title: KO PGC rep1

status: Public on Jan 30 2014

description: replicate 1

hyb_protocol: According to the manufacturer's recommendations.

scan_protocol: The arrays were washed and stained according to the manufacturer's recommendations and scanned in a GeneChip scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al., Journal of American Statistical Association, 99(468), 909-917, 2004). Scatter plots were performed using in-house developed functions in Matlab.

source_name: KO PGC rep1

extract_protocol: RNA was extracted from ESCs and sorted PGCLCs using the RNeasy Mini Kit (Qiagen, Hilden, Germany)

value: PGC

tag: genotype/variation

value: Tcfap2c KO


title: Ctrl PGC rep1

type: RNA

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Ctrl PGC rep1

label_protocol: According to the manufacturer's recommendations.

tag: cell type

value: control


title: Ctrl PGC rep2

description: replicate 2

source_name: Ctrl PGC rep2


title: hFib1

status: Public on Mar 23 2014

description: Human parental D1 fibroblast

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina) background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor

organism: Homo sapiens

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

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

value: Human parental D1 fibroblast

tag: potency, inductors

value: Unipotent


title: KO PGC rep2

description: replicate 2

source_name: KO PGC rep2


title: Ctrl ESC rep2

description: replicate 2

source_name: Ctrl ESC rep2

value: ESC


title: Ctrl ESC rep1

description: replicate 1

source_name: Ctrl ESC rep1


title: KO ESC rep1

description: replicate 1

source_name: KO ESC rep1


title: TSLacZTX

status: Public on Jan 28 2014

description: TSLacZTX

hyb_protocol: cRNA was hybridized for 16h to Mouse Genome 430 2.0 GeneChip expression arrays (Affymetrix).

scan_protocol: The arrays were washed and stained and stained automatically on a GeneChip Fluidics station 450 (Affymetrix) and scanned in a GeneChip scanner 3000 (Affymetrix, Santa Clara, CA, USA).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA. Scatter plots were performed using in-house developed functions in Matlab.

source_name: TSLacZTX

label_protocol: Biotin labeling and fragmentation were performed according to the Affymetrix user manual.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality was tested using the Agilent 2100 Bioanalyzer (Agilent Technologies). 100 ng total RNA were used for cDNA synthesis

value: Mouse trophoblast stem cell LacZ cell line

tag: culture medium

value: TX


title: TSL5TX

value: Mouse trophoblast stem cell L5 cell line


title: TSLacZTS

description: TSLacZTS

source_name: TSLacZTS

value: TS


title: TSL5TS


title: tetraploid nuclear transfer #1 rep1

status: Public on Jul 11 2013

description: tNT#1 rep1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina). Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model. Variance stabilization was Background correction performed using the log2 scaling and gene expression normalization was calculated with the method implemented in the lumi package of R-Bioconductor.

source_name: tetraploid nuclear transfer #1 rep1

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

tag: tetraploid

value: Yes

tag: strain

value: mixed strain


title: CD45+ blood cells FLT3-WT rep1

status: Public on Jun 04 2013

description: replicate 1

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: Primary data was processed with GeneSpring 11.0 software (Silicon Genetics, Redwood City, CA). Data postprocessing was performed with in-house developed functions in Matlab

source_name: CD45+ blood cells FLT3-WT rep1

label_protocol: Labeled samples were hybridized overnight with the Gene Expression Hybridization kit to a Whole Human Genome Microarray (G4112F 45.000 probes corresponding to 32.600 genes Agilent Technologies) following the Manufacturer's instructions

extract_protocol: Hemogenic progenitors (CD31+CD45-) and blood cells (CD45+) derived from hESCs were sorted out at day 15 of EB development for gene expression profiling14,33. The following transgenic hESC lines were used: EV, FLT3-TKD, MLLAF4/FLT3-TKD and MLLAF4/FLT3-WT. Cells were collected and stabilized in Prep-Protec solution (Miltenyi Biotech) until RNA extraction. RNA was isolated using the NucleoSpin RNAII kit, and its quality checked in the Agilent 2100 Bioanalyzer platform (Agilent Technologies). For the linear T7-based amplification, 100ng of each total RNA sample was used

value: CD45+ blood cells

tag: precursor

value: No


title: CD45+ blood cells FLT3-TKD/MLLAF4 rep2

description: replicate 2

source_name: CD45+ blood cells FLT3-TKD/MLLAF4 rep2


title: nuclear transfer #2 rep1

description: NT#2 rep1

source_name: nuclear transfer #2 rep1


title: tetraploid nuclear transfer #4 rep1

description: tNT#4 rep1

source_name: tetraploid nuclear transfer #4 rep1


title: TSGFPTS

description: TSGFPTS

source_name: TSGFPTS

value: Mouse trophoblast stem cell EGFP cell line


title: tetraploid nuclear transfer #2 rep1

description: tNT#2 rep1

source_name: tetraploid nuclear transfer #2 rep1


title: tetraploid nuclear transfer #5 rep1

description: tNT#5 rep1

source_name: tetraploid nuclear transfer #5 rep1


title: nuclear transfer #1 rep1

description: NT#1 rep1

source_name: nuclear transfer #1 rep1


title: tetraploid nuclear transfer #6 rep1

description: tNT#6 rep1

source_name: tetraploid nuclear transfer #6 rep1


title: CD45+ blood cells FLT3-WT/MLLAF4 rep1

description: replicate 1

source_name: CD45+ blood cells FLT3-WT/MLLAF4 rep1


title: tetraploid nuclear transfer #3 rep1

description: tNT#3 rep1

source_name: tetraploid nuclear transfer #3 rep1


title: CD45+ blood cells FLT3-TKD/MLLAF4 rep1

description: replicate 1

source_name: CD45+ blood cells FLT3-TKD/MLLAF4 rep1


title: CD45+ blood cells FLT3-TKD rep2

description: replicate 2

source_name: CD45+ blood cells FLT3-TKD rep2


title: CD45- hemogenic precursors FLT3-WT/MLLAF4 rep2

description: replicate 1

value: CD45- hemogenic precursors


title: Ctrl_NSC_24

status: Public on May 13 2014

description: replicate 1

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

extract_protocol: 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 14h)

value: neural stem cell

tag: time

tag: treated


title: CD45+ blood cells EV rep1

description: replicate 1

source_name: CD45+ blood cells EV rep1

value: EV


title: CD45+ blood cells FLT3-TKD rep1

description: replicate 1

source_name: CD45+ blood cells FLT3-TKD rep1


title: CD45- hemogenic precursors FLT3-TKD/MLLAF4 rep2

description: replicate 1


title: CD45- hemogenic precursors FLT3-WT/MLLAF4 rep1

description: replicate 1


title: TSGFPTX

description: TSGFPTX

source_name: TSGFPTX


title: CD45+ blood cells FLT3-WT rep2

description: replicate 2

source_name: CD45+ blood cells FLT3-WT rep2


title: CD45- hemogenic precursors FLT3-WT rep2

description: replicate 2

source_name: CD45- hemogenic precursors FLT3-WT rep2


title: CD45- hemogenic precursors FLT3-WT rep1

description: replicate 1

source_name: CD45- hemogenic precursors FLT3-WT rep1


title: CD45- hemogenic precursors FLT3-TKD rep1

description: replicate 1


title: CD45- hemogenic precursors FLT3-TKD rep2

description: replicate 2


title: CD45- hemogenic precursors EV rep1

description: replicate 1

source_name: CD45- hemogenic precursors EV rep1


title: CD1vivo rep2

status: Public on May 03 2012

description: replicate 2

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: CD1vivo rep2

extract_protocol: 150 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumna TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

tag: growth condition

value: in vivo


title: CD1vivo rep1

description: replicate 1

source_name: CD1vivo rep1


title: CD1ISM1 rep3

description: replicate 3

source_name: CD1ISM1 rep3


title: CD45- hemogenic precursors EV rep2

description: replicate 2

source_name: CD45- hemogenic precursors EV rep2


title: CD1vivo rep3

description: replicate 3

source_name: CD1vivo rep3


title: C1a1

status: Public on Aug 10 2012

description: EpiSC

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),  background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

tag: spot14 gfp

value: EpiSC


title: mESC

description: ESC


title: Spot14+ rep1

status: Public on Nov 02 2012

description: replicate 1

hyb_protocol: The amplification and array hybridisation were performed by Biolytix AG Switzerland as followed according to the manufacturer's procedures: the OvationTM RNA amplification SystemV2 (NuGEN Inc.) was used to generate cDNA followed by a cleanup step using Agencourt Beads RNA clean (Agnecourt Beckman Coulter Genomics). Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip Expression 3' Amplification Reagent Hybridization Controls and the Hybridization Module of GeneChip Hybridization Wash and Stain Kit and mixed with amplified cDNA samples. GeneChip Arrays Mouse Genome 430 2.0  were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip Fluidics Station 450 and scanning with GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al. Journal of American Statistical Association 99(468) 909-917 2004). Scatter plots were performed using in-house developed functions in Matlab.

source_name: Spot14+ rep1

label_protocol: Fragmentation and biotin labelling was done with the NuGEN Encore Biotin Module (NuGEN Inc.)

extract_protocol: RNA was extracted using the NucleoSpin XS Kit (Macherey&Nagel)

tag: spot14 gfp status

value: Spot14 GFP positive


title: Lin+iPSCs11

description: iPSCs generated from OG2 lineage-positive bone marrow cells, line 1.1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

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

extract_protocol: 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).

tag: tissue

value: bone marrow

value: iPSCs from lineage-positive bone marrow cells

tag: potency

value: pluripotent


title: Lin-iPSCs7

description: iPSCs generated from OG2 lineage-negative bone marrow cells, line 7.

value: iPSCs from lineage-negative bone marrow cells


title: Spot14+ rep3

description: replicate 3

source_name: Spot14+ rep3


title: Lin-OG2-BM

description: Lineage-negative bone marrow cells isolated from OG2 mice.

value: lineage-negative bone marrow cells

value: unipotent


title: E5

description: EpiSC


title: T9

description: EpiSC


title: Spot14- rep2

description: replicate 2

source_name: Spot14- rep2

value: Spot14 GFP negative


title: E3

description: EpiSC


title: OG2.2

description: EpiSC


title: MEF-iPSC

description: iPSCs generated from OG2 MEFs.

source_name: MEF-iPSC

value: iPSCs from MEFs


title: Lin-iPSCs112

description: iPSCs generated from OG2 lineage-negative bone marrow cells, line 1.1.2.


title: Spot14- rep1

description: replicate 1

source_name: Spot14- rep1


title: Spot14- rep3

description: replicate 3

source_name: Spot14- rep3


title: OG2-ESC

description: OG2 ES cells.

value: embryonic stem (ES) cells


title: Lin-iPSCs9

description: iPSCs generated from OG2 lineage-negative bone marrow cells, line 9.


title: Spot14+ rep2

description: replicate 2

source_name: Spot14+ rep2


title: OG2.1

description: EpiSC


title: CD1ISM1 rep1

description: replicate 1

source_name: CD1ISM1 rep1


title: CD45- hemogenic precursors FLT3-TKD/MLLAF4 rep1

description: replicate 1

value: Yes


title: CD1ISM1 rep2

description: replicate 2

source_name: CD1ISM1 rep2


title: CD1HTF rep3

description: replicate 3

source_name: CD1HTF rep3

value: HTF


title: CD1HTF rep1

description: replicate 1

source_name: CD1HTF rep1


title: CD1HTF rep2

description: replicate 2

source_name: CD1HTF rep2


title: B6vivo rep3

description: replicate 3

source_name: B6vivo rep3


title: CD1KSOM rep1

description: replicate 1

source_name: CD1KSOM rep1

value: KSOM


title: B6vivo rep2

description: replicate 2

source_name: B6vivo rep2


title: B6ISM1 rep3

description: replicate 3

source_name: B6ISM1 rep3


title: B6ISM1 rep1

description: replicate 1

source_name: B6ISM1 rep1


title: B6vivo rep1

description: replicate 1

source_name: B6vivo rep1


title: B6HTF rep2

description: replicate 2

source_name: B6HTF rep2


title: B6HTF rep3

description: replicate 3

source_name: B6HTF rep3


title: B6HTF rep1

description: replicate 1

source_name: B6HTF rep1


title: B6KSOM rep1

description: replicate 1

source_name: B6KSOM rep1


title: B6KSOM rep2

description: replicate 2

source_name: B6KSOM rep2


title: B6ISM1 rep2

description: replicate 2

source_name: B6ISM1 rep2


title: B6KSOM rep3

description: replicate 3

source_name: B6KSOM rep3


title: 4F iNSC (early) rep1

description: replicate 1

source_name: 4F iNSC (early) rep1

extract_protocol: RNA samples to be analysed on microarrays were prepared using QIAGEN RNeasy columns with on-column DNA digestion. 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).

tag: nsc like


title: 5F iNSC rep1

description: replicate 1

source_name: 5F iNSC rep1


title: 4F iNSC (late) rep1

description: replicate 1

source_name: 4F iNSC (late) rep1


title: Control NSC rep2

description: replicate 2

source_name: Control NSC rep2


title: KO ESC rep2

description: replicate 2

source_name: KO ESC rep2

value: ESC

value: Tcfap2c KO


title: Control NSC rep1

description: replicate 1

source_name: Control NSC rep1


title: 5F iNSC rep2

description: replicate 2

source_name: 5F iNSC rep2


title: Fibroblast rep1

description: replicate 1

source_name: Fibroblast rep1

value: No


title: 4F iNSC (late) rep2

description: replicate 2

source_name: 4F iNSC (late) rep2


title: 4F iNSC (early) rep2

description: replicate 2

source_name: 4F iNSC (early) rep2


title: C4 aOBSC rep1

status: Public on Apr 27 2012

description: replicate 1

hyb_protocol: 10 µg of fragmented cRNA were hybridized to the mouse MOE 430 2.0 array (Affymetrix, Santa Clara, CA), containing 39000 transcript variants from 34000 well -characterized mouse genes. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: Scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix) Data analyses were performed using GeneChip Operating Software (GCOS).

data_processing:
CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al., Journal of American Statistical Association, 99(468), 909-917, 2004).
Data postprocessing and graphics were performed using in-house developed functions in Matlab®.

source_name: C4 rep1

label_protocol: Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA). cDNA was synthesized from 2.5 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (10 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

extract_protocol: Total RNA was extracted from aOBSC cultures using the Trizol reagent (Invitrogen) and purified with Qiagen RNeasy Mini Kit separation columns (Qiagen Cat.: 74104).

value: olfatory bulb stem cells

tag: fgf2 and egf addition frequency

value: Every 4 days


title: C2 aOBSC rep3

description: replicate 3

source_name: C2 rep3

value: Every 2 days


title: C4 aOBSC rep3

description: replicate 3

source_name: C4 rep3


title: C4 aOBSC rep2

description: replicate 2

source_name: C4 rep2


title: C2 aOBSC rep1

description: replicate 1

source_name: C2 rep1


title: Control aOBSC rep2

description: replicate 2

source_name: Ctr rep2

value: Every 1 day


title: Control aOBSC rep3

description: replicate 3

source_name: Ctr rep3


title: C2 aOBSC rep2

description: replicate 2

source_name: C2 rep2


title: Control aOBSC rep1

description: replicate 1

source_name: Ctr rep1


title: Donor V- rep1

status: Public on Mar 19 2012

description: replicate 1

source_name: Donor V sorted p75 negative Inferior Turbinate stem cells (ITSC)

extract_protocol: 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)

tag: p75 positive

value: Inferior Turbinate stem cells


title: Donor II- rep1

description: replicate 1

source_name: Donor II sorted p75 negative Inferior Turbinate stem cells (ITSC)


title: HUESC6 rep2

description: replicate 1

source_name: Human Embryonic Stem Cells HUESC6

value: Embryonic Stem Cells


title: Donor V rep1

description: replicate 1

source_name: Donor V sorted p75 positive Inferior Turbinate stem cells (ITSC)


title: Donor I- rep1

description: replicate 1

source_name: Donor I sorted p75 negative Inferior Turbinate stem cells (ITSC)


title: HUESC6 rep1

description: replicate 1


title: Donor IV rep1

description: replicate 1

source_name: Donor IV sorted p75 positive Inferior Turbinate stem cells (ITSC)


title: Donor IV- rep1

description: replicate 1

source_name: Donor IV sorted p75 negative Inferior Turbinate stem cells (ITSC)


title: Donor III- rep1

description: replicate 1

source_name: Donor III sorted p75 negative Inferior Turbinate stem cells (ITSC)


title: Donor II rep1

description: replicate 1

source_name: Donor II sorted p75 positive Inferior Turbinate stem cells (ITSC)


title: Donor I rep1

description: replicate 1

source_name: Donor I sorted p75 positive Inferior Turbinate stem cells (ITSC)


title: iPS16

status: Public on Apr 02 2011

description: line 2

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina) background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

source_name: hiPSC line 2 derived from HT16

value: hiPSC line 2 derived from HT16

tag: cell potency

value: Pluripotent


title: Donor III rep1

description: replicate 1

source_name: Donor III sorted p75 positive Inferior Turbinate stem cells (ITSC)

tag: cell type


title: FS

description: FS

source_name: FS human foreskin fibroblasts

value: FS human foreskin fibroblasts

value: Unipotent


title: iPS3

description: line 2

source_name: hiPSC line 2 derived from HT3

value: hiPSC line 2 derived from HT3


title: BJ

description: BJ

source_name: BJ human foreskin fibroblasts

value: BJ human foreskin fibroblasts


title: HT3

description: line 3

source_name: HT3 Human fibroblast-like testis cells

value: HT3 Human fibroblast-like testis cells


title: YoungBlastocysts rep2

status: Public on Aug 16 2011

description: replicate 2

scan_protocol: Standard Agilent scanning protocol with Agilent G2505B Microarray Scanner

data_processing: Feature extraction was performed using Agilent Feature Extraction software v.9.5. Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in Matlab.

source_name: YoungBlastocysts rep2

label_protocol: Turbo Labeling CY3 Kit (MDS Analytical Technologies) was used to label the amplified RNA with Cy3

extract_protocol: Ttotal DNA-free RNA was used as input for labelled cRNA synthesis (RNeasy Mini Kit) following the manufacturer's instructions (no DNase treatment)

value: B6C3 F1

value: Blastocysts

tag: age

value: Young


title: YoungBlastocysts rep1

description: replicate 1

source_name: YoungBlastocysts rep1


title: HuES6

description: bulk harvest at semi-sub confluence

source_name: HuES6 hESCs

value: HuES6 hESCs


title: HT16

description: line 16

source_name: HT16 Human fibroblast-like testis cells

value: HT16 Human fibroblast-like testis cells


title: ClimactericBlastocysts rep1

description: replicate 1

source_name: ClimactericBlastocysts rep1

value: Climacteric


title: NCL

description: bulk harvest at semi-sub confluence

source_name: NCL3 hESCs

value: NCL3 hESCs


title: YoungOoplasts rep1

description: replicate 1

source_name: YoungOoplasts rep1

value: Ooplasts


title: ClimactericOoplasts rep1

description: replicate 1

source_name: ClimactericOoplasts rep1


title: ClimactericBlastocysts rep2

description: replicate 2

source_name: ClimactericBlastocysts rep2


title: Epi-Sox2, rep2

status: Public on Feb 24 2011

description: Biological replicate 2 of 2.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

Non-normalized data is available in the 'GSE17984_non-normalized_data.txt' file, which is linked to the Series GSE17984 record as a supplementary file.

source_name: EpiSC GOF18 male (overexpressing Sox2) cultured in condition EpiSC medium (CM)

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).

tag: gender

value: male

value: epiblast stem cells


title: T9-EpiSC, rep1

description: Biological replicate 1 of 1.

source_name: EpiSC T9 grown on medium-density CF1 MEFs in UM, 2d -Fgf2, harv. w/o MEFs


title: EpiSC-GFP+, rep1

description: Biological replicate 1 of 2.

source_name: EpiSC E3 grown in CM and FACS-sorted for Oct4-GFP+


title: Epi-Sox2, rep1

description: Biological replicate 1 of 2.


title: EpiSC-GFP+, rep2

description: Biological replicate 2 of 2.


title: EpiSC-GFP-, rep2

description: Biological replicate 2 of 2.

source_name: EpiSC E3 grown in CM and FACS-sorted for Oct4-GFP-


title: EpiSC-GFP-, rep1

description: Biological replicate 1 of 2.


title: ESC, rep2

description: Biological replicate 2 of 2.

source_name: ESC male

value: embryonic stem cells


title: EpiSC, rep2

description: Biological replicate 2 of 2.

source_name: EpiSC GOF18 male


title: ESC, rep1

description: Biological replicate 1 of 2.


title: EpiSC, rep1

description: Biological replicate 1 of 2.


title: gPSr line 3

status: Public on Jan 23 2011

description: cell line 3

source_name: germ Pluripotent Stem cells from OG2-ROSA

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).

value: C57BL6 x 129sv

tag: genome/variation

value: Oct4-GFP x Lacz transgenic

value: germline-derived pluripotent stem (gPS) cells

value: Pluripotent


title: gPS line 1 (biol rep2)

description: cell line 1

source_name: germ Pluripotent Stem cells from OG2

tag: strain

value: Oct4-GFP transgenic


title: ESC rep2 (biol rep2)

description: replicate 2

source_name: Embryonic Stem Cells

value: embryonic stem (ES) cells


title: GSCr line 2

description: cell line 2

source_name: Germ Stem Cells OG2-ROSA

value: germline stem cells (GSCs)

value: Unipotent


title: gPS line 3 (biol rep2)

description: cell line 3


title: gPS line 2 (biol rep2)

description: cell line 2


title: GSCr line 1

description: cell line 1


title: gPSr line 1

description: cell line 1


title: GSCr line 3

description: cell line 3


title: GSC line 3 (biol rep2)

description: cell line 3

source_name: Germ Stem Cells OG2


title: gPSr line 2

description: cell line 2


title: ESC rep1 (biol rep2)

description: replicate 1


title: GSC line 2 (biol rep2)

description: cell line 2


title: EpiSox2mL2, rep2

status: Public on Dec 31 2010

description: replicate 2 of 2.

source_name: EpiSC GOF18 male overexpressing Sox2 cultured in condition EpiSC medium (CM)

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 10h).


title: EpiSCf, rep2

description: replicate 2 of 2.

source_name: EpiSC OG2 female

value: female


title: GSC line 1 (biol rep2)

description: cell line 1


title: P19-Sox2, rep1

description: replicate 1 of 2.

source_name: P19 embryonic carcinoma cell overexpressing Sox2


title: EpiSox2mE1, rep2

description: replicate 2 of 2.

source_name: EpiSC GOF18 male overexpressing Sox2 cultured in condition ESC medium (ESC like1)


title: EpiSCm, rep1

description: replicate 1 of 2.


title: Epi-Sox2f, rep2

description: replicate 2 of 2.

source_name: EpiSC OG2 female overexpressing Sox2


title: EpiSox2mE1, rep1

description: replicate 1 of 2.


title: EpiSox2mE2, rep1

description: replicate 1 of 2.

source_name: EpiSC GOF18 male overexpressing Sox2 cultured in condition ESC medium (ESC like2)


title: P19-Sox2, rep2

description: replicate 2 of 2.


title: F9-Sox2, rep1

description: replicate 1 of 2.

source_name: F9 embryonic carcinoma cell overexpressing Sox2


title: EpiSCf, rep1

description: replicate 1 of 2.


title: EpiSox2mE2, rep2

description: replicate 2 of 2.


title: EpiSox2mL2, rep1

description: replicate 1 of 2.


title: P19 EC, rep2

description: replicate 2 of 2.

source_name: P19 embryonic carcinoma cell


title: P19 EC, rep1

description: replicate 1 of 2.


title: EpiSCm, rep2

description: replicate 2 of 2.


title: ESCm, rep2

description: replicate 2 of 2.


title: ESCf, rep2

description: replicate 2 of 2.

source_name: ESC OG2 female


title: F9-Sox2, rep2

description: replicate 2 of 2.


title: ESCf, rep1

description: replicate 1 of 2.


title: Epi-Sox2f, rep1

description: replicate 1 of 2.


title: F9 EC, rep2

description: replicate 2 of 2.

source_name: F9 embryonic carcinoma cell


title: F9 EC, rep1

description: replicate 1 of 2.


title: ESCm, rep1

description: replicate 1 of 2.

source_name: ESC male


title: ePSC-R, rep2

status: Public on Dec 08 2010

description: Biological replicate 2 of 2.

hyb_protocol: Standard Illumina hybridization protocol. Purified and labelled cRNA was hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina)  according to the manufacturer's instructions.  After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare).

scan_protocol: Standard Illumina scanning protocol. Chips were scanned using the iScan reader (Illumina) and accompanying software.

data_processing: The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.

label_protocol: 500 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).

extract_protocol: RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion.

value: EpiSC-like iPS cell reverted (ePSC reverted)

value: pluripotent


title: ePSC-RC2, rep2

description: Biological replicate 2 of 2.


title: ePSC-RC1, rep1

description: Biological replicate 1 of 2.


title: ePSC-R, rep1

description: Biological replicate 1 of 2.


title: ePSC-RC1, rep2

description: Biological replicate 2 of 2.


title: ePSC-RC2, rep1

description: Biological replicate 1 of 2.


title: ePSC C1, rep2

description: Biological replicate 2 of 2.

value: epiblast stem cell-like induced pluripotent stem cell (EpiSC-like iPS cell; ePSC)


title: ePSC L7, rep1

description: Biological replicate 1 of 2.


title: ePSC L7, rep2

description: Biological replicate 2 of 2.


title: EpiSC GOF18, rep1

description: Biological replicate 1 of 2.

value: epiblast stem cell (EpiSC)


title: ePSC L4, rep2

description: Biological replicate 2 of 2.


title: ePSC C3, rep1

description: Biological replicate 1 of 2.


title: EpiSC OG2, rep2

description: Biological replicate 2 of 2.


title: ePSC L4, rep1

description: Biological replicate 1 of 2.


title: EpiSC GOF18, rep2

description: Biological replicate 2 of 2.


title: ESC OG2, rep1

description: Biological replicate 1 of 2.

source_name: ESC

value: embryonic stem cell (ESC)


title: EpiSC OG2, rep1

description: Biological replicate 1 of 2.


title: EpiSC T9b, rep1

description: Biological replicate 1 of 2.


title: ePSC C1, rep1

description: Biological replicate 1 of 2.


title: MEF, rep1

description: Biological replicate 1 of 2.

source_name: MEF

value: mouse embryonic fibroblast (MEF)

value: unipotent


title: EpiSC T9b, rep2

description: Biological replicate 2 of 2.


title: ESC OG2, rep2

description: Biological replicate 2 of 2.


title: MEF, rep2

description: Biological replicate 2 of 2.


title: ePSC C3, rep2

description: Biological replicate 2 of 2.


title: 20M rep2

status: Public on Nov 16 2010

description: Replicate 2

hyb_protocol: Hybridized for 18 hrs onto MouseRef-8 v2 gene expression BeadChips (Illumina) following the manufacturer's instructions.

scan_protocol: Chips were scanned using the iScan reader and accompanying software.

source_name: PGC 20M dpp

value: male

value: 20 days

value: primordial germ cells


title: 16M rep1

description: Replicate 1

source_name: PGC 16M dpp

value: 16 days


title: 16M rep2

description: Replicate 2


title: 20M rep1

description: Replicate 1


title: 14M rep1

description: Replicate 1

source_name: PGC 14M dpp

value: 14 days


title: 18M rep1

description: Replicate 1

source_name: PGC 18M dpp

value: 18 days


title: 10M rep2

description: Replicate 2

source_name: PGC 10M dpp

value: 10 days


title: 12M rep1

description: Replicate 1

source_name: PGC 12M dpp

value: 12 days


title: 10M rep1

description: Replicate 1


title: 8M rep2

description: Replicate 2

source_name: PGC 8M dpp

value: 8 days


title: 18M rep2

description: Replicate 2


title: 8M rep1

description: Replicate 1


title: 17.5M rep1

description: Replicate 1

source_name: PGC E17.5M

value: embryonic day 17.5


title: 18.5M rep1

description: Replicate 1

source_name: PGC E18.5M

value: embryonic day 18.5


title: 14.5M rep1

description: Replicate 1

source_name: PGC E14.5M

value: embryonic day 14.5


title: 14.5M rep2

description: Replicate 2


title: 12M rep2

description: Replicate 2


title: 13.5M rep2

description: Replicate 2

source_name: PGC E13.5M

value: embryonic day 13.5


title: 17.5M rep2

description: Replicate 2


title: 18.5M rep2

description: Replicate 2


title: 18.5F rep1

description: Replicate 1

source_name: PGC E18.5F

value: female


title: 17.5F rep2

description: Replicate 2

source_name: PGC E17.5F


title: 15.5M rep2

description: Replicate 2

source_name: PGC E15.5M

value: embryonic day 15.5


title: 15.5M rep1

description: Replicate 1


title: 13.5M rep1

description: Replicate 1


title: 12.5M rep2

description: Replicate 2

source_name: PGC E12.5M

value: embryonic day 12.5


title: 12.5M rep1

description: Replicate 1


title: 16.5M rep2

description: Replicate 2

source_name: PGC E16.5M

value: embryonic day 16.5


title: 16.5M rep1

description: Replicate 1

value: male


title: 18.5F rep2

description: Replicate 2


title: 15.5F rep2

description: Replicate 2

source_name: PGC E15.5F


title: 16.5F rep2

description: Replicate 2

source_name: PGC E16.5F


title: 15.5F rep1

description: Replicate 1


title: 13.5F rep1

description: Replicate 1

source_name: PGC E13.5F


title: 12.5F rep2

description: Replicate 2

source_name: PGC E12.5F


title: 17.5F rep1

description: Replicate 1


title: 14.5F rep1

description: Replicate 1

source_name: PGC E14.5F


title: 16.5F rep1

description: Replicate 1


title: 11.5 rep2

description: Replicate 2

source_name: PGC E11.5

value: undefined

value: embryonic day 11.5


title: 12.5F rep1

description: Replicate 1

value: primordial germ cells


title: 13.5F rep2

description: Replicate 2


title: 14.5F rep2

description: Replicate 2


title: 11.5 rep1

description: Replicate 1


title: iPS4F rep3

status: Public on Jun 14 2010

description: replicate 3

source_name: iPS4F (induced with Oct4, Sox2, Klf4, c-myc), male

value: pluripotent


title: H1 hESC rep1

status: Public on Jun 22 2010

description: replicate 1

source_name: H1 human ESCs grown on low-density CF1 MEFs

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

value: Pluripotent

value: H1 hESC


title: ESCm rep1

description: Replicate 1

source_name: ESCm OG2

tag: genotype

value: +/+ Oct4-GFP

value: embryonic stem (ES) cells


title: 2F hNiPS rep2

description: replicate 2

source_name: Two factors (Oct4, Klf4) human iPS cells from hNSCs

value: Multipotent

value: 2F hNiPS


title: iPS6F rep3

description: replicate 3

source_name: iPS6F (induced with Oct4, Sox2, Klf4, c-myc, Brg1, Baf155), male

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h)


title: H9 hESC rep1

description: replicate 1

source_name: H9 human ESCs grown on low-density CF1 MEFs

value: H9 hESC


title: iPS6F rep1

description: replicate 1


title: 1F hNiPS rep1

description: replicate 1

source_name: One factor (Oct4) human iPS cells from hNSCs

value: 1F hNiPS


title: 2F hNiPS rep1

description: replicate 1


title: iPS6F rep2

description: replicate 2


title: H1 hESC rep2

description: replicate 2


title: H9 hESC rep2

description: replicate 2


title: 1F hNiPS rep2

description: replicate 2


title: HUiPS rep2

description: replicate 2

source_name: Human iPS cells from human umbilical cord blood USSC

value: HUiPS


title: HUiPS rep1

description: replicate 1


title: USSC rep2

description: replicate 2

source_name: Human umbilical cord blood unrestricted somatic stem cells

value: Unipotent

value: USSC


title: USSC rep1

description: replicate 1


title: iPS4F rep2

description: replicate 2


title: MEF rep3

description: replicate 3

source_name: MEF OG2 male

value: unipotent

value: MEF


title: iPS4F rep1

description: replicate 1

value: male


title: ESC rep3

description: replicate 3

source_name: ESC OG2

value: ESC


title: MEF rep2

description: replicate 2


title: ESC rep2

description: replicate 2


title: pESC-B rep2

status: Public on Jan 23 2010

description:
pESC-B: Mouse parthenogenetic ESC (Embryonic Stem Cell) SSEA-1 sorted.
Replicate  2.

hyb_protocol: Standard Illumina hybridization protocol. Purified and labelled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare). Samples were exclusively hybridized as biological replicates.

scan_protocol: Standard Illumina scanning protocol. Scanned using the iScan reader (Illumina) and accompanying software.

source_name: parthenogenetic ESC SSEA-1 sorted

label_protocol: Specifically, 400 ng of total RNA per sample was used as input into a linear amplification protocol for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions, which involved synthesis of T7-linked double-stranded cDNA and 10-12 hrs of in-vitro transcription (IVT) incorporating biotin-labelled nucleotides.

value: parthenogenetic

value: embryonic stem cell, SSEA-1 sorted


title: hNSC, rep1

status: Public on Sep 23 2009

description: replicate 1 of 2.

source_name: Neural stem cells

extract_protocol: 400 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 10h).

value: multipotent


title: 2F hNiPS, rep2

description: replicate 2 of 2.

source_name: 2F (Oct4,Klf4) hiPS from hNSC

value: pluripotent


title: H9 hESC, rep1

description: replicate 1 of 2.

source_name: H9 ESCs


title: pESC-B rep1

description:
pESC-B: Mouse parthenogenetic ESC (Embryonic Stem Cell) SSEA-1 sorted.
Replicate  1.


title: pNSC rep1

description:
pNSC: Mouse parthenogenetic NSC (Neural Stem Cell).
Replicate  1.

source_name: parthenogenetic NSC

value: neural stem cell


title: MEF rep1

description: replicate 1


title: H1 hESC, rep1

description: replicate 1 of 2.

source_name: H1 ESCs


title: 1F hNiPS, rep2

description: replicate 2 of 2.

source_name: 1F (Oct4) hiPS from hNSC


title: piPS-2F rep2

description:
piPS-2F: Mouse parthenogenetic induced pluripotent cells derived from NSC overexpressing Oct4 and Klf4.
Replicate  2.

source_name: parthenogenetic iPS from NSC overexpressing Oct4 and Klf4

value: pluripotent cells, derived from NSC overexpressing Oct4 and Klf5


title: H9 hESC, rep2

description: replicate 2 of 2.


title: hNSC, rep2

description: replicate 2 of 2.


title: fESC-B rep2

description:
fESC: Mouse female ESC (Embryonic Stem Cell) OG2.
Replicate  2.

source_name: female ESC OG2

value: female

value: embryonic stem cell OG2


title: piPS-2F rep1

description:
piPS-2F: Mouse parthenogenetic induced pluripotent cells derived from NSC overexpressing Oct4 and Klf4.
Replicate  1.

value: pluripotent cells, derived from NSC overexpressing Oct4 and Klf4


title: H1 hESC, rep2

description: replicate 2 of 2.


title: ESC rep1

description: replicate 1


title: fNSC rep2

description:
fNSC: Mouse female NSC (Neural Stem Cell).
Replicate  2.

source_name: female NSC


title: 1F hNiPS, rep1

description: replicate 1 of 2.


title: fESC-B rep1

description:
fESC: Mouse female ESC (Embryonic Stem Cell) OG2.
Replicate  1.


title: 2F hNiPS, rep1

description: replicate 1 of 2.


title: pNSC rep2

description:
pNSC: Mouse parthenogenetic NSC (Neural Stem Cell).
Replicate  2.


title: fNSC rep1

description:
fNSC: Mouse female NSC (Neural Stem Cell).
Replicate  1.


title: ESC rep2

status: Public on Jul 29 2009

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol. Quality-checked cRNA samples were hybridized as biological or technical duplicates for 18 h onto mouse-8 v2 expression BeadChips (Illumina), washed, and stained following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.

scan_protocol: Standard Illumina scanning protocol. Scanned following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.

source_name: Embryonic Stem Cells

label_protocol:
400 ng of total DNA-free RNA was used as input for cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

value: Embryonic Stem Cells

value: Pluripotent


title: gPS line 3

description: cell line 3

source_name: germ Pluripotent Stem cells

value: germ Pluripotent Stem cells


title: gPS line 2

description: cell line 2


title: ESC rep1

description: replicate 1


title: Post_K4

status: Public on Sep 15 2008

type: genomic

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

country: USA

institute: University of Texas at Austin

description: H3K4 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter

hyb_protocol: Approximately 8.25μg of DNA was hybridzed per array using the Affymetrix hybridization kit.   For these 7 array sets, 4 arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

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

data_processing: Data was quantile normalized and analyzed with TileMap. Log2(IP/Input) fold changes (fc) and TileMap moving average (ma) statistics were reported in BAR files.

label: Biotin

molecule: genomic DNA

source_name: H3K4me3 ChIP DNA from E11.5 posterior limb buds

label_protocol: Samples (37.5-44μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: Rosa Gli3TFLAG c/c females mice were crossed with Prrx1Cre homozygous male drivers and litters were taken at E11.5. Embryos (generally 9) were dissected and forelimbs and hindlimbs were dissected into PBS, trypsinized in 300μl trypsin-EDTA for 5 minutes at 37º, inactivated by adding 700μl of DMEM with 10% calf serum, and cross-linked with 1% formaldehyde for 30 minutes.  ChIP and LMPCR was performed according to our previous protocol (Vokes et al., 2007) with the following modifications.  Chromatin was sonicated in 2ml of buffer 3 using 10x30 second pulses on a Branson 450 Sonifier (3 pulses on setting 4, then 7 on setting 5).  For whole genome arrays, three ChIP reactions were set up in parallel with 500μl each (with 15μl of each biological sample reserved for an input control) – single promoter arrays used a single ChIP sample. At the final step, the samples were pooled and enrichment was validated using qPCR.  For LMPCR, the pooled samples were divided into three and processed in parallel using 0.25mM  dATP, dCTP, dGTP, 0.2mM dTTP and 0.05mM dUTP with 27 total cycles and then re-pooled after PCR cleanup. Each pooled set of reaction yielded >38μg of amplified sample. The linearity of amplification was confirmed by comparing qPCR values with the values from the unamplified samples.

tag: Age

value: E11.5 mouse limb buds (posterior 2/3d)

tag: Amplification method

value: LMPCR

tag: Antibody

source_name: Input DNA from E11.5 posterior limb buds

tag: Input DNA


title: Post_PanH3

description: PanH3 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter

source_name: Pan Histone H3 ChIP DNA from E11.5 posterior limb buds

value: Histone H3


title: Post_K27

description: H3K27 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter

source_name: H3K27me3 ChIP DNA from E11.5 posterior limb buds


title: Ant_PanH3

description: PanH3 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter

source_name: Pan Histone H3 ChIP DNA from E11.5 anterior limb buds

value: E11.5 mouse limb buds (anterior 1/3d)

source_name: Input DNA from E11.5 anterior limb buds


title: GSC line 4

description: cell line 4

source_name: Germ stem cells

value: Germ stem cells

value: Unipotent


title: Ant_K4

description: H3K4 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter

source_name: H3K4me3 ChIP DNA from E11.5 anterior limb buds


title: Ant_K27

description: H3K27 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter

source_name: H3K27me3 ChIP DNA from E11.5 anterior limb buds


title: GSC line 2

description: cell line 2


title: Gli3Promoter_mm8

description: GLI3 ChIP Biological Rep 1-3, promoter

source_name: FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds

value: E11.5 mouse limb buds

value: FLAG M2 mouse monoclonal

source_name: Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds


title: Gli3Genome_mm8_3

description: GLI3 ChIP Biological Rep 1-3, chip C


title: Gli1Promoter_mm8

description: GLI1 ChIP Biological Rep 1-3, promoter

source_name: FLAG ChIP DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds

source_name: Input DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds


title: gPS line 1

description: cell line 1


title: Gli3Genome_mm8_1

description: GLI3 ChIP Biological Rep 1-3, chip A


title: GSC line 3

description: cell line 3


title: Gli3Mut_Y

description:
Gli3 loss-of-function mutant limb bud at E11.5, biological rep3
Forelimbs from  embryo 1030 (Gli3-/-) Gli3 mutant

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP).  • Transfer 200μl of hyb solution to each array, then tape holes and parafilm.  • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: Age: E11.5 Forelimbs

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

growth_protocol: Mouse forelimbs dissected from day 11.5 mouse embryos

extract_protocol: Shh mutant phenotypes were manually identified as wild-type or mutants. All other samples were snap frozen in liquid N2 and genotyped. Either single or dual samples of equivalent genotyped samples (2-4 forelimbs) were used for all other samples. All samples contained 5μg of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinus™ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: E11.5 Forelimbs


title: time point twelve rep 3

status: Public on May 05 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_time point twelve rep 3

hyb_protocol: ~1ug label and fragmented applied for 16hrs 40OC

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Francisella tularensis subsp. tularensis SCHU S4

source_name: time point twelve rep 3

label_protocol: RNA amplification step was introduced as follows: all RNA samples that were generated from F. tularensis SchuS4-infected and noninfected BMMs were randomized on a single 96-well plate and the MessageAmp II-Bacteria kit (Ambion, Foster City, CA) was used to amplify 0.5 to 1 μg of mixture of F. tularensis and BMM RNAs according to manufacturer's instructions. Briefly, RNAs were concentrated to 5 μl, denatured for 10 min at 70°C, polyadenylated using E.coli polyA polymerase for 15 min at 37°C, and reverse transcribed for 2 h at 42°C using ArrayScript and polydT primer with a T7 tail.  Second strand synthesis was performed immediately after first strand cDNA synthesis for 2 h at 16°C. Purified cDNA was mixed with 75 nmol of biotin-16-UTP (Roche Applied Science, Mannheim, Germany) and concentrated to 18 μl. Biotin-labeled complementary pathogen-host RNA was amplified at 37°C in an overnight 40 μl in vitro transcription reaction. The amount of target consisting of macrophage and F. tularensis cRNAs was determined by Absorbance measurements at 260 nm. The quality and the size of the amplified targets were determined on a Agilent 2100 Bioanalyzer using the Pico analysis kit (Agilent Technologies, Palo Alto, CA). The amount of F. tularensis cRNA was estimated by quantitative RT-PCR of the FTT0243 locus, as described below, using a standard curve method (Applied Biosystems, Foster City, CA). F.tularensis RNA extracted from a bacterial suspension in TSB-C was used for the RNA standard curve.

growth_protocol: Bone marrow cells were isolated from femurs of 6-10 week-old, C57BL/6J female mice (Jackson Laboratories, Bar Harbor, ME, USA) and differentiated into macrophages for 5 days at 37°C and 7% CO2, in 1g/L glucose Dulbecco's Modified Eagle Medium (DMEM, Invitrogen) supplemented with 10% fetal bovine serum (FBS, Invitrogen), 10% L-conditioned medium {de Chastellier, 1993 #28}, and 2 mM L-glutamine in non tissue culture-treated Petri dishes. After 5 days, loosely adherent BMMs were washed with PBS, harvested by incubation in chilled cation-free PBS on ice for 10 min, resuspended in complete medium and replated in either 6-, 12- or 24-well cell culturetreated plates at a density of 1x106, 5x105 or 1x105 macrophages/well, respectively. BMMs were further incubated at 37°C under 7% CO2 atmosphere for 48 h, with replenishing complete medium 24 h before infection. For infections, bacterial suspensions were diluted in complete medium and 1.5, 1 or 0.5 ml was added to chilled BMMs at an appropriate multiplicity of infection (MOI) of 50, unless stated otherwise. Bacteria were centrifuged onto macrophages at 400 x g for 10 min at 4°C, and infected BMMs incubated for 20 min at 37°C under 7% CO2 atmosphere including an initial, rapid warm up in a 37°C water bath to synchronize bacterial uptake. Infected BMMs were 23 then washed 5 times with DMEM to remove extracellular bacteria, incubated for an additional 60 min in complete medium containing 100 μg/ml gentamicin to kill extracellular bacteria and thereafter in gentamicin-free medium until processing.

extract_protocol: At each time point, samples were washed 3 times with sterile PBS to remove residual extracellular bacteria, and both BMMs and bacteria were lysed directly in the wells by the addition of 1 ml TRIzol (Invitrogen, Carlsbad, CA) and pipetting 10 times. Samples were transferred to microtubes, 200 ìl chloroform were added, vials were vortexed, and centrifuged at 16,000 x g for 15 min. The RNA-containing aqueous phase was collected from each sample and passed through a Qiashredder column (Qiagen, Valencia, CA) at 21,000 x g for 2 min.

treatment_protocol: BMMs seeded in 12-well plates were infected with Schu S4 at a MOI of either 200 (0, 1, 2 and 4 h time points), 50 (8, 12 h time points) or 25 (16 and 24 h time points). The use of different MOIs in this experimental design was required to recover sufficient amount of bacterial RNA at all time points analyzed but did not affect the timing of the Francisella intracellular cycle, therefore generating biologically comparable samples. Time zero samples were generated by adding bacteria (MOI 200; 108/well) directly to BMMs that had been washed with PBS, followed by the immediate addition of lysis buffer, as described below. Uninfected controls were generated at both 0 and 24h post infection.

tag: Schu 4


title: GSC line 1

description: cell line 1


title: time point twelve rep 1

description: Gene expression data from_time point twelve rep 1

source_name: time point twelve rep 1


title: Gli3WT_U

description:
Gli3 wild type limb bud at E11.5, biological rep1
Forelimbs from  embryo 1024 (Gli3 +/+;Smo n/+) considered wild-type


title: Gli3WT_V

description:
Gli3 wild type limb bud at E11.5, biological rep2
Forelimbs from  embryo 1026 (Gli3 +/-;Smo n/+) considered wild-type


title: Gli3WT_W

description:
Gli3 wild type limb bud at E11.5, biological rep3
Forelimbs from  embryo 1027 (Gli3 +/-;Smo n/+) considered wild-type


title: SmoGli3_CONT_M

description:
Control for Smo and Gli3 double knock-out limb bud at E11.5, biological rep1
Forelimbs from  embryo 1002 (Gli3+/-;Smo+/+) considered wild-type


title: SmoGli3_I

description:
Smo and Gli3 double knock-out limb bud at E11.5, biological rep1
Forelimbs from  embryo 981 (Gli3-/-;Smo n/c) double mutant


title: SmoM2_T

description:
Smo gain-of-function mutant limb bud at E11.5, biological rep3
Forelimbs from two embryos

source_name: Genotype: Prrx1Cre +/-;RosaSmoM2 c/+

value: E11.5 Forelimbs, Genotype:Prrx1Cre +/-;RosaSmoM2 c/+


title: Comparison of mouse wild type 8-cell stage with Cdx2 knock-down 8-cell stage

status: Public on Dec 30 2008

description: Biological duplicates of mouse 8-cell stage.

hyb_protocol: 800 micrograms of Cy3 and Cy5 labeled cRNA was used for the array hibridization. The hybridization experiments were duplicated in a reciprocal labeling manner to reduce dye integration bias. The array hybridization was carried out standard Agilent hybridization protocol using SSC buffer.

scan_protocol: Hybridized slides were scanned using the Agilent GeneArray scanner.

data_processing: Scanned microarray results were processed with Feature Extraction software (ver. 7.5, Agilent). The data merge were carried out using Rosetta Luminator software.

source_name: Total RNA from murine wild type 8-cell stage labeled with Cyanine-5 (red).

label_protocol: 500 micrograms of total RNA was labeled using a Low Input Linear Amplification kit (Agilent) following the manufacturer’s instructions.

extract_protocol: TriZol procedure

treatment_protocol: Wild type

tag: Tissue

value: 8 cell

source_name: Total RNA from murine Cdx2 mutant 8-cell stage labeled with Cyanine-3 (green).

treatment_protocol: Cdx2 knock-down


title: SmoGli3_J

description:
Smo and Gli3 double knock-out limb bud at E11.5, biological rep2
Forelimbs from  embryo 982 (Gli3-/-;Smo n/c) double mutant


title: Gli3Mut_AA

description:
Gli3 loss-of-function mutant limb bud at E11.5, biological rep1
Forelimbs from  embryo 1032 (Gli3-/-) Gli3 mutant


title: time point eight rep 3

description: Gene expression data from_time point eight rep 3

source_name: time point eight rep 3


title: Gli3Mut_BB

description:
Gli3 loss-of-function mutant limb bud at E11.5, biological rep2
Forelimbs from  embryo 1033 (Gli3-/-) Gli3 mutant


title: SmoGli3_L

description:
Smo and Gli3 double knock-out limb bud at E11.5, biological rep3
Forelimbs from  embryo 1006 (Gli3-/-;Smo n/c) double mutant


title: SmoGli3_CONT_P

description:
Control for Smo and Gli3 double knock-out limb bud at E11.5, biological rep2
Forelimbs from  embryo 940 (Gli3+/+;Smo n/+) considered wild-type


title: SmoM2_Q

description:
Smo gain-of-function mutant limb bud at E11.5, biological rep1
Forelimbs from two embryos


title: Comparison of mouse wild type blastocsyt stage with Cdx2 knock-down blastocsyt stage

description: Biological triplicates of mouse blastocyst stage.

hyb_protocol: 800 micrograms of Cy3 and Cy5 labeled cRNA was used for the array hibridization. The hybridization experiments were triplicated in a reciprocal labeling manner to reduce dye integration bias. The array hybridization was carried out standard Agilent hybridization protocol using SSC buffer.

source_name: Total RNA from murine wild type blastocyst stage labeled with Cyanine-5 (red).

value: Blastoyst

source_name: Total RNA from murine wild type blastocyst stage labeled with Cyanine-3 (green).


title: Shh_WT_G

description:
Shh wild type limb bud at E11.5, biological rep3
Forelimbs from phenotypically wt embryos 968 and 969; genotype is mixture of Shh +/+ and Shh +/- forelimbs

source_name: Genotype Shh +/+ and +/- mixture

value: E11.5 Forelimbs, Genotype Shh +/+ and +/- mixture


title: Shh_Mut_C

description:
Shh loss-of-function mutant limb bud at E11.5, biological rep3
Forelimbs from Shh mutants 964 and 965

source_name: Genotype Shh -/-

value: E11.5 Forelimbs, Genotype Shh -/-


title: SmoM2_S

description:
Smo gain-of-function mutant limb bud at E11.5, biological rep2
Forelimbs from two embryos


title: Shh_WT_H

description:
Shh wild type limb bud at E11.5, biological rep4
Forelimbs from phenotypically wt embryos 970 and 971; genotype is mixture of Shh +/+ and Shh +/- forelimbs


title: Shh_Mut_A

description:
Shh loss-of-function mutant limb bud at E11.5, biological rep1
Forelimbs from Shh mutants 946 and 947


title: Shh_WT_F

description:
Shh wild type limb bud at E11.5, biological rep2
Forelimbs from phenotypically wt embryos 956 and 957; genotype is mixture of Shh +/+ and Shh +/- forelimbs


title: Shh_WT_E

description:
Shh wild type limb bud at E11.5, biological rep1
Forelimbs from phenotypically wt embryos 948 and 949; genotype is mixture of Shh +/+ and Shh +/- forelimbs


title: Shh_Mut_D

description:
Shh loss-of-function mutant limb bud at E11.5, biological rep4
Forelimbs from Shh mutants 966 and 967


title: Gli3Genome_mm8_5

description: GLI3 ChIP Biological Rep 1-3, chip E


title: POST_10_10

description:
posterior limb bud at E11.5, biological rep3
posterior 2/3 of forelimb pooled litter

source_name: Genotype: Swiss-Webster (wild-type)

value: E11.5 Forelimbs, Genotype:Swiss-Webster (wild-type)


title: Gli3Genome_mm8_6

description: GLI3 ChIP Biological Rep 1-3, chip F


title: time point eight rep 2

description: Gene expression data from_time point eight rep 2

source_name: time point eight rep 2


title: Gli3Genome_mm8_2

description: GLI3 ChIP Biological Rep 1-3, chip B

source_name: FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds


title: Gli3Genome_mm8_4

description: GLI3 ChIP Biological Rep 1-3, chip D

source_name: Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds


title: ANT_10_12

description:
anterior limb bud at E11.5, biological rep3
anterior 1/3 of forelimb pooled litter


title: ANT_10_10

description:
anterior limb bud at E11.5, biological rep2
anterior 1/3 of forelimb pooled litter


title: POST_10_09

description:
posterior limb bud at E11.5, biological rep1
posterior 2/3 of forelimb pooled litter


title: ANT_10_09

description:
anterior limb bud at E11.5, biological rep1
anterior 1/3 of forelimb pooled litter


title: Shh_Mut_B

description:
Shh loss-of-function mutant limb bud at E11.5, biological rep2
Forelimbs from Shh mutants 954 and 955


title: time point twelve rep 2

description: Gene expression data from_time point twelve rep 2

source_name: time point twelve rep 2


title: 04_RA_EB

status: Public on Apr 20 2007

description: Neuralized Embryoid Bodies treated with 500nM Retinoic Acid

data_processing: dChip

label: SAPE

source_name: Embryoid bodies + Retinoic acid

growth_protocol: EBs were grown in DFNB media (Wichterle et al, 2002 Cell 110:385-397.

extract_protocol: Trizol

treatment_protocol: ES cells were differentiated to Embryoid bodies (EBs). After plating in suspension for 2 days, EBs were treated with 500nM retinoic acid

tag: Strain

value: YFP3.1 ES Cells with constitutively expressed Gli1FLAG. 3 days post-differentiation with 500nM retinoic acid


title: 08_RAHh_EB

description: Neuralized Embryoid Bodies treated with 500nM Retinoic Acid and 1μM of Hh agonist (HH-Ag)

source_name: Embryoid bodies + Retinoic acid + Hh stimulation

treatment_protocol: ES cells were differentiated to Embryoid bodies (EBs). After plating in suspension for 2 days, EBs were treated with 500nM retinoic acid and 1μM of Hh agonist (HH-Ag)

value: YFP3.1 ES Cells with constitutively expressed Gli1FLAG. 3 days post-differentiation with 500nM retinoic acid and 1μM of Hh agonist (HH-Ag).


title: 07_RAHh_EB

tag: YFP3.1 ES Cells with constitutively expressed Gli1FLAG. 3 days post-differentiation with 500nM retinoic acid and 1μM of Hh agonist (HH-Ag).


title: 02_RA_EB

source_name: Embryoid Bodies + Retinoic Acid


title: 06_RAHh_EB

source_name: Embryoid bodies + Retionic acid + Hh stimulation

value: YFP3.1 Cells with constitutively expressed Gli1FLAG. 3 days post-differentiation with 500nM retinoic acid and 1μM of Hh agonist (HH-Ag)


title: 05_RAHh_EB


title: 03_RA_EB

value: YFP3.1 ES Cells with constitutively expressed GLi1FLAG. 3 days post-differentiation with 500nM retinoic acid


title: 01_RA_EB

source_name: Embryoid bodies + Retinoic Acid


title: Gli3Genome_mm8_7

description: GLI3 ChIP Biological Rep 1-3, chip G

value: LMPCR


title: POST_10_12

description:
posterior limb bud at E11.5, biological rep2
posterior 2/3 of forelimb pooled litter


title: US22502648_251357810007_S01_44k_CGH

description: This is biological replicate #2 technical replicate #1. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

hyb_protocol: Arrays were hybridized by competitive hybridization using 5µg of labeled material per channel using the Oligo CGH hybridization kit (Agilent Technologies). The hybridizations were done in Agilent SureHyb hybridization chambers and in an Agilent rotating hyb oven at a speed of 10rpm for 72 hours at 65º C. Samples were washed sequentially for 5 minutes at room temperature using Oligo aCGH wash buffer 1, 1 minute at 37º C using Oligo aCGH wash buffer 2, 1 minute in acetonitrile at room temperature and 30 seconds in stabilization and drying solution (all from Agilent technologies).

scan_protocol: Finished arrays were scanned using an Agilent scanner. The settings were 10µm resolution and the PMT setting of both channels was at 100. Array images were extracted using Agilent’s Feature Extraction Software (version 8.5.1.1) using the standard CGH protocol included with the software. The settings included spatial detrending of the extracted array data and a linear median normalization

data_processing: The Value column is the Log Ratio of the two channels

source_name: Neuralized EBs Input Biological Rep#2 Technical Rep#2

label_protocol: 2 µg of amplified DNA was labeled with Cy3-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization

extract_protocol: Chromatin prep and shearing, crosslinks reversed, LMPCR amplification

treatment_protocol: Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)

tag: Mouse embryoid bodies treated to express neuronal progenitors

source_name: Neuralized EBs ChIP Biological Rep#2 Technical Rep#2

label_protocol: 2 µg of amplified DNA was labeled with Cy5-dUTP (Perkin Elmer) using the Bioprime Array CGH kit (Invitrogen) per Agilent’s recommended protocol. 5 µg of amplified material was used for each channel during hybridization


title: US22502648_251357810004_S01_44k_CGH

description: This is biological replicate #1 technical replicate #4. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#1 Technical Rep#4

tag: Neuralized Embryoid bodies treated with 500nM retinoic acid and 1µm of HH Agonist (HH-Ag)

source_name: Neuralized EBs Input Biological Rep#1 Technical Rep#4


title: US22502648_251357810013_S01_44k_CGH

description: This is biological replicate #3 technical replicate #3. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#3 Technical Rep#3

source_name: Neuralized EBs Input Biological Rep#3 Technical Rep#3


title: US22502648_251357810001_S01_44k_CGH

description: This is biological replicate #1, technical replicate #1. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset

source_name: Neuralized EBs Input Biological Rep#1 Technical Rep#1

source_name: Neuralized EBs ChIP Biological Rep#1 Technical Rep#1


title: US22502648_251357810006_S01_44k_CGH

source_name: Neuralized EBs Input Biological Rep#2 Technical Rep#1

source_name: Neuralized EBs ChIP Biological Rep#2 Technical Rep#1


title: US22502648_251357810011_S01_44k_CGH

description: This is biological replicate #3 technical replicate #1. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.


title: US22502648_251357810008_S01_44k_CGH

description: This is biological replicate #2 technical replicate #3. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#2 Technical Rep#3

source_name: Neuralized EBs Input Biological Rep#2 Technical Rep#3


title: US22502648_251357810002_S01_44k_CGH

description: This is biological replicate #1 technical replicate #2. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs Input Biological Rep#1 Technical Rep#2

source_name: Neuralized EBs ChIP Biological Rep#1 Technical Rep#2


title: US22502648_251357810003_S01_44k_CGH

description: This is biological replicate #1 technical replicate #3. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#1 Technical Rep#3

source_name: Neuralized EBs Input Biological Rep#1 Technical Rep#3


title: US22502648_251357810009_S01_44k_CGH

description: This is biological replicate #2 technical replicate #4. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#2 Technical Rep#4

source_name: Neuralized EBs Input Biological Rep#2 Technical Rep#4


title: US22502648_251357810012_S01_44k_CGH

description: This is biological replicate #3 technical replicate #2. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs Input Biological Rep#3 Technical Rep#2

source_name: Neuralized EBs ChIP Biological Rep#3 Technical Rep#2


title: US22502648_251357810014_S01_44k_CGH

description: This is biological replicate #3 technical replicate #4. All control spots were removed from this dataset because they have redundant names. If needed, they are present in the attached original dataset.

source_name: Neuralized EBs ChIP Biological Rep#3 Technical Rep#4

source_name: Neuralized EBs Input Biological Rep#3 Technical Rep#4