title: M0 452-2244 T8

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description: Sample tested for the presence of genomic aberrations. Data shown in Supplementary Figure of the manuscript.

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011). Slight modifications were introduced WGA products processed with the PCR-based labeling approaches. Here, the hybridization mix consisted of 5.0 µg of Cot1-DNA (Roche Diagnostics), 12 µl of 10x Blocking Reagent (Agilent Technologies), 60 µl of 2x Hi RPM Hybridization Buffer, 1% (v/v) of both Tween20 and Igepal and 19 µl of both test and reference DNA. For each hybridization 100 µl of the hybridization mix was applied on the array and hybridized at 65◦C for 24 h. Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature, twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing: Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 7.0  Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 7.0. Centralization algorithm was set to a threshold of 6.0 and bin size of 10. To avoid false positive calls, aberration filters were applied to define the minimum log2 ratio (0.4 ) and the minimum region size of 10000 kbp.

source_name: EpCAM+ single cell from M0-stage prostate cancer patient

label_protocol: PCR-based labeling using incorporation of dye-conjugated dNTPs.  WGA products were labeled by PCR in the presence of Cy5 or Cy3 conjugated dCTP and dUTP. Incorporation of the fluorescent dyes using the dNTPs provided the advantage that adapters flanking each amplicon in the WGA product could be removed prior to aCGH hybridization, thereby avoiding unspecific cross-hybridization of test sample with reference DNA and oligonucleotide probes on the array. For each sample two 50µl PCR reactions were run in parallel each comprising 5 µl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 µM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 µM of dATP and dGTP, 315 µM of dCTP and dTTP, 35 µM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 µl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 µl of the template DNA. Labeling products were pooled and purified using the Amicon Ultra 0.5 System (100 kDa cut-off). DNA yields and dye incorporation rates were quantified using the NanoDrop ND-1000 Instrument.

growth_protocol: VCaP cell line was grown in Dulbecco's Modified Eagle's Medium (PAN-Biotech) supplemented with 10% fetal calf serum (FCS) (PAN-Biotech), 4 mM L-Glutamic acid (PAN-Biotech) and 1% of Penicillin/Streptomycin solution (PEN STREP) (PAN-Biotech).

extract_protocol: Total genomic DNA (bulk DNA) was extracted using the Dbeasy Blood & Tissue Kit (QIAgen) following manufacture's instructions. All single cells, cell pools (few hundred cells) and microdissected specimens from formalin fixed paraffin embedded (FFPE) tumor tissue were amplified using the Ampli1™ WGA Kit (Silicon Biosystems).

tag: cell line/clinical sample

value: clinical sample

tag: tumor sample/healthy donor

value: tumor sample

tag: amplified/unamplified dna

value: amplified - Ampli1 WGA

tag: primary/reamplified wga

value: reamplified WGA  (Czyz et al., 2014, PLoS One)

tag: labeling protocol

value: PCR-based labeling (Czyz et al., 2014, PLoS One)

value: male

source_name: Healthy donor: cord blood; cell pool WGA (WGA product obtained from large number of cells)

value: Clinical sample

value: healthy donor


title: M0 363-1086 T2

status: Public on Oct 20 2014

type: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: gender

source_name: Healthy donor: cord blood; a pool of 4 single-cell WGA products from the same donor


title: M1 PC-719 T1

source_name: EpCAM+ single cell from M1-stage prostate cancer patient


title: M0 452-2244 T3


title: M1 PC-719 T2

source_name: Healthy donor: cord blood bulk gDNA


title: M0 348-1035 T1


title: M0 333-1003 T2


title: M0 452-2244 T4


title: PBL #2

description: Sample used to demonstrate the performance of single cell aCGH - negative control. Data shown in Supplementary Figure of the manuscript.

source_name: Peripheral blood leukocyte of healthy volunteer


title: N-29-2022-Ep3

source_name: EpCAM+ single cell from cancer-free male patient


title: N-24-1193-Ep1


title: M0 330-998 T2


title: M0 336-1006 T3


title: N-21-1101-Ep2


title: PBL #1


title: 13wk7-SZ

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

description: Spatial Regulation of Articular Cartilage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 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: RMA by software Partek

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: SZ

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: All animal studies were approved by the NICHD/NIH Animal Care and Use Committee.

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

treatment_protocol: normal postnatal 1wk tissue

tag: tissue

value: Superficial Zone of the Articular Cartilage

tag: age

value: 1 wk


title: N-30-2024-Ep4


title: VCaP sc #6

description: Sample used to demonstrate the performance of single cell aCGH - positive control. Data shown in Supplementary Figure of the manuscript.

source_name: VCaP prostate cancer cell line

value: cell line (ATCC)


title: VCaP gDNA

value: unamplified

value: Klenow Based labeling-standard Protocol of the Agilent Genomic DNA Enzymatic Labeling Kit Agilent p/n 5190-0447


title: 12wk6-DZ

source_name: DZ

value: Deep Zone of the Articular Cartilage


title: 15wk7-DZ


title: 14wk7-MZ

source_name: MZ

value: Mid-Zone of the Articular Cartilage


title: diseased_sample_rep4

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

description:
Sample_10_D
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.

hyb_protocol: hyb protocol according to Microarrays Inc

scan_protocol: Scanned on GenePix 4000B, using GenePix Pro 4.1.1.44

data_processing:
log2 of quantile normalized ratio of medians (Cy3/Cy5) with negative flag values, empty or unnamed spots removed (intersect of probes between samples).
Quantile normalization performed after the above pre-selection steps.
We used R: A Language and Environment for Statistical Computing, R Core Team, R Foundation for Statistical Computing, Vienna, Austria, 2013 (http://www.R-project.org).

source_name: human meniscus_diseased

label_protocol: label protocol according to Microarrays Inc

extract_protocol: mRNA was extracted from human primary meniscal progenitor cells (MPC) using the RNeasy Mini kit (Quiagen, Hilden, Germany).

tag: disease state

value: late stages of osteoarthritis (D)

tag: cell type

value: primary meniscal progenitor cells (MPC)


title: 10wk6-SZ


title: lessDiseased_sample_rep3

description:
Sample_3_LD
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.

source_name: human meniscus_less diseased

value: late stages of osteoarthritis (LD)


title: 9wk5-DZ


title: lessDiseased_sample_rep1

description:
Sample_1_LD
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.


title: lessDiseased_sample_rep2

description:
Sample_2_LD
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.


title: 8wk5-MZ


title: 5wk4-MZ


title: 11wk6-MZ


title: lessDiseased_sample_rep4

description:
Sample_7_LD
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.


title: 6wk4-DZ


title: 7wk5-SZ


title: Podoplanin-low LEC, rep 2

city: Vienna

first: Bernhard

last: Schweighofer

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: Sample name: PODO-LOW_2

hyb_protocol: Purified and fragmented cRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays following the manufacturer’s recommendations.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analysed in CARMAweb 1.5, using the RMA (robust multi-array average) method.

source_name: LEC, podoplanin low expressing population

label_protocol: Biotinylated cRNA were prepared using the GeneChip HT 3' IVT Express Kit.

growth_protocol: Cells were routinely cultured in EGM-2 (Lonza)

treatment_protocol: Cells were not treated in a special way, but flow-sorted according to differences in FSC and SSC values

value: lymphatic endothelial cell

tag: cell population

value: podoplanin low expressing population


title: Podoplanin-low LEC, rep 3

description: Sample name: PODO-LOW_3


title: diseased_sample_rep3

description:
Sample_9_D
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.


title: 4wk4-SZ


title: Podoplanin-low LEC, rep 1

description: Sample name: PODO-LOW_1


title: Podoplanin-high LEC, rep 3

description: Sample name: PODO-HIGH_3

source_name: LEC, podoplanin high expressing population

value: podoplanin high expressing population


title: Podoplanin-high LEC, rep 1

description: Sample name: PODO-HIGH_1


title: Neurons differentiated from amyotrpic lateral sclerosis patient NSCs

first: Nasir

last: Malik

address: 50 South Drive/Room 1146

department: NIAMS

institute: NIH

description: NSC derived neurons from Amyotropic lateral sclerosis patient with SOD1 mutation

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with the Gene Expression package of Illumina's Genome Studio software

source_name: Day 42 differentiated astrocytes

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

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: NSC differentiated astrocytes


title: Podoplanin-high LEC, rep 2

description: Sample name: PODO-HIGH_2


title: adenocarcinoma 1d

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA (fresh/frozen) of different organs of non-cancer individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v10.5 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

source_name: Colorectal tissue, m-FCM sorted nuclei

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Multiple haematoxylin-eosin stained cryostatic sections were used as references to increase the epithelian cell component. DAPI stained nuclei suspentions were prepared and measured by multiparameter FACS 440-Sorted. DNA was extracted using Archive Pure DNA kit (5 Prime), amplified with Enzo Bioscore Screening and Amplification kit and Whole Genome Amplification kit WGA2 (Sigma-Aldrich) and purified with QIAquick Purification kit (Qiagen).

value: Colorectal tissue, m-FCM sorted nuclei

tag: ploidy status

value: diploid

value: M

source_name: Fresh/frozen DNA pool from different organs of non-cancer individuals

value: M/F


title: Amyotropic lateral sclerosis patient NSCs passage 5

description: iPSC-derived NSCs from Amyotropic lateral sclerosis patient with SOD1 mutation

source_name: cultured neural stem cell line

value: neural stem cell

tag: passage

value: passage 5


title: diseased_sample_rep2

description:
Sample_8_D
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.


title: 2wk3-MZ

value: 1 wk


title: Neurons differentiated from Niemann Pick C Type 1 patient NSCs

description: NSC derived neurons from Niemann Pick C Type 1 patient with NPC1 I1071T mutation

source_name: Day 14 differentiatied neurons

value: NSC differentiated neurons

value: Neurons differentiated from NSCs for 14 days


title: Niemann Pick C Type 1 patient NSC passage 3

description: iPSC-derived NSCs from Niemann Pick C Type 1 patient with NPC1 I1071T mutation

value: passage 3


title: 1wk3-SZ

value: Superficial Zone of the Articular Cartilage


title: 1988-T74-RMS_N

city: Tokyo

first: Riki

last: Nishimura

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

label: Biotin

source_name: ERMS tumor specimen

label_protocol: Affymetrix standard protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from resected fresh tumor blocks or freeze tumor blocks.

tag: disease

value: RMS

tag: histology subtype

value: ERMS


title: 2012-T13-RMS_N

description: Hybridized to 250K_Nsp


title: AJHCC10

status: Public on Oct 19 2014

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: HCC

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

value: Advanced HCC


title: diseased_sample_rep1

description:
Sample_6_D
DE analysis (D vs. LD) based on ratio of medians (Cy3/Cy5).   Cy5 was not a control label in the sense of housekeeping genes; there was no RNA at all hybridized. The Cy5 channel was used for background measurement only.

value: late stages of osteoarthritis (D)

value: primary meniscal progenitor cells (MPC)


title: AJHCC07


title: AJHCC09


title: AJHCC12


title: AJHCC04

value: Early HCC


title: AJHCC02


title: AJHCC08


title: AJHCC05


title: AJHCC06


title: sirUBF oligo #2 transfected NIH3T3 rep 2

city: East Melbourne

first: Elaine

last: Sanij

state: VIC

address: 1 St Andrews Place

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Mouse GeneChip Gene 1.0 ST arrays using Affymetrix hybridization kit materials for 18 hours at 45C

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics station 450 and scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing: The data were analyzed with using the affy and limma packages.

label_protocol: 100 ng total RNA was used to prepare 2.5 ug amplified, fragmented and biotin labeled cDNA using the NuGen Applause WT-Amp ST RNA amplification system

growth_protocol: NIH3T3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) at 37oC

extract_protocol: total RNA was extracted using Qiagen RNA extraction kit as per manufacturer's protocol

treatment_protocol: NIH3T3 cells were incubated with Dharmafect 2 reagent (Dharmacon) to transfect siRNA at 40 nM. Mock transfected cells were incubated with Dharmafect 2 reagent without siRNA. Total RNA was exctracted 48 hours after transfection

value: immortalized mouse fibroblasts

tag: cell line


title: 1987-T33-RMS_N

description: Hybridized to 250K_Nsp


title: CT-receptor-KO osteoclasts treated 3

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: C57Bl/6 mouse

hyb_protocol: Following fragmentation the cRNA were hybridized for 16 hr at 45C on the arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (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 200.

source_name: Murine osteoclasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix IVT labeling protocol from 5 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Osteoclast precursor cells were isolated from the bone marrow of 12 weeks old mice and differentiated for 4 days in α-MEM containing 10 nM 1,25(OH)2 Vitamin D3. For the next 6 days they additionally received M-CSF (20 ng/ml) and RANKL (40 ng/ml) to allow terminal differentiation. The conditioned medium was collected from day 1-4 of culture (osteoclast precursor cells) or from day 7-10 of culture (mature osteoclasts).

extract_protocol: RNA was isolated using the RNeasyMini kit (Qiagen).

treatment_protocol: For binding assays mature osteoclasts were incubated for 2 hours with 10-11 M 125I-salmon calcitonin (CT) in the absence or presence of 10-8 M salmon CT.

tag: genetic background

tag: genotype

value: Calcr-/-

value: Osteoclasts

tag: treatment

value: Calcitonin


title: AJHCC03


title: sirUBF oligo #2 transfected NIH3T3 rep 3


title: 1991-T27-RMS_N

description: Hybridized to 250K_Nsp


title: AJHCC11


title: AJHCC01


title: 1985-T38-RMS_N

description: Hybridized to 250K_Nsp


title: sirUBF oligo #2 transfected NIH3T3 rep 1


title: 2012-T1-RMS-ICH-ERMS_N

description: Hybridized to 250K_Nsp


title: 1992-T2-RMS_N

description: Hybridized to 250K_Nsp


title: CT-receptor-KO osteoclasts treated 2

description: C57Bl/6 mouse


title: WT osteoclasts untreated 3

description: C57Bl/6 mouse

value: wildtype

value: untreated


title: sirEGFP transfected NIH3T3 rep 3


title: CT-receptor-KO osteoclasts untreated 3

description: C57Bl/6 mouse


title: sirUBF oligo #1 transfected NIH3T3 rep 2


title: Mock transfected (no siRNA) NIH3T3 rep 2


title: WT osteoclasts untreated 1

description: C57Bl/6 mouse


title: WT osteoclasts treated 2

description: C57Bl/6 mouse


title: sirUBF oligo #1 transfected NIH3T3 rep 3


title: 1993-T-RMS_N

description: Hybridized to 250K_Nsp


title: WT osteoclasts untreated 2

description: C57Bl/6 mouse


title: sirEGFP transfected NIH3T3 rep 1


title: sirEGFP transfected NIH3T3 rep 2


title: Mock transfected (no siRNA) NIH3T3 rep 1


title: CT-receptor-KO osteoclasts untreated 1

description: C57Bl/6 mouse


title: CT-receptor-KO osteoclasts treated 1

description: C57Bl/6 mouse


title: sirUBF oligo #1 transfected NIH3T3 rep 1


title: CT-receptor-KO osteoclasts untreated 2

description: C57Bl/6 mouse


title: Mock transfected (no siRNA) NIH3T3 rep 3


title: AGS cell_490_rep1

status: Public on Oct 18 2014

city: Hong Kong

first: Jing

last: Shen

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, cuhk, Shatin NT

department: sbs

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression after transfection with miR-490-3p mimics

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cell,transfected, 72h

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: Total RNA was isolated using TRIzol reagent.

treatment_protocol: Cells were transfected with control mimics or miR-490-3p mimics for 72 hours.

value: AGS

value: miR-490-3p mimic


title: AGS cell_ctrl_rep1

description: Gene expression after transfection with control mimics

value: control


title: WT osteoclasts treated 3

description: C57Bl/6 mouse


title: HNO223 stable knockdown CTTN clone 2 rep 2 vs. HNO223 control clone 2 rep 2

city: Heidelberg

first: Madeleine

last: Gross

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: CTTN-2-rep2 vs. Luci-2-rep2

hyb_protocol: Hybridization was done according to the standard protocol of Agilent.

scan_protocol: Scanning was performed on an Agilent Scanner.

data_processing: Data were extracted and preprocessed by Agilent Feature Extraction Software Version 10.7. Normalization and filtering was performed using the in-house-developed ChipYard analysis software (http://www.dkfz.de/genetics/ChipYard/).

source_name: HNO223_CTTN KO

label_protocol: Labeling was done according to the standard protocol of Agilent.

growth_protocol: Stable transfections of the plasmid containing cortactin and control shRNA in HNO223 were performed. Cells were selected with zeocin.

extract_protocol: Total RNA isolation was done using the Rneasy Kit (Qiagen) according to manufacturer`s instructions.

value: Head and neck squamous cell carcinoma (HNSCC)

tag: genotype/variation

value: CTTN knockdown

tag: sample type


title: WT osteoclasts treated 1

description: C57Bl/6 mouse


title: AGS cell_490_rep2


title: HNO223 stable knockdown CTTN clone 2 rep 2 vs. HNO223 control clone 1 rep 2

description: CTTN-2-rep2 vs. Luci-1-rep2


title: AGS cell_ctrl_rep2


title: vagina 35d control animal #3

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

description: 35d control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.  Output data are averages.
Gene expression was standardized against GAPDH as a housekeeping gene and analyzed by the 2−ΔΔCT method.
The file "Normalized_data.txt" is available on the series record and reports average normalized signal (against housekeeping gene). e.g.,  avg 2^-ΔCt, where -ΔCt = -( average Ct_Target − average Ct_HKG).
The file "Fold_change_data.txt" is available on the series record and reports average infected/average control (i.e., average oviduct 28d infected /average oviduct 28d control) ratios.

label: SYBR Green

source_name: Vagina Control

label_protocol: PCR assays were performed using the RT2Profiler PCR array for mouse cytokines and chemokines (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 0.5 ug total RNA using the RT2 First Strand Kit (SA Biosciences). Real-time PCR were performed on an Eppendorf Mastercycler ep realplex2 system (Eppendorf, Hamburg, Germany)

growth_protocol: female C3H/HeJ mice, 6 -to 8 -week old, (Jackson Laboratories, Sacramento, CA) were pretreated with 2.5 mg medroxyprogesterone acetate (SICOR Pharmaceuticals) on Days -10 and -3 before infection.  mice were infected via vaginal challenge with 5 x 102 inclusion-forming units (IFUs) of C. trachomatis, serovar D in 0.01 mL of Eagle Minimal essential media (MEM, Gibco) on Day 0.  Control mice were also pretreated with medroxyprogesterone acetate, but were sham infected with Eagle Minimal essential media (MEM, Gibco) alone.  Vaginal swabs were obtained twice weekly after infection and cell cultures were performed to monitor infection.

extract_protocol: Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified through RNeasy columns (Qiagen, Valencia, CA) according the manufacturer's instructions.

treatment_protocol: Mice were killed on day 28 (n = 3 for control and infected) in experiment 1 and day 35 (n = 3 for control and infected) in experiment 2.  Vaginal tissue, uterine horns and the oviducts were collected and processed for superarray analysis.

value: Vagina

value: female

value: 6-8 weeks

tag: strain


title: vagina 35d infected animal #3

description: 35d infected

source_name: Vagina Infected

tag: gender


title: vagina 35d control animal #1

description: 35d control

tag: tissue


title: vagina 35d control animal #2

description: 35d control

tag: age


title: vagina 35d infected animal #2

description: 35d infected


title: LNCaP_siRUNX1_DHT

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from LNCaP cells  treated with DHT 10 nM after trasfected with siRUNX1

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS.  Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA 48 h before hormone treatment. Cells were treated with vehicle or DHT (10 nM).

value: LNCaP

value: prostate cancer

tag: sirna

tag: ligand

value: DHT 10 nM


title: vagina 35d infected animal #1

description: 35d infected


title: vagina 28d control animal #3

description: 28d control


title: HNO223 stable knockdown CTTN clone 2 rep 1 vs. HNO223 control clone 1 rep 1

description: CTTN-2-rep1 vs. Luci-1-rep1

tag: cell type


title: vagina 28d control animal #2

description: 28d control


title: HNO223 stable knockdown CTTN clone 1 rep 2 vs. HNO223 control clone 1 rep 2

description: CTTN-1-rep2 vs. Luci-1-rep2


title: vagina 28d control animal #1

description: 28d control


title: LNCaP_siRUNX1_Veh

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after trasfected with siRUNX1

value: Vehicle


title: HNO223 stable knockdown CTTN clone 1 rep 1 vs. HNO223 control clone 2 rep 1

description: CTTN-1-rep1 vs. Luci-2-rep1


title: CD10-A375. 1.

city: Fukuoka

first: Junna

last: Oba

address: 3-1-1 Maidashi, Higashi-ku

department: Dermatology

institute: Kyushu University

description: biological replicate 1

data_processing: The data were normalised using average normalisation with Illumina Genome Studio v1.

source_name: A375 melanoma cells

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays.

extract_protocol: RNA was extracted with QIAGEN RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with BIORAD Experion System.

value: human melanoma cell

tag: transfection

value: CD10 transgenic

tag: origin

value: ATCC® CRL-1619™


title: mock-A375. 3.

description: biological replicate 7

value: mock transgenic


title: HNO223 stable knockdown CTTN clone 2 rep 1 vs. HNO223 control clone 2 rep 1

description: CTTN-2-rep1 vs. Luci-2-rep1


title: LNCaP_siControl_Veh

description: Gene expression data from LNCaP cells treated with vehicle (ethanol) after transfected with siControl

value: siControl


title: LNCaP_siControl_DHT

description: Gene expression data from LNCaP cells treated with DHT 10 nM after transfected with siControl


title: HNO223 stable knockdown CTTN clone 1 rep 1 vs. HNO223 control clone 1 rep 1

description: CTTN-1-rep1 vs. Luci-1-rep1


title: mock-A375. 1.

description: biological replicate 5


title: vagina 28d infected animal #2

description: 28d infected


title: mock-A375. 4.

description: biological replicate 8


title: CD10-A375. 3.

description: biological replicate 3


title: CD10-A375. 2.

description: biological replicate 2


title: vagina 28d infected animal #1

description: 28d infected


title: uterine horn 35d infected animal #3

description: 35d infected

source_name: Uterine horn Infected

value: Uterine horn


title: uterine horn 35d control animal #1

description: 35d control

source_name: Uterine horn Control


title: mock-A375. 2.

description: biological replicate 6


title: uterine horn 35d control animal #2

description: 35d control


title: CD10-A375. 4.

description: biological replicate 4


title: uterine horn 28d control animal #3

description: 28d control


title: uterine horn 35d infected animal #1

description: 35d infected


title: uterine horn 28d control animal #1

description: 28d control


title: uterine horn 28d infected animal #3

description: 28d infected


title: oviduct 35d control animal #3

description: 35d control

source_name: Oviduct Control

value: Oviduct


title: uterine horn 28d infected animal #2

description: 28d infected


title: oviduct 35d control animal #2

description: 35d control


title: vagina 28d infected animal #3

description: 28d infected


title: oviduct 35d control animal #1

description: 35d control


title: oviduct 35d infected animal #3

description: 35d infected

source_name: Oviduct Infected


title: oviduct 35d infected animal #2

description: 35d infected


title: oviduct 35d infected animal #1

description: 35d infected


title: oviduct 28d control animal #3

description: 28d control


title: oviduct 28d control animal #1

description: 28d control


title: oviduct 28d infected animal #3

description: 28d infected


title: uterine horn 35d control animal #3

description: 35d control


title: oviduct 28d infected animal #2

description: 28d infected


title: uterine horn 35d infected animal #2

description: 35d infected


title: uterine horn 28d control animal #2

description: 28d control


title: uterine horn 28d infected animal #1

description: 28d infected


title: oviduct 28d control animal #2

description: 28d control


title: Mammary glands, Balb/c mice, 24day culture + Vitamin D5

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Mouse Whole Genome Microarrays in hybridization buffer. Arrays were hybridized at 37° C for 18 hrs. in a shaking incubator and washed at 46° C for 30 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner at 5 µm resolution.

data_processing:
CodeLink Expression Analysis software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).
Intensity values are normalized to the median intensity of each array.

source_name: Balb/c mice

label_protocol: First and second strand cDNA was prepared from the pooled Total RNA samples.  Biotinylated cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: Both ERKO models were originally developed on a C57BL6/129SV background; C57/BL6 mice were used in the present studies as wild-type (WT) controls. All mice were genotyped prior to use in order to confirm their ER status. Briefly, 4-week-old female mice (C57/BL, αERKO, or βERKO) that had been pretreated with 1 μg estrogen and 1 mg progesterone for 9 days were sacrificed by CO2 asphyxiation and thoracic pairs of mammary glands were excised aseptically. Mammary glands were then incubated on silk rafts in serum-free organ culture using chemically defined Waymouth medium.

extract_protocol: Mammary glands were collected from five mice per group (WT, αERKO, βERKO) and snap-frozen in liquid N2.  Purified total RNA was extracted individually from each gland using the Ambion RiboPure RNA isolation kit (Life Technologies, Carlsbad, CA) and was quantitated using the OD260/280 ratio for each sample. Equal mass amounts of total RNA from each gland were pooled to yield a sample representing RNA from mammary glands from every mouse in each group.

treatment_protocol: In WT mice, in vivo pre-treatment with E (1μg) and P (1 mg) is required to support mammary gland responsiveness to hormones in organ culture.  WT and ERKO mice were treated with 25 ng EGF + 1 mg P daily for 5 consecutive days; mammary glands were collected and processed as whole mounts for evaluations of morphology.  Freshly harvested mammary glands were incubated in Waymouth’s MB 752/1 medium supplemented with insulin (I; 5 μg/ml), prolactin (PRL; 5 μg/ml), aldosterone (A; 1 μg/ml), and hydrocortisone (F; 1 μg/ml) for 10 days (defined as the growth promotion phase). On Day 3 of the growth promotion phase, glands were exposed to the polycyclic aromatic hydrocarbon carcinogen, 7,12-dimethylbenz[a]anthracene (DMBA; 2 μg/ml) for 24 h. After completion of the 10-day growth promotion phase, glands were grown for an additional 14 days in medium containing insulin only (5 μg/ml; regression phase).

tag: strain background

value: Balb/c

value: wild type

value: 4 wks

value: mammary gland


title: oviduct 28d infected animal #1

description: 28d infected

value: female


title: Mammary glands, C57 mice, 24day culture, no DMBA


title: Mammary glands, ESR1 KO, 24day culture

value: αERKO


title: Mammary glands, ESR2 KO, 24day culture

value: βERKO


title: Mammary glands, C57 mice, 24day culture + DMBA


title: Mammary glands, C57 mice, 10day culture, no DMBA


title: Mammary glands, Balb/c mice, 24day culture


title: PAPC_rep2

status: Public on Oct 17 2014

city: Kawasaki-city

first: Shigeo

last: Ohta

state: Kanagawa

address: 1-394, Kosugi-machi, Nakahara-ku

department: Department of Biochemistry and Cell Biology

institute: Institute of Development and Aging Sciences, Graduate School of Medicine, Nippon Medical School

description:
Gene expression after exposure to PAPC
AR1704_02

hyb_protocol: Hybridization were performed using Gene Expression Hybridization Kit  (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and the fragmentation mixture were hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven (10r.p.m.).  Wash were performed using Gene Expression Wash Buffers Pack  (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol: GE1_1105_Oct12 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. 2% of the probe sets with the highest and the lowest values were excluded and normalized the mean signal intensity value to 2500.

source_name: THP-1 cell, PAPC, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low-Input QuickAmp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit according to the manufacturers’ protocol (Qiagen, Valencia, CA, USA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: THP-1 cells were exposed for 4 h to PAPC, OxPAPC, H2[1.3%]OxPAPC or H2[5%]OxPAPC that had been air-oxidized for 3 days with 0, 1.3 or 5% H2.

value: monocyte


title: OxPAPC_rep2

description:
Gene expression after exposure to OxPAPC
AR1704_05

source_name: THP-1 cell, OxPAPC, replicate 2


title: H2[5%]OxPAPC_rep1

description:
Gene expression after exposure to H2[5%]OxPAPC
AR1704_10

source_name: THP-1 cell, H2[5%]OxPAPC, replicate 1


title: H2[1.3%]OxPAPC_rep3

description:
Gene expression after exposure to H2[1.3%]OxPAPC
AR1704_09

source_name: THP-1 cell, H2[1.3%]OxPAPC, replicate 3


title: Id3 spleen 4 (IgM)

type: protein

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Culture supernatant harvested following lipopolysaccharide stimulation for 6 days

hyb_protocol: Autoantigen array  protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX

scan_protocol: Genepix Pro 6.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: Heat map figures and statistical tests were generated using Matlab software (http://www.mathworks.com/products/matlab/) (Mathworks).

label: Cy5 labeled anti-IgM

molecule: protein

source_name: Splenic follicular B cell

label_protocol: autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG) and 635nm (cy5 labeled anti-IgM)

growth_protocol: B cells were sort-purified from Id3-/- submandibular gland tissue and spleen.  Sera were also assayed.

extract_protocol: update

treatment_protocol: B cells were sort purified from spleen, cLN and SMG tissue of Id3-/- mice.  Cells (1x10^5 /well) were cultured in 5% RPMI 1640, stimulated with LPS (25 μg/mL) for 6 days, and supernatants harvested.  Sera from SS mice were harvested by cardiac puncture immediately following euthanasia.  Blood was allowed to clot for two hours and centrifuged at 2,000 g for twenty minutes.  Serum was removed and stored at -20°C until use. These undiluted supernatant samples and sera were used to perform the autoantigen array.

value: Splenic follicular B cell


title: Id3 spleen 6 (IgM)


title: Id3 spleen 3 (IgM)


title: Id3 spleen 5 (IgM)


title: B6 spleen 3 (IgM)


title: Id3 SMG 2 (IgM)

source_name: Submandibular salivary gland B cell

value: Submandibular salivary gland B cell


title: B6 spleen 4 (IgM)


title: B6 LN 6 (IgM)

source_name: Cervial lymph node follicular B cell

value: Cervial lymph node follicular B cell


title: B6 spleen 5 (IgM)


title: B6 LN 4 (IgM)


title: B6 LN 5 (IgM)


title: B6 LN 3 (IgM)


title: Pooled normal,  tech rep2 [set 2]

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description:
Normal-2
Gene expression in human prostate adjacent normal tissues

hyb_protocol: The fragmented and labeled aRNA (600ng) were hybridized onto Agilent’s 8x60k format Human LINC RNA array using Agilent Technologies Gene Hybridization protocol.

scan_protocol: The arrays were scanned using Agilent's C Scanner following the scan protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain mean signals which were background corrected, log transformed and normalized using using Limma package.

source_name: Pool of 10 patient's prostate adjacent normal tissues

label_protocol: The samples were labeled using One Color Quick Amp Labeling kit following Manufacturer's (Agilent Technologies) protocol. The protocol incorporates Cyanine 3-CTP to the target (aRNA) material.

growth_protocol: Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. Cells were harvested at confluency 70%.

extract_protocol: Total RNAs were prepared using the RNeasy kit (QAIGEN, Valencia CA) following the manufacturer's recommendations. The prostate epithelial cell RNA was purchased from Biochain (Cat # R1234201-50, Newark CA).  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After prostatectomy, the pathologist examined tumor part and adjacent normal part of prostate. Two biopsy needle amount tissues were obtained from 10 pair of samples and tissues were immersed in RNAlater (Ambion, Austin TX). After 24 hr at 4C, samples were stored at -80C.


title: Epithelial, rep2 [set 2]

description:
Epithelial-2
Gene expression in normal prostate cells

source_name: Normal epithelial prostatic cells

value: Prostate Normal epithelial cells


title: Pooled normal,  tech rep1 [set 2]

description:
Normal-1
Gene expression in human prostate adjacent normal tissues

value: Pool of 10 patient's prostate adjacent normal tissues


title: H2[5%]OxPAPC_rep2

description:
Gene expression after exposure to H2[5%]OxPAPC
AR1704_11

source_name: THP-1 cell, H2[5%]OxPAPC, replicate 2


title: H2[1.3%]OxPAPC_rep1

description:
Gene expression after exposure to H2[1.3%]OxPAPC
AR1704_07

source_name: THP-1 cell, H2[1.3%]OxPAPC, replicate 1


title: PAPC_rep1

description:
Gene expression after exposure to PAPC
AR1704_01

source_name: THP-1 cell, PAPC, replicate 1


title: OxPAPC_rep1

description:
Gene expression after exposure to OxPAPC
AR1704_04

source_name: THP-1 cell, OxPAPC, replicate 1


title: Epithelial, rep1 [set 2]

description:
Epithelial-1
Gene expression in normal prostate cells


title: H2[1.3%]OxPAPC_rep2

description:
Gene expression after exposure to H2[1.3%]OxPAPC
AR1704_08

source_name: THP-1 cell, H2[1.3%]OxPAPC, replicate 2


title: PAPC_rep3

description:
Gene expression after exposure to PAPC
AR1704_03

source_name: THP-1 cell, PAPC, replicate 3


title: OxPAPC_rep3

description:
Gene expression after exposure to OxPAPC
AR1704_06

source_name: THP-1 cell, OxPAPC, replicate 3


title: H2[5%]OxPAPC_rep3

description:
Gene expression after exposure to H2[5%]OxPAPC
AR1704_12

source_name: THP-1 cell, H2[5%]OxPAPC, replicate 3


title: HNO223 stable knockdown CTTN clone 1 rep 2 vs. HNO223 control clone 2 rep 2

description: CTTN-1-rep2 vs. Luci-2-rep2

source_name: HNO223_CTTN KO

value: Head and neck squamous cell carcinoma (HNSCC)

value: CTTN knockdown

value: control


title: Id3 LN 5 (IgM)


title: Id3 LN 3 (IgM)


title: Id3 LN 4 (IgM)


title: B6 serum 6 (IgM)

description: Serum

source_name: Serum

value: Serum


title: Id3 LN 6 (IgM)


title: Id3 spleen 4 (IgG)

label: Cy3 labeled anti-IgG


title: Id3 spleen 6 (IgG)


title: B6 spleen 3 (IgG)


title: B6 spleen 4 (IgG)


title: Id3 spleen 5 (IgG)


title: B6 spleen 5 (IgG)


title: Id3 spleen 3 (IgG)


title: Id3 serum 5 (IgM)

description: Serum


title: B6 serum 5 (IgM)

description: Serum


title: Id3 serum 4 (IgM)

description: Serum


title: B6 serum 4 (IgM)

description: Serum


title: Id3 serum 3 (IgM)

description: Serum


title: Id3 serum 6 (IgM)

description: Serum


title: B6 serum 3 (IgM)

description: Serum


title: B6 LN 6 (IgG)


title: Id3 SMG 2 (IgG)


title: B6 LN 4 (IgG)


title: B6 LN 5 (IgG)


title: B6 LN 3 (IgG)


title: Id3 LN 4 (IgG)


title: Id3 LN 6 (IgG)


title: B6 serum 5 (IgG)

description: Serum


title: B6 serum 6 (IgG)

description: Serum


title: B6 serum 4 (IgG)

description: Serum


title: Id3 LN 5 (IgG)


title: Id3 LN 3 (IgG)


title: Id3 serum 6 (IgG)

description: Serum


title: Id3 serum 4 (IgG)

description: Serum


title: Id3 serum 5 (IgG)

description: Serum


title: B6 spleen 1 (IgM)

label_protocol: Autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG) and 635nm (cy5 labeled anti-IgM)


title: B6 spleen 2 (IgM)


title: Id3 LN 1 (IgM)


title: B6 LN 2 (IgM)


title: Id3 spleen 1 (IgM)


title: Id3 spleen 2 (IgM)


title: B6 serum 2 (IgM)

description: Serum


title: B6 LN 1 (IgM)


title: B6 serum 1 (IgM)

description: Serum


title: B6 serum 3 (IgG)

description: Serum


title: Id3 LN 2 (IgM)


title: Id3 serum 1 (IgM)

description: Serum


title: B6 spleen 2 (IgG)


title: Id3 SMG 1 (IgG)


title: Id3 spleen 2 (IgG)


title: B6 spleen 1 (IgG)


title: Id3 serum 2 (IgM)

description: Serum


title: Id3 spleen 1 (IgG)


title: Id3 SMG 1 (IgM)


title: Id3 serum 3 (IgG)

description: Serum


title: Human Female with Syndromic Intellectual disability_2_CGH-array

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

country: Spain

institute: Hospital Universitari i Politecnic La Fe

hyb_protocol: Hybridization protocol was the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol Version 4.0.

scan_protocol: Scanning was made with Agilent G2565BA. For feature extraction we used the Agilent Feature Extraction Software 9.5.31.  The extraction protocol and metrics were  the Agilent protocol CGH-v4_95_Feb07 and the QC Metric Set CGH_QCM_Feb07.

data_processing: The algorithm used are the Z-score and/or ADM-2. The supplementary files containing the normalized log2 ratios are available on the sample records. These files contain normalized log2 ratio representing test/reference.

source_name: Peripheral blood DNA

label_protocol: test  and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS

extract_protocol: DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.

value: test

source_name: pooled peripheral blood DNA from 37 healthy females

value: reference


title: B6 LN 2 (IgG)


title: Id3 serum 1 (IgG)

description: Serum


title: Id3 LN 1 (IgG)


title: Id3 LN 2 (IgG)


title: B6 serum 2 (IgG)

description: Serum


title: B6 serum 1 (IgG)

description: Serum


title: Id3 serum 2 (IgG)

description: Serum


title: B6 LN 1 (IgG)


title: KO 1h TPA rep1

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: RNA was hybridised to Mouseref-6 arrays (approx. 47,000 transcripts, Illumina Inc, USA).

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw intensity values were VST transformed and quantile normalised

source_name: mouse embryonic fibroblasts

label_protocol: The RNA were biotinylated and amplified using an Illumina TotalPrep RNA Amplification Kit (Ambion by Life Technologies).

growth_protocol: MEFs were grown in DMEM supplemented with 10% FBS, penicillin [100 units/ml], streptomycin [100 µg/ml] and sodium pyruvate [1 mM] prior to treatment.

extract_protocol: Total RNA was extracted from cells using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 100ng/ml TPA.

value: male

tag: developmental stage

value: day 13.5 embryo

value: DUSP5 knockout (KO)


title: WT 3h TPA rep1

value: wild type (WT)


title: KO 3h TPA rep1


title: WT 3h TPA rep2


title: KO 0h TPA rep2


title: WT 1h TPA rep1


title: WT 1h TPA rep3


title: WT 0h TPA rep2


title: Serum.C8

city: Shenyang

first: Xinghua

last: Gao

state: Liaoning

address: No.155  Nanjing  North  Street

department: Department  of  Dermatology

country: China

institute: No.1  Hospital  of  China  Medical  University

description:
controls
Genome-wide miRNA profiling in serum

scan_protocol: The global miRNA profiling was performed by using the TaqMan® Low Density Array (TLDA) Human microRNA Panel version 1.0 (Capitalbio, Beijing, China). n/a

data_processing: Raw cycle threshold (Ct) values were calculated using SDS 2.3 and RQ manager 1.2 software (Applied Biosystems) and applied automatic baselines and threshold settings. Raw cycle threshold (Ct) values were calculated using SDS 2.3 and RQ manager 1.2 software (Applied Biosystems) and applied automatic baselines and threshold settings.

label: FAM

source_name: healthy children

label_protocol: manufacturer's instructions

extract_protocol: Total RNA was extracted from serum and urine samples with miRNeasy kit (#217004, QIAGEN) according to the manufacturer’s protocol for liquid samples.

tag: source

value: serum

tag: phenotype

value: healthy


title: KO 0h TPA rep3


title: KO 1h TPA rep2


title: WT 1h TPA rep2


title: KO 1h TPA rep3


title: WT 0h TPA rep3


title: Epithelial, rep3 [set 1]

description: Gene expression in normal prostate cells

hyb_protocol: The fragmented and labeled cRNA (1.5ug) were hybridized onto Invitrogen's 2x105k format Human NCODE array using Agilent Technologies Gene Hybridization protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 021441_ncRNA_v1_human_FE_grid_template) to obtain mean signals which were background corrected, log transformed and normalized using using Limma package.

label_protocol: The samples were labeled using One Color Quick Amp Labeling kit following Manufacturer's (Agilent Technologies) protocol. The protocol incorporates Cyanine 3-CTP to the target (cRNA) material.

extract_protocol: PC3 cell RNAs were prepared using the RNeasy kit (QAIGEN, Valencia CA) following the manufacturer's recommendations. The prostate epithelial cell RNA was purchased from Biochain (Cat # R1234201-50, Newark CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment


title: KO 3h TPA rep2


title: WT 0h TPA rep1


title: Epithelial, rep2 [set 1]


title: PC3, rep3 [set 1]

description: Gene expression in androgen insensitive prostate cancer cells

source_name: PC3 prostate cancer cells

tag: cell line

value: Prostate Cancer cells


title: KO 0h TPA rep1


title: Epithelial, rep1 [set 1]


title: KO 3h TPA rep3


title: WT 3h TPA rep3


title: Serum.C7


title: Serum.C5


title: Serum.C4


title: Serum.C3


title: Serum.C2


title: Serum.C6


title: Serum.C1


title: HFD_WT3

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall

department: Department of Molecular & Integrative

institute: University of Illinois at Urbana-Champaign

description: replicate 3

data_processing: The data were processed in R (2.15.0) using limma (3.12.3) using the neqc function, which does a normexp background correction using negative control probes, quantile normalization using negative and positive control probes and log2 transformation.

source_name: Liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions

extract_protocol: Details can be found in Kim DH, Xiao Z, Kwon S, Sun X, Tkac D, Ryerson D, Choi SE, Ma P, Wi S, Chiang CM, Palvimo J, Chen LF, Kemper B, and J. K. Kemper (2014) A dysregulated Acetyl/SUMO switch of FXR promotes hepatic inflammation in obesity. EMBO Journal,

tag: obesity status

value: obese

tag: expression construct

value: FXR-WT

value: 8 weeks

value: liver


title: ND_217_Q3

description: replicate 3

value: lean


title: HFD_WT1

description: replicate 1


title: Serum-AD.A7

description:
cases
Genome-wide miRNA profiling in serum

source_name: Atopic dermatitis children

value: Atopic dermatitis


title: Serum-AD.A5


title: Serum-AD.A8


title: Serum-AD.A4


title: Serum-AD.A1


title: Serum-AD.A2


title: Serum-AD.A3


title: Serum-AD.A6


title: SK-N-BE(2) FOXP1 T72

city: Cologne

first: Sandra

last: Ackermann

address: Kerpener Str. 62, Geb. 26, UG

department: Pediatric Oncology and Hematology

institute: University Hospital of Cologne

description: Gene expression after 72 hr in FOXP1-induced SK-N-BE(2)

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

data_processing: Data normalization using the quantile algorithm, Reference: G. K. Smyth. Limma: linear models for microarray data. In: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, 2005. pp. 397-420.

source_name: Cell line

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: Cells were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

tag: transgene

tag: time point


title: ND_217_Q1

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

tag: strain

tag: gender


title: ND_WT2

description: replicate 2

tag: age

tag: tissue


title: R26-LSL-KITD816V:Vav-iCre fetal liver rep1

city: Bonn

first: Natalie

last: Haas

address: Sigmund-Freud-Str. 25

department: Department of Developmental Pathology

institute: University of Bonn Medical School/ Institute of Pathology

description:
9249051014_D
replicate 1

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

source_name: Mouse fetal liver

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol provided by the manufacturer. Quality control was performed with Agilent Bioanalyser.

value: Embryo

value: fetal liver

tag: genotype/variation


title: PC3, rep1 [set 1]

tag: cell type


title: HFD_WT2

description: replicate 2


title: HFD_217_R2

description: replicate 2


title: ND_WT1

description: replicate 1


title: R26-LSL-KITD816V:Vav-iCre fetal liver rep3

description:
9249051014_F
replicate 3


title: R26-LSL-KITD816V:Vav-iCre fetal liver rep2

description:
9249051014_E
replicate 2


title: Urine.C3

description:
controls
Genome-wide miRNAs profiling in serum

value: urine


title: Urine.C2


title: HFD_217_R1

description: replicate 1


title: HFD_217_R3

description: replicate 3


title: SK-N-BE(2) FOXP1 T24

description: Gene expression after 24 hr in FOXP1-induced SK-N-BE(2)


title: ND_217_Q2

description: replicate 2


title: SK-N-BE(2) FOXP1 T12

description: Gene expression after 12 hr in FOXP1-induced SK-N-BE(2)


title: Urine-AD.A1

description:
cases
Genome-wide miRNAs profiling in serum


title: SK-N-BE(2) FOXP1 T0

description: Gene expression after 0 hr in FOXP1-induced SK-N-BE(2)

value: 0 h


title: PC3, rep2 [set 1]


title: Urine-AD.A2


title: Urine.C1


title: Urine-AD.A3


title: SK-N-BE(2) GFP T72

description: Gene expression after 72 hr in GFP-induced SK-N-BE(2)

value: GFP


title: Control fetal liver rep3

description:
9249051014_C
replicate 3

value: R26-LSL-KITD816V single transgenic


title: treatment,biological rep3

city: hefei

first: Shanshan

last: Xie

state: anhui

address: No.130 changjiang west road

institute: Anhui agricultural university

description: Gene expression data from Bacillus subtilis in response to rice seedlings

hyb_protocol: Complex probes were hybridized to eachGeneChip® B. subtilisGenome Array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

organism: Bacillus subtilis

label_protocol: A total of 1000ng of total RNA was labelled using the Genisphere HSR labelling Kit.

growth_protocol: B. subtilis OKB105 was grown in LB at 37℃for 12 h. Cells were harvested by centrifugation at 8000 rpm for 15 min at 4℃, resuspended in distilled water and adjusted to a final concentration of 106 cfu ml-1.

extract_protocol: Total RNA was extracted using the Bacterial RNA Kit according to the manufacturer’s instructions.

treatment_protocol: 50 ml 106 cfu/ml B. subtilis OKB105 suspensions incubating with 30 rice seedlings for 2 h were harvested for following microarray analysis, and OKB105 cells that without interacting with rice were used as control.

tag: treatment

value: in response to rice seedlings


title: SK-N-BE(2) GFP T24

description: Gene expression after 24 hr in GFP-induced SK-N-BE(2)


title: treatment,biological rep1

source_name: Bacillus subtilis in response to rice seedlings


title: control, biological rep2

description: Gene expression data from Bacillus subtilis without exposing to rice seedlings

value: without exposing to rice seedlings


title: 35S-AFL1_stress_rep2

city: Taipei

first: Verslues

middle: Edwin

last: Paul

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: A volume of 44 µl of Alexa555-labeled cDNA was denatured at 98℃ for 3 min and cooled to room temperature. The cDNA solution was mixed with 11µl of 10x Agilent blocking agent followed by 55 µl of 2x Agilent hybridization buffer. The 100 µl of reaction mix was hybridized to Agilent Arabidopsis (V4) Gene Expression Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides. Scan resolution 5mm, Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 021169_D_F_20100217) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: seedlings, low water potential

label_protocol: 15 µg of total RNA was annealed to Oligo dTV DNA primer, and cDNA was synthesized in a reverse transcription reaction with an amino allyl modified dUTP. The amino allyl labeled cDNA was then coupled to Alexa 555 dye (Invitrogen) containing a NHS-ester leaving group. Unreacted NHS-ester Alexa dyes were quenched with addition of 4.5 µl of 4 M hydroxylamine and removed by PCR clean up kit (QIAGEN).

growth_protocol: Seedlings were growtn for sevenb days on agar plates containing half strength Murashige-Skoog media with 2 mM MES buffer (pH 5.7) and kept under continuous light (80-100 micromol photons m-2sec-1 at 23 C.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plant Mini Kit according to the manufacturers protocol.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After seven days of growth, seedlings were transferred either to fresh plates of control media or to agar plates infused with polyethylene glycol 8000 (PEG) to impose low water potential (-1.2 MPa) stress.  Samples were collected 10 h after transfer.

value: whole seedling

tag: genotype

value: Transgenic 35S:YFP-AFL1

tag: genetic background


title: control, biological rep1

source_name: Bacillus subtilis without exposing to rice seedlings


title: control, biological rep3


title: Control fetal liver rep1

description:
9249051014_A
replicate 1

tag: developmental stage

value: Vav-iCre single transgenic


title: CHP-212 FOXP1 T72

description: Gene expression after 72 hr in FOXP1-induced CHP-212


title: Control fetal liver rep2

description:
9249051014_B
replicate 2


title: 35S-AFL1_stress_rep3


title: SK-N-BE(2) GFP T12

description: Gene expression after 12 hr in GFP-induced SK-N-BE(2)


title: treatment,biological rep2


title: SK-N-BE(2) GFP T0

description: Gene expression after 0 hr in GFP-induced SK-N-BE(2)


title: 35S-AFL1_stress_rep1


title: CHP-212 FOXP1 T24

description: Gene expression after 24 hr in FOXP1-induced CHP-212


title: CHP-212 FOXP1 T12

description: Gene expression after 12 hr in FOXP1-induced CHP-212


title: Wild type_stress_rep2

value: wild type (Col-0)


title: CHP-212 GFP T24

description: Gene expression after 24 hr in GFP-induced CHP-212


title: Wild type_stress_rep3


title: CHP-212 FOXP1 T0

description: Gene expression after 0 hr in FOXP1-induced CHP-212


title: CHP-212 GFP T72

description: Gene expression after 72 hr in GFP-induced CHP-212


title: Human Female low BMD_5

city: Chang sha

first: shishi

last: min

state: Hunan

address: Lu shan  road

department: College of life sciences

institute: Hunan Normal University

hyb_protocol: Affymetrix GeneChip Human Exon 1.0 ST arrays were hybridized with 11 μg of labeled sense DNA.

scan_protocol: Array scanning was performed according to the protocol described in WT Sense Target Labeling Assay Manual

data_processing: All the expression data of the 10 samples had been preprocessed using robust multichip average (RMA) normalization.

source_name: Healthy female_low_BMD

label_protocol: Double-stranded cDNA was synthesized by using the Superscript Choice System, followed by an in vitro transcription reaction with a T-7 (dT24) primer to produce biotinylated cRNA. The full-length cRNAs were fragmented to 20 to 200 bp and hybridized to Affymetrix GeneChip Human Exon 1.0 ST Array. 100 ng of total RNA was amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.

growth_protocol: One hundred and fifty milliliters of peripheral blood were drawn for each selected subject.

extract_protocol: Genomic DNA was extracted from the freshly isolated PBMs. Total RNA from monocytes was extracted using a Qiagen RNeasy Mini Kit . RNA integrity was assessed by using an Agilent 2100 Bioanalyzer .

treatment_protocol: Monocyte isolation：A monocyte negative isolation kit (Order No. 130-091-153, Miltenyi Biotec Inc., Auburn, CA, USA) was used to isolate circulating monocytes from 150mL whole blood.

value: blood

value: Peripheral blood monocytes

tag: Sex

value: female


title: Human Female low BMD_4


title: Human Female low BMD_2


title: Human Female low BMD_3


title: Human Female high BMD_5

source_name: Healthy female_high_BMD


title: Human Female low BMD_1


title: Human Female high BMD_4


title: Wild type_stress_rep4


title: 35S-AFL1_control_rep3

source_name: seedlings, unstressed


title: Human Female high BMD_3


title: Wild type_stress_rep1


title: Human Female high BMD_1


title: 35S-AFL1_control_rep2


title: Human Female high BMD_2


title: Wild type_control_rep4


title: IMR-32 FOXP1 T72

description: Gene expression after 72 hr in FOXP1-induced IMR-32


title: CB 18th day embryo_muscle sample 2

city: Hyderabad

first: Tarun

middle: K

last: Bhattacharya

address: Rajendranagar

country: India

institute: Directorate of Poultry Research

description: Gene expression at embryonic stage.

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanning was done using Agilent Technologies G2505C scanner.

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Gallus gallus

source_name: Muscle of 18th day embryonic stage of control broiler bird

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double-stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis, Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Chickens were reared following standard managemental protocol at the Institute farm from where fertile eggs were collected. The fertile eggs were kept in the Institute hatchery for embryonic development.

extract_protocol: Total RNA was extracted using the TRIzol method as recommended by manufacturer's protocol.

treatment_protocol: Embryo of Aseel bird was used as treatment group and embryo of broiler bird was used as control group. Aseel was slow-growing bird while control broiler was fast-growing line.

tag: breed

value: broiler

value: muscle of embryo

value: 18th day embryo


title: CHP-212 GFP T0

description: Gene expression after 0 hr in GFP-induced CHP-212

tag: cell line


title: Human Male with Syndromic Intellectual disability_2_CGH-array

value: male

tag: sample type

value: test

source_name: pooled peripheral blood DNA from 11 healthy males

value: reference


title: CHP-212 GFP T12

description: Gene expression after 12 hr in GFP-induced CHP-212

value: GFP


title: IMR-32 FOXP1 T12

description: Gene expression after 12 hr in FOXP1-induced IMR-32


title: IMR-32 FOXP1 T0

description: Gene expression after 0 hr in FOXP1-induced IMR-32

value: 0 h


title: Human Female with Syndromic Intellectual disability_1_CGH-array

source_name: Peripheral blood DNA

source_name: pooled peripheral blood DNA from 11 healthy females


title: Wild type_control_rep2


title: IMR-32 FOXP1 T24

description: Gene expression after 24 hr in FOXP1-induced IMR-32


title: Human Male with Syndromic Intellectual disability_1_CGH-array


title: 35S-AFL1_control_rep1


title: CB 18th day embryo_muscle sample 1

description: Gene expression at embryonic stage.


title: Aseel 18th day embryo_muscle sample 2

description: Gene expression at embryonic stage.

source_name: Muscle of 18th day embryonic stage of Aseel bird

value: Aseel


title: IMR-32 GFP T72

description: Gene expression after 72 hr in GFP-induced IMR-32


title: Aseel 18th day embryo_muscle sample 1

description: Gene expression at embryonic stage.


title: CB 7th day embryo_sample 2

description: Gene expression at embryonic stage.

scan_protocol: Scanned using Agilent Technologies G2505C scanner.

source_name: 7th day embryo of control broiler bird

extract_protocol: Total RNA was isolated using TRIZOL method. Total RNA and cRNA Purification Kit: Qiagen’s RNeasy Mini Kit (Cat#74104) was used.

value: whole embryo

value: 7th day embryo


title: Wild type_control_rep1

value: whole seedling


title: Wild type_control_rep3


title: IMR-32 GFP T24

description: Gene expression after 24 hr in GFP-induced IMR-32


title: IMR-32 GFP T12

description: Gene expression after 12 hr in GFP-induced IMR-32


title: Aseel 7th day embryo_sample 2

description: Gene expression at embryonic stage.

source_name: 7th day embryo of Aseel bird


title: CB 7th day embryo_sample 1

description: Gene expression at embryonic stage.


title: IMR-32 GFP T0

description: Gene expression after 0 hr in GFP-induced IMR-32


title: Ashbya_gossypii_VTT_D-101398_0h_DTT_addition_(at_9.5h_culture)_rep2

status: Public on Oct 16 2014

city: Braga

first: Tatiana

middle: Quinta

last: Aguiar

address: Campus de Gualtar

country: Portugal

institute: Centre of Biological Engineering of the Universisty of Minho

hyb_protocol: Hybridization was performed in a NimbleGen Hybridization System according to the Roche NimbleGen Arrays User’s Guide: Gene Expression Arrays v5.0 (http://www.nimblegen.com/).

scan_protocol: Scanning was performed in a NimbleGen MS 200 Microarray Scanner according to the Roche NimbleGen Arrays User’s Guide: Gene Expression Arrays v5.0 (http://www.nimblegen.com/).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. 2003 - PMID: 12925520), quantile normalization (Bolstad et al. 2003 - PMID: 12538238), and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Eremothecium gossypii

source_name: A. gossypii VTT D-101398_immediatly after addition of DTT at 9.5h of culture

label_protocol: Double-stranded cDNA was labelled with Cy3 fluorescent dye (NimbleGen One-Color DNA Labeling Kit) according to the NimbleGen Arrays User’s Guide: Gene Expression Arrays v5.0 (http://www.nimblegen.com/).

growth_protocol: A. gossyppii pre-cultures were inoculated with 10^6 spores and grown for 14-17 h at 30C and 200 rpm in 250 ml Erlenmeyer flasks containing 50 ml of AFM (1% (w/v) yeast extract, 1% (w/v) tryptone, 2% (w/v) glucose and 0.1% (w/v) myo-inositol) with 200 μg/ml G418. Biostat® CT bioreactors (maximum working volume of 2.5 l) containing 1.5 l or 2 l of AFM plus 200 μg/ml G418 were inoculated to an initial biomass of 0.13 ± 0.08 g/l and cultures were grown at 30°C, pH 6.0 and 500 rpm, with 1.0 volume of gas per volume of culture per minute aeration.

extract_protocol: Total RNA extraction from frozen mycelium was carried out using the RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s instructions for isolation of total RNA from filamentous fungi. RNA concentration and purity were determined using a NanoDrop ND-1000 (NanoDrop Technologies) and integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mycelial samples from the recombinant strains (VTT D-101398 and correspending empty vector control strain) were collected from duplicate bioreactor cultivations 4h, 7h, 10h and 13.5/14h after inoculation. After 9.5 h, DTT was added to two independent A. gossypii VTT D-101398 cultures at a final concentration of 10 mM. Samples from DTT-treated cultures were collected 0.5h, 1h and 4h after DTT addition. Mycelium was rapidly separated from the culture supernatant by filtration through Whatman GF/B glass fibre filters, washed with two sample volumes of 0.9% (w/v) NaCl, frozen immediately in liquid nitrogen and stored at -80ºC.

value: VTT D-101398 secreting recombinant EGI

value: mycelia


title: Ashbya_gossypii_VTT_D-101398_0.5h_DTT_rep2

source_name: A. gossypii VTT D-101398_0.5h after DTT addition

value: 0.5h after DTT addition


title: Ashbya_gossypii_VTT_D-101398_0h_DTT_addition_(at_9.5h_culture)_rep1

value: immediatly after addition of DTT at 9.5h of culture


title: Ashbya_gossypii_VTT_D-101398_1h_DTT_rep2

source_name: A. gossypii VTT D-101398_1h after DTT addition

value: 1h after DTT addition


title: Ashbya_gossypii_VTT_D-101398_4h_DTT_rep2

source_name: A. gossypii VTT D-101398_4h after DTT addition

value: 4h after DTT addition


title: Ashbya_gossypii_VTT_D-101398_0.5h_DTT_rep1


title: Ashbya_gossypii_empty_vector_14h_culture_rep2

source_name: A. gossypii empty vector control_14h of culture

value: empty vector control strain

value: 14h of culture


title: Ashbya_gossypii_empty_vector_7h_culture_rep2

source_name: A. gossypii empty vector control_7h of culture

value: 7h of culture


title: Ashbya_gossypii_VTT_D-101398_1h_DTT_rep1


title: Ashbya_gossypii_VTT_D-101398_4h_DTT_rep1


title: Ashbya_gossypii_empty_vector_10h_culture_rep2

source_name: A. gossypii empty vector control_10h of culture

value: 10h of culture


title: Aseel 7th day embryo_sample 1

description: Gene expression at embryonic stage.


title: P26

city: Yufu

first: Takahiro

last: Narimatsu

state: Oita

address: Hasamamachi Idaigaoka 1-1

department: Medicine

institute: Oita University

description: peripheral blood cells of 10 healthy male voluteers were used as the source of control DNA

hyb_protocol: dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65C for 24 h

scan_protocol: A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm

data_processing: Microarray images were analyzed by using FEATURE EXTRACTION v.9.1.3.1, v.9.5.1.1 or v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_91 or CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy5 (tumor) to Cy3 (Control) was calculated. Aberrant regions were determined by the Aberration Detection Method-2 algorithm at a threshold of 6.0 in DNA Analytics. To detect gains and losses of chromosomal regions, we set the values of parameters for aberration filters as follows: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.10, maximum number of aberrant regions 10000, and percentage penetrance per feature 0.

source_name: primary ccRCC

label_protocol: Agilent Genomic DNA Labeling Kit Plus(Agilent)

extract_protocol: standard proteinase K-digestion method

value: primary ccRCC

value: male

tag: site

value: kidney

tag: Stage

source_name: peripheral blood cells

value: peripheral blood cells


title: Ashbya_gossypii_empty_vector_4h_culture_rep2

source_name: A. gossypii empty vector control_4h of culture

tag: time point

value: 4h of culture


title: P27


title: P29

value: female


title: Ashbya_gossypii_empty_vector_14h_culture_rep1

tag: strain


title: P30


title: Ashbya_gossypii_empty_vector_10h_culture_rep1


title: P20


title: P21


title: P25


title: P23


title: P24


title: P28


title: P22


title: Ashbya_gossypii_empty_vector_7h_culture_rep1


title: P19


title: Ashbya_gossypii_VTT_D-101398_4h_culture_rep2

source_name: A. gossypii VTT D-101398_4h of culture

value: VTT D-101398 secreting recombinant endoglucanase I (EGI)


title: Ashbya_gossypii_VTT_D-101398_10h_culture_rep2

source_name: A. gossypii VTT D-101398_10h of culture


title: P18


title: P11


title: Ashbya_gossypii_empty_vector_4h_culture_rep1


title: Ashbya_gossypii_VTT_D-101398_13.5h_culture_rep2

source_name: A. gossypii VTT D-101398_13.5h of culture

value: 13.5h of culture


title: Ashbya_gossypii_VTT_D-101398_7h_culture_rep2

source_name: A. gossypii VTT D-101398_7h of culture

value: mycelia


title: Ashbya_gossypii_VTT_D-101398_7h_culture_rep1


title: P14


title: P16


title: Ashbya_gossypii_VTT_D-101398_10h_culture_rep1


title: P12


title: Ashbya_gossypii_VTT_D-101398_13.5h_culture_rep1


title: P15


title: Ashbya_gossypii_VTT_D-101398_4h_culture_rep1


title: scc2-4+ exp2, biological rep4

city: Stockholm

first: Lena

last: Ström

address: Berzelius väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
scc2-4+ 2_4
Gene expression data from scc2-4 cell with break induction on Chr. VI

hyb_protocol: According to manufacturer’s (Affymetrix)  instructions

data_processing:
Gene expression data was pre-processed using RMA normalization in R (library affy), which include Background correction, qunatile normalization and expression calculation, and with batch adjustments using ComBat.R. Then, each run was checked for technical variation and adjustments for batch effects were carried out. In the second experiment run, one sample was excluded because of non-biological variation. In each run, samples were tested for differential expression (FDR≤0.05) between different strains, and within strains but between absence and presence of DSB. Selected probesets were annotated using DAVID software and NetAffxTM (Affymetrix), and heatmaps were generated using Cluster software and visualized in TreeView. Mathematica 7.0 or R 2.9.2 was used for all calculations.
Pleaes note that the GeneChip  Yeast Genome 2.0 Array (GPL2529) contains  probe sets to detect transcripts from both Saccharomyces cerevisiae  and Schizosaccharomyces pombe, but only the data for S.  cerevisiae were included in the analysis, which makes the number of probe sets to be 5864 in the  sample data table.

organism: Saccharomyces cerevisiae

source_name: Scc2-4 cells +DSB

growth_protocol: YEP media supplemented with 2% raffinose

extract_protocol: Total RNA was isolated after zymolase treatment for 1h at 30°C, using Invitrogen PureLink Micro-to-Midi Total RNA Purification System. Sample quantity and quality was assessed with a spectrophotometer (ND-1000, NanoDrop technologies) and Agilent Bioanalyzer 2100

treatment_protocol: Log phase yeast cells were arrested in G2/M. The temperature was raised and 30 minutes later galactose was added to induce one DSB in cells containing the recognition site for the HO enzyme. Ninety minutes later, cells were harvested.

tag: strain background

value: haploid and of W303 origin

value: Scc2 deficient

tag: break induction on chr.iv

value: yes


title: P8

tag: tissue

tag: age


title: P10


title: scc2-4+ exp2, biological rep2

description:
scc2-4+ 2_2
Gene expression data from scc2-4 cell with break induction on Chr. VI

scan_protocol: According to manufacturer’s (Affymetrix)  instructions

tag: genotype/variation


title: scc2-4+ exp2, biological rep3

description:
scc2-4+ 2_3
Gene expression data from scc2-4 cell with break induction on Chr. VI

label_protocol: According to manufacturer’s (Affymetrix)  instructions


title: P13


title: P6


title: P9


title: scc2-4- exp2, biological rep4

description:
scc2-4- 2_4
Gene expression data from scc2-4 cell without break induction on Chr. VI

source_name: Scc2-4 cells -DSB

value: no


title: P4


title: scc2-4- exp2, biological rep3

description:
scc2-4- 2_3
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: P3


title: scc2-4- exp2, biological rep2

description:
scc2-4- 2_2
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: P5


title: P7


title: scc2-4+ exp2, biological rep1

description:
scc2-4+ 2_1
Gene expression data from scc2-4 cell with break induction on Chr. VI


title: WT+ exp2, biological rep2

description:
WT+ 2_2
Gene expression data from WT cell with break induction on Chr. VI

source_name: WT cells +DSB

value: wild type


title: WT+ exp2, biological rep3

description:
WT+ 2_3
Gene expression data from WT cell with break induction on Chr. VI


title: P2


title: WT+ exp2, biological rep1

description:
WT+ 2_1
Gene expression data from WT cell with break induction on Chr. VI


title: P1


title: WT- exp2, biological rep4

description:
WT-2_4
Gene expression data from WT cell without break induction on Chr. VI

source_name: WT cells -DSB


title: M20M

description: normal renal cortex obtained from each patient was used as the source of control DNA

source_name: metastasis of ccRCC

value: metastasis of ccRCC

value: bone

source_name: normal renal cortex

value: normal renal cortex


title: WT- exp2, biological rep3

description:
WT-2_3
Gene expression data from WT cell without break induction on Chr. VI


title: scc2-4- exp2, biological rep1

description:
scc2-4- 2_1
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: WT- exp2, biological rep2

description:
WT-2_2
Gene expression data from WT cell without break induction on Chr. VI


title: M19M

value: pancreas


title: M18M

value: male


title: scc2-4+ exp1, biological rep2

description:
scc2-4+ 1_2
Gene expression data from scc2-4 cell with break induction on Chr. VI


title: M17M

value: small intestine


title: scc2-4+ exp1, biological rep1

description:
scc2-4+ 1_1
Gene expression data from scc2-4 cell with break induction on Chr. VI


title: WT- exp2, biological rep1

description:
WT-2_1
Gene expression data from WT cell without break induction on Chr. VI


title: M13M

value: lung


title: scc2-4+ exp1, biological rep3

description:
scc2-4+ 1_3
Gene expression data from scc2-4 cell with break induction on Chr. VI


title: M16M

value: urinary bladder


title: scc2-4- exp1, biological rep3

description:
scc2-4- 1_3
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: WT+ exp1, biological rep3

description:
WT+ 1_3
Gene expression data from WT cell with break induction on Chr. VI


title: M15M


title: M12M

value: skin


title: WT+ exp1, biological rep2

description:
WT+ 1_2
Gene expression data from WT cell with break induction on Chr. VI


title: scc2-4- exp1, biological rep1

description:
scc2-4- 1_1
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: scc2-4- exp1, biological rep2

description:
scc2-4- 1_2
Gene expression data from scc2-4 cell without break induction on Chr. VI


title: M11M

value: adrenal gland


title: WT+ exp1, biological rep1

description:
WT+ 1_1
Gene expression data from WT cell with break induction on Chr. VI


title: M14M

value: psoas muscle


title: M10M


title: P17

description: peripheral blood cells of 10 healthy male voluteers were used as the source of control DNA

value: primary ccRCC

value: kidney

value: peripheral blood cells


title: M4M


title: WT- exp1, biological rep3

description:
WT- 1_3
Gene expression data from WT cell without break induction on Chr. VI

value: haploid and of W303 origin


title: WT- exp1, biological rep2

description:
WT- 1_2
Gene expression data from WT cell without break induction on Chr. VI

value: no


title: M7M

description: normal renal cortex obtained from each patient was used as the source of control DNA


title: M6M


title: M8M


title: M9M

value: epidural membrane


title: M5M

value: metastasis of ccRCC

value: female

value: brain


title: M2M

value: normal renal cortex


title: M3M

value: male


title: WT- exp1, biological rep1

description:
WT-1_1
Gene expression data from WT cell without break induction on Chr. VI

value: wild type


title: M1M

value: lung


title: M20P


title: 8-12 wk Duct Cell-3

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

description: replicate 3

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

source_name: 8-12 wk Duct Cell

label_protocol: NuGen Amplication and Biotin Labeling Kit V2

extract_protocol: PicoPure Kit

value: pancreas

tag: cell population

value: Duct Cell


title: 8-12 wk Duct Cell-2

description: replicate 2


title: M19P


title: M18P


title: 8-12 wk Duct Cell-1

description: replicate 1


title: Human Male with Syndromic Intellectual disability_SNP-array

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix chromosome Analysis suite (ChAS version 2,0,1,2). Copy number values for individual SNPs were extracted and converted from CEL files.

source_name: Peripheral blood DNA

label_protocol: As per manufacturer (Affymetrix)

tag: gender


title: 8-12 wk Alpha Cell-3

description: replicate 3

source_name: 8-12 wk Alpha Cell

value: Alpha Cell


title: 8-12 wk Duct Cell-4

description: replicate 4


title: M10P


title: 8-12 wk Alpha Cell-2

description: replicate 2


title: M13P


title: M15P


title: 8-12 wk Alpha Cell-4

description: replicate 4


title: 8-12 wk Alpha Cell-5

description: replicate 5


title: M14P


title: M9P


title: P0 Alpha Cell-4

description: replicate 4

source_name: P0 Alpha Cell


title: M12P

source_name: primary ccRCC


title: 8-12 wk Alpha Cell-1

description: replicate 1


title: M17P


title: M8P


title: M16P


title: M11P


title: M7P


title: 8-12wk Beta Cell-4

description: replicate 4

source_name: 8-12 wk Beta Cell

value: Beta Cell


title: P0 Alpha Cell-1

description: replicate 1


title: P0 Alpha Cell-3

description: replicate 3


title: M6P

value: primary ccRCC


title: 8-12wk Beta Cell-3

description: replicate 3


title: M2P

value: kidney


title: 8-12wk Beta Cell-2

description: replicate 2


title: M5P


title: P15 Beta Cell-4

description: replicate 4

source_name: P15 Beta Cell


title: M1P


title: 8-12wk Beta Cell-1

description: replicate 1


title: M3P


title: P15 Beta Cell-1

description: replicate 1


title: P15 Beta Cell-3

description: replicate 3


title: P15 Beta Cell-2

description: replicate 2


title: P0 Alpha Cell-2

description: replicate 2


title: M4P


title: P0 Beta Cell-2

description: replicate 2

source_name: P0 Beta Cell


title: 23-3373-m24

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

description: biological replicate 5

data_processing: The raw data were log2 transformed and processed with background correction and quantile normalization using R statistical packages.  Linear models and empirical Bayes method in Lima (Smyth, Stat Appl Genet Mol Biol 2004; 3:Article3) were used to access the differential expression between the wild types and transgenics.

source_name: 24 wk transgenic, mild line rep5

growth_protocol: Mice were housed in microinsular cages in a dedicated mouse room in the Lerner Research Institute's virarium.  Animals were fed a standard diet.

extract_protocol: Mice were euthanized by carbon dioxide inhalation, and hearts were excised postmortem.  Total RNA was extracted with Trizol Reagent (Invitrogen), DNase-treated using the DNA-free Kit (Ambion), and cleaned up using the RNeasy Kit (Qiagen) following manufacturers' protocols.  RNA concentrations and quality were confirmed on a Nanodrop ND-1000 spectrophotometer and Agilent Bio-analyzer.

value: FVB/N

tag: transgenic line

tag: genotype

value: transgenic

value: 24 weeks

value: Whole heart


title: 24-2084-s24

description: biological replicate 5

source_name: 24 wk transgenic, severe line rep5


title: 21-3374-m24

description: biological replicate 4

source_name: 24 wk transgenic, mild line rep4


title: 22-3745-wm3

description: biological replicate 2

source_name: 3 wk wildtype, mild line rep2

value: wildtype

value: 3 weeks


title: P0 Beta Cell-3

description: replicate 3

tag: developmental stage


title: 19-2797-ws24

description: biological replicate 2

source_name: 24 wk wildtype, severe line rep2

value: female


title: 18-2813-ws24

description: biological replicate 1

source_name: 24 wk wildtype, severe line, rep1


title: E17.5 Beta Cell-3

description: replicate 3

source_name: E17.5 Beta Cell


title: E17.5 Beta Cell-1

description: replicate 1


title: E17.5 Beta Cell-2

description: replicate 2


title: P0 Beta Cell-1

description: replicate 1


title: E15.5 Beta Cell -2

description: replicate 2

source_name: E15.5 Beta Cell


title: 17-3743-wm3

description: biological replicate 1

source_name: 3 wk wildtype, mild line rep1


title: 20-2800-s24

description: biological replicate 4

source_name: 24 wk transgenic, severe line rep4


title: E15.5 Beta Cell -1

description: replicate 1


title: 15-2464-s24

description: biological replicate 3

source_name: 24 wk transgenic, severe line rep3


title: 16-1757-m3

description: biological replicate 3

source_name: 3 wk transgenic, mild line rep3


title: E1.5 Neurog3-null cells-2

description: replicate 2

source_name: E1.5 Neurog3-null cells

value: Neurog3-null cells


title: 13-1417-s3

description: biological replicate 3

source_name: 3 wk transgenic, severe line rep3


title: KD control replicate 2

city: Austin

first: Jonghwan

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

description: Gene expression data

hyb_protocol: A hybridization mixture of the fragmented DNA and probe array control was prepared, followed by hybridization to the probe array during a 16 hour incubation.

scan_protocol: GeneChips were scanned by Affymetrix Scanner 3000

data_processing: Expression data were normalized using a robust multiple array (RMA).

source_name: embryonic stem cells

label_protocol: cDNA synthesis was performed with qScript cDNA supermix (Qunata), followed by labelling with Cy3.

growth_protocol: Mouse J1 ES cells were maintained in DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 20% fetal bovine serum (FBS), 2mM of L-glutamine, 100uM of non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 100uM of β-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor (LIF, Chemicon) and 50U/ml of penicillin/streptomycin. ES cells were cultured in 0.1% gelatin coated dishes.

extract_protocol: Total RNA was isolated from cultured cells using RNeasy plus mini kit (Qiagen).

tag: treatment

value: control knockdown

value: J1 ES cells


title: E15.5 Endocrine Progenitor-2

description: replicate 2

source_name: E15.5 Endocrine Progenitor

value: wild type

value: Endocrine Progenitor


title: 11-2639-s24

description: biological replicate 2

source_name: 24 wk transgenic, severe line rep2


title: Oct4 KD replicate 2

description: Gene expression data

value: Oct4 knockdown

tag: cell line


title: E1.5 Neurog3-null cells-3

description: replicate 3

value: pancreas


title: E1.5 Neurog3-null cells-1

description: replicate 1


title: E1.5 Neurog3-null cells-4

description: replicate 4


title: E15.5 Endocrine Progenitor-1

description: replicate 1


title: 10-3731-ws3

description: biological replicate 2

source_name: 3 wk wildtype, severe line rep2


title: KD control replicate 1

description: Gene expression data


title: E15.5 Beta Cell -3

description: replicate 3

value: Beta Cell


title: 14-3317-m24

description: biological replicate 3

source_name: 24 wk transgenic, mild line rep3


title: E15.5 Endocrine Progenitor-3

description: replicate 3


title: Arid3a KD replicate 2

description: Gene expression data

value: Arid3a knockdown


title: 12-1522-m3

description: biological replicate 2

source_name: 3 wk transgenic, mild line rep2


title: E15.5 Acinar-2

description: replicate 2

source_name: E15.5 Acinar

value: Acinar


title: Oct4 KD replicate 1

description: Gene expression data


title: E15.5 Acinar-1

description: replicate 1


title: 9-2659-m24

description: biological replicate 2

source_name: 24 wk transgenic, mild line rep2

value: FVB/N


title: Arid3a KD replicate 1

description: Gene expression data


title: E15.5 Acinar-3

description: replicate 3


title: E15.5 Progenitor-2

description: replicate 2

source_name: E15.5 Progenitor

value: Progenitor


title: 8-3128-s3

description: biological replicate 2

source_name: 3 wk transgenic, severe line rep2

value: transgenic


title: 7-3002-wm24

description: biological replicate 2

source_name: 24 wk wildtype, mild line rep2

value: 24 weeks

value: Whole heart


title: E11.5 Sox9-3

description: replicate 3


title: E15.5 Progenitor-1

description: replicate 1


title: E11.5 Sox9-4

description: replicate 4


title: BirA control replicate 2

description: Gene expression data

value: BirA control


title: E15.5 Progenitor-3

description: replicate 3


title: Arid3a OE-High replicate 1

description: Gene expression data

value: Arid3a overexpression high

tag: sample type

value: single colony


title: 6-3197-m3

description: biological replicate 1

source_name: 3 wk transgenic, mild line rep1

value: female

value: 3 weeks


title: E11.5 Sox9-2

description: replicate 2

value: wild type


title: Arid3a OE-High replicate 2

description: Gene expression data

value: J1 ES cells