title: Mouse with thyroid hormone receptor mutation - replication 2

value: ThrbPV (ThrbPV/PV)


title: N2_4

status: Public on Sep 22 2015

type: RNA

city: Goettingen

first: Michal

last: Turek

address: Am Fassberg 11

department: Sleep and Waking

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

description: Gene expression in N2 wild type sleeping L4 larvae

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65uC in the Hybridization Oven (Agilent).

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B).

data_processing: Intensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2, replicate 4

label_protocol: 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer’s recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 21.5°C. For each sample 200 L4 sleeping animals were picked individually with a platinum wire pick and were immediately placed into a tube containing one ml of Trizol (Invitrogene).

extract_protocol: RNA was extracted from the Trizol using standard procedure.

treatment_protocol: For performing the experiment ‘‘Low RNA Input linear Amplification Kit Plus, One Color’’ protocol (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5282)were used following the manufacturer’s standard protocol.

tag: tissue

value: whole animal

tag: gender

value: hermaphrodite

tag: age

value: L4 sleep

tag: genotype/variation

value: N2 wild type sleeping L4 larvae


title: N2_1 in pretzel-stage embryos

description: Gene expression in N2 wild type pretzel-stage embryos

source_name: N2, replicate 1

growth_protocol: C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 21.5°C. For each sample approximately 3000 pretzel-stage embryos were picked individually with a platinum wire pick and were immediately placed into a tube containing one ml of Trizol (Invitrogene).

value: pretzel-stage embryo

value: N2 wild type pretzel-stage embryos


title: N2_1


title: aptf-1_3

description: Gene expression in aptf-1(gk794) mutant sleeping L4 larvae

source_name: aptf-1(gk794) mutant, replicate 3

value: aptf-1(gk794) mutant sleeping L4 larvae


title: Mouse with RAS - replication 3

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

country: USA

institute: NCI

hyb_protocol: Hybriddized biotinylated-aRNA accordig to the manufacturer prorocol.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software. Data processing and analysis were done by affy, limma, xps, et al R/Bioconductor packages.

label: biotin

organism: Mus musculus

source_name: RAS - replication 3

label_protocol: Biotin labelled accordig to the manufacturer prorocol.

extract_protocol: Total RNA from thyroids was isolated using TRIzol (Invitrogen, Carlsbad, CA) as indicated by the protocol of the manufacturer.

tag: background strain

value: mixed background of C57Bl/6n, C129 and FVB strains

value: RAS mutation (KrasG12D)


title: N2_2

source_name: N2, replicate 2


title: MPP KO 1

status: Public on Sep 21 2015

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

description:
strategy for knock out: A lambda phage clone containing exon 11 (encoding the DNA binding domain) of Erg was retrieved using the REC screening system. LoxP sites were subsequently introduced on each of the exon using homologous recombination in E.coli and the resulting targeting construct was introduced into E14.1 ES cells by electroporation followed by blastocyst injections and breeding for germ line transmission. The Frt-flanked Neostop cassette was subsequently removed by crossing with a Flp deleter line resulting in mice heterozygous for the Erg flox  (Erg fl) allele. Mice with the Erg fl allele were bred with mice harbouring the Mx1-Cre allele. Ergfl/fl; Mx1Cre and Ergfl/fl mice were treated with 5 intraperitoneal injections (two days interval) of 200 µl polyinosinic-polycytidylic acid (pIpC) (1.5 mg/ml) to obtain full knockout of Erg in bone marrow cells. Cells were sorted 2 weeks after the first pIpC injection.
Erg KO murine Multipotential progenitor

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol, according to manufacturers specifications

scan_protocol: standard Affymetrix protocol

data_processing: Cell intensity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). The data was normalized using the RMA function from the Bioconductor package affy in R.

label: Biotin

source_name: Sorted MPPs (LSKCD150+CD48-) from bone marrow samples

label_protocol: 2.5ug of amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Murine bone marrow cells were enriched for cKit+ and hematopoietic cells were sorted by FACS.

extract_protocol: Total RNA from sorted cells were isolated with RNeasy Micro Kit (Qiagen). Samples were prepared in triplicates for each genotype. 20 ng of total RNA was amplified using Ovation Pico WTA system V2 (Nugene) according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/cs/microarrays-and-qpcr/ovation-pico-wta-system-v2/manufacturers instructions.

tag: origin

value: Bone Marrow

tag: sorting strategy

value: Lineage-, Sca-1+, c-kit+, CD150-.

tag: strain

value: C57Bl/6 (at least 6 generations).

tag: genotype

value: Erg -/-

tag: Sex

value: male

tag: cell type

value: murine multipotential progenitor

tag: condition

value: Erg KO


title: Mouse with double mutatons - replication 1

source_name: double mutatons - replication 1

value: ThrbPV/PV and KrasG12D


title: HSC KO 2

description:
strategy for knock out: A lambda phage clone containing exon 11 (encoding the DNA binding domain) of Erg was retrieved using the REC screening system. LoxP sites were subsequently introduced on each of the exon using homologous recombination in E.coli and the resulting targeting construct was introduced into E14.1 ES cells by electroporation followed by blastocyst injections and breeding for germ line transmission. The Frt-flanked Neostop cassette was subsequently removed by crossing with a Flp deleter line resulting in mice heterozygous for the Erg flox (Erg fl) allele. Erg +/-  mice were generated by crossing Erg fl/+ mice with a general Cre deleter mouse.
Erg KO murine stem cell

source_name: Sorted HSCs (LSKCD150+CD48-) from bone marrow samples

value: Lineage-, Sca-1+, c-kit+, CD150+, CD48-.

value: Erg +/-

value: HSC


title: MPP WT 2

description:
strategy for knock out: A lambda phage clone containing exon 11 (encoding the DNA binding domain) of Erg was retrieved using the REC screening system. LoxP sites were subsequently introduced on each of the exon using homologous recombination in E.coli and the resulting targeting construct was introduced into E14.1 ES cells by electroporation followed by blastocyst injections and breeding for germ line transmission. The Frt-flanked Neostop cassette was subsequently removed by crossing with a Flp deleter line resulting in mice heterozygous for the Erg flox  (Erg fl) allele. Mice with the Erg fl allele were bred with mice harbouring the Mx1-Cre allele. Ergfl/fl; Mx1Cre and Ergfl/fl mice were treated with 5 intraperitoneal injections (two days interval) of 200 µl polyinosinic-polycytidylic acid (pIpC) (1.5 mg/ml) to obtain full knockout of Erg in bone marrow cells. Cells were sorted 2 weeks after the first pIpC injection.
Wild type murine Multipotential progenitor

value: Erg flox/flox

value: WT


title: Mouse with thyroid hormone receptor mutation - replication 3

value: ThrbPV (ThrbPV/PV)


title: HSC WT 3

description:
strategy for knock out: A lambda phage clone containing exon 11 (encoding the DNA binding domain) of Erg was retrieved using the REC screening system. LoxP sites were subsequently introduced on each of the exon using homologous recombination in E.coli and the resulting targeting construct was introduced into E14.1 ES cells by electroporation followed by blastocyst injections and breeding for germ line transmission. The Frt-flanked Neostop cassette was subsequently removed by crossing with a Flp deleter line resulting in mice heterozygous for the Erg flox (Erg fl) allele. Erg +/-  mice were generated by crossing Erg fl/+ mice with a general Cre deleter mouse.
Wild type murine stem cell

value: Erg +/+


title: HSC WT 2


title: Mouse with RAS - replication 1

source_name: RAS - replication 1

value: mixed background of C57Bl/6n, C129 and FVB strains


title: aptf-1_1

source_name: aptf-1(gk794) mutant, replicate 1

value: whole animal

value: hermaphrodite

value: L4 sleep

value: aptf-1(gk794) mutant sleeping L4 larvae


title: aptf-1_2

source_name: aptf-1(gk794) mutant, replicate 2


title: HSC KO 3

value: Bone Marrow

value: C57Bl/6 (at least 6 generations).


title: MPP KO 3

value: Lineage-, Sca-1+, c-kit+, CD150-.

value: Erg -/-

value: male

value: murine multipotential progenitor


title: MPP KO 2

value: Erg KO


title: aptf-1_4

source_name: aptf-1(gk794) mutant, replicate 4


title: MPP WT 1


title: Mouse with double mutatons - replication 3

source_name: double mutatons - replication 3

value: ThrbPV/PV and KrasG12D


title: Mouse with double mutatons - replication 2

source_name: double mutatons - replication 2


title: HSC KO 1

value: Lineage-, Sca-1+, c-kit+, CD150+, CD48-.

value: Erg +/-

value: HSC


title: aptf-1_2 in pretzel-stage embryos

description: Gene expression in aptf-1(gk794) mutant pretzel-stage embryos

value: pretzel-stage embryo


title: Mouse with thyroid hormone receptor mutation - replication 1

value: mixed background of C57Bl/6n, C129 and FVB strains

value: ThrbPV (ThrbPV/PV)


title: TK AngII Balb/C 3

city: Helsinki

first: Riikka

last: Kivelä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki and Wihuri Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Chipster software (www.chipster.csc.fi)

source_name: Mouse heart left ventricle

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

extract_protocol: Total RNA was isolated from left ventricle with TRIsure reagent (Bioline) and further purified with NucleoSpin RNA II (Macherey-Nagel). Quality control was performed with Agilent Bioanalyser.

value: Balb/C

value: Male

value: Bmx deficient


title: WT AngII Balb/C 3

value: wild type


title: WT AngII Balb/C 1


title: TK Sham Balb/C 3


title: KO Sham C57Bl/6J 2


title: HSC WT 1

value: Bone Marrow

value: C57Bl/6 (at least 6 generations).

value: Erg +/+

value: WT


title: WT Sham Balb/C 2


title: TK AngII Balb/C 1


title: TK AngII Balb/C 2


title: DMSO control  6 day  treatment, biological rep1

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
DM
Gene expression data from DMSO treated AML cells

hyb_protocol: Hybridized to Human 2.0 ST GeneChip probe array (PN 902113)

scan_protocol: The array image is generated by a high-resolution GeneArray Scanner 3000 7G (Affymetrix, Santa Clara, CA)

data_processing:
The data were analyzed with GeneChip® Command Console® Software (AGCC) using Affymetrix default analysis settings.
According to default settings in Affymetrix Transcriptome Analysis Console

organism: Homo sapiens

source_name: IDH1 mutant AML treated with DMSO control

label_protocol: The sscDNA is chemically fragmented and biotin-labeled made into a hybridization cocktail using hybridization kit (PN 901524) according to the Affymetrix Genechip protocol

growth_protocol: Serum free media containing recombinant human cytokines 10 ng/mL IL-3, 25 ng/mL IL-6, 50 ng/mL SCF, 100 ng/mL TPO, 50 ng/mL FLT-3L, 1:500 primocin (50 mg/mL; InvivoGen) and 40 mg/mL Low Density Lipoprotein (Sigma) for 12-16 h.

extract_protocol: Total RNA extracted was extracted using RNeasy Micro kit according to Manufacturers protocol (Qiagen, Valencia, CA). RNA was amplified to single strand cDNA using the NuGEN Ovation pico WTA System V2 (PN 3302).

treatment_protocol: Following pre-incubation, viable cells were seeded at 1.5 - 3 x 105 cells per 500 mL media in a 48-well plate and treated with 0.3% DMSO and 3 mM GSK990 or GSK321 inhibitors were treated for 6 days followed by RNA extraction.

value: AML mononuclear cells


title: TK Sham Balb/C 1


title: WT Sham C57Bl/6J 3


title: KO AngII C57Bl/6J 3


title: WT AngII Balb/C 2


title: TK Sham Balb/C 2


title: KO AngII C57Bl/6J 2


title: Active inhibitor  6 day  treatment, biological rep3

description:
DM
Gene expression data from GSK321 treated AML cells

source_name: IDH1 mutant AML treated with GSK321


title: WT Sham Balb/C 3


title: Inactive inhibitor  6 day  treatment, biological rep2

description:
ID2
Gene expression data from GSK990 treated AML cells

source_name: IDH1 mutant AML treated with GSK990


title: DMSO control  6 day  treatment, biological rep2


title: WT Sham Balb/C 1


title: WT Sham C57Bl/6J 2


title: WT Sham C57Bl/6J 1


title: KO Sham C57Bl/6J 1


title: Active inhibitor  6 day  treatment, biological rep2

description:
AD2
Gene expression data from GSK321 treated AML cells


title: KO Sham C57Bl/6J 3


title: Inactive inhibitor  6 day  treatment, biological rep1

description:
ID1
Gene expression data from GSK990 treated AML cells


title: WT AngII C57Bl/6J 3


title: WT AngII C57Bl/6J 1


title: KO AngII C57Bl/6J 1


title: Active inhibitor 6 day treatment, biological rep1

description:
AD1
Gene expression data from GSK321 treated AML cells


title: LT339_3

city: Pittsburgh

first: Kathleen

middle: F

last: Richards

state: PA

address: 5117 Centre Avenue Suite 1.8

department: Cancer Virology Program

institute: University of Pittsburgh Cancer Institute

description:
Replicate 3
stable cell line generated by lentiviral transduction and selection

hyb_protocol: 250 ng of cRNA were hybridized to the Illumina HT12 chip according to protocols provided by the manufacturer

scan_protocol: Arrays were scanned using an Illumina iScan

data_processing: Data was analyzed using GenomeStudio 1.9.0 using cubic spline normalization

source_name: cells expressing tumor-derived LT-339 rep3

label_protocol: Biotinylated cRNA were prepared from 250 ng of total RNA using TotalPrep (Ambion, Austin, TX)

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

tag: cell line

value: BJ-hTERT


title: LT339.LFCDK_3

source_name: cells expressing tumor-derived LT-339 with a mutated LxCxE motif rep3


title: Empty_2

description:
Replicate 2
stable cell line generated by lentiviral transduction and selection

source_name: cells expressing empty vector rep2


title: LT339.LFCDK_1

description:
Replicate 1
stable cell line generated by lentiviral transduction and selection

source_name: cells expressing tumor-derived LT-339 with a mutated LxCxE motif rep1


title: LT339.LFCDK_2

source_name: cells expressing tumor-derived LT-339 with a mutated LxCxE motif rep2


title: Kras-p53 SAHA

status: Public on Sep 20 2015

city: Munich

first: Jens

middle: T

last: Siveke

address: Ismaninger Str. 22

department: 2. Med. Klinik

institute: Klinikum rechts der Isar, Technical University Munich

hyb_protocol: Following fragmentation, 6 ug of aRNA were hybridized to an Affymetrix Mouse Genome 430 PM 16-Array Plate for 16 hr at 45C. For hybridization, washing and staining an Affymetrix GeneTitan system was used.

scan_protocol: GeneChips were scanned using an Affymetrix GeneTitan system.

data_processing: Summarized probe set signals were calculated by using the RMA algorithm with the Affymetrix GeneChip Expression Console Software. Software After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated.

source_name: Kras-p53 mice treated with SAHA

label_protocol: Biotinylated aRNA were prepared from 250 ng total RNA according to the Affymetrix GeneChip 3’ IVT Express Kit user manual (2008).

extract_protocol: Total RNA was isolated using Qiagen RNeasy Isolation Kit. RNA quality was assessed on an Agilent 2100 Bioanalyser, RNA 6000 Pico Series II Chips (Agilent).

treatment_protocol: Cells were treated either with JQ1 (100 nM) or SAHA (2000 nM) or vehicle 10% (2-Hydroxypropyl)-β-cyclodextrin (Sigma-Aldrich) or as combination therapy (JQ1 100 nM, SAHA 1000 nM) for 6 hours.

value: Pancreatic ductal adenocarcinoma (PDAC)


title: LT339_1

source_name: cells expressing tumor-derived LT-339 rep1


title: LT339+sT_2

source_name: cells expressing tumor-derived LT-339 and sT rep2


title: Kras-p53 JQ1

source_name: Kras-p53 mice treated with JQ1


title: Empty_1

source_name: cells expressing empty vector rep1


title: LT339+sT_3

source_name: cells expressing tumor-derived LT-339 and sT rep3


title: LT339_2

source_name: cells expressing tumor-derived LT-339 rep2


title: lung_SP_day6_rep3

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Gene expression profiling after 6 days SP  infection
SP d6-3

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SP d6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from harvested lungs using Trizol/phenol chloroform extraction followed by precipitation.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Mice were exposed to either PBS, 1918 influenza virus, Pneumococcus or 1918 influenza virus followed  by pneumoccocus 72hrs later. At 3,4,5 or 6 days post-viral infection lung tissue was harvested and RNA isolated for microarray analysis.

value: BALB/c

value: Lung

tag: pathogen

value: SP

tag: time p.i.

value: day 6


title: MPP WT 3

source_name: Sorted MPPs (LSKCD150+CD48-) from bone marrow samples

value: Lineage-, Sca-1+, c-kit+, CD150-.

value: Erg flox/flox

value: male

value: murine multipotential progenitor


title: lung_SP_day4_rep3

description:
Gene expression profiling after 4 days SP  infection
SP d4-3

source_name: SP d4

value: day 4


title: LT339+sT_1

source_name: cells expressing tumor-derived LT-339 and sT rep1


title: lung_SP_day4_rep2

description:
Gene expression profiling after 4 days SP  infection
SP d4-2


title: Kras-p53 vehicle

source_name: Kras-p53 mice treated with vehicle


title: lung_SP_day5_rep1

description:
Gene expression profiling after 5 days SP  infection
SP d5-1

source_name: SP d5

value: day 5


title: lung_SP_day6_rep1

description:
Gene expression profiling after 6 days SP  infection
SP d6-1


title: Kras-p53 JQ1+SAHA

source_name: Kras-p53 mice treated JQ1-SAHA combination


title: lung_SP_day6_rep2

description:
Gene expression profiling after 6 days SP  infection
SP d6-2


title: lung_SP_day5_rep3

description:
Gene expression profiling after 5 days SP  infection
SP d5-3


title: lung_SP_day5_rep2

description:
Gene expression profiling after 5 days SP  infection
SP d5-2


title: Empty_3

source_name: cells expressing empty vector rep3


title: lung_1918 SP_day4_rep3

description:
Gene expression profiling after 4 days 1918+SP  infection
1918 SP d4-3


title: lung_SP_day4_rep1

description:
Gene expression profiling after 4 days SP  infection
SP d4-1


title: lung_1918 SP_day6_rep3

description:
Gene expression profiling after 6 days 1918+SPs infection
1918 SP d6-3


title: lung_1918 SP_day5_rep2

description:
Gene expression profiling after 5 days 1918+SP  infection
1918 SP d5-2


title: lung_1918 SP_day5_rep3

description:
Gene expression profiling after 5 days 1918+SP  infection
1918 SP d5-3


title: lung_1918 SP_day6_rep1

description:
Gene expression profiling after 6 days 1918+SP  infection
1918 SP d6-1


title: lung_1918 SP_day6_rep2

description:
Gene expression profiling after 6 days 1918+SP  infection
1918 SP d6-2


title: lung_1918 SP_day5_rep1

description:
Gene expression profiling after 5 days 1918+SP  infection
1918 SP d5-1


title: lung_1918 SP_day4_rep2

description:
Gene expression profiling after 4 days 1918+SP  infection
1918 SP d4-2


title: lung_1918 SP_day4_rep1

description:
Gene expression profiling after 4 days 1918+SP s infection
1918 SP d4-1


title: lung_1918_day4_rep3

description:
Gene expression profiling after 4 days 1918 influenza virus infection
1918 d4-3


title: lung_1918_day4_rep2

description:
Gene expression profiling after 4 days 1918 influenza virus infection
1918 d4-2


title: INSULIN+LY294002 Replicate 2

city: singapore

first: Lena

last: Ho

state: -- Please Select --

address: 8A BIomedical Grove 05-40 Immnuos

country: Singapore

institute: Institute of Medical Biology

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on U133_Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were processed with Agilent GeneSpring GX13 using RMA summarization, quantile normalization and baseline transformed using median of all samples. Probe sets with intensity values below the 20th percentile or whose intensity values did not change more than 1.5-fold (ANOVA p-value<0.05) between any pair of conditions were omitted from further analysis

source_name: hESC 12 hours INSULIN + LY294002

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT PLUS protocol from 100ng total RNA.

growth_protocol: mTSER1 and Matrigel

extract_protocol: Qiagen RNAeasy

treatment_protocol: Accutase-dissociated hESC were seeded in mTSER1 at equal density into 24 well plates. 24 hours later, the medium was changed to non-supplemented DMEM/F12 for 2 hours. Wells receiving LY294002 were pretreated with 2.5 μM of the drμg for 15 minutes. ELA or INSULIN were then added to a final concentration of 5 μM or 20 nM respectively. The cells were harvested 12 hours later for their RNA using Qiagen’s RNeasy kit.

value: hESC

tag: treatment

value: INSULIN + LY294002


title: lung_1918_day3_rep1

description:
Gene expression profiling after 3 days 1918 influenza virus infection
1918 d3-1

value: day 3


title: lung_1918_day6_rep2

description:
Gene expression profiling after 6 days 1918 influenza virus infection
1918 d6-2


title: lung_1918_day3_rep3

description:
Gene expression profiling after 3 days 1918 influenza virus infection
1918 d3-3


title: INSULIN Replicate 1

source_name: hESC 12 hours INSULIN

value: INSULIN


title: lung_1918_day6_rep1

description:
Gene expression profiling after 6 days 1918 influenza virus infection
1918 d6-1


title: INSULIN Replicate 2


title: lung_1918_day3_rep2

description:
Gene expression profiling after 3 days 1918 influenza virus infection
1918 d3-2


title: lung_1918_day4_rep1

description:
Gene expression profiling after 4 days 1918 influenza virus infection
1918 d4-1


title: lung_PBS_rep3

description:
Gene expression profiling after 8 days PBS
Mock-3

source_name: Mock

value: PBS

value: Day 8


title: Wild type, self filling loop replicate-3

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description:
WFL4
MW22

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: raw data were processed using the R/Bioconductor package limma for background correction and quantile normalization

source_name: Wild type, self filling loop

label_protocol: standard Illumina protocol

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

treatment_protocol: C57Bl/6 mice  were anesthetized with ketamine/xylazine. Aseptic surgery was performed to resect 2.5 cm of ileum 3 cm proximal to the ileal-cecal value with anastomosis to the ileum. In contrast to human surgery, colons are not removed in our mouse model. DSS experiments were performed as previously described. After 5 weeks, mice were humanely euthanized. Intestinal loops and sham tissues were collected for RNA, protein, and histology. Loop, sham ileum, and sham colon contents were collected and snap frozen at −80°C for microbiota analysis.

tag: group

value: WFL

value: WT

value: Loop

tag: surgery

value: self-filling


title: ELA Replicate 2

source_name: hESC 12 hours ELA

value: ELA


title: lung_1918_day5_rep2

description:
Gene expression profiling after 5 days 1918 influenza virus infection
1918 d5-2

value: BALB/c

tag: tissue

value: Lung


title: lung_1918_day5_rep1

description:
Gene expression profiling after 5 days 1918 influenza virus infection
1918 d5-1


title: Wild type, self empty loop replicate-4

description:
WEL4
MW23

source_name: Wild type, self empty loop

value: WEL

value: self-emptying


title: lung_PBS_rep2

description:
Gene expression profiling after 8 days PBS
Mock-2


title: lung_PBS_rep4

description:
Gene expression profiling after 8 days PBS
Mock-4


title: lung_1918_day6_rep3

description:
Gene expression profiling after 6 days 1918 influenza virus infection
1918 d6-3

value: day 6


title: IL10 knockout, self empty loop replicate-2

description:
KEL3
MW21

source_name: IL10 knockout, self empty loop

value: KEL

value: IL10 KO


title: INSULIN+LY294002 Replicate 1

value: hESC

value: INSULIN + LY294002


title: ELA+LY294002 Replicate 1

source_name: hESC 12 hours ELA + LY294002


title: Control Replicate 2

source_name: hESC 12 hours Vehicle Control

value: Vehicle


title: lung_1918_day5_rep3

description:
Gene expression profiling after 5 days 1918 influenza virus infection
1918 d5-3

value: day 5


title: IL10 knockout, self filling loop replicate-3

description:
KFL3
MW20

source_name: IL10 knockout, self filling loop

value: KFL


title: ELA Replicate 3


title: ELA+LY294002 Replicate 2


title: Control Replicate 3


title: ELA Replicate 1


title: Wild type, sham surgery, Ileum replicate-3

description:
WSL3
MW17
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.

source_name: Wild type, sham surgery, Ileum

value: WSL

value: Ileum

value: Sham


title: Control Replicate 1


title: Root grown under -Fe of ys3 mutant vs. WT plants Replicate 1

city: Tokyo

first: Tomoko

last: Nozoye

address: 1-1-1 yayoi bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Replicate 1 of 2. Root of WT vs. ys3 mutant. Fe-deficient.

hyb_protocol: Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.detrended processed signal intensities.

organism: Zea mays

source_name: ys3 mutant - Fe-deficient

label_protocol: Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Maize plants were germinated in a 5-L plastic container for 4 days, and then transferred to a 20-L plastic container with air bubbling. Fe deficiency was initiated 8 days after germination by transfer of the plants to Fe(III)-EDTA-free culture medium. Maize plants grown hydroponically under Fe-sufficient or Fe-deficient conditions for 5 days were harvested at the same time.

extract_protocol: RNA was prepared using RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cultivar

value: Root

source_name: WT - Fe-deficient

value: Alice


title: Wild type, sham surgery, Cecum replicate-2

description:
WSR2
MW12
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.

source_name: Wild type, sham surgery, Cecum

value: WSR

tag: genotype/variation

value: WT

value: Cecum


title: IL10 knockout, self empty loop replicate-1

description:
KEL2
MW14

value: Loop

value: self-emptying


title: Root grown under -Fe of ys1 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Root of WT vs. ys1 mutant. Fe-deficient.

source_name: ys1 mutant - Fe-deficient


title: Root grown under +Fe of ys3 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Root of WT vs. ys3 mutant. Fe-sufficient.

source_name: WT - Fe-sufficient

source_name: ys3 mutant - Fe-sufficient


title: Root grown under +Fe of ys3 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Root of WT vs. ys3 mutant. Fe-sufficient.


title: Wild type, sham surgery, Cecum replicate-3

description:
WSR3
MW19
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.


title: Wild type, self empty loop replicate-3

description:
WEL3
MW16

value: WEL


title: Root grown under -Fe of ys3 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Root of WT vs. ys3 mutant. Fe-deficient.


title: IL10 knockout, self filling loop replicate-2

description:
KFL2
MW13

value: IL10 KO

value: self-filling


title: Root grown under +Fe of ys1 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Root of WT vs. ys1 mutant. Fe-sufficient.

source_name: ys1 mutant - Fe-sufficient


title: Root grown under -Fe of ys1 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Root of WT vs. ys1 mutant. Fe-deficient.


title: CD34+ hematopoietic progenitor cells, pre-miR-NC1, replicate 3

city: Modena

first: Elena

last: Tenedini

state: MO

address: Via Campi, 287

department: Biomedical Sciences

country: Italy

institute: University of Modena and Reggio Emilia

description: CD34+ hematopoietic progenitor cells treansfected with pre-miR-NC1 (Ambion Pre-miR miRNA Precursor Molecule—Negative Control # 1)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 Scanner.

data_processing: The data were analyzed with RMA procedure using Bioconductor packages and standard Affymetrix CDF libraries.

source_name: CD34+ hematopoietic progenitor cells from cord blood

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

growth_protocol: CD34+ hematopoietic progenitor cells were cultured in IMDM with the addiction of 20% BIT serum substitute, 2mM L-Glu, 1x P/S, IL-3 (10ng/mL), IL-6 (10ng/mL), TPO (20ng/mL), FLT-3L (50ng/mL), SCF (50ng/mL).

extract_protocol: 24 hours post tranfection, cells were collected and mirVana kit (Ambion) was used for total cellular RNA extraction according to the manufacturer's instructions.

treatment_protocol: After 2 days of culture, CD34+ hematopoietic progenitor cells were transfected with the Amaxa Nucleofector Device, using the Human CD34 Cell Nucleofection Kit, accordingly to the manufacturer’s instructions (Amaxa Biosystem, Cologne, Germany), and 5µg of either the Pre-miR miRNA Precursor Molecule—Negative Control # 1 (NC1) or the hsa-mir-299-5p Pre-miR miRNA Precursor Molecule (299-5p) (Ambion, Austin, TX, USA) and pulsed with the program U-008.

value: Negative control 1


title: Wild type, sham surgery, Ileum replicate-2

description:
WSL2
MW10
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.


title: CD34+ hematopoietic progenitor cells, pre-miR-299-5p, replicate 2

description: CD34+ hematopoietic progenitor cells treansfected with pre-miR-299-5p (Ambion hsa-mir-299-5p Pre-miR miRNA Precursor Molecule)


title: CD34+ hematopoietic progenitor cells, pre-miR-NC1, replicate 2


title: lung_PBS_rep1

description:
Gene expression profiling after 8 days PBS
Mock-1

source_name: Mock

value: BALB/c

value: Lung

value: PBS

value: Day 8


title: Root grown under +Fe of ys1 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Root of WT vs. ys1 mutant. Fe-sufficient.


title: CD34+ hematopoietic progenitor cells, pre-miR-299-5p, replicate 3


title: Wild type, self filling loop replicate-2

description:
WFL2
MW8

source_name: Wild type, self filling loop

value: WFL


title: Shoot grown under -Fe of ys3 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Shoot of WT vs. ys3 mutant. Fe-deficient.

value: Shoot


title: Shoot grown under -Fe of ys3 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Shoot of WT vs. ys3 mutant. Fe-deficient.


title: IL10 knockout, self filling loop replicate-1

description:
KFL1
MW6

value: KFL


title: Wild type, self empty loop replicate-2

description:
WEL2
MW9


title: DEN_WT_Liver_SEC_rep2

city: Houston

first: Brian

last: York

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing: Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.

source_name: Mouse liver sinusoidal endothelial cell

label_protocol: cRNA were prepared with the Illumina TotalPrep 96 RNA amplification kit

growth_protocol: Male C57Bl/6 mice were injected intraperitoneally with 25mg/kg DEN at post-natal day 25. Tumor progression was monitored for 9 months post-injection. Age-matched untreated animals were used as controls.

extract_protocol: RNA was isolated from primary hepatocytes, MΦ, and SEC using the Ambion Purelink RNA Mini Kit

value: liver

value: sinusoidal endothelial cell

tag: gender

value: male


title: DEN_WT_Liver_SEC_rep1


title: DEN_WT_Liver_MP_rep2

source_name: Mouse liver macrophage

value: macrophage


title: CD34+ hematopoietic progenitor cells, pre-miR-299-5p, replicate 1


title: Wild type, sham surgery, Ileum replicate-1

description:
WSL1
MW3
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.

value: WSL

value: WT

value: Ileum

value: Sham


title: Wild type, sham surgery, Cecum replicate-1

description:
WSR1
MW5
Sham tissues represent surgical control mouse that received an abdominal laparotomy but not surgical intervention of the intestinal tissue.

value: WSR

value: Cecum


title: Shoot grown under -Fe of ys1 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Shoot of WT vs. ys1 mutant. Fe-deficient.

value: Alice


title: Wild type, self empty loop replicate-1

description:
WEL1
MW2

source_name: Wild type, self empty loop

value: WEL

value: Loop

value: self-emptying


title: DEN_WT_Liver_MP_rep1


title: Ring1B I53A/I53A rep2

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: Gene expression of E14Tg2a-derived Ring1B I53A/I53A mESCs

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 il of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Mouse GE 8x60K microarray (Agilent; G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 2x1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 2x1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned on a Nimblegen scanner at 2um resolution and 25% gain to generate single channel TIFF images.

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain non-background subtracted and spatially detrended processed signal intensities.  Duplicate probe intensity values were replaced with their arithmetic mean. Normalised values were produced using the limma package (R/Bioconductor) by quantile normalisation across all samples. The output file provides log2 normalised intensity values for the 55,681 unique probes (excluding control probes), available in sample table.
Differential Expression Analysis:  The limma package was used to calculate fold-changes and p-values for differential expression using the empirical Bayes statistics for differential expression (eBayes) framework. To assign probes to gene names we created a custom probe annotation by downloading a list of mouse transcripts from Ensembl, and identifying probes which map to any transcript with no more than one mismatch, deletion, or insertion. We then used the probe sequences as input to the online version of RepeatMasker using the cross_match search engine and setting “Speed/Sensitivity” to “slow” and “DNA source” to “mouse”. Probes were only included in subsequent analysis if they mapped to transcripts from exactly one gene, and had less than 50 % repetitive sequence as identified by RepeatMasker. The Benjamini-Hochberg method was used to adjust p-values for multiple testing. A probe was considered differentially expressed if it had a fold change greater than 2 or less than 0.5 and an adjusted p-value of less than 0.05. Three biological replicates were used per sample. Final processed data is included as a supplementary file (‘processed_data.txt’, available on the series record) which contains the following information:     Sample independent information  ProbeName (Agilent probe ID)  sequence (Agilent probe sequence)  transcript (Ensembl transcript ID/s)  ensGene (Ensembl gene name)  ens.chr (chromosome/s)  ens.TSS.mm10 (transcription start site/s - mm10)  SystematicName (Gene symbol or gene location – mm10).    Sample dependent information (X denotes e14, KO_G6 or I53A)   X.logFC (log2 (intensityX/intensityWT))   X.pval (p value).   X.padj (p value following BH multiple testing correction).  X (log2 normalised intensity value for X)  X.mean (mean log2 normalised intensity value for X)  X.up (genes which are upregulated in X vs. e14s)  X.down (genes which are downregulated in X vs. e14s)

molecule: polyA RNA

source_name: E14Tg2a-derived Ring1B I53A/I53A ESCs replicate 2

label_protocol: 1ug of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent – 5188-5282) and the mixture labelled with cyanine 3 (Cy3) using the Amino Allyl MessageAmp™ II with Cy™3 kit (Ambion; AM1795) according to manufacturer’s instructions.

growth_protocol: ES cells were grown in GMEM supplemented with 10% fetal bovine serum (FBS), 1,000 units/ml LIF, non-essential amino acids, sodium pyruvate, 2-β-mercaptoethanol and L-glutamine.

extract_protocol: RNA was prepared using RNeasy mini kit (Qiagen) according to manufacturer’s protocol, including a DNaseI (Qiagen) treatment for 15min at room temperature

value: Ring1B I53A/I53A

value: ESC


title: Ring1B I53A/I53A rep1

source_name: E14Tg2a-derived Ring1B I53A/I53A ESCs replicate 1


title: Ring1B I53A/I53A rep3

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain non-background subtracted and spatially detrended processed signal intensities.  Duplicate probe intensity values were replaced with their arithmetic mean. Normalised values were produced using the limma package (R/Bioconductor) by quantile normalisation across all samples. The output file provides log2 normalised intensity values for the 55,681 unique probes (excluding control probes) , available in sample table.
Differential Expression Analysis:  The limma package was used to calculate fold-changes and p-values for differential expression using the empirical Bayes statistics for differential expression (eBayes) framework. To assign probes to gene names we created a custom probe annotation by downloading a list of mouse transcripts from Ensembl, and identifying probes which map to any transcript with no more than one mismatch, deletion, or insertion. We then used the probe sequences as input to the online version of RepeatMasker using the cross_match search engine and setting “Speed/Sensitivity” to “slow” and “DNA source” to “mouse”. Probes were only included in subsequent analysis if they mapped to transcripts from exactly one gene, and had less than 50 % repetitive sequence as identified by RepeatMasker. The Benjamini-Hochberg method was used to adjust p-values for multiple testing. A probe was considered differentially expressed if it had a fold change greater than 2 or less than 0.5 and an adjusted p-value of less than 0.05. Three biological replicates were used per sample. Final processed data is included as a supplementary file (‘processed_data.txt’, available on the series record) which contains the following information:     Sample independent information  ProbeName (Agilent probe ID)  sequence (Agilent probe sequence)  transcript (Ensembl transcript ID/s)  ensGene (Ensembl gene name)  ens.chr (chromosome/s)  ens.TSS.mm10 (transcription start site/s - mm10)  SystematicName (Gene symbol or gene location – mm10).    Sample dependent information (X denotes e14, KO_G6 or I53A)   X.logFC (log2 (intensityX/intensityWT))   X.pval (p value).   X.padj (p value following BH multiple testing correction).  X (log2 normalised intensity value for X)  X.mean (mean log2 normalised intensity value for X)  X.up (genes which are upregulated in X vs. e14s)  X.down (genes which are downregulated in X vs. e14s)

source_name: E14Tg2a-derived Ring1B I53A/I53A ESCs replicate 3


title: Shoot grown under +Fe of ys3 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Shoot of WT vs. ys3 mutant. Fe-sufficient.

value: Shoot


title: MGO2015_026

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: patient derived pancreatic carcinoma xenograft Bo63

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with cyanine-5-CTP (Cy5)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumor Bo63 soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol: Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Nude mice were treated with daily i.p. injection of SaHa and JQ1 or corresponding vehicle for 21 days (SAHA 25 mg/kg 1-0-0 (once per day in the morning) and JQ1 50 mg/kg 0-0-1 (one per day in the evening), treatment was imitated when tumor size reached 200 mm³ +/- 20 mm³.

tag: tissue type


title: Shoot grown under +Fe of ys3 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Shoot of WT vs. ys3 mutant. Fe-sufficient.


title: Ring1B -/- rep3

description: Gene expression of E14Tg2a-derived Ring1B -/- mESCs

source_name: E14Tg2a-derived Ring1B -/- ESCs replicate 1

value: Ring1B knockout


title: CD34+ hematopoietic progenitor cells, pre-miR-NC1, replicate 1

value: Negative control 1


title: Shoot grown under -Fe of ys1 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Shoot of WT vs. ys1 mutant. Fe-deficient.

source_name: WT - Fe-deficient


title: Ring1B -/- rep2

value: male


title: UTX_WT_Liver_SEC_rep1

value: liver

value: sinusoidal endothelial cell


title: IL10 knockout, self empty loop replicate-3

description:
KEL1
MW7

source_name: IL10 knockout, self empty loop

value: KEL

value: IL10 KO


title: UTX_WT_Liver_SEC_rep2


title: UTX_WT_Liver_MP_rep2

value: macrophage


title: Shoot grown under +Fe of ys1 mutant vs. WT plants Replicate 2

description: Replicate 2 of 2. Shoot of WT vs. ys1 mutant. Fe-sufficient.


title: Shoot grown under +Fe of ys1 mutant vs. WT plants Replicate 1

description: Replicate 1 of 2. Shoot of WT vs. ys1 mutant. Fe-sufficient.


title: WT AngII C57Bl/6J 2

source_name: Mouse heart left ventricle

value: Male

value: wild type


title: TLR4 knockout, self empty loop replicate-3

description:
koTE3
MX6

source_name: TLR4 knockout, self empty loop

value: koTE

value: TLR4 KO


title: TLR4 knockout, self empty loop replicate-1

description:
koTE1
MX4

value: Loop


title: UTX_WT_Liver_MP_rep1


title: TLR4 knockout, self empty loop replicate-2

description:
koTE2
MX5

value: self-emptying


title: E14Tg2a rep2

description: Gene expression of E14Tg2a mouse embryonic stem cells (mESCs)

source_name: E14Tg2a ESCs replicate 2

value: wildtype


title: E14Tg2a rep1

source_name: E14Tg2a ESCs replicate 1

value: ESC


title: DEN_WT_PH_rep1

source_name: Mouse liver hepatocyte

value: hepatocyte


title: Ring1B -/- rep1

value: Ring1B knockout


title: MGO2015_023

value: patient derived pancreatic carcinoma xenograft


title: TLR4 knockout, self filling loop replicate-2

description:
koTF2
MX2

source_name: TLR4 knockout, self filling loop

value: koTF

value: self-filling


title: E14Tg2a rep3

source_name: E14Tg2a ESCs replicate 3

value: male


title: TLR4 knockout, self filling loop replicate-3

description:
koTF3
MX3


title: MGO2015_024


title: MGO2015_022

description: Bo63-JQ1-SAHA_treatment control


title: DEN_WT_PH_rep2

value: liver


title: UTX_WT_PH_rep2


title: UTX_WT_PH_rep1


title: MGO2015_025


title: TLR4 knockout, self filling loop replicate-1

description:
koTF1
MX1


title: T-bet KO, replicate 3

status: Public on Sep 19 2015

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

description: OT1 cells sorted at d6 of Listeria-OVA infection of T-bet KO mice

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: RMA, Genepattern, The Sample data table contains raw expression data post RMA, excluding unlabeled probes or duplicate probes (that showed identical value).

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Glass slide teasing Flow sorting

treatment_protocol: 1X10^4 cells from WT or KO mice were co-transferred into cogenically matched recipient mice. Mice were infected with LCMV or Listeria-OVA the next day. On day6 of infection cells are purified by Facs Aria sorting.

tag: age

value: 6 weeks

value: Spleen

value: T-bet KO

tag: phenotypic marker


title: T-bet KO, replicate 2

source_name: OT1 cells sorted at d6 of Listeria-OVA infection of T-bet KO mice

tag: strain

value: Male


title: T-bet WT, replicate 3

description: OT1 cells sorted at d6 of Listeria-OVA infection of T-bet WT mice

value: T-bet WT


title: T-bet WT, replicate 1

source_name: OT1 cells sorted at d6 of Listeria-OVA infection of T-bet WT mice


title: Zeb2 KO, replicate 1

description: P14 cells sorted at d6 of LCMV infection of Zeb2 KO mice

value: Zeb2 KO


title: T-bet WT, replicate 2


title: Zeb2 KO, replicate 2

source_name: P14 cells sorted at d6 of LCMV infection of Zeb2 KO mice


title: T-bet KO, replicate 1


title: MGO2015_020

description: Bo63-JQ1-SAHA_treatment control


title: MGO2015_021

description: Bo63-JQ1-SAHA_treatment control


title: C2C12 cells infected with  Ad-PGC-1alpha

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: Gene expression data from C2C12 myotubes infected with Ad-PGC-1alpha

hyb_protocol: Hybridization was performed at 45 degrees celcius for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

source_name: C2C12 cells infected with  Ad-PGC-1alpha

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis with the Ambion WT Expression Kit (PN4411974). Fragmentation and terminal labeling was peformed with the AffymetrixGeneChip WT Terminal Labeling Kit (PN 900671)

growth_protocol: Human primary hepatocytes were supplied in Hepatocyte medium (BD). HepG2 cells were grown in EMEM supplemented with 10% FBS. C2C12 cells were grown in DMEM with 20% FBS, and differentiated in DMEM containing 2% donor equine serum and 1uM insulin for 7 days.

extract_protocol: Using the Rneasy kit from Qiagen according to manufacturer's protocol

treatment_protocol: Adenoviruses were added directly to the culture medium and cells were collected 24hr later. For experiments involving siRNA transfetions, cells were transfected with the indicated siRNAs 48hr prior to infection with adenoviruses encoding either GFP ("Ad-GFP") or PGC-1alpha ("Ad-PGC-1alpha").

tag: tissue of origin

value: Muscle

value: C2C12 myotubes


title: Zeb2 WT, replicate 1

description: P14 cells sorted at d6 of LCMV infection of Zeb2 WT mice

value: Zeb2 WT


title: Zeb2 WT, replicate 2

source_name: P14 cells sorted at d6 of LCMV infection of Zeb2 WT mice


title: Liver_metastasis_case2

city: okayama city

first: Tomokazu

last: Fuji

state: Okayama

address: 2-5-1 Shikata-cho

department: Department of Gastroenterological Surgery

institute: Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences

hyb_protocol: After heat treatment at 100°C for 5 minutes, Cy3-labelled miRNA was mixed with miRNA Complete Labeling and Hyb kit <5190-0456> (Agilent Technologies) and hybridized to SurePrint G3 Human miRNA microaaray kit 8x60k Rel.21.0 < G4872A#070156>(Agilent Technologies) for 20 hours at 55°C/20rpm in a rotating Agilent hybridization oven.   After hybridization, microarrays were washed  at room temperature with Gene Expression Wash Pack <5188-5242> (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Scanner (G2539A) using Scan Control <version A.8.5.1> (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction <version 10.10.1.1> (Agilent Technologies) using default parameters (FE protocol: miRNA_1010_Sep10 and Grid template: 070156_D_F_20141006).  Date processing was performed using GeneSpring GX <version 13.0.0> (Agilent Technologies).The expression level of each probe was sum of 20 spots raw intensity with the background subtracted. The target miRNA which were not detected at any spots were represented as “undetected” and set at expression level “0.1”. Data was 90 percentile normalized followed by excluding the target miRNA that were not detected in all samples.

source_name: case2 Liver T

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA using the miRNA Complete Labeling and Hyb kit <5190-0456> (Agilent) according to the manufacturer's instructions.

extract_protocol: The total miRNA was isolated from frozen tissue specimens by miRNeasy mini kit <217004 > (Qiagen) and analyzed in Agilent 2100 Bioanalyzer <G2939A> (Agilent Technologies) according to the manufacture’s protocol.

tag: case

tag: cancer status

value: metastatic lesion


title: Liver_normal_case2

source_name: case2 Liver N

value: normal non-cancerous tissue


title: Colon_normal_case2

source_name: case2 Colon N

value: rectum


title: C2C12 cells infected with Ad-GFP

description: Gene expression data from C2C12 myotubes infected with Ad-GFP

source_name: C2C12 cells infected with Ad-GFP

tag: cell type

value: Ad-GFP


title: mc38_cc1l_72h_rep3

city: Montreal

first: Gregory

last: VOISIN

state: Québec

address: 6825 rue Saint Denis

country: Canada

institute: Atelerics

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and rsn normalized.

source_name: colon cancer cell expressing CEACAM1-L, grown for 72h in medium containing 10% serum

growth_protocol: Cell culture medium containing 10% serum and proper selection antibiotics was used to culture cells

value: metastatic murine colon cancer cells syngeneic to C57BL/6 mice, expressing CEACAM1-L


title: Wild type, self filling loop replicate-1

description:
WFL1
MW1

source_name: Wild type, self filling loop

value: WFL

value: WT

value: Loop

value: self-filling


title: Colon_normal_case1

source_name: case1 Colon N

value: colon


title: mc38_ct_72h_rep1

source_name: colon cancer cell deficient of CEACAM1, grown for 72h in medium containing 10% serum

value: metastatic murine colon cancer cells syngeneic to C57BL/6 mice, devoid of CEACAM1


title: HepG2 cells infected with SiControl Ad-GFP

description: Gene expression data from HepG2 cells transfected with control siRNAs and then infected with Ad-GFP

value: Liver

value: HepG2 cells

value: SiControl, Ad-GFP


title: HepG2 cells infected with SiControl Ad-PGC-1alpha

description: Gene expression data from HepG2 cells transfected with control siRNAs and then infected with Ad-PGC-1alpha

value: SiControl, Ad-PGC-1alpha


title: HepG2 cells infected with SiHSF1 Ad-GFP

description: Gene expression data from HepG2 cells transfected with siRNAs targeting HSF1 and then infected with Ad-GFP

source_name: HepG2 cells infected with SiHSF1 Ad-GFP

value: SiHSF1, Ad-GFP


title: mc38_cc1l_72h_rep2


title: Colon_tumor_case1

source_name: case1 Colon T

value: primary tumor


title: mc38_cc1s_72h_rep1

source_name: colon cancer cell expressing CEACAM1-S, grown for 72h in medium containing 10% serum

value: metastatic murine colon cancer cells syngeneic to C57BL/6 mice, expressing CEACAM1-S


title: HepG2 cells infected with Ad-GFP

description: Gene expression data from HepG2 cells infected with Ad-GFP

source_name: HepG2 cells infected with Ad-GFP


title: mc38_ct_72h_rep3


title: mc38_ct_72h_rep4


title: HepG2 cells infected with SiHSF1 Ad-PGC-1alpha

description: Gene expression data from HepG2 cells transfected with  siRNAs targeting HSF1 and then infected with Ad-PGC-1alpha

value: SiHSF1, Ad-PGC-1alpha


title: mc38_cc1s_72h_rep4


title: mc38_cc1s_72h_rep2


title: mc38_cc1l_72h_rep1


title: mc38_ct_72h_rep2


title: HepG2 cells infected with Ad-PGC-1alpha

description: Gene expression data from HepG2 cells infected with Ad-PGC-1alpha

source_name: HepG2 cells infected with Ad-PGC-1alpha


title: mc38_cc1l_72h_rep4


title: mc38_cc1s_72h_rep3


title: Colon_tumor_case2

source_name: case2 Colon T

value: rectum


title: Liver_metastasis_case1

source_name: case1 Liver T

value: liver

value: metastatic lesion


title: Liver_normal_case1

source_name: case1 Liver N

value: normal non-cancerous tissue


title: HepG2 cells infected with AD-PGC-1beta

description: Gene expression data from HepG2 cells infected with Ad-PGC-1beta

source_name: HepG2 cells infected with AD-PGC-1beta


description: Gene expression data from Human primary hepatocytes donor 5 infected with Ad-PGC-1alpha

value: primary hepatocytes


title: Human primary hepatocytes donor 5 infected with Ad-GFP

description: Gene expression data from human primary hepatocytes donor 5 infected with Ad-GFP

value: Ad-GFP


description: Gene expression data from Human primary hepatocytes donor 2 infected with Ad-PGC-1alpha


description: Gene expression data from Human primary hepatocytes donor 1 infected with Ad-PGC-1alpha


title: Human primary hepatocytes donor 2 infected with Ad-GFP

description: Gene expression data from human primary hepatocytes donor 2 infected with Ad-GFP


title: Human primary hepatocytes donor 1 infected with Ad-GFP

description: Gene expression data from human primary hepatocytes donor 1 infected with Ad-GFP


description: Gene expression data from Human primary hepatocytes donor 3 infected with Ad-PGC-1alpha


title: Human primary hepatocytes donor 3 infected with Ad-GFP

description: Gene expression data from human primary hepatocytes donor 3 infected with Ad-GFP


title: 20123850 Ileum Low gain-low intake

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing: The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).

organism: Bos taurus

source_name: ileum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Steers were fed a standard concentrate diet for 84 days.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform.  RNA pellets were centrifuged through RNeasy Plus Mini Kit columns (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions to remove genomic DNA.

treatment_protocol: Animals most divergent from the bivariate mean from in each of the four phenotypic Cartesian quadrants for gain x intake were selected and small intestine tissue samples were collected and t. The transcriptomes of the three sections of the small intestineduodenum, jejunum and ileum from the 16 animals selected were evaluated by microarray.

value: ileum

tag: phenotype

value: low gain-low intake


title: 20123611 Ileum High gain-low intake

value: high gain-low intake


title: 20123593 Ileum Low gain-low intake


title: 20123806 Ileum High gain-high intake

value: high gain-high intake


title: 20123841 Ileum High gain-high intake


title: 20124206 Ileum High gain-high intake


title: 20123891 ileum High gain-low intake


title: 20123591 Ileum High gain-low intake


title: 20123661 Ileum Low gain-low intake


title: 20124257 Ileum Low gain-high intake

value: low gain-high intake


title: 20124211 Ileum Low gain-high intake


title: 20123852 Ileum Low gain-high intake


title: 20123915 Ileum Low gain-low intake


title: 20123812 Ileum High gain-low intake


title: 20123636 Ileum Low gain-high intake


title: 20123616 Ileum High gain-high intake


title: Human primary hepatocytes donor 4 infected with Ad-GFP

description: Gene expression data from human primary hepatocytes donor 4 infected with Ad-GFP

value: Liver


title: 20124257 Jejunum Low gain-high intake

source_name: jejunum

value: jejunum


title: 20123850 Jejunum Low gain-low intake


title: 20123636 Jejunum Low gain-high intake


title: 20123661 jejunum Low gain-low intake


title: 20123915 Jejunum Low gain-low intake


title: 20123852 Jejunum Low gain-high intake


title: 20123593 Jejunum Low gain-low intake


title: 20123812 Jejunum High gain-low intake


title: 20123891 Jejunum High gain-low intake


title: 20124211 Jejunum Low gain-high intake


title: 20123611 Jejunum High gain-low intake


description: Gene expression data from Human primary hepatocytes donor 4 infected with Ad-PGC-1alpha


title: 20123616 Jejunum High gain-high intake


title: 20124206 Jejunum High gain-high intake


title: 20124211 Duodenum Low gain-high intake

source_name: duodenum

value: duodenum


title: 20123850 Duodenum Low gain-low intake


title: 20123591 Jejunum High gain-low intake


title: 20123852 Duodenum Low gain-high intake


title: 20123891 Duodenum High gain-low intake


title: 20123661 Duodenum Low gain-low intake


title: 20124257 Duodenum Low gain-high intake


title: 20123593 Duodenum Low gain-low intake


title: 20123841 Jejunum High gain-high intake


title: 20123806 Jejunum High gain-high intake


title: 20123812 Duodenum High gain-low intake


title: 20123591 Duodenum High gain-low intake


title: 20123611 Duodenum High gain-low intake


title: 20123915 Duodenum Low gain-low intake


title: 20123636 Duodenum Low gain-high intake


title: 20124206 Duodenum High gain-high intake


title: 20123616 Duodenum High gain-high intake


title: 20123806 Duodenum High gain-high intake


title: FD Fetus Brain 2

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description:
Dye-swap (Cy3/Cy5) of FD Fetus Brain vs. Control
Control Fetus Brain (Cy5) x FD Fetus Brain (Cy3)

hyb_protocol: Hybridization kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing:
Software: Feature Extraction ver 9.5.3.1
Normalization: LOWESS (locally weighted linear regression)

source_name: Fetal brain, maternal food deprivation

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: C57BL/6J mice were purchased from Japan SLC Co. Ltd. (Hamamatsu, Japan). The animals were housed at the Animal Institution in Showa University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum. As per the supplier's (CLEA) information, CE-2 includes 51.4% nitrogen free extracts, 24.9% crude protein, 8.6% moisture, 6.7% crude ash, 4.6% crude fat, and 3.7% crude fiber. The physiological fuel value is 346.7 kcal per 100 g chow. All animal experiments were started after a period of acclimation of at least one week. Pregnant animals were obtained by housing females with males (1-2 females/male). The day the vaginal plug was observed was designated embryonic day 0 (ED0) and gestation day 0 (GD0).

extract_protocol: Kit: QIAGEN, RNeasy Mini

treatment_protocol: Control (normal diet), FD (Food Deprived for overnight at GD17) treatment diet, FR (Food Restricted from GD10 to 17) treatment diet.

tag: strain/background

value: fetal brain

tag: maternal diet

value: food deprivation

source_name: Fetal brain, maternal control diet

value: ad libitum


title: 11 RAW PA(+) aP2(+)

city: Sapporo

first: Masato

last: Furuhashi

institute: Sapporo Medical University School of Medicine

description: Gene expression after 24 hr incubation in macrophages with palmitic acid (+)and FABP4 (+)

hyb_protocol: For each sample, the Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 h in a rotating hybridization oven.

scan_protocol: After washing, microarrays were scanned using an Agilent microarray scanner (Agilent Technologies).

data_processing: Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software, which performs background subtractions, such as error modeling, adjusting for additive and multiplicative noise. Normalization was performed using Agilent GeneSpring GX (per chip normalization: 75 percentile shift; per gene normalization: none).

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (+), replicate 2

label_protocol: Starting with 50 ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer’s protocol.

growth_protocol: Mouse RAW264.7 macrophages were cultured in DMEM supplemented with 10% heat-inactivated FBS, 50 U/ml penicillin and 50 μg/ml streptomycin at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (Qiagen, Hilden, Germany), and RNA quality was assessed by using an Agilent 2100 Bioanalyzer.

treatment_protocol: RAW264.7 macrophages were treated with and without 200 nM recombinant FABP4 in the absence and presence of 0.2 mM palmitic acid in the medium supplemented with 0.5% fatty acid-free BSA

value: macrophage


title: FR Fetus Brain 2

description:
Dye-swap (Cy3/Cy5) of FR Fetus Brain vs. Control
Control Fetus Brain (Cy5) x FR Fetus Brain (Cy3)

source_name: Fetal brain, maternal food restriction

value: food restriction


title: 12 RAW PA(+) aP2(+)

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (+), replicate 3


title: 9 RAW PA(+) aP2(-)

description: Gene expression after 24 hr incubation in macrophages with palmitic acid (+)and FABP4 (-)

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (-), repicate 3


title: 142101

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the hybridization kit according the Agilent protocol

scan_protocol: We used a Surescan provided by Agilent and controled by SureScan Software

data_processing: the data was processed on Cytogenomics 2.9.1.3 using the Default Analysis Method - CGH v2 proposed by Agilent

molecule: genomic DNA

source_name: Glioblastoma

label_protocol: DNA was labeled with the sureTag labeling kit accirding the agilent protocol

extract_protocol: DNA was extracted from fresh, frozen or formol fixed-paraffin embedded fragments using Qiamp DNA mini kit.

value: Glioblastoma

source_name: Female DNA control provided in SureTag Labeling Kit

tag: sample type

value: commercial DNA from cell lines


title: FR Fetus Brain 1

description:
Dye-swap (Cy3/Cy5) of Control vs. FR Fetus Brain
Control Fetus Brain (Cy3) x FR Fetus Brain (Cy5)


title: fresh pool3

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

institute: IRCCS AOU San Martino-IST

hyb_protocol: hybridization was performed in Agilent Oven for 17 hours at 65°C 10 rpm.

scan_protocol: After washing and scanning using Agilent Scanner G2505C, data were extracted using Feature Extraction software v10.7, protocol GE1_1100_Jul11.

data_processing: Tab-delimited text files containing FE results were acquired and analyzed in R v3.1.3 software environment (www.r-project.org) using the limma package v3.22.7 (Smyth 2005). To perform a quantitative analysis, only spots with positive signal minus background (“gBGSubSignal” FE field name) were used in the following analysis as “detected” spots. In each two-groups comparison, probes with less than 75% of detected spots across all arrays in one of the two groups were removed from the analysis. Similarly, arrays with a number of detected spots smaller than a predefined cutoff (equal to the average number of detected spots minus two times the standard deviation across all arrays) were removed. Background corrected intensities (gBGSubSignal) of duplicate spots on each array were averaged. Data were then log2-transformed and normalized for between-array comparison using scale normalization (Yang 2002; Yang 2003). Differential expression analysis between groups was carried out using Student's t-test (unpaired, two-tailed, unequal variance). Probes with False Discovery Rate (FDR) < 0.1 (Benjamini 1995) and fold-change between the two groups larger than 3 were selected as differentially expressed genes.

source_name: pool of 10 oocytes

label_protocol: Five ng of total RNA were amplified using Ovation Pico WTA System V2 (NuGEN Technologies, San Carlos, CA) then labelled according to Agilent Enzymatic Labelling Kit, 3 ug was hybridized to Human GE 4x44K v2 Microarray Kit (Agilent Technologies) containing probes for 41,000 human transcripts

extract_protocol: Total RNA was extracted from each pool of 8-10 oocytes using the miRNeasy Micro kit (Qiagen, Helden, Germany), according to the manufacturer’s procedure. Quantification and quality control of total RNA were performed by RNA 6000 Pico kit on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: protocol

value: fresh

value: female


title: 20123841 Duodenum High gain-high intake

tag: tissue


title: fresh pool2


title: 10 RAW PA(+) aP2(+)

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (+), replicate 1


title: 6years pool2

source_name: pool of 9 oocytes

value: criopreserved for more than 6 years


title: 7 RAW PA(+) aP2(-)

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (-), repicate 1


title: 6 RAW PA(-) aP2(+)

description: Gene expression after 24 hr incubation in macrophages with palmitic acid (-)and FABP4 (+)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (+), replicate 3


title: 6years pool4


title: 4 RAW PA(-) aP2(+)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (+), replicate 1


title: 1 RAW PA(-) aP2(-)

description: Gene expression after 24 hr incubation in macrophages with palmitic acid (-)and FABP4 (-)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (-), replicate 1


title: 3years pool2

source_name: pool of 8 oocytes

value: criopreserved for more than 3 years


title: 2 RAW PA(-) aP2(-)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (-), replicate 2


title: ILD sample 50

status: Public on Sep 18 2015

city: Pittsburgh

first: SungHwan

last: Kim

address: 200 Lothrop, BST W1200

institute: University of Pittsburgh

description:
LT126767LL
6-digit tissue label
micro RNA

hyb_protocol: Hybridized to Agilent-021827 or Agilent-031181 miRNA arrays according to Agilent instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B).

data_processing: Probes from the two arrays were matched using gene symbols, and loess normalization was applied using affy package in R. Probes whose mean value of normalized expression (loess normalization) was less than 1.7 were filtered.

source_name: flash frozen lung tissues, ILD

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the QuickAmp kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).

growth_protocol: Not applicable.

extract_protocol: 30 ug of whole lung was homogenized with Trizol, and then total RNA was extracted using the QiaCube system (Qiagen, Valencia CA).

treatment_protocol: Not applicable.

value: lung

tag: disease status

value: interstitial lung disease (ILD)

tag: scaled bmi

tag: scaled age


title: ILD sample 47

description:
LT118801RU
6-digit tissue label
micro RNA


title: ILD sample 48

description:
LT123131RL
6-digit tissue label
micro RNA


title: ILD sample 49

description:
LT124161RL
6-digit tissue label
micro RNA


title: ILD sample 46

description:
LT118629RL
6-digit tissue label
micro RNA


title: 5 RAW PA(-) aP2(+)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (+), replicate 2


title: ILD sample 51

description:
LT128191LL
6-digit tissue label
micro RNA


title: ILD sample 52

description:
LT134279LL
6-digit tissue label
micro RNA


title: ILD sample 53

description:
LT134776LL
6-digit tissue label
micro RNA


title: 3years pool3

tag: gender


title: 6years pool1


title: fresh pool1


title: 3 RAW PA(-) aP2(-)

source_name: RAW264.7 macrophages, Palmitic acid (-), FABP4 (-), replicate 3


title: 3years pool1


title: 8 RAW PA(+) aP2(-)

source_name: RAW264.7 macrophages, Palmitic acid (+), FABP4 (-), repicate 2


title: 3years pool4


title: ILD sample 42

description:
LT100707RL
6-digit tissue label
micro RNA


title: ILD sample 43

description:
LT102695LL
6-digit tissue label
micro RNA


title: ILD sample 44

description:
LT111916LL
6-digit tissue label
micro RNA


title: ILD sample 45

description:
LT116004RL
6-digit tissue label
micro RNA


title: ILD sample 41

description:
LT099879RL
6-digit tissue label
micro RNA


title: ILD sample 40

description:
LT094532RL
6-digit tissue label
micro RNA


title: ILD sample 37

description:
LT087826LL
6-digit tissue label
micro RNA


title: ILD sample 34

description:
LT080750LL
6-digit tissue label
micro RNA


title: ILD sample 36

description:
LT087663RL
6-digit tissue label
micro RNA


title: ILD sample 35

description:
LT082461RL
6-digit tissue label
micro RNA


title: ILD sample 39

description:
LT094217RM
6-digit tissue label
micro RNA


title: ILD sample 33

description:
LT078404RM
6-digit tissue label
micro RNA


title: ILD sample 27

description:
LT062121LL
6-digit tissue label
micro RNA


title: ILD sample 32

description:
LT077082RU
6-digit tissue label
micro RNA


title: ILD sample 26

description:
LT050079RL
6-digit tissue label
micro RNA


title: ILD sample 28

description:
LT062141RL
6-digit tissue label
micro RNA


title: ILD sample 31

description:
LT076421LL
6-digit tissue label
micro RNA


title: ILD sample 24

description:
LT046539RL
6-digit tissue label
micro RNA


title: ILD sample 25

description:
LT047152LL
6-digit tissue label
micro RNA


title: ILD sample 23

description:
LT042151RL
6-digit tissue label
micro RNA


title: ILD sample 17

description:
LT030347RL
6-digit tissue label
micro RNA


title: ILD sample 19

description:
LT033422RL
6-digit tissue label
micro RNA


title: ILD sample 18

description:
LT030662LL
6-digit tissue label
micro RNA


title: ILD sample 29

description:
LT067200LU
6-digit tissue label
micro RNA


title: ILD sample 20

description:
LT036383LL
6-digit tissue label
micro RNA


title: ILD sample 21

description:
LT039091RL
6-digit tissue label
micro RNA


title: ILD sample 22

description:
LT041723RL
6-digit tissue label
micro RNA


title: ILD sample 38

description:
LT090666LL
6-digit tissue label
micro RNA


title: ILD sample 14

description:
LT022251RL
6-digit tissue label
micro RNA


title: FD Fetus Brain 1

description:
Dye-swap (Cy3/Cy5) of Control vs. FD Fetus Brain
Control Fetus Brain (Cy3) x FD Fetus Brain (Cy5)

source_name: Fetal brain, maternal control diet

source_name: Fetal brain, maternal food deprivation


title: ILD sample 16

description:
LT026534RL
6-digit tissue label
micro RNA


title: ILD sample 15

description:
LT022562LL
6-digit tissue label
micro RNA


title: ILD sample 13

description:
LT021748RL
6-digit tissue label
micro RNA


title: ILD sample 30

description:
LT069585RL
6-digit tissue label
micro RNA


title: ILD sample 12

description:
LT021461RM
6-digit tissue label
micro RNA


title: ILD sample 11

description:
LT017533RM
6-digit tissue label
micro RNA


title: ILD sample 10

description:
LT017495RL
6-digit tissue label
micro RNA


title: ILD sample 8

description:
LT011501RL
6-digit tissue label
micro RNA


title: ILD sample 6

description:
LT006946RM
6-digit tissue label
micro RNA


title: ILD sample 9

description:
LT012933RL
6-digit tissue label
micro RNA


title: ILD sample 5

description:
LT005256RL
6-digit tissue label
micro RNA


title: ILD sample 4

description:
LT002902RU
6-digit tissue label
micro RNA


title: ILD sample 7

description:
LT007259RU
6-digit tissue label
micro RNA


title: ILD sample 3

description:
LT000379LU
6-digit tissue label
micro RNA


title: COPD sample 96

description:
LT286056RU
6-digit tissue label
micro RNA

source_name: flash frozen lung tissues, COPD

value: chronic obstructive pulmonary disease (COPD)


title: COPD sample 94

description:
LT273284LL
6-digit tissue label
micro RNA


title: COPD sample 95

description:
LT285906LL
6-digit tissue label
micro RNA


title: ILD sample 2

description:
LT000216LL
6-digit tissue label
micro RNA


title: COPD sample 136

description:
LT020426LU
6-digit tissue label
micro RNA


title: COPD sample 93

description:
LT270247RU
6-digit tissue label
micro RNA


title: COPD sample 91

description:
LT262371RM
6-digit tissue label
micro RNA


title: COPD sample 92

description:
LT263636RU
6-digit tissue label
micro RNA


title: COPD sample 97

description:
LT291449RL
6-digit tissue label
micro RNA


title: COPD sample 87

description:
LT253131RU
6-digit tissue label
micro RNA


title: COPD sample 88

description:
LT255244RU
6-digit tissue label
micro RNA


title: COPD sample 89

description:
LT255718RU
6-digit tissue label
micro RNA


title: COPD sample 90

description:
LT261141RU
6-digit tissue label
micro RNA


title: COPD sample 85

description:
LT249811RU
6-digit tissue label
micro RNA


title: COPD sample 86

description:
LT249917LL
6-digit tissue label
micro RNA


title: COPD sample 83

description:
LT245084RU
6-digit tissue label
micro RNA


title: COPD sample 79

description:
LT243058RU
6-digit tissue label
micro RNA


title: COPD sample 80

description:
LT244399LU
6-digit tissue label
micro RNA


title: COPD sample 82

description:
LT245031LL
6-digit tissue label
micro RNA


title: COPD sample 81

description:
LT244480LU
6-digit tissue label
micro RNA


title: COPD sample 78

description:
LT238765RL
6-digit tissue label
micro RNA


title: COPD sample 77

description:
LT238531RU
6-digit tissue label
micro RNA


title: COPD sample 76

description:
LT237439RU
6-digit tissue label
micro RNA


title: COPD sample 84

description:
LT245983LU
6-digit tissue label
micro RNA


title: COPD sample 75

description:
LT234774LU
6-digit tissue label
micro RNA


title: COPD sample 71

description:
LT223106RU
6-digit tissue label
micro RNA


title: COPD sample 70

description:
LT220968RU
6-digit tissue label
micro RNA


title: COPD sample 64

description:
LT203541RU
6-digit tissue label
micro RNA


title: COPD sample 68

description:
LT213735RU
6-digit tissue label
micro RNA


title: COPD sample 67

description:
LT213352LU
6-digit tissue label
micro RNA


title: COPD sample 69

description:
LT215341RU
6-digit tissue label
micro RNA


title: COPD sample 74

description:
LT233821RL
6-digit tissue label
micro RNA


title: COPD sample 65

description:
LT210463LU
6-digit tissue label
micro RNA


title: COPD sample 60

description:
LT198612RL
6-digit tissue label
micro RNA


title: COPD sample 66

description:
LT212777RU
6-digit tissue label
micro RNA


title: COPD sample 59

description:
LT197511LU
6-digit tissue label
micro RNA


title: COPD sample 61

description:
LT199384RL
6-digit tissue label
micro RNA


title: COPD sample 62

description:
LT200930RL
6-digit tissue label
micro RNA


title: COPD sample 63

description:
LT203231RM
6-digit tissue label
micro RNA


title: COPD sample 58

description:
LT196677RU
6-digit tissue label
micro RNA


title: COPD sample 55

description:
LT190004RU
6-digit tissue label
micro RNA


title: COPD sample 56

description:
LT194473RU
6-digit tissue label
micro RNA


title: COPD sample 52

description:
LT184901RU
6-digit tissue label
micro RNA


title: COPD sample 53

description:
LT185970RL
6-digit tissue label
micro RNA


title: COPD sample 51

description:
LT184772RL
6-digit tissue label
micro RNA


title: COPD sample 57

description:
LT195871RU
6-digit tissue label
micro RNA


title: COPD sample 72

description:
LT229669RU
6-digit tissue label
micro RNA


title: COPD sample 49

description:
LT177956LL
6-digit tissue label
micro RNA


title: COPD sample 50

description:
LT184423LL
6-digit tissue label
micro RNA


title: COPD sample 54

description:
LT186521RU
6-digit tissue label
micro RNA


title: COPD sample 48

description:
LT176510LU
6-digit tissue label
micro RNA


title: COPD sample 47

description:
LT172093RL
6-digit tissue label
micro RNA


title: COPD sample 45

description:
LT165114RU
6-digit tissue label
micro RNA


title: COPD sample 46

description:
LT168128RU
6-digit tissue label
micro RNA


title: COPD sample 43

description:
LT162479RU
6-digit tissue label
micro RNA


title: COPD sample 40

description:
LT152653LU
6-digit tissue label
micro RNA


title: COPD sample 41

description:
LT154785RU
6-digit tissue label
micro RNA


title: COPD sample 37

description:
LT140046RU
6-digit tissue label
micro RNA


title: COPD sample 73

description:
LT233620RU
6-digit tissue label
micro RNA


title: COPD sample 42

description:
LT156041LU
6-digit tissue label
micro RNA


title: COPD sample 28

description:
LT112597RU
6-digit tissue label
micro RNA


title: COPD sample 30

description:
LT118064RL
6-digit tissue label
micro RNA


title: COPD sample 29

description:
LT115251RU
6-digit tissue label
micro RNA


title: COPD sample 31

description:
LT126327LU
6-digit tissue label
micro RNA


title: COPD sample 26

description:
LT095342LU
6-digit tissue label
micro RNA


title: COPD sample 27

description:
LT108067RU
6-digit tissue label
micro RNA


title: COPD sample 32

description:
LT134121RU
6-digit tissue label
micro RNA


title: COPD sample 36

description:
LT139691RU
6-digit tissue label
micro RNA


title: COPD sample 33

description:
LT134719RU
6-digit tissue label
micro RNA


title: COPD sample 38

description:
LT144769RL
6-digit tissue label
micro RNA


title: COPD sample 34

description:
LT136415RU
6-digit tissue label
micro RNA


title: COPD sample 25

description:
LT089723LL
6-digit tissue label
micro RNA


title: COPD sample 44

description:
LT163771RU
6-digit tissue label
micro RNA


title: COPD sample 39

description:
LT148377LU
6-digit tissue label
micro RNA


title: COPD sample 24

description:
LT084808LU
6-digit tissue label
micro RNA


title: COPD sample 21

description:
LT083950RU
6-digit tissue label
micro RNA


title: COPD sample 22

description:
LT084038RM
6-digit tissue label
micro RNA


title: COPD sample 23

description:
LT084406RU
6-digit tissue label
micro RNA


title: COPD sample 35

description:
LT138418LU
6-digit tissue label
micro RNA


title: COPD sample 20

description:
LT083759RL
6-digit tissue label
micro RNA


title: COPD sample 17

description:
LT076617LL
6-digit tissue label
micro RNA


title: COPD sample 16

description:
LT076181LI
6-digit tissue label
micro RNA


title: COPD sample 15

description:
LT075462RU
6-digit tissue label
micro RNA


title: COPD sample 18

description:
LT080176RU
6-digit tissue label
micro RNA


title: COPD sample 9

description:
LT053283RU
6-digit tissue label
micro RNA


title: COPD sample 13

description:
LT070403LL
6-digit tissue label
micro RNA


title: COPD sample 11

description:
LT058691LU
6-digit tissue label
micro RNA


title: COPD sample 10

description:
LT057972LU
6-digit tissue label
micro RNA


title: COPD sample 12

description:
LT060717LU
6-digit tissue label
micro RNA


title: COPD sample 6

description:
LT034070LU
6-digit tissue label
micro RNA


title: COPD sample 14

description:
LT072387LU
6-digit tissue label
micro RNA


title: COPD sample 7

description:
LT037710RU
6-digit tissue label
micro RNA


title: ILD sample 183

description:
LT186388LL
6-digit tissue label
micro RNA


title: COPD sample 1

description:
LT002501RL
6-digit tissue label
micro RNA


title: COPD sample 2

description:
LT005419RU
6-digit tissue label
micro RNA


title: COPD sample 8

description:
LT041389RL
6-digit tissue label
micro RNA


title: COPD sample 3

description:
LT017275LL
6-digit tissue label
micro RNA


title: COPD sample 4

description:
LT024967LU
6-digit tissue label
micro RNA


title: ILD sample 181

description:
LT002410RM
6-digit tissue label
micro RNA


title: ILD sample 182

description:
LT091552LL
6-digit tissue label
micro RNA


title: COPD sample 19

description:
LT081498RL
6-digit tissue label
micro RNA


title: ILD sample 180

description:
LT161434RL
6-digit tissue label
micro RNA


title: ILD sample 179

description:
LT295133LL
6-digit tissue label
micro RNA


title: ILD sample 176

description:
LT231373LU
6-digit tissue label
micro RNA


title: ILD sample 175

description:
LT231101RL
6-digit tissue label
micro RNA


title: ILD sample 156

description:
LT157253RL
6-digit tissue label
micro RNA


title: ILD sample 157

description:
LT158011LL
6-digit tissue label
micro RNA


title: COPD sample 5

description:
LT028427LU
6-digit tissue label
micro RNA


title: ILD sample 164

description:
LT187987LL
6-digit tissue label
micro RNA


title: ILD sample 146

description:
LT109097LL
6-digit tissue label
micro RNA


title: ILD sample 165

description:
LT188161LL
6-digit tissue label
micro RNA


title: ILD sample 141

description:
LT092669LU
6-digit tissue label
micro RNA


title: ILD sample 122

description:
LT285671LU
6-digit tissue label
micro RNA


title: ILD sample 123

description:
LT287158LU
6-digit tissue label
micro RNA


title: ILD sample 124

description:
LT288719RL
6-digit tissue label
micro RNA


title: ILD sample 119

description:
LT280282RL
6-digit tissue label
micro RNA


title: ILD sample 121

description:
LT282601LL
6-digit tissue label
micro RNA


title: ILD sample 118

description:
LT279828RU
6-digit tissue label
micro RNA


title: ILD sample 116

description:
LT277002LL
6-digit tissue label
micro RNA


title: ILD sample 117

description:
LT277811RL
6-digit tissue label
micro RNA


title: ILD sample 115

description:
LT266817LL
6-digit tissue label
micro RNA


title: ILD sample 127

description:
LT299181LU
6-digit tissue label
micro RNA


title: ILD sample 126

description:
LT297451LU
6-digit tissue label
micro RNA


title: A2 iPS cells, 7d, cholesterol deficient, biological replicate 4

city: Sioux Falls

first: Kevin

middle: R

last: Francis

state: SD

department: Cellular Therapies

institute: Sanford Research

description:
A2_7day_4
SLOS iPS cells removed from mTeSR1 media, 7 days culture

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Standard manufacturing protocols were followed for preparation of arrays, washes, and sample loading.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek software. GCRMA background correction was applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: A2 iPS cells_7d_cholesterol deficient

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

growth_protocol: Control (BJ) and SLOS (A2) iPS cell lines cultured in cholesterol rich conditions (0 hr) were transferred to cholesterol deficient conditions.  RNA was isolated after 2, 3, 4, 5, and 7 days cholesterol deficient culture.

extract_protocol: Samples were collected by scraping and snap frozen in dry ice. All RNA samples were prepared using PicoPure RNA isolation kit. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Cholesterol rich pluripotent  culture consisted of human ES cell media (including 20% KOSR, 7.5 ng/mL bFGF) on a MEF feeder layer.  Cholesterol deficient culture was performed in mTeSR1 defined pluripotent conditions devoid of feeders.

tag: cell line

value: SLOS iPS cell line

tag: genotype/vairation

value: DHCR7 mutant

tag: cultured in

value: cholesterol deficient condition

tag: time point

value: 7 days


title: A2 iPS cells, 5d, cholesterol deficient, biological replicate 4

description:
A2_5day_4
SLOS iPS cells removed from mTeSR1 media, 5 days culture

source_name: A2 iPS cells_5d_cholesterol deficient

value: 5 days


title: A2 iPS cells, 7d, cholesterol deficient, biological replicate 3

description:
A2_7day_3
SLOS iPS cells removed from mTeSR1 media, 7 days culture


title: A2 iPS cells, 5d, cholesterol deficient, biological replicate 3

description:
A2_5day_3
SLOS iPS cells removed from mTeSR1 media, 5 days culture


title: A2 iPS cells, 7d, cholesterol deficient, biological replicate 2

description:
A2_7day_2
SLOS iPS cells removed from mTeSR1 media, 7 days culture


title: A2 iPS cells, 5d, cholesterol deficient, biological replicate 2

description:
A2_5day_2
SLOS iPS cells removed from mTeSR1 media, 5 days culture


title: ILD sample 114

description:
LT266802RL
6-digit tissue label
micro RNA


title: ILD sample 113

description:
LT264283RL
6-digit tissue label
micro RNA


title: ILD sample 120

description:
LT280851LL
6-digit tissue label
micro RNA


title: ILD sample 125

description:
LT295717RL
6-digit tissue label
micro RNA


title: A2 iPS cells, 5d, cholesterol deficient, biological replicate 1

description:
A2_5day_1
SLOS iPS cells removed from mTeSR1 media, 5 days culture


title: ILD sample 112

description:
LT259072LU
6-digit tissue label
micro RNA


title: ILD sample 111

description:
LT253677RL
6-digit tissue label
micro RNA


title: A2 iPS cells, 4d, cholesterol deficient, biological replicate 4

description:
A2_4day_4
SLOS iPS cells removed from mTeSR1 media, 4 days culture

source_name: A2 iPS cells_4d_cholesterol deficient

value: 4 days


title: A2 iPS cells, 3d, cholesterol deficient, biological replicate 4

description:
A2_3day_4
SLOS iPS cells removed from mTeSR1 media, 3 days culture

source_name: A2 iPS cells_3d_cholesterol deficient

value: 3 days


title: A2 iPS cells, 4d, cholesterol deficient, biological replicate 1

description:
A2_4day_1
SLOS iPS cells removed from mTeSR1 media, 4 days culture


title: A2 iPS cells, 4d, cholesterol deficient, biological replicate 3

description:
A2_4day_3
SLOS iPS cells removed from mTeSR1 media, 4 days culture


title: A2 iPS cells, 4d, cholesterol deficient, biological replicate 2

description:
A2_4day_2
SLOS iPS cells removed from mTeSR1 media, 4 days culture


title: A2 iPS cells, 7d, cholesterol deficient, biological replicate 1

description:
A2_7day_1
SLOS iPS cells removed from mTeSR1 media, 7 days culture


title: ILD sample 110

description:
LT253371RL
6-digit tissue label
micro RNA


title: A2 iPS cells, 3d, cholesterol deficient, biological replicate 3

description:
A2_3day_3
SLOS iPS cells removed from mTeSR1 media, 3 days culture


title: ILD sample 109

description:
LT251947LL
6-digit tissue label
micro RNA


title: ILD sample 108

description:
LT251693LL
6-digit tissue label
micro RNA


title: A2 iPS cells, 3d, cholesterol deficient, biological replicate 1

description:
A2_3day_1
SLOS iPS cells removed from mTeSR1 media, 3 days culture


title: A2 iPS cells, 3d, cholesterol deficient, biological replicate 2

description:
A2_3day_2
SLOS iPS cells removed from mTeSR1 media, 3 days culture


title: ILD sample 107

description:
LT249481LU
6-digit tissue label
micro RNA


title: ILD sample 106

description:
LT248906LL
6-digit tissue label
micro RNA


title: ILD sample 105

description:
LT244824RU
6-digit tissue label
micro RNA


title: A2 iPS cells, 2d, cholesterol deficient, biological replicate 3

description:
A2_2day_3
SLOS iPS cells removed from mTeSR1 media, 2 days culture

source_name: A2 iPS cells_2d_cholesterol deficient

value: 2 days


title: A2 iPS cells, 2d, cholesterol deficient, biological replicate 2

description:
A2_2day_2
SLOS iPS cells removed from mTeSR1 media, 2 days culture


title: ILD sample 104

description:
LT243794RL
6-digit tissue label
micro RNA


title: ILD sample 102

description:
LT239116RM
6-digit tissue label
micro RNA


title: ILD sample 101

description:
LT236710RL
6-digit tissue label
micro RNA


title: ILD sample 103

description:
LT242161RL
6-digit tissue label
micro RNA


title: ILD sample 100

description:
LT236519LL
6-digit tissue label
micro RNA


title: A2 iPS cells, 0hr, cholesterol rich, biological replicate 4

description:
A2_0hr_4
SLOS iPS cells removed from MEF feeders, 20% KOSR medium

source_name: A2 iPS cells_0hr_cholesterol rich

value: cholesterol rich condition


title: A2 iPS cells, 0hr, cholesterol rich, biological replicate 2

description:
A2_0hr_2
SLOS iPS cells removed from MEF feeders, 20% KOSR medium


title: ILD sample 99

description:
LT236045LL
6-digit tissue label
micro RNA


title: ILD sample 96

description:
LT232073LU
6-digit tissue label
micro RNA


title: ILD sample 97

description:
LT234205RL
6-digit tissue label
micro RNA


title: ILD sample 98

description:
LT235441RL
6-digit tissue label
micro RNA


title: A2 iPS cells, 2d, cholesterol deficient, biological replicate 4

description:
A2_2day_4
SLOS iPS cells removed from mTeSR1 media, 2 days culture


title: BJ iPS cells, 7d, cholesterol deficient, biological replicate 2

description:
BJ_7day_2
Control iPS cells removed from mTeSR1 media, 7 days culture

source_name: BJ iPS cells_7d_cholesterol deficient

value: BJ

value: Human iPS cells

value: wild-type (control)


title: A2 iPS cells, 0hr, cholesterol rich, biological replicate 3

description:
A2_0hr_3
SLOS iPS cells removed from MEF feeders, 20% KOSR medium


title: A2 iPS cells, 0hr, cholesterol rich, biological replicate 1

description:
A2_0hr_1
SLOS iPS cells removed from MEF feeders, 20% KOSR medium


title: ILD sample 93

description:
LT228241RL
6-digit tissue label
micro RNA


title: ILD sample 94

description:
LT228772LL
6-digit tissue label
micro RNA


title: ILD sample 95

description:
LT228897LL
6-digit tissue label
micro RNA


title: BJ iPS cells, 7d, cholesterol deficient, biological replicate 1

description:
BJ_7day_1
Control iPS cells removed from mTeSR1 media, 7 days culture


title: BJ iPS cells, 5d, cholesterol deficient, biological replicate 4

description:
BJ_5day_4
Control iPS cells removed from mTeSR1 media, 5 days culture

source_name: BJ iPS cells_5d_cholesterol deficient


title: A2 iPS cells, 2d, cholesterol deficient, biological replicate 1

description:
A2_2day_1
SLOS iPS cells removed from mTeSR1 media, 2 days culture


title: BJ iPS cells, 7d, cholesterol deficient, biological replicate 3

description:
BJ_7day_3
Control iPS cells removed from mTeSR1 media, 7 days culture


title: ILD sample 90

description:
LT221687RM
6-digit tissue label
micro RNA


title: ILD sample 89

description:
LT220661RL
6-digit tissue label
micro RNA


title: ILD sample 91

description:
LT221782LL
6-digit tissue label
micro RNA


title: BJ iPS cells, 4d, cholesterol deficient, biological replicate 4

description:
BJ_4day_4
Control iPS cells removed from mTeSR1 media, 4 days culture

source_name: BJ iPS cells_4d_cholesterol deficient


title: ILD sample 88

description:
LT214473RL
6-digit tissue label
micro RNA


title: BJ iPS cells, 4d, cholesterol deficient, biological replicate 3

description:
BJ_4day_3
Control iPS cells removed from mTeSR1 media, 4 days culture


title: BJ iPS cells, 5d, cholesterol deficient, biological replicate 2

description:
BJ_5day_2
Control iPS cells removed from mTeSR1 media, 5 days culture


title: ILD sample 87

description:
LT213606RL
6-digit tissue label
micro RNA


title: BJ iPS cells, 7d, cholesterol deficient, biological replicate 4

description:
BJ_7day_4
Control iPS cells removed from mTeSR1 media, 7 days culture