title: Human_islet_1_1B4_NR4A3siRNA_48hr_100mMH2O2_2hr

city: Minato-ku

first: Yuzuru

last: Otsuka

state: Tokyo

department: Department of Nutrition

institute: Toita Women's College

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 treated with siRNA of NR4A3 and treated with 100mM H2O2 2hr
H1_1B4SiH2O2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60 C for 30 minutes in a reaction volume of 55 microl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 microl of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome microarray arrays 4x44K v2(G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven with 10rpm.  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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_feb07 and Grid: 014850_D_F_20101031) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were further normalized using GeneSpringGX10 using default parameters of recommended protocol with Median shift normalization to the 75th percentile and baseline transformed to the median of all samples.
The normalized_data_full.txt contains normalized signal intensity for each sample, their average and comparison data. Average of 3 samples of siRNA of NR4A3 treated group was compared with average of 3 control samples of nucleaase free water group. One sample of H2O2 treated after siRNA of NR4A3 treated group was also compared to the average of control group. One sample of H2O2 treated but siRNA was not added group was also compared to the average of control group.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared with 100 ng RNA from 3 dishes using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the Hitachi UV Spectrophotometer.

growth_protocol: Human Islet derived hybrid cell of 1.1B4 was cultured in RPMI-1640 medium supplemented with 10% FBS with Penicilin (50 IU/ml) - Streptomycine (50 micro g/ml) in humidified air at 37 C with 5% CO2.

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations.  The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cells of 1.1B4 was cultured (0.5 x 100000 cells/ml) in 12 dishes with siRNA of NR4A3 (or 12 dishes with nuclase free water) and after 48hr, culture medium was changed to RPMI-1640, then 24hr later 9 dishes total RNA was isolated. Remaining 3 dishes were added 100mM H2O2 and incubated 2hr, then RNA was isolated. The RNA of 3 dishes of same treatment was combined and applied to an array. Twelve dishes with nuclease free water were also treated as same.

value: pancreatic islet derived hybrid cells

value: siRNA of NR4A3

tag: incubated with

value: 100mM H2O2 for 2hr


title: Human_islet_1_1B4_100mM_H2O2_2hr

status: Public on Sep 15 2016

type: RNA

country: Japan

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 treated without siRNA of NR4A3 but treated with 100mM H2O2 2hr
H1_1B4H2O2

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: DLX5_miR_2

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

country: USA

institute: University of Southern California

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array.Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: gingival fibroblast

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: alpha-MEM+10% FBS.

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Cells were transfected with ｌentivirus vectors which carry artificial microRNA sequences. Total RNA was extracted from gingival fibroblasts 120h after infection.

value: gingival fibroblast

tag: transfection construct


title: RUNX2long_miR_3


title: Ket77 [GRC11052226]

type: genomic

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

description: Genomic DNA extracted from blood was genotyped using Affymetrix platform

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
Affymetrix Power Tools (APT) Software Package (version 1.12.0) has been used for data analysis. Application 'apt-probeset-genotype' has been used for making genotype calls.
Processed data (along with sample metadata) is provided for each sample (*alleles_affy.txt). Processed data include genotype data for each rs number;
#ID_REF = Affymetrix probe set ID
#VALUE = Genotype Call
#RS_NUMBER = dbSNP_RS_ID
Dataset is also converted into PLINK format (http://pngu.mgh.harvard.edu/~purcell/plink/). Files SIBERIA.bed, SIBERIA.bim, SIBERIA.fam are provided.

molecule: genomic DNA

source_name: Central Siberia_Ket

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Ket

tag: region

value: Central Siberia

tag: gender

value: Male

tag: tissue

value: blood


title: BPA-CTL-U2

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

description:
5539777026_E_Grn.idat
Litter 2
Sample name: 5539777026_E

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile normalized using Illumina BeadSpace

organism: Mus musculus

source_name: Mouse Uterus

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

extract_protocol: Each sample was placed in 1 ml TRIzol solution (Thermo Fisher  Scientific,Waltham, MA, USA), and total RNA was purified by  using the Qiagen RNeasy Plus Mini kit according to manufacturer  instructions.

treatment_protocol: Pregnant dams were either exposed to 5/mg/kg/day of BPA IP or DMSO control. At 6 weeks offspring were oopherectomized. At 8 weeks offspring were either injected with 300ng estradiol or DMSO control.

tag: strain

tag: in utero exposure

value: BPA

tag: 8wk treatment

value: DMSO

tag: age

value: 8 weeks

value: uterus


title: Human_islet_1_1B4_cell_control3

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 without siRNA of NR4A3 and H2O2
H1_1B4Cont3


title: NpBI-206AS_NotInduced

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Torino

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

scan_protocol: Scanning was performed with the GeneChip® Scanner 3000 7G, controlled by Affymetrix GeneChip® Command Console software (AGCC).

data_processing: CEL files have been analyzed with Partek Genomic Suite 6.4, with the following parameters: probe filtering skip, background correction RMA, quantile normalization, probeset summarization Median Polish.

source_name: RD18 NpBI-206AS cells NOT-INDUCED

label_protocol: Labeling was performed with GeneChip® WT Plus Kit following the Affymetrix 150ng Total RNA Target Labeling protocol.

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 2 mM l-glutamine, 100 U/ml penicillin, and 0.1 mg/ml streptomycin.

extract_protocol: 1 µg of total RNA was extracted using Trizol, according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 6 days (induced) or left untreated (non-induced).

value: RD18 NpBI-206AS

value: embryonal Rhabdomyosarcoma (ERMS) cell line

tag: treated with

value: none (NI; untreated)


title: NpBI-22_Induced_rep1

source_name: RD18 NpBI-22 cells INDUCED

value: RD18 NpBI-22

value: doxycycline for 6 days (IND)


title: Human_islet_1_1B4_NR4A3siRNA_48hr3

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 treated with siRNA of NR4A3 but no H2O2
H1_1B4NR4A3Si3

value: pancreatic islet derived hybrid cells


title: NC_miR


title: BPA-CTL-U3

description:
5539777026_F_Grn.idat
Litter 3
Sample name: 5539777026_F


title: Ket80 [GRC11052227]


title: NpBI-22_Induced_rep2


title: NpBI-22_NotInduced_rep1

source_name: RD18 NpBI-22 cells NOT-INDUCED


title: Human_islet_1_1B4_cell_control2

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 without siRNA of NR4A3 and H2O2
H1_1B4Cont2


title: BPA-CTL-U1

description:
5539777026_D_Grn.idat
Litter 1
Sample name: 5539777026_D


title: NpBI-22_NotInduced_rep2


title: T80 shArid1A Myr-PI3K [DNAse-seq]

type: SRA

city: Boston

first: Falong

last: Lu

state: Massachusetts

address: 200 Longwood Ave, WAB 159

department: Program of Cellular and Molecular Medicine

institute: Boston Children's Hospital / HHMI

description: processed data file: 2016_OCCC_differential_DHSs_3fold.xlsx

library_source: genomic

data_processing:
RNA-seq data analysis: Reads of RNA-seq were mapped to the human genome (hg19) with TopHat v2.0.6. All programs were run with default parameters unless otherwise specified. Uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1. Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Dnase-seq data analysis: Reads of DNase-seq were mapped to the human genome (hg19) using Bowtie v0.12.9. We use ‘-m 1’ parameter for unique hits mapping. The reads with mapping quality (MAPQ) ≤ 10 or redundant reads that mapped to the same location with the same orientation were removed from further analysis in each library.  Differential DHSs with 3-fold difference were called using ChIPDiff (Xu et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each gene or region of differential DHSs.

source_name: T80 shArid1A Myr-PI3K

extract_protocol:
Total RNA were extracted from samples using Trizol reagent. NEBNext Ultra Directional RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. For DNase-seq, the nuclei were digested with DNase I (Roche) at 60 U/ml final concentration at 37°C for 5 minutes. The reactions were stopped by adding stop buffer containing EDTA and proteinase K. DNA was purified by phenyl-chloroform extraction and ethanol precipitation. Small fragments around 150 bp were selected with SPRIselect (Beckman Coulter).
RNA-seq libraries were prepared following the manual of NEBNext Ultra Directional RNA Library Prep Kit.For DNase-seq, DNA obtained after DNase treatment were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: cell line background

value: human ovarian epithelial cell line

tag: genotype/variation

value: shArid1A Myr-PI3K


title: Human_islet_1_1B4_cell_control1

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 without siRNA of NR4A3 and H2O2
H1_1B4Cont1


title: Ket75 [GRC11052224]


title: BPA-E2-U3

description:
5539777026_C_Grn.idat
Litter 3
Sample name: 5539777026_C

value: Estradiol


title: Human_islet_1_1B4_NR4A3siRNA_48hr2

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 treated with siRNA of NR4A3 but no H2O2
H1_1B4NR4A3Si2

value: siRNA of NR4A3


title: DLX5_miR_4

value: gingival fibroblast


title: BPA-E2-U2

description:
5539777026_B_Grn.idat
Litter 2
Sample name: 5539777026_B


title: Ket74 [GRC11052223]

value: Ket

value: Central Siberia

value: Male


title: Ket73 [GRC11052222]

value: blood


title: Ket76 [GRC11052225]


title: BPA-E2-U1

description:
5539777026_A_Grn.idat
Litter 1
Sample name: 5539777026_A

value: BPA

value: 8 weeks


title: T80 [DNAse-seq]

value: WT


title: T80 shArid1A [DNAse-seq]

source_name: T80 shArid1A


title: Ket71 [GRC11052220]


title: CTL-CTL-U1

description:
5539777011_E_Grn.idat
Litter 1
Sample name: 5539777011_E

value: DMSO

value: uterus


title: Ket72 [GRC11052221]


title: CTL-E2-U2

description:
5539777011_D_Grn.idat
Litter 2
Sample name: 5539777011_D


title: Ket70 [GRC11052219]


title: T80 Myr-PI3K [mRNA-seq]

description: processed data file: 2016_OCCC_FPKM_all.xlsx

library_source: transcriptomic

source_name: T80 Myr-PI3K


title: CTL-CTL-U2

description:
5539777011_F_Grn.idat
Litter 2
Sample name: 5539777011_F


title: T80 shArid1A [mRNA-seq]


title: Ket67 [GRC11052216]

description: Genomic DNA extracted from blood was genotyped using Affymetrix platform


title: T80 shArid1A Myr-PI3K [mRNA-seq]


title: T29 shArid1A Myr-PI3K [mRNA-seq]

source_name: T29 shArid1A Myr-PI3K


title: Evenk64 [GRC11052190]

source_name: North Central Siberia_Evenk

value: Evenk

value: North Central Siberia


title: Ket68 [GRC11052217]


title: T29 Myr-PI3K [mRNA-seq]

source_name: T29 Myr-PI3K


title: T80 Myr-PI3K [DNAse-seq]


title: T80 [mRNA-seq]


title: Evenk58 [GRC11052189]


title: T29 shArid1A [mRNA-seq]

source_name: T29 shArid1A


title: T29 [mRNA-seq]


title: Evenk46 [GRC11052187]


title: Ket69 [GRC11052218]


title: Evenk45 [GRC11052186]


title: CTL-E2-U1

description:
5539777011_C_Grn.idat
Litter 1
Sample name: 5539777011_C


title: P19 EC cells, BMS961, 48h

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

hyb_protocol: The arrays were washed and stained with streptavidine-phycoerythrin in an Affymetrix GeneChip® Fluidics station 450 using the script protocol F450-0007.

scan_protocol: Arrays were scanned with the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Expression values were generated with the Affymetrix software Expression Console version 1.1 using sketch quantile normalization and median polish summarization as in Robust Multiarray analysis. For comparing P19 EC cells’ generated transcriptomes with the previously described for the F9 EC cells model system (Mendoza-Parra et al, 2011) we have normalized all raw CELL files with the Affymetrix software Expression Console prior further analyses.

source_name: P19 cells treated with BMS961 48h

label_protocol: For transcriptomics analysis by microarrays hybridization, 250ng of extracted RNA was used for cDNA reverse transcription including a biotin-labelling procedure then hybridized on Affymetrix GeneChip® Mouse Gene 1.0 ST array (Affymetrix, Santa Clara, CA, USA) as described in the manufacture’s protocols (GeneChip® whole transcript sense target labelling assay manual: P/N 701880 Rev.4).

growth_protocol: F9 EC cells were cultures in Dubelcco’s modified Eagle’s medium supplemented with 10% fetal Calf serum. In a similar manner, P19 cell’s medium was supplemented with 5% fetal Calf serum and 5% delipidated Calf serum. In both cases the medium was complemented with 40ug/ml Gentamicin. F9 or P19 EC cells were cultured in monolayer conditions seeded in gelatine-coated tissue culture plates (0.1%).

extract_protocol: Total RNA was extracted from EC cells treated with either ATRA or RAR-specific agonists during different period of times, using the GENEElute RNA extraction kit (Sigma). 2ug of the extracted RNA was used for reverse transcription (AMV-RTase, Roche; Oligo(dT) New England Biolabs; 1h; 42°C). Transcribed cDNA was diluted ten folds and used for real-time quantitative PCR (Roche instrument LC480).

treatment_protocol: For cell differentiation induction, ATRA was added to plates in a final concentration of 1x10-6 M at different time points. For RAR subtype-specific agonists’ treatment, cells were incubated with BMS961 (RARg specific; final concentration 1x10-7 M), BMS753 (RARa specific; final concentration 1x10-6 M) or BMS641 (RARb specific; final concentration 1x10-7 M).

value: P19 embryonal carcinoma cells

tag: agent

tag: time point


title: P19 EC cells, BMS961, 6h

source_name: P19 cells treated with BMS961 6h


title: P19 EC cells, BMS961, 72h

source_name: P19 cells treated with BMS961 72h


title: P19 EC cells, BMS961, 24h

source_name: P19 cells treated with BMS961 24h


title: P19 EC cells, BMS641, 72h

source_name: P19 cells treated with BMS641 72h


title: P19 EC cells, BMS961, 2h

source_name: P19 cells treated with BMS961 2h


title: Evenk32 [GRC11052184]


title: Evenk53 [GRC11052188]


title: P19 EC cells, BMS641, 6h

source_name: P19 cells treated with BMS641 6h


title: Evenk30 [GRC11052183]


title: P19 EC cells, BMS641, 48h

source_name: P19 cells treated with BMS641 48h


title: Human_islet_1_1B4_NR4A3siRNA_48hr1

description:
Gene expression of human panceatic islet drived 1.1B4 cell by Agilent human GE 4X44Kv2 treated with siRNA of NR4A3 but no H2O2
H1_1B4NR4A3Si1

value: pancreatic islet derived hybrid cells


title: Evenk29 [GRC11052182]


title: Evenk25 [GRC11052181]


title: Evenk44 [GRC11052185]


title: Evenk16 [GRC11052178]


title: Evenk19 [GRC11052179]


title: U-2 (CD117+)

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
Replicate 2
SAMPLE 8

scan_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: bone marrow

extract_protocol: RNA was extracted from 2 x 106 cells for each sample using the RNeasy Mini Plus kit from Qiagen, as per the manufacturer’s protocol. Following DNase treatment, total RNA was sequenced and analyzed at the Yale Center for Genome Analysis

treatment_protocol: 2x106 cells were treated with 3ug/ml of SCF IN SAMPLE10 , 11 AND 12 for 48 hours.

value: 3 months

value: Bone marrow


title: P19 EC cells, BMS753, 72h

source_name: P19 cells treated with BMS753 72h


title: Evenk14 [GRC11052177]


title: U-1 (CD117+)

description:
Replicate 1
SAMPLE 7


title: P19 EC cells, BMS753, 48h

source_name: P19 cells treated with BMS753 48h


title: P19 EC cells, BMS753, 6h

source_name: P19 cells treated with BMS753 6h


title: P19 EC cells, BMS753, 24h

source_name: P19 cells treated with BMS753 24h


title: Evenk10 [GRC11052176]


title: P19 EC cells, BMS641, 24h

source_name: P19 cells treated with BMS641 24h


title: Evenk22 [GRC11052180]

source_name: North Central Siberia_Evenk


title: P19 EC cells, BMS641, 2h

source_name: P19 cells treated with BMS641 2h


title: P19 EC cells, BMS753, 2h

source_name: P19 cells treated with BMS753 2h


title: C-3 (CD117+)

description:
Replicate 3
SAMPLE 6


title: SCF2 (CD117+, treat)

description:
Replicate 2
SAMPLE 11


title: SCF3 (CD117+, treat)

description:
Replicate 3
SAMPLE 12


title: SCF1 (CD117+, treat)

description:
Replicate 1
SAMPLE 10


title: Evenk04 [GRC11052175]


title: C-2 (CD117+)

description:
Replicate 2
SAMPLE 5


title: Evenk02 [GRC11052174]


title: Dolgan118 [GRC11056546]

source_name: North Central Siberia_Dolgan

value: Dolgan


title: Dolgan096 [GRC11056545]


title: P19 EC cells, ATRA, 72h

source_name: P19 cells treated with ATRA 72h

value: ATRA


title: Dolgan068 [GRC11056543]


title: A-2 (CD117-)

description:
Replicate 2
SAMPLE 2


title: U-3 (CD117+)

description:
Replicate 3
SAMPLE 9


title: Dolgan067 [GRC11056542]


title: Dolgan055 [GRC11056541]


title: P19 EC cells, ATRA, 6h

source_name: P19 cells treated with ATRA 6h


title: A-3 (CD117-)

description:
Replicate 3
SAMPLE 3


title: Dolgan042 [GRC11056540]


title: C-1 (CD117+)

description:
Replicate 1
SAMPLE 4


title: Dolgan033 [GRC11056539]


title: P19 EC cells, ATRA, 24h

source_name: P19 cells treated with ATRA 24h


title: P19 EC cells, EtOH, rep4

source_name: P19 cells treated with EtOH rep4

value: EtOH


title: P19 EC cells, ATRA, 48h

source_name: P19 cells treated with ATRA 48h


title: A-1 (CD117-)

description:
Replicate 1
SAMPLE 1


title: P19 EC cells, EtOH, rep1

source_name: P19 cells treated with EtOH rep1


title: Buryat51 [GRC11052156]

source_name: South Central Siberia_Buryat

value: Buryat

value: South Central Siberia


title: P19 EC cells, EtOH, rep3

source_name: P19 cells treated with EtOH rep3


title: P19 EC cells, EtOH, rep2

source_name: P19 cells treated with EtOH rep2


title: Dolgan025 [GRC11056537]

value: Male

value: blood


title: Ly6C[Hi]-Mono_rep1

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
Ly6C high monocytes, replicate 1
Gene expression of ECM TAM

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6) Copyright © 2012).

source_name: C57BL/6 Cx3cr1gfp/+  spleen

growth_protocol: Cells were sorted from fresh tissues, either orthotopic colorectal cancer tumors (Ly6C high infiltrating, F4/80 TAM), colon ( lamina propria steady state macrophages) or spleen (Ly6C high monocytes) of Cx3cr1gfp/+ mice. All tissues were homogenized using Collagenase VIII, stained with antibodies and filtered before sorting.

extract_protocol: RNA was prepared using the microRNeasy Kit (QIAGEN). RNA purity was assessed with ND-100 Nanodrop (Peqlab) and BioAnalyzer 2100 (Agilent). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: No treatment was applied.

value: male

tag: genotype

value: spleen

value: Ly6C high monocytes


title: Ly6C[Hi]-TAMs_rep2

description:
Ly6C high Tumor infiltrating macrophages, replicate 2
Gene expression of ECM TAM

source_name: C57BL/6 Cx3cr1gfp/+  ortotopic colorectal tumor

label_protocol: according to the instruction manual, as described in the Affymetrix website

value: ortotopic colorectal tumor


title: Buryat49 [GRC11052155]


title: Dolgan090 [GRC11056544]


title: Ly6C[Hi]-Mono_rep2

description:
Ly6C high Monocytes, replicate 2
Gene expression of ECM TAM

value: mixed

value: Ly6C high Monocytes


title: SS-MF_rep2

description:
steady state colonic lamina propria macrophages, replicate 2
Gene expression of ECM TAM

source_name: C57BL/6 Cx3cr1gfp/+  colon

value: female

value: colon


title: SS-MF_rep1

description:
steady state colonic lamina propria macrophages, replicate 1
Gene expression of ECM TAM


title: F4/80[Hi]_rep2

description:
F4/80 high Tumor associated macrophages (TAM), replicate 2
Gene expression of ECM TAM


title: Buryat47 [GRC11052154]


title: Dolgan029 [GRC11056538]

value: North Central Siberia


title: Buryat40 [GRC11052152]


title: Ly6C[Hi]-TAMs_rep1

description:
Ly6C high Tumor infiltrating macrophages, replicate 1
Gene expression of ECM TAM


title: Buryat44 [GRC11052153]


title: F4/80[Hi]_rep1

description:
F4/80 high Tumor associated macrophages (TAM), replicate 1
Gene expression of ECM TAM


title: Buryat34 [GRC11052150]


title: Control mice-1 aorta

city: Iowa City

first: Ajit

last: Vikram

state: Iowa

address: 431 Newton Rd. 400 EMRB

department: Internal Medicine

institute: University of Iowa

description: Sample name: PFM-Aorta-1

hyb_protocol: As per manufacturers instructions

scan_protocol: As per manufacturers instructions

data_processing: The raw data was normalized to 6 dilution series of positive controls to minimize inter-run variability. To eliminate noise and false positive results the mean and twice of standard deviation of eight negative controls in each lane was deducted from the raw value of individual miRNAs count, and after deduction, miRNAs with negative values were eliminated and considered as not expressed. The data for aorta and serum was separately processed and analyzed. We received raw data in excel file from the core facility and we processed data on Microsoft Excel (2010).

source_name: Aorta

label_protocol: As per manufacturers instructions

extract_protocol: Thoracic aorta was carefully isolated and total RNA was isolated using miRNeasy Kit.

value: Swiss-Webster

tag: mouse type

value: pathogen-free

value: Aorta


title: Control mice-2 aorta

description: Sample name: PFM-Aorta-2


title: Buryat28 [GRC11052149]


title: Control mice-3 aorta

description: Sample name: PFM-Aorta-3


title: Buryat23 [GRC11052147]


title: RBCs stored for 20 days with 1uM SNP_case_rep2

city: Guangzhou

first: xie

middle: xu

last: hong

address: Guangzhou First People's Hospital,NO.1.Panfu Road

department: Department of Blood Transfusion

country: China

institute: Guangzhou First People's Hospital

description: miRNA expression in RBCs stored for 20 days with 1uM SNP

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: RBC

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: Healthy,male type O RBCs were stored in blood bank refrigerator at 4±2℃.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Healthy,male type O RBCs were stored in blood bank refrigerator at 4±2℃for 20 days, and then added with 1uM SNP.

tag: blood type

value: type O

value: 20 Days with 1uM SNP


title: RBCs stored for 20 days with 1uM SNP_case_rep3


title: Buryat19 [GRC11052146]

value: Buryat

value: South Central Siberia


title: Buryat15 [GRC11052145]

value: Male

value: blood


title: Buryat08 [GRC11052143]


title: Buryat06 [GRC11052142]


title: germ-free mice-2 aorta

description: Sample name: GFM-Aorta-2

value: germ-free


title: RBCs stored for 20 days_case_rep3

description: miRNA expression in RBCs stored for 20 days

value: male

value: 20 Days


title: Buryat04 [GRC11052141]


title: RBCs stored for 20 days with 1uM SNP_case_rep1


title: Buryat39 [GRC11052151]


title: healthy, male type O donors_control_rep2

description: miRNA expression in healthy,male type O donors

value: 0 Day


title: RBCs stored for 20 days_case_rep2


title: RBCs stored for 20 days_case_rep1


title: germ-free mice-1 aorta

description: Sample name: GFM-Aorta-1


title: Buryat01 [GRC11052140]


title: Buryat27 [GRC11052148]


title: healthy, male type O donors_control_rep3


title: healthy, male type O donors_control_rep1


title: 18_SQ11-92T

status: Public on Sep 14 2016

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description:
92T
Gene Expression data

hyb_protocol: Biotin-labeled cDNAs were hybridized overnight to Human HTA 2.0 arrays. Wash and stain of these GeneChip microarrays was carried out under strictly controlled conditions with the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix Scanner.

data_processing: The data were analyzed with Affymetrix® Expression Console™ software version 1.1 using Affymetrix default analysis settings with RMA normalization and general background correction.

source_name: lung SCC

label_protocol: Approximately 100 ng of total RNA were reverse transcribed and labeled by biotin (biotin-labeled cDNA) according to standard Affymetrix protocols used by NCI core facility (LMT/Affymetrix Group, Frederick National Laboratory for Cancer Research, http://atp.ncifcrf.gov/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/microarray/service-details/).

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

value: lung squamous cell carcinoma

tag: tumor size(cm)

tag: pt

tag: pn

tag: pm

tag: 7th pstage

value: IA

tag: smoking status

value: Current

tag: pack-year

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: death

value: dead

tag: days before death/censor


title: 17_SQ11-91T

description:
91T
Gene Expression data

tag: tissue

tag: gender

tag: age

value: Ever

value: alive


title: 76_SQ11-90T

description:
90T
Gene Expression data

value: IIA

value: relapsed


title: 72_SQ11-71T

description:
71T
Gene Expression data

value: IIB


title: 6_SQ11-9T

description:
9T
Gene Expression data


title: 16_SQ11-83T

description:
83T
Gene Expression data


title: 13_SQ11-66T

description:
66T
Gene Expression data

value: Female


title: 75_SQ11-81T

description:
81T
Gene Expression data

value: Male


title: 50_SQ13-8T_2

description:
8T
Gene Expression data


title: 5_SQ11-7T

description:
7T
Gene Expression data

value: IB


title: P19 EC cells, ATRA, 2h

source_name: P19 cells treated with ATRA 2h

tag: cell type

value: P19 embryonal carcinoma cells

tag: agent

value: ATRA

tag: time point


title: 14_SQ11-69T

description:
69T
Gene Expression data

tag: tumor size(cm)


title: 12_SQ11-62T

description:
62T
Gene Expression data

tag: pt


title: 63_SQ11-48T

description:
48T
Gene Expression data

tag: pn


title: 71_SQ11-67T

description:
67T
Gene Expression data

tag: pm


title: 66_SQ11-46T

description:
46T
Gene Expression data

tag: 7th pstage


title: 4_SQ11-4T

description:
4T
Gene Expression data

tag: smoking status


title: 64_SQ11-54T

description:
54T
Gene Expression data

value: Never

tag: pack-year


title: 65_SQ11-57T

description:
57T
Gene Expression data

tag: relapse


title: 73_SQ11-77T

description:
77T
Gene Expression data

tag: days before relapse/censor


title: 70_SQ11-63T

description:
63T
Gene Expression data

tag: death


title: 49_SQ13-5T

description:
5T
Gene Expression data

tag: days before death/censor


title: 11_SQ11-56T

description:
56T
Gene Expression data

tag: tissue


title: germ-free mice-3 aorta

description: Sample name: GFM-Aorta-3

tag: strain

value: Swiss-Webster

tag: mouse type

value: germ-free

value: Aorta


title: 77_SQ11-99T

description:
99T
Gene Expression data

value: lung squamous cell carcinoma

tag: gender

tag: age

value: Current


title: 61_SQ11-40T

description:
40T
Gene Expression data

value: dead


title: 62_SQ11-42T

description:
42T
Gene Expression data


title: 74_SQ11-80T

description:
80T
Gene Expression data

value: Ever


title: 57_SQ11-24T

description:
24T
Gene Expression data


title: 3_SQ11-3T

description:
3T
Gene Expression data

value: not relapsed

value: alive


title: 60_SQ11-37T

description:
37T
Gene Expression data

value: relapsed


title: 48_SQ11-232T

description:
232T
Gene Expression data

value: IA


title: 107_SQ11-235T

description:
235T
Gene Expression data

value: IIA


title: 104_SQ11-220T

description:
220T
Gene Expression data

value: Male


title: 105_SQ11-223T

description:
223T
Gene Expression data

value: IIB


title: 9_SQ11-29T

description:
29T
Gene Expression data


title: 55_SQ11-21T

description:
21T
Gene Expression data


title: 2_SQ11-2T

description:
2T
Gene Expression data


title: 44_SQ11-216T

description:
216T
Gene Expression data

value: Female


title: 103_SQ11-215T

description:
215T
Gene Expression data


title: 19_SQ11-98T

description:
98T
Gene Expression data

value: IB


title: 47_SQ11-230T

description:
230T
Gene Expression data


title: 1_SQ11-1T

description:
1T
Gene Expression data


title: 40_SQ11-203T

description:
203T
Gene Expression data


title: 58_SQ11-27T

description:
27T
Gene Expression data


title: 56_SQ11-23T

description:
23T
Gene Expression data


title: 45_SQ11-221T

description:
221T
Gene Expression data


title: 10_SQ11-30T

description:
30T
Gene Expression data


title: 41_SQ11-207T

description:
207T
Gene Expression data


title: 42_SQ11-209T

description:
209T
Gene Expression data


title: 106_SQ11-228T

description:
228T
Gene Expression data


title: 59_SQ11-28T

description:
28T
Gene Expression data


title: 102_SQ11-214T

description:
214T
Gene Expression data


title: 43_SQ11-211T

description:
211T
Gene Expression data


title: 39_SQ11-201T

description:
201T
Gene Expression data


title: 46_SQ11-229T

description:
229T
Gene Expression data


title: 101_SQ11-196T

description:
196T
Gene Expression data


title: 97_SQ11-174T

description:
174T
Gene Expression data


title: 96_SQ11-172T

description:
172T
Gene Expression data


title: 99_SQ11-181T

description:
181T
Gene Expression data


title: 95_SQ11-169T

description:
169T
Gene Expression data


title: 35_SQ11-179T

description:
179T
Gene Expression data


title: 37_SQ11-193T

description:
193T
Gene Expression data


title: 33_SQ11-161T

description:
161T
Gene Expression data


title: 98_SQ11-180T

description:
180T
Gene Expression data


title: 94_SQ11-168T

description:
168T
Gene Expression data


title: 29_SQ11-155T

description:
155T
Gene Expression data


title: 88_SQ11-146T

description:
146T
Gene Expression data


title: 51_SQ11-144T

description:
144T
Gene Expression data


title: 27_SQ11-173T

description:
173T
Gene Expression data


title: 32_SQ11-167T

description:
167T
Gene Expression data


title: 30_SQ11-156T

description:
156T
Gene Expression data


title: 28_SQ11-153T

description:
153T
Gene Expression data


title: 90_SQ11-152T

description:
152T
Gene Expression data


title: 89_SQ11-149T

description:
149T
Gene Expression data


title: 34_SQ11-165T

description:
165T
Gene Expression data


title: 93_SQ11-159T

description:
159T
Gene Expression data


title: 26_SQ11-148T

description:
148T
Gene Expression data


title: 92_SQ11-158T

description:
158T
Gene Expression data


title: 91_SQ11-154T

description:
154T
Gene Expression data


title: 8_SQ11-14T

description:
14T
Gene Expression data


title: 25_SQ11-143T

description:
143T
Gene Expression data


title: 83_SQ11-131T

description:
131T
Gene Expression data


title: 52_SQ13-10T

description:
10T
Gene Expression data


title: 87_SQ11-138T

description:
138T
Gene Expression data


title: 86_SQ11-134T

description:
134T
Gene Expression data


title: 84_SQ11-132T

description:
132T
Gene Expression data


title: 31_SQ13-9T

description:
9T
Gene Expression data


title: 68_SQ11-123T

description:
123T
Gene Expression data


title: 78_SQ11-105T

description:
105T
Gene Expression data


title: 54_SQ11-10T

description:
10T
Gene Expression data


title: 53_SQ13-11T

description:
11T
Gene Expression data


title: 7_SQ11-11T

description:
11T
Gene Expression data


title: 22_SQ11-113T

description:
113T
Gene Expression data


title: 69_SQ11-126T

description:
126T
Gene Expression data


title: 38_SQ11-198T

description:
198T
Gene Expression data


title: 100_SQ11-183T

description:
183T
Gene Expression data


title: 23_SQ11-116T

description:
116T
Gene Expression data


title: 81_SQ11-114T

description:
114T
Gene Expression data


title: 21_SQ11-111T

description:
111T
Gene Expression data


title: 80_SQ11-110T

description:
110T
Gene Expression data


title: 36_SQ11-190T

description:
190T
Gene Expression data


title: 20_SQ11-101T

description:
101T
Gene Expression data


title: 24_SQ11-120T

description:
120T
Gene Expression data


title: 67_SQ11-121T

description:
121T
Gene Expression data


title: 82_SQ11-128T

description:
128T
Gene Expression data


title: 85_SQ11-133T

description:
133T
Gene Expression data


title: TNF/iNOS-producing dendritic cells, replicate B

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

hyb_protocol: Samples were hybridized to Affymetrix Mouse Genome 430 2.0 arrays following the standard Affymetrix procedures.

scan_protocol: Arrays were scanned with an Affymetrix GCS 3000 7G scanner.

data_processing: Affymetrix MAS5.0 procedure

source_name: mouse TNF/iNOS-producing dendritic cells

label_protocol: The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA).

growth_protocol: EG7 tumor was injected in C57BL/6 and after 7 days of tumor growth mice were treated with adoptive  CD8+ T cells specific to recognize  OVA antigen. After 3 days mice were sacrified and tumor masses used to isolate cells.CD11b+NO+Ly6C+Ly6G- live cells were FACS sorted from tumor masses pooled from 12 mice. 2 samples from two different experiments were obtained.

extract_protocol: CD11b+NO+Ly6C+Ly6G- cells were prepared for  for the extraction of total RNA by using TRIzol reagent

treatment_protocol: After 3 days mice were sacrified and tumor masses used to isolate cells.CD11b+NO+Ly6C+Ly6G- live cells were FACS sorted from tumor masses pooled from 12 mice for each sample. 2 samples from two different experiments were obtained.


title: Embryonic thymospheres 1

city: Heidelberg

first: Olga

last: Ucar

address: Im Neuenheimer Feld 280

department: Developmental Immunology

country: Germany

institute: German Cancer Research Center

description:
252800522015_1_3
Gene expression in thymospheres (colonies derived in vitro from thymic epithelial stem cells, which have the ability to form spheres).

hyb_protocol: 0,25 ug of cRNA were hybridized for 17 hr at 65°C on Agilent Mouse Gene Expression Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C .

data_processing: The scanned images were analysed with Feature Extraction Software 10.7.3.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: embryonic mouse thymus_sphere culture

label_protocol: 25 ng of total RNA was used for cRNA synthesis and Cy3 labelling using Agilent Low Input Quick Amp Labeling Kit.

growth_protocol: Fresh thymic digests were plated into ultra low attachment plates in sphere culture medium and placed in CO2 incubator. Fresh medium was added at day 5 in vitro. Spheres were collected on day 7 in vitro.

extract_protocol: RNA extraction was performed using TRIzol/chloroform method; absolute ethanol was used for precipitation at -20°C, the RNA pellet was washed twice with 80% ethanol and dissolved in H2O. RNA concentration and integrity were analysed by Eukaryote Total RNA pico Series II chip on a 2100 Bioanalyzer (Agilent). 25 ng of total RNA was used for cDNA synthesis using Agilent Low Input Quick Amp Labeling Kit.

treatment_protocol: Sphere culture medium contained B27 supplement, hydrocortisone, insulin, EGF and bFGF.

value: embryonic day 14.5

value: primary thymospheres


title: Embryonic thymospheres 2

description:
252800522015_1_4
Gene expression in thymospheres (colonies derived in vitro from thymic epithelial stem cells, which have the ability to form spheres).


title: Adult thymospheres 2

description:
252800522015_1_2
Gene expression in thymospheres (colonies derived in vitro from thymic epithelial stem cells, which have the ability to form spheres).

source_name: adult mouse thymus_sphere culture

value: 5-6 weeks


title: miR-155-/- BMM, Mtb 8h, rep 3, val

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Mtb-infected miR-155-/- BMM

hyb_protocol: Samples were hybridized according to the Whole Transcript Sense Target Labeling protocol: Heat cocktail mix at 99°C for 5 minutes, 45°C for 5 minutes, and then centrifuge at 13,200g for 1 minute. Transfer 200uL of hyb solution to each array. Hybridize 16 hours at 45°C at 60rpm. Wash and stain using fluidics protocol FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 14) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization.
BrainArray version 14: MoEx10stv1_Mm_ENTREZG

source_name: miR-155-/- BMM, Mtb 8h

label_protocol: Total RNA samples were labeled as described in the Whole Transcript Sense Target Labeling protocol (Affymetrix)

growth_protocol: Bone marrow-derived macrophages (BMM) were cultured in complete RPMI (cRPMI; plus 10% FBS, 2 mM l-glutamine, penicillin and streptomycin) with recombinant human CSF-1 (50 ng/ml) for 6 days.

extract_protocol: Total RNA was isolated from cells using TRIzol (Invitrogen) according to manufacturer's instructions. Prior to labeling, sample integrity was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: On day 7, BMM were infected with Mtb H37Rv strain (MOI 5), followed by washing 2X with PBS. BMM were infected with H37Rv for 8 hours prior to RNA extraction.

tag: genotype/variation

tag: cell type

value: BMM

tag: infection

value: Mtb H37Rv strain (MOI 5)

tag: timepoint

tag: series

value: validation


title: TNF/iNOS-producing dendritic cells, replicate C

growth_protocol: EG7 tumor was injected in C57BL/6 and after 7 days of tumor growth mice were treated with adoptive  CD8+ T cells specific to recognize  OVA antigen. After 3 days mice were sacrified and tumor masses used to isolate cells.CD11b+NO+Ly6C+Ly6G- live cells were FACS sorted from tumor masses pooled from 12 mice. 3 samples from 3 different experiments were obtained.

extract_protocol: CD11b+NO+Ly6C+Ly6G- cells were prepared for for the extraction of total RNA by using TRIzol reagent

treatment_protocol: After 3 days mice were sacrified and tumor masses used to isolate cells.CD11b+NO+Ly6C+Ly6G- live cells were FACS sorted from tumor masses pooled from 12 mice for each sample. 3 samples from 3 different experiments were obtained.


title: miR-155-/- BMM, Mtb 8h, rep 2, val

description: Mtb-infected miR-155-/- BMM


title: 79_SQ11-109T

description:
109T
Gene Expression data

value: lung squamous cell carcinoma

tag: tumor size(cm)

tag: pt

tag: pn

tag: pm

tag: 7th pstage

value: Current


title: 15_SQ11-72T

description:
72T
Gene Expression data

tag: smoking status

tag: pack-year

tag: relapse

value: not relapsed

tag: days before relapse/censor

tag: death

value: dead


title: TNF/iNOS-producing dendritic cells, replicate A

tag: strain


title: miR-155-/- BMM, 0h, rep 2, val

description: naïve miR-155-/- BMM

value: naïve


title: Adult thymospheres 1

description:
252800522015_1_1
Gene expression in thymospheres (colonies derived in vitro from thymic epithelial stem cells, which have the ability to form spheres).

tag: age

tag: tissue


title: miR-155-/- BMM, 0h, rep 3, val

description: naïve miR-155-/- BMM

tag: genotype/variation

tag: cell type


title: miR-155-/- BMM, 0h, rep 1, val

description: naïve miR-155-/- BMM

tag: infection

tag: timepoint


title: miR-155-/- BMM, Mtb 8h, rep 1, val

description: Mtb-infected miR-155-/- BMM

tag: series


title: WT BMM, Mtb 8h, rep 3, val

description: Mtb-infected WT BMM

source_name: WT BMM, Mtb 8h

value: WT


title: WT BMM, Mtb 8h, rep 2, val

description: Mtb-infected WT BMM


title: WT BMM, Mtb 8h, rep 1, val

description: Mtb-infected WT BMM


title: WT BMM, Mtb 24h, rep 3

description: Mtb-infected WT BMM

source_name: WT BMM, Mtb 24h

treatment_protocol: On day 7, BMM were infected with Mtb H37Rv strain (MOI 5), followed by washing 2X with PBS. BMM were infected with H37Rv for 4, 8, 24, or 48 hours prior to RNA extraction.

value: timecourse


title: WT BMM, Mtb 24h, rep 1

description: Mtb-infected WT BMM


title: WT BMM, 0h, rep 3, val

description: naïve WT BMM

source_name: WT BMM, 0h


title: WT BMM, Mtb 48h, rep 3

description: Mtb-infected WT BMM

source_name: WT BMM, Mtb 48h


title: WT BMM, Mtb 8h, rep 3

description: Mtb-infected WT BMM


title: WT BMM, Mtb 24h, rep 2

description: Mtb-infected WT BMM


title: WT BMM, Mtb 48h, rep 2

description: Mtb-infected WT BMM


title: WT BMM, 0h, rep 1, val

description: naïve WT BMM


title: WT BMM, 0h, rep 2, val

description: naïve WT BMM


title: WT BMM, Mtb 48h, rep 1

description: Mtb-infected WT BMM


title: shCtrl

city: Beijing

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: The expression profiles of lncRNA and mRNA were compared between shZNF717-HepG2 and blank control group.

hyb_protocol: The Cy3TM-labeled samples were hybridized according to the manufacturer’s protocol (Arraystar Inc).

scan_protocol: The slides were scanned usingthe Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: shCtrl-HepG2 cells

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for RNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: disease state

value: liver cancer

tag: cell line

value: control


title: shZNF717

source_name: shZNF717-HepG2 cells

value: ZNF717 knockdown


title: WT BMM, Mtb 8h, rep 1

description: Mtb-infected WT BMM


title: WT BMM, Mtb 8h, rep 2

description: Mtb-infected WT BMM


title: WT BMM, Mtb 4h, rep 2

description: Mtb-infected WT BMM

source_name: WT BMM, Mtb 4h


title: WT BMM, 0h, rep 3

description: naïve WT BMM


title: WT BMM, Mtb 4h, rep 3

description: Mtb-infected WT BMM


title: WT BMM, Mtb 4h, rep 1

description: Mtb-infected WT BMM


title: A. thaliana salt, high conc., late time point rep 2

city: Kolkata

first: Malay

last: Das

state: West Bengal

address: 86/1 College Street

department: Biological Sciences

country: India

institute: Presidency University

description: Gene expression of early and late time points after moderate and high conc. of NaCl treatments

hyb_protocol: As per Agilent recommedations

scan_protocol: Data were extracted by using an Agilent scanner and an Agilent Feature Extraction program.

data_processing: Background corrected and multiplicatively de-trended hybridization signals were imported to GeneSpring (G3784AA, version 2011) for log2 transformation and data normalization.

organism: Arabidopsis thaliana

source_name: shoot tissues, 500mM NaCl treatment, 27h post treatment harvest

label_protocol: Cy3 labelling by using the one colour low-amp quick amplification labeling kit (Agilent technologies)

growth_protocol: Four weeks old, soil grown Arabidopsis thaliana, Col 0 plants were treated either with 250 or 500 mM NaCl solution by flush flooding, while the control group was watered.

extract_protocol: Triazol extraction of total RNA and subsequent purification with Rneasy mini spin columns

treatment_protocol: Tissues were harvested at 3h and 27h post NaCl treatment of moderate (250mM) and high (500 mM) concentrations.

tag: protocol

value: 500mM NaCl treatment

tag: time point

value: 27h post treatment harvest

value: shoots freeze frozen


title: A. thaliana salt, moderate conc., late time point rep 2

source_name: shoot tissues, 250mM NaCl treatment, 27h post treatment harvest

value: 250mM NaCl treatment


title: A. thaliana salt, high conc., late time point rep 3


title: A. thaliana salt, moderate conc., late time point rep 1


title: A. thaliana salt, moderate conc., late time point rep 3


title: WT BMM, 0h, rep 2

description: naïve WT BMM

value: BMM


title: WT BMM, 0h, rep 1

description: naïve WT BMM


title: A. thaliana control regular watering late time point rep 3

source_name: shoot tissues, regular watering,  27h time point

value: regular waterin

value: 27h time point


title: A. thaliana salt, high conc., late time point rep 1


title: A. thaliana control regular watering late time point rep 1

value: regular watering


title: A. thaliana control regular watering late time point rep 2


title: A. thaliana salt, high conc., early time point rep 3

source_name: shoot tissues, 500mM NaCl treatment, 3h post treatment harvest

value: 3h post treatment harvest


title: A. thaliana salt, high conc., early time point rep 1


title: A. thaliana salt, moderate conc., early time point rep 1

source_name: shoot tissues, 250mM NaCl treatment, 3h post treatment harvest


title: A. thaliana salt, moderate conc., early time point rep 3


title: A. thaliana salt, high conc., early time point rep 2


title: A. thaliana UV-B late time point rep 2

description: Gene expression of mid and late time points after UV-B treatments

source_name: shoot tissues, 8h UV exposed, late time points

growth_protocol: Four weeks old Arabidopsis thaliana, Col 0 plants grown on soil were exposed to UV-B radiation.

treatment_protocol: Plants were exposed to UV-B radiation plus PAR (400-700 nm) of 140 µmol m-2 s^{-1}. The biological effective UV-B radiation, weighted after generalized plant action spectrum (Caldwell, 1971) and normalized at 300 nm were 1.31 kJ m^{-2} for 4 h.

value: 8h UV exposed

value: late time points


title: A. thaliana control regular watering early time point rep 2

source_name: shoot tissues, regular watering,  3h time point

value: 3h time point


title: A. thaliana control regular watering early time point rep 3


title: A. thaliana UV-B late time point rep 1

source_name: shoot tissues,8h UV exposed, late time points


title: A. thaliana control regular watering early time point rep 1


title: A. thaliana UV-B late time point rep 3


title: A. thaliana control plants late time point rep 2

source_name: shoot tissues, control plants, late time points

value: control plants


title: A. thaliana control plants late time point rep 1


title: A. thaliana control plants late time point rep 3


title: A. thaliana salt, moderate conc., early time point rep 2


title: A. thaliana UV-B mid time point rep 3

source_name: shoot tissues,4h UV exposed, mid time points

value: 4h UV exposed

value: mid time points


title: A. thaliana UV-B mid time point rep 1


title: A. thaliana UV-B mid time point rep 2


title: A. lyrata salt, high conc., late time point rep 3

organism: Arabidopsis lyrata subsp. lyrata

growth_protocol: Six weeks old, soil grown Arabidopsis lyrata ssp. lyrata plants were treated either with 250 or 500 mM NaCl solution by flush flooding, while the control group was watered.


title: A. lyrata salt, high conc., late time point rep 2


title: A. thaliana control mid time point rep 1

source_name: shoot tissues, control plants, mid time points


title: A. thaliana control mid time point rep 3


title: A. lyrata salt, moderate conc., late time point rep 3


title: A. lyrata salt, moderate conc., late time point rep 1


title: A. lyrata salt, moderate conc., late time point rep 2


title: A. thaliana flower bud rep 3

description: Gene expression of 6 weeks old A. thaliana plants

source_name: Healthy flower buds freeze frozen

growth_protocol: Sterilized seeds of A. thaliana, col 0 were placed on top of eppendorf tube containg 0.65% agar, stratified for 2-3 days and and were grown hydroponically

treatment_protocol: Roots and flower buds from 6 weeks old plants of A. thaliana were harvested in liquid nitrogen

value: Flower buds


title: A. thaliana flower bud rep 2


title: A. thaliana control mid time point rep 2


title: A. thaliana flower bud rep 4


title: 1201C1_NR-NSPC (Long culture)

city: Shinjuku-ku

first: Keiko

last: Sugai

address: 35 Shinanomachi

institute: Keio University School of Medicine

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The image was analyzed using Chromosome Analysis Suite (ChAS) Software.
Copy Number data

label: Biotin

source_name: iPS-derived NSPC

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: iPSCs were grown according to standard conditions. Neural induction was perfomed by dual SMAD inhibition. iPS-derived NSPCs were expanded by neurosphere culture technique.

extract_protocol: Genomic DNA was extracted from cultured cells by Qiagen DNA Blood and Tissue Kit. DNA quality and quantity was assessed using a Spectrophotometer.

treatment_protocol: None.

tag: ethnicity

value: African-American

tag: Sex

value: Female


title: 1201C1_EB-NSPC (Long culture)


title: 1210B2_EB-NSPC


title: A. lyrata control regular watering late time point rep 2


title: A. thaliana flower bud rep 1


title: A. lyrata control regular watering late time point rep 3


title: A. thaliana root rep 4

source_name: Healthy roots freeze frozen

value: Roots


title: A. lyrata control regular watering late time point rep 1

value: shoots freeze frozen


title: A. lyrata salt, high conc., early time point rep 3

value: 250mM NaCl treatment


title: 1231A3_NR-NSPC (Long culture)


title: 1201C1_EB-NSPC


title: 1201C1_iPSC

source_name: iPSC


title: 1231A3_iPSC


title: A. thaliana root rep 3


title: 1231A3_EB-NSPC (Long culture)


title: 1201C1_NR-NSPC


title: 1210B2_NR-NSPC (Long culture)


title: 1231A3_EB-NSPC


title: 1210B2_iPSC


title: A. lyrata salt, high conc., early time point rep 2


title: A. lyrata salt, high conc., early time point rep 1


title: A. thaliana root rep 1


title: 1210B2_EB-NSPC (Long culture)


title: A. thaliana drought late time point rep 1

description: Gene expression of early and late time points after drought treatments

source_name: shoot tissues, 11 days after withdrawal of watering

growth_protocol: Sterilized seeds of A. thaliana, col 0 Three weeks old Arabidopsis thaliana, Col0 plants were stopped watering for the treatment groups, while the control group was watered on regular intervals.

treatment_protocol: Tissue was harvested 8d after drought treatment for the early time point, while 11d for late time point.

value: shoot

value: 11 days after withdrawal of watering


title: 1231A3_NR-NSPC


title: A. thaliana root rep 2


title: A. lyrata salt, moderate conc., early time point rep 3


title: A. thaliana drought late time point rep 3


title: 1210B2_NR-NSPC


title: A. thaliana drought late time point rep 2


title: A. lyrata salt, moderate conc., early time point rep 1


title: A. lyrata salt, moderate conc., early time point rep 2


title: A. thaliana control late time point rep 3

source_name: shoot tissues, regular watering


title: A. lyrata control regular watering early time point rep 3


title: A. thaliana control late time point rep 2


title: A. thaliana control late time point rep 1


title: A. lyrata control regular watering early time point rep 2


title: A. lyrata control regular watering early time point rep 1


title: A. lyrata UV-B late time point rep 3

growth_protocol: Six weeks old Arabidopsis lyrata ssp. lyrata plants grown on soil were exposed to UV-B radiation.


title: A. thaliana control early time point rep 3


title: A. thaliana drought early time point rep 3

source_name: shoot tissues, 8 days after withdrawal of watering

value: 8 days after withdrawal of watering


title: A. lyrata UV-B late time point rep 1


title: A. lyrata UV-B late time point rep 2


title: A. lyrata salt, high conc., late time point rep 1

source_name: shoot tissues, 500mM NaCl treatment, 27h post treatment harvest

value: 27h post treatment harvest


title: A. thaliana drought early time point rep 2


title: A. thaliana drought early time point rep 1


title: A. thaliana control early time point rep 2

value: regular watering


title: A. lyrata control plants late time point rep 2


title: A. lyrata control plants late time point rep 3


title: High-OCT4_biological rep4

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 150 Bergen Street

department: Department of Medicine

institute: New Jersey Medical School, Rutgers School of Biomedical Health Science

description: Global gene expression data from MDA-MB-231 breast cancer cell with high-OCT4 expression

hyb_protocol: Fragmented samples were hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays and then washed and stained following the manufacturer’s protocols.

scan_protocol: GeneChip arrays were scanned on a GeneChip Scanner 3000 7G (Agilent/Affymetrix)

data_processing: Background corrected hybridization intensities were imported into BRB-Array Tools Version 4.4.0 log2-transformed and robust multi-array average (RMA) normalized.

source_name: MDA-MB-231_transfected with pEGFP1-Oct3/4 and then selected with neomycin_high-Oct4

label_protocol: Total RNA (100 ng) was converted into cDNA, cRNA, and fragmented according to the manufacturer's protocol with the assistance of the Biomek FXP  Target Prep Express with GeneChip HT 3' IVT Express Kit.

growth_protocol: MDA-MB-231 cells from ATCC were transfected with pEGFP1-Oct3/4 and then selected with neomycin

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen) and quality was assessed on the Agilent Bioanalyzer 2100.

treatment_protocol: Stable transfectants were sorted based on GFP intensity using the FACSDiva (BD Biosciences). Sorting was done using the top and lower 5% GFP cells and the population in the middle of the two extreme subsets and were designated Oct4hi, Oct4med and Oct4lo.

value: Breast cancer cell derived from metastatic site

tag: phenotype

value: MDA-MB-231 with OCT4-high


title: A. thaliana control early time point rep 1


title: High-OCT4_biological rep3


title: A. lyrata UV-B mid time point rep 2

source_name: shoot tissues, 4h UV exposed, mid time points


title: sigA overexpression_24h

city: Bielefeld

first: Hironori

last: Taniguchi

institute: Bielefeld University

description:
Three replicates:
sigA overexpression_24h_4 (sigA overexpression_24h_4.csv, WT(pVWEx1-sigA) Cy3, WT(pVWEx1) Cy5)
sigA overexpression_24h_5 (sigA overexpression_24h_5.csv, WT(pVWEx1-sigA) Cy3, WT(pVWEx1) Cy5)
sigA overexpression_24h_6 (sigA overexpression_24h_6.csv, WT(pVWEx1) Cy3, WT(pVWEx1-sigA) Cy5)
Inoculation in CGXII with 4% glucose at initial OD (λ600) of 1

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the data was done with the software package EMMA 2 (Dondrup et al., 2009). Genes which expression was upregulated or downregulated in WT(pVWEx1-sigA) were taken into account for further analysis (FDR < 0.05, M-value > 1 for upregulation, M-value < -1 for downregulation).

label: Cy3, Cy5

organism: Corynebacterium glutamicum

source_name: C. glutamicum WT(pVWEx1)

label_protocol: cDNA synthesis were performed as described previously (Netzer et al., 2004; Polen et al., 2007).

growth_protocol: C. glutamicum strains WT(pVWEx1) and WT(pVWEx1-sigA) were cultured in LB medium with 56 mM of glucose and 25 μg/mL of kanamycin and inoculated into CGXII medium with 222 mM of glucose and 25 μg/mL of kanamycin for adaptation to glucose as carbon source. Cells were cultured overnight and inoculated into 50 mL of CGXII medium with 222 mM of glucose, 50 μM of IPTG and 25 μg/mL of kanamycin at the initial OD of 1. Cells were harvested 8 hours after inoculation in the early exponential growth phase (OD between 6 and 8) and after 24 hours in the stationary phase.

extract_protocol: RNA isolation was performed as described previously (Wendisch, 2003). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality.

value: control

tag: time

value: 24 hours after inoculation

source_name: C. glutamicum WT(pVWEx1-sigA)

value: sigA overexpression


title: A. lyrata UV-B mid time point rep 3

value: 4h UV exposed

value: mid time points


title: High-OCT4_biological rep1


title: sigA overexpression_8h

description:
Three replicates:
sigA overexpression_8h_4 (sigA overexpression_8h_4.csv, WT(pVWEx1) Cy3, WT(pVWEx1-sigA) Cy5)
sigA overexpression_8h_5 (sigA overexpression_8h_5.csv, WT(pVWEx1-sigA) Cy3, WT(pVWEx1) Cy5)
sigA overexpression_8h_6 (sigA overexpression_8h_6.csv, WT(pVWEx1-sigA) Cy3, WT(pVWEx1) Cy5)
Inoculation in CGXII with 4% glucose at initial OD (λ600) of 1

value: 8 hours after inoculation


title: A. lyrata UV-B mid time point rep 1


title: Medium-OCT4_biological rep2

description: Global gene expression data from MDA-MB-231 breast cancer cell with mdium-OCT4 expression

source_name: MDA-MB-231_transfected with pEGFP1-Oct3/4 and then selected with neomycin_medium-Oct4

value: MDA-MB-231 with OCT4-Medium


title: A. lyrata control mid time point rep 3

value: control plants


title: A. lyrata control plants late time point rep 1

value: late time points

value: shoots freeze frozen


title: Chaos3/3 C3HxB6 F2_5

type: mixed

city: Ithaca

first: John

last: Schimenti

state: NY

address: College of Veterinary Medicine T9014A

department: Biomedical Scinces

institute: Cornell University

description:
17320
US83000170_252741411108_S01_CGH_107_Sep09

hyb_protocol: Manufacterer's protocol

scan_protocol: Images were scanned using Agilent’s SureScan Microarray Scanner

data_processing:
Agilent’s Cytogenomics software was used for spot identification and signal quantification, following default Linear and LOWESS  normalization of test/reference ratios and background correction.
Criteria for calling amplifications/deletions were as follows: minimum number of contiguous probes >= 3, minimum avg. absolute log2 ratio >= 0.25.

source_name: bone tumor

label_protocol: Manufacterer's protocol

growth_protocol: Tumors developed spontaneously within female mice with the MCM4Chaos3/Chaos3 point mutation

extract_protocol: Genomic DNA was isolated from primary tumors by solubilizing in lysis buffer (50 mMTris-HCl pH 8.0; 100 mM EDTA pH 8.0; 100 mM NaCl; 1% SDS; 0.5 mg/ml ProteinaseK) for 3 hours at 55°, phenol/chloroform extraction, precipitation of the DNA in 0.8 volumes isopropanol, followed by spooling and washes in 70% then 100% ethanol.

value: Chaos3/3 C3HxB6 F2

value: MCM4Chaos3/Chaos3 point mutation

tag: gender

value: female

value: bone tumor

tag: # of cnvs

source_name: reference wild-type DNAs from C57Bl/6J and C3HeB/FeJ

value: C57Bl/6J and C3HeB/FeJ

value: wild type

tag: sample type

value: reference DNA


title: Chaos3/3 C3HxB6 F2_4

description:
17651
US83000170_252741411107_S01_CGH_107_Sep09

source_name: uterine tumor

tag: strain

tag: tissue

value: uterine tumor


title: A. lyrata control mid time point rep 2

source_name: shoot tissues, control plants, mid time points


title: nore1-1_DAE24-2

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

hyb_protocol: Microarray chips were hybridized using Agilent’s Gene Expression Hybridization Kit and washed with Agilent’s Gene Expression Wash Buffer Kit.

scan_protocol: An Agilent SureScan Microarray Scanner

data_processing:
Scanned images were analyzed and quantified using Agilent Feature Extraction software (version 11.5). Log2 intensities of the probes were first normalized using quantile normalization. Applicable cutoffs for reliable signals in probes were determined by Gaussian curve fitting (Signal ≥ 5.583)
Probes targeting multiple genes were ignored and data was analyzed based on gene expression, not on transcript expression

source_name: nore1-1, DAE24

label_protocol: Total RNA was amplified and labeled using Agilent's one-color Low Input Quick Amp Labeling kit

growth_protocol: Arabidopsis were grown in the soil for 21~33 days in 16:8 light-dark (LD) cycle

extract_protocol: Total RNA was isolated using WelprepTM Total RNA Isolation Reagent

treatment_protocol: Plants were harvested at 6 hr after light-on.

tag: genotype/variation

tag: age

value: 24 days old

value: 3 or 4th leaves


title: Low-OCT4_biological rep4

description: Global gene expression data from MDA-MB-231 breast cancer cell with low-OCT4 expression

source_name: MDA-MB-231_transfected with pEGFP1-Oct3/4 and then selected with neomycin_low-Oct4

value: Breast cancer cell derived from metastatic site

value: MDA-MB-231 with OCT4-low


title: Chaos3/3 C3H Congenic_6

description:
20889
US83000170_252741411105_S01_CGH_107_Sep09

source_name: mammary tumor

value: Chaos3/3 C3H Congenic

value: mammary tumor


title: Chaos3/3 C3H Congenic_7

description:
20724
US83000170_252741411106_S01_CGH_107_Sep09


title: Low-OCT4_biological rep3


title: A. lyrata control mid time point rep 1

value: control plants

value: mid time points


title: nore1-1_DAE20-2

source_name: nore1-1, DAE20

value: 20 days old


title: Low-OCT4_biological rep2


title: A. lyrata drought late time point rep 2

source_name: shoot tissues, 11 days after withdrawal of watering

growth_protocol: Five weeks old Arabidopsis lyrata ssp. lyrata plants grown on soil were stopped watering for the treatment groups, while the control group was watered on regular intervals.

value: 11 days after withdrawal of watering

value: shoots freeze frozen


title: A. lyrata drought late time point rep 3


title: nore1-1_DAE16-2

source_name: nore1-1, DAE16

value: 16 days old


title: Low-OCT4_biological rep1


title: A. lyrata drought late time point rep 1


title: nore1-1_DAE12-2

source_name: nore1-1, DAE12

value: 12 days old


title: Chaos3/3 C3H Congenic_4

description:
20894
US83000170_252741411076_S01_CGH_107_Sep09

value: Chaos3/3  C3H Congenic

value: MCM4Chaos3/Chaos3 point mutation

value: female

value: C57Bl/6J and C3HeB/FeJ


title: Col_DAE24-2

source_name: Col, DAE24

value: wild type

value: 24 days old


title: Chaos3/3 C3H Congenic_2

description:
19959
US83000170_252741411074_S01_CGH_107_Sep09

value: reference DNA


title: Chaos3/3 C3H Congenic_5

description:
20164
US83000170_252741411104_S01_CGH_107_Sep09


title: 1201C1_T2_NR-NSPC

hyb_protocol: The cRNAs were hybridized to each array according to the manufacturer's instructions.

data_processing:
The array image was acquired using Afymetrix Genechip Command Console.
affymetrix-algorithm-name = ExpressionStat  affymetrix-algorithm-version = 5.0

source_name: iPS-derived NSPC

label_protocol: As per manufacturer (Affymetrix 3'-IVT Kit)

extract_protocol: Total RNA was extracted by QIAzol lysis reagent, followed by 2-propanol precipitate and DNase treatment

value: African-American

value: Female


title: A. lyrata control late time point rep 3

source_name: shoot tissues, regular watering

value: regular watering


title: Medium-OCT4_biological rep1

value: Breast cancer cell derived from metastatic site

value: MDA-MB-231 with OCT4-Medium


title: A. lyrata control late time point rep 2


title: 1210B2_T2_NR-NSPC


title: 1231A3_T2_NR-NSPC


title: Col_DAE16-2

source_name: Col, DAE16

value: 3 or 4th leaves


title: A. lyrata control late time point rep 1


title: Chaos3/3 C3H Congenic_1

description:
20138
US83000170_252741411073_S01_CGH_107_Sep09

value: mammary tumor


title: Chaos3/3 C3HxB6 F2_2

description:
16694
US83000170_252741411103_S01_CGH_107_Sep09

value: Chaos3/3 C3HxB6 F2


title: nore1-1_DAE24-1


title: A. lyrata drought early time point rep 3

source_name: shoot tissues, 8 days after withdrawal of watering

value: 8 days after withdrawal of watering

value: shoots freeze frozen


title: Chaos3/3 C3H Congenic_3

description:
20626
US83000170_252741411075_S01_CGH_107_Sep09

value: Chaos3/3 C3H Congenic


title: High-OCT4_biological rep2

source_name: MDA-MB-231_transfected with pEGFP1-Oct3/4 and then selected with neomycin_high-Oct4

value: MDA-MB-231 with OCT4-high


title: Chaos3/Chaos3 C3H Congenic

description:
20892
US83000170_252741411072_S01_CGH_107_Sep09

value: Chaos3/Chaos3 C3H Congenic

value: MCM4Chaos3/Chaos3 point mutation

value: female


title: Col_DAE12-2

source_name: Col, DAE12

value: wild type

value: 12 days old


title: Chaos3/3 C3HxB6 F1_2

description:
16898
US83000170_252741411070_S01_CGH_107_Sep09

value: Chaos3/3 C3HxB6 F1

source_name: reference wild-type DNAs from C57Bl/6J and C3HeB/FeJ

value: C57Bl/6J and C3HeB/FeJ

value: reference DNA


title: Chaos3/3 C3HxB6 F2_1

description:
18656
US83000170_252741411102_S01_CGH_107_Sep09


title: A. lyrata drought early time point rep 2

description: Gene expression of early and late time points after drought treatments


title: 1231A3_T1_NR-NSPC

value: African-American

value: Female


title: 1210B2_T1_NR-NSPC


title: 1201C1_T2_EB-NSPC


title: Chaos3/3 C3HxB6 F1_1

description:
18333
US83000170_252741411101_S01_CGH_107_Sep09


title: Chaos3/3 C3HxB6 F2_3

description:
16815
US83000170_252741411071_S01_CGH_107_Sep09


title: A. lyrata drought early time point rep 1


title: 1201C1_T1_NR-NSPC


title: nore1-1_DAE20-1

value: 20 days old

value: 3 or 4th leaves


title: A. lyrata control early time point rep 2

value: regular watering


title: Col_DAE24-1

value: 24 days old


title: A. lyrata flower bud rep 4

description:
Healthy flower buds snap frozen
Gene expression of 6 weeks old A. lyrata ssp. lyrata plants

source_name: Flower buds

growth_protocol: Sterilized seeds of A. lyrata ssp. lyrata, col 0 were placed on top of eppendorf tube containg 0.65% agar, stratified for 7 days and and were grown hydroponically

treatment_protocol: Roots and flower buds from 6 weeks old plants of A. lyrata ssp. lyrata were harvested in liquid nitrogen

value: Flower buds


title: A. lyrata control early time point rep 1

value: shoots freeze frozen


title: Col_DAE20-1

source_name: Col, DAE20


title: nore1-1_DAE16-1

value: 16 days old


title: 1210B2_T2_EB-NSPC


title: 1231A3_T2_EB-NSPC


title: nore1-1_DAE12-1


title: 1201C1_T1_EB-NSPC


title: Col_DAE12-1


title: A. lyrata flower bud rep 3


title: A. lyrata flower bud rep 2


title: Col_DAE20-2


title: A. lyrata flower bud rep 1


title: 1210B2_T2_iPSC

source_name: iPSC


title: A. lyrata root rep 4

description:
Healthy roots snap frozen
Gene expression of 6 weeks old A. lyrata ssp. lyrata plants

source_name: Roots

value: Roots


title: 1201C1_T2_iPSC


title: 1210B2_T1_EB-NSPC


title: 1231A3_T1_EB-NSPC


title: 1231A3_T2_iPS


title: A. lyrata root rep 2


title: 1201C1_T1_iPSC


title: Col_DAE16-1


title: 1231A3_T1_iPSC


title: A. lyrata root rep 1


title: Mouse MyD88 KO fed with high-fat diet

status: Public on Sep 13 2016

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data from MyD88 liver specific KO mice. Total liver tissue under high fat diet.

hyb_protocol: Affymetrix hybridization control and hybridization wash and stain kit.

scan_protocol: The wash and stain protocols were runned on an Affy 450 station. The chips were scanned according to the Affymetrix standard procedure.

data_processing: Affymetrix Gene Expression Console and APT suite tool. Normalization: RMA-sketch procedure; signal detection p-values: DABG procedure.

source_name: Mouse (C57Bl6) liver tissue

label_protocol: Biotinylated cRNAs were prepared according to the standard Ambion WT expression kit from 100ng of total RNA  followed by Affymetrix WT terminal labeling kit.

growth_protocol: two groups of mice:  Myd88 WT and MyD88 liver conditional KO were recruited for this experiment

extract_protocol: Liver RNA extraction was done using Tripure (Roche). After extraction RNAs from 4 to 5 mice per group were pooled, mice were selected based on their RNA quality.

treatment_protocol: each group of mice were fed either with control diet (composition: 9.4% fat) or high-fat containing diet (composition: 60% fat)

value: total liver

tag: genotype

value: ALB Cre MyD88 lox/lox

tag: diet

value: high-fat

value: 16 weeks


title: Liver MyD88 KO mice fed with control diet

description: Gene expression data from MyD88 liver specific KO mice. Total liver tissue under normal diet.

value: control


title: A. lyrata root rep 3


title: 1210B2_T1_iPSC


title: nonviral 4F stromal primed fetal liver iPSC clone 3 p11

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V3.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 3, passage 11

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: cell type

tag: passage

value: non-integrated stromal primed fetal liver iPSC generated in the Zambidis laboratory


title: Cord Blood CD34+ progenitors Sample 2

description: Individual sample

source_name: Cord Blood CD34+ progenitors Sample 2_Day 0

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: nonviral 4F stromal primed fetal liver iPSC clone 6 p11

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 6, passage 11


title: hESC (ESO3) p76

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 76 (ES Cell International)

value: Undifferentiated hESC


title: nonviral 4F stromal primed cord blood iPSC clone 2 p9

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone 2, passage 9

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: nonviral 4F stromal primed cord blood iPSC clone E5C4 p11

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C4, passage 11


title: hESC (H1) p35

description: Individual sample

source_name: H1 human Embryonic Stem Cells, Passage 35 (NIH Code WA01)


title: viral fibroblast iPSC line IMR90-4

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-4

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.


title: nonviral 7F stromal primed cord blood iPSC clone 6.13 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.13, passage 14


title: nonviral 7F stromal primed cord blood iPSC clone 6.11 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.11, passage 14


title: nonviral 7F stromal primed cord blood iPSC clone E1C4 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C4, passage 12


title: Cord Blood CD34+ progenitors Sample 3

description: Individual sample

source_name: Cord Blood CD34+ progenitors Sample 3_Day 0


title: Liver MyD88 WT fed with high-fat diet

description: Gene expression data from Liver MyD88 WT mice. Total liver tissue under high-fat diet.

value: MyD88 lox/lox


title: Liver MyD88 wild-type mice fed with control diet

description: Gene expression data from Liver MyD88 WT mice. Total liver tissue under normal diet


title: nonviral 4F stromal primed cord blood iPSC clone E5C3 p11

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C3, passage 11


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p14

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.2, passage 14


title: hESC (H9) p45

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 49 (NIH Code WA09)


title: hESC (H9) p51

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 51 (NIH Code WA09)


title: nonviral 4F stromal primed cord blood iPSC clone E5C4 p9

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C4, passage 9


title: viral fibroblast iPSC line IMR90-1

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-1


title: nonviral 7F stromal primed cord blood iPSC clone E1C3 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C3, passage 12


title: nonviral 4F stromal primed fetal liver iPSC clone 1 p9

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 1, passage 9


title: nonviral 4F stromal primed cord blood iPSC clone E5C1 p9

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 9


title: nonviral 7F stromal primed cord blood iPSC clone E1C11 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C11, passage 12


title: nonviral Keratinocyte iPSC clone 1 p13

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 3, passage 13

value: nonviral Keratinocyte iPSC clone 3

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory


title: Adult Fibroblasts Sample 1

description: Individual sample

source_name: Adult Fibroblasts Sample 1

value: Adult Fibroblasts Sample 1

value: Provided by R.A. Reijo-Pera (Stanford).


title: A. lyrata control early time point rep 3

source_name: shoot tissues, regular watering

tag: protocol

value: regular watering

value: shoots freeze frozen


title: Adult Fibroblasts Sample 2

description: Individual sample

source_name: Adult Fibroblasts Sample 2

value: Adult Fibroblasts Sample 2

tag: cell line


title: nonviral 7F stromal primed cord blood iPSC clone E1C2 p12

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C2, passage 12


title: nonviral Keratinocyte iPSC clone 1 p14

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 1, passage 14

value: nonviral Keratinocyte iPSC clone 1


title: viral 4F Adult Fibroblast iPSC clone HUF5 p15

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF5, passage 15

value: Provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009)


title: nonviral 7F Adult fibroblast iPSC clone WT2 p20

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone WT2, passage 20

value: non-integrated Adult Fibroblast iPSC generated in the Zambidis laboratory


title: viral 4F Adult Fibroblast iPSC clone HUF17 p10

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF17, passage 10


title: hESC (ES03) p87

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 87 (ES Cell International)


title: nonviral 7F Neonatal fibroblast iPSC clone 7ta p44

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) neonatal Fibroblast iPSC clone 7ta, passage 44

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 324:797-801 (2009).


title: Cord Blood CD34+ progenitors Sample 1

description: Individual sample

source_name: Cord Blood CD34+ progenitors_Day 0

value: Cord Blood CD34+ progenitors_Day 0


title: Bone Marrow CD34+ progenitors

description: Individual sample

source_name: Bone Marrow CD34+ progenitors_Day 0

value: Bone Marrow CD34+ progenitors_Day 0

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: Fetal Liver CD34+ progenitors

description: Individual sample

source_name: Fetal Liver CD34+ progenitors_Day 0

value: Fetal Liver CD34+ progenitors_Day 0


title: nonviral 7F Adult fibroblast iPSC clone WT4 p15

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone WT4, passage 15


title: Fetal Fibroblasts

description: Individual sample

source_name: Fetal Fibroblasts

value: Fetal Fibroblasts


title: viral 4F Adult Fibroblast iPSC clone HUF1 p11

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF1, passage 11


title: Adult keratinocytes

description: Individual sample

source_name: Adult keratinocytes

value: Adult keratinocytes

value: Isolated from hair folicle in Zambidis laboratory, as per Peters et al. Human Embryonic and Induced Pluripotent Stem Cells, Springer Protocols Handbooks, Part 2:202-227. 2011


title: viral 4F Adult Fibroblast iPSC clone HUF3 p20

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF3, passage 20


description: Individual sample

source_name: mobilized peripheral blood CD34+ progenitors_Day 0


title: Y30F-DMSO_rep-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from COS-1 cell over-expressing mCCRP-V5 and FLAG-hGR Y30F treated with 0.1% DMSO

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

organism: Chlorocebus aethiops

source_name: COS-1, 0.1% DMSO

label_protocol: Gene expression analysis was conducted using Agilent Whole Human Genome 4x44 multiplex format oligo arrays (014850) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: COS-1 cells were cultured in Dulbecco’s Modified Eagle Medium (Cat# 11965-092, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum in a humidified 5% CO2 incubator at 37 °C.

extract_protocol: Total RNAs were extracted from COS-1 cells using Trizol (Invitrogen) and purified with QIAGEN RNeasy kit (QIAGEN, Hilden, Germany) according to a manufacture’s protocol.

treatment_protocol: COS-1 cells were transiently transfected with expression plasmids by reverse transfection technique using FuGENE 6 (Promega, Madison, WI) according to the manufacturer’s protocol. After 40 hours from the transfection, cells were treated with vehicle 0.1% DMSO or 100 nM dexamethasone for 6 hours.

tag: transfection contsruct


title: Y30F-DEX_rep-1

description: Gene expression from COS-1 cell over-expressing mCCRP-V5 and FLAG-hGR Y30F treated with 100nM dexamethasone

source_name: COS-1, 100 nM dexamethasone


title: Y30F-DMSO_rep-2


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C2, passage 13

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.

data_processing: Data were extracted with Gene Expression Module 1.9.0 in GenomeStudio V2011.1 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C2, passage 13


title: Y30F-DEX_rep-3


title: Y30E-DMSO_rep-1

description: Gene expression from COS-1 cell over-expressing mCCRP-V5 and FLAG-hGR Y30E treated with 0.1% DMSO

value: FLAG-hGR


title: Y30E-DMSO_rep-2


title: Y30F-DEX_rep-2


title: Y30E-DEX_rep-3

description: Gene expression from COS-1 cell over-expressing mCCRP-V5 and FLAG-hGR Y30E treated with 100 nM dexamethasone


title: Y30E-DEX_rep-2


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+10, passage 13

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+10, passage 13

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: Y30F-DMSO_rep-1


title: nonviral 7 factor  neonatal Fibroblast iPSC clone 7ta, passage 50

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) neonatal Fibroblast iPSC clone 7ta, passage 50


title: Y30E-DMSO_rep-3


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+2, passage 19

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+2, passage 19


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C1.2, passage 13

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C1.2, passage 13


title: hESC (H9) p38

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 38 (NIH Code WA09)

value: Undifferentiated hESC


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p18 (sp-CB_iPSC-6.2-7FE p15)

description: Individual sample

source_name: nonviral 7F  (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed cord blood iPSC clone 6.2 passage 15

value: nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 15


title: Y30E-DEX_rep-1


title: hESC (ESO3) p88

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 88 (ES Cell International)


title: nonviral 4 factor stromal primed Cord Blood iPSC clone E5C1, passage 30

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 30


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C2, passage 9, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C2, passage 9, P4 after conversion to a naïve state with L3i

value: non-integrated Adult Fibroblast iPSC generated in the Zambidis laboratory, converted to a naïve state with L3i


title: nonviral 4 factor stromal primed cord blood iPSC clone E5C3 passage 18

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 18


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C1.2, passage 9, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C1.2, passage 9, P4 after conversion to a naïve state with L3i


title: LP-1_rep2_261884

city: Washington

first: Robert

last: Hawley

state: DC

address: 2300 I Street NW, Suite 431

department: Anatomy and Regenerative Biology

institute: George Washington University

description:
Gene expression data from LP-1 multiple myeloma cells
SAMPLE 2.2

hyb_protocol: Hybridization of cRNA on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays was performed by Expression Analysis.

scan_protocol: Scanning of GeneChip arrays was performed by Expression Analysis.

data_processing: The data were analyzed with GeneSpring software (Agilent Technologies) using default settings and the RMA normalization and summarization algorithm.

source_name: LP-1 multiple myeloma cells

label_protocol: Biotinylated cRNA was prepared by Expression Analysis (Durham, NC).

growth_protocol: Cells for gene expression profiling were cultured in RPMI 1640 with GlutaMAX (Life Technologies) supplemented with 4% fetal bovine serum.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

treatment_protocol: LP-1/Cfz cells were profiled for gene expression after 1 week of growth in the absence of carfilzomib together with parental LP-1 cells which had not been selected in the drug.


title: LP-1_rep1_261886

description:
Gene expression data from LP-1 multiple myeloma cells
SAMPLE 2.1


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+10 passage 17, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+10, passage 17, P4 after conversion to a naïve state with L3i

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory, converted to a naïve state with L3i


title: nonviral 4 factor stromal primed cord blood iPSC clone E17C6 passage 14

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 14


title: LP-1_rep3_261885

description:
Gene expression data from LP-1 multiple myeloma cells
SAMPLE 2.3


title: hESC (H7) p42

description: Individual sample

source_name: H7 human Embryonic Stem Cells, Passage 42 (NIH Code WA07)


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+2, passage 17, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+2, passage 17, P4 after conversion to a naïve state with L3i


title: nonviral 7 factor  neonatal Fibroblast iPSC clone 7ta, passage 47, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) neonatal Fibroblast iPSC clone 7ta, passage 47, P4 after conversion to a naïve state with L3i

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 324:797-801 (2009)., converted to a naïve state with L3i


title: nonviral 4 factor stromal primed cord blood iPSC clone E5C3 passage 22, P5 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 22, P5 after conversion to a naïve state with L3i


title: LP-1/Cfz_rep2_261889

description:
Gene expression data from LP-1/Cfz multiple myeloma cells resistant to 12 nM carfilzomib
SAMPLE 1.2


title: nonviral 4 factor stromal primed Cord Blood iPSC clone E5C1, passage 27, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 27, P4 after conversion to a naïve state with L3i


title: nonviral 7F  stromal primed cord blood iPSC clone 6.2 passage 26, P7 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7F  (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed cord blood iPSC clone 6.2 passage 26, P7 after conversion to a naïve state with L3i


title: TNBC tumor FFPE block 5443C/03

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

description:
9284936060_G
FBB-370

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on Illumina iScan microarray scanner

data_processing: The data were exported from GenomeStudio and normalised using quantile normalisation with the beadarray library in R

source_name: triple negative breast cancer, tumor area, FFPE block

label_protocol: Whole-Genome DASL (cDNA-mediated Annealing, Selection, Extension, and Ligation) Gene Expression Assay (Illumina, San Diego, California) was used, carried out as per manufacturer’s instructions. Two hundred nanograms of total RNA was used in the procedure.

extract_protocol: RNA isolation was performed using the QIAGEN RNeasy FFPE Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s protocol. The RNeasy FFPE kit includes traditional RNeasy MinElute series columns for RNA purification, and additionally gDNA Eliminator columns, which allow for the removal from the sample of genomic DNA that contaminates the isolated RNA. The blocks were cut into 5 μm-thick sections. In RNA isolation, 5 sections were used per one examination. The material was deparaffinized using xylene and, after supernatant removal, rinsed in alcohol. RNA concentration was evaluated using the Nanodrop ND-1000 microspectrophotometer. No routine RNA quality analysis was carried out.

tag: patient group

value: TNBC patient with brain metastasis (BM)

tag: patient age at breast cancer diagnosis

tag: disease stage at diagnosis

tag: tumor grade

tag: patient age at metastatic disease

tag: location of metastatic disease

value: with brain metastases


title: hESC (H7) p42, P6 after conversion to a naïve state with L3i

description: Individual sample

source_name: H7 human Embryonic Stem Cells, Passage 42 (NIH Code WA07), P6 after conversion to a naïve state with L3i

tag: sample type

value: Undifferentiated hESC, converted to a naïve state with L3i


title: TNBC tumor FFPE block 06-15694

description:
9284936060_J
FBB-325

value: TNBC patient without brain metastasis (BM)

value: other than central nervous system


title: LP-1/Cfz_rep1_261887

description:
Gene expression data from LP-1/Cfz multiple myeloma cells resistant to 12 nM carfilzomib
SAMPLE 1.1


title: TNBC tumor FFPE block 49642/09

description:
9284936060_H
FBB-194


title: nonviral 4 factor stromal primed cord blood iPSC clone E17C6 passage 27, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 27, P4 after conversion to a naïve state with L3i


title: hESC (ESO3) p87, P7 after conversion to a naïve state with L3i

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 87 (ES Cell International), P7 after conversion to a naïve state with L3i


title: nonviral 4F stromal primed GCSF-mobilized peripheral blood iPSC clone E29C4 p8 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed GCSF-mobilized peripheral blood iPSC clone E29C4 passage 8

value: non-integrated stromal primed GCSF-mobilized peripheral blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 13294/06

description:
9284936060_K
FBB-295


title: TNBC tumor FFPE block 00-19211

description:
9284936060_L
FBB-327