title: Monocytes from RA patient number 9 (RA_9)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 9, labelled as RA_9

value: patient number 9

value: RA


title: Monocytes from RA patient number 7 (RA_7)

status: Public on Jun 14 2012

type: RNA

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 7, labelled as RA_7

hyb_protocol: label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol. label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol. label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the FS450_0001 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood monocytes

label_protocol:
label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 3-5 µg of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)
label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 300 ng of total RNA was amplified and labelled using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit according to Affymetrix instruction
label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 100 ng of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)

extract_protocol: RNA was collected by using the RNeasy mini kit (Qiagen)

treatment_protocol: only for Affymetrix chips where monocytes were stimulated in vitro by TNFα, IFNα2a and IFNγ

tag: cell type

value: Monocytes

tag: individual

value: patient number 7

tag: disease state


title: Monocytes from healthy donor number 9

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 9, labelled as ND_9

value: healthy donor number 9

value: healthy


title: Monocytes from RA patient number 11 (RA_11)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 11, labelled as RA_11

value: patient number 11


title: Monocytes from healthy donor number 24

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 24, labelled as ND_24

value: healthy donor number 24


title: vestibular macula (bv/+) at E16.5, biological rep3

status: Public on Oct 21 2012

city: Coralville

first: Botond

last: Banfi

state: Iowa

address: 2501 Crosspark Road

department: Anatomy and Cell Biology

country: USA

institute: University of Iowa

description:
pooled vestibular maculas from the utricule and saccule
vm_Het_3

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Affymetrix Model 7G upgraded scanner

data_processing:
Raw microarray CEL files were imported into Partek Genomics Suite. Signal intensities for the probe-sets were quantile normalized and median polished using Robust Multichip Average background correction. Prior to analysis, two data sets were generated: the first data set contained probe-set intensity data that were not corrected for a batch effect [available as a Series Supplementary file], and the second data set contained probe-set intensity data that were batch-corrected [included in the sample data table] in Partek Genomics Suite (batch 1: Het(bv+)_1, Het(bv+)_2, and Homoz(bvbv)_1; batch 2: Het(bv+)_3, Het(bv+)_4, Homoz(bvbv)_2, Homoz(bvbv)_3). The downstream analysis of the batch-corrected and non-corrected data sets was identical. The signal intensities of exon probe-sets were used to calculate the overall expression level of each gene represented in MJAY. Normalized probe-set intensities (Inorm) were calculated by dividing the background-subtracted signal intensities of exon and exon-junction probe-sets by the background-subtracted gene-expression signal of the corresponding gene. We used 2 (in log2 scale) as background level for exon and exon-exon junction probe-sets and 3 (in log2 scale) as background level for gene expression data. Probe-sets that do not match any NCBI reference transcript were filtered out.
MJAY_r2.pgf
MJAY_r2.full.mps

organism: Mus musculus

source_name: vestibular macula (bv/+) at E16.5

label_protocol: Sense-strand cDNA targets were generated using the NuGEN WT-Ovation Exon Module and biotinylated using the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol: Mouse vestibular maculas isolated by laser capture microdissection from mouse embryos at E16.5

extract_protocol: Inner ears of mouse embryos (E16.5) were embedded in Tissue-Tek O.C.T. Compound and frozen in liquid nitrogen. The embryos were genotyped, and the selected inner ear samples were cryosectioned. Sections were further processed for laser-capture microdissection using the Arcturus Histogene Frozen Section Staining kit. The manufacturer’s staining protocol was modified in that RNAse inhibitor (ProtectRNA, Sigma) was added to every solution in the kit that contains more than 5% water. The vestibular macula was captured from the inner ear sections using the Laser Capture Microdissection system (Pixcell II). RNA was isolated from the captured tissue using the PicoPure RNA isolation kit (Arcturus). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.

treatment_protocol: not applicable

tag: background strain

value: Bronx waltzer (bv)

tag: genotype

value: heterozygous (bv/+)

tag: developmental stage

tag: tissue

value: vestibular maculas


title: Monocytes from healthy donor number 14

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 14, labelled as ND_14

value: healthy donor number 14


title: Monocytes from healthy donor number 7

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 7, labelled as ND_7

value: healthy donor number 7


title: Monocytes from healthy donor number 18

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 18, labelled as ND_18

value: healthy donor number 18


title: vestibular macula (bv/bv) at E16.5, biological rep1

description:
pooled vestibular maculas from the utricule and saccule
vm_Homoz_1

source_name: vestibular macula (bv/bv) at E16.5

value: homozygous (bv/bv)


title: vestibular macula (bv/bv) at E16.5, biological rep3

description:
pooled vestibular maculas from the utricule and saccule
vm_Homoz_3


title: vestibular macula (bv/bv) at E16.5, biological rep2

description:
pooled vestibular maculas from the utricule and saccule
vm_Homoz_2


title: Monocytes from healthy donor number 12

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 12, labelled as ND_12

value: healthy donor number 12


title: cerebellum (bv/+) at P15, biological rep2

description:
cerebellum total RNA from one (bv/+) mouse
Het_2

data_processing:
Raw microarray CEL files were imported into Partek Genomics Suite. Signal intensities for the probe-sets were quantile normalized and median polished using Robust Multichip Average background correction. The signal intensities of exon probe-sets were used to calculate the overall expression level of each gene represented in MJAY. Normalized probe-set intensities (Inorm) were calculated by dividing the background-subtracted signal intensities of exon and exon-junction probe-sets by the background-subtracted gene-expression signal of the corresponding gene. We used 2 (in log2 scale) as background level for exon and exon-exon junction probe-sets and 3 (in log2 scale) as background level for gene expression data. Probe-sets that do not match any annotated transcript were filtered out.
MJAY_r2.pgf
MJAY_r2.full.mps

source_name: cerebellum (bv/+) at P15

growth_protocol: Mouse cerebellum was isolated at P15.

extract_protocol: RNA was also extracted from the cerebellums of mice at P15, using the Trizol Reagent (Invitrogen). The cerebellar RNA was treated with DNase and further purified using the RNeasy mini kit (Qiagen). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.

tag: age

value: cerebellum


title: cerebellum (bv/bv) at P15, biological rep1

description:
cerebellum total RNA from one (bv/bv) mouse
Homoz_1

source_name: cerebellum (bv/bv) at P15


title: cerebellum (bv/bv) at P15, biological rep2

description:
cerebellum total RNA from one (bv/bv) mouse
Homoz_2


title: cerebellum (bv/+) at P15, biological rep4

description:
cerebellum total RNA from one (bv/+) mouse
Het_4


title: vestibular macula (bv/+) at E16.5, biological rep1

description:
pooled vestibular maculas from the utricule and saccule
vm_Het_1


title: vestibular macula (bv/+) at E16.5, biological rep2

description:
pooled vestibular maculas from the utricule and saccule
vm_Het_2


title: Monocytes from RA patient number 2 (RA_2)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 2, labelled as RA_2

value: patient number 2


title: Monocytes from RA patient number 5 (RA_5)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 5, labelled as RA_5

value: patient number 5

value: RA


title: Monocytes from RA patient number 3 (RA_3)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 3, labelled as RA_3

value: Monocytes

value: patient number 3


title: Monocytes from RA patient number 4 (RA_4)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 4, labelled as RA_4

value: patient number 4


title: Monocytes from SLE patient number 21 (SL_21)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 21, labelled as SL_21

value: patient number 21

value: SLE


title: cerebellum (bv/bv) at P15, biological rep4

description:
cerebellum total RNA from one (bv/bv) mouse
Homoz_4

value: Bronx waltzer (bv)


title: cerebellum (bv/+) at P15, biological rep3

description:
cerebellum total RNA from one (bv/+) mouse
Het_3

value: heterozygous (bv/+)


title: cerebellum (bv/bv) at P15, biological rep3

description:
cerebellum total RNA from one (bv/bv) mouse
Homoz_3


title: Monocytes from SLE patient number 16 (SL_16)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 16, labelled as SL_16

value: patient number 16


title: Monocytes from SLE patient number 14 (SL_14)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 4, labelled as SL_14


title: Monocytes from SLE patient number 5 (SL_5)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 5, labelled as SL_5


title: Monocytes from SLE patient number 13 (SL_13)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 13, labelled as SL_13

value: patient number 13


title: Monocytes from SLE patient number 11 (SL_11)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 11, labelled as SL_11

value: patient number 11


title: Monocytes from SLE patient number 10 (SL_10)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 10, labelled as SL_10

value: patient number 10


title: Monocytes from SLE patient number 7 (SL_7)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 7, labelled as SL_7

value: patient number 7


title: cerebellum (bv/+) at P15, biological rep1

description:
cerebellum total RNA from one (bv/+) mouse
Het_1


title: Monocytes from SLE patient number 4 (SL_4)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 4, labelled as SL_4


title: Monocytes from SLE patient number 1 (SL_1)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 1, labelled as SL_1

value: patient number 1


title: Monocytes from SLE patient number 3 (SL_3)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 3, labelled as SL_3


title: Monocytes from SLE patient number 8 (SL_8)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 8, labelled as SL_8

value: patient number 8


title: Chilko salmon 83620 held at 19.0C, Second

status: Public on May 31 2012

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

hyb_protocol: Each fish examined in the array experiments was run on a single slide against a reference control that was a pool of RNA from all of the fish used in the experiment. Data was normalized using the print-tip LOESS method. Microarray data were expressed in terms of normalized (background corrected) log2 ratios between each fish and the reference control.  All slides were processed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). All steps from washing, hybridization, denaturation, and slide drying were carried out automatically.

scan_protocol: Fluorescent images were scanned using a Perkin Elmer ScanArray Express, adjusting the PMT gain for optimized visualization of each image. The images were quantified using Imagene.

data_processing: Expression data were managed using a local installation of BASE. BASE was customized slightly to support Imagene two-file formatting. Each slide was normalized in BASE using the print-tip LOESS method. The number of missing values, mean signal-to-noise log-ratio and quality metrics from arrayQualityMetrics and arrayQuality in Bioconductor were used to assess slide quality.  Slides were removed from further experimental analysis if two or more plots were flagged on the arrayQualityMetrics report after data normalization, if more than 40% missing spots were identified by the SNR and missing spots report, if there were more than 30% missing spots and an experimentally low SNR value as identified by the SNR and missing spots report, or if the slide had spatial problems as identified by the plots from the arrayQuality package and substantiated by the spatial plots score of the raw microarray data in the arrayQualityMetrics report. The data for each retained slide was further processed to remove poor-quality spots. Flagged spots were treated as missing, as were spots with a SNR less than 2. In a set of slides considered a single data set, probes with more than 50% missing values were removed prior to statistical analysis. For procedures such as PCA that require matrices without missing values, missing data were imputed using an average of the existing probe intensities. The submitted data includes all probes and imputed data is not included.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: gill

label_protocol: Amplified RNA (5 micrograms) was reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer's instructions. Briefly, the cDNA was purified using Zymo-25 Clean-Up columns (Zymo Research) and eluted using the 2X coupling buffer, supplied by Invitrogen. During dye labelling, samples were process individually: the DMSO was added to the Alexa dye tube, followed by cDNA and incubated for 1h at room temperature. A standard reference design was used in the microarray experiments where the reference was comprised of a mixture of RNA from all individuals used in the study. All individual samples to be run on the arrays were fluorescently tagged with Alexa 555 and the mixed reference sample was labelled with Alexa 647. Labelled samples were cleaned up using Zymo-25 Clean-up columns by adding 300 microliters of DNA wash buffer to the pooled Alexa labelled cDNAs. The columns were centrifuged at 12500 rpm for 30 sec. The cDNA probes were washed 3 times with DNA Wash Buffer, centrifuged as above and re-centrifuged to dry followed by elution with 9 microliters of 1XTE buffer. The probes were combined with 2 microliters of Poly dA and denatured for 10 minutes at 80C. Following denaturation, 125 microliters of Ambion SlideHybe3 Buffer was added to the probes and held at 65 degrees C until the Tecan-HS4800 Pro Hybridization Station was ready for injection.

extract_protocol: Freshly sampled gill tissues were quickly frozen in liquid nitrogen and stored at -80 degrees C until RNA extractions were performed. At each of the subsequent steps leading up the hybridization of microarray slides, samples were randomized to minimize the impact of technical artefacts. The -80 degrees C samples were removed and processed immediately by adding 0.4 ml of TRI-reagent and one stainless steel 3 mm ball. Samples were extracted using a Biomek FXP automated liquid-handling instrument with the Ambion MagMax-96 for Microarrays Total RNA Isolation Kit, according to the manufacturer's instructions and robotic scripts. Total RNA was Purity was assessed by measuring the A260/A280 ratio for purity and quantity. Total RNA (1 micrograms) was used as a template for RNA amplification using the Ambion MessageAmp II-96 aRNA Amplification Kit. Amplification steps were performed using one 96-well plate.

value: gill

tag: alternative identifier

tag: survival status

value: Survival

tag: temperature (c)

tag: stock

value: Chilko

tag: Sex

value: M

label: Alexa 647

source_name: gill from all samples in the series

extract_protocol: tbd

tag: sample type

value: Pooled RNA reference


title: Chilko salmon 83621 held at 19.0C, Second


title: Chilko salmon 83616 held at 19.0C, Second


title: Chilko salmon 83622 held at 19.0C, Second


title: Chilko salmon 83619 held at 19.0C, Second


title: Monocytes from SLE patient number 2 (SL_2)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 2, labelled as SL_2

value: Monocytes

value: patient number 2


title: Chilko salmon 83618 held at 19.0C, Second


title: Chilko salmon 83617 held at 19.0C, Second


title: Chilko salmon 83615 held at 19.0C, Second


title: Chilko salmon 83614 held at 19.0C, Mortality

value: Mortality


title: Chilko salmon 83613 held at 19.0C, Mortality


title: Chilko salmon 83611 held at 19.0C, Mortality

value: F


title: Monocytes from SLE patient number 9 (SL_9)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from SLE patient number 9, labelled as SL_9

value: patient number 9

value: SLE


title: Chilko salmon 83610 held at 19.0C, Mortality


title: Chilko salmon 83612 held at 19.0C, Mortality


title: Chilko salmon 83607 held at 19.0C, Mortality


title: Chilko salmon 83602 held at 14.0C, Second


title: Chilko salmon 83606 held at 14.0C, Second


title: Chilko salmon 83609 held at 19.0C, Mortality


title: Chilko salmon 83599 held at 14.0C, Mortality


title: Chilko salmon 83603 held at 14.0C, Second


title: Adams salmon 83590 held at 19.0C, Mortality

value: Adams


title: Chilko salmon 83595 held at 14.0C, Mortality


title: Chilko salmon 83600 held at 14.0C, Mortality


title: Chilko salmon 83608 held at 19.0C, Mortality


title: Chilko salmon 83604 held at 14.0C, Second


title: Chilko salmon 83598 held at 14.0C, Mortality


title: Chilko salmon 83605 held at 14.0C, Second


title: Adams salmon 83594 held at 19.0C, Second


title: Chilko salmon 83596 held at 14.0C, Mortality


title: Chilko salmon 83597 held at 14.0C, Mortality


title: Adams salmon 83591 held at 19.0C, Mortality


title: Adams salmon 83592 held at 19.0C, Second


title: Adams salmon 83588 held at 19.0C, Mortality


title: Adams salmon 83593 held at 19.0C, Second


title: Chilko salmon 83601 held at 14.0C, Second


title: Monocytes from RA patient number 1 (RA_1)

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from RA patient number 1, labelled as RA_1

value: RA


title: Adams salmon 83586 held at 14.0C, Mortality


title: Adams salmon 83583 held at 14.0C, Mortality


title: Adams salmon 83587 held at 19.0C, Mortality


title: Adams salmon 83585 held at 14.0C, Mortality


title: THP1_13_CDP870 24h

status: Public on May 03 2012

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: gene expression from stimulated cell lines

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 2.0 Plus Array (Affymetrix GeneChipHybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using GCRMA

source_name: THP1-cells stimulated with CDP870 for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: as previously published by Schulze et al, Genes and Immunity 2008

extract_protocol: RNA extracted using RNEasy (Qiagen) according to the manufacturers guidelines

tag: cell line

tag: treatment

tag: time


title: THP1_12_CDP870 24h

treatment_protocol: as previously published by Schulze et al, Genes and Immunity 2008


title: Adams salmon 83584 held at 14.0C, Mortality


title: THP1_11_CDP870 24h


title: Adams salmon 83589 held at 19.0C, Mortality


title: THP1_15_CDP870 6h

source_name: THP1-cells stimulated with CDP870 for 6h


title: THP1_05_IFX 24h

source_name: THP1-cells stimulated with Infliximab for 24h

value: Infliximab


title: THP1_07_IFX 24h


title: LN.TR.14w.B6#1

status: Public on Apr 21 2012

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: CCD11b- CD11c- B220- CD19- CD8- CD3+CD4+CD25+

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: lymph nodes

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: mechanical dissociation/ double sorted

value: 14 weeks

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method

value: MoFlo double-sorting

value: male


title: THP1_14_CDP870 6h


title: ABD.TR.14w.B6#1

source_name: Epi Fat

extract_protocol: collagenase 2 digestion/ double sorted


title: LN.TR.14w.B6#3


title: T.8Eff.Sp.OT1.48hr.LisOva#1

description: T.8Eff.Sp.OT1.48hr.LisOva#1, Mice were infected with 5e3 cfu Lm-Ova. 24 hours later 1e6 OT1 cells were transferred.  48 hour post-transfer time point.

source_name: spleen

extract_protocol: frosted microscope teasing, dissection/trimming  Dynal CD8 negative isolation, FACSaria

value: 6 weeks

value: C57BL/6J (B6.SJL)

value: dissection/trimming


title: ABD.TR.14w.B6#3


title: THP1_09_IFX 6h

source_name: THP1-cells stimulated with Infliximab for 6h


title: T.8Eff.Sp.OT1.48hr.LisOva#2

description: T.8Eff.Sp.OT1.48hr.LisOva#2, B6.SJL (CD45.1) mice were infected with 5x10e3 CFU Lm-Ova. 24 hours later 1x10e6 CD45.2 OT1 T cells were transferred into infected recipient mice.  OT1 cells were isolated 48 hours post-transfer.

extract_protocol: frosted microscope teasing, dissection/trimming  Dynal CD8 negative isolation, iCyt Reflection sorter


title: THP1_16_CDP870 6h


title: THP1_10_IFX 6h


title: T.8Eff.Sp.OT1.24hr.LisOva#3

description: T.8Eff.Sp.OT1.24hr.LisOva#3, B6.SJL (CD45.1) mice were infected with 5x10e3 CFU Lm-Ova. 24 hours later 1x10e6 CD45.2 OT1 T cells were transferred into infected recipient mice.  OT1 cells were isolated 24 hours post-transfer.


title: THP1_04_unstim

source_name: THP1-cells unstimulated


title: THP1_06_IFX 24h


title: T.8Eff.Sp.OT1.12hr.LisOva#2

description: T.8Eff.Sp.OT1.12hr.LisOva#2, B6.SJL (CD45.1) mice were infected with 5x10e3 CFU Lm-Ova. 24 hours later 1x10e6 CD45.2 OT1 T cells were transferred into infected recipient mice.  OT1 cells were isolated 12 hours post-transfer.

extract_protocol: frosted microscope teasing, dissection/trimming  Dynal CD8 negative isolation,  iCyt Reflection sorter


title: T.8Eff.Sp.OT1.12hr.LisOva#3

description: T.8Eff.Sp.OT1.12hr.LisOva#3, B6.SJL (CD45.1) mice were infected with 5x10e3 CFU Lm-Ova. 24 hours later 1x10e6 CD45.2 OT1 T cells were transferred into infected recipient mice.  OT1 cells were isolated 12 hours post-transfer.


title: ABD.TR.14w.B6#2


title: Tgd.vg5+24ahi.Th#2

description: Tgd.vg5+24ahi.Th#2, Thymus TCRgammadelta Vg5+ CD24hi

source_name: thymus

extract_protocol: Glass Tissue Grinder  ACK Lysis Buffer  TCRd isolation kit

value: 5 weeks

value: TCRd+ Vg5+ CD24hi


title: Tgd.vg5+24ahi.Th#1

description: Tgd.vg5+24ahi.Th#1, Thymus TCRgammadelta Vg5+ CD24hi

extract_protocol: Glass Tissue Grinder  ACK Lysis Buffer  TCRd Isolation Kit


title: T.8Eff.Sp.OT1.12hr.LisOva#1

description: T.8Eff.Sp.OT1.12hr.LisOva#1, Mice were infected with Lm-Ova. 24 hours later 1e6 OT1 cells were transferred.  12 hour post-transfer time point.


title: T.8Eff.Sp.OT1.24hr.LisOva#2

description: T.8Eff.Sp.OT1.24hr.LisOva#2, Mice were infected with 5e3 cfu Lm-Ova. 24 hours later 1e6 OT1 cells were transferred.  24 hour post-transfer time point.


title: Tgd.vg3+24ahi.e17.Th#3

description: Tgd.vg3+24ahi.e17.Th#3, Thymus B6 E17 TCRgammadelta Vg3+ CD24hi

extract_protocol: Glass Tissue Grinder  ACK Lysis Buffer  Flow Sorting

value: 17 days

value: TCRd+ Vg3+ CD24hi

value: both (pooled)


title: Tgd.vg3+24ahi.e17.Th#2

description: Tgd.vg3+24ahi.e17.Th#2, Thymus B6 E17 TCRgammadelta Vg3+ CD24hi


title: THP1_02_unstim


title: THP1_03_unstim


title: THP1_08_IFX 6h


title: T.8Eff.Sp.OT1.24hr.LisOva#1

description: T.8Eff.Sp.OT1.24hr.LisOva#1, Mice were infected with5e3 cfu Lm-Ova. 24 hours later 1e6 OT1 cells were transferred.  24 hour post-transfer time point.

extract_protocol: frosted microscope teasing, dissection/trimming  CD8 T cells were pre-purified with Dynal CD8 negative isolation kit.  OTI cells were sorted on an iCyt Reflection sorter.


title: Tgd.vg3+24ahi.e17.Th#1

description: Tgd.vg3+24ahi.e17.Th#1, Thymus B6 E17 TCRgammadelta Vg3+ CD24hi


title: Tgd.vg2+24alo.Th#1

description: Tgd.vg2+24alo.Th#1, Thymus TCRgammadelta Vg2+ CD24lo

extract_protocol: Glass Tissue Grinder  CD24-biotin Anti-biotin Magnetic Depletion

value: TCRd+ Vg2+ CD24lo


title: Tgd.vg1+vd6+24alo.Th#3

description: Tgd.vg1+vd6+24alo.Th#3, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24lo

extract_protocol: Glass Tissue Grinder  CD8 Dynal Magnetic Bead Depletion  Flow Sorting

value: TCRd+ Vg1.1+ Vd6.3+ CD24lo


title: Tgd.vg1+vd6+24ahi.Th#3

description: Tgd.vg1+vd6+24ahi.Th#3, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24hi

value: TCRd+ Vg1.1+ Vd6.3+ CD24hi


title: Tgd.vg1+vd6-24ahi.Th#1

description: Tgd.vg1+vd6-24ahi.Th#1, Thymus TCRgammadelta Vg1.1+ CD24hi

value: TCRd+ Vg1.1+ Vd6.3- CD24hi


title: Tgd.vg1+vd6-24alo.Th#2

description: Tgd.vg1+vd6-24alo.Th#2, Thymus TCRgammadelta Vg1.1+ CD24lo

value: TCRd+ Vg1.1+ Vd6.3- CD24lo


title: Tgd.vg1+vd6-24ahi.Th#3

description: Tgd.vg1+vd6-24ahi.Th#3, Thymus TCRgammadelta Vg1.1+ CD24hi


title: Tgd.vg1+vd6-24ahi.Th#2

description: Tgd.vg1+vd6-24ahi.Th#2, Thymus TCRgammadelta Vg1.1+ CD24hi


title: Tgd.vg1+vd6+24ahi.Th#2

description: Tgd.vg1+vd6+24ahi.Th#2, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24hi


title: Tgd.vg1+vd6-24alo.Th#1

description: Tgd.vg1+vd6-24alo.Th#1, Thymus TCRgammadelta Vg1.1+ CD24lo


title: MM-Liv/Mb-4C2

status: Public on Mar 28 2012

type: genomic

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description:
4C Amplified DNA was compared to Background DNA
RAW and gff data in MM6, matrix data in MM9

hyb_protocol: The Cy3 and Cy5 labelled DNA was purified with Qiaquick PCR purification kit (Qiagen Cat. N. 28106) and eluted in 30 ul of hybridization solution (GlassHybTM Hybridization solution, Clontech). It was denatured and incubated in the presence of 50 ug mouse Cot1 DNA at 45°C for 1 hour. Before hybridisation the slides were washed in sodium borohydride solution (0.25g sodium borohydride in 100 ml 2x saline sodium citrate buffer SSC and 0.05% sodium dodecil sulfate) at 42°C for 30 min. After that the slides were washed twice in 1X SSC at room temperature for 5 minutes, followed by 3 washes in 0.2X SSC at RT for 2 min. The treated slides were spin-dried in a centrifuge at 200 g for 1 min. They were then incubated in 70% ethanol for 30 min at room temperature and spin dried at 2000rpm for 1 min.. Equal amounts of Cy3 and Cy5 labelled probes were combined and 50 ul was applyed onto each slide. The hybridisation was performed in hyb chambers ( Corning CMT Hyb chambers) at 50°C for 18 hours. Washing of microarrays were done according to GlassHybTM Hybridization Solution kit User Manual (Clontech). Following rinsing the slides in water, the slides were washed at room temperature i) for 10 min in wash buffer, II) for 15 min in a solution containing 2 ml wash buffer, 19 ml water and 1 ml 20X SSC, iii) for 15 min in a solution containing 2 ml wash buffer, 0.25 ml 20 x SSC, 19.75 ml water, and iv) for 15 min in a solution containing 22 ml water, 0.238 ml 20 x SSC. Finally, the slides were rinsed in water and spin-dried at 200 g.

scan_protocol: A Gene Array List(GAL) file was generated according to the format described for ScanArray Express, version 3.0. After washing, the hybridized arrays were scanned immediately using ScanArray 4000 scanner (Packard BioChip technologies) at wavelengths of 543nm for Cy3, and 633nm for Cy5. Data were analysed with ScanArray Express version 3.0 (Packard BioChip technologies) to produce the GPR files.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

source_name: Maternally Mutated Liv MboI

label_protocol: 200-400ng nested PCR product was labeled in PCR reaction with Cy3 (for background sample) dye (Amersham Biosciences PA53021) or Cy5 (for signal sample) dyes (Amersham Biosciences PA55021). Forward and rewerse primers were 5'-TTTGGCCCTTGGACATTGTCAT-3' and 5'-CCGATCTCTGAAAAG GATCATT-3'. The Cycling conditions were 94°C 3min, (24 times 94°C 30 sec-60°C 30 sec- 65°C 5min) 65°C 3min.times 94°C 30 sec-60°C 30 sec- 65°C 5min) 65°C 3min.

growth_protocol: The 142* strain mouse with 3 of the 4 CTCF target sites mutated in a 129/SvJ background 9 was crossed with the recombinant SD7 strain. Neonatal livers were collected 2 days post-partum. All animal experiments have been approved of by the local ethical committee at Uppsala.

extract_protocol: The DNA samples were amplified by nested-PCR. The high-fidelity DNA polymerase Phusion (Finnzymes, Finland) was used for first round amplification. The PCR condition is 98°C 30 sec followed by 35 x (98°C 10 sec, 70°C 30 sec, 72°C 1 min). The first round primers were 5'-CTGGTTTTGGGGTTCAGTGA-3' and 5'-TAGCAGAGAGTATGGGGGCCA-3'. For the second round of PCR, the first round PCR product was diluted 100-fold and DyNAzyme EXT (Finnzymes, Finland) was added: 94°C 3 min, 30x(94°C 30 sec, 60°C 30 sec, 72°C 1.5 min). Nested primers were 5'-TTTGGCCCTTGGACATTGTCAT-3' and 5'-CCGATCTCTGAAAAG GATCATT-3'.

treatment_protocol: Neonatal mice liver cells or differentiated and undifferentiated embryonic stem cells were dispersed and fixed in 2% formaldehyde for 10 min at room temperature (21 °C), and the reaction was then quenched with 0.125 M glycine. After two washes with PBS, the pellet was resuspended in cold lysis buffer (10 mM Tris HCl, 10 mM NaCl, 0.2% NP-40) with freshly added protease inhibitors (complete protease inhibitor cocktail tablets; Roche) and lysed on ice for 10 min. After the recovery of crosslinked nuclei by centrifugation at 600g for 5 min, the pellet (4 g DNA) was resuspended in 1 Mse I buffer (New England Biolabs), including 0.1% SDS, and was incubated at 37 °C for 1 h with shaking. We added 2% (final concentration) Triton-X 100 and incubated it at 37 °C for 1 h before adding 800 units (U) MseI (50,000 U/ml; New England Biolabs) and incubating the mixture overnight at 37 °C with shaking. The restriction enzyme was inactivated by the addition of 1.6% SDS (final concentration) and was incubated at 65 °C for 20 min. The digestion mixture was diluted (usually to 1–2 ng/l final concentration of genomic DNA) with 1 T4 ligase buffer (NEB), including 1% Triton X-100, and was incubated at 37 °C for 1 h. We ligated 4 ml of the digested DNA sample for 1 week at 4 °C with 4,000 cohesive units T4 ligase added all at once. After addition of 100 g/ml proteinase K, the samples were incubated at 65 °C overnight. Before DNA purification by phenol extraction and ethanol precipitation, the samples were incubated for 30 min at 37 °C with 0.5 g/ml RNase A.

tag: enzyme

value: MboI

tag: cell type

value: Liver

tag: mutation

value: MM

tag: dna type

value: 4C Amplified DNA

treatment_protocol: genomic DNA

value: Background DNA

value: genomic DNA


title: PM-Liv/MS-4C1

source_name: Paternally Mutated Liv MseI

value: MseI

value: PM

source_name: gDNA/MseI


title: ESC/Mb-4C2

source_name: ESC 4C treated with Mbo1

growth_protocol: Murine embryonic stem cells were maintained in vitro on a monolayer of mitoticaly inactivated mouse embryonic fibroblast (feeders) at 37oC in humidified air with 5% CO2, grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% serum, 0.1mM ß- mercaptoethanol, 50U/ml penicillin, 50 mg streptomycin, 0.1 mM non-essential amino acids (all from GIBCO) and 500 pM LIF (Chemicon). To ensure a rich population of stem cells, they were grown for one passage in gelatin-coated dishes without feeders. To assess the contamination of feeder cells in the population of undifferentiated ES cells, we use GFP-expressing feeder cells. In our preparations of undifferentiated ES cells for 4C analysis, the feeder cells was always <1% of the ES cell population. Differentiated cells were obtained by maintaining the cells for two weeks in LIF-deficient culture medium. To assess the differentiation status, RNA was extracted using Tryzol ® , cDNA prepared using a cDNA kit from Biorad and PCR assays using previously published primers and conditions for Oct-4, Gata-4.

value: ESC


title: MM-Liv/MS-4C2

source_name: Maternally Mutated Liv MseI


title: ESC/Ms-4C1


title: Tgd.vg2+24alo.Th#2

description: Tgd.vg2+24alo.Th#2, Thymus TCRgammadelta Vg2+ CD24lo

extract_protocol: Glass Tissue Grinder  CD24-biotin Anti-Biotin Magnetic Depletion

tag: age

value: 6 weeks

value: dissection/trimming

value: male


title: PM-Liv/MS-4C2


title: ESC/Ms-4C2


title: Tgd.vg1+vd6+24alo.Th#1

description: Tgd.vg1+vd6+24alo.Th#1, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24lo


title: PM-Liv/Mb-4C1

source_name: Paternally Mutated Liv MboI


title: PM-Liv/Mb-4C2


title: Tgd.vg1+vd6+24ahi.Th#1

description: Tgd.vg1+vd6+24ahi.Th#1, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24hi


title: dESC/Mb-4C2

source_name: dESC 4C treated with Mbo1

value: dESC


title: dESC/Ms-4C2


title: LN.TR.14w.B6#2

description: CCD11b- CD11c- B220- CD19- CD8- CD3+CD4+CD25+

value: 14 weeks

value: MoFlo double-sorting


title: PDS4_1

status: Public on Feb 01 2012

city: Prague

first: Ondrej

last: Seda

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University in Prague

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Transcriptomic data: after evaluation of the hybridization, the quality control and the data normalization by robust multi-array analysis (RMA), the gene expression was compared between the PD.SHR4a and PD strains utilizing PARTEK Genomics Suite (Partek, Inc.).

organism: Rattus norvegicus

source_name: PD.SHR4 rat liver

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: The animals were sacrificed and  liver tissue was snap frozen in liquid nitrogen for further analyses of gene expression.

extract_protocol: We extracted total RNA from the liver of 4-month-old males of both strains using phenol-chloroform and purified with the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol. The quality of the total RNA was verified by the Agilent 2100 Bioanalyzer system.

tag: tissue

value: liver

tag: diet

value: standard chow


title: PD_3

source_name: PD rat liver


title: ESC/Mb-4C1

value: MboI


title: PD_1


title: MM-Liv/MS-4C1

value: Liver


title: GN.Arth.SynF#2

status: Public on Dec 28 2011

source_name: Synovial Fluid

value: CD11b+ Ly6-G+


title: dESC/Mb-4C1

value: 4C Amplified DNA


title: GN.Arth.SynF#3


title: Mo.6C-II-.BM#2

description: Mo.6C-II-.BM#2, B220neg CD3neg CD115+ Ly-6C/Glo CD43+

source_name: Bone marrow

extract_protocol: Flushed femurs and tibias; RBC lysed with ACK buffer

value: 8 weeks

value: B220neg CD3neg CD115+ Ly-6C/Glo CD43+


title: GN.Arth.SynF#1


title: Mo.6C-II-.BM#1

description: Mo.6C-II-.BM#1, B220neg CD3neg CD115+ Ly-6C/Glo CD43+


title: PD_2


title: GN.UrAc.PC#1

description: GN.UrAc.PC#1, GN.UrAc.PC

source_name: Peritoneal Cavity

extract_protocol: Treated with 10% Uric Acid


title: MM-Liv/Mb-4C1

value: MM

value: Background DNA

value: genomic DNA


title: GN.UrAc.PC#3

description: GN.UrAc.PC#3, GN.UrAc.PC

extract_protocol: Treated with 3% Thioglycollate

value: 6 weeks


title: GN.Thio.PC#3

description: GN.Thio.PC#3, GN.Thio.PC

value: dissection/trimming


title: dESC/Ms-4C1

value: MseI


title: GN.Arth.BM#1

description: GN.Arth.BM#1, GN.Arth.BM

extract_protocol: Flushed BM with syringe

value: male


title: Tgd.vg1+vd6+24alo.Th#2

description: Tgd.vg1+vd6+24alo.Th#2, Thymus TCRgammadelta Vg1.1+ Vd6.3+ CD24lo

value: TCRd+ Vg1.1+ Vd6.3+ CD24lo


title: Mo.6C-II-.BM#3

description: Mo.6C-II-.BM#3, B220neg CD3neg CD115+ Ly-6C/Glo CD43+


title: GN.Arth.BM#2

description: GN.Arth.BM#2, GN.Arth.BM


title: GN.Thio.PC#2

description: GN.Thio.PC#2, GN.Thio.PC


title: GN.Arth.BM#3

description: GN.Arth.BM#3, GN.Arth.BM


title: DC.pDC.8+.MLN#2

description: DC.pDC.8+.MLN#2, Mesenteric lymph node CD8+ plasmacytoid dendritic cells  CD11cint/CD8a+/CD4+/B220+/GR1+  (samples from 8/25/10+12/01/10 pooled together)

source_name: Mesenteric LN

extract_protocol: gentle teasing using forceps, Liberase DL + DNase I digestion 15 min at 37C  depletion of NK1.1, CD3e, CD19 and TER119 positive cells using MACS system

value: PI SA-PECy7

value: B220-FITC CD45-APC CD11c-eFluor780 GR1-PE CD8-eFluor450


title: MF.169+11chi.SLN#2

description: MF.169+11chi.SLN#2, CD169+CD11c high macrophage from skin-draining lymph nodes

source_name: Skin-draining LN

extract_protocol: Digested with Liberase for 20 minutes

value: B220 CD90 Ly-6G CD103 SiglecF

value: CD11b+ CD169+ CD11chigh


title: DC.pDC.8+.SLN#1

description: DC.pDC.8+.SLN#1, Skin lymph node CD8+ plasmacytoid dendritic cells  CD11cint/CD8a+/CD4+/B220+/GR1+

source_name: Skin LN


title: MF.169+11chi.SLN#1

description: MF.169+11chi.SLN#1, CD169+CD11c high macrophage from skin-draining lymph nodes


title: DC.pDC.8+.SLN#3

description: DC.pDC.8+.SLN#3, Skin lymph node CD8+ plasmacytoid dendritic cells  CD11cint/CD8a+/CD4+/B220+/GR1+


title: DC.8-4-11b-.SLN#5

description: DC.8-4-11b-.SLN#5, CD11c+, CD8a-, CD4-, CD11b- DCs (triple negative)

source_name: subcutaneous LN

extract_protocol: Blendzyme liberase III + DNase digestion - CD3, CD19, NK1.1, GR1, Ter119 MACS depletion

value: CD11b-FITC CD4-PE CD11c-eFluor780 CD8a-eFluor450 CD45-APC


title: DC.pDC.8+.MLN#1

description: DC.pDC.8+.MLN#1, Mesenteric lymph node CD8+ plasmacytoid dendritic cells  CD11cint/CD8a+/CD4+/B220+/GR1+  (samples from 8/26/10+11/30/10 pooled together)


title: DC.8-4-11b+.SLN#4

description: DC.8-4-11b+.SLN#4, CD11c+, CD8a-, CD4-, CD11b+ DCs (double negative)


title: Ep.MEChi.Th#1

description: Ep.MEChi.Th#1, Medullary Epithelial Cells, MHC II hi

source_name: thymus

extract_protocol: Digestion Flow sorting


title: GN.UrAc.PC#2

description: GN.UrAc.PC#2, GN.UrAc.PC

value: CD11b+ Ly6-G+


title: DC.8-4-11b-.SLN#4

description: DC.8-4-11b-.SLN#4, CD11c+, CD8a-, CD4-, CD11b- DCs (triple negative)


title: MF.11cloSer.SI#5

description: MF.11cloSer.SI#5, Small Intestinal CD11c-lo CD103-CD11b+ MF

source_name: intestine

extract_protocol: Standard (Re-purified: 98.6% pure)

value: 7 weeks

value: PI CD3 B220

value: CD45+ MHCII+ CD11c-lo CD11b+


title: DC.8-4-11b+.SLN#3

description: DC.8-4-11b+.SLN#3, double negative: CD11c+, CD11b+, CD4-, CD8-

extract_protocol: digestion using Liberase III + DNase I - CD3, CD19, GR1, NK1.1, Ter-119 using MACS beads

value: CD45-APC CD11b-FITC CD11c-eFluor780 CD4-PE CD8a-eFluor450


title: MF.11cloSer.SI#4

description: MF.11cloSer.SI#4, Small Intestinal CD11c-lo CD103-CD11b+ MF

extract_protocol: Standard (Re-purified: 98% pure)


title: MF.11cloSer.SI#3

description: MF.11cloSer.SI#3, Small Intestinal CD11c-lo CD103-CD11b+ MF

extract_protocol: Standard (Re-purified: 94.5% pure)


title: DC.8-4-11b+.SLN#2

description: DC.8-4-11b+.SLN#2, double negative: CD11c+, CD11b+, CD4-, CD8-


title: MF.11cloSer.SI#2

description: MF.11cloSer.SI#2, Small Intestinal CD11c-lo CD103-CD11b+ MF


title: DC.pDC.8+.SLN#2

description: DC.pDC.8+.SLN#2, Skin lymph node CD8+ plasmacytoid dendritic cells  CD11cint/CD8a+/CD4+/B220+/GR1+


title: MF.11cloSer.Salm3.SI#4

description: MF.11cloSer.Salm3.SI#4, Small Intestinal CD11c-lo serosal Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

source_name: small intestine

extract_protocol: According to SOP

value: CD45+ MHCII+ Gr1- CD11c-lo CD11b+


title: MF.11cloSer.Salm3.SI#1

description: MF.11cloSer.Salm3.SI#1, Small Intestinal CD11c-lo serosal Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 99.5% pure)


title: MF.103-11b+.Lu#2

description: MF.103-11b+.Lu#2, MHCII+CD11c+CD103-CD11b+CD24-

source_name: lung

extract_protocol: Collagenase

value: 8 weeks

value: SiglecF CD3 DX5 B220

value: MHCII+ CD11c+ CD103- CD11b+ CD24-


title: MF.11cloSer.Salm3.SI#3

description: MF.11cloSer.Salm3.SI#3, Small Intestinal CD11c-lo serosal Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 97.6% pure)

value: 6 weeks

value: dissection/trimming


title: DC.103-11b+F4/80lo.Kd#2

description: DC.103-11b+F4/80lo.Kd#2, Kidney CD103- CD11b+ F4/80lo DC

source_name: kidney

extract_protocol: Liberase 30 minutes

value: male


title: DC.103-11b+F4/80lo.Kd#3

description: DC.103-11b+F4/80lo.Kd#3, Kidney CD103- CD11b+ F4/80lo DC


title: MF.103-11b+.Lu#1

description: MF.103-11b+.Lu#1, MHCII+CD11c+CD103-CD11b+CD24-


title: MF.103-11b+.Salm3.SI#4

description: MF.103-11b+.Salm3.SI#4, Small Intestinal CD11c-hi CD103-CD11b+ Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

value: CD45+ MHCII+ Gr1- CD11c-hi CD11b+ CD103- F480+


title: MF.103-11b+.Salm3.SI#2

description: MF.103-11b+.Salm3.SI#2, Small Intestinal CD11c-hi CD103-CD11b+ Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 94.4% pure)


title: Ago2CLIP_infected_24h

status: Public on Nov 10 2011

type: SRA

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

library_source: transcriptomic

data_processing: Adapter-trimmed sequencing libraries were mapped against an index composed of both the human (UCSC hg19, http://genome.ucsc.edu) and HCMV Towne (Genbank FJ616285.1) genomes, using Bowtie software (version 0.12.7, with parameters -k 1 -m 10 -l 25 --best). Custom Perl scripts were used to overlap mapped coordinates with smRNA annotations, which were obtained from miRBase 16.0 (http://www.mirbase.org) and the UCSC Table Browser.

growth_protocol: Primary human foreskin fibroblasts were cultured as previously described (Sanders J Virol 2008) and maintained within passages 16 to 20.

extract_protocol:
The Illumina Small RNA Sample Prep v1.5 kit was used to prepare smRNA-seq samples and CLIP-seq libraries were generated as described (Yeo Nat Struct Mol Biol 2008; Zisoulis Nat Struct Mol Biol 2010).
library_strategy: CLIP-seq

treatment_protocol: For infections, G0-synchronized cells were trypsinized, re-suspended in the presence of HCMV, and plated at near confluence. All infections were performed with the wild-type Towne strain at an MOI of 3. For mock infections, tissue culture supernatant (spent media from 3 days of culture) containing 1% DMSO was used in place of virus stock.

value: human foreskin fibroblasts (HFF)

tag: antibody

value: HCMV infected


title: MF.11cloSer.Salm3.SI#2

description: MF.11cloSer.Salm3.SI#2, Small Intestinal CD11c-lo serosal Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 94% pure)

tag: Sex


title: Ago2CLIP_mock_24h

value: mock infected


title: DC.8-4-11b-.SLN#3

description: DC.8-4-11b-.SLN#3, CD11c+, CD8a-, CD4-, CD11b- DCs (triple negative)

value: PI SA-PECy7

value: CD11b-FITC CD4-PE CD11c-eFluor780 CD8a-eFluor450 CD45-APC


title: Ago1CLIP_infected_24h


title: Ago1CLIP_infected_72h


title: MF.103-11b+.Salm3.SI#3

description: MF.103-11b+.Salm3.SI#3, Small Intestinal CD11c-hi CD103-CD11b+ Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 90.3% pure)


title: MF.103-11b+.Salm3.SI#1

description: MF.103-11b+.Salm3.SI#1, Small Intestinal CD11c-hi CD103-CD11b+ Macrophages, Day 3 post-infection with oral Salmonella Typhimurium

extract_protocol: According to SOP (Re-purified: 96.5% pure)


title: DC.103+11b-.Lu#5

extract_protocol: 15min Liberase Blend

value: MHCII+ CD11c+ CD103+ CD11b


title: DC.103-11b+F4/80lo.Kd#1

description: DC.103-11b+F4/80lo.Kd#1, Kidney CD103- CD11b+ F4/80lo DC


title: MF.11cloSer.SI#1

description: MF.11cloSer.SI#1, Small Intestinal CD11c-lo CD103-CD11b+ MF

extract_protocol: Standard (No re-purification: 94% pure)

value: 7 weeks

value: PI CD3 B220


title: DC.103-11b+24+.Lu#1

description: DC.103-11b+24+.Lu#1, MHCII+CD11c+CD103-CD11b+CD24+

value: MHCII+ CD11c+ CD103- CD11b+ CD24+


title: B1a.Sp#4

description: B1a.Sp#4, CD19+CD45R+IgM++AA4.1-CD23-CD43+CD5+

source_name: spleen

extract_protocol: Spleen ground between 2 glass slides to prepare single cell suspension, ACK lysis of RBCs, 2x flow sorting

value: CD3 Ter119 Ly6c GR-1 CD11b


title: B1a.Sp#6

description: B1a.Sp#6, CD19+CD45R+IgM++AA4.1-CD23-CD43+CD5+

value: 9 weeks


title: Ago1CLIP_mock_72h


title: Ago1CLIP_mock_24h


title: B1a.Sp#5

description: B1a.Sp#5, CD19+CD45R+IgM++AA4.1-CD23-CD43+CD5+

value: 8 weeks


title: Ago2CLIP_infected_72h


title: DC.103+11b-.Lu#4

value: SiglecF CD3 DX5 B220


title: Ago2CLIP_mock_72h


title: preT.ETP-2A.Th#4

status: Public on Sep 07 2011

description: preT.ETP-2A.Th#4, DN1-DN2 transitional population

extract_protocol: Filter/syringe plunger teasing, ACK lysis  Lin+ magnetic depletion (Dynobeads), 2 rounds of sorting, 2d sort directly into trizol

value: 6 weeks

value: Lin= CD4, CD8a, TCRb, TCRgd, CD11b, CD11c, NK1.1, Gr1, Ter119; additional B cell exclusion markers CD19, CD138, B220, IgL-kappa, IgL-lamda

value: Lin-/lo CD25int CD44+ cKit+


title: preT.DN3-4.Th#1

description: preT.DN3-4.Th#1, DN3-DN4 transitional thymocytes

value: Lin= CD4, CD8a, TCRb, TCRgd, CD11b, CD11c, NK1.1, Gr1, CD19, Ter119

value: Lin-/lo CD25int CD44- CD28+

value: dissection/trimming

value: male


title: preT.DN2B.Th#2

description: preT.DN2B.Th#2, DN2b thymocytes

value: Lin-/lo CD25hi CD44+ cKitint


title: preT.DN3-4.Th#2

description: preT.DN3-4.Th#2, DN3-DN4 transitional thymocytes


title: DC.103-11b+24+.Lu#2

description: DC.103-11b+24+.Lu#2, MHCII+CD11c+CD103-CD11b+CD24+


title: preT.DN2B.Th#1

description: preT.DN2B.Th#1, DN2b thymocytes


title: preT.DN2A.Th#2

description: preT.DN2A.Th#2, DN2a thymocytes

value: Lin-/lo CD25hi CD44+ cKithi


title: preT.DN2-3.Th#3

description: preT.DN2-3.Th#3, DN2-DN3 transitional thymocytes

value: Lin-/lo CD25hi CD44Int


title: preT.DN2A.Th#1

description: preT.DN2A.Th#1, DN2a thymocytes


title: MLP.FL#3

description: MLP.FL#3, lineage-AA4.1+CD117++IL7R-CD45R-

source_name: Fetal Liver

extract_protocol: ground between 2 glass slides, ACK lysis of RBCs, 1x flow sorting

value: 15 days

value: Ly6c TER119 CD3 GR1 CD11b

value: CD19- IgM- CD43+ CD24intermediate AA4.1+ CD45R- CD117++ IL7R-

value: both (pooled)


title: MLP.BM#1

description: MLP.BM#1, Bone Marrow MLP

extract_protocol: Syringe disruption, Flow sorting

value: TER119- Ly6c- CD3- Gr1- CD11b-


title: MLP.BM#3

description: MLP.BM#3, lineage-AA4.1+CD117++IL7R+CD45R-

extract_protocol: disruption using 1ml syringe, ACK lysis of RBCs, 1x flow sorting

value: 10 weeks

value: TER119 Ly6c CD11b GR1 CD3


title: preT.ETP-2A.Th#3

description: preT.ETP-2A.Th#3, DN1-DN2 transitional population

value: 6 weeks


title: SC.STSL.FL#1

description: SC.STSL.FL#1, lineage-IgM-CD24-CD117+IL7R-CD150-CD48- AA4.1+CD43+

extract_protocol: Ground between 2 glass slides, ACK lysis of RBCs

value: 14 days


title: MLP.BM#4

description: MLP.BM#4, lineage-AA4.1+CD1117++IL7R-CD45R-

value: 11 weeks


title: SC.GMP.BM#3

description: SC.GMP.BM#3, Lineage- sca1- ckithi  iCD34+ FcgRhi

extract_protocol: Flushed femurs and tibias, lysed with ACK buffer

value: 8 weeks

value: CD11b TER119 Gr-1 B220 CD3

value: Lineage- sca1- ckithi CD34+ FcgRhi


title: SC.LTSL.FL#1

description: SC.LTSL.FL#1, lineage- CD150+CD48- AA4.1+ CD43+

value: dissection/trimming


title: MLP.BM#2

description: MLP.BM#2, Bone Marrow MLP

value: male


title: preT.DN2-3.Th#2

description: preT.DN2-3.Th#2, DN2-DN3 transitional thymocytes

value: Lin= CD4, CD8a, TCRb, TCRgd, CD11b, CD11c, NK1.1, Gr1, CD19, Ter119


title: SC.LTSL.FL#2

description: SC.LTSL.FL#2, IgM-CD24-CD117+IL7R-CD150+CD48-AA4.1+CD43+


title: SC.GMP.BM#2

description: SC.GMP.BM#2, Lineage- sca1- ckithi CD34+ FcgRhi


title: SC.CDP.BM#1

description: SC.CDP.BM#1, 2/22/11 sample CDP

extract_protocol: Syringe Flushing

value: CD11b TER119 Ly6G CD3e CD45R

value: Sca1- Flt3+ MCSFR+ cKitlo


title: SC.CDP.BM#3

description: SC.CDP.BM#3, Bone Marrow CDP


title: preT.DN3-4.Th#3

description: preT.DN3-4.Th#3, DN3-DN4 transitional thymocytes

value: Lin-/lo CD25int CD44- CD28+


title: SC.CDP.BM#2

description: SC.CDP.BM#2, Bone Marrow CDP


title: SC.GMP.BM#1

description: SC.GMP.BM#1, Lineage- sca1- ckithi CD34+ FcgRhi


title: MLP.FL#1

description: MLP.FL#1, lineage -, AA4.1+,CD117++ Il7R- CD45R-

extract_protocol: ground between 2 glass slides, ACK lysis of RBcs, 1x flow sorting

value: 15 days

value: CD19- IgM- CD43+ CD24intermediate AA4.1+ CD45R- CD117++ IL7R-


title: SC.STSL.FL#3

description: SC.STSL.FL#3, IgM-CD24-CD117+IL7R-CD150-CD48-AA4.1+CD43+

value: Ly6c TER119 CD3 GR1 CD11b

value: both (pooled)


title: SC.MDP.BM#2

description: SC.MDP.BM#2, 2/8/11 sample   Combine with 2/15/11 sample for 10,000 cells for analysis

value: Sca1- Flt3+ MCSFR+ cKithi


title: SC.MDP.BM#1

description: SC.MDP.BM#1, 5000 mdp in 250ul trizol for pooling

value: 6 weeks


title: MLP.FL#2

description: MLP.FL#2, lineage - AA4.1+CD117++IL7R-CD45R-


title: SC.LTSL.FL#3

description: SC.LTSL.FL#3, IgM-CD24-CD117+IL7R-CD150+CD48-AA4.1+CD43+

value: TER119 Ly6c CD11b GR1 CD3


title: St.31-38-44-.SLN#2

status: Public on Aug 11 2011

description: St.31-38-44-.SLN#2, cutaneous lymph node CD44- double negative stromal cell

source_name: cutaneous LN

extract_protocol: Enzymatic digestion, MACS CD45 depletion sorting

value: CD45 gp38 CD31 CD44


title: St.31-38-44-.SLN#3

description: St.31-38-44-.SLN#3, lymph node stromal cells negative for CD31, gp38 and CD44

extract_protocol: Enzymatic digestion, MACS CD45 depletion, sorting


title: SC.MDP.BM#3

description: SC.MDP.BM#3, 2.15.11 sample.   Combine with 2.8.11 sample for 10,000 total


title: LEC.SLN#4

description: LEC.SLN#4, LECs from the SLN

extract_protocol: Dissection and enzymatic digestion, AutoMACS enrichment of CD45- cells, Aria sorting

value: CD45 TER119


title: LEC.SLN#3

description: LEC.SLN#3, LECs from the SLN


title: LEC.SLN#2

description: LEC.SLN#2, LECs from the SLN


title: FRC.SLN#5

description: FRC.SLN#5, FRCs from the SLN


title: LEC.MLN#3

description: LEC.MLN#3, gp38+CD31+D45- cells

extract_protocol: LN isolation, enzymatic digestion, AutoMACS depletion of CD45+ cells', Aria sorting

value: 6 days


title: LEC.SLN#1

description: LEC.SLN#1, LECs from the SLN


title: LEC.MLN#2

description: LEC.MLN#2, gp38+CD31+CD45-

extract_protocol: LN isolation, enzymatic digestion, AutoMACS depletion of CD45+ cells, Aria sorting


title: FRC.SLN#6

description: FRC.SLN#6, FRCs from the SLN


title: FRC.SLN#1

description: FRC.SLN#1, FRCs from the SLN


title: FRC.MLN#3

description: FRC.MLN#3, gp38+CD31-CD45-


title: LEC.MLN#5

description: LEC.MLN#5, gp38+CD31+CD45- cells


title: FRC.MLN#6

description: FRC.MLN#6, gp38+CD31-CD140a+CD45- cells


title: Fi.Sk#4

description: Fi.Sk#4, gp38+CD31-CD140a+CD45- cells from the ears

source_name: Skin

extract_protocol: Removal of ears, Cut up tissue with razor blades, Enzymatic digestion, Aria sorting


title: Fi.MTS15+.Th#1

description: Fi.MTS15+.Th#1, N/A

extract_protocol: Digestion, Flow Sorting

value: CD45- PDGFRa+ MTS15+


title: FRC.MLN#7

description: FRC.MLN#7, gp38+CD31-CD140a+CD45- cells

value: dissection/trimming


title: LEC.MLN#6

description: LEC.MLN#6, gp38+CD31+CD45- cells

value: male


title: FRC.MLN#5

description: FRC.MLN#5, gp38+CD31-CD140a+CD45- cells


title: Fi.Sk#1

description: Fi.Sk#1, gp38+CD31-CD140a+CD45- cells from the ears

extract_protocol: Removal of ears, Dicing of tissue w/ razor blades, Enzymatic Digestion, Aria sorting


title: Fi.Sk#3

description: Fi.Sk#3, gp38+CD31-CD140a+CD45- cells from the ears


title: FRC.MLN#8

description: FRC.MLN#8, gp38+CD31-CD140a+CD45-


title: Fi.Sk#2

description: Fi.Sk#2, gp38+CD31-CD140a+CD45- cells from the ears

extract_protocol: Removal of ears, Cutting of tissue with razor blades, Enzymatic digestion, Aria sorting


title: Fi.MTS15+.Th#3

description: Fi.MTS15+.Th#3, N/A


title: Ep.MEChi.Th#3

description: Ep.MEChi.Th#3, Thymic Medullary Epithelial Cells, MHCIIhi

value: CD45- EpCAm+ Ly51- MHCIIhi


title: Fi.MTS15+.Th#2

description: Fi.MTS15+.Th#2, N/A


title: St.31-38-44-.SLN#1

description: St.31-38-44-.SLN#1, cutaneous lymph node CD44- double negative stromal cell


title: GN.Thio.PC#1

description: GN.Thio.PC#1, GN.Thio.PC

extract_protocol: Treated with 3% Thioglycollate

value: CD11b+ Ly6-G+


title: FRC.SLN#3

description: FRC.SLN#3, FRCs from the SLN


title: BEC.SLN#4

description: BEC.SLN#4, BECs from the SLN


title: BEC.MLN#8

description: BEC.MLN#8, gp38-CD31+CD45- cells

value: 6 weeks old


title: BEC.SLN#3

description: BEC.SLN#3, BECs from the SLN


title: BEC.MLN#4

description: BEC.MLN#4, gp38-CD31+CD45- cells

extract_protocol: LN isolation, enzymatic digest, AutoMACS depletion of CD45+ cells, Aria sorting


title: BEC.MLN#7

description: BEC.MLN#7, gp38-CD31+CD45- cells

extract_protocol: LN isolation, enzymatic digestion, AutoMACS depletion of CD45+ cells, Aria sorting of populations


title: BEC.MLN#3

description: BEC.MLN#3, gp38-D31+CD45- cells

extract_protocol: LN Isolation, Enzymatic Digest, AutoMACS depletion of CD45+ cells, Aria sorting


title: BEC.MLN#6

description: BEC.MLN#6, gp38-CD31+CD45- cells

extract_protocol: LN Isolation, enzymatic digestion, AutoMACS depletion of CD45+ cells, Aria sorting of populations


title: B.Fo.MLN#1

description: B.Fo.MLN#1, CD19+CD45R+CD23+CD21/35+

extract_protocol: single cell suspension using frosted glass slides, 1x flow sorting

value: 8 weeks

value: CD3 TER119 GR1 Ly6c AA4.1 CD24 IgM CD43


title: BEC.SLN#5

description: BEC.SLN#5, BECs from the SLN


title: B.Fo.MLN#2

description: B.Fo.MLN#2, CD19+CD45R+CD23+CD21/35+

value: 9 weeks


title: B.Fo.LN#2

description: B.Fo.LN#2, CD19+CD45R+CD23+CD21/35+

source_name: Subcutaneous LN


title: B.Fo.MLN#3

description: B.Fo.MLN#3, CD19+CD45R+CD23+CD21/35+


title: Ep.MEChi.Th#2

description: Ep.MEChi.Th#2, Thymic Medullary Epithelial Cells, MHCIIhi

extract_protocol: Digestion, Flow sorting


title: BEC.SLN#1

description: BEC.SLN#1, BECs from the SLN


title: ChIP-Seq analysis of WCE in BM-MSC cells; Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE

status: Public on Mar 31 2011

city: Cambridge

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5687
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
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:
**********************************************************************

ANALYSIS FILE NAME: GSM669946_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6565
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0145
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0611
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM669946_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6775
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC Input 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 57 Library Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0145
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0611
POISSON_PERCENTILE: 60

**********************************************************************

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:07--ChIP:MC:20100628:07:BM-MSC:WCE

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: genomic DNA from digynic placenta 5

status: Public on Jun 30 2011

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

description: digynic placental sample TP84

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Data in the table were processed by background normalization using GenomeStudio v1.0.5 that subtracts a background value derived by averaging the signals of built-in negative control bead types. Probes with detection p value less than 0.05 in at least one sample were eliminated

label: Cy5 and Cy3

source_name: digynic placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard techniques and purified using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: placenta

tag: disease state

value: digyny


title: ChIP-Seq analysis of H3K9ac in ADMSC cells; Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5761
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM670020_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.1_rel2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:06--ChIP:XZ:20100104:04:ADMSC:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4989
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K9ac 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.4059
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.395
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.994
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5558
POISSON_PERCENTILE: 74

**********************************************************************

ANALYSIS FILE NAME: GSM670020_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac-Lib:XZ:20100107:06--ChIP:XZ:20100104:04:ADMSC:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6538
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.5254
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5474
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9974
IROC_PERCENTILE: 84
POISSON_SCORE: 0.5802
POISSON_PERCENTILE: 96

**********************************************************************

ANALYSIS FILE NAME: GSM670020_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac-Lib:XZ:20100107:06--ChIP:XZ:20100104:04:ADMSC:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6748
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: ADMSC H3K9ac 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 1 Library Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.5254
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5474
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9974
IROC_PERCENTILE: 84
POISSON_SCORE: 0.5802
POISSON_PERCENTILE: 96

**********************************************************************

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100827:09--ChIP:XZ:20100824:09:ADMSC:H3K9Ac

value: ADMSC

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac


title: genomic DNA from digynic placenta 6

description: digynic placental sample TP61


title: genomic DNA from digynic placenta 10

description: digynic placental sample TP85


title: genomic DNA from diandric placenta 3

description: diandric placental sample TP24

source_name: diandric placenta

value: diandry


title: genomic DNA from diandric placenta 8

description: diandric placental sample TP9


title: genomic DNA from digynic placenta 9

description: digynic placental sample TP69


title: genomic DNA from diandric placenta 4

description: diandric placental sample TP54

value: Male


title: genomic DNA from diandric placenta 6

description: diandric placental sample TP57


title: ChIP-Seq analysis of H3K4me3 in human ADMSC cells; Lib:XZ:20100107:01--ChIP:XZ:20091228:08:ADMSC:H3K4Me3

status: Public on Nov 12 2010

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:01--ChIP:XZ:20091228:08:ADMSC:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3798
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621458_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:01--ChIP:XZ:20091228:08:ADMSC:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4640
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.557
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5364
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.991
IROC_PERCENTILE: 6
POISSON_SCORE: 0.6556
POISSON_PERCENTILE: 82

**********************************************************************

ANALYSIS FILE NAME: GSM621458_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:01--ChIP:XZ:20091228:08:ADMSC:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4914
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K4me3 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.557
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5364
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.991
IROC_PERCENTILE: 6
POISSON_SCORE: 0.6556
POISSON_PERCENTILE: 82

**********************************************************************

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100107:01--ChIP:XZ:20091228:08:ADMSC:H3K4Me3

value: genomic DNA

value: Primary Cell Culture

value: Millipore

value: Histone H3K4me3


title: genomic DNA from diandric placenta 9

description: diandric placental sample TP49


title: genomic DNA from diandric placenta 7

description: diandric placental sample TP76


title: genomic DNA from diandric placenta 5

description: diandric placental sample TP74


title: genomic DNA from digynic placenta 7

description: digynic placental sample TP60


title: genomic DNA from diandric placenta 1

description: diandric placental sample TP6


title: genomic DNA from diandric placenta 2

description: diandric placental sample TP7


title: genomic DNA from diandric placenta 10

description: diandric placental sample TP86


title: genomic DNA from digynic placenta 8

description: digynic placental sample TP56


title: genomic DNA from digynic placenta 4

description: digynic placental sample TP3


title: genomic DNA from digynic placenta 1

description: digynic placental sample TP1


title: T cell dependent immune responses: B cell activation and differentiation Group2 early germinal center Bcells (GC1) Chip2

status: Public on Mar 29 2011

description: Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.

source_name: B cell subsets

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.

growth_protocol: Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: strain

value: BALB/c

value: female

value: Spleen

value: early germinal center Bcells (GC1)


title: T cell dependent immune responses: B cell activation and differentiation Group2 early germinal center Bcells (GC1) Chip1

tag: cell type


title: T cell dependent immune responses: B cell activation and differentiation Group1 follicular B cells (Fo), Chip 2

value: follicular B cells (Fo)


title: T cell dependent immune responses: B cell activation and differentiation Group1 follicular B cells (Fo), Chip 3


title: ChIP-Seq analysis of H3K9ac in human BM-MSC cells; Lib:MC:20100706:05--ChIP:MC:20100628:05:BM-MSC:H3K9Ac

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:05--ChIP:MC:20100628:05:BM-MSC:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3782
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621442_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:05--ChIP:MC:20100628:05:BM-MSC:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4697
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.4196
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4141
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9969
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5151
POISSON_PERCENTILE: 69

**********************************************************************

ANALYSIS FILE NAME: GSM621442_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:05--ChIP:MC:20100628:05:BM-MSC:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4971
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMDMSC H3K9ac 57
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 57 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.4196
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4141
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9969
IROC_PERCENTILE: 86
POISSON_SCORE: 0.5151
POISSON_PERCENTILE: 69

**********************************************************************

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; Lib:MC:20100706:05--ChIP:MC:20100628:05:BM-MSC:H3K9Ac

value: healthy

value: BM-MSC

value: Unknown

value: Rikshospitalet University Hospital

value: SDS lysis

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human ADMSC cells; Lib:XZ:20100107:04--ChIP:XZ:20100104:02:ADMSC:H3K36Me3

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100107:04--ChIP:XZ:20100104:02:ADMSC:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3889
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621446_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:04--ChIP:XZ:20100104:02:ADMSC:H3K36Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4741
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2387
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9812
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5719
POISSON_PERCENTILE: 69

**********************************************************************

ANALYSIS FILE NAME: GSM621446_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:04--ChIP:XZ:20100104:02:ADMSC:H3K36Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 1 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5015
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ADMSC H3K36me3 1
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 1 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2387
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9812
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5719
POISSON_PERCENTILE: 69

**********************************************************************

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib:XZ:20100107:04--ChIP:XZ:20100104:02:ADMSC:H3K36Me3

value: ADMSC

value: Female

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3