title: HIEG clamp Muscle 13-14 Control

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68073.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5880; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.93; Parameter Scan Time = 12:10:48; Parameter PMT Volts = 530; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5617; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.93; Parameter Scan Time = 12:10:48; Parameter PMT Volts = 540; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5632; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

source_name: Muscle 14 Control after HIEG clamp

tag: skeletal muscle biopsie after clamp;sex = female; Age = 49 years

source_name: Muscle 13 Control before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = female; Age = 49 years; Phenotype = lean


title: HepG2 high glucose rep3

status: Public on Jun 04 2010

type: RNA

city: incheon

first: DeokHoon

last: Kim

address: 7-45 songdo-dong yeonsu-ku

country: South Korea

institute: Lee Gil Ya cancer and diabets institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile in Illumina genome studio v2010.1

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cell line

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

growth_protocol: HepG2 celline was cultured in 25mM glucose DMEM with 10% FBS and 100U/ml penicillin/streptomycin.

extract_protocol: RNA was extracted with RNeasy kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Experion (Bio-rad)

treatment_protocol: 2.7mM glucose was treated in low glucose condition. 25mM glucose was treated in high glucose condition.

tag: cell line

tag: cell culture condition

value: high glucose


title: HIEG clamp Muscle 5-6 Control

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68071.gif

hyb_protocol: The labelled cDNA with cy5 ( before HIEG clamp) and cy3 (after HIEG clamp) from the same subject were pooled and hybridized simultaneously on Stanford microarray.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6040; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 11:28:09; Parameter PMT Volts = 540; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5582; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.49; Parameter Scan Time = 11:28:09; Parameter PMT Volts = 500; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5590; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Muscle 6 Control after HIEG clamp

label_protocol: 10ug aRNA were labeled with cyanine (Cy) 3 or Cy5 dyes during a random-primed reverse transcription reaction using the superscript II (Invitrogen, France).

extract_protocol: Total RNA was extracted from basal and after HIEG clamp biopsies with guanidinium thiocyanate method. RNA concentrations and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France. 500ng of total RNA were amplified using the MessageAmp antisense RNA kit (Ambion, Austin, TX).

tag: skeletal muscle biopsie after clamp;sex = male; Age = 42 years

source_name: Muscle 5 Control before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = male; Age = 42 years; Phenotype = lean


title: [E-TABM-722] do96_HNF4a_liver_ARP31046_mmuC57BL612_SAN03

status: Public on Jun 03 2010

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description:
do96_HNF4a_liver_ARP31046_mmuC57BL612_SAN03.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: HNF4a

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
chip_seq | sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles. doi:10.1016/j.ymeth.2009.03.001

tag: strain

tag: developmentalstage

value: adult

tag: organismpart

value: liver

tag: sex

value: male

tag: individual

tag: chip antibody

tag: chip catalog number


title: HIEG clamp Muscle 11-12 Control

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68072.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5880; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 11:57:45; Parameter PMT Volts = 530; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5609; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.56; Parameter Scan Time = 11:57:45; Parameter PMT Volts = 540; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

source_name: Muscle 12 Control after HIEG clamp

tag: skeletal muscle biopsie after clamp;sex = male; Age = 41 years

source_name: Muscle 11 Control before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = male; Age = 41 years; Phenotype = lean


title: [E-TABM-722] do96_HNF4a_liver_ARP31046_mmuC57BL612_SAN02

description:
do96_HNF4a_liver_ARP31046_mmuC57BL612_SAN02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: Soybean_Tamahomare_Fullygrown2

city: Bunkyo-ku yayoi

first: Tomoyo

last: Narikawa

state: Tokyo

country: Japan

institute: University of Tokyo

description: Gene expression data from beans of Tamahomare at reproductive development

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

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

data_processing:
MAS5.0 was used to format the microarray data into CHP files.
The data were subsequently analyzed with Normalized Message Router (NMR) using Bioconductor and R.

label: biotin

organism: Glycine max

source_name: soybean seed green and fully grown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Both species were geown under the same condition.

extract_protocol: total RNAwas extracted using RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Samples were stored at -80C until RNA extraction.

tag: cultivar

value: Tamahoamare

tag: developmental stage

value: Fully grown


title: HIEG clamp Muscle 1-2 Control

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68069.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6040; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.91; Parameter Scan Time = 11:12:40; Parameter PMT Volts = 520; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5569; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.91; Parameter Scan Time = 11:12:40; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5578; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

source_name: Muscle 2 Control after HIEG clamp

tag: skeletal muscle biopsie after clamp;sex = female; Age = 48 years

source_name: Muscle 1 Control before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = female; Age = 48 years; Phenotype = lean


title: [E-TABM-722] do96_HNF4a_liver_ARP31046_mmuC57BL612_CRI01

description:
do96_HNF4a_liver_ARP31046_mmuC57BL612_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: [E-TABM-722] do600_HNF4a_liver_ARP31046_tc1S2_CRI02

description:
do600_HNF4a_liver_ARP31046_tc1S2_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: HNF4a
Factor Value [GENOTYPE]: contains human chromosome 21

growth_protocol: TC1 mouse | growth | The protocol describing the mouse strain TC1 can be found at http://dx.doi.org/10.1126/science.1114535

tag: genotype

value: contains human chromosome 21


title: [E-TABM-722] do601_CEBPA_liver_sc9314_tc1S2_CRI02

description:
do601_CEBPA_liver_sc9314_tc1S2_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: CEBPA
Factor Value [GENOTYPE]: contains human chromosome 21

value: CEBPA


title: HepG2 high glucose rep2

description: replicate 2

tag: cell line

tag: cell culture condition


title: [E-TABM-722] do601_CEBPA_liver_sc9314_tc1S2_CRI01

description:
do601_CEBPA_liver_sc9314_tc1S2_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: CEBPA
Factor Value [GENOTYPE]: contains human chromosome 21


title: HIEG clamp Muscle 3-4 Control

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68070.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6320; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.13; Parameter Scan Time = 11:45:02; Parameter PMT Volts = 530; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5598; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.13; Parameter Scan Time = 11:45:02; Parameter PMT Volts = 530; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5606; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

source_name: Muscle 4 Control after HIEG clamp

tag: skeletal muscle biopsie after clamp;sex = female; Age = 47 years

source_name: Muscle 3 Control before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = female; Age = 47 years; Phenotype = lean


title: [E-TABM-722] do573_CEBPA_liver_sc9314_tc1S4_CRI01

description:
do573_CEBPA_liver_sc9314_tc1S4_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: CEBPA
Factor Value [GENOTYPE]: contains human chromosome 21

tag: strain

tag: developmentalstage


title: [E-TABM-722] do576_CEBPA_liver_sc9314_tc1S5_CRI01

description:
do576_CEBPA_liver_sc9314_tc1S5_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: CEBPA
Factor Value [GENOTYPE]: contains human chromosome 21

tag: organismpart

tag: sex


title: [E-TABM-722] do502_HNF4a_liver_ARP31046_tc1R329m2_CRI01

description:
do502_HNF4a_liver_ARP31046_tc1R329m2_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: HNF4a
Factor Value [GENOTYPE]: contains human chromosome 21

tag: individual

tag: chip antibody


title: Mutant 2

city: San Francisco

first: Xin

last: Chen

state: CA

country: USA

institute: UCSF

description: Gene expression data from Ihh mutant mice

hyb_protocol: Standard Affy Array protocol by Gladstone Array Core

data_processing: RMA  normalization

source_name: Ihh mutant mouse colon 2

growth_protocol: P9 to p12 control or mutant mice were harvested and colon tissues were dissected out, put immediately into Trizol.

extract_protocol: Total RNA was isolated according to Trizol protocol.

tag: tissue

value: colon

tag: genotype/variation

value: Ihh mutant


title: Control 1

description: Gene expression data from wildtype mice

scan_protocol: Standard Affy Array protocol by Gladstone Array Core

source_name: Wild type mouse colon 1

value: wild type


title: islet of non-pregnant mice 1

city: Bunkyo-Ku

first: Hirotaka

last: Watada

address: 2-1-1 Hongo

department: Medicine, Metabolism and Endocrinology

institute: Juntendo University

description: Gene expression data from islet of non-pregnant mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

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

source_name: islet of non-pregnant mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

extract_protocol: RNA was extracted using the QIAGEN Rneasy mini kit (QIAGE N, Valencia, CA) according to the manufacture's instructions.

treatment_protocol: Pancreatic islet were isolated from control and 12.5 dpc mice by collagenase digestion method.

value: pancreatic islet

tag: status

value: non-pregnant

tag: time

value: 0 dpc


title: MRTFA-B double knockout brain

city: Dallas

first: Mayssa

middle: H.

last: Mokalled

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center at Dallas

description: Gene expression data from MRTF-A-/-;MRTF-BF/F;GFAP-Cre  mouse brain at P1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MRTF-A-/-;MRTF-BF/F;GFAP-Cre mouse brain at P0

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

extract_protocol:
Cortical brain tissues were extracted from three control MRTFA-/-;MRTF-BFlox/Flox and three MRTF-A-/-;MRTF-BF/F;GFAP-Cre mice at postnatal day 0.  Extracts were pooled in control and double knockout groups.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: brain cortex

value: MRTF-A-/-;MRTF-BF/F;GFAP-Cre

tag: age


title: Mutant 1

source_name: Ihh mutant mouse colon 1

label_protocol: Standard Affy Array protocol by Gladstone Array Core


title: Soybean_Tamahomare_Fullygrown1

tag: cultivar

tag: developmental stage


title: [E-TABM-722] do502_HNF4a_liver_ARP31046_tc1R329m2_CRI02

description:
do502_HNF4a_liver_ARP31046_tc1R329m2_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: HNF4a
Factor Value [GENOTYPE]: contains human chromosome 21

tag: genotype

tag: chip catalog number


title: [E-TABM-722] do217_Input_liver_none_tc128_1m9_CRI01

description:
do217_Input_liver_none_tc128_1m9_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: input_DNA
Factor Value [GENOTYPE]: contains human chromosome 21

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://dx.doi.org/10.1016/j.ymeth.2009.03.001

value: none, input DNA


title: Soybean_Tamahomare_Bean5mm1

source_name: soybean seed when the bean's length is 5mm

value: Bean 5mm


title: HepG2 high glucose rep1

description: replicate 1

tag: cell line

tag: cell culture condition

value: high glucose


title: Soybean_Tamahomare_Bean5mm2


title: [E-TABM-722] do20_Input_liver_none_mmuTC1R024_CRI03

description:
do20_Input_liver_none_mmuTC1R024_CRI03.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: input_DNA
Factor Value [GENOTYPE]: contains human chromosome 21

tag: strain

value: adult

value: liver


title: [E-TABM-722] do16_Input_liver_none_mmuC57BL6_CRI02_h0_t0

description:
do16_Input_liver_none_mmuC57BL6_CRI02_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: input_DNA

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://dx.doi.org/10.1016/j.ymeth.2009.03.006

tag: developmentalstage

value: male


title: [E-TABM-722] do20_Input_liver_none_mmuTC1R024_CRI02

description:
do20_Input_liver_none_mmuTC1R024_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: input_DNA
Factor Value [GENOTYPE]: contains human chromosome 21

tag: organismpart


title: [E-TABM-722] do16_Input_liver_none_mmuC57BL6_CRI01_h0_t0

description:
do16_Input_liver_none_mmuC57BL6_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: input_DNA

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://dx.doi.org/10.1016/j.ymeth.2009.03.005

tag: sex


title: [E-TABM-722] do20_Input_liver_none_mmuTC1R024_CRI01

description:
do20_Input_liver_none_mmuTC1R024_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: input_DNA
Factor Value [GENOTYPE]: contains human chromosome 21

tag: individual


title: [E-TABM-722] do600_HNF4a_liver_ARP31046_tc1S2_CRI01

description:
do600_HNF4a_liver_ARP31046_tc1S2_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: TC1 mouse
Factor Value [IMMUNOPRECIPITATE]: HNF4a
Factor Value [GENOTYPE]: contains human chromosome 21

tag: chip antibody


title: Control brain

description: Gene expression data from MRTFA-/-;MRTF-BFlox/Flox  mouse brain at P0

tag: tissue

value: MRTFA-/-;MRTF-BFlox/Flox


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 38

city: Groningen

first: Lude

last: Franke

state: Groningen

department: Genetics

country: Netherlands

institute: University Medical Centre Groningen

description: Gene expression from whole visceral adipose tissue from unrelated Dutch severely obese individuals.

hyb_protocol: 750 ng of complementary RNA was hybridized to Illumina HumanHT12 BeadChips (Illumina, San Diego, CA, USA)

scan_protocol: Illumina BeadArray Reader, data was handled through Illumina BeadStudio Gene Expression module v3

data_processing:
Raw data generated using Illumina BeadStudio Gene Expression module v3.
Processed data generated using custom software: Quantile normalized log2 transformed expression intensity. Subsequently, per sample the intensities have been centered to zero and subsequently scaled such that each individual has a standard deviation of 1 in probe intensities

source_name: Total RNA from whole visceral adipose tissue.

label_protocol: Wedge biopsies of visceral adipose tissue (omentum magus) were taken during surgery. RNA was isolated using the Qiagen Lipid Tissue Mini Kit (Qiagen, Hilden, Germany, 74804) and RNA quality and concentration was assessed with an Agilent Bioanalyzer (Agilent Technologies, Waldbronn, Germany, 5067-1521). Starting with 200 ng of RNA, the Ambion Illumina TotalPrep Amplification Kit was used for anti-sense RNA synthesis, amplification, and purification, according to the manufacturer's protocol (Applied Biosystems/Ambion, Austin, TX, USA).

value: Whole visceral adipose tissue


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 76

extract_protocol: Qiagen Lipid Tissue Mini Kit (Qiagen, Hilden, Germany, 74804)


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 98


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 69


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 107


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 53


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 102


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 52


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 75


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 84


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 70


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 79


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 50


title: HepG2 high glucose rep6

description: replicate 6

source_name: HepG2 cell line


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 45


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 103


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 95


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 88


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 49


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 109


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 74


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 51


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 65


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 93


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 66


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 40


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 43


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 63


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 60


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 73


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 115


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 85


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 77


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 57


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 42


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 97


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 39


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 104


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 56


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 44


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 71


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 92


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 112


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 100


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 83


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 58


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 101


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 64


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 114


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 62


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 61


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 59


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 89


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 113


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 111


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 55


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 68


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 48


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 110


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 65

description: Gene expression from whole subcutaneous adipose tissue from unrelated Dutch severely obese individuals.

source_name: Total RNA from whole subcutaneous adipose tissue.

label_protocol: Wedge biopsies of subcutaneous adipose tissue (abdominal) were taken during surgery. RNA was isolated using the Qiagen Lipid Tissue Mini Kit (Qiagen, Hilden, Germany, 74804) and RNA quality and concentration was assessed with an Agilent Bioanalyzer (Agilent Technologies, Waldbronn, Germany, 5067-1521). Starting with 200 ng of RNA, the Ambion Illumina TotalPrep Amplification Kit was used for anti-sense RNA synthesis, amplification, and purification, according to the manufacturer's protocol (Applied Biosystems/Ambion, Austin, TX, USA).

value: Whole subcutaneous adipose tissue


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 106


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 72


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 90


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 87


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 37


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 86


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 36


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 99


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 114


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 78


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 104


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 109


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 71


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 38


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 112


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 46


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 108


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 85


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 103


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 58


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 69


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 105


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 78


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 93


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 95


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 70


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 77


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 43


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 52


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 40


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 36


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 53


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 86


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 49


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 90


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 79


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 88


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 66


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 48


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 42


title: Whole visceral adipose tissue RNA from Dutch severely obese individual 47


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 73


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 59


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 37


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 96


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 91


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 102


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 68


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 97


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 107


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 41


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 57


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 61


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 50


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 101


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 110


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 75


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 98


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 115


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 76


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 100


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 55


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 44


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 106


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 74


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 99


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 105


title: Gli1FLAG GNP Chip

type: genomic

city: Stanford

first: Eunice

last: Lee

address: 318 Campus Drive

department: Developmental Biology

institute: Stanford University

description:
Gli1-FLAG GNP ChIP biological replicates 1, 2, 3.

The RosaGli1FLAG mice were reported by Vokes et al., Development. 2007 May;134(10):1977-89.
The Math1-Cre mice were reported by Matei et al., Dev Dyn. 2005 Nov;234(3):633-50.

hyb_protocol: At least 5 ug DNA was hybridzed per array using GeneChip Hybridization, Wash, and Stain kit (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was quantile normalized and analyzed with TileMap. Log2(IP/Input) fold changes (fc) for each probe, and TileMap moving average (ma) statistics for each probe, are reported in the BAR files. fc.bar and ma.bar are generated by CisGenome software (previously TileMap). The high-confidence binding regions reported in the paper are listed in the 'Gli1FLAG_GNP_Chip.bed' and 'Gli1FLAG_MB_Chip.bed' files.

source_name: Gli1-FLAG ChIP DNA from P8 RosaGli1-FLAG;Math1Cre granule neuron precusors

label_protocol: Samples (5-7.5 ug DNA) were fragmented and biotin-labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: For GNPs, RosaGli1-FLAG c/c mice were crossed with Math1Cre mice and litters were taken at P8. Cerebellum was dissected into PBS and granule neuron precursor cells were isolated as previously described (Wechsler-Reya and Scott 1999).  Medulloblastoma tumors were isolated from RosaGli1-FLAG c/c;Ptc+/- mice.

extract_protocol: Freshly isolated GNPs or tumor cells were then cross-linked with 1% formaldehyde for 30 minutes.  ChIP and LMPCR was performed as previously described (Vokes et al., 2007).  Prior to hybridization on promoter arrays, enrichment was verified by qPCR.

treatment_protocol: Not applicable.

value: normal cerebellum

tag: cell type

value: granule neuron precursors

tag: antibody

value: FLAG M2 mouse monoclonal

source_name: Total chromatin input from P8 RosaGli1-FLAG;Math1Cre granule neuron precursors


title: Gli1FLAG MB Chip

description:
Gli1-FLAG MB ChIP biological replicates 1, 2, 3.

The RosaGli1FLAG mice were reported by Vokes et al., Development. 2007 May;134(10):1977-89.
The Math1-Cre mice were reported by Matei et al., Dev Dyn. 2005 Nov;234(3):633-50.
The Ptch1+/- mice were reported by Goodrich et al., Science. 1997 Aug 22;277(5329):1109-13.

source_name: Gli1-FLAG ChIP DNA from RosaGli1-FLAG;Math1Cre;Ptc+/- medulloblastoma

value: Adult

value: medulloblastoma tumor

source_name: Total chromatin input from RosaGli1-FLAG;Math1Cre;Ptc+/- medulloblastoma


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 87


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 56


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 84


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 47


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 72


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 39


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 113


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 89


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 63


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 62


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 83


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 45


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 111


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 54


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 92


title: Whole subcutaneous adipose tissue RNA from Dutch severely obese individual 51


title: H4_HC48h

city: Charlestown

first: Lei

last: Lu

address: 114, 16th Street

institute: Massachusetts General Hospital

description: gene expression data for H4 treated with HC for 48 h

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCRMA in R/Bioconductor

source_name: human fetal small intestinal epithelial cell, HC 48h

label_protocol: Affymetrix GeneChip 3' IVT Express

growth_protocol: Cells are grown on 10-cm petri-dish until reach 90% confluency

extract_protocol: Qiagen RNaeasy KIT

treatment_protocol: H4 cells were treated with 1mM hydrocortisone for 12, 24, 48 hours or 5 days

tag: origin

value: fetal

tag: treatment

value: hydrocortisone


title: UD-G-05

city: Boston

first: Wenzhong

last: xiao

state: MA

address: 55 Fruit Street, GRB 1302

description: Gene expression data from Microfluidics isolated human neutrophils, GM-CSF and IFNg stimulated

hyb_protocol: the labeled cDNA was hybridized onto GeneChip™ Human Genome U133 Plus 2.0 Arrays according to standard Affymetrix protocol

scan_protocol: Chips were washed and scanned as recommended by the Ovation System User Guide (version 1.0).

data_processing: Low level analysis was performed using dChip using the perfect match only option.

source_name: Density centrifugation with Ficoll-dextran human neutrophils, Unstimulated

label_protocol: cDNA was synthesized using Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies) from 20 ng of total RNA as starting material.

growth_protocol: Freshly drawn peripheral blood was anti-coagulated with sodium heparin and was directly processed for cell isolation by microfluidics (designated as unstimulated) or stimulated before cell isolation. In addition to microfluidic processing, leukocytes were isolated using density gradient techniques from both unstimulated and stimulated whole blood.

extract_protocol: RNA extraction followed a modified commercial protocol (QIAGEN RNeasy Plus). To remove genomic DNA, 350 l of guanadinium isothiocyanate with detergent (Qiagen RLT Plus Buffer) was added to the thawed, original lysate along with 2 mercaptoethaol (Sigma) at 20 l/ml. This combined lysate was then processed according to manufacturer protocols (Qiagen RNeasy Plus Kit) yielding purified total RNA analyzed on an Agilent Bioanalyzer 2100 system.

treatment_protocol: Stimulated cells were treated with LPS (50 ng/ml) or GM-CSF (20 ng/ml) + IFN-g(100 IU/ml) (abbreviated as GM+I) for 16 hours on a rocker at 37 °C in 5% CO2 atmosphere before cell isolation.

value: human neutrophils

tag: isolation

tag: condition

value: Unstimulated

tag: subject


title: H4_HC24h

description: gene expression data for H4 treated with HC for 24 h

source_name: human fetal small intestinal epithelial cell, HC 24h


title: H4_HC12h

description: gene expression data for H4 treated with HC for 12 h

source_name: human fetal small intestinal epithelial cell, HC 12h


title: UC-G-03

source_name: Microfluidics isolated  human neutrophils, Unstimulated

value: Microfluidics isolated


title: UC-G-05


title: Unst_2

description: Gene expression data from Microfluidics isolated human neutrophils, Unstimulated


title: UD-G-02

value: Density centrifugation with Ficoll-dextran


title: UD-G-06


title: T84

description: gene expression data for T84

source_name: human colonic epithelial cell

value: adult


title: H4_ctrl

description: gene expression data for H4

source_name: human fetal small intestinal epithelial cell

value: control


title: Unst_1

source_name: Microfluidics isolated human neutrophils, Unstimulated


title: UD-G-04


title: UC-G-02


title: H4_HC5d

description: gene expression data for H4 treated with HC for 5d

source_name: human fetal small intestinal epithelial cell, HC 5 day

value: 5 d


title: UC-G-04


title: Unst_3


title: HealthyControl60

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

description: Gene expression of healthy controls

hyb_protocol: According to the standard Affymetrix protocol, with some modifications.

scan_protocol: Affymetrix GeneChip 3000 7G scanner

data_processing: The data were processed using dChip (Build: April 9 2009) using default analysis setting and invariant set normalization.

label_protocol: Biotinylated cRNA were prepared following the standard Affymetrix protocol from 4 ug total RNA.

extract_protocol: Peripheral blood was collected and lysis buffer (bicarbonate-buffered ammonium chloride solution, 0.826%NH4Cl, 0.1% KHC03, 0.0037%Na4EDTA in H2O) was added at a ratio of 20:1 (lysis buffer:blood). Samples were then incubated at room temperature until erythrocyte lysis was complete (5–7 min). Leukocytes were recovered by centrifugation (400 g, 48C) and washed once in ice-cold phosphate buffered saline. Leukocyte pellets were then resuspended in 8ml RLT buffer (Qiagen) and the samples sheared ten times with an 18-gauge needle attached to a 10-ml syringe. Samples were then immediately frozen and kept at 270 8C until RNA extraction was required. Total cellular RNA was isolated from the leukocyte pellets using a commercial kit (RNeasy, Qiagen).

tag: sample type

tag: age (yrs)

tag: age group

value: F


title: HealthyControl63

description: Gene expression of healthy controls

value: M


title: UC-G-06


title: HealthyControl59

description: Gene expression of healthy controls


title: HealthyControl62

description: Gene expression of healthy controls

value: Ped


title: HealthyControl57

description: Gene expression of healthy controls


title: HealthyControl56

description: Gene expression of healthy controls


title: HealthyControl54

description: Gene expression of healthy controls


title: Unst_4


title: UD-G-03


title: HealthyControl61

description: Gene expression of healthy controls


title: HealthyControl58

description: Gene expression of healthy controls


title: HealthyControl53

description: Gene expression of healthy controls


title: HealthyControl51

description: Gene expression of healthy controls


title: HealthyControl50

description: Gene expression of healthy controls


title: HealthyControl49

description: Gene expression of healthy controls


title: HealthyControl52

description: Gene expression of healthy controls


title: HealthyControl47

description: Gene expression of healthy controls


title: HealthyControl55

description: Gene expression of healthy controls


title: HealthyControl46

description: Gene expression of healthy controls


title: HealthyControl44

description: Gene expression of healthy controls


title: HealthyControl41

description: Gene expression of healthy controls


title: HealthyControl40

description: Gene expression of healthy controls


title: HealthyControl48

description: Gene expression of healthy controls


title: HealthyControl39

description: Gene expression of healthy controls


title: HealthyControl42

description: Gene expression of healthy controls


title: HealthyControl43

description: Gene expression of healthy controls


title: HealthyControl36

description: Gene expression of healthy controls


title: HealthyControl35

description: Gene expression of healthy controls


title: HealthyControl25

description: Gene expression of healthy controls


title: HealthyControl33

description: Gene expression of healthy controls


title: HealthyControl26

description: Gene expression of healthy controls


title: HealthyControl29

description: Gene expression of healthy controls


title: HealthyControl23

description: Gene expression of healthy controls


title: HealthyControl38

description: Gene expression of healthy controls


title: HealthyControl30

description: Gene expression of healthy controls


title: HealthyControl45

description: Gene expression of healthy controls


title: HealthyControl28

description: Gene expression of healthy controls


title: HealthyControl31

description: Gene expression of healthy controls


title: HealthyControl32

description: Gene expression of healthy controls


title: HealthyControl34

description: Gene expression of healthy controls


title: HealthyControl24

description: Gene expression of healthy controls


title: HealthyControl27

description: Gene expression of healthy controls


title: HealthyControl22

description: Gene expression of healthy controls


title: HealthyControl18

description: Gene expression of healthy controls


title: HealthyControl20

description: Gene expression of healthy controls


title: HealthyControl21

description: Gene expression of healthy controls


title: HealthyControl19

description: Gene expression of healthy controls


title: HealthyControl15

description: Gene expression of healthy controls


title: HealthyControl11

description: Gene expression of healthy controls


title: HealthyControl10

description: Gene expression of healthy controls


title: HealthyControl9

description: Gene expression of healthy controls


title: HealthyControl17

description: Gene expression of healthy controls


title: HealthyControl14

description: Gene expression of healthy controls


title: HealthyControl13

description: Gene expression of healthy controls


title: HealthyControl16

description: Gene expression of healthy controls


title: HealthyControl6

description: Gene expression of healthy controls


title: HealthyControl3

description: Gene expression of healthy controls


title: HealthyControl5

description: Gene expression of healthy controls


title: HealthyControl1

description: Gene expression of healthy controls


title: BurnPatient56_Mid

description: Gene expression of burn patient

value: burn

tag: hours post injury

tag: sampling time group

value: Mid

tag: total burn surface area (tbsa, %)

tag: injury inhalation

value: No

tag: survival

value: Yes

tag: hospital length of stay (days)


title: BurnPatient55_Early

description: Gene expression of burn patient

value: Adult

tag: sex

value: Early


title: HealthyControl8

description: Gene expression of healthy controls


title: BurnPatient54_Mid

description: Gene expression of burn patient


title: BurnPatient57_Mid

description: Gene expression of burn patient


title: HealthyControl4

description: Gene expression of healthy controls


title: BurnPatient57_Early

description: Gene expression of burn patient


title: HealthyControl2

description: Gene expression of healthy controls


title: HealthyControl7

description: Gene expression of healthy controls


title: HealthyControl12

description: Gene expression of healthy controls


title: HealthyControl37

description: Gene expression of healthy controls


title: BurnPatient56_Early

description: Gene expression of burn patient


title: BurnPatient53_Mid

description: Gene expression of burn patient


title: BurnPatient55_Mid

description: Gene expression of burn patient


title: BurnPatient53_Early

description: Gene expression of burn patient


title: BurnPatient52_Early

description: Gene expression of burn patient


title: BurnPatient52_Mid

description: Gene expression of burn patient


title: BurnPatient54_Early

description: Gene expression of burn patient


title: BurnPatient51_Early

description: Gene expression of burn patient


title: BurnPatient51_Mid

description: Gene expression of burn patient


title: BurnPatient49_Mid

description: Gene expression of burn patient


title: BurnPatient49_Early

description: Gene expression of burn patient


title: BurnPatient48_Mid

description: Gene expression of burn patient


title: BurnPatient47_Mid

description: Gene expression of burn patient


title: BurnPatient47_Early

description: Gene expression of burn patient


title: BurnPatient41_Early

description: Gene expression of burn patient


title: BurnPatient42_Early

description: Gene expression of burn patient


title: BurnPatient50_Mid

description: Gene expression of burn patient


title: BurnPatient44_Mid

description: Gene expression of burn patient


title: BurnPatient42_Mid

description: Gene expression of burn patient


title: BurnPatient45_Mid

description: Gene expression of burn patient


title: BurnPatient44_Early

description: Gene expression of burn patient


title: BurnPatient45_Early

description: Gene expression of burn patient


title: BurnPatient50_Early

description: Gene expression of burn patient


title: BurnPatient40_Mid

description: Gene expression of burn patient


title: BurnPatient48_Early

description: Gene expression of burn patient


title: BurnPatient46_Mid

description: Gene expression of burn patient


title: BurnPatient40_Early

description: Gene expression of burn patient


title: BurnPatient43_Early

description: Gene expression of burn patient


title: BurnPatient43_Mid

description: Gene expression of burn patient


title: BurnPatient41_Mid

description: Gene expression of burn patient


title: BurnPatient38_Mid

description: Gene expression of burn patient


title: BurnPatient38_Early

description: Gene expression of burn patient


title: BurnPatient39_Mid

description: Gene expression of burn patient


title: BurnPatient37_Early

description: Gene expression of burn patient


title: BurnPatient36_Mid

description: Gene expression of burn patient


title: BurnPatient39_Early

description: Gene expression of burn patient


title: BurnPatient34_Early

description: Gene expression of burn patient


title: BurnPatient37_Mid

description: Gene expression of burn patient


title: BurnPatient35_Mid

description: Gene expression of burn patient


title: BurnPatient30_Early

description: Gene expression of burn patient


title: BurnPatient32_Mid

description: Gene expression of burn patient


title: BurnPatient46_Early

description: Gene expression of burn patient


title: BurnPatient32_Early

description: Gene expression of burn patient


title: BurnPatient33_Early

description: Gene expression of burn patient


title: BurnPatient31_Early

description: Gene expression of burn patient


title: BurnPatient36_Early

description: Gene expression of burn patient


title: BurnPatient33_Mid

description: Gene expression of burn patient


title: BurnPatient31_Mid

description: Gene expression of burn patient


title: BurnPatient28_Mid

description: Gene expression of burn patient


title: BurnPatient29_Early

description: Gene expression of burn patient


title: BurnPatient34_Mid

description: Gene expression of burn patient


title: BurnPatient29_Mid

description: Gene expression of burn patient


title: BurnPatient28_Early

description: Gene expression of burn patient


title: BurnPatient35_Early

description: Gene expression of burn patient


title: BurnPatient27_Early

description: Gene expression of burn patient


title: BurnPatient26_Mid

description: Gene expression of burn patient


title: BurnPatient27_Mid

description: Gene expression of burn patient


title: BurnPatient24_Early

description: Gene expression of burn patient


title: BurnPatient26_Early

description: Gene expression of burn patient


title: BurnPatient25_Mid

description: Gene expression of burn patient


title: BurnPatient23_Mid

description: Gene expression of burn patient


title: BurnPatient22_Mid

description: Gene expression of burn patient


title: BurnPatient23_Early

description: Gene expression of burn patient


title: BurnPatient22_Early

description: Gene expression of burn patient


title: BurnPatient20_Mid

description: Gene expression of burn patient


title: BurnPatient25_Early

description: Gene expression of burn patient


title: BurnPatient21_Early

description: Gene expression of burn patient


title: BurnPatient20_Early

description: Gene expression of burn patient


title: BurnPatient21_Mid

description: Gene expression of burn patient


title: BurnPatient18_Mid

description: Gene expression of burn patient


title: BurnPatient30_Mid

description: Gene expression of burn patient


title: BurnPatient19_Mid

description: Gene expression of burn patient


title: BurnPatient19_Early

description: Gene expression of burn patient


title: BurnPatient17_Early

description: Gene expression of burn patient


title: BurnPatient16_Mid

description: Gene expression of burn patient


title: BurnPatient18_Early

description: Gene expression of burn patient


title: BurnPatient16_Early

description: Gene expression of burn patient


title: BurnPatient17_Mid

description: Gene expression of burn patient


title: BurnPatient15_Mid

description: Gene expression of burn patient


title: BurnPatient15_Early

description: Gene expression of burn patient


title: BurnPatient13_Mid

description: Gene expression of burn patient


title: BurnPatient14_Early

description: Gene expression of burn patient


title: BurnPatient14_Mid

description: Gene expression of burn patient


title: BurnPatient13_Early

description: Gene expression of burn patient


title: BurnPatient12_Mid

description: Gene expression of burn patient


title: BurnPatient11_Mid

description: Gene expression of burn patient


title: BurnPatient12_Early

description: Gene expression of burn patient


title: BurnPatient11_Early

description: Gene expression of burn patient


title: [E-TABM-722] do505_HNF4a_liver_ARP31046_hsaHH1294_CRI01

description:
do505_HNF4a_liver_ARP31046_hsaHH1294_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: HNF4a

tag: developmentalstage

tag: organismpart

value: liver

value: male

tag: individual

tag: chip antibody

tag: chip catalog number


title: [E-TABM-722] do206_CEBPA_liver_sc9314_hsa1294_CRI02

description:
do206_CEBPA_liver_sc9314_hsa1294_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: CEBPA

value: CEBPA


title: BurnPatient9_Early

description: Gene expression of burn patient


title: BurnPatient10_Mid

description: Gene expression of burn patient


title: BurnPatient5_Mid

description: Gene expression of burn patient


title: BurnPatient8_Early

description: Gene expression of burn patient


title: BurnPatient7_Early

description: Gene expression of burn patient


title: Tconv activated

city: Okayama

first: Mayuko

last: Yamamoto

address: 675-1, Fujisaki, Naka-ku

department: Cell Biology Institute, Research Center

institute: Hayashibara Biochemical Laboratories Inc.

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min.  Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath.

scan_protocol: Following hybridization, the slides were washed and dried prior to a high-resolution scan on a GenePix 4000B (Molecular Devices, Inc, CA, USA).  Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.  We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.  We normalized biases in net intensity between the one fluorescent dye channel in a microarray by using the global normalization option in Array-Pro Analyzer Ver4.5.  Analyzed data were selected by using MicroArray Data Analysis Tool (Filgen, Inc.).

source_name: Tconv activated

label_protocol: Chemically synthesized oligoribonucleotides (Ambion), or purified miRNAs were labeled with the mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer. Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were first used to append a poly-nucleotide tail.  The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy5 dye (GE Healthcare Bio-Science Corp., Piscataway, NJ, USA).  Unincorporated dyes were removed with a second glass fiber filter-based cleaning procedure.

extract_protocol: To isolate miRNA fractions from total RNA, 8.8μｇ total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per the manufacturer’s recommendation.

tag: cell type

value: Tconv cell


title: [E-TABM-722] do205_Input_liver_none_hsa1294_CRI02

description:
do205_Input_liver_none_hsa1294_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: input_DNA

value: none, input DNA


title: BurnPatient8_Mid

description: Gene expression of burn patient


title: BurnPatient9_Mid

description: Gene expression of burn patient


title: BurnPatient10_Early

description: Gene expression of burn patient


title: BurnPatient7_Mid

description: Gene expression of burn patient


title: BurnPatient6_Mid

description: Gene expression of burn patient


title: [E-TABM-722] do206_CEBPA_liver_sc9314_hsa1294_CRI01

description:
do206_CEBPA_liver_sc9314_hsa1294_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: CEBPA

value: adult


title: [E-TABM-722] do205_Input_liver_none_hsa1294_CRI01

description:
do205_Input_liver_none_hsa1294_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: input_DNA


title: HOZOT cocultured with mouse stroma cells

tag: cell line

value: Treg cell line


title: BurnPatient4_Early

description: Gene expression of burn patient

tag: sample type


title: BurnPatient4_Mid

description: Gene expression of burn patient

tag: age (yrs)


title: BurnPatient2_Mid

description: Gene expression of burn patient

tag: age group


title: Ye478 re-watering, biological rep3

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from maize inbred line Ye478 after re-watering

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

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

organism: Zea mays

source_name: The shoot tissue of the seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The total RNA was extracted by the TRIzol method (Invitrogen, USA). Mesocotyls were ground in liquid nitrogen, and 50-100 mg of frozen tissue was transferred into a tube with 1 ml TRIzol. Next, RNA was isolated, dried and dissolved in 50 µl DEPC-H2O. RNA quality and concentration were determined by 1.0% agarose gel electrophoresis and spectrophotometry.

tag: tissue

value: shoot

tag: developmental stage

value: three-leaf stage seedlings

tag: genotype

tag: protocol

value: re-watering


title: BurnPatient6_Early

description: Gene expression of burn patient

value: M

tag: hours post injury

tag: sampling time group

tag: total burn surface area (tbsa, %)

tag: injury inhalation

tag: survival


title: BurnPatient3_Mid

description: Gene expression of burn patient

value: burn

value: Ped

tag: sex

tag: hospital length of stay (days)


title: [E-TABM-722] do204_CEBPA_liver_sc9314_hsa1323_CRI02

description:
do204_CEBPA_liver_sc9314_hsa1323_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: CEBPA

tag: developmentalstage

tag: organismpart

tag: individual

tag: chip antibody

tag: chip catalog number


title: [E-TABM-722] do203_Input_liver_none_hsa1323_CRI01

description:
do203_Input_liver_none_hsa1323_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: input_DNA


title: BurnPatient1_Mid

description: Gene expression of burn patient

tag: sample type

tag: age (yrs)

tag: age group

value: F

value: Mid

value: No


title: [E-TABM-722] do204_CEBPA_liver_sc9314_hsa1323_CRI01

description:
do204_CEBPA_liver_sc9314_hsa1323_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: BurnPatient3_Early

description: Gene expression of burn patient

value: Early

value: Yes


title: BurnPatient5_Early

description: Gene expression of burn patient


title: BurnPatient2_Early

description: Gene expression of burn patient

value: Adult


title: [E-TABM-722] do199_HNF4a_liver_ARP31046_hsaHH1308_CRI01

description:
do199_HNF4a_liver_ARP31046_hsaHH1308_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: HNF4a

value: liver

value: male


title: [E-TABM-722] do137_Input_liver_none_hsaHH1308_CRI01

description:
do137_Input_liver_none_hsaHH1308_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: input_DNA

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://dx.doi.org/10.1016/j.ymeth.2009.03.004

value: none, input DNA


title: [E-TABM-722] do199_HNF4a_liver_ARP31046_hsaHH1308_CRI02

description:
do199_HNF4a_liver_ARP31046_hsaHH1308_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Homo sapiens
Factor Value [IMMUNOPRECIPITATE]: HNF4a

value: adult


title: [E-TABM-722] do578_Input_liver_none_mdo1_CRI01

description:
do578_Input_liver_none_mdo1_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: input_DNA

organism: Monodelphis domestica


title: BurnPatient1_Early

description: Gene expression of burn patient


title: [E-TABM-722] do247_CEBPA_liver_sc9314_mdo3_CRI02

description:
do247_CEBPA_liver_sc9314_mdo3_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: CEBPA

value: CEBPA


title: Ye478 moderate drought, biological rep3

description: Gene expression data from maize inbred line Ye478 under moderate drought stress

tag: tissue

value: shoot

tag: developmental stage

tag: genotype

value: moderate drought stress


title: Han21 re-watering, biological rep3

description: Gene expression data from maize inbred line Han21 after re-watering

value: three-leaf stage seedlings

tag: protocol

value: re-watering


title: Ye478 control, biological rep3

description: Gene expression data from maize inbred line Ye478 as control

value: control


title: Ye478 severe drought, biological rep3

description: Gene expression data from maize inbred line Ye478 severe drought stress

value: severe drought stress


title: Subject 926, Replicate 4

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Gene expression data from reconstituted human epidermis

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Derived from neonatal foreskin

label_protocol: Total RNA was converted to biotin-labeled cRNA GeneChip target using Ambion Message Amp II- Biotin Enhanced Kit according to manufacture's recommendations.  Biotin-labeled cRNA was purified using the Qiagen RNeasy kit and a total of 20 μg of cRNA was fragmented randomly to ~200 bp at 94°C for 35 min (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc).

growth_protocol: Reconstructed human EpiDerm™ EPI-200 tissues prepared from four different neonatal foreskin donors (254, 1188, 219 and 926) were acquired from MatTek Corporation (Ashland, MA).   Five tissues from each donor were placed into 6-well plates with 1ml/tissue/well of pre-warmed (37°C) NMM media (MatTek Corp.) and incubated overnight at 37°C.

extract_protocol: Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).

treatment_protocol: Following overnight incubation in MMM Media, individual epidermal tissues were peeled from the tissue insert and placed into 2 ml of RNAlater® (Ambion/ABI, Foster City, CA) pre-loaded into a 24-well plate.  After 24 hours incubation under 4°C, the RNAlater® submersed tissues were transferred into a 2 ml Seal-Rite® microcentrifuge tube (USA Scientific Inc, Ocala, FL) and all excess RNAlater® was removed from the tissue by gentle pipetting.  The tissues were stored at -80°C until RNA was isolated.

tag: subject/donor

tag: gender

value: Male

value: cultured epidermis

tag: replicate


title: Han21 severe drought, biological rep3

description: Gene expression data from maize inbred line Han21 severe drought stress


title: W_MoB

city: Laramie

first: Mark

last: Gomelsky

state: WY

institute: University of Wyoming

description: Photosynthetic conditions (10 W/m2, sealed flasks), medium with Tungsten and  Molibdenium

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: RMA processing for corresponding experimental series was used for data analysis and mentioned in the papers; MAS 5.0 values are depositied here for consistensy with other submissions

organism: Cereibacter sphaeroides 2.4.1

source_name: medium with Tungsten and  Molibdenium

label_protocol: according to Affymetrix protocol

extract_protocol: RNA isolated with bead beater + RNeasy kits

tag: strain


title: Subject 926, Replicate 5


title: T cells

city: Tokyo

first: Shinsuke

last: Yuasa

address: 35-Shinanomachi Shinjuku-ku

institute: Keio University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 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 (G2505CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-105_Apr08 and Grid: 014850_D_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: T cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol and RNeasy Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: iPSCs and ESCs were collected by standard collagenase treatment. Activated T cells were collected by cell scraping.

tag: cell type

value: T cells


title: Subject 926, Replicate 3


title: WC

description: Photosynthetic conditions (10 W/m2, sealed flasks), medium with Tungsten instead of Molibdenium


title: W_MoA

growth_protocol: Photosynthetic conditions (10 W/m2, sealed flasks), medium with Tungsten and  Molibdenium


title: TiPSCs

source_name: TiPSCs

value: TiPSCs


title: Han21 control, biological rep3

description: Gene expression data from maize inbred line Han21 as control


title: HDF-iPSCs

description: Kindly gifted from Dr. Yamanaka.

source_name: HDF-iPSCs

value: HDF-iPSCs


title: Subject 254, Replicate 5


title: WB

growth_protocol: Photosynthetic conditions (10 W/m2, sealed flasks), medium with Tungsten instead of Molibdenium


title: Subject 926, Replicate 1


title: Han21 moderate drought, biological rep3

description: Gene expression data from maize inbred line Han21 under moderate drought stress


title: Medulloblastoma, biological replicate 4

description: medulloblastoma, biological replicate 4

hyb_protocol: Samples were hybridized for 16 hours at 45° at 60rpm, according to manufacturer's instructions (Affymetrix).

scan_protocol: Affymetrix GeneChiP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction was applied to probe intensities. Gene expression indices were calculated from the background-corrected core probe intensities using the dChip model.  Differential gene expression was determined using SAM analysis.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Gli1FLAG;Ptc+/- tumor

label_protocol: Samples were fragmented and biotin-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: RosaGli1-FLAG c/c mice (Vokes et al., 2007) were crossed with Math1Cre (Matei et al., 2005) mice and litters were taken at P8 to isolate Gli1-FLAG-expressing GNPs. Ptc+/- GNPs were purified from P8 Ptc+/- mice (Goodrich et al., 1997).  Cerebellums were dissected into PBS and GNPs were isolated as previously described (Wechsler-Reya and Scott 1999).  Medulloblastoma tumors were isolated from RosaGli1-FLAG c/c;Math1-Cre;Ptc+/- mice.

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen). Ribosomal RNA reduction was performed using RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen).  cDNA synthesis and amplification were done using GeneChip WT cDNA Synthesis Kit (Affymetrix).

treatment_protocol: not applicable

tag: age

value: Adult

tag: disease state

value: medulloblastoma


title: Ye478 re-watering, biological rep1

description: Gene expression data from maize inbred line Ye478 after re-watering


title: Ye478 re-watering, biological rep2


title: ESCs

description: Kindly gifted from Dr. Nakatsuji.

source_name: ESCs

value: ESCs


title: Ye478 severe drought, biological rep2


title: BurnPatient24_Mid

description: Gene expression of burn patient

value: burn

tag: sex

value: M

tag: hours post injury

tag: sampling time group

value: Mid

tag: total burn surface area (tbsa, %)

tag: injury inhalation

value: Yes

tag: survival

tag: hospital length of stay (days)


title: Subject 926, Replicate 2

tag: tissue


title: Subject 254, Replicate 4


title: WA

source_name: medium with Tungsten instead of Molibdenium


title: Medulloblastoma, biological replicate 3

description: medulloblastoma, biological replicate 3

tag: genotype


title: Mo C

description: Photosynthetic conditions (10 W/m2, sealed flasks), normal medium (Mo)

source_name: normal medium


title: Subject 254, Replicate 3


title: Ye478 moderate drought, biological rep2

value: shoot

tag: developmental stage

tag: protocol

value: moderate drought stress


title: Medulloblastoma, biological replicate 2

description: medulloblastoma, biological replicate 2


title: Subject 254, Replicate 2

tag: subject/donor

tag: gender


title: Mo B

growth_protocol: Photosynthetic conditions (10 W/m2, sealed flasks), normal medium (Mo)

tag: strain


title: Medulloblastoma, biological replicate 1

description: medulloblastoma, biological replicate 1

tag: cell type


title: Mo A


title: Ptc+/- GNPs at P8, biological replicate 2

source_name: Ptc+/- GNPs

tag: age

value: normal

value: granule neuron precursor cells

value: Ptc+/-


title: Ptc+/- GNPs at P8, biological replicate 1

tag: disease state


title: [E-TABM-722] do76_HNF4a_liver_ARP31046_cfa4_SAN01

description:
do76_HNF4a_liver_ARP31046_cfa4_SAN01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: HNF4a

organism: Canis lupus familiaris

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
chip_seq | sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles. doi:10.1016/j.ymeth.2009.03.001

tag: developmentalstage

value: adult

tag: organismpart

value: liver

tag: sex

value: male

tag: individual

tag: chip antibody

tag: chip catalog number


title: [E-TABM-722] do76_HNF4a_liver_ARP31046_cfa4_SAN02

description:
do76_HNF4a_liver_ARP31046_cfa4_SAN02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: high salt, 45 minutes C

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); high salt stress (1.5% NaCl) during 45 min

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 1.5 %; Cultures were collected at 45 min after addition of NaCl


title: high salt, 7 minutes C

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); high salt stress (1.5% NaCl) during 7 min

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions; salt stress was induced by the addition of NaCl to the exponentially grown (A600 = 0.4 ± 0.03) cultures to the final concentration of 1.5 %; Cultures were collected at 7 min after addition of NaCl


title: Gli1FLAGCre+ GNPs at P8, biological replicate 1

source_name: Gli1FLAG GNPs


title: 2010_401, photosynthetic, 10 W/m2

description: Rhodobacter sphaeroides 2.4.1, Laramie

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); no salt stress

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions without salt stress


title: [E-TABM-722] do75_HNF4a_liver_ARP31046_cfa3_SAN03

description:
do75_HNF4a_liver_ARP31046_cfa3_SAN03.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: Gli1FLAGCre+ GNPs at P8, biological replicate 2


title: Subject 219, Replicate 5

value: Male

value: cultured epidermis

tag: replicate


title: Ye478 moderate drought, biological rep1

tag: tissue

value: three-leaf stage seedlings


title: Ye478 control, biological rep2

tag: genotype

value: control


title: Han21 re-watering, biological rep1

tag: developmental stage

value: re-watering


title: Subject 254, Replicate 1


title: Han21 re-watering, biological rep2

tag: protocol


title: Subject 219, Replicate 2

tag: subject/donor


title: Ye478 control, biological rep1


title: Han21 severe drought, biological rep2

value: severe drought stress


title: Subject 219, Replicate 4

tag: gender


title: Han21 moderate drought, biological rep2


title: Subject 219, Replicate 3


title: [E-TABM-722] do75_HNF4a_liver_ARP31046_cfa3_SAN02

description:
do75_HNF4a_liver_ARP31046_cfa3_SAN02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: [E-TABM-722] do261_Input_liver_none_cfa3_CRI01

description:
do261_Input_liver_none_cfa3_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: input_DNA

value: none, input DNA


title: [E-TABM-722] do75_HNF4a_liver_ARP31046_cfa3_CRI01

description:
do75_HNF4a_liver_ARP31046_cfa3_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: HNF4a


title: Subject 1188, Replicate 4


title: Ye478 severe drought, biological rep1


title: Subject 1188, Replicate 3


title: Subject 219, Replicate 1


title: Subject 1188, Replicate 5


title: Han21 control, biological rep2


title: Subject 1188, Replicate 2


title: Subject 1188, Replicate 1


title: Han21 control, biological rep1


title: Han21 moderate drought, biological rep1


title: Gr0 T16 biological rep 2

status: Public on Jun 02 2010

city: Zurich

first: Alessandro

last: Fammartino

address: Universitaettstrasse 2

department: IPAS

country: Switzerland

institute: ETHZ

description: Gene expression data from flag leaf of Gr0 inoculated with T16

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

data_processing: The data were analyzed with Microarray AGCC software. Probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002) and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Log ratio data for the comparisons are included in supplementary files on the series record.

organism: Triticum aestivum

source_name: Triticum aestivum flag leaf symptomatic

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The field experiment was designed in randomized complete blocks with four replicates. Each plot was seeded by hand and consisted of two 10 foot rows with 3.5 grams of seed per row. A total of 8 treatments were tested. These included two wheat genotypes (null segregant Greina and KP4-Greina) each inoculated with the 3 bunt races (T1/T5/T16) and each with no inoculation (Untreated). In addition to a high inoculum load, plots were seeded early in the spring when soil temperatures were cool which are most favorable to induce high levels of infection. Individual plants were scored for bunt symptoms 16 weeks after sowing, during dough stages of the new formed seeds

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

treatment_protocol: A concentrated aqueous suspension of T. caries teliospores was made of each pathogenic race. A few drops of the suspension were added to the seeds in a 50 ml test tube and then vortexed to evenly distribute spores on the seeds and to adhere spores to seeds. The spores were applied at a high rate to the point seeds were visibly darkened with spores to generate a high infection pressure. Flag leaves from 20 plants were collected from each plot from plants showing smut symptoms on the ears, in the case of treated plots, while flag leaves from asymptomatic ears from untreated plots. One plot was considered a biological replicate and RNA extraction was performed from a mix of all the leaves collected.

value: leaf

tag: genotype/variation

tag: treatment

value: Zadoks stages 85-87 of wheat growth


title: GrKP4 T1 biological rep 3

description: Gene expression data from flag leaf of GrKP4 inoculated with T1

tag: age


title: GrKP4 T16 biological rep 2

description: Gene expression data from flag leaf of GrKP4 inoculated with T16


title: Han21 severe drought, biological rep1

value: shoot


title: Gr0 T1 biological rep 2

description: Gene expression data from flag leaf of Gr0 inoculated with T1


title: Gr0 T16 biological rep 3


title: Gr0 T1 biological rep 1


title: GrKP4 untreated biological rep 3

description: Gene expression data from flag leaf of GrKP4 not inoculated

source_name: Triticum aestivum flag leaf healthy

value: untreated


title: GrKP4 T16 biological rep 3


title: GrKP4 untreated biological rep 2


title: GrKP4 T1 biological rep 2


title: beta-cells_non-diabetic condition_surgical specimen7

first: Lorella

last: Marselli

address: One Joslin Place

department: Joslin Diabetes Center and the Department of Medicine

institute: Harvard Medical School

description:
Gene expression data from surgical samples
Surgical-861

hyb_protocol: Biotinylated cRNA was fragmented to nucleotide stretches of 30-200 nucleotides and hybridized for 16hr at 45C to the Affymetrix Human X3P array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

data_processing: Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.

source_name: human beta-cells_non-diabetic

label_protocol: Amplified RNA  was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).

extract_protocol: Total RNA was extracted from each population of laser captured β–cells using PicoPure RNA Isolation Kit (Arcturus) and amplified by T7-based linear amplification using T7-oligo-dT-primers. RNA amplification was performed using RiboAmp HS RNA Amplification Kit (Arcturus) following the manufacture’s protocol.

treatment_protocol: Pancreas specimens obtained from surgical samples and islet grafts recovered from the transplanted mice were placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed in diethylpyrocarbonate (DEPC)-treated water for 30 sec, and dehydrated in 70% ethanol for 30 sec, 100% ethanol (rinsing), 100% ethanol twice for 1 min, and xylene for 4 minutes. Sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer for 30 minutes at 42°C, and the samples stored at -80°C.

value: pancreatic islets

tag: cell type

value: beta-cell

value: non-diabetic condition

value: female

tag: age (years)

tag: bmi (body mass index, kg/m2)


title: transplanted beta-cells_hyperglycemic condition_donor2_sample_a

description:
Gene expression data from transplanted islets
1M-NT060606-4L

source_name: human beta-cells exposed to mild hyperglycemia in transplant site

value: hyperglycemic condition


title: transplanted beta-cells_hyperglycemic condition_donor2_sample_c

description:
Gene expression data from transplanted islets
1M-NT060606-5R

value: male


title: Gr0 T16 biological rep 1


title: transplanted beta-cells_hyperglycemic condition_donor1_sample_b

description:
Gene expression data from transplanted islets
111705-5LHuGraft


title: transplanted beta-cells_hyperglycemic condition_donor1_sample_a

description:
Gene expression data from transplanted islets
111705-5RHuGraft


title: GrKP4 T16 biological rep 1


title: transplanted beta-cells_hyperglycemic condition_donor2_sample_b

description:
Gene expression data from transplanted islets
1M-NT060606-4B


title: beta-cells_non-diabetic condition_surgical specimen5

description:
Gene expression data from surgical samples
Surgical-564


title: transplanted beta-cells_hyperglycemic condition_donor1_sample_c

description:
Gene expression data from transplanted islets
111705-5NHuGraft


title: GrKP4 T1 biological rep 1


title: beta-cells_non-diabetic condition_surgical specimen6

description:
Gene expression data from surgical samples
Surgical-850


title: Gr0 T1 biological rep 3


title: GrKP4 untreated biological rep 1


title: Gr0 untreated biological rep 3

description: Gene expression data from flag leaf of Gr0 not inoculated


title: Gr0 untreated biological rep 2


title: beta-cells_non-diabetic condition_surgical specimen2

description:
Gene expression data from surgical samples
Surgical-799


title: Gr0 untreated biological rep 1


title: beta-cells_non-diabetic condition_surgical specimen1

description:
Gene expression data from surgical samples
Surgical-760