title: post_MBT_rep3


title: control_rep4

status: Public on Apr 20 2017

type: RNA

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol on GeneChip Scanner 3000.

data_processing: R/Bioconductor, rma normalization, default parameters.

label: biotin

molecule: total RNA

organism: Xenopus tropicalis

source_name: late blastula embryos, control morpholino

label_protocol: Standard Affymetrix protocol.

growth_protocol: Xenopus tropicalis eggs were collected, in vitro fertilized, microinjected and cultivated following standard procedures. Embryos were staged according to Nieuwkoop and Faber (1967).

extract_protocol: Total RNA of 10 embryos was extracted using Trizol (Ambion) and phenol/chloroform. The RNA was precipitated with 70% isopropanol and cleaned using the RNeasy Cleanup Kit (Qiagen) including DNaseI-on-column digestion.

treatment_protocol: Radial injections were performed at the 2-4 cell stage with 30ng BRG1 morpholino (CCATTGGAGGGTCTGGGGTGGACAT) or 60ng control morpholino and cultivated until late blastula stage.

tag: tissue

value: embryos

tag: developmental stage

value: late blastula

tag: morpholino

value: control

tag: replicate


title: control_rep3


title: Scrb_LG_biological replicate 1

city: Ann Arbor

first: Zhuoxian

last: Meng

state: Michigan

address: 210 Washtenaw Ave

country: USA

institute: University of Michigan

description: Gene expression data from C2C12 myotubes transduced with siScramble retrovirus and treated with 1 mM glucose for 12 h.

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Data was analyzed using the affy Bioconductor packages implemented in the R-statistical environment. RMA was used to fit log2 expression values.

organism: Mus musculus

source_name: C2C12 mouse cell line

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

treatment_protocol: C2C12 myoblasts were transduced with retroviruses expressing shRNAs targeting control or mouse Baf60c, differentiated into myotubes, and treated with 1mM or 10 mM glucose for 12 h, followed by RNA extraction.

tag: cell line

tag: protocol


title: control_rep2


title: brg1_rep3

source_name: late blastula embryos, brg1 morpholino


title: brg1_rep1


title: pre_MBT_rep1

source_name: pre-MBT embryos

growth_protocol: Xenopus tropicalis eggs were collected, in vitro fertilized and cultivated following standard procedures. Embryos were staged according to Nieuwkoop and Faber (1967). After fertilization, we collected one sample in the 4-cell stage as negative GS17 control. For the preMBT time-point, we collected around the ~1000 cell stage and then every 20-25 minutes for approximately 60-100min. We choose 20-25 min breaks depending on how long the embryos need in average for the first cell divisions. 120-150 minutes after collecting the last preMBT sample, we started again to collect every 20-25 min samples until we observed dorsal lip formation. In order to find the preMBT sample closest to the MBT, we performed qPCR analysis with MBT-marker GS17. For the preMBT time-point, we took the last sample without GS17 expression. As postMBT, we choose the sample ~40min before upcoming of dorsal lip formation, because this timepoint is in accordance to the timepoint of the comparative microarray analysis.

value: pre midblastula transition (MBT)


title: control_rep1


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Small Intestine Tissue; renlab.H3K27ac.STL002SB.02.01

status: Public on Apr 19 2017

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Small Intestine Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY365
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19846
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

molecule: genomic DNA

organism: Homo sapiens

source_name: Small Intestine tissue; renlab.H3K27ac.STL002SB.02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sra sample accession

tag: disease

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: Small Intestine

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

tag: biosamplemodel

value: Generic

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue; renlab.H3K27ac.STL002SX.02.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY342
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19842
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14062
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Spleen


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue; renlab.H3K27ac.STL003SG.02.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY94
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19850
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11872
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Sigmoid Colon tissue; renlab.H3K27ac.STL003SG.02.01

value: Sigmoid Colon

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Liver Tissue; renlab.H3K27ac.STL011LI.02.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY369
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19824
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: coronary artery disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Liver

value: coronary artery disease. No history of hypertension or diabetes.


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Right Ventricle Tissue; renlab.H3K27ac.STL003RV.03.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19852
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12222
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K27ac.STL003RV.03.01

value: Right Ventricle

value: Autopsy

value: Caucasian


title: Reference Epigenome: ChIP-Seq H3K27ac from Human Right Ventricle Tissue; renlab.H3K27ac.STL001RV.03.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq H3K27ac from Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY54
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19863
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Right Ventricle tissue; renlab.H3K27ac.STL001RV.03.01

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: Generic

value: Histone H3K27ac

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Ovary Tissue; renlab.H3K27ac.STL002OV.02.01

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Ovary Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY308
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19836
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Ovary

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: premalignant NKT 1

city: Durham

first: Yuan

last: Zhuang

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed using default settings in RMA, and differential expression determined using limma, available from Bioconductor. For inclusion of WT samples that were not originally part of the microarray, WT data (also obtained from an Affymetrix microarray, GSE15907) was downloaded from Immgen, and combined and re-normalized acoording to the Emperical Bayes' method using Arraymining webtool (www.arraymining.net/)

source_name: Sorted NKT cells from 3 week old mice

label_protocol: Approximately 10 μg of amplified cRNA was labeled, hybridized to GeneChip Mouse Genome 430A 2.0 array (Affymetrix)

extract_protocol: Total RNA was extracted using an RNAqueous Kit (Life Technology) according to manufacturer’s protocol

tag: strain

value: L-DKO

tag: cell type

value: Sorted NKT cells from 3 week old mice


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue; renlab.H3K27ac.STL003PO.02.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY92
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19826
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11875
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL003PO.02.01

value: Shin Lin, Stanford University

value: Primary Tissue

value: Psoas Muscle

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male


title: premalignant NKT 2


title: Mia2 ctrl-2_3999650017_G

city: Baltimore

first: Asma

last: Begum

state: MD

address: 1650 Orleans street, CRBI Room-230

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Hybridization on Illumina HumanHT-12 v4 Expression BeadChips, and the staining and detection of cRNAs with the iScan system were performed according to the manufacturer’s recommendations (Illumina Inc., San Diego, USA).

scan_protocol: GenomeStudio 2011.1 software (Illumina Inc.) and its Gene Expression Analysis Module (version 1.9.0) were used for signal extraction and quantile normalization.

label: Biotin

source_name: Pancratic ductal adenocarcinoma

growth_protocol: Capan-1 and MIA PaCa-2 cell lines were purchased from American Type Culture Collection (Manassas, VA) global bio-resource center and authenticated by short tandem repeat profiling at the Johns Hopkins Genetics Core Resources Facility.  All cell lines were cultured in Dulbecco’s modified Eagle medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Harlan, Indianapolis, IN), 1% penicillin–streptomycin (Invitrogen), and 1% L-glutamine (Invitrogen). Cells are replate for passage every 72 -96 hours.

extract_protocol: Total RNA was purified from cells with the RNAeasy® Mini kit (Qiagen). RNA was quantified with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc.). RNA integrity was assessed with a Bioanalyzer 2100 machine and the RNA6000 Nano kit (Agilent Technologies Inc.). All samples had a RNA integrity number of at least 7.00. No signs of DNA contamination were detected. We used 500 ng of total RNA per sample. We used the Illumina Total Prep RNA Amplification Kit (Ambion, Life Technologies) to generate biotinylated, amplified cRNA, according to the manufacturer’s recommendations.

treatment_protocol: Capan-1 amd MIA PaCa2  cell line expressing scrambled shRNA or shRNAs against FAK are puromycin resistant and grew in 1.5 ug/ml and 3.5 ug/ml puromycin supplemented growth media, respectively. Knock down of FAK were induced by adding 50 ng/ml doxycycline in medium for 96 hours.

tag: hairpin backbone

value: PLKO.1 tet-on

tag: selection marker

value: Puromycin

tag: shRNA

value: ctrl


title: Capan1 ctrl-2_3999650017_H

data_processing: GenomeStudio 2011.1 software (Illumina Inc.) and its Gene Expression Analysis Module (version 1.9.0) were used for signal extraction and quantile normalization.

label_protocol: We used 500 ng of total RNA per sample. We used the Illumina Total Prep RNA Amplification Kit (Ambion, Life Technologies) to generate biotinylated, amplified cRNA, according to the manufacturer’s recommendations.


title: Capan1 sh1209-1_3999650017_D


title: Capan1 shFAK1319-2_3999650017_L


title: Capan1 ctrl-1_3999650017_B


title: premalignant NKT 3


title: Capan1 shFAK1319-1_3999650017_F


title: tumor CD1dtet+ 1

source_name: Lymphoma cells from payer's patch of 20 week old mice


title: Capan1 sh1209-2_3999650017_J


title: tumor CD1dtet-

source_name: Lymphoma cells from thymus of 37 week old mice


title: Uninfected THP-1 cells

city: Lucknow

first: Dr. Bhupendra

middle: Narain

last: Singh

state: Uttar Pradesh

address: Jankipuram Extension, Sec.-10, Sitapur Road

department: Microbiology

country: India

institute: CSIR-CDRI Lucknow

description: Control

data_processing:
Analysis was performed by Expression suite software v1.0.3. ΔΔCt method was employed for data analysis. U6 snRNA was used as endogenous contarol for data normalization. Total RNA from uninfected THP-1 cells was considered reference sample to calculate fold change.  Ct Max is 40 cycle.
Fold Change worksheet reports test/control (i.e., H37Rv infected THP-1 cells /Uninfected THP-1) ratios.

label: FAM

source_name: human leukemic monocytes cell line derived macrophages

label_protocol: Total 1 μg RNA per sample were reverse transcribed to cDNA with Megaplex Human Pool A and Pool B stem loop RT primers (version 3.0) (Invitrogen) and TaqMan MicroRNA RT kit (Invitrogen) as per manufacturer´s instructions for TLDA experiments.

growth_protocol: 3 million THP-1 cells grown in RPMI-1640 complete media were PMA treated and incubated for 48 hrs at 5% CO2 and 37ᵒC temperature for differentiation into macrophages.

extract_protocol: Total RNAs were isolated from infected and uninfected THP-1 samples by using Ambion mirVana miRNA isolation kit. RNA samples having 260/ 280 and 260/230 ratios above 1.8 were considered good and proceeded further for downstream applications.

treatment_protocol: After 48 hrs monolayer cells were washed thrice with prewarmed PBS at 37ᵒC, complete RPMI-1640 medium was added and left for 12 hrs so that macrophages achieve normal physiology. Then mycobacterium inoculum was added at MOI 10:1 (10 million per flask) and incubated for 4 hrs at 5% CO2 and 37ᵒC for maximum phagocytosis of mycobacterium.

tag: infected

value: uninfected


title: Mia2 sh1209-2_3999650017_I


title: H37Rv infected THP-1 cells

description: Test

value: H37Rv infected


title: Mia2 ctrl-1_3999650017_A


title: Mia2 sh1319-1_3999650017_E


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL001GA.03.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY58
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19861
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Gastric

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: Generic

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL002GA.02.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19840
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14004
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Shin Lin, Stanford University

value: Primary Tissue

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue; renlab.H3K27ac.STL003GA.02.01

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Gastric Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK339
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19832
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue; renlab.H3K27ac.STL001LG.02.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY361
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19844
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13947
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Lung

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue; renlab.H3K27ac.STL001PO.03.01

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Psoas Muscle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY52
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19858
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Psoas Muscle tissue; renlab.H3K27ac.STL001PO.03.01

value: Psoas Muscle

value: Generic

value: Histone H3K27ac

value: Biorupter


title: tumor CD1dtet+ 2

source_name: Lymphoma cells from payer's patch of 18 week old mice

value: L-DKO


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue; renlab.H3K27ac.STL003SX.02.01

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK348
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19834
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11852
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Shin Lin, Stanford University

value: Primary Tissue

value: Spleen

value: 500 micrograms


title: Mia2 sh1209-1_3999650017_C

value: PLKO.1 tet-on

value: Puromycin


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue; renlab.H3K27ac.STL003AD.03.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK321
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19854
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Adrenal Gland tissue; renlab.H3K27ac.STL003AD.03.01

value: Adrenal Gland

value: Autopsy

value: Caucasian

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Mia2 sh1319-2_3999650017_K


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue; renlab.H3K27ac.STL002EG.02.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY336
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19838
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: iron deficiency, bipolar

value: Esophagus

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue; renlab.H3K27ac.STL002AO.03.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY160
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19856
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Aorta

value: Generic

value: Histone H3K27ac

value: Biorupter

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells; renlab.H3K9me3.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id:
Design description: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK136
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7830
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K9me3.BMP4M.01.01

tag: sample alias

tag: sample common name

value: H1 BMP4 Derived Mesendoderm Cultured Cells

tag: molecule

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K9me3

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue; renlab.H3K27ac.STL003EG.02.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK324
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19830
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11826
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

tag: sra sample accession

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Esophagus

value: Autopsy

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue; renlab.H3K27ac.STL003AO.02.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY46
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19848
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11864
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

value: Aorta

tag: biosamplemodel

value: Generic

value: Histone H3K27ac

value: Biorupter


title: jejunum_High Zinc_d63_f_1_890

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

hyb_protocol: The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for one colour gene expression.

data_processing: The data were analysed by using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA [1] from Bioconductor [2]. Quantile normalisation of the data was performed between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes was removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1 and 3) the gene/probe must be expressed in each of the samples in an experimental condition (e.g. in ileum d 14 control).

organism: Sus scrofa

source_name: jejunum, High Zinc, d63, f

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA was used on the eight pack array.  Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies).

growth_protocol: The piglets were of the Tempo x Topigs 20 genotype. At the start of the study the piglets were divided per pen in a way that the mean body weight and its variation per pen were similar. The piglets were weaned at a mean age of 28 ± 1.5 d. The piglets received creep feed during the suckling period. The mean body weight of the piglets one day prior to the start of the study was 7.9 kg. The piglets were housed in floor pens (1.75 x 3.00 m) with 12 piglets per pen. Male (boars) and female piglets were equally distributed over pens and litter mates were divided equally over pens as far as possible. The piglets were fed ad libitum using a dry feed dispenser. The diets were provided as pellets. The animals had free access to water via an automatic drinking device.    The ingredient and calculated nutrient composition of the weaning diet and the starter diet (control). The diets were formulated to be nutritionally adequate using data on the composition and nutritional value of feed ingredients according to CVB (2011).  After weaning, the piglets were fed the same weaning diet during the period of d 0 till 14. From d 14 till 23 after weaning the experimental piglet diets were provided containing either a regular or a high zinc concentration (analysed zinc concentrations 100 and 2690 mg/kg, respectively). The contrast in Zn concentration was realised by supplementing ZnO to the control diet. From   d 23 till 35 the piglets in both treatment groups received the same starter piglet diet with a regular Zn concentration (analysed 100 mg Zn per kg).

extract_protocol: Total RNA was extracted from 50 to 100 mg tissue mucosal scrapings of jejunum and ileum. The jejunum and ileum samples were homogenised using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenised tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently a phase separation with chloroform was performed as described by the manufacturer Life Technologies. The RNA was precipitated and dissolved and quantified by absorbance measurements at 260 nm.

tag: tissue

value: jejunum

tag: treatment

value: High Zinc

tag: age

tag: block

tag: pen

tag: gender

value: f

tag: sow

tag: animal


title: jejunum_Control_d63_m_3_890

source_name: jejunum, Control, d63, m

treatment_protocol: From d 14 till 23 after weaning the experimental piglet diets were provided containing either a regular or a high zinc concentration (analysed zinc concentrations 100 and 2690 mg/kg, respectively). The contrast in Zn concentration was realised by supplementing ZnO to the control diet.

value: Control

value: m


title: jejunum_Control_d63_m_1_890


title: jejunum_High Zinc_d63_f_3_796


title: jejunum_Control_d63_m_1_796


title: jejunum_Control_d63_m_2_890


title: jejunum_High Zinc_d63_m_3_890

source_name: jejunum, High Zinc, d63, m


title: jejunum_High Zinc_d63_f_2_890


title: jejunum_High Zinc_d51_m_1_878

source_name: jejunum, High Zinc, d51, m


title: jejunum_High Zinc_d51_f_2_878

source_name: jejunum, High Zinc, d51, f


title: jejunum_Control_d63_f_2_796

source_name: jejunum, Control, d63, f


title: jejunum_Control_d51_m_3_878

source_name: jejunum, Control, d51, m


title: jejunum_High Zinc_d63_f_2_796


title: jejunum_High Zinc_d51_f_3_878


title: jejunum_Control_d51_m_3_873


title: jejunum_Control_d51_m_2_878


title: jejunum_High Zinc_d51_m_1_873


title: F4437Nsp, Patient

type: genomic

city: Sao Paulo

first: Cibele

last: Masotti

state: São Paulo

address: Rua do Matao, 277.

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description: Hybridized to 250K_Nsp

hyb_protocol: Mapping 500K arrays were washed and stained in the Affymetrix Fluidics Station 450, then hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.

scan_protocol: Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GeneChip Scanner 3000 7G.

data_processing:
CEL-Files were analyzed using the BRLMM-algorithm, implemented in the Genotyping Console software (Affymetrix, USA), to produce genotype calls, stored in the corresponding CHP-Files.
Genotypes primarily generated under Genome version hg18 (GRCh36.1) were converted to hg19 with UCSC LiftOver tool.

source_name: OOMMSC

label_protocol: Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 250ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005).

growth_protocol: We established OOMMSC primary cultures according to previously published protocol [Bueno et al. 2009] and expanded to 70-90% confluence.

extract_protocol: Total DNA isolation was performed with NucleoSpin tissue kit (Macherey-Nagel), following manufacturer’s recommendations. DNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis.

treatment_protocol: No specific treatment was used in cells cultures.

tag: cell type

value: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures

tag: phenotype

value: Nonsyndromic cleft lip/palate (NSCL/P)

value: Male


title: F4257Nsp, Patient

description: Hybridized to 250K_Nsp

value: Female


title: jejunum_Control_d51_m_1_873


title: F5614Nsp, Patient

description: Hybridized to 250K_Nsp


title: F6130Nsp, Patient

description: Hybridized to 250K_Nsp


title: F8000Nsp, Control

description: Hybridized to 250K_Nsp

tag: disease state


title: jejunum_High Zinc_d51_f_3_873


title: F5716Nsp, Control

description: Hybridized to 250K_Nsp


title: F4219Nsp, Patient

description: Hybridized to 250K_Nsp


title: F6081Nsp, Patient

description: Hybridized to 250K_Nsp


title: jejunum_Control_d51_f_2_873

source_name: jejunum, Control, d51, f


title: F5715Nsp, Control

description: Hybridized to 250K_Nsp


title: F5662Nsp, Patient

description: Hybridized to 250K_Nsp


title: F6023Nsp, Patient

description: Hybridized to 250K_Nsp


title: F5647Nsp, Patient

description: Hybridized to 250K_Nsp


title: F5610Nsp, Patient

description: Hybridized to 250K_Nsp


title: F5686Nsp, Patient

description: Hybridized to 250K_Nsp


title: jejunum_High Zinc_d51_m_2_873


title: F4317Nsp, Patient

description: Hybridized to 250K_Nsp


title: F6010Nsp, Patient

description: Hybridized to 250K_Nsp


title: jejunum_High Zinc_d42_m_1_798

source_name: jejunum, High Zinc, d42, m


title: jejunum_Control_d42_m_1_798

source_name: jejunum, Control, d42, m


title: F3506Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3497Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3496Nsp, Patient

description: Hybridized to 250K_Nsp


title: jejunum_Control_d42_f_3_798

source_name: jejunum, Control, d42, f


title: jejunum_High Zinc_d42_m_3_798


title: jejunum_Control_d42_f_2_798


title: F3507Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_High Zinc_d63_f_1_890

source_name: ileum, High Zinc, d63, f

value: ileum


title: F3491Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3488Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3484Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_Control_d63_m_1_890

source_name: ileum, Control, d63, m


title: F3479Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_Control_d63_m_3_890


title: F3476Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_High Zinc_d63_m_1_796

source_name: ileum, High Zinc, d63, m


title: Human trisomy 21 embryo 6

city: México

first: Esther

last: Lopez-Bayghen

address: Av. IPN 2508 San Pedro Zac

department: Toxicología

country: Mexico

institute: Cinvestav-IPN

description:
Biological replicate 6 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)

hyb_protocol: Samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Scanned on an Innopsys InnoScan 710 laser scan.

data_processing: Images were imported as .tiff and analyzed using BlueFuse Multi 4.3(25799) Software.

source_name: Human reference DNA

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Whole Genome Amplification performed with Sureplex following manufacturer's instructions.

tag: sample type

value: SureRef reference DNA

source_name: Trophectoderm human embryo cells

value: Human embryo trophectoderm cells biopsied at day 5 by conventional method


title: Human trisomy 21 embryo 2

description:
Biological replicate 2 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 21 embryo 5

description:
Biological replicate 5 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 21 embryo 4

description:
Biological replicate 4 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_Control_d63_m_2_890


title: Human trisomy 21 embryo 7

description:
Biological replicate 7 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 21 embryo 1

description:
Biological replicate 1 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_High Zinc_d63_f_2_890


title: F3468Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3474Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3480Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_Control_d63_m_1_796


title: Human trisomy 18 embryo 5

description:
Biological replicate 5 of 5. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 18
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 21 embryo 3

description:
Biological replicate 3 of 7. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 21
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_High Zinc_d63_f_3_796


title: F3493Nsp, Patient

description: Hybridized to 250K_Nsp


title: Human trisomy 18 embryo 4

description:
Biological replicate 4 of 5. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 18
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_Control_d63_f_3_796

source_name: ileum, Control, d63, f


title: F3463Nsp, Patient

description: Hybridized to 250K_Nsp


title: Human trisomy 18 embryo 3

description:
Biological replicate 3 of 5. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 18
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 18 embryo 2

description:
Biological replicate 2 of 5. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 18
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_High Zinc_d63_f_2_796


title: F3458Nsp, Patient

description: Hybridized to 250K_Nsp


title: Human non-trisomy embryo 9

description:
Biological replicate 9 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human trisomy 18 embryo 1

description:
Biological replicate 1 of 5. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo with a trisomy in chromosome 18
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: F3459Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3462Nsp, Patient

description: Hybridized to 250K_Nsp


title: Human non-trisomy embryo 7

description:
Biological replicate 7 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human non-trisomy embryo 8

description:
Biological replicate 8 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human non-trisomy embryo 6

description:
Biological replicate 6 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human non-trisomy embryo 5

description:
Biological replicate 5 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: Human non-trisomy embryo 4

description:
Biological replicate 4 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_Control_d63_f_2_796


title: ileum_High Zinc_d51_m_1_878

source_name: ileum, High Zinc, d51, m


title: ileum_High Zinc_d51_f_3_878

source_name: ileum, High Zinc, d51, f


title: ileum_Control_d51_m_3_878

source_name: ileum, Control, d51, m


title: Human non-trisomy embryo 3

description:
Biological replicate 3 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: F3440Nsp, Patient

description: Hybridized to 250K_Nsp


title: Human non-trisomy embryo 2

description:
Biological replicate 2 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: ileum_Control_d51_m_1_878


title: Human non-trisomy embryo 1

description:
Biological replicate 1 of 9. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as an embryo lacking trisomies in chromosomes 18 and 21.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: F3439Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3434Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3436Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_High Zinc_d51_f_2_878


title: ileum_High Zinc_d51_m_1_873


title: ileum_Control_d51_m_2_878


title: brain-old-4

city: Stanford

first: Joseph

middle: Michael

last: Castellano

address: 770 Welch Road

institute: Stanford University

description:
DOld25
Gene expression data from brain samples isolated from mice treated with human old plasma.

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60 rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G using the Affymetrix GeneChip Command Console Software.

data_processing: The data were analyzed by Bioconductor/R 3.1.2 and RMA was applied as normalization method.

source_name: Hippocampi from aged NSG mice treated with human old plasma

label_protocol: Affymetrix WT Plus kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Affymetrix WT Terminal Labeling and Hybridization kit.

extract_protocol: RNA was extracted according to procedures performed by the Translational Applications Service Center at Stanford University.

treatment_protocol: Aged mice treated with different groups of human plasma were sacrificed following 6 intravenous injections, and hippocampi were dissected from brain tissue for analysis by whole genome microarray.

tag: strain/background

value: NSG (005557 Jackson Labs)

value: mean 14 months

value: human old plasma

value: hippocampal tissue


title: ileum_Control_d51_m_3_873


title: brain-old-6

description:
DOld27
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: ileum_High Zinc_d51_f_3_873


title: ileum_Control_d51_m_1_873


title: brain-old-3

description:
DOld24
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: brain-old-7

description:
DOld28
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: brain-old-5

description:
DOld26
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: ileum_High Zinc_d51_m_2_873


title: ileum_High Zinc_d42_m_1_798

source_name: ileum, High Zinc, d42, m


title: brain-old-1

description:
DOld22
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: F3413Nsp, Patient

description: Hybridized to 250K_Nsp


title: ileum_High Zinc_d42_m_3_798


title: F3430Nsp, Patient

description: Hybridized to 250K_Nsp


title: brain-old-2

description:
DOld23
Gene expression data from brain samples isolated from mice treated with human old plasma.


title: ileum_Control_d51_f_2_873

source_name: ileum, Control, d51, f


title: ileum_Control_d42_f_3_798

source_name: ileum, Control, d42, f


title: F3427Nsp, Patient

description: Hybridized to 250K_Nsp

source_name: OOMMSC


title: F3404Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3478Nsp, Patient

description: Hybridized to 250K_Nsp


title: brain-young-5

description:
CYoung19
Gene expression data from brain samples isolated from mice treated with human young plasma.

source_name: Hippocampi from aged NSG mice treated with human young plasma

value: human young plasma


title: brain-young-4

description:
CYoung18
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: brain-young-6

description:
CYoung20
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: F3324Nsp, Patient

description: Hybridized to 250K_Nsp


title: F3292Nsp, Patient

description: Hybridized to 250K_Nsp


title: brain-cord-7

description:
BCord14
Gene expression data from brain samples isolated from mice treated with human cord plasma.

source_name: Hippocampi from aged NSG mice treated with human cord plasma

value: human cord plasma


title: ileum_High Zinc_d42_m_2_798

value: High Zinc


title: ileum_Control_d42_f_2_798

value: f


title: brain-young-1

description:
CYoung15
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: brain-cord-4

description:
BCord11
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: brain-young-3

description:
CYoung17
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: brain-cord-6

description:
BCord13
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: brain-cord-3

description:
BCord10
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: ileum_Control_d42_m_1_798

source_name: ileum, Control, d42, m

value: Control


title: brain-cord-2

description:
BCord09
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: brain-cord-5

description:
BCord12
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: brain-cord-1

description:
BCord08
Gene expression data from brain samples isolated from mice treated with human cord plasma.


title: brain-young-7

description:
CYoung21
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: brain-young-2

description:
CYoung16
Gene expression data from brain samples isolated from mice treated with human young plasma.


title: brain-PBS-7

description:
APBS07
Gene expression data from brain samples isolated from mice treated with PBS.

source_name: Hippocampi from aged NSG mice treated with PBS

value: PBS


title: brain-PBS-2

description:
APBS02
Gene expression data from brain samples isolated from mice treated with PBS.


title: brain-PBS-4

description:
APBS04
Gene expression data from brain samples isolated from mice treated with PBS.


title: brain-PBS-6

description:
APBS06
Gene expression data from brain samples isolated from mice treated with PBS.


title: brain-PBS-5

description:
APBS05
Gene expression data from brain samples isolated from mice treated with PBS.


title: brain-PBS-1

description:
APBS01
Gene expression data from brain samples isolated from mice treated with PBS.


title: F1403Nsp, Patient

description: Hybridized to 250K_Nsp

value: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures


title: brain-PBS-3

description:
APBS03
Gene expression data from brain samples isolated from mice treated with PBS.


title: B-104_150501

city: Okayama

first: TAKAYUKI

last: IWAMOTO

address: 2-5-1 Shikata-cho, Kitaku

country: Japan

institute: Okayama university hospital

data_processing: Gene expression profiling was performed using Affymetrix U133A gene chips. Expression data were normalized using the MAS5 algorithm, mean centered to 600, and log2 transformed before further analysis.

source_name: Breast

label_protocol: standard Affymetrix protocol

growth_protocol: Core needle biopsy (Cx) primary cancer specimens were collected at Okayama University Hospital in Japan from hormone receptor positive /HER2 negative patients that subsequently received two weeks of neoadjuvant hormone therapy. Thirty clinical TNM stage I and II women were enrolled in this study.

extract_protocol: Specimens for gene expression analysis were collected into RNA and later stored at -80°C.

treatment_protocol: Patients received preoperative hormone therapy daily for two weeks before surgery. Premenopausal patients received tamoxifen (40 mg) and postmenopausal patients received letrozole (2.5 mg). All patients underwent a mastectomy or breast-conserving surgery.

tag: paired

value: Post

tag: age at diagnosis

tag: pathological ihc er

tag: pathological ihc pr

tag: pathological ihc her2

tag: t cm

tag: cn

tag: m

tag: historogical grade

tag: histologic subtypes

tag: type of hormone

tag: type of operation


title: B-87_150501


title: B-83_150501


title: B-92_150501


title: B-76_150501


title: B-91_150501


title: B-54_150501


title: B-74_150501


title: B-95_150501


title: B-73_150501


title: B-36_150501


title: B-65_150501


title: B-29_150501


title: B-56_150501


title: B-79_150501


title: B-68_150501


title: B-55_150501


title: B-28_150501


title: B-53_150501


title: B-27_150501


title: B-23_150501


title: B-18_150501


title: B-16_150501


title: B-17_150501


title: LM3/LV-shKindlin-2

city: Fuzhou City

first: Lin

last: Jie

state: Fujian Province

address: No.134, Dong Street

department: Pathology

country: China

institute: Fujian Provincial Hospital

description: Gene expression after Kindlin-2 was knockdown

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25X fragmentation buffer and 10X blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4*44K Microarrays (v2, Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (version 11.0.1.1). Quantile normalization and subsequent data processing were performed with GeneSpring GX v12.1 software package (Agilent). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: LM3 cells infected with shRNA targeting Kindlin-2 knockdown lentivirus vector

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LM3 cell line were maintained in DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: RNA was extracted using TRIzol® Reagent (Invitrogen) and cleaned-up using RNasey Mini Kit(Qiagen) following the manufacturer's recommendations. RNA quantification and quality were assured by NanoDrop ND-1000 spectrophotometer. RNA Integrity and gDNA contamination were tested by denaturing agarose gel electrophoresis.

treatment_protocol: LM3 cells were infected with lentivirus expressing shRNA targeting Kindlin-2 and control shRNA, respectively, then the stable knockdown cells were selected.

tag: cell line

tag: cell type

value: hepatocellular carcinoma cells

tag: kindlin-2 expression status

value: Kindlin-2 low expression


title: LM3/LV-shcontrol

description: Gene expression when Kindlin-2 was not knockdown

source_name: LM3 cells infected with control shRNA knockdown lentivirus vector

value: Kindlin-2 high expression


title: B-24_150501


title: B-14_150501


title: A-95_150501

value: Pre

value: Pos

value: Scirrhous carcinoma

value: AI

value: Bp


title: A-76_150501

value: Mucinous carcinoma


title: A-104_150501

value: Neg

value: lobular carcinoma


title: A-83_150501

value: IHC 2;/FISH-

value: Papillotubular carcinoma

value: TAM


title: jejunum_10%rye_d28_72

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies). The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays where scanned using the DNA microarray scanner with Sure scan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 μm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for one colour gene expression.

data_processing: The data were analysed by using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA (Gentleman et al., 2005) from Bioconductor (Gentleman et al., 2004). Quantile normalisation of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure , 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1 and 3) the gene/probe must be expressed in each of the samples in the experimental condition.

organism: Gallus gallus

source_name: jejunum, 10%rye, d28, 72

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies, using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA, and 600 ng of labelled cRNA was used on the eight pack array.

growth_protocol: Male broilers were housed in floor pens (40 birds per pen at d0) in a mechanically  ventilated room provided with facilities to control temperature, ventilation and lighting. The surface area of the pens was 1.5 m2. Each pen contained a feeding trough and three drink cups. Wood shavings were used as bedding material and bedding material was ‘topped up’ (ca. 1 kg/pen) at d 30 due to poor litter condition. The broiler unit was continuously illuminated during the first two days. From day three onwards the broiler house was illuminated according to the schedule 18L:6D with a light intensity of 20 lux at bird level. Temperature inside the experimental room was increased to 36°C one day before arrival of the chicks. From d1 the temperature was gradually decreased to 20°C  according a fixed scheme. Relative humidity was gradually increased from 60 (d0) to 75% (d35) during the experiment.

extract_protocol: Total RNA was extracted from 50 to 100 mg jejunum tissue. All samples were homogenised using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenised tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently, Direct-zol™ RNA MiniPrep Kit by Zymo Research was used as described by the manufacturer. The RNA was quantified by absorbance measurements at 260 nm.

treatment_protocol: The experimental diets were formulated according to commercial broiler diets. For each feeding period (starter, grower and finisher), diets were formulated to meet or exceed the nutrient requirements recommended by Ross 308 Guidelines for broiler chickens. The broilers received a standard starter and finisher broiler diet, whereas during the grower period (d 15 to 28) the three experimental grower diets were provided. Besides the 0% rye diet, two diets with different levels (5 and 10%) of rye inclusion were used. A standard Dutch broiler diet usually contains a high level of wheat (25-50%). To prevent interaction with other insoluble NSP sources, maize (low in insoluble NSP) instead of wheat (intermediate in insoluble NSP) was included as the main cereal in the diets. To compensate for the lower energy value of rye compared to maize, the inclusion of lard was increased with increasing rye inclusion level. Diets were formulated to be iso-nitrogenous and iso-caloric. Diets were not supplemented with NSP degrading enzymes. Starter diets were offered to all birds from day-old until 14 days of age, grower diets from 15 to 28 days and finisher diets from 29 to 35 days. The diets and water were provided ad libitum. All diets were pelleted (3.2 mm). After pelletizing, the starter diet was crumbled, whereas the grower and finisher diets were provided as pellets.

tag: tissue

value: jejunum

tag: age

tag: treatment

value: 10% rye

tag: pool

tag: gender

value: Male


title: A-92_150501

tag: paired

tag: age at diagnosis

tag: pathological ihc er

tag: pathological ihc pr


title: A-65_150501

tag: pathological ihc her2

tag: t cm

tag: cn

tag: m


title: A-79_150501

tag: historogical grade

tag: histologic subtypes

tag: type of hormone

tag: type of operation

value: BT


title: jejunum_10%rye_d28_69

source_name: jejunum, 10%rye, d28, 69

tag: tissue


title: A-56_150501


title: A-55_150501


title: jejunum_10%rye_d28_66

source_name: jejunum, 10%rye, d28, 66

tag: age


title: A-74_150501

value: Tubular carcinoma


title: A-91_150501


title: jejunum_10%rye_d28_71

source_name: jejunum, 10%rye, d28, 71

tag: treatment


title: A-54_150501


title: B-9_150501

value: Post


title: B-52_150501


title: A-52_150501

value: Pre


title: jejunum_10%rye_d28_68

source_name: jejunum, 10%rye, d28, 68

tag: pool


title: jejunum_10%rye_d28_70

source_name: jejunum, 10%rye, d28, 70

tag: gender


title: B-86_150501

tag: paired


title: A-68_150501

tag: age at diagnosis

value: Pos


title: A-86_150501

tag: pathological ihc er


title: B-7_150501

tag: pathological ihc pr


title: A-73_150501

tag: pathological ihc her2


title: A-87_150501

tag: t cm

value: Solid-tubular carcinoma


title: jejunum_10%rye_d28_67

source_name: jejunum, 10%rye, d28, 67


title: A-53_150501

tag: cn

value: Scirrhous carcinoma

value: AI


title: A-28_150501

tag: m


title: A-27_150501

tag: historogical grade

value: Bp


title: jejunum_5%rye_d28_60

source_name: jejunum, 5%rye, d28, 60

value: 5% rye


title: A-23_150501

tag: histologic subtypes


title: A-29_150501

tag: type of hormone


title: A-17_150501

tag: type of operation


title: jejunum_5%rye_d28_63

source_name: jejunum, 5%rye, d28, 63

tag: tissue


title: A-7_150501


title: A-16_150501


title: A-24_150501


title: jejunum_10%rye_d28_65

source_name: jejunum, 10%rye, d28, 65

tag: age


title: A-36_150501


title: A-18_150501

value: Unknown


title: jejunum_5%rye_d28_61

source_name: jejunum, 5%rye, d28, 61

tag: treatment


title: jejunum_5%rye_d28_62

source_name: jejunum, 5%rye, d28, 62

tag: pool


title: A-14_150501

value: IHC 2;/FISH-


title: jejunum_5%rye_d28_57

source_name: jejunum, 5%rye, d28, 57

tag: gender


title: jejunum_5%rye_d28_58

source_name: jejunum, 5%rye, d28, 58


title: jejunum_0%rye_d28_56

source_name: jejunum, 0%rye, d28, 56

value: 0% rye


title: A-9_150501

source_name: Breast

tag: paired


title: jejunum_0%rye_d28_51

source_name: jejunum, 0%rye, d28, 51


title: jejunum_0%rye_d28_52

source_name: jejunum, 0%rye, d28, 52


title: jejunum_0%rye_d28_50

source_name: jejunum, 0%rye, d28, 50


title: jejunum_0%rye_d28_49

source_name: jejunum, 0%rye, d28, 49


title: jejunum_0%rye_d28_55

source_name: jejunum, 0%rye, d28, 55


title: F6081Sty, Patient

description: Hybridized to 250K_Sty

source_name: OOMMSC

tag: cell type

value: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures

tag: phenotype

value: Nonsyndromic cleft lip/palate (NSCL/P)


title: F8000Sty, Control

description: Hybridized to 250K_Sty

tag: disease state

value: Control

value: Female


title: jejunum_0%rye_d28_54

source_name: jejunum, 0%rye, d28, 54

value: jejunum

value: Male


title: F6023Sty, Patient

description: Hybridized to 250K_Sty


title: F6130Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_0%rye_d28_53

source_name: jejunum, 0%rye, d28, 53


title: F5992Sty, Control

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_47

source_name: jejunum, 10%rye, d21, 47

value: 10% rye


title: F5715Sty, Control

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_46

source_name: jejunum, 10%rye, d21, 46


title: jejunum_10%rye_d21_48

source_name: jejunum, 10%rye, d21, 48


title: F4257Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_45

source_name: jejunum, 10%rye, d21, 45


title: F6010Sty, Patient

description: Hybridized to 250K_Sty


title: F5959Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_43

source_name: jejunum, 10%rye, d21, 43


title: F5647Sty, Patient

description: Hybridized to 250K_Sty


title: F4437Sty, Patient

description: Hybridized to 250K_Sty


title: F5662Sty, Patient

description: Hybridized to 250K_Sty


title: F5614Sty, Patient

description: Hybridized to 250K_Sty


title: F4219Sty, Patient

description: Hybridized to 250K_Sty


title: F3507Sty, Patient

description: Hybridized to 250K_Sty


title: F5716Sty, Control

description: Hybridized to 250K_Sty


title: F4317Sty, Patient

description: Hybridized to 250K_Sty


title: F5686Sty, Patient

description: Hybridized to 250K_Sty


title: F5610Sty, Patient

description: Hybridized to 250K_Sty


title: F3506Sty, Patient

description: Hybridized to 250K_Sty


title: F3497Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_42

source_name: jejunum, 10%rye, d21, 42


title: F3491Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_10%rye_d21_41

source_name: jejunum, 10%rye, d21, 41


title: F3484Sty, Patient

description: Hybridized to 250K_Sty


title: F3493Sty, Patient

description: Hybridized to 250K_Sty


title: F3496Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_5%rye_d21_37

source_name: jejunum, 5%rye, d21, 37


title: jejunum_5%rye_d21_39

source_name: jejunum, 5%rye, d21, 39


title: F3479Sty, Patient

description: Hybridized to 250K_Sty


title: F3478Sty, Patient

description: Hybridized to 250K_Sty


title: F3480Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_5%rye_d21_38

source_name: jejunum, 5%rye, d21, 38


title: jejunum_5%rye_d21_35

source_name: jejunum, 5%rye, d21, 35


title: jejunum_5%rye_d21_36

source_name: jejunum, 5%rye, d21, 36


title: F3476Sty, Patient

description: Hybridized to 250K_Sty


title: F3488Sty, Patient

description: Hybridized to 250K_Sty


title: Patient F6130

description: Gene expression data from mesenchymal stem cells derived from OOM.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.

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

data_processing: Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method. We excluded from the expression data the Affymetrix controls and probe sets classified as ‘rescue->FLmRNA->unmapped’ (poorly aligning to transcriptome, Homo sapiens NetAffx annotation release 32, 2011-06-21), also removing probe sets with cross hybridization potential.

source_name: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures (OOMMSC)

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

growth_protocol: We established OOMMSC primary cultures according to previously published protocol [Bueno et al. 2009] and expanded to 70-90% confluence. We confirmed the mesenchymal immunophenotype of a representative sample of cell cultures through flow cytometry analysis with fluorescent antibodies for markers CD29 (adhesion), CD31 (endothelial), CD45 (hematopoietic), CD73 or CD166, CD90, and CD105 (mesenchymal).

extract_protocol: Total RNA isolation was performed with NucleoSpin RNA II kit (Macherey-Nagel), following manufacturer’s recommendations. RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.

value: Orbicularis Oris Muscle


title: jejunum_5%rye_d21_34

source_name: jejunum, 5%rye, d21, 34


title: F3462Sty, Patient

description: Hybridized to 250K_Sty

source_name: OOMMSC


title: Patient F6081


title: Control F8000


title: F3463Sty, Patient

description: Hybridized to 250K_Sty


title: F3474Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_0%rye_d21_29

source_name: jejunum, 0%rye, d21, 29


title: jejunum_0%rye_d21_30

source_name: jejunum, 0%rye, d21, 30


title: jejunum_0%rye_d21_28

source_name: jejunum, 0%rye, d21, 28


title: F3459Sty, Patient

description: Hybridized to 250K_Sty


title: Patient F6010


title: jejunum_0%rye_d21_27

source_name: jejunum, 0%rye, d21, 27


title: F3458Sty, Patient

description: Hybridized to 250K_Sty


title: Patient F5959


title: F3468Sty, Patient

description: Hybridized to 250K_Sty


title: Control F5716


title: Control F5992


title: Patient F6023


title: F3413Sty, Patient

description: Hybridized to 250K_Sty


title: F3440Sty, Patient

description: Hybridized to 250K_Sty


title: F3430Sty, Patient

description: Hybridized to 250K_Sty


title: F3436Sty, Patient

description: Hybridized to 250K_Sty


title: F3427Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_0%rye_d21_25

source_name: jejunum, 0%rye, d21, 25


title: F1403Sty, Patient

description: Hybridized to 250K_Sty


title: Patient F5610


title: F3292Sty, Patient

description: Hybridized to 250K_Sty


title: F3324Sty, Patient

description: Hybridized to 250K_Sty


title: F3434Sty, Patient

description: Hybridized to 250K_Sty


title: F3439Sty, Patient

description: Hybridized to 250K_Sty


title: F3404Sty, Patient

description: Hybridized to 250K_Sty


title: jejunum_0%rye_d14_23

source_name: jejunum, 0%rye, d14, 23


title: Patient F5614


title: Patient F3507


title: Patient F4219


title: jejunum_0%rye_d14_22

source_name: jejunum, 0%rye, d14, 22


title: Patient F4257


title: Patient F4317


title: Patient F3496


title: jejunum_0%rye_d14_21

source_name: jejunum, 0%rye, d14, 21


title: Patient F3497


title: Patient F5662


title: Patient F5686


title: jejunum_0%rye_d14_20

source_name: jejunum, 0%rye, d14, 20


title: Patient F3491


title: Patient F3493


title: jejunum_0%rye_d14_24

source_name: jejunum, 0%rye, d14, 24


title: jejunum_0%rye_d21_26

source_name: jejunum, 0%rye, d21, 26


title: Patient F5647


title: Patient F3488


title: Patient F3476


title: jejunum_0%rye_d14_19

source_name: jejunum, 0%rye, d14, 19


title: Control F5715


title: jejunum_0%rye_d14_16

source_name: jejunum, 0%rye, d14, 16


title: jejunum_0%rye_d14_18

source_name: jejunum, 0%rye, d14, 18


title: Patient F3459

source_name: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures (OOMMSC)


title: Patient F3480


title: Patient F3479


title: Patient F3474


title: Patient F3439


title: Patient F3478


title: Patient F3436


title: jejunum_0%rye_d14_13

source_name: jejunum, 0%rye, d14, 13


title: Patient F3468


title: Patient F3484


title: Patient F3463


title: jejunum_0%rye_d14_17

source_name: jejunum, 0%rye, d14, 17


title: jejunum_0%rye_d14_15

source_name: jejunum, 0%rye, d14, 15


title: Patient F3458


title: Patient F3462


title: Patient F3440


title: jejunum_0%rye_d14_14

source_name: jejunum, 0%rye, d14, 14


title: jejunum_0%rye_d14_12

source_name: jejunum, 0%rye, d14, 12


title: jejunum_0%rye_d14_11

source_name: jejunum, 0%rye, d14, 11


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells; renlab.H3K9me3.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id:
Design description: ChIP-Seq Analysis of H3K9me3 in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK526
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7838
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K9me3.BMP4M.02.01

tag: sample alias

tag: sample common name

value: H1 BMP4 Derived Mesendoderm Cultured Cells

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

tag: batch

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue; renlab.H3K27ac.STL001SG.02.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK229
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19828
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Sigmoid Colon tissue; renlab.H3K27ac.STL001SG.02.01

tag: sra sample accession

value: Shin Lin, Stanford University

value: Primary Tissue

value: Sigmoid Colon

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

tag: biosamplemodel

value: Generic

value: Histone H3K27ac

value: Active Motif


title: Patient F3434

tag: tissue

value: Orbicularis Oris Muscle

tag: gender

value: Female

value: Nonsyndromic cleft lip/palate (NSCL/P)


title: Patient F3430


title: jejunum_0%rye_d14_10

source_name: jejunum, 0%rye, d14, 10

value: jejunum

tag: age

tag: treatment

value: 0% rye

tag: pool


title: Patient F3413

tag: phenotype


title: Patient F3404


title: Patient F3292


title: jejunum_0%rye_d14_8

source_name: jejunum, 0%rye, d14, 8


title: Patient F3324


title: Patient F3427


title: jejunum_0%rye_d14_7

source_name: jejunum, 0%rye, d14, 7


title: Patient F4437


title: jejunum_0%rye_d14_9

source_name: jejunum, 0%rye, d14, 9


title: jejunum_0%rye_d14_4

source_name: jejunum, 0%rye, d14, 4


title: cr cy 0116

city: Ithaca

first: Tim

middle: L.

last: Setter

state: NY

address: 517 Bradfield Hall

department: Crop & Soil Sci; Plant Breeding & Genetics

institute: Cornell University

description: images were analyzed using ScanAlyze software, version 2.35

hyb_protocol: see: Plant Molec. Biol. 128: 896-910.

scan_protocol: ScanArray 5000, GSI lumonics at 10um

data_processing: see: Proc. Natl. Acad. Sci. USA 95: 14863-14868

organism: Zea mays

source_name: well watered Vp1

label_protocol: aminoallyl

extract_protocol: Qiagen kit

tag: endosperm 10 d after pollination

source_name: well watered vp1 mutant


title: wy cy 0220

source_name: water stressed vp1 mutant


title: jejunum_0%rye_d14_5

source_name: jejunum, 0%rye, d14, 5


title: Patient F1403

source_name: Orbicularis Oris Muscle Mesenchymal Stem Cells Primary Cultures (OOMMSC)


title: wr wy 1121

source_name: water stressed Vp1


title: cr wr 0806


title: wy cy 0212


title: wy cy 1121


title: wr wy 0815


title: wr wy 1126


title: cr cy 0804


title: jejunum_0%rye_d14_6

source_name: jejunum, 0%rye, d14, 6


title: wr cr 0218


title: cr cy 0117


title: wr cr 0211


title: jejunum_0%rye_d14_3

source_name: jejunum, 0%rye, d14, 3


title: 10%_rye_6h_b

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

institute: Animal Sciences Group

description: Gene expression analysis after 6 hours of incubation in IPEC-J2 cells

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies) The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: Agilent microarray slides (G2519F Sus scrofa Agilent-035953, costumized in situ oligonucleotide array printed in 8 patches of 60K) harbouring 43,803 probes, were used and scanned using the DNA microarray scanner with Surescan high resolution Technology (Agilent Technologies). Agilent Scan Control with resolution of 5µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression. Background substacted signal intensity (gBGSubSigna) in the Metadata sheet are provided for all probes (ID_REF) on the array.

source_name: IPEC-J2_10% rye diet_6 hours_replica 2

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling. 500 ng RNA of each sample was amplified and labelled with the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling kit and 600 ng of Cy3 labelled cRNA was used for hybridisation on each patch.

extract_protocol: Total RNA was isolated from mucosal scrapings with TRIzol® reagent (Invitrogen) and treated with DNase. The RNA was further purified using QIAamp MinElute Virus Spin Kit columns (Qiagen, Venlo, the Netherlands) according to the manufacturers’ instructions.

tag: cell line

tag: cell type

value: Intestinal Porcine Epithelial Cells


title: 10%_rye_2h_b

description: Gene expression analysis after 2 hours of incubation in IPEC-J2 cells

source_name: IPEC-J2_10% rye diet_2 hours_replica 2


title: 10%_rye_6h_a

source_name: IPEC-J2_10% rye diet_6 hours_replica 1


title: 10%_rye_2h_a

source_name: IPEC-J2_10% rye diet_2 hours_replica 1


title: 5%_rye_2h_b

source_name: IPEC-J2_5% rye diet_2 hours_replica 2


title: C6h_b

source_name: IPEC-J2_no additive_6 hours_replica 2


title: ZnO_6h_b

source_name: IPEC-J2_ZNO_6 hours_replica 2


title: 5%_rye_2h_a

source_name: IPEC-J2_5% rye diet_2 hours_replica 1


title: C2h_b

source_name: IPEC-J2_no additive_2 hours_replica 2


title: 0%_rye_6h_a

source_name: IPEC-J2_0% rye diet_6 hours_replica 1


title: C2h_a

source_name: IPEC-J2_no additive_2 hours_replica 1


title: 5%_rye_6h_b

source_name: IPEC-J2_5% rye diet_6 hours_replica 2


title: 0%_rye_2h_b

source_name: IPEC-J2_0% rye diet_2 hours_replica 2


title: ZnO_2h_b

source_name: IPEC-J2_ZNO_2 hours_replica 2


title: 0%_rye_2h_a

source_name: IPEC-J2_0% rye diet_2 hours_replica 1


title: 0%_rye_6h_b

source_name: IPEC-J2_0% rye diet_6 hours_replica 2


title: Amox_2h_b

source_name: IPEC-J2_amoxicillin_2 hours_replica 2


title: ZnO_6h_a

source_name: IPEC-J2_ZNO_6 hours_replica 1


title: C6h_a

source_name: IPEC-J2_no additive_6 hours_replica 1


title: Amox_2h_a

source_name: IPEC-J2_amoxicillin_2 hours_replica 1


title: Amox_6h_a

source_name: IPEC-J2_amoxicillin_6 hours_replica 1


title: 5%_rye_6h_a

source_name: IPEC-J2_5% rye diet_6 hours_replica 1


title: Amox_6h_b

source_name: IPEC-J2_amoxicillin_6 hours_replica 2


title: sputum from lung cancer patient 3

status: Public on Apr 18 2017

city: Chandigarh

first: Indu

last: Verma

state: Outside U.S. & Canada

address: Dept. of Biochemistry, PGIMER

department: Biochemistry

institute: Post Graduate Institute of Medical Education and Research (PGIMER)

hyb_protocol: For hybridization, labeled cDNA probes generated from aRNA obtained from M. tb in PTB patient sputum was mixed with the labeled reference cDNA probe prior to purification with Microcon YM10 filter (Millipore). For each sputum sample from PTB patients, the M. tb arrays were hybridized over night with the mixed labeled cDNA probes including a Cy3/Cy5 dye swap for 4/7 samples (Fontan et al, 2008)

scan_protocol: The microarrays were scanned and processed with an Axon 4000B scanner and GenePix Pro 6.1 software, respectively.

data_processing: Normalized by the print-tip Lowess method; intensity ratio data obtained used to perform Significance Analysis of Microarrays (SAM) with Multiarray Viewer Software on the TMEV website for determination of differentially expressed genes; ≥ 2 fold change at a false discovery rate of < 2% were considered significantly differentially expressed.

organism: Mycobacterium tuberculosis

source_name: 7H9 broth-grown M. tb

label_protocol: The synthesis and fluorescent labeling of cDNA with Cy3 or Cy5 from aRNA was accomplished by first performing reverse transcriptase (RT) reaction with Superscript II RT followed by labeling with Klenow fragment using Bioprime Kit (Invitrogen) following a published method (Schlingemann 2005).

growth_protocol: For using as reference, M. tb H37Rv was grown in Middlebrook 7H9 broth to mid-log phase

extract_protocol: Sputum samples after collection were immediately transferred to Primestore molecular transport media (Longhorn vaccines and diagnostics). Total RNA from sputum samples in primestore was isolated using RNAzol as per manufacturer's protocol.  An RNA amplification strategy was used (MessageAmp II-bacteria RNA amplification kit- Ambion) (Schlingemann etal., 2005; Garton et al., 2008)

treatment_protocol: Expectorated sputum were immediately transferred to Primestore molecular transport media after collection.

tag: bacterial strain

tag: human tissue source

value: none (broth-grown)

organism: uncultured bacterium

source_name: sputum from lung cancer patient 3

value: speciation not done

value: sputum

tag: diagnosis

value: lung cancer


title: sputum from lung cancer patient 2

source_name: sputum from lung cancer patient 2


title: sputum from lung cancer patient 5

source_name: sputum from lung cancer patient 5


title: sputum from lung cancer patient 3 (dye flip)


title: sputum from lung cancer patient 2 (dye flip)


title: sputum from lung cancer patient 4 (dye flip)

source_name: sputum from lung cancer patient 4


title: sputum from lung cancer patient 4


title: ZnO_2h_a

source_name: IPEC-J2_ZNO_2 hours_replica 1


title: sputum from lung cancer patient 1 (dye flip)

source_name: sputum from lung cancer patient 1


title: sputum from lung cancer patient 1


title: sputum from pulmonary tuberculosis patient 7

source_name: sputum from PTB patient 7

value: tuberculosis


title: sputum from pulmonary tuberculosis patient 6

source_name: sputum from PTB patient 6


title: sputum from pulmonary tuberculosis patient 4

source_name: sputum from PTB patient 4


title: sputum from pulmonary tuberculosis patient 2

source_name: sputum from PTB patient 2


title: sputum from pulmonary tuberculosis patient 5 (dye flip)

source_name: sputum from PTB patient 5


title: sputum from pulmonary tuberculosis patient1(dye flip)

source_name: sputum from PTB patient 1


title: sputum from pulmonary tuberculosis patient 3

source_name: sputum from PTB patient 3


title: sputum from pulmonary tuberculosis patient1


title: sputum from pulmonary tuberculosis patient 7 (dye flip)


title: sputum from pulmonary tuberculosis patient 3 (dye flip)

source_name: sputum from patient 3


title: sputum from pulmonary tuberculosis patient 5


title: DAKO_brown_adipose_7months_replicate2

city: Bar Harbor

first: Christoph

last: Preuss

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
replicate 2
Sample name: 3267_DKO_B_7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Brown adipose tissue

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

extract_protocol: RNA was extracted from 3, 7 and 12-month old mice for tumor and non-tumor brown adipose tissue from all four genotypes using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Cat. No.74804). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were raised with a light-dark cycle with lights on at 7am and off at 7pm, and free access to water and food (no. 2019, Teklad Global Rodent, 9% fat; Harlan Laboratories, Madison, WI). For sacrifice, mice were anesthetized with sodium pentobarbital (Somnotol; MTC Pharmaceuticals, Hamilton, Ontario, Canada). After cardiac puncture, organs were rapidly removed, weighed, and frozen. Experiments were approved by the Canadian Council on Animal Care-accredited animal facility committee of CHU Sainte-Justine Hospital.

value: brown adipose

tag: background strain

tag: genotype

value: ATGL/HSL double Knockout (DAKO)

value: 7 months


title: DAKO_brown_adipose_12months_replicate1

description:
replicate 1
Sample name: 3515_DKO_B_12

value: 12 months


title: DAKO_white_adipose_3months_replicate2

description:
replicate 2
Sample name: 3481_DKO_W_3

source_name: White adipose tissue

value: white adipose

value: 3 months


title: DAKO_brown_adipose_12months_replicate2

description:
replicate 2
Sample name: 3519_DKO_B_12


title: DAKO_white_adipose_3months_replicate4

description:
replicate 4
Sample name: 3542_DKO_W_3


title: DAKO_brown_adipose_14months_replicate1

description:
replicate 1
Sample name: 3277_DKO_B_14

value: 14 months


title: DAKO_brown_adipose_3months_replicate3

description:
replicate 3
Sample name: 3482_DKO_B_3


title: DAKO_brown_adipose_14months_replicate5

description:
replicate 5
Sample name: 3518_DKO_B_14


title: DAKO_white_adipose_3months_replicate1

description:
replicate 1
Sample name: 3480_DKO_W_3


title: DAKO_brown_adipose_3months_replicate4

description:
replicate 4
Sample name: 3484_DKO_B_3


title: DAKO_brown_adipose_3months_replicate5

description:
replicate 5
Sample name: 3542_DKO_B_3


title: DAKO_brown_adipose_7months_replicate3

description:
replicate 3
Sample name: 3446_DKO_B_7


title: DAKO_brown_adipose_7months_replicate1

description:
replicate 1
Sample name: 3234_DKO_B_7


title: DAKO_brown_adipose_14months_replicate3

description:
replicate 3
Sample name: 3391_DKO_B_14


title: DAKO_brown_adipose_7months_replicate4

description:
replicate 4
Sample name: 3448_DKO_B_7


title: DAKO_brown_adipose_14months_replicate2

description:
replicate 2
Sample name: 3335_DKO_B_14


title: DAKO_brown_adipose_12months_replicate3

description:
replicate 3
Sample name: 3521_DKO_B_12


title: DAKO_brown_adipose_14months_replicate4

description:
replicate 4
Sample name: 3392_DKO_B_14


title: DAKO_white_adipose_3months_replicate3

description:
replicate 3
Sample name: 3482_DKO_W_3


title: DAKO_brown_adipose_12months_replicate4

description:
replicate 4
Sample name: 3468_DKO_B_12


title: HSLAKO_white_adipose_3months_replicate1

description:
replicate 1
Sample name: 3491_HAKO_W_3

value: HSL Single Knockout


title: DAKO_brown_adipose_3months_replicate2

description:
replicate 2
Sample name: 3481_DKO_B_3


title: HSLAKO_white_adipose_3months_replicate4

description:
replicate 4
Sample name: 3531_HAKO_W_3


title: HSLAKO_white_adipose_3months_replicate3

description:
replicate 3
Sample name: 3493_HAKO_W_3


title: HSLAKO_brown_adipose_12months_replicate1

description:
replicate 1
Sample name: 3464_HAKO_B_12


title: DAKO_brown_adipose_3months_replicate1

description:
replicate 1
Sample name: 3480_DKO_B_3


title: HSLAKO_brown_adipose_12months_replicate2

description:
replicate 2
Sample name: 3465_HAKO_B_12


title: HSLAKO_brown_adipose_12months_replicate3

description:
replicate 3
Sample name: 3466_HAKO_B_12


title: HSLAKO_white_adipose_3months_replicate2

description:
replicate 2
Sample name: 3492_HAKO_W_3


title: HSLAKO_brown_adipose_7months_replicate1

description:
replicate 1
Sample name: 3429_HAKO_B_7


title: HSLAKO_brown_adipose_3months_replicate4

description:
replicate 4
Sample name: 3492_HAKO_B_3


title: HSLAKO_brown_adipose_3months_replicate2

description:
replicate 2
Sample name: 3531_HAKO_B_3


title: HSLAKO_brown_adipose_3months_replicate1

description:
replicate 1
Sample name: 3493_HAKO_B_3


title: ATGLAKO_white_adipose_3months_replicate_5

description:
replicate 5
Sample name: 289_AAKO_W_3

value: ATGL Single Knockout


title: HSLAKO_brown_adipose_7months_replicate2

description:
replicate 2
Sample name: 3479_HAKO_B_7


title: ATGLAKO_brown_adipose_12months_replicate_1

description:
replicate 1
Sample name: 291_AAKO_B_12


title: HSLAKO_brown_adipose_3months_replicate3

description:
replicate 3
Sample name: 3491_HAKO_B_3


title: ATGLAKO_brown_adipose_12months_replicate_3

description:
replicate 3
Sample name: 293_AAKO_B_12


title: ATGLAKO_brown_adipose_7months_replicate_3

description:
replicate 3
Sample name: 285_AAKO_B_7


title: ATGLAKO_brown_adipose_7months_replicate_2

description:
replicate 2
Sample name: 284_AAKO_B_7


title: ATGLAKO_white_adipose_3months_replicate_2

description:
replicate 2
Sample name: 256_AAKO_W_3


title: ATGLAKO_white_adipose_3months_replicate_3

description:
replicate 3
Sample name: 257_AAKO_W_3


title: ATGLAKO_white_adipose_3months_replicate_4

description:
replicate 4
Sample name: 258_AAKO_W_3


title: ATGLAKO_brown_adipose_12months_replicate_4

description:
replicate 4
Sample name: 249_AAKO_B_12


title: ATGLAKO_brown_adipose_12months_replicate_2

description:
replicate 2
Sample name: 292_AAKO_B_12


title: ATGLAKO_brown_adipose_7months_replicate_4

description:
replicate 4
Sample name: A278_AAKO_B_7


title: ATGLAKO_brown_adipose_3months_replicate_5

description:
replicate 5
Sample name: A290_AAKO_B_3


title: HSLAKO_brown_adipose_7months_replicate3

description:
replicate 3
Sample name: Lipl_23_HAKO_B_7


title: ATGLAKO_brown_adipose_7months_replicate_1

description:
replicate 1
Sample name: 279_AAKO_B_7


title: ATGLAKO_brown_adipose_3months_replicate_3

description:
replicate 3
Sample name: A258_AAKO_B_3


title: ATGLAKO_brown_adipose_3months_replicate_2

description:
replicate 2
Sample name: A257_AAKO_B_3


title: ATGLAKO_brown_adipose_3months_replicate_4

description:
replicate 4
Sample name: A289_AAKO_B_3


title: Control_wildtype_white_adipose_3months_replicate_3

description:
replicate 3
Sample name: 295_WT_W_3

value: Control


title: Control_wildtype_white_adipose_3months_replicate_2

description:
replicate 2
Sample name: 294_WT_W_3


title: ATGLAKO_white_adipose_3months_replicate_1

description:
replicate 1
Sample name: 255_AAKO_W_3


title: Control_wildtype_white_adipose_3months_replicate_1

description:
replicate 1
Sample name: 253_WT_W_3


title: ATGLAKO_brown_adipose_3months_replicate_1

description:
replicate 1
Sample name: A255_AAKO_B_3


title: HSLAKO_brown_adipose_7months_replicate4

description:
replicate 4
Sample name: Lipl_24_HAKO_B_7


title: Control_wildtype_brown_adipose_12months_replicate_2

description:
replicate 2
Sample name: 208_WT_B_12


title: Control_wildtype_brown_adipose_12months_replicate_4

description:
replicate 4
Sample name: 231_WT_B_12


title: Control_wildtype_brown_adipose_7months_replicate_3

description:
replicate 3
Sample name: 265_WT_B_7


title: Control_wildtype_brown_adipose_7months_replicate_1

description:
replicate 1
Sample name: 263_WT_B_7


title: Control_wildtype_brown_adipose_12months_replicate_1

description:
replicate 1
Sample name: 207_WT_B_12