title: swd2.2delta cells-replica 2-FW and RV strands

source_name: swd2.2delta cells grown at 34°C for 3 hours, replica 2


title: swd2.2delta cells-replica 1-FW and RV strands

status: Public on Apr 17 2014

type: RNA

city: Lyon

first: Vincent

last: Vanoosthuyse

address: 46 allée d'Italie

department: Laboratoire de Biologie Moléculaire de la Cellule

country: France

institute: CNRS

description: strand-specific expression data from fission yeast cells lacking Swd2.2 grown for 3 hours at 34°C

hyb_protocol: 5 µg of cDNAs were then hybridized on a GeneChip S.pombe Tiling 1.0FR Array (Affymetrix), according to the manufacturer's instructions.

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

data_processing:
CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0
Series supplementary files contain RMA normalized data and UTR ratio
corresponds to the chromosome followed by the position on the given chromosome of the 1st nucleotide of the probe
Raw data were normalized with Partek Genomic Suite software 6.5 (Partek Inc., St. Louis, MO, US) using Robust Multiarray Average (RMA) statistical algorithm, which includes RMA background correction, quantile normalization and log2 transformation.
UTR ratios
Columns ABCDE:  Gene of interest (E) with its position on the chromosome (ABCD)
Columns FGHI: Genomic positions of the 5'UTR, the coding sequence (CDS) and the 3'UTR of the gene of interest
Columns JKL:  Average signal intensity recorded in swd2.2+ cells for the 5'UTR (column J), the CDS (column K) and the 3'UTR (column L) of the gene
Columns MNO:  Average signal intensity recorded in swd2.2delta cells for the 5'UTR (column M), the CDS (column N) and the 3'UTR (column O) of the gene
Column P UTR ratio swd2.2+: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2+ cells
Column Q UTR ratio swd2.2delta: Ratio of the average signal intensity recorded in the 3'UTR versus the CDS in swd2.2delta cells
Column R UTR ratio swd2.2delta/UTR ratio swd2.2+

label: biotin

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: swd2.2delta cells grown at 34°C for 3 hours, replica 1

label_protocol: Extracted RNA were purified using the miRNeasy mini kit (Qiagen), dosed using a nanodrop and their quality were assessed using a Bioanalyzer 2100 (Agilent). To prepare cDNAs, 250 ng of RNA were then amplified using the WT Expression Kit (Ambion). The resulting cDNAs were then dosed (nanodrop) and their quality assessed using a Bioanalyzer 2100 (Agilent). 5,5 µg of cDNAs were then fragmented and labelled using the GeneChIP WT Terminal Labelling Kit (Affymetrix)

growth_protocol: cells were grown in rich YES+ Adenine medium for one generation (3 hours) at 34°C

extract_protocol: RNA was extracted from 2.10^8 cells according to the procedure described in (Wilhelm et al., 2008; Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243.).

tag: genotype

tag: genetic background


title: Breast Cancer Sample BC1807

city: Frankfurt

first: Thomas

last: Karn

address: Theodor-Stern-Kai 7

country: Germany

description: Gene expression data from primary breast tumors

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Homo sapiens

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturers instructions

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

treatment_protocol: samples were snap frozen and stored at -80°C

tag: gender

value: female

tag: tissue

value: pretreatment surgical biopsy

tag: cohort

value: HH


title: Breast Cancer Sample BC1809


title: Breast Cancer Sample BC1804


title: Breast Cancer Sample BC1808


title: LNCaPEV_pre D

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: LNCaP cells with EV control

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

growth_protocol: LNCaP cells grown in RPMI & 10% FBS

extract_protocol: Total RNA was extracted using the QIAGEN AllPrep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

tag: cell line

value: LNCaP

tag: expression

value: vector control


title: Breast Cancer Sample BC1794


title: Breast Cancer Sample BC1806


title: Breast Cancer Sample BC1805


title: LNCaPEV_pre E

description: E


title: Swd2.2+ cells-replica 3-FW and RV strands

description: strand-specific expression data from wild-type fission yeast grown for 3 hours at 34°C

source_name: swd2.2+ cells grown at 34°C for 3 hours, replica 3


title: LNCaPHes6_pre C

description: C

source_name: LNCaP cells with Hes6 overexpression

value: Hes6 overexpression


title: Swd2.2+ cells-replica 2-FW and RV strands

source_name: swd2.2+ cells grown at 34°C for 3 hours, replica 2


title: Breast Cancer Sample BC1787


title: LNCaPHes6_pre B

description: B


title: Breast Cancer Sample BC1788


title: Swd2.2+ cells-replica 1-FW and RV strands

source_name: swd2.2+ cells grown at 34°C for 3 hours, replica 1


title: Breast Cancer Sample BC1796


title: Breast Cancer Sample BC1721


title: Breast Cancer Sample BC1782


title: Breast Cancer Sample BC1713


title: Breast Cancer Sample BC1722


title: Breast Cancer Sample BC1781


title: LNCaPHes6_pre A

description: A


title: Breast Cancer Sample BC1704


title: 8839265049_G

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

country: USA

institute: Mayo Clinic

hyb_protocol: Standard Illumina Hybridization Protocol

scan_protocol: Standard Illumina Scanning Protocol

data_processing: The image was processed using Illumina's GenomeStudio Software, and the probe level data was quantile normalized across samples with no background subtraction

source_name: Sinonasal sarcoma

label_protocol: 200ng of RNA from each sample was subjected to Human WG-DASL Assay with Human HT12 v4.0 BeadChips (Illumina)

extract_protocol: Total RNA was extracted from FFPE materials using miRNeasy FFPE Kit (Qiagen)

tag: fusion

value: PAX3 fusion


title: 8839265049_F

value: PAX3/MAML3 fusion


title: Breast Cancer Sample BC1700


title: Breast Cancer Sample BC1699


title: Breast Cancer Sample BC1685


title: 8839265049_H


title: 8839265049_C

source_name: ARMS

value: NO FUSION


title: CD34+/CD38+ CML sample #845

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix 3'IVT protocol

scan_protocol: Affymetrix 3'IVT protocol

data_processing: RMA

source_name: CML

label_protocol: Affymetrix 3'IVT protocol

extract_protocol: RNeasy mikro kit (Qiagen)

tag: cell type

value: sorted CD34+/CD38+ CML


title: Breast Cancer Sample BC1683


title: Breast Cancer Sample BC1687


title: CD34+/CD38- Cord blood sample #899

source_name: Cord blood

value: sorted CD34+/CD38- Cord blood


title: 8839265049_D


title: CD34+/CD38+ Cord Blood sample #900

source_name: Cord Blood

value: sorted CD34+/CD38+ Cord Blood


title: Breast Cancer Sample BC1698


title: 8839265049_E


title: CD34+/CD38- CML sample #844

value: sorted CD34+/CD38- CML


title: CD34+/CD38- CML sample #841


title: Breast Cancer Sample BC1682


title: CD34+/CD38- PB CML sample #422

value: sorted CD34+/CD38- PB CML


title: 8839265046_L


title: 8839265046_K

source_name: MPNST


title: CD34+/CD38+ CML sample #842


title: Breast Cancer Sample BC1677


title: 8839265046_J


title: 8839265049_B


title: Breast Cancer Sample BC1673


title: CD34+/CD38+ PB CML sample #421

value: sorted CD34+/CD38+ PB CML


title: 8839265046_I

source_name: Schwannoma


title: CD34+/CD38- CML sample #838


title: 8839265046_H

source_name: Neurofibroma


title: Breast Cancer Sample BC1671


title: 8839265046_E

source_name: DFSP


title: 8839265046_G


title: CD34+/CD38+ CML sample #839


title: Breast Cancer Sample BC1669


title: Breast Cancer Sample BC1670


title: 8839265046_D

source_name: FTS


title: Breast Cancer Sample BC1672


title: Breast Cancer Sample BC1665


title: 8839265030_L


title: 8839265046_F


title: 8839265030_K


title: 8839265030_I


title: 8839265030_J


title: Breast Cancer Sample BC1663


title: Breast Cancer Sample BC1657


title: Breast Cancer Sample BC1662


title: 8839265030_E

source_name: Melanoma


title: Breast Cancer Sample BC1659

source_name: primary breast cancer tissue


title: Breast Cancer Sample BC1431


title: Breast Cancer Sample BC1434


title: 8839265030_D


title: 8803836089_L


title: Breast Cancer Sample BC1667


title: 8803836089_K

source_name: SYT


title: 8839265030_F

source_name: GIST


title: 8803836089_J


title: 8803836089_I


title: Breast Cancer Sample BC1430


title: Mixture of cancer and normal tissue from patient 1,2,5

city: Nanjing

first: Wen

last: Zhu

state: Jiangsu

address: 300 Guangzhou Road

department: Respiratory Medicine

country: China

institute: The First Affiliated Hospital, Nanjing Medical University

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: After a filtering procedure, 39000 human lncRNAs ( 4765 from RefSeq, 12754 from ENSEMBL, 8195 lincRNA from John Rinn lab, 1289 from NRED (ncRNA Expression Database), 17203 from H-InvDB, 2975 from ENCODE, 529 from CombinedLit, 1053 from Antisense ncRNA pipeline, 407 Hox ncRNAs, 481 UCRs, and 848 from Chen Ruisheng lab (Institute of Biophysics, Chinese Academy of Science). ) were selected for the following analysis. We first did quantile normalization for the microarray data (containing the 39000 lncRNAs and 32000 mRNAs in the microarray) of 4 paired tumor-normal samples. Then, the data was log2-scale transformed. Missing values were imputed using the random forest unsupervised classification algorithm (details are described in Supplementary Methods).

source_name: Mixture of cancer  tissue from patient 1,2,5

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: pulmonary adenocarcinoma

tag: patient number

source_name: Mixture of adjacent normal tissue from patient 1,2,5

value: normal lung tissue


title: Cancer and normal tissue from patient 5

source_name: Cancer tissue from patient 5

source_name: Adjacent normal tissue from patient 5


title: Cancer and normal tissue from patient 2

source_name: Cancer tissue from patient 2

source_name: Adjacent normal tissue from patient 2


title: Cancer and normal tissue from patient 1

source_name: Cancer tissue from patient 1

source_name: Adjacent normal tissue from patient 1


title: 8803836089_F


title: 8803836089_G


title: 8803836075_H

source_name: Rhabdomyosarcoma, embryonal


title: 8803836075_I


title: STAP-2-/-, biological rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description:
KO1
Acute colitis model was induced to STAP-2-/- mice by addition of 1.75% DSS in drinking water for 7 days.
Pool from 3 mice.

hyb_protocol: After labeling, rates of dye incorporation and quantification were measured with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and were then fragmented for 30 min at 60°C in the dark. The labeled 1,650 ng of each cRNA sample was then hybridized on Agilent 4 × 44K whole mouse genome arrays (Agilent Design #026655) at 65°C for 17 h with rotation in the dark. Hybridization was performed using a Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: After washing in GE washing buffer, slides were scanned with an Agilent Microarray Scanner G2505C.

data_processing: Feature Extraction software (Version 10.7.1.1) employing defaults for all parameters was used to convert images into gene expression data. Raw data were imported into GeneSpring GX 12.0 (Agilent Technologies) for database management and quality control. For normalization in GeneSpring, the threshold raw signal was set to 1.0 and the global normalization algorithm (percentile shift) was used with a percentile target of 75. This normalized data was used for identifying differentially expressed genes, in which KO group were compared to WT group as control.

organism: Mus musculus

source_name: DSS-treated colons derived from STAP-2-/- mice

label_protocol: One hundred nanogram of total RNA with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent Technologies) was reverse transcribed into double strand cDNAs by AffinityScript multiple temperature reverse transcriptase and amplified for 2 h at 40°C. Resulting cDNAs were subsequently used for in vitro transcription by T7-polymerase and labeled with cyanine-3-labeled cytosine triphosphate (Perkin Elmer) for 2 h at 40°C using a Low Input Quick-Amp Labeling Kit ver. 6.5 (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA of the entire colon tissues, which was immediately stored in RNAlater solution at -80 °C (Life Technologies, Carlsbad, CA), was purified using TissueLyser at 20 Hz and RNeasy kit (QIAGEN, Venlo, Netherlands) according to the manufacturer's instructions.

treatment_protocol: Wild type (WT) and STAP-2-/- mice were administered 1.75% DSS for 3 days and sacrificed to isolate mRNA from colon tissue.

tag: strain/background

tag: genotype/variation

tag: age

value: fourteen weeks

value: colon

tag: treatment

value: DSS


title: 8803836075_E


title: 8803836089_E


title: 8803836089_B

source_name: Sinonasal sarcoma


title: 8803836075_D

source_name: BFH


title: STAP-2-/-, biological rep2

description:
KO2
Acute colitis model was induced to STAP-2-/- mice by addition of 1.75% DSS in drinking water for 7 days.
Pool from 3 mice.


title: 8803836075_F

source_name: Schwannoma


title: 8803836089_H


title: 8803836089_C


title: WT, biological rep1

description:
WT1
Acute colitis model was induced to WT mice by addition of 1.75% DSS in drinking water for 7 days.
Pool from 3 mice.

source_name: DSS-treated colons derived from WT mice

value: wild type


title: whirly cells alone

city: Stockholm

first: Hayrettin

last: Guven

address: Nobels Vag 16

department: MTC

country: Sweden

institute: Karolinska Institute

hyb_protocol: Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan scanner.

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.3.1) using the RMA method.

source_name: Immortalized human foreskin fibroblast cells

label_protocol: 150ng total RNA was used to generate sense strand cDNA using Ambion WT Expression kit that was fragmented and biotinylated using Affymetrix Gene Chip WT Terminal Labeling Kit.

growth_protocol: Whirly  cells were plated (0.5 X 106) in 10 cm dishes coated with collagen (Rat tail) (Corning) in IMDM medium for 5 days.

extract_protocol: Total RNA was prepared from 5-day-old monolayers of Whirly fibroblasts using Ambion's RNAqueous-4PCR kit (Invitrogen).

treatment_protocol: Cells were trypsinized in trypsin-EDTA solution and then washed once with complete medium and once with PBS.

tag: clone

value: whirly

value: BJhTERT


title: 8803836075_C


title: 8803836075_G


title: 8803836075_B


title: whirly cells confronted with PC3 mRFP cells

value: confronted with PC3 mRFP cells


title: WT, biological rep2

description:
WT2
Acute colitis model was induced to WT mice by addition of 1.75% DSS in drinking water for 7 days.
Pool from 3 mice.


title: Pooled sample at d5, left plantaris, young mice

status: Public on Apr 16 2014

city: Lexington

last: Chaillou

state: KY

address: University of Kentucky, Department of Physiology, 800 Rose Street

institute: Department of Physiology

description: Gene expression data from left plantaris muscle, d5

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL data were generated using Affymetrix Command Console software and the data analysis was performed using Partek Genomics Suite.

source_name: Left plantaris muscle, d5

label_protocol: Biotinylated cDNA were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (Ambion WT Expression kit and Affymetrix WT Terminal Labeling kit).

growth_protocol: Male C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME), 5 months of age were housed in a temperature- and humidity-controlled facility on a 14:10 h light:dark cycle with access to food and water ad libitum

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

tag: time

value: Skeletal muscle

tag: strain

value: 5 months


title: Pooled sample at d3, left plantaris, young mice

description: Gene expression data from left plantaris muscle, d3

source_name: Left plantaris muscle, d3


title: Pooled sample at d7, left plantaris, young mice

description: Gene expression data from left plantaris muscle, d7

source_name: Left plantaris muscle, d7


title: CGS27023A and BIPBIPU 4

city: Yokohama

first: shunsuke

last: iriyama

address: 2-2-1, Hayabuchi, Tsuzuki-ku,

institute: Shiseido Research Center

description: Gene expression by treatment of CGS27023A and BIPBIPU of epidermis after 4 days

hyb_protocol: 1.65 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 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Epidermis of skin equivalent, CGS27023A and BIPBIPU, Day4, replicate 4

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

extract_protocol: RNA was prepared using the Isogen reagent (Nippon Gene, Toyama, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Skin equivalent model (EFT-400, MatTek) was cultured in medium EFT-400-ASY with CGS27023A and/or BIPBIPU.

value: keratinocyte in epidermis of skin equivalent model


title: Pooled sample at d10, left plantaris, young mice

description: Gene expression data from left plantaris muscle, d10

source_name: Left plantaris muscle, d10


title: Pooled sample at d14, left plantaris, young mice

description: Gene expression data from left plantaris muscle, d14

source_name: Left plantaris muscle, d14


title: CGS27023A and BIPBIPU 3

source_name: Epidermis of skin equivalent, CGS27023A and BIPBIPU, Day4, replicate 3


title: Pooled sample at d1, left plantaris, young mice

description: Gene expression data from left plantaris muscle, d1

source_name: Left plantaris muscle, d1


title: BIPBIPU 3

description: Gene expression by treatment of BIPBIPU of epidermis after 4 days

source_name: Epidermis of skin equivalent, BIPBIPU, Day4, replicate 3


title: CGS27023A 4

description: Gene expression by treatment of CGS27023A of epidermis after 4 days

source_name: Epidermis of skin equivalent, CGS27023A, Day4, replicate 4


title: BIPBIPU 1

source_name: Epidermis of skin equivalent, BIPBIPU, Day4, replicate 1


title: CGS27023A and BIPBIPU 1

source_name: Epidermis of skin equivalent, CGS27023A and BIPBIPU, Day4, replicate 1


title: USC_pt8_week24

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, washing and scanning were performed according to the manufacturer's instructions.

scan_protocol: BeadArrays were  scanned using an Illumina BeadArray Reader. Scanner settings were set at a default for DirectHyb.

data_processing: Raw data were extracted using Illumina Genometudio Gene Expression Module v1.1. The data were transformed using variance stabilizing transformation (vst) and normalised using robust spline normalization with Bioconductor package lumi in R. Gene filtering was applied to retain only genes with IQR>0.5 (measure of the spread of the middle 50% of the intensity scores for each gene > 0.5 on a log base 2 scale). Technical batch effects associated with sample collection at three different sites were removed using ComBat (Johnson and Rabinovic, Biostatistics, 2007).

source_name: primary CD4+ T cells

label_protocol: Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini (>1 million cells) or micro (≤1 million cells) kit in accordance with the prescribed protocol provided with the kits. Quality control was performed with Agilent 2100 Bioanalyzer.

value: primary CD4+ T cells

value: Maraviroc

tag: infection

value: HIV

tag: patient id

tag: recruitment site

value: USC

tag: time point

value: week 24


title: USC_pt9_week0

value: baseline

value: week 0


title: BIPBIPU 4

source_name: Epidermis of skin equivalent, BIPBIPU, Day4, replicate 4


title: Pooled sample at d0 (control obtained after 2 weeks of hindlimb suspension), left plantaris, young mice

description: Gene expression data from left plantaris muscle, d0

source_name: Left plantaris muscle, d0

tag: tissue


title: Control 4

description: Gene expression of epidermis after 4 days

source_name: Epidermis of skin equivalent, control Day4, replicate 4


title: CGS27023A 2

source_name: Epidermis of skin equivalent, CGS27023A, Day4, replicate 2


title: USC_pt8_week0


title: USC_pt8_week4

value: week 4


title: USC_pt9_week24


title: USC_pt9_week4


title: Control 2

source_name: Epidermis of skin equivalent, control Day4, replicate 2


title: CGS27023A 1

source_name: Epidermis of skin equivalent, CGS27023A, Day4, replicate 1


title: Control 3

source_name: Epidermis of skin equivalent, control Day4, replicate 3


title: BIPBIPU 2

source_name: Epidermis of skin equivalent, BIPBIPU, Day4, replicate 2


title: USC_pt7_week4


title: USC_pt4_week24


title: USC_pt5_week24


title: USC_pt5_week0


title: USC_pt5_week4


title: USC_pt1_week4


title: USC_pt7_week24


title: UCLA_pt13_week24

value: UCLA


title: USC_pt7_week0


title: USC_pt4_week4


title: UCLA_pt15_week0


title: USC_pt1_week0


title: UCLA_pt15-week4


title: USC_pt3_week0


title: UCLA_pt15_week24


title: USC_pt1_week24


title: UCLA_pt12_week4


title: UCLA_pt12_week24


title: LS723 Salt A

city: Laurel

first: Atin

last: Datta

state: MD

address: 8301 Muirkirk Rd

department: CFSAN/DVA

institute: FDA

description: LS723 Salt A.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ListeriaChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with RMA using R/bioconductor.

label: Biotin

organism: Listeria monocytogenes

source_name: ∆lstC_mid-log BHI with 7% NaCl 37°C

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

growth_protocol: Cultures were grown to mid-log phase (Abs600 = 0.0.5 ± 0.05) in BHI broth or BHI broth with 7% NaCl at 37°C.

extract_protocol: RNA was extracted using the Ambion RiboPure Bacterial kit following the manufacturer's protocol except for the use of a 20 minute cell disruption step.

treatment_protocol: Bacterial cells were collected via centrifugation, discarding the supernatant. The pellet was then immediately processed via the extract protocol.

value: ∆lstC mutant

tag: culture condition

value: high salt; BHI with 7% NaCl at 37°C

tag: growth phase

value: mid-long


title: UCLA_pt13_week0


title: UCLA_pt13_week4


title: USC_pt4_week0


title: UCLA_pt12_week0


title: UCLA_pt10_week24


title: USC_pt3_week24


title: USC_pt3_week4


title: LS723 Salt C

description: LS723 Salt C.CEL


title: LS723 Salt B

description: LS723 Salt B.CEL


title: LS723 Reg C

description: LS723 Reg C.CEL

source_name: ∆lstC_mid-log BHI 37°C

value: normal; BHI at 37°C


title: UCLA_pt10_week4


title: UCLA_pt9_week24


title: UCLA_pt9_week4


title: UCLA_pt9_week0


title: UCLA_pt8_week0


title: UCLA_pt8_week24


title: UCLA_pt8_week4


title: UCLA_pt10_week0


title: LS723 Reg B

description: LS723 Reg B.CEL


title: UCLA_pt6_week4


title: LS723 Reg A

description: LS723 Reg A.CEL


title: UCLA_pt5_week0


title: UCLA_pt6_week24


title: LS411 Salt C

description: LS411 Salt C.CEL

source_name: WT_mid-log BHI with 7% NaCl 37°C

value: wild type


title: LS411 Salt A

description: LS411 Salt A.CEL


title: UCLA_pt4_week24


title: UCLA_pt5_week4


title: LS411 Salt B

description: LS411 Salt B.CEL


title: UCLA_pt6_week0


title: UCLA_pt5_week24


title: LS411 Reg C

description: LS411 Reg C.CEL

source_name: WT_mid-log BHI 37°C


title: LS411 Reg B

description: LS411 Reg B.CEL


title: gastric normal 5

city: Changchun

first: Jihan

last: Wang

address: 126, Xinmin Street

institute: Jilin University

hyb_protocol: the labeled cDNA samples were used as probes to hybridize to the array chips by incubation at 45℃ and rotated at 60rpm for 17 h with Eukaryotic Hybridization Control Kit and Hybridization, Wash and Stain Kit(affymetrix),Fluidics washing is Hybridization, Wash and Stain KitFS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software.using RMA to get the gene core signal from each probe.
probe group file: HuEx-1_0-st-v1.r2.pgf
meta-probeset file: HuEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: human

label_protocol: 1 μg RNA template was used to reversely transcribed into cDNA and cDNA samples were digested into cDNA fragments with endonucleases and then labeled with the IVT labeling Kit provided by Affymetrix

growth_protocol: tissues dissected from surgery patients

extract_protocol: Tissue RNA was isolated using Trizol and further purified using the RNeasy Mini kit according to the manufacturer’s instructions.

treatment_protocol: All tissues were taken from surgery room and snap-frozen and stored in liquid nitrogen within 10 min after the resection, for RNA extraction.

tag: gender

value: female

value: normal


title: UCLA_pt4_week0

tag: cell type


title: UCLA_pt3_week24


title: LS411 Reg A

description: LS411 Reg A.CEL


title: gastric normal 4


title: UCLA_pt4_week4


title: CGS27023A 3

source_name: Epidermis of skin equivalent, CGS27023A, Day4, replicate 3

value: keratinocyte in epidermis of skin equivalent model


title: UCLA_pt3_week0

value: primary CD4+ T cells


title: gastric normal 3


title: UCLA_pt2_week24

value: Maraviroc


title: UCSD_pt11_week24

value: HIV

value: UCSD


title: UCLA_pt2_week0


title: UCLA_pt2_week4


title: gastric normal 1


title: UCLA_pt3_week4


title: UCSD_pt9_week24

value: week 24


title: gastric cancer 5

value: gastric cancer


title: UCSD_pt10_week4


title: UCSD_pt10_week0

value: baseline

value: week 0


title: UCSD_pt11_week4

value: week 4


title: gastric normal 2

value: male


title: UCSD_pt9_week4


title: CGS27023A and BIPBIPU 2

source_name: Epidermis of skin equivalent, CGS27023A and BIPBIPU, Day4, replicate 2


title: UCSD_pt8_week24


title: UCSD_pt9_week0


title: gastric cancer 3


title: gastric cancer 1


title: gastric cancer 4


title: UCSD_pt10_week24


title: gastric cancer 2


title: UCSD_pt6_week4


title: Control 1

source_name: Epidermis of skin equivalent, control Day4, replicate 1


title: UCSD_pt8_week0

source_name: primary CD4+ T cells


title: UCSD_pt5_week24


title: UCSD_pt2_week24


title: UCSD_pt5_week0


title: UCSD_pt6_week0


title: UCSD_pt2_week0


title: UCSD_pt8_week4


title: UCSD_pt1_week24


title: UCSD_pt1_week0


title: siSRC1 without glucose, biological rep2

city: Houston

first: David

last: Lonard

state: TX

address: 1 Baylor Plaza

department: Mol & Cell Biology-Mol.Regulation

institute: Baylor College of Medicine

description: siSRC-1 without glucose

hyb_protocol: 15 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Genome Array. GeneChips were washed, then stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000.

data_processing: The data were analyzed using RMAExpress Version: 1.0.4 with default analysis settings.

source_name: A549 Cells

label_protocol: Biotinylated cRNA was produced using the standard Affymetrix protocol.

growth_protocol: A549 cell lines were cultured in DMEM supplemented with 10% fetal calf serum (FCS), penicillin, and streptomycin (100 U/mL). Twenty-four hours prior to transfection, A549 cells were plated in 6-well plates.

extract_protocol: RNAs was isolated using the RNeasy mini Kit (QIAGEN).

treatment_protocol: Cells were transfected with control or SRC-1 targeting siRNA using DharmaFECT 1 according to the manufacturer's protocol. Transfected cells were changed to medium supplemented with 10% dialyzed FCS and incubated for 36 hours before the indicated treatment with DMEM with or without glucose supplemented with 10% dialyzed FCS.

value: siSRC1 without glucose

tag: cell line


title: UCSD_pt2_week4


title: siSRC1 with glucose, biological rep1

description: siSRC-1 with glucose

value: siSRC1 with glucose


title: A4 Replicate 2

city: College Station

first: James

last: Winkler

address: 3122 TAMU

institute: Texas A&M University

description:
Fitness Calculation: Mutant growth rate / WT growth rate - 1
Conditions: 0.65 M NaCl, minimal media + glucose (0.5% w/v) + 50 ug/ml tryptophan
Measurement: 96 well plate, TECAN Infinite M200

hyb_protocol: Microarray samples were hybridized and washed according to the manufacturer's instructions for two color prokaryotic microarrays.

scan_protocol: Slides were scanned with an Axon 4200A GenePix Scanner at 5um resolution. PMT was equal to 600 for both dye channels

data_processing: Data were normalized using the LOWESS algorithm and analyzed for statistical significance using the MeV package

organism: Escherichia coli

source_name: A4, osmotolerant mutant

label_protocol: RNA was converted to amino-allyl cDNA using Superscript III RT, purified by ethanol precipitation, and resuspended in dye coupling buffer. Cy3 and Cy5 were utilized to label the experimental samples and reference as specified by GE Amersham.

growth_protocol: Grown in glucose M9 media supplemented with 0.55 M NaCl

extract_protocol: Samples were grown to mid exponential phase (OD approx 0.5). Cultures were then harvested with rapid filtration and resuspended in RNALater to stop RNA degradation. The Zymo Quick-RNA miniprep kit was used to extract pure RNA for subsequent analysis

value: Adaptive mutant

tag: population

tag: average fitness

organism: Escherichia coli BW25113

value: unevolved parent strain

tag: strain description

value: E. coli BW25113 with F oriTs integrated at mbhA and hyfC


title: sictrl  without glucose, biological rep2

description: siControl without glucose

tag: treatment

value: sictrl  without glucose


title: sictrl with glucose, biological rep1

description: siControl with glucose

value: sictrl with glucose


title: siSRC1 with glucose, biological rep2

description: siSRC-1 with glucose


title: sictrl without glucose, biological rep1

description: siControl without glucose

value: sictrl without glucose


title: A4 Replicate 1

tag: genotype/variation


title: Fibroblast PLS patient 36

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description:
FBpat36
Gene expression data from human fibroblasts

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 Plus 2.0 Array (Affymetrix)  in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

source_name: Human fibroblasts from PLS case 36

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: Qiagen RNeasy Extraction Kit was used for RNA extraction according to manufacturers' instructions

value: skin

value: fibroblasts

tag: disease

value: primary lateral sclerosis (PLS)


title: siSRC1 without glucose, biological rep1

description: siSRC-1 without glucose


title: Fibroblast sporadic ALS case 23

description:
FBpat23
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 23

value: sporadic amyotrophic lateral sclerosis (SALS)


title: sictrl with glucose, biological rep2

description: siControl with glucose


title: Fibroblast sporadic ALS case 31

description:
FBpat31
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 31


title: Fibroblast PLS patient 25

description:
FBpat25
Gene expression data from human fibroblasts

source_name: Human fibroblasts from PLS case 25


title: Fibroblast sporadic ALS case 26

description:
FBpat26
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 26


title: Fibroblast PLS patient 22

description:
FBpat22
Gene expression data from human fibroblasts

source_name: Human fibroblasts from PLS case 22


title: Fibroblast sporadic ALS case 27

description:
FBpat27
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 27


title: Fibroblast sporadic ALS case 21

description:
FBpat21
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 21


title: A2 Replicate 1

source_name: A2, osmotolerant mutant

tag: strain


title: G6 Replicate 2

source_name: G6, osmotolerant mutant

value: E. coli BW25113 with an integrated F tra operon at the trp locus, plus additional F oriT sequences integrated at mbhA and hyfC


title: A2 Replicate 2


title: G5 Replicate 1

source_name: G5, osmotolerant mutant


title: Fibroblast PLS patient 16

description:
FBpat16
Gene expression data from human fibroblasts

source_name: Human fibroblasts from PLS case 15


title: Fibroblast Control case 14

description:
FBCon14
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 14


title: G5 Replicate 2


title: G3 Replicate 1

source_name: G3, osmotolerant mutant


title: G2 Replicate 1

source_name: G2, osmotolerant mutant


title: G2 Replicate 2


title: Fibroblast UMND case 20

description:
FBpat20
Gene expression data from human fibroblasts

source_name: Human fibroblasts from UMND case 20

value: UMND


title: Fibroblast sporadic ALS case 18

description:
FBpat18
Gene expression data from human fibroblasts

source_name: Human fibroblasts from sporadic ALS case 18


title: G6 Replicate 1


title: Fibroblast Control case 13

description:
FBCon13
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 13


title: Fibroblast Control case 2

description:
FBCon2
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 2


title: G3 Replicate 2


title: Fibroblast Control case 11

description:
FBCon11
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 11


title: UCSD_pt6_week24

source_name: primary CD4+ T cells

value: primary CD4+ T cells

value: Maraviroc

tag: infection

value: HIV

value: UCSD

value: week 24


title: Fibroblast Control case 3

description:
FBCon3
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 3


title: Fibroblast PLS patient 15

description:
FBpat15
Gene expression data from human fibroblasts


title: 48 hr negative control + insulin 5

status: Public on Apr 15 2014

city: Ottawa

first: Ella

last: Atlas

state: Ontario

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Sample 34

hyb_protocol: Samples were hybridized to Agilent SurePrint G3 Human Gene Expression 8X60K microarrays (Agilent Technologies) for 17 hours at 65C with a rotation speed of 10 rpm, washed according to the manufacturer’s instructions

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: preadipocyte_vehicle control (ethanol) and 100nM insulin for 48 hrs

label_protocol: Biological samples were labelled with cyanine 5-CTP (Cy5) dye, while the commercially available Stratagene human reference RNA was labelled with cyanine 3-CTP (Cy3) dye.

growth_protocol: Primary human preadipocytes (purchased from Zenbio, Inc., Research Triangle Park, NC) from donors with body mass indices < 24.99 were maintained in Preadipocyte Medium (ZenBio) at 37C and 5% CO2 according to the supplier's instructions.

extract_protocol: Total RNA was extracted and DNase treated using RNeasy Mini Plus Kits (Qiagen, Mississauga, Canada). Quantification of RNA was performed using a NanoDrop 2000 (Thermo Scientific, Waltham, USA) and RNA quality was determined using a BioAnalyzer (Agilent Technologies, Santa Clara, USA). RNA samples with A260/A280 ratios > 1.8 and RNA integrity numbers (RIN) > 8.0 were used in this study. Total RNA was used for subsequent microarray hybridization and real-time PCR analysis.

treatment_protocol: Confluent preadipocytes were treated with media containing 500 µM 3-isobutyl-1-methylxanthine (IBMX), 33 µM biotin  17 µM pantothenate (all Sigma-Aldrich, St Louis, MO) and 100 nM insulin (Roche Applied Science) for 2 days. On day 2, 5 µM troglitazone (Sigma-Aldrich) was added with or without 100 nM insulin to the media with either 50 µM BPA or 1 µM dexamethasone (DEX) (Sigma-Aldrich) or vehicle (ethanol). On day 4 (48 hours post-exposure), cells were washed, pelleted and used for RNA isolation. Also included was a 1 µM dexamethasone (DEX) with insulin treated sample at 96 hours post-treatment.

tag: gender (donor)

value: female

value: Differentiating human primary preadipocyte

tag: treated with

value: vehicle control (ethanol) and 100nM insulin for 48 hours

source_name: reference RNA

tag: sample type

value: Stratagene human reference RNA


title: 48 hr DEX 4

description: Sample 31

source_name: preadipocyte_1 uM DEX and 100 nM insulin for 48 hrs

value: 1 uM dexamethasone (DEX) and 100 nM insulin for 48 hours


title: 48 hr 25 uM BPA + insulin 5

description: Sample 37

source_name: preadipocyte_25 uM BPA and 100 nM insulin for 48 hrs

value: 25 uM bisphenol A (BPA) and 100 nM insulin for 48 hours


title: 48 hr 50 uM BPA + insulin 4

description: Sample 30

source_name: preadipocyte_50 uM BPA and 100 nM insulin for 48 hrs

value: 50 uM bisphenol A (BPA) and 100 nM insulin for 48 hours


title: Fibroblast Control case 1

description:
FBCon1
Gene expression data from human fibroblasts

source_name: Human fibroblasts from control case 1

tag: tissue

value: skin

value: fibroblasts


title: UCSD_pt11_week0

value: baseline

tag: patient id

tag: recruitment site

tag: time point

value: week 0


title: 48 hr 50 uM BPA + insulin 5

description: Sample 38

tag: cell type


title: 96 hr DEX 5

description: Sample 40

source_name: preadipocyte_1 uM DEX and 100 nM insulin for 96 hrs

value: 1 uM dexamethasone (DEX) and 100 nM insulin for 96 hours


title: 48 hr negative control 5

description: Sample 33

source_name: preadipocyte_vehicle control (ethanol) for 48 hrs

value: vehicle control (ethanol) for 48 hours


title: 48 hr 25 uM BPA 4

description: Sample 27

source_name: preadipocyte_25 uM BPA for 48 hrs

value: 25 uM bisphenol A (BPA) for 48 hours


title: 48 hr 25 uM BPA + insulin 4

description: Sample 29


title: 96 hr DEX 4

description: Sample 32


title: 48 hr 25 uM BPA 5

description: Sample 35


title: 48 hr negative control + insulin 3

description: Sample 18


title: 48 hr negative control 4

description: Sample 25


title: 48 hr 25 uM BPA + insulin 3

description: Sample 21


title: 48 hr DEX 5

description: Sample 39


title: 48 hr 50 uM BPA 3

description: Sample 20

source_name: preadipocyte_50 uM BPA for 48 hrs

value: 50 uM bisphenol A (BPA) for 48 hours


title: 96 hr DEX 2

description: Sample 16


title: 96 hr DEX 3

description: Sample 24


title: 48 hr negative control + insulin 4

description: Sample 26


title: 48 hr 25 uM BPA 3

description: Sample 19


title: 48 hr 50 uM BPA 4

description: Sample 28


title: 48 hr negative control 3

description: Sample 17


title: 48 hr DEX 3

description: Sample 23


title: 48 hr 50 uM BPA + insulin 2

description: Sample 14


title: 48 hr DEX 2

description: Sample 15


title: 48 hr 50 uM BPA 5

description: Sample 36


title: 48 hr 50 uM BPA + insulin 3

description: Sample 22


title: UCSD_pt1_week4

value: primary CD4+ T cells

value: Maraviroc

value: HIV

value: UCSD

value: week 4


title: 48 hr DEX 1

description: Sample 7

value: female

value: Differentiating human primary preadipocyte

value: Stratagene human reference RNA


title: 48 hr negative control 2

description: Sample 9


title: 48 hr 50 uM BPA + insulin 1

description: Sample 6

value: 50 uM bisphenol A (BPA) and 100 nM insulin for 48 hours


title: 48 hr 25 uM BPA 2

description: Sample 11


title: 48 hr 50 uM BPA 2

description: Sample 12


title: 48 hr negative control + insulin 2

description: Sample 10

value: vehicle control (ethanol) and 100nM insulin for 48 hours


title: 48 hr negative control 1

description: Sample 1


title: 48 hr 25 uM BPA + insulin 1

description: Sample 5

value: 25 uM bisphenol A (BPA) and 100 nM insulin for 48 hours


title: 48 hr 25 uM BPA 1

description: Sample 3


title: 48 hr 25 uM BPA + insulin 2

description: Sample 13


title: human colon, sample 46

city: Chicago

first: Sonia

last: Kupfer

state: IL

address: 900 East 57th Street, MB#9

department: Department of Medicine

institute: University of Chicago

description: Distal colonic biopsies from healthy African American subjects

data_processing: The Illumina GenomeStudio software was used to extract the signal intensities of each gene expression probe, which were then further preprocessed using the lumi package of Bioconductor in R. The preprocessing included background correction of the gene expression data, followed by variance-stabilizing transformation (VST), log2-transformation and quantile normalization. BLAT was used to map the probe sequences onto the RefSeq transcriptome. All probes mapping to multiple Entrez Gene IDs were excluded, and only probes with unique perfect matches to autosomal genes were kept. Probes that encompass a common SNP (MAF ≥ 5%) in either 1000 Genomes AFR or EUR populations were further excluded. Lastly, probes with an Illumina detection p-value < 0.01 in at least one individual were kept.

source_name: colon

label_protocol: Ambion MessageAmp kit for Illumina arrays

extract_protocol: Maxwell 16 Tissue LEV Total RNA Purification Kit (Promega)

value: colon

tag: batch

tag: gender

value: M

value: yes


title: human colon, sample 41


title: human colon, sample 43


title: human colon, sample 44


title: 48 hr negative control + insulin 1

description: Sample 2


title: human colon, sample 47


title: human colon, sample 40


title: human colon, sample 48


title: human colon, sample 38


title: 96 hr DEX 1

description: Sample 8

value: 1 uM dexamethasone (DEX) and 100 nM insulin for 96 hours


title: human colon, sample 39


title: human colon, sample 42


title: human colon, sample 37


title: human colon, sample 27


title: human colon, sample 36


title: human colon, sample 33


title: human colon, sample 25


title: human colon, sample 26


title: human colon, sample 22


title: human colon, sample 18


title: human colon, sample 23


title: human colon, sample 20


title: human colon, sample 28


title: human colon, sample 19


title: human colon, sample 21


title: human colon, sample 14


title: human colon, sample 15


title: human colon, sample 13


title: human colon, sample 32


title: human colon, sample 11


title: KK10-specific CD8+ T cells No Pept Pt 289151

first: Gaurav

middle: Das

last: Gaiha

state: MA

address: 400 Technolology Square

department: Ragon Institute

institute: Massachusetts General Hospital

description:
HIV-specific CD8+ T cells No Pept
3671 -  289151 No Pept.AVG_Signal

hyb_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol

data_processing: Quantile Normalized  & Background Subtracted

growth_protocol: RPMI-1640, with 10% FBS

extract_protocol:
Nugen Pico Amplification/Labeling
Ambion RNAqueous micro kit, catalogue number AM1931

treatment_protocol:
No Peptide
10 ng/mL of KK10 peptide

value: KK10-specific CD8+ T cells


title: human colon, sample 6


title: human colon, sample 5


title: human colon, sample 10

value: F


title: human colon, sample 7


title: human colon, sample 2


title: human colon, sample 9


title: human colon, sample 4


title: human colon, sample 1


title: human colon, sample 24


title: human colon, sample 8


title: Bulk CD8 T cells Pt 289151

description:
Bulk CD8+ T cells
3673 -  289151 Bulk.AVG_Signal

scan_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol

treatment_protocol:
Bulk
10 ng/mL of KK10 peptide

value: Bulk CD8+ T cells


title: KK10-specific CD8+ T cells No Pept Pt 529440

description:
HIV-specific CD8+ T cells No Pept
3677 -  529440 No Pept.AVG_Signal

label_protocol: Per Washington University Microarray Core Laboratory Illumina BeadArray Protocol


title: KK10-specific CD8+ T cells +Pept Pt 289151

description:
HIV-specific CD8+ T cells +Pept
3672 -  289151 Pept.AVG_Signal

treatment_protocol:
Peptide
10 ng/mL of KK10 peptide


title: KK10-specific CD8+ T cells +Pept Pt 690641

description:
HIV-specific CD8+ T cells No Pept
3675 -  690641 Pept.AVG_Signal


title: human colon, sample 3


title: human colon, sample 12


title: Bulk CD8 T cells Pt 690641

description:
Bulk CD8+ T cells
3676 -  690641 Bulk.AVG_Signal


title: Bulk CD8 T cells Pt 529440

description:
Bulk CD8+ T cells
3679 -  529440 Bulk.AVG_Signal


title: PANC-1_GW3

first: Nicholes

last: Candelaria

state: Texas

address: 3605 Cullen Boulevard SERC (Building 545), Rm 3023

department: Cellular and Molecular Biology

institute: University of Houston

description: GW3965-treated, 72 hours, replicate 3

data_processing: Data was normalized and background-corrected using R Program, lumi package. Comparisons were done with R program limma package. For our analyses, only probes that align to a single gene on the human genome as defined by Ensembl were used in the final data set.

source_name: pancreatic gland, pancreus, adenocarcinoma, epithelial

label_protocol: cRNA were prepared and labeled with Cy3 dye using Illumina TotalPrep-96RNA Amplification Kit and Illumina Whole-Genome Gene Expression Direct Hybridisation Kit

growth_protocol: BxPC-3 cells were propogated in DMEM/F12 media, whereas MIA-PaCa-2 and PANC-1 cells were maintained in DMEM. All cell culture media was supplemented with 10% FBS.

extract_protocol: RNA was extracted using the Qiagen Rneasy Kit.

treatment_protocol: Cells were treated with 10 μM GW 3965 or ethanol (vehicle) for 72 hours prior to harvest and RNA isolation.

tag: cell line

tag: p53 status

value: Negative

tag: agent


title: PANC-1_GW2

description: GW3965-treated, 72 hours, replicate 2


title: KK10-specific CD8+ T cells +Pept Pt 476597

description:
HIV-specific CD8+ T cells +Pept
3681 -  476597 Pept.AVG_Signal


title: PANC-1_Control2

description: Untreated control, replicate 2

value: ethanol (vehicle)


title: KK10-specific CD8+ T cells No Pept Pt 690641

description:
HIV-specific CD8+ T cells No Pept
3674 -  690641 No Pept.AVG_Signal


title: PANC-1_Control3

description: Untreated control, replicate 3


title: PANC-1_GW1

description: GW3965-treated, 72 hours, replicate 1


title: KK10-specific CD8+ T cells No Pept Pt 476597

description:
HIV-specific CD8+ T cells +Pept
3680 -  476597 No Pept.AVG_Signal


title: MIA-PaCa-2_GW3

description: GW3965-treated, 72 hours, replicate 3


title: PANC-1_Control1

description: Untreated control, replicate 1


title: MIA-PaCa-2_Control2

description: Untreated control, replicate 2


title: BxPC-3_GW3

description: GW3965-treated, 72 hours, replicate 3


title: MIA-PaCa-2_Control3

description: Untreated control, replicate 3


title: MIA-PaCa-2_GW1

description: GW3965-treated, 72 hours, replicate 1


title: MIA-PaCa-2_Control1

description: Untreated control, replicate 1


title: BxPC-3_GW1

description: GW3965-treated, 72 hours, replicate 1


title: BxPC-3_Control3

description: Untreated control, replicate 3


title: BxPC-3_Control1

description: Untreated control, replicate 1


title: BxPC-3_Control2

description: Untreated control, replicate 2


title: female frontal cortex rep6

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description: 3153 12 cortex female M115 5_17

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Partek Genomics Suite  Incorporated, Saint Louis, MO) for further characterization of sexually dimorphic geneexpression in female cerebella.

source_name: female_frontal cortex

label_protocol: 100ng of total RNA was used to produce an amplified pool of biotin-labeled RNA corresponding to the polyadenylated-mRNA fraction.

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

value: SJL/JOrlCrl

tag: Sex

tag: age

value: 10 weeks

value: frontal cortex


title: male cerebellum rep5

description: 3158 17 cerebellum male M108 5_17

tag: strain

value: male

value: cerebellum


title: MIA-PaCa-2_GW2

description: GW3965-treated, 72 hours, replicate 2

hyb_protocol: Standard Illumina hybridization protocol


title: male cerebellum rep3

description: 3156 15 cerebellum male M106 5_17


title: female cerebellum rep5

description: 3164 23 cerebellum female M114 5_17

value: female


title: female cerebellum rep2

description: 3161 20 cerebellum female M103 4_25


title: female cerebellum rep6

description: 3165 24 cerebellum female M115 5_17


title: 48 hr 50 uM BPA 1

description: Sample 4

value: Differentiating human primary preadipocyte

value: 50 uM bisphenol A (BPA) for 48 hours

value: Stratagene human reference RNA


title: female frontal cortex rep5

description: 3152 11 cortex female M114 5_17


title: male cerebellum rep1

description: 3154 13 cerebellum male M104 4_25


title: female cerebellum rep4

description: 3163 22 cerebellum female M113 5_17


title: female cerebellum rep3

description: 3162 21 cerebellum female M112 5_17


title: male cerebellum rep2

description: 3155 14 cerebellum male M105 4_25


title: female frontal cortex rep2

description: 3149 8 cortex female M103 4_25


title: female cerebellum rep1

description: 3160 19 cerebellum female M102 4_25


title: female frontal cortex rep4

description: 3151 10 cortex female M113 5_17


title: male cerebellum rep4

description: 3157 16 cerebellum male M107 5_17


title: BxPC-3_GW2

description: GW3965-treated, 72 hours, replicate 2


title: male frontal cortex rep2

description: 3143 2 cortex male M105 4_25

source_name: male_frontal cortex


title: male frontal cortex rep3

description: 3144 3 cortex male M106 5_17


title: WT3-3

city: Boston

middle: E.

last: Clapham

address: Enders 1309

department: Cardiology

institute: HHMI/Boston Children's Hospital/Harvard Medical School

description: Replicate 3

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio software

source_name: WT mESC

label_protocol: Biotinylation using Illumina¨ TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: Embryonic stem cell medium was composed of KO-DMEM supplemented with 15% FBS, glutamate, nonessential amino acids, 2-mercaptoethanol (all from Gibco/Life Science Technologies), 103 U/mL LIF (Millipore/GE Healthcare) and 10 mM MgCl2. Cells were grown on the layer of irradiated mouse embryonic fibroblasts. In cultured ES cells, the media was changed daily and cells were split 1:5 every other day. For feeder-free conditions, mESC were depleted of feeder cells by pre-plating on gelatin-coated plates and cultured on 0.1% gelatin-coated plates for 3 passages with 2x103 U/mL LIF.

extract_protocol: Total RNA was extracted from cells using Qiagen RNAeasy Plus mini Kit

value: mouse embryonic stem cells 3x passaged without feeder cells

tag: genotype

value: WT

tag: genetic background


title: female frontal cortex rep3

description: 3150 9 cortex female M112 5_17


title: female frontal cortex rep1

description: 3148 7 cortex female M102 4_25


title: male frontal cortex rep6

description: 3147 6 cortex male M109 5_17


title: male cerebellum rep6

description: 3159 18 cerebellum male M109 5_17


title: male frontal cortex rep4

description: 3145 4 cortex male M107 5_17


title: male frontal cortex rep1

description: 3142   1 cortex male M104 4_25


title: male frontal cortex rep5

description: 3146 5 cortex male M108 5_17


title: KO9-3

description: Replicate 3

source_name: TRPM7-/- mESC


title: KO9-1

description: Replicate 1


title: WT3-2


title: Breast cancer 11

city: Jeddah

first: Manikandan

last: Jayapal

address: King Fahd Medical Research Center | King Abdulaziz University | PO BOX 80216, Jeddah 21589. KSA.

country: Saudi Arabia

institute: King Abdulaziz University

description: Fresh Tissue

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

source_name: Breast cancer fresh tissue

label_protocol: 1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples for amplification with the Pico kit were isolated from fresh tissues using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturersâ€™ suggestions followed by an additional amplification step using Nugen Exon Module.

value: breast cancer tumor

tag: histological type

value: IDC

tag: age (y)

tag: grade

tag: site

value: L

tag: er   (1= positive, 0=nagative)

tag: pr   (1= positive, 0= negative)

tag: her2  (1=positive, 0=negative)

tag: triple negative (1= yes, 0= no)


title: Breast cancer 33

description: Fresh Tissue

tag: tissue

value: R


title: WT3-1

description: Replicate 1

scan_protocol: Standard Illumina scanning protocol

tag: cell type


title: Breast cancer 44

description: Fresh Tissue

value: Mixed


title: Breast cancer 27

description: Fresh Tissue


title: Breast cancer 43

description: Fresh Tissue


title: Breast cancer 16

description: Fresh Tissue

value: ILC


title: Breast cancer 42

description: Fresh Tissue


title: Breast cancer 21

description: Fresh Tissue


title: Breast cancer 1

description: Fresh Tissue

value: Mucinous


title: Breast cancer 39

description: Fresh Tissue


title: Bulk CD8 T cells Pt 476597

city: Cambridge

description:
Bulk CD8+ T cells
3682 -  476597 Bulk.AVG_Signal

value: Bulk CD8+ T cells


title: Breast cancer 37

description: Fresh Tissue


title: Breast cancer 12

description: Fresh Tissue


title: Breast cancer 18

description: Fresh Tissue


title: Breast cancer 32

description: Fresh Tissue


title: Breast cancer 25

description: Fresh Tissue


title: Breast cancer 13

description: Fresh Tissue


title: Breast cancer 41

description: Fresh Tissue


title: Breast cancer 24

description: Fresh Tissue


title: Breast cancer 14

description: Fresh Tissue


title: KO9-2

description: Replicate 2


title: Breast cancer 28

description: Fresh Tissue

value: Poorly diff


title: Breast cancer 17

description: Fresh Tissue


title: KK10-specific CD8+ T cells +Pept Pt 529440

description:
HIV-specific CD8+ T cells +Pept
3678 -  529440 Pept.AVG_Signal

value: KK10-specific CD8+ T cells


title: Breast cancer 36

description: Fresh Tissue


title: Breast cancer 30

description: Fresh Tissue


title: Breast cancer 10

description: Fresh Tissue


title: Breast cancer 8

description: Fresh Tissue


title: Breast cancer 7

description: Fresh Tissue


title: Breast cancer 9

description: Fresh Tissue


title: Breast cancer 6

description: Fresh Tissue


title: Normal breast CEGMR 5

description: Fresh Tissue

source_name: Normal Breast tissue

value: normal breast

value: Normal


title: Breast cancer 2

description: Fresh Tissue


title: Epitrochlearis muscle, whey protein hydrolysate administrated after 2h exercise, biological rep1

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with theDistribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Rattus norvegicus

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was purified with an RNeasy Fibrous Tissue Mini Kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Rats were acclimated to swimming exercise by three days of pre-training. One day before the experiment, they were fed 5 g of a restricted diet (MF, Oriental Yeast Co., Ltd., Osaka, Japan). On the day of the experiment, rats swam for 2 hours. Immediately following exercise, rats were given one of two isoenergetic test solutions by gavage. These solutions contained 44 kJ in a four-test dose that represented about 15% of daily energy needs and included either a mixed meal containing carbohydrate and amino acid mixture (AAM) or a mixed meal containing carbohydrate and whey protein hydrolysate (WPH; Meiji Co., Ltd., Japan).

value: Sprague-Dawley

tag: gender

value: male

value: 6 weeks

tag: treatment

value: whey protein hydrolysate

value: epitrochlearis muscle


title: Normal breast CEGMR 3

description: Fresh Tissue


title: Epitrochlearis muscle, amino acid mixture administrated after 2h exercise, biological rep1

value: amino acid mixture


title: Case NE 43

city: Rockville

first: Paula

middle: Lisa

last: Hyland

address: 6120 Executive Blvd

department: DCEG

institute: NCI, NIH

description: Gene expression data

hyb_protocol: 20 ug fragmented cRNA were hybridized for 16 hr at 45C on GeneChip H133-A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression data were processed and normalized using Bioconductor Affy package, based on the Robust Multichip Average (RMA) for single-channel Affymetrix chips

source_name: NE Tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA and following clean-up with Qiagen Rneasy Mini Kit were performed according to the manufacturers instructions

tag: group

value: BE case

value: NE


title: Case NE 40

description: Gene expression data


title: Case BE 43

description: Gene expression data

source_name: BE Tissue

value: BE


title: Epitrochlearis muscle, whey protein hydrolysate administrated after 2h exercise, biological rep2

tag: age


title: Case NE 39

description: Gene expression data


title: Case BE 39

description: Gene expression data


title: Case NE 41

description: Gene expression data


title: Epitrochlearis muscle, amino acid mixture administrated after 2h exercise, biological rep2

tag: strain


title: Epitrochlearis muscle, amino acid mixture administrated after 2h exercise, biological rep4


title: Normal breast CEGMR 1

description: Fresh Tissue


title: Case BE 38

description: Gene expression data


title: Case BE 40

description: Gene expression data


title: Epitrochlearis muscle, whey protein hydrolysate administrated after 2h exercise, biological rep4


title: Case NE 38

description: Gene expression data


title: Case NC 39

description: Gene expression data

source_name: NC Tissue

value: NC


title: Case NC 41

description: Gene expression data


title: Case NC 43

description: Gene expression data


title: Case BE 41

description: Gene expression data


title: Epitrochlearis muscle, whey protein hydrolysate administrated after 2h exercise, biological rep3


title: Normal breast CEGMR 2

description: Fresh Tissue


title: Case NE 37

description: Gene expression data


title: Case NC 40

description: Gene expression data


title: Epitrochlearis muscle, amino acid mixture administrated after 2h exercise, biological rep3


title: Case BE 37

description: Gene expression data


title: Case NC 37

description: Gene expression data


title: Case NE 36

description: Gene expression data


title: Case NC 38

description: Gene expression data


title: Case BE 36

description: Gene expression data


title: Case NC 35

description: Gene expression data


title: Case BE 35

description: Gene expression data


title: Case NE 35

description: Gene expression data


title: Case BE 30

description: Gene expression data


title: Case NE 33

description: Gene expression data


title: Normal breast CEGMR 4

description: Fresh Tissue


title: Case BE 33

description: Gene expression data


title: Case BE 34

description: Gene expression data


title: Case NC 33

description: Gene expression data


title: Case NE 30

description: Gene expression data


title: Case NE 34

description: Gene expression data


title: Case NC 36

description: Gene expression data


title: Case NC 30

description: Gene expression data


title: Case BE 31

description: Gene expression data


title: Case NC 29

description: Gene expression data


title: Case NC 34

description: Gene expression data


title: Case NE 31

description: Gene expression data


title: Case NE 28

description: Gene expression data


title: Case NE 27

description: Gene expression data


title: Case NE 29

description: Gene expression data


title: Case BE 29

description: Gene expression data


title: Case BE 28

description: Gene expression data


title: Case NE 26

description: Gene expression data


title: Case NC 31

description: Gene expression data


title: Case BE 27

description: Gene expression data


title: Case NC 28

description: Gene expression data


title: Case BE 26

description: Gene expression data


title: Case NC 26

description: Gene expression data


title: Case NC 27

description: Gene expression data


title: Case BE 25

description: Gene expression data


title: Case NC 24

description: Gene expression data


title: Case BE 23

description: Gene expression data


title: Case NC 25

description: Gene expression data


title: Case NE 23

description: Gene expression data


title: Case NE 22

description: Gene expression data


title: Case NE 21

description: Gene expression data


title: Case NE 25

description: Gene expression data


title: Oocyte_climacteric_rep3

city: Rostock

first: Marcin

last: Siatkowski

address: Ernst-Heydemann-Str. 8

institute: IBIMA

description: Gene expression of climacteric mouse oocyte

hyb_protocol: Fragmentation (1650 ng Cy3-labeled amplified RNA) and hybridization were performed following the hybridization pro- cedure recommended by the array manufacturer (Agilent Tech- nologies), with a modification given by the manufacturer of the Turbo Labeling CY3 Kit.

scan_protocol: Microarray wash and detection of the labeled RNA on GeneChips were performed according to the instructions of Agilent Technologies. Gene expression profiling was performed using Agilent’s Whole Mouse Genome Oligo Microarrays (4 44k, each array with 41 174 features).

data_processing: Array image acquisition and feature extraction was performed using the Agilent G2505B Microarray Scanner and Feature Extraction software version 9.5 (Agilent Technologies).

source_name: Oocyte, climacteric B6C3F1 mice, 58 +/- 10 weeks of age, replicate 3

label_protocol: Three micrograms of amplified RNA were labeled with Cy3 using Arcturus Turbo Labeling CY3 Kit (MDS Analytical Technologies GmbH, Germany). Concentration and frequency of incorporation (FOI) were measured using the NanoPhotometer (Implen, Munich, Germany).

growth_protocol: B6C3F1 mice (C57Bl/6J · C3H/HeN) aged 3, 8 and 52 weeks (prepubertal, mid-age, climacteric) were maintained and used for experiments according to the ethical permit issued by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV) of the state of North Rhine-Westphalia, Germany. Throughout the extended time of this study, mice were reared, housed, fed ad libitum and primed for superovulation.

extract_protocol: RNA (samples in 300 μL RLT buffer with 1% β-mercapt- oethanol) was isolated using RNeasy Micro Kit as described by the manufacturer (Qiagen, no DNase treatment). An examina- tion of total RNA on an Agilent 2100 Bioanalyzer and RNA Pico 6000 Lab-Chip kit confirmed the extraction of high-quality RNA, which was then prepared for gene expression profiling. Arcturus RiboAmp HS Plus Amplification Kit (MDS Analytical Technologies GmbH, Germany) was used to amplify total RNA (two rounds of amplification) according to manufacturer’s instructions. After the second round of amplification, ampli- fied RNA was eluted with 15 μL RE buffer. Concentration of amplified RNA was measured using Agilent Bioanalyzer 2100 and RNA 6000 Lab-Chip kit.

treatment_protocol: Mice were injected with 10 IU PMSG and 10 IU hCG i.p. 48 hours apart, and sacrificed by cervical dislocation 14 h after hCG injection. Metaphase II oocytes were retrieved from the oviductal ampullae, and freed of cumulus cells and zonae pellucidae, before lysing in SDS lysis buffer (4% SDS, 100 mM Tris/HCl pH 7.5, 0.1 M DTT, total volume 70 µL).

value: oocyte

value: 58 +/- 10 weeks of age

tag: developmental stage

value: climacteric


title: Oocyte_mature_age_rep3

description: Gene expression of mature age mouse oocyte

source_name: Oocyte, mature B6C3F1 mice, 8 +/- 1 weeks of age, replicate 3

value: 8 +/- 1 weeks of age

value: mature age


title: Case BE 24

description: Gene expression data


title: Oocyte_climacteric_rep2

source_name: Oocyte, climacteric B6C3F1 mice, 58 +/- 10 weeks of age, replicate 2


title: Oocyte_mature_age_rep2

source_name: Oocyte, mature B6C3F1 mice, 8 +/- 1 weeks of age, replicate 2


title: Case BE 22

description: Gene expression data


title: Case NC 21

description: Gene expression data


title: Oocyte_prepubertal_rep2

description: Gene expression of prepubertal mouse oocyte

source_name: Oocyte, prepubertal B6C3F1 mice, 3 weeks of age, replicate 2

value: 3 weeks of age

value: prepubertal


title: Case NC 20

description: Gene expression data


title: Case BE 21

description: Gene expression data


title: Case BE 20

description: Gene expression data


title: Case NC 22

description: Gene expression data


title: Oocyte_climacteric_rep1

source_name: Oocyte, climacteric B6C3F1 mice, 58 +/- 10 weeks of age, replicate 1


title: Oocyte_mature_age_rep1

source_name: Oocyte, mature B6C3F1 mice, 8 +/- 1 weeks of age, replicate 1


title: Case BE 19

description: Gene expression data


title: Case NE 20

description: Gene expression data


title: Case BE 18

description: Gene expression data


title: Oocyte_prepubertal_rep1

source_name: Oocyte, prepubertal B6C3F1 mice, 3 weeks of age, replicate 1


title: Oocyte_prepubertal_rep3

source_name: Oocyte, prepubertal B6C3F1 mice, 3 weeks of age, replicate 3


title: Case NE 24

description: Gene expression data


title: Case NC 23

description: Gene expression data


title: Case NE 19

description: Gene expression data


title: Case NE 18

description: Gene expression data


title: Case NE 15

description: Gene expression data


title: Case NC 19

description: Gene expression data


title: Case BE 17

description: Gene expression data


title: Case BE 16

description: Gene expression data


title: Case NC 17

description: Gene expression data


title: Case NC 18

description: Gene expression data


title: Case NE 17

description: Gene expression data


title: Case BE 15

description: Gene expression data


title: Case NE 16

description: Gene expression data


title: Case NE 14

description: Gene expression data


title: Case NC 15

description: Gene expression data


title: KYSE140 treated B2

city: Beijing

first: Yang

last: Xu

address: No.17 Panjiayuan Nanli, Chaoyang district

institute: Cancer Hospital

description: Gene expression data from KYSE140 treated with cisplatin for 12 hrs.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

source_name: KYSE140 treated with CDDP for 12 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: KYSE140 cells were clutured in RPMI 1640 media with 10% fetal bovin serum (FBS) and antibiotics

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

treatment_protocol: KYSE140 cells were treated with 10mM of cisplatin for 12 hrs or left untreated

tag: cell line

value: 10mM of cisplatin for 12 hrs


title: Case NC 16

description: Gene expression data


title: Case NE 13

description: Gene expression data


title: KYSE140 treated B1


title: KYSE140 untreated

description: Gene expression data from KYSE140 untreated.

source_name: KYSE140 untreated

value: Untreated


title: Case BE 14

description: Gene expression data


title: Case NC 14

description: Gene expression data


title: Case NE 12

description: Gene expression data


title: Case BE 12

description: Gene expression data


title: Case NC 12

description: Gene expression data


title: gastric cancer 5

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

description: Gene expression data from gastric cancer (diffuse type including por2, por2>por1, por2+sig, pathological stage III, GC23s)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for aprx. 16 hr at 45C on GeneChip Human Genome U133 Plus2.0 Array. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip operating software (GCOS) version 1.4 using Affymetrix default analysis setting and mask-file (Affymetrix, hgu133_plus_2norm) scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 10000.

source_name: gastric cancer tissue

label_protocol: Biotinylated cRNA were prepared according to two-cycle Affymetrix protocol from 100 ng total RNA (GeneChip Expression Analysis Technical Manual 702232 Rev. 2 & 3, 702731 Rev. 3, Affymetrix)

extract_protocol: Total RNA extraction was performed using ISOGEN lysis buffer and isopropanol precipitation method (Nippon Gene).

value: stomach

tag: tumor or normal

value: tumor

tag: tumor type


title: Case NC 13

description: Gene expression data


title: gastric cancer 4

description: Gene expression data from gastric cancer (diffuse type including por2, por2>por1, por2+sig, pathological stage III, GC60)


title: pancreatic cancer 1

description: Gene expression data from pancreatic cancer (PC3)

source_name: pancreatic cancer tissue

value: pancreas

value: pancreatic cancer (PC3)


title: Case BE 13

description: Gene expression data

value: BE case


title: Case NE 11

description: Gene expression data

value: NE


title: Case NC 11

description: Gene expression data


title: Case BE 11

description: Gene expression data

value: BE


title: Case BE 9

description: Gene expression data


title: Case BE 10

description: Gene expression data


title: Case NE 8

description: Gene expression data


title: Case NC 10

description: Gene expression data

value: NC


title: Case BE 8

description: Gene expression data


title: gastric cancer 1

description: Gene expression data from gastric cancer (diffuse type including por2, por2>por1, por2+sig, pathological stage III, GC16)


title: Case NE 9

description: Gene expression data


title: Case NC 9

description: Gene expression data


title: Case NE 7

description: Gene expression data


title: gastric cancer 2

description: Gene expression data from gastric cancer (diffuse type including por2, por2>por1, por2+sig, pathological stage III, GC40)


title: Case NC 7

description: Gene expression data


title: Case NC 6

description: Gene expression data


title: Case BE 6

description: Gene expression data


title: Starved Replicate 8

city: St Louis

last: Shaw

address: 660 S Euclid

department: Anatomy

institute: Washington University School of Medicine

hyb_protocol: Reactions were purified using QIAQuick PCR purification columns (Qiagen), and labeled RNA was hybridized to clones arrayed on a 2x2-cm field under a plastic HybriSlip (Grace BioLabs) in a humidified cassette (TeleChem) for 15 h at 65 degrees C

scan_protocol: After the arrays were washed, fluorescence intensities were measured on an Agilent scanner.

data_processing: Data from the 4,659 ESTs present were background subtracted, mean normalized and subjected to loess transformation using Standardization and Normalization of MicroArray Data (http://pevsnerlab.kennedykrieger.org/snomadinput.html). The two most extreme values were identified from each condition (control, sleep deprived and starved) and removed.

organism: Drosophila melanogaster

source_name: fly head, starved, 7 hours

label_protocol: Three milligrams of poly(A) mRNA was used as a template for each of cDNA synthesis reactions using Superscript II (GibcoBRL) in the presence of fluorescently labeled Cy3- or Cy5-dCTP (Amersham).

growth_protocol: Three day old female cyc01 mutants were monitored under baseline conditions for 2 days in dark;dark.

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

treatment_protocol: On the third day, they were either sleep deprived for 7 h according to standard procedures or starved for 7 h by replacing their food with 1% agar.

tag: light conditions

value: dark;dark

tag: genotype

value: 7 d

value: Female

value: head

source_name: fly head


title: Case BE 7

description: Gene expression data

source_name: BE Tissue


title: Starved Replicate 7


title: Case NE 6

description: Gene expression data

source_name: NE Tissue


title: Case NE 4

description: Gene expression data


title: wt_MEFs_CATCHIT_(20121012_538386_2)

type: genomic

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CATCH-IT profiling of mouse embryonic fibroblasts expressing wildtype-Chd1

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: The standard deviates of the bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 computedby NimbleGen were computed. The supplementary gff and wig files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.

molecule: genomic DNA

source_name: CATCH-IT pulldown

label_protocol: Standard NimbleGen protocol

extract_protocol: CATCH-IT was performed as previously described (PMID: 23602475) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested and washed with 1X PBS. Nuclei were isolated by hypotonic lysis of cells in ice-cold NE1 buffer (20mM HEPES-KOH (ph 7.9), 10mM KCl, 1mM MgCl2, 0.1% Triton X-100, 1mM DTT, 20% Glycerol). MNase digest, Biotin coupling, chromatin extraction, streptavidin pulldown, urea wash and DNA isolation were then performed as previously described.

value: mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: expressing wildtype-Chd1

source_name: Input chromatin

extract_protocol: Same as for ch1


title: Case NC 8

description: Gene expression data

source_name: NC Tissue


title: Case NC 4

description: Gene expression data


title: Starved Replicate 4


title: Starved Replicate 5


title: 1-MLL1 KO-AUY922 rep1

city: cambridge

first: yaoyu

last: chen

state: Massachusetts

address: 250 Mass ave

department: ONC

institute: NIBR

description: Gene expression data from vec control cells treated with 10uM MDV

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: 1-MLL1 KO-AUY922

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All lines were cultured in RPMI-1640 supplemented with 10% FCS prior to treatment with 0.1% DMSO or 100nM AUY922 for 3h.

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 300K cells were seeded in 6 wells prior to treatment for 3 h

value: MLL1 KO


title: Starved Replicate 6


title: Case NE 2

description: Gene expression data


title: Starved Replicate 3


title: Case BE 4

description: Gene expression data


title: 1-MLL1 KO-DMSO rep3

source_name: 1-MLL1 KO-DMSO

value: DMSO


title: Case BE 2

description: Gene expression data


title: 1-MLL1 KO-AUY922 rep3

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 10uM MDV


title: Case NE 3

description: Gene expression data


title: Case NC 3

description: Gene expression data


title: K510R_MEFs_CATCHIT_(20121012_538427_2)

description: CATCH-IT profiling of mouse embryonic fibroblasts expressing K510R-Chd1

tag: transgene


title: 1-MLL1 KO-AUY922 rep2


title: Case BE 3

description: Gene expression data


title: KD_MEFs_CATCHIT_(20121012_559018)

description: CATCH-IT profiling of mouse embryonic fibroblasts expressing a short hairpin RNA to knockdown expression of Chd1

value: expressing short hairpin CHd1i1 RNAi (to knockdown Chd1 expression)


title: Starved Replicate 2


title: Case NC 2

description: Gene expression data


title: Starved Replicate 1


title: Sleep Deprived Replicate 7

source_name: fly head, sleep deprived, 7 hours


title: Sleep Deprived Replicate 8


title: 1-MLL1 KO-DMSO rep2

description: Gene expression data from W741C/T877A overexpressing cells treated with 0.1% DMSO


title: control_MEFs_CATCHIT_(20131025_559020)

description: CATCH-IT profiling of control mouse embryonic fibroblasts

value: expressing short hairpin control


title: Case NE 1

description: Gene expression data


title: 1-MLL1 WT-AUY922 rep3

description: Gene expression data from F876L/T877A AR overexpressing cells treated with 0.1% DMSO

source_name: 1-MLL1 WT-AUY922

value: wild type


title: Ink4a/Arf+/+_Ezh2_-/-

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used  to prepare the Hybridization Cocktail. The kit contains mix for target  dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled  control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat  #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM,  respectively. These control oligos serve as positive controls for  hybridization. Biotin-labeled sense targets were diluted in hybridization  buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes.  Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged  at maximum speed for 1 minute prior to loading into the GeneChip® array  cartridge.  Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60  RPM. Upon hybridization, GeneChip cartridges were washed and stained with  GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station  450 following the FS450_0007 standard protocol. The cartridge is then loaded  into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are scanned using default parameters. Affymetrix GeneChip  Command Console software (AGCC) was used to acquire GeneChip images and  generate .DAT and .CEL files.

data_processing:
Microarray data is analyzed using Affy and Limma packages in R.
In Matrix, for each probe its normalized expression, log2 fold change between KO and WT, p-value and its respective annotation is presented.

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA.  Double stranded cDNA synthesis and related cRNA amplification was performed  with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse  transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip®  WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the  protocol were performed according to manufacturer’s specifications. Efficacy  of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

growth_protocol: MEF cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

extract_protocol: Total RNA was cleaned -up with RNAesy Qiagen purification kit.

treatment_protocol: Total RNA was extracted from exponentially growing MEF cells previously tryptinizied and collected.

value: MEF


title: Ink4a/Arf-/-_Ezh2_-/-_rep2


title: Ink4a/Arf+/+_Ezh2_fx/fx


title: Case NE 10

description: Gene expression data


title: 1-MLL1 WT-AUY922 rep2


title: Sleep Deprived Replicate 6


title: Ink4a/Arf-/-_Ezh2_fx/fx_rep1


title: Ink4a/Arf-/-_Ezh2_fx/fx_rep2


title: Sleep Deprived Replicate 5


title: 1-MLL1 WT-AUY922 rep1

description: Gene expression data from T877A AR overexpressing LNCaPs treated with 0.1% DMSO


title: 1-MLL1 WT-DMSO rep1

description: Gene expression data from vec control cells treated with 0.1% DMSO

source_name: 1-MLL1 WT-DMSO


title: gastric cancer 3

description: Gene expression data from gastric cancer (diffuse type including por2, por2>por1, por2+sig, pathological stage III, GC54b)

value: stomach

value: tumor


title: Sleep Deprived Replicate 4


title: 1-MLL1 WT-DMSO rep2


title: TGF-beta1 treated (24 hours) CDP 2

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: TGF-beta1 treated (24 hours) CDP

label_protocol: biotin

growth_protocol: MPP and CDP were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Seré et al., 2012).

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

treatment_protocol: Cells were treated with 10 ng/ml recombinant human TGF-β1 (R&D Systems, Minneapolis, USA) for 2, 4, 6, 12 and 24 h as described (Felker et al., 2010) or left untreated.

value: common dendritic cell progenitor


title: Sleep Deprived Replicate 2


title: TGF-beta1 treated (24 hours) CDP 3


title: 1-MLL1 KO-DMSO rep1


title: TGF-beta1 treated (24 hours) CDP 1


title: Ink4a/Arf-/-_Ezh2_-/-_rep1


title: Sleep Deprived Replicate 1


title: Sleep Deprived Replicate 3


title: TGF-beta1 treated (12 hours) CDP 2

source_name: TGF-beta1 treated (12 hours) CDP


title: 1-MLL1 WT-DMSO rep3


title: TGF-beta1 treated (12 hours) CDP 1


title: TGF-beta1 treated (8 hours) CDP 2

source_name: TGF-beta1 treated (8 hours) CDP


title: TGF-beta1 treated (8 hours) CDP 3


title: TGF-beta1 treated (12 hours) CDP 3


title: 168hr_SPIO_3

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Gene expression data from mouse lung tissue 168hr after SPIO nanparticle exposure

hyb_protocol: Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

source_name: Lung tissue from mice 168hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3

label_protocol: Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Male balb/c mice (N=5 per condition) were exposed to the SPIO nanoparticle aerosol (365 ug total mass), or a sham control (i.e. just humidified helium-oxygen-HEPA-filtered air atmosphere), for 4 hrs.  All mice were sacrificed with an overdose of sodium pe

value: lung

tag: Sex

value: male

value: Balb/c

value: SPIO

tag: exposure time


title: TGF-beta1 treated (8 hours) CDP 1


title: TGF-beta1 treated (4 hours) CDP 2

source_name: TGF-beta1 treated (4 hours) CDP


title: TGF-beta1 treated (4 hours) CDP 3


title: 168hr_SPIO_4

source_name: Lung tissue from mice 168hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4

tag: tissue


title: 168hr_SPIO_5

source_name: Lung tissue from mice 168hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: 168hr_SPIO_2

source_name: Lung tissue from mice 168hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: TGF-beta1 treated (2 hours) CDP 3

source_name: TGF-beta1 treated (2 hours) CDP

tag: cell type


title: Case BE 1

description: Gene expression data

source_name: BE Tissue

value: BE case

value: BE


title: TGF-beta1 treated (2 hours) CDP 1


title: TGF-beta1 treated (4 hours) CDP 1


title: Untreated common dendritic cell progenitor (CDP) 3


title: 168hr_SPIO_1

source_name: Lung tissue from mice 168hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: 96hr_SPIO_4

description: Gene expression data from mouse lung tissue 96hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 96hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4


title: Untreated common dendritic cell progenitor (CDP) 2


title: Untreated common dendritic cell progenitor (CDP) 1


title: TGF-beta1 treated (2 hours) CDP 2


title: 96hr_SPIO_5

source_name: Lung tissue from mice 96hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: 96hr_SPIO_3

source_name: Lung tissue from mice 96hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3


title: 96hr_SPIO_1

source_name: Lung tissue from mice 96hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: 48hr_SPIO_3

description: Gene expression data from mouse lung tissue 48hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 48hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3


title: TGF-beta1 treated (24 hours) MPP 2

source_name: TGF-beta1 treated (24 hours) MPP

value: multipotent progenitor


title: 48hr_SPIO_5

source_name: Lung tissue from mice 48hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: TGF-beta1 treated (12 hours) MPP 2

source_name: TGF-beta1 treated (12 hours) MPP


title: 48hr_SPIO_2

source_name: Lung tissue from mice 48hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: TGF-beta1 treated (12 hours) MPP 3


title: TGF-beta1 treated (24 hours) MPP 3


title: 96hr_SPIO_2

source_name: Lung tissue from mice 96hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: TGF-beta1 treated (24 hours) MPP 1


title: 48hr_SPIO_1

source_name: Lung tissue from mice 48hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: 24hr_SPIO_4

description: Gene expression data from mouse lung tissue 24hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 24hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4


title: TGF-beta1 treated (8 hours) MPP 2

source_name: TGF-beta1 treated (8 hours) MPP


title: 24hr_SPIO_3

source_name: Lung tissue from mice 24hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3


title: 48hr_SPIO_4

source_name: Lung tissue from mice 48hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4


title: TGF-beta1 treated (8 hours) MPP 3


title: 24hr_SPIO_5

source_name: Lung tissue from mice 24hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: TGF-beta1 treated (12 hours) MPP 1


title: 24hr_SPIO_1

source_name: Lung tissue from mice 24hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: TGF-beta1 treated (2 hours) MPP 3

source_name: TGF-beta1 treated (2 hours) MPP


title: TGF-beta1 treated (8 hours) MPP 1


title: TGF-beta1 treated (4 hours) MPP 1

source_name: TGF-beta1 treated (4 hours) MPP


title: 6hr_SPIO_3

description: Gene expression data from mouse lung tissue 6hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 6hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3


title: 6hr_SPIO_2

source_name: Lung tissue from mice 6hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: TGF-beta1 treated (2 hours) MPP 2


title: 0hr_SPIO_5

description: Gene expression data from mouse lung tissue 0hr after SPIO nanparticle exposure

source_name: Lung tissue from mice 0hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: TGF-beta1 treated (4 hours) MPP 3


title: TGF-beta1 treated (2 hours) MPP 1


title: 6hr_SPIO_4

source_name: Lung tissue from mice 6hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep4


title: 6hr_SPIO_5

source_name: Lung tissue from mice 6hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep5


title: TGF-beta1 treated (4 hours) MPP 2


title: 6hr_SPIO_1

source_name: Lung tissue from mice 6hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep1


title: 0hr_SPIO_3

source_name: Lung tissue from mice 0hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep3


title: 24hr_SPIO_2

source_name: Lung tissue from mice 24hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: Untreated multipotent progenitor (MPP) 2

source_name: Untreated multipotent progenitor (MPP)


title: 0hr_SPIO_2

source_name: Lung tissue from mice 0hr after inhalation exposure with SPIO nanoparticle aerosol, biological rep2


title: Untreated multipotent progenitor (MPP) 1