients' serum


title: mirN4

source_name: Normal donor 4


title: 24_(miRNA-4_0)

value: Non-responder


title: mirN3

source_name: Normal donor 3


title: mirN2

source_name: Normal donor 2


title: Papain_3days

source_name: papain


title: DLBCL, non-GCB, Patient 4


title: DLBCL, GCB, Patient 6


title: 15_(miRNA-4_0)


title: PCLBCL-LT, Patient 2

value: PCLBCL-LT


title: PCLBCL-LT, Patient 1


title: HCMV

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

description: HCMV NR-1 successfully established latency in HPCs

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

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

data_processing: Raw data were normalized by MAS 5.0/RMA algorithm, Affy packages in R.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) / Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) / Ovation® Pico WTA System V2(Cat#3302， NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: CD34+ HPCs were cultured with StemPro-34 SFM plus cytokines SCF (100 ng/mL),  IL-3 (50 ng/mL), and GM-CSF (25 ng/mL) at 37c in 5% CO2

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

treatment_protocol: To reactive HCMV from latent infection, CD34+ HPCs infected with NR-1 were treated with phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA) for 24 h and then incubated with human foreskin fibroblast (HFF)

value: HCMV infected human CD34+ HPCs


title: mESC_biorep3

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

hyb_protocol: hybridized to the Affymetrix Mouse 430 2.0 chips (PAN Facility Stanford).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner

data_processing: Data sets analyzed using the Affimetrix Expression and Transcriptome Analysis Console.. Data from CEL files were loaded and preprocessed using the oligo package (v. 1.38.0; package = pd.mogene.2.0.st ) in R (v. 3.3.1). Raw expression values were log2 transformed and normalized using the Robust Multi-Array Average method from the oligo package.

source_name: Embryonic stem cells

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from cells using TRIzol according to manufacturer’s instructions (Invitrogen). RNA was purified using RNAeasy MinElute Cleanup (Qiagen)

value: Undifferentiated embryonic stem cells

tag: strain/genotype

value: C.FVB-Tg(CAG-luc, GFP)L2G85Chco/FathJ

tag: passage

value: < passage 20


title: Mock

description: human CD34+ HPCs

source_name: human CD34+ HPCs

tag: cell type

value: Normal human CD34+ HPCs


title: ES_HLC_biorep1

source_name: Differentiated ESC

value: mESC differentiated into hepatocyte like cells


title: ES_HLC_biorep3


title: Ad_Hep_biorep2

source_name: Liver

value: Adult Hepatocytes


title: ES_HLC_biorep2


title: Identification of miR-185-5p target genes in T24

source_name: mock

tag: cell line

value: bladder cancer

tag: transfection

value: no transfection

source_name: miR-185-5p transfected cell line


title: mESC_biorep4


title: Ad_Hep_biorep1


title: Ad_Hep_biorep3


title: Identification of miR-107 target genes in T24

source_name: miR-107 transfected cell line


title: mESC_biorep1


title: mESC_biorep2


title: Identification of miR-320c target genes in T24

source_name: miR-320c transfected cell line


title: Identification of miR-30a-5p target genes in PC3

value: prostate cancer

source_name: miR-30a-5p transfected cell line


title: lncN4

description: Gene expression data from healthy donor plasma cells

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Expression data has been normalized using RMA procedure at the probe cluster ID annotation level. Cross-hybridization probes were filtered-out. We combined annotated probes with both Ensembl transcripts (GRCh37/hg19 assembly) and lncRNAs from v4 database on LNCipedia repository (http://www. lncipedia.org/), based on the chromosome localization of the target sequence identified by each probe; afterwards, we considered only probes univocally referable to lncRNA transcripts (i.e. that do not overlap with Ensembl transcripts). To summarize probes related to each lncRNA, we considered their median expression value

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).


title: Identification of miR-135-3p target genes in SAS

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

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

value: SAS

value: oral squamous cell carcinoma

source_name: miR-135-3p transfected cell line


title: shCCP6

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: This is CCP6-depleted D3 ESCs

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

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

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

source_name: CCP6-depleted D3 ESCs

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit according to The GeneChip® WT Terminal Labeling and Hybridization User Manual

treatment_protocol: D3 ESCs were infected with shCtrl or shCCP6 retrovirus for 48hr. 5x105  D3 ESCs were harvested after trypzinization.

value: CCP6 knockdown


title: Identification of miR-184 target genes in PC3

source_name: miR-184 transfected cell line


title: lncN3

value: healthy control

value: CD138+ plasma cells


title: Identification of miR-320b target genes in T24

source_name: miR-320b transfected cell line


title: lncN2


title: 5_(HuEx-1_0-st-v2)

source_name: At early stage of the disease

value: Non-responder

value: peripheral blood mononuclear cells extracted from RA patients' serum


title: IL13 21d, biological rep3

city: Iowa City

first: Alejandro

middle: A

last: Pezzulo

state: IA

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

description: Gene expression data from human airway epithelia exposed to vehicle or IL13 20ng/mL for 21 days

hyb_protocol: Five micrograms of purified cDNA product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.  The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Gene 1.0 ST arrays (Part No. 901085), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing: The data were analyzed with Partek Genomics Suite. RMA with background subtraction, quantile normalization and log2 transformation was performed.

source_name: Human airway epithelia 21 days IL13

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility.  Briefly, 50 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v2 (NuGEN Technologies, San Carlos, CA, Cat. #3302) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.

growth_protocol: Well-differentiated cultures of human airway epithelia were obtained from the in vitro models and cell culture core of the University of Iowa

treatment_protocol: DMEM/F12 media with Ultroser G was replaced every two days. 20ng/mL recombinant human IL13 in PBS was added to treatment groups with every media change for 21 days

value: human airway epithelia primary culture

tag: agent


title: IL13 21d, biological rep1


title: Differentially expressed genes by knocking down of PHLDA2-2 in PANC-1

first: Naohiko

address: 1-8-1, Inohana

institute: Chiba University

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

value: pancreatic cancer

source_name: si-PHLDA2-2 transfected cell line


title: Identification of miR-451a and miR-144-3p/5p target genes in 786-O

value: renal cell carcinoma

source_name: miR-451a and miR-144-3p/5p co-transfected cell line

value: miR-451a and miR-144-3p/5p


title: Identification of miR-455-3p target genes in 786-O

source_name: miR-455-3p transfected cell line


title: Identification of miR-451a and miR-144-3p/5p target genes in A498


title: Identification of miR-30a-3p target genes in PC3

source_name: miR-30a-3p transfected cell line


title: IL13 21d, biological rep2


title: Propofol 2

city: Milwaukee

first: Xiaowen

last: Bai

state: WI

address: 8701 Watertown Plank Road

department: Anesthesiology

institute: Medical College of Wisconsin

description: 7 day old mice received an intraperitoneal injection of 50mg/kg propofol or 50mg/kg intralipid vehicle control, with a total exposure of 3h.  This was followed by a 3h washout.  Mice were sacrificed, hippocampal tissues were collected, and RNA was extracted prior to profiling.

hyb_protocol: labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar)

scan_protocol: arrays were scanned by the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that at least 2 out of 8 samples have flags in Present or Marginal (“All Targets Value - mRNAs”) were chosen for differentially expressed mRNAs screening

source_name: hippocampus

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 mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar

extract_protocol: After mouse hippocampus tissues were lysed in the QIAzol lysis reagent (Qiagen Inc., Valencia, CA), chloroform was thoroughly mixed with the samples, set for 5 minutes before centrifuged.  Supernatants were transferred into a new tube and mixed with isopropanol and centrifuged again for pellets. After washed with 75% ethanol for one time, the pellets were dried and dissolved in RNase free water. The quantity and purity of RNA were validated using a Nanodrop spectrophotometer (Thermo scientific).

value: hippocampus

value: 7 days-old


title: Differentially expressed genes by knocking down of PHLDA2-3 in PANC-1

last: Seki

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

source_name: si-PHLDA2-3 transfected cell line


title: Control 4

treatment_protocol: 7 day old mice received an intraperitoneal injection of 50mg/kg propofol or 50mg/kg intralipid vehicle control, with a total exposure of 3h.  This was followed by a 3h washout.  Mice were sacrificed, hippocampal tissues were collected, and RNA was extracted prior to profiling.


title: Vehicle 21d, biological rep3

source_name: Human airway epithelia 21 days vehicle

value: control


title: Vehicle 21d, biological rep1


title: Vehicle 21d, biological rep2


title: Propofol 3


title: Propofol 4


title: Propofol 1


title: siRHOQ3

status: Public on Nov 13 2017

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

institute: SUN YAT-SEN UNIVERSITY

description: Gene expression data from normal human

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: Biotin

source_name: HCT-116 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: DMEM added with 10%FBS

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Scramble siRNA or siRHOQ

value: colorectal cell line

tag: knockdown

value: siRHOQ


title: Control 3


title: Control 1


title: siRHOQ2

description: Gene expression data from normal human


title: Control 2


title: siRHOQ1

description: Gene expression data from normal human


title: NC3

description: Gene expression data from normal human

value: scramble siRNA


title: NC2

description: Gene expression data from normal human


title: IFNa_a_HUHH0011_Mock_18h_1_RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). 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 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene 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: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.  No outliers were identified in this study.

source_name: HUH cells, Mock-inoculated, 18h, bioreplicate 1

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: HUH VP30 cells , seeded at 3x10^5 cells/well in 12-well plates one day prior to treatment

extract_protocol: RNA samples were collected by lysing cells directly in TRIzol.  Lysates were scraped into a tube, vortexed thoroughly and directly frozen at -80°C.

treatment_protocol: Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 250 U/ml of human interferon α and 250 U/ml of human interferon β(PBL Biosciences).  Mock-treated cells were given normal culture medium only.  Mock and treated cells were incubated at 37°C until sample collection time points.

value: HUH VP30

tag: parental cell line

value: HUH

tag: genotype/variation

value: HUH cells stably transfected with Ebola VP30

tag: time

value: Mock


title: IFNa_a_HUHH0011_Mock_12h_3_RNA

source_name: HUH cells, Mock-inoculated, 12h, bioreplicate 3

tag: treatment


title: IFNa_a_HUHH0011_Mock_18h_2_RNA

source_name: HUH cells, Mock-inoculated, 18h, bioreplicate 2


title: IFNa_a_HUHH0011_IFN_18h_4_RNA

source_name: HUH cells, IFN-inoculated, 18h, bioreplicate 4

value: IFN alpha and beta


title: IFNa_a_HUHH0011_Mock_12h_4_RNA

source_name: HUH cells, Mock-inoculated, 12h, bioreplicate 4


title: IFNa_a_HUHH0011_Mock_6h_3_RNA

source_name: HUH cells, Mock-inoculated, 6h, bioreplicate 3


title: IFNa_a_HUHH0011_Mock_6h_2_RNA

source_name: HUH cells, Mock-inoculated, 6h, bioreplicate 2


title: IFNa_a_HUHH0011_Mock_12h_1_RNA

source_name: HUH cells, Mock-inoculated, 12h, bioreplicate 1


title: IFNa_a_HUHH0011_Mock_12h_2_RNA

source_name: HUH cells, Mock-inoculated, 12h, bioreplicate 2


title: IFNa_a_HUHH0011_Mock_6h_1_RNA

source_name: HUH cells, Mock-inoculated, 6h, bioreplicate 1


title: IFNa_a_HUHH0011_IFN_12h_3_RNA

source_name: HUH cells, IFN-inoculated, 12h, bioreplicate 3


title: IFNa_a_HUHH0011_Mock_6h_4_RNA

source_name: HUH cells, Mock-inoculated, 6h, bioreplicate 4


title: NC1

description: Gene expression data from normal human


title: IFNa_a_HUHH0011_Mock_18h_4_RNA

source_name: HUH cells, Mock-inoculated, 18h, bioreplicate 4


title: IFNa_a_HUHH0011_IFN_18h_3_RNA

source_name: HUH cells, IFN-inoculated, 18h, bioreplicate 3


title: IFNa_a_HUHH0011_IFN_12h_1_RNA

source_name: HUH cells, IFN-inoculated, 12h, bioreplicate 1


title: IFNa_a_HUHH0011_IFN_12h_2_RNA

source_name: HUH cells, IFN-inoculated, 12h, bioreplicate 2


title: IFNa_a_HUHH0011_IFN_12h_4_RNA

source_name: HUH cells, IFN-inoculated, 12h, bioreplicate 4


title: Identification of miR-135-5p target genes in SAS

city: Chiba

department: Functional Genomics

source_name: mock

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: SAS

value: oral squamous cell carcinoma

value: no transfection

source_name: miR-135-5p transfected cell line


title: IFNa_a_HUHH0011_IFN_18h_2_RNA

source_name: HUH cells, IFN-inoculated, 18h, bioreplicate 2


title: IFNa_a_HUHH0011_IFN_6h_4_RNA

source_name: HUH cells, IFN-inoculated, 6h, bioreplicate 4


title: IFNa_a_HUHH0011_IFN_6h_3_RNA

source_name: HUH cells, IFN-inoculated, 6h, bioreplicate 3


title: IFNa_a_HUHH0011_IFN_18h_1_RNA

source_name: HUH cells, IFN-inoculated, 18h, bioreplicate 1


title: Identification of miR-199-3p target genes in PC3

value: prostate cancer

source_name: miR-199-3p transfected cell line


title: Wnt5a_treated_SV40LT-HFL-cells_rep1

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Gene expression data after Wnt5a stimulation

hyb_protocol: Hybridization to Affymetrix Human Gene 2.1 ST Array was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.

scan_protocol: Array plates were scanned using a GeneTitan scanner.

data_processing: Preprocessing in Affymetrix Expression Console (EC) Software (v. 1.4.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

source_name: SV40LT-HFL cells_Wnt5a_treated

label_protocol: Total RNA was converted to sense strand cDNA using Ambion WT Expression kit. For fragmentation and labeling WT GeneChip WT target Labeling kit was used.

growth_protocol: SV40LT-HFL cells and hFLPC were maintained in DMEM supplemented with 10% human AB serum containing media in presence of 30 ng/ml HGF, 20 ng/ml EGF, 10 ng/ml bFGF, 5 ng/ml VEGF, 2 ng/ml IL-6 and 10 ng/ml FGF-9.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were cultured in 1% human AB serum containing media for 6 hours and treated with Wnt 3a or Wnt 5a at 100 ng/ml for 12 hours.


title: Identification of miR-455-5p target genes in 786-O

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

value: renal cell carcinoma

source_name: miR-455-5p transfected cell line


title: IFNa_a_HUHH0011_IFN_6h_1_RNA

source_name: HUH cells, IFN-inoculated, 6h, bioreplicate 1


title: Wnt3a_treated_SV40LT-HFL-cells_rep3

description: Gene expression data after Wnt3a stimulation

source_name: SV40LT-HFL cells_Wnt3a_treated


title: untreated_SV40LT-HFL-cells_rep2

description: Gene expression data using PBS as vehicle control

source_name: SV40LT-HFL cells_untreated


title: untreated_SV40LT-HFL-cells_rep1


title: Wnt3a_treated_SV40LT-HFL-cells_rep2


title: untreated_SV40LT-HFL-cells_rep3


title: IFNa_a_HUHH0011_IFN_6h_2_RNA

source_name: HUH cells, IFN-inoculated, 6h, bioreplicate 2


title: Wnt5a_treated_SV40LT-HFL-cells_rep3


title: Wnt5a_treated_SV40LT-HFL-cells_rep2


title: Wnt3a_treated_SV40LT-HFL-cells_rep1


title: Wnt5a_treated_hFLPC_rep3

value: human fetal liver progenitor cells (hFLPC)


title: RaeI shCTRL HiC

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

library_source: genomic

data_processing:
General HiC processing: Paired reads were aligned to combined human/viral reference genomes with HiCUP version 0.5.0 using default parameters (Wingett et al., 2015) to generate a set of interactions. We used the human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence. Only alignments with mapq scores equal to or greater than 30 were retained.
Chromosome-resolution heatmaps of interactions were determined from the HiCUP-filtered interchromosomal Hi-C interactions in sam format. Expected interactions were calculated using the following equation for each chromosome pair, where chrA represents the number of single end interchromosomal reads containing chrA, chrB represents the number of single end interchromosomal reads containing chrB, totalPairs represents the total number of interchromosomal paired end reads, and all represents the total number of interchromosomal single end reads, which is equal to 2 x totalPairs: (((chrA/all)*(chrB/(all-chrA)))+((chrB/all)*(chrA/(all-chrB)))) * total_pairs.
Lamin association analysis: The set of lamin interacting domains from Tig3 cells (Guelen et al., 2008) was downloaded from the UCSC genome browser (Kent et al., 2002). Hi-C interactions identified by HiCUP were processed into a format readable by the HiTC package (Servant, 2015) using 1 Mb bins for the human genome and 1 kb bins for the viral genome. We performed further analyses on these interaction matrices in R (R Core Team, 2016). First a full interaction matrix for all autosomes was constructed. Next, for each bin, the mean of interaction counts with LAD bins was calculated as was the mean of interaction counts with non-LAD bins. Correlations were then performed across all autosomal bins with the LAD mean vector and the non-LAD mean vector. A logistic regression was performed on the LAD and non-LAD correlation values estimate the probability with which each genome region would interact with lamin. Next, we calculated the probability that each viral bin interacted with the lamin by applying the logistic regression model of the autosomal LAD correlations to the viral interaction data.
Genome_build: human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence
Supplementary_files_format_and_content: Chromsome-resolution heatmap generation results in two plain text files *interchrom_raw_counts_label.txt and *obs_exp_log2_label.txt. The *interchrom_raw_counts_label.txt contains a labeled 26 x 26 matrix for the raw counts of interchromosomal interactions between whole chromosomes. The *obs_exp_log2_label.txt file contains the same labeled 26 x 26 matrix, with raw interchromosomal counts normalized as described above.
Supplementary_files_format_and_content: Lamin association analysis results in plain text files ending in *allCounts.txt, which contains three columns, the first two are individual genomic bins and the third column is the number of interactions between those two bins.

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: RaeI cells

growth_protocol: EBV-positive Daudi, KemIII, RaeI, and Raji cells were maintained under standard conditions (Phan et al., 2016). K562 (C. B. Lozzio and B. B. Lozzio, 1975), EBV- and KSHV-positive BC-1 (Cesarman et al., 1995) and EBV-positive Namalwa (Klein et al., 1972) cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) fetal bovine serum (Invitrogen) in 5% CO2 at 37 °C.  EBV-positive Akata-Zta cells (Ramasubramanyan et al., 2015) were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech). The HPV16-positive 20863 (Jeon et al., 1995) and HPV31-positive 9E (De Geest et al., 1993) keratinocyte cell lines were grown in F-medium, 3:1 (v/v) F-12-DMEM, 5% fetal bovine serum, 400 ng/ml hydrocortisone, 5 µg/ml insulin, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 100 U/ml penicillin, and 100 µg/ml streptomycin, in the presence of irradiated 3T3-J2 feeder cells, as described previously (Chapman et al., 2014). Irradiated feeder cells were removed by versene treatment before the cells were harvested.

extract_protocol:
In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI as described (Rao et al., 2014) with slight modifications. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0 and transferred to new tubes.
Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0. After library amplification, SPRI beads were added as directed to purify the amplified DNA.

treatment_protocol: All cells except Akata-Zta were untreated. 5 million cells per experiment were fixed for in situ Hi-C as previously described (Rao et al., 2014). Akata-Zta cells were pretreated with 200 μM acyclovir for 1 hour before reactivation of the lytic cycle with 500 ng/mL doxycycline. After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotech). 5 million cells each of LGNFR+ and LGNFR- were fixed for in situ Hi-C as previously described (Rao et al. 2014)

value: RaeI

value: shCTRL


title: Wnt5a_treated_hFLPC_rep2


title: Wnt3a_treated_hFLPC_rep3


title: untreated_hFLPC_rep2


title: Wnt3a_treated_hFLPC_rep2


title: shCtrl

description: This is control D3 ESCs

source_name: shCtrl D3 ESCs

tag: genotype

value: Control


title: Wnt3a_treated_hFLPC_rep1


title: Wnt5a_treated_hFLPC_rep1


title: untreated_hFLPC_rep3


title: MES/CSC-96hr_untreated

status: Public on Nov 12 2017

city: Cleveland

first: Mary

middle: Rose

last: Doherty

state: Ohio

address: 2103 Cornell Road

department: Pathology

institute: CWRU

description: SAMPLE 8

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio

label: Standard Illumina Label

source_name: Transformed Human Mammary Epithelial cells

label_protocol: Standard Illumina protocol

growth_protocol: Transformed HMEC (Ep/non-CSC, MES/CSC) were cultured as previously described (Junk et al., 2013, Neoplasia15(9):1100-1109)

extract_protocol: RNA was extracted using the RNeasy mini kit (QIAGEN)

treatment_protocol: Transformed HMEC (Ep/non-CSC, MES/CSC) were treated with 100IU/ml IFNβ as indictated

value: Transformed HMEC (MES/CSC)

value: untreated

tag: cell source

value: Female Adult Mammary Epithelial cells obtained from reduction mammoplasty (transformed:shP16, shP53, c-MYC, RASG12V)


title: Ep/non-CSC-96hr_untreated

description: SAMPLE 4

value: Transformed HMEC (Ep/non-CSC)


title: untreated_hFLPC_rep1


title: MES/CSC-4hr_IFNβ

description: SAMPLE 6

value: IFNβ


title: MES/CSC-0hr_untreated

description: SAMPLE 5


title: Ep/non-CSC-96hr_IFNβ

description: SAMPLE 3


title: MES/CSC-96hr_IFNβ

description: SAMPLE 7


title: Ep/non-CSC-4hr_IFNβ

description: SAMPLE 2


title: PC3_humanPSMAoverexpressed_4

status: Public on Nov 11 2017

city: Boston

first: Charalambos

last: Kaittanis

state: MA

address: 55 Fruit St, White 427

department: GCMI

institute: Massachusetts General Hospital

description: PSMA-expressing cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GenePattern GCRMA with quantile normalization

source_name: PC3 human prostate cancer cell line in RPMI_PSMA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: PC3 cells grown in RPMI

extract_protocol: Trizol

treatment_protocol: PC3-PSMA cells were transfected with the pLNCX-PSMA plasmid, whereas PC3-Ctrl with the vector alone, using the FUGENE 6 reagent ( 3 ug plasmid DNA with 2 ug FUGENE in serum-free medium for 30 min; recovery in complete media for 72 h, followed by puromycin selection)

value: PSMA overexpression


title: Ep/non-CSC_0h_untreated

description: SAMPLE 1


title: PC3_wildtype_2

description: Control cells

source_name: PC3 human prostate cancer cell line in RPMI_vector only

value: wildtype


title: PC3_humanPSMAoverexpressed_5

description: PSMA-expressing cells


title: PC3_wildtype_3

description: Control cells


title: PC3_humanPSMAoverexpressed_6

description: PSMA-expressing cells


title: PC3_wildtype_1

description: Control cells


title: LNCaP_untreated_3

description: Control cells

source_name: LNCaP human prostate cancer cell line in RPMI

growth_protocol: LNCaP cells grown in RPMI

treatment_protocol: Control LNCaP cells grown in RPMP (untreated); LNCaP PSMA-knockdown (knockdown via transduced shRNA from TransOmics; knockdown completed in 11/18/13)

value: LNCaP

value: control


title: LNCaP_PSMAknockdown_2

description: Knockdown cells

value: PSMA KD


title: LNCaP_PSMAknockdown_1

description: Knockdown cells


title: LNCaP_untreated_1

description: Control cells


title: ND85 CCR4 CCR6

city: Charleston

first: Chrystal

last: Paulos

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: MUSC

hyb_protocol: Standard.OneArray Hybridization chamber with Hybridization buffer

scan_protocol: “OneArray® Microarray Scanner

data_processing: Automated company-provided analyses, after normalizing with median scaling normalization method, then take average of repeated data from the same sample.

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Primary Cell Culture (T cell media)

extract_protocol: T cell isolation from PBMC

treatment_protocol: Sorted based on receptor of interest

value: Cells that are CD46-positive


title: CCR4 CCR6 ND65


title: LNCaP_PSMAknockdown_3

description: Knockdown cells


title: ND90 CCR4 CCR6


title: LNCaP_untreated_2

description: Control cells


title: lncN1

source_name: Normal donor 1

value: healthy control

value: CD138+ plasma cells


title: IFNa_a_HUHH0011_Mock_18h_3_RNA

source_name: HUH cells, Mock-inoculated, 18h, bioreplicate 3

value: HUH VP30

value: HUH

value: HUH cells stably transfected with Ebola VP30

value: Mock


title: 26 neg ND64

source_name: NEG

value: Cells that are CD26-negative


title: 26 neg ND65


title: ND85 CD26 int

source_name: INT

value: Cells that are CD26-intermediate (positive and relatively normal expression)


title: ND90 CD26 neg


title: CCR4 CCR6 ND64


title: ND90 CD26 int


title: ND90 bulk

value: Cells that are CD4-positive


title: ND90 CD26 hi

source_name: HI

value: Cells that are CD26-high (positive and relatively high expression)


title: ND85 CD26 hi


title: 26 hi ND65


title: ND85 bulk


title: 26 int ND63


title: 26 hi ND63


title: 26 hi ND64


title: CD4 ND64


title: CD4 ND65


title: healthy woman skin biological rep3

city: Krasnoyarsk

first: Anna

last: Komina

address: Partizana Zheleznyaka

department: Pathological physiology

country: Russia

institute: Krasnoyarsk State Medical University

hyb_protocol: Hybridization on arrays in Affymetrix® miRNA 4.1 Array Strip (Affymetrix, Santa Clara, USA) using the GeneChip® GeneAtlas™ Hybridization and Stain Module (Ref. 902135) reagents (Affymetrix, Santa Clara, CA, USA) 48°C for 20 h

scan_protocol: Washing array strips on the GeneAtlas™ Microarray System Fluidic Station using the GeneChip® GeneAtlas™ Hybridization and Stain Module buffers and solutions (Ref. 902135) (Affymetrix, Santa Clara, CA, USA) and detecting on the Imaging Station of the GeneAtlas™ Microarray System

data_processing:
Data were analyzed using Expression Console and Transcriptome Analysis Console 3.0 software (Affymetrix, USA).
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_1
program-name = Expression Console
program-version = 1.4.0.38

source_name: healthy woman skin

label_protocol: 8 ul of total RNA samples containing from 130 to 270 ng microRNA were labeled with biotin using Affymetrix® Flash Tag™ Biotin HSR (Ref. 901913, Affymetrix, Santa Clara, CA, USA)

growth_protocol: Skin biopsies were obtained from patients with androgenetic alopecia and healthy volunteers after obtaining informed consent.

extract_protocol: For RNA extraction skin tissues were washed in 0,01M PBS after RNA-later and homogenized mechanically with liquid nitrogen. Total RNA was isolated using RecoverAll™ Total Nucleic Acid Isolation kit (Cat# AM1975, Ambion, Vilnius, Lithuania)

treatment_protocol: Skin samples were stored in RNA-later at -20C before RNA isolation

tag: subject status

value: healthy individual

tag: gender

value: female

tag: age

tag: tissue

value: skin biopsy

tag: tissue subtype

value: healthy woman skin

tag: molecule subtype

value: microRNA


title: man skin biological rep4

source_name: man skin

value: male

value: man skin


title: healthy woman skin biological rep1


title: man skin biological rep2


title: HCC827-OR

city: Sendagi, Bunkyou-ku

first: Akiko

last: Takahashi

state: Tokyo

department: Pulmonary medicine

institute: Nippon Medical School Hospital

description: osimertinib resistant HCC827

hyb_protocol: Biotin-labeled cDNA was injected into Genechip Human Gene 2.0 ST array and hybridized with probe in Genechip Hybridization Oven 645. The array was washed using Genechip Hybridization, Wash and Stain Kit and stained by phycoerythrin. GeneChip Fluidics Station 450 was used.

scan_protocol: Fluorescent signal by phycoerythrin staining of cDNA hybridized to the probe in the array was measured using a GeneChip Scanner 3000 7G. Data was acquired using analysis software GeneChip Command Console.

data_processing: Data was normalized in a data mining software (GeneSpring GX Version12.6) using the RMA 16 Summarization algorithm. Confidence level was all. Baseline transformation was not performed. All scanned transcript cluster data were obtained.

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and  apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA  strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the  Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded  cDNA is required for fragmentation and labeling.

extract_protocol: Total RNA from cells was extracted using Rneasy Plus Mini (QIAGEN) Kit according to the manufacturer’s protocol.

value: osimertinib resistant


title: man skin biological rep3


title: man skin biological rep5


title: PC-9-AR

description: afatinib resistant PC9

value: afatinib resistant


title: HCC827-AR

description: afatinib resistant HCC827


title: healthy woman skin biological rep4


title: PC-9

description: the parent cells PC9

value: EGFR mutation positive(del.19)


title: man skin biological rep1


title: PC-9-OR

description: osimertinib resistant PC9


title: alopecia skin biological rep1

source_name: alopecia skin

value: hair loss patient

value: alopecia skin


title: 3170

status: Public on Nov 10 2017

city: Hangzhou

first: Chengliang

last: Zhou

state: Zhejiang

address: No. 866th, Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

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 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data.

source_name: Ovarian granulosa cells, PCOS with with normal testosterone level

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: RNA was extracted from oGCs using the miRNeasy mini kit (Qiagen).Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Ovarian granulosa cells were obtained by follicular aspiration from women undergoing oocyte retrieval for IVF. For each patient, cells from multiple follicles and consequently follicular fluid were pooled. oGCs from each patient were extracted as described (9) and stored in Trizol (Thermo Fisher Scientific) at −80°C.

value: Female

tag: cell type

value: Ovarian granulosa cells

tag: disease state


title: alopecia skin biological rep2