title: Peripheral whole blood-control-U1-C058

source_name: Peripheral whole blood, control, U1, C058

tag: group

tag: diabetes status

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: other medication

tag: tissue

tag: technical replicate

value: replicate 1

tag: sentrix id and position


title: 534

status: Public on Dec 05 2014

type: RNA

city: Aurora

first: Andrés

middle: F.

last: Henao-Martínez

state: Colorado

address: 12700 E. 19th Avenue.

department: Medicine

country: USA

institute: University of Colorado Denver

hyb_protocol: Standard Agilent microarray protocol

scan_protocol: Standard Agilent microarray protocol

data_processing: Array data were quantile normalized and log2-transformed prior to statistical analysis performed with Partek software. Principal components analysis was then used to perform additional QC and to detect and exclude potential technical outlier samples

molecule: total RNA

organism: Mus musculus

label_protocol: Standard Agilent microarray protocol

extract_protocol: Gene expression profiling of heart tissue was performed on the Agilent G3 SurePrint 8x60 mouse gene expression one-color microarray platform

tag: strain

tag: gender

value: male

tag: age

value: 8 weeks

tag: injected with

value: tissue-derived trypomastigotes (Tulahuen strain)

tag: parasite dose

value: Heart


title: 530


title: Peripheral whole blood-AIM-L-C056

city: Prague

first: Michal

last: Kolář

address: Pod Vodárenskou věží 2

country: Czech Republic

institute: Institute of Computer Science, Academy of Sciences of the Czech Republic

hyb_protocol: The cRNA samples (1.5 μg) were hybridized on HumanWG-6 v2 Expression BeadChips (Illumina Inc.) according to manufacturer’s protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected using the Illumina background model and quantile normalised with GenomeStudio Version 2010.3.0.30128

label: biotin

organism: Homo sapiens

source_name: Peripheral whole blood, AIM, L, C056

label_protocol: The cRNA was amplified using Illumina® TotalPrep™ RNA Amplification Kit, precipitated and controlled on Nanodrop (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies).

extract_protocol: Samples of peripheral whole blood were collected from all subjects using commercial 3 ml Vacutainer sets with EDTA. The tubes were inverted several times and 2.4 ml of the content was immediately mixed with 7.6 ml RNAlater (Applied Biosystems) in 15 ml tubes, stabilized blood samples were inverted several times until they were homogenous and the samples were stored in -70°C. The RNA was isolated from 1.8 ml aliquot of stabilized blood with RiboPure-Blood Kit (Applied Biosystems), precipitated and purified with GLOBINclear–Human kit (Applied Biosystems).

value: AIM

tag: pair

value: L

tag: Sex

value: Male

tag: age [year]

value: no

tag: smoking status

value: yes

tag: height [cm]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

value: whole blood


title: Sry_3/ IgG_3a

type: genomic

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: SRY experimental sample 3 is compared to IgG control sample 3

hyb_protocol: The ChIP-Chip hybridization used a Roche Nimblegen's Rat ChIP-chip 3×720K RefSeq Promoter Array. The enrichment for each probe on the array was calculated as the log ratio of the intensities of hybridization for SRY or SOX9 ChIP DNA (Cy5) to control DNA from IgG control (Cy3). Array contained on average 4,000 bp of promoter for each of 15,287 promoters in the rat genome corresponding to 15,600 RefSeq transcripts (approximately 3880 bp upstream and 970 bp downstream from transcription start site). Two different comparative (ChIP vs ChIP) hybridizations experiments were performed, each encompassing 4 samples (2 treatment and 2 control) and 4 array sets. The first was a dye balance design as follows: C1 in the green channel against V1 in the red channel; V1 in the green channel against C2 in the red channel; C2 in the green channel against V2 in the red channel; V2 in the green channel against C1 in the red channel. The second one was a dye swap design as follows: C1 in the green channel against V1 in the red channel; V1 in the green channel against C1 in the red channel; C2 in the green channel against V2 in the red channel; V2 in the green channel against C2 in the red channel.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each hybridization experiment raw data from both the Cy3 can Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), and data checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2). The R codes that were used for analysis and annotation are available in the following website: http//www.skinner.wsu.edu. All the tiling array Chip data was deposited in the NCBI GEO site. Within each array, probes were separated into groups by GC content and each group was separately normalized using the LOESS normalization procedure. This allowed for groups with optimal GC content, which exhibited a reduced quality issue, to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure. Following normalization the probe's normalized M values (and then A) were replaced with the median value of all probe M values (and then A) within a sliding window of 600 bp, due to the size of DNA fragments used. Following normalization each probe's M value represents the median intensity difference between Cy5 and Cy3 of a 600 bp window. Significance was assigned to probe differences between experimental (SRY or SOX9) and IgG control by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of M. Regions of interest were then determined by combining consecutive probes with significance p-values less than 10−3. Significance was assigned to probe differences between experimental and control by calculating the median value of the increasing differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the mean. A Z-score and P-value were computed from that distribution with the use of R code analysis. The statistically significant peaks of hybridization were identified and P-value associated with each peak presented. Each peak of interest was then annotated for the gene. Every promoter exceeding the intensity threshold was considered positive for SRY or SOX9 binding. The final list of SRY or SOX9 targets includes the promoter-proximal regions that made the threshold in an average of the three replicates. Hybridization signals for all the candidate promoters that were within the cutoff line (p≤1×10−7) were plotted (average of the three replicates), Supplemental Figure S1. The genes that were not in the list but seemed to be masked by IgG negative signals were designated as questionable positives. These questionable positive promoters were manually chosen and confirmed by PCR, Supplemental Figure S2.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study.  Value definitions for processed data files: #ClusterID= ID and chrolosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control),  #Chromosome= Chromosome number, #cSTART= Cluster start site,  #cSTOP= Cluster stop site,  #meanM= mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group,  #meanA= mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group,  #minP= p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files. P-value must be p<1.0E-5 or less for inclusion,  #nProbes= number of consecutive probes with p<1.0E-5 included in cluster,  #CG= CG content of cluster,  #CpG= CpG content of cluster, and #CpGdensity= number of CpGs per hundred base pairs.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: SRY ChIP DNA from embryonic day 13 gonads

label_protocol: SRY or SOX9 ChIP DNA where labeled with Cy5 and control DNA from IgG control were labeled with Cy3

extract_protocol: Harlan Sprague-Dawley rats were used for the study. All the rats were kept in a temperature controlled environment and given food and water ad libitum. Estrous cycles of female rats were monitored by cellular morphology from vaginal smears. Rats in early estrus were paired with males overnight and mating confirmed by sperm positive smears, denoted day 0 of pregnancy. Pregnant rats were euthanized at embryonic day 13 (E13) of pregnancy, and embryonic gonads were collected for chromatin immunoprecipitation. Sex was determined by PCR using primers specific for Sry on genomic DNA isolated from embryo tails was preformed by using 1 μl of genomic DNA with the consensus SRY primers 5′ CGGGATCCATGTCAAGCGCC CCATGAATGCATTTATG 3′ and 5′ GCGGAATTCACTTTAGCCCTCCGATGAGGCTGA TAT 3′, producing a PCR product of 240 base pairs (bp). PCR was performed using an annealing temperature of 55°C for 30 cycles. All procedures were approved by the Washington State University Animal Care and Use Committee (IACUC approval # 02568-026). A modified ChIP (cChIP) assay was adopted from O'Neill et al., (2006) and performed according to Bhandari et al (2011).  To run ChIP assay, male and female gonads (gonad+mesonephros) were dissected from approximately twenty to twenty five 13 dpc (12–18 tail somite stage) rat embryos per array and snap-frozen in liquid nitrogen. Drosophila SL2 cells were used as a carrier. Densely-grown cells (approximately 5×107 cells) were pelleted and washed three times in ice-cold PBS, 5 mM sodium butyrate and resuspended in 0.5 ml NB buffer (15 mM Tris-HCL, pH 7.4, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM 2-mercaptoethanol, 0.1 mM PMSF). Frozen testis samples were thawed, mixed with SL2 cells and homogenized to make single cell suspension. Nuclei were pelleted, resuspended in 20 ml NB buffer, 5% (vol/vol) sucrose, pelleted and resuspended again in 5 ml digestion buffer (50 mM Tris-HCl pH 7.4, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF). Following micrococcal nuclease digestion (NEB, USA) for 10 minutes at 37 degree, the digested samples were gently spun (800×g) for 10 minutes and supernatant set aside on ice. The pellet was resuspended in 250 ul incubation buffer (50 mM Nacl, 20 mM Tris HCl pH 7.5, 20 mM Na-butyrate, 5 mM Na2EDTA, and 0.1 mM PMSF) and again centrifuged gently for 10 minutes. Both the supernatants were pooled and a fraction (50 ul) out of it was kept aside to use as input. The remaining supernatant was incubated with either non-immune IgG or anti-SRY or anti-Gata4 antibodies at 4°C overnight. After incubation with 100 µl of preswollen protein A-Sepharose beads (Sigma) for 2 h at 4°C, the bead-bound immunoprecipitates were centrifuged gently and washed five times with wash buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 5 mM Na butyrate and 50–150 mM NaCl). The protein-DNA complexes were incubated at room temperature with elution buffer (1% SDS in TE) and centrifuged at 11500×g at 4°C for 10 minutes. Elution was repeated two times and eluted DNA was pooled. Co-immunoprecipitated DNA was purified by proteinase K digestion, phenol/chloroform extraction, and ethanol precipitation. Final concentration of immunoprecipitated DNA varied from 100 to 300 ng per assay. Two rounds of PCR reactions were run for 25 cycles before evaluating samples by gel electrophoresis. Identity of the PCR-amplified fragments was verified by sequencing. The conditions for the native-ChIP (not including cross linking) were optimized for immunoprecipitating with SRY and SOX9 antibodies. The native-ChIP was used to identify high affinity binding sites and reduce low affinity sites, and was validated with PCR for Sox9, Tcf21 and Ntf3. To run a replicate of the ChIP assay, at least twenty male gonads from thirty 13 dpc (12–18 tail somite stage) rat embryos were used per array. All three ChIP experiments were with different biological samples. Drosophila SL2 cells (American Type Culture Collection (ATCC) Catalog no. CRL-1963) were used as a carrier. Densely-grown cells (approximately 5×107 cells) were pelleted and washed three times in ice-cold phosphate buffered salve (PBS), 5 mM sodium butyrate and resuspended in 0.5 ml NB buffer (15 mM Tris-HCL, pH 7.4, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM 2-mercaptoethanol, 0.1 mM PMSF). Testis samples were mixed with SL2 cells and homogenized to make single cell suspension. Nuclei were pelleted, resuspended in 10 ml NB buffer, 5% (vol/vol) sucrose, pelleted and resuspended again in 1.5 ml digestion buffer (50 mM Tris-HCl pH 7.4, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF). Following micrococcal nuclease digestion (NEB, USA) for 5 minutes at 28°C, the digested samples were gently spun (800× g) for 15 minutes and supernatant set aside on ice. The pellet was resuspended in 250 ul digestion buffer and again centrifuged gently at 800× g for 15 minutes at 4 degrees. Both the supernatants were pooled and a fraction (50 ul) out of it was kept aside to use as input. The remaining supernatant was incubated with either non-immune IgG or anti-SRY (Santa Cruz, CA, USA) or anti-SOX9 (ABcam, CA, USA) antibodies at 4°C overnight. The specificity of these antibodies on western blots have been previously described and validated. After incubation with 100 µl of pre-swollen protein A-Sepharose beads (SL2 DNA blocked) for 2 h at 4°C, the bead-bound immunoprecipitates were centrifuged gently and washed five times with wash buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 5 mM Na butyrate and 50–150 mM NaCl). The protein-DNA complexes were incubated at room temperature with elution buffer (1% SDS in TE) and centrifuged at 11500× g for 10 minutes. Elution was repeated two times and eluted DNA was pooled. Co-immunoprecipitated DNA was purified by phenol/chloroform extraction, and ethanol precipitation. Final concentration of immunoprecipitated DNA varied from 200 to 500 ng per assay. Three different experiments and ChIP assays were performed. Exactly 30 ng of immunoprecipitated DNA from each assay was amplified by whole genome amplification kit developed by Sigma (Sigma #WGA2 50 RXN). At least five separate whole genome amplifications were performed and DNA was pooled. Pooled whole genome amplified DNA was purified by using Promega's Wizard SV40 PCR cleanup kit (Promega). Purified DNA was checked on the gel and sent to Nimblegen for ChIP-chip hybridization (Nimblegen, Iceland).

treatment_protocol: SRY- experimental

tag: developmental stage

value: Embryonic day 13 (E13)

value: Harlan Sprague-Dawley

tag: tissue

value: gonads

source_name: IgG ChIP DNA from embryonic day 13 gonads

treatment_protocol: IgG- Control


title: Peripheral whole blood-AIMD6-D-C053

source_name: Peripheral whole blood, AIMD6, D, C053

tag: group

value: D

value: Female

tag: diabetes status

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: Young without severe cognitive disability_23

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

country: Poland

institute: Jagiellonian University

data_processing: GeneSpring software was used with default workflow-type; single-color analysis

source_name: Blood white cells

extract_protocol: RNA extraction from blood samples with use of PAXgene system (PreAnalytiX)

tag: age

value: Young

tag: condition

value: without severe cognitive disability

tag: cell type

value: white blood cell


title: Sry_1/ IgG_1a

description: SRY experimental sample 1 is compared to IgG control sample 1

growth_protocol: Harlan Sprague-Dawley rats were used for the study. All the rats were kept in a temperature controlled environment and given food and water ad libitum. Estrous cycles of female rats were monitored by cellular morphology from vaginal smears. Rats in early estrus were paired with males overnight and mating confirmed by sperm positive smears, denoted day 0 of pregnancy. Pregnant rats were euthanized at embryonic day 13 (E13) of pregnancy, and embryonic gonads were collected for chromatin immunoprecipitation.

tag: strain


title: Young without severe cognitive disability_21


title: 529

tag: gender

value: male

value: 8 weeks

tag: injected with

tag: parasite dose


title: Sry_2/ IgG_2a

description: SRY experimental sample 2 is compared to IgG control sample 2

tag: developmental stage


title: Young without severe cognitive disability_22


title: 525

value: none (control)

tag: tissue

value: Heart


title: 526


title: Peripheral whole blood-AIM-X1-C039

source_name: Peripheral whole blood, AIM, X1, C039

tag: group

value: AIM

tag: pair

tag: Sex

tag: age [year]

tag: smoking status

tag: height [cm]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

value: replicate 1


title: Peripheral whole blood-AIM-L1-C037dup

source_name: Peripheral whole blood, AIM, L1, C037

tag: diabetes status

value: no

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: 524

tag: strain

tag: gender

tag: age

tag: injected with

tag: parasite dose

tag: tissue


title: 523


title: Young without severe cognitive disability_20

tag: condition

tag: cell type


title: Young without severe cognitive disability_19


title: Peripheral whole blood-AIM-S1-C036

source_name: Peripheral whole blood, AIM, S1, C036

tag: group

tag: pair

tag: Sex

tag: age [year]

tag: smoking status

tag: height [cm]

tag: acei

tag: betablockers

value: yes

tag: diuretics

tag: ca blockers

tag: statins


title: YPIIIanaerobvsaerob_stat_GEO_sample02

city: Umea

first: Kemal

last: Avican

address: Building 6L

department: Department of Molecular Biology

country: Sweden

institute: Umea University

description: Biological replicate 2 of 4.

hyb_protocol: 300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions

scan_protocol: The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6

data_processing: Microarray data processing was done using the Limma package (Smyth, 2005) from the R/Bioconductor framework (Gentleman et al., 2004). Unprocessed array intensity values were read-in using function read.maimages and overall array and hybridization qualities were assessed by evaluation of control probe intensities and exploratory data analysis. Quality assessed/controlled intensities were subsequently normalized using the variance stabilization normalization method (Huber et al., 2002) with background substraction as implemented in the vsn2 function of the Bioconductor package vsn.

organism: Yersinia pseudotuberculosis YPIII

source_name: WT_aerobic_stationary phase

label_protocol: RNA samples were labelled either with Cy3 (anaerob) or Cy5 (aerob) using the ULS fluorescent labelling kit (Kreatech, Germany)

growth_protocol: Y. pseudotuberculosis wild-type strain YPIII was grown at 25°C in LB medium supplemented with 10 g/l glucose and 0.2 M HEPES buffer under aeration or under an-aerobic growth conditions (in a nitrogen atmosphere) to stationary phase. Addition of the HEPES buffer was required to avoid acidification of the medium below pH 5.0 due to mixed acid fermentation, resulting in a significant growth reduction/stop. Additional glucose was added to maximize energy production and growth rate under aerobic growth condi-tions. Absence of oxygen in the culture medium was tested by gas chromatography (GC-WLD, Carlo Erba Vega Series 6000) coupled with a detector coupled with an integrator (Spectra-Physics, SP4270) using a Poropak QS (100-120 Mesh) column and helium (Westalen 4.6) at 300 kPa.

extract_protocol: RNA extraction was performed using the SV Total RNA Isolation System (Promega)

tag: strain

value: YPIII pIB1 wild type

tag: growth condition

value: aerobic

tag: growth phase

value: stationary phase

source_name: WT_anaerobic_stationary phase

value: YPIII pIB1 wild type anaerob


title: Peripheral whole blood-AIM-T1-C030

source_name: Peripheral whole blood, AIM, T1, C030

value: Male

tag: diabetes status

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: fibrates

tag: other medication

tag: tissue

value: whole blood

tag: technical replicate

tag: sentrix id and position


title: 511

value: Balb/c

tag: gender

tag: age

tag: injected with

value: tissue-derived trypomastigotes (Tulahuen strain)

tag: parasite dose


title: YPIIIanaerobvsaerob_stat_GEO_sample03

description: Biological replicate 3 of 4.


title: YPIIIanaerobvsaerob_stat_GEO_sample04

description: Biological replicate 4 of 4.


title: Young without severe cognitive disability_16

value: Young

tag: condition

value: without severe cognitive disability

tag: cell type

value: white blood cell


title: 512

tag: strain

value: male

value: 8 weeks


title: Peripheral whole blood-AIM-T-C029_1

source_name: Peripheral whole blood, AIM, T, C029

tag: group

value: AIM

tag: pair

value: T

tag: Sex

tag: age [year]

tag: smoking status

tag: height [cm]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins


title: Young without severe cognitive disability_15

tag: age


title: Young without severe cognitive disability_18


title: YPIIIanaerobvsaerob_stat_GEO_sample01

description: Biological replicate 1 of 4.

tag: growth condition

tag: growth phase

value: anaerobic

value: exponential phase


title: 506

tag: gender

tag: injected with

value: none (control)

tag: parasite dose

tag: tissue

value: Heart


title: YPIIIanaerobvsaerob_log_GEO_sample04

description: Biological replicate 4 of 4.

source_name: WT_aerobic_exponential phase

growth_protocol: Y. pseudotuberculosis wild-type strain YPIII was grown at 25°C in LB medium supplemented with 10 g/l glucose and 0.2 M HEPES buffer under aeration or under an-aerobic growth conditions (in a nitrogen atmosphere) to exponential phase (OD600=0.5). Addition of the HEPES buffer was required to avoid acidification of the medium below pH 5.0 due to mixed acid fermentation, resulting in a significant growth reduction/stop. Additional glucose was added to maximize energy production and growth rate under aerobic growth condi-tions. Absence of oxygen in the culture medium was tested by gas chromatography (GC-WLD, Carlo Erba Vega Series 6000) coupled with a detector coupled with an integrator (Spectra-Physics, SP4270) using a Poropak QS (100-120 Mesh) column and helium (Westalen 4.6) at 300 kPa.

tag: strain

value: YPIII pIB1 wild type

value: aerobic

source_name: WT_anaerobic_exponential phase


title: Young without severe cognitive disability_17

tag: condition

tag: cell type


title: Peripheral whole blood-AIM-T-C029_2

tag: group

tag: pair

tag: Sex

value: Male

tag: age [year]

tag: diabetes status

value: no

tag: smoking status

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: fibrates

tag: other medication

tag: technical replicate

value: replicate 2

tag: sentrix id and position


title: Peripheral whole blood-control-F-C023

source_name: Peripheral whole blood, control, F, C023

value: control

value: F

value: Female

value: yes

tag: height [cm]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: tissue

value: whole blood

value: replicate 1


title: 508

tag: strain

value: Balb/c

tag: gender

value: male

tag: age

value: 8 weeks

tag: injected with

value: tissue-derived trypomastigotes (Tulahuen strain)

tag: parasite dose


title: Young without severe cognitive disability_13

value: Young

tag: condition

value: without severe cognitive disability

tag: cell type

value: white blood cell


title: 505

value: none (control)

value: Heart


title: YPIIIanaerobvsaerob_log_GEO_sample03

description: Biological replicate 3 of 4.

value: YPIII pIB1 wild type

tag: growth condition

value: aerobic

tag: growth phase

value: exponential phase

value: anaerobic


title: 504


title: Young without severe cognitive disability_14


title: Peripheral whole blood-control-K-C022

source_name: Peripheral whole blood, control, K, C022

tag: group

value: control

tag: pair

value: K

tag: Sex

value: Female

tag: age [year]

tag: diabetes status

tag: smoking status

value: no

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: fibrates

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-AIM-Y-C019

source_name: Peripheral whole blood, AIM, Y, C019

value: AIM

value: Y

tag: height [cm]

tag: acei

tag: betablockers

value: yes

tag: diuretics

tag: ca blockers

tag: statins

tag: tissue

value: whole blood

value: replicate 1


title: Young without severe cognitive disability_11

tag: age

value: Young

tag: condition

value: without severe cognitive disability

tag: cell type


title: Peripheral whole blood-AIM-H-C048

source_name: Peripheral whole blood, AIM, H, C048

tag: group

tag: pair

value: H

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

tag: weigth [kg]


title: 503

tag: strain

value: Balb/c

tag: gender

value: male

value: 8 weeks

tag: injected with

value: none (control)

tag: parasite dose

value: Heart


title: Young without severe cognitive disability_9

value: white blood cell


title: 470

value: tissue-derived trypomastigotes (Tulahuen strain)


title: Peripheral whole blood-AIM-M1-C016

source_name: Peripheral whole blood, AIM, M1, C016

value: Male

tag: height [cm]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: fibrates

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: 466

tag: age

tag: tissue


title: Peripheral whole blood-AIM-Z-C013

source_name: Peripheral whole blood, AIM, Z, C013

tag: group

tag: pair

value: Z

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

value: no

tag: weigth [kg]

tag: statins


title: ESAM(Bright)

city: Suita

first: Tomohiko

last: Ishibashi

state: Osaka

address: C9, 2-2, Yamadaoka

department: Department of Hematology and Oncology

country: Japan

institute: Osaka University Graduate School of Medicine

hyb_protocol: 2.0 µg of Cy3-labelled cDNA was filled up to 50 µl containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: collagenase-treated bone, CD34(+) CD38(-) ESAM(Bright)

label_protocol: cDNA were amplified by Ovation Pico WTA System V2 (NuGEN Technologies) from 6.5 ng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared from 2.0 µg cDNA using SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

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

treatment_protocol: Trabecular tissues of the femora were treated with 2 mg/mL collagenase IV and DNase and gently agitated for 1 h at 37°C. Mononuclear cells were collected using Ficoll-Paque PLUS (GE Healthcare Life Sciences, Piscataway, NJ).

value: bone marrow

tag: gender

value: female


title: YPIIIanaerobvsaerob_log_GEO_sample02

description: Biological replicate 2 of 4.

tag: strain

value: YPIII pIB1 wild type

tag: growth condition

value: aerobic

tag: growth phase

value: exponential phase

value: anaerobic


title: ESAM(High)

source_name: collagenase-treated bone, CD34(+) CD38(-) ESAM(High)


title: Young without severe cognitive disability_8

source_name: Blood white cells

value: Young

tag: condition

value: without severe cognitive disability

tag: cell type


title: Peripheral whole blood-control-C-C010

source_name: Peripheral whole blood, control, C, C010

value: control

value: C

tag: height [cm]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: fibrates

tag: other medication

value: yes

value: whole blood

tag: technical replicate

value: replicate 1

tag: sentrix id and position


title: Peripheral whole blood-control-T-C014

source_name: Peripheral whole blood, control, T, C014

tag: group

tag: pair

value: T

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

tag: weigth [kg]

tag: statins

tag: tissue


title: Young without severe cognitive disability_10

tag: age

tag: condition

tag: cell type

value: white blood cell


title: Young without severe cognitive disability_12


title: 464

tag: strain

tag: gender

value: male

value: 8 weeks

tag: injected with

value: tissue-derived trypomastigotes (Tulahuen strain)

tag: parasite dose

value: Heart


title: Peripheral whole blood-control-Q-C011

source_name: Peripheral whole blood, control, Q, C011

value: Q

value: Female

value: no

tag: height [cm]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: fibrates

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: YPIIIanaerobvsaerob_log_GEO_sample01

description: Biological replicate 1 of 4.

value: YPIII pIB1 wild type

tag: growth condition

value: aerobic

tag: growth phase

value: exponential phase

value: anaerobic


title: 463

tag: strain

tag: age

value: none (control)

tag: tissue


title: @52055800915952052113413827183092

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Affy-169 : 200.0 ng at 45 degree_C during 17 hours

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and Gene Level-RMA sketch as normalization method.

extract_protocol: Trizol

value: whole neocortex

tag: amount in (µg)

tag: rin number

tag: genotype/variation

value: wild type


title: @52055800915940050513413631664282


title: 461

tag: gender

tag: injected with

tag: parasite dose


title: Young with severe cognitive disability_6

value: Young

tag: condition

value: severe cognitive disability and early dementia

tag: cell type


title: Young with severe cognitive disability_7

value: white blood cell


title: Young with severe cognitive disability_5


title: @52055800915951052113413827199401


title: Young with severe cognitive disability_4


title: 454

value: Balb/c

value: male


title: @52055800915951052113413827199418


title: Young with severe cognitive disability_3


title: Young with severe cognitive disability_2


title: HEK_Native_2

city: Penzberg

first: Fabian

last: Birzele

address: Nonnenwald 2

department: Pharmaceutical Sciences

country: Germany

institute: Roche Diagnostics GmbH

hyb_protocol: The hybridization mix was loaded onto the arrays and incubated in a roller device for 16 hrs. Hybridization solution was removed, arrays were washed, stained

scan_protocol: Scanned with an Affymetrix GeneChip Scanner 3000 (7G)

data_processing: Partek Genomics suite was used to process CEL files, perform normalization and QC as well as to identify differentially regulated genes between native and CD44 transfected HEK293 cells using ANOVA.

molecule: polyA RNA

source_name: cell culture, native HEK293 cells

label_protocol: standard Affymtrix protocol

growth_protocol: For cloning and expression of human CD44 (EMBL accession number M24915) the sequence was codon optimized (Geneart, Germany) and CD44s was expressed using a pcDNA3.1(-) vector (Invitrogen, Germany). PCR was performed with a denaturation step at 94°C for 2 min, followed by 30 cycles of denaturation at 94°C for 30 sec, annealing at 58°C for 30 sec, and extension at 68°C for 45 sec, with a final extension of 7 minutes at 68°C (Expand High Fidelity PCR Kit, Roche). The PCR product and the vector were digested with EcoRI/HindIII restriction endonucleases, and DNA fragments were resolved by 1% agarose gel electrophoresis,purified from gels (GFX PCR DNA and Gel Band Purification Kit) and ligated (Rapid DNA Ligation Kit, Roche). Vectors were transferred into XL-10 Gold super-competent cells (Stratagene, The Netherlands) by heat shock and transformed cells were isolated form agar plates containing 100µg/ml Ampicilin. Vector DNA from transfected cells was isolated using the High Pure Plasmid Isolation Kit (Roche, Germany).

extract_protocol: HEK293-CD44s Clone 4, expressing an average level of HA, was picked for profiling gene expression using Affymetrix Human Genome U133plus 2.0 arrays. Total RNA was prepared using the RNeasy Mini Kit (Qiagen, Germany), Microarray RNA Target Synthesis Kit T7 and RNeasy Mini-Spin Columns (Roche, Germany) and a hybridization mix was created consisting of 30 µl of fragmented cRNA solution mixed with control oligonucleotide, staggered control cRNAs, herring sperm DNA, acetylated BSA and hybridization buffer in a total volume of 300 µl. All kit procedures were performed according to the manufacturers’ instructions.

treatment_protocol: no treatment

tag: cd44 transfected


title: @52055800915951052113413827199328


title: Young with severe cognitive disability_1


title: 453

value: 8 weeks

value: tissue-derived trypomastigotes (Tulahuen strain)


title: 450

value: Heart


title: HEK_Native_1


title: HEK_Native_3


title: @52055800915951052113413827199320


title: HEK_CD44s-Transfected_3

source_name: cell culture, HEK transfected with CD44s

value: yes


title: 448


title: Cdx2-/fl / Lgr5-EGFP SI organoids_SI med 2

status: Public on Dec 04 2014

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: full organoids

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Mouse Gene ST 1.1 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the rma_sketch algorithm (target signal = 100) using Affy Powertools (APT) software (Affymetrix).

source_name: Cdx2-/fl / Lgr5-EGFP small intestinal organoids cultured into SI med_(ENR)

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Cdx2-/fl small intestinal (Control SI), Cdx2null small intestinal (Cdx2null SI) and Cdx2-/fl stomach (Control Sto) clonal organoids grown into ENRWfg (Sto med). Cdx2-/fl SI organoids and Cdx2-/fl Sto organoids have been also cultured in ENR (SI med) to induce differentiation. After some passages of clonal organoids expansion, RNA was isolated from Control SI, Cdx2null SI and Control Sto Lgr5-EGFPhi FACS sorted stem cell populations and from small intestinal and stomach full organoids in different culture conditions and hybridized on Affymetrix Mouse Gene ST 1.1 arrays.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

tag: tissue/cell type

value: small intestinal organoids

tag: genotype

value: Cdx2-/fl / Lgr5-EGFP


title: HEK_CD44s-Transfected_1


title: Peripheral whole blood-AIMD6-C-C005

source_name: Peripheral whole blood, AIMD6, C, C005

tag: group

tag: pair

value: C

tag: Sex

value: Male

tag: age [year]

tag: diabetes status

value: no

tag: smoking status

tag: height [cm]

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication

value: whole blood

tag: technical replicate

value: replicate 1

tag: sentrix id and position


title: Cdx2-/fl / Lgr5-EGFP Sto organoids_Sto med 1

description: full organoids

source_name: Cdx2-/fl / Lgr5-EGFP stomach organoids cultured into Sto med_(ENRWfg)

tag: tissue/cell type

value: stomach organoids

tag: genotype


title: Cdx2-/fl / Lgr5-EGFP SI organoids_Sto med

description: full organoids

source_name: Cdx2-/fl / Lgr5-EGFP small intestinal organoids cultured into Sto med_(ENRWfg)


title: 459

tag: strain

tag: gender

tag: age

tag: injected with

tag: parasite dose

tag: tissue


title: Cdx2-/fl / Lgr5-EGFP SISCs 2

description: Lgr5 high expression level

source_name: FACS sorted control small intestinal stem cells from Cdx2-/fl / Lgr5-EGFP intestinal organoids

value: FACS sorted small intestinal stem cells


title: @52055800915940050513413631664200

value: whole neocortex

tag: amount in (µg)

tag: rin number

tag: genotype/variation


title: Cdx2-/fl / Lgr5-EGFP SI organoids_SI med 3

description: full organoids

value: SI_SI med (ENR)_1


title: Cdx2-/fl / Lgr5-EGFP StoScs 2

description: Lgr5 high expression level

source_name: FACS sorted control stomach stem cells from Cdx2-/fl / Lgr5-EGFP stomach organoids

value: FACS sorted stomach stem cells


title: HEK_CD44s-Transfected_2

tag: cd44 transfected


title: Cdx2-/fl / Lgr5-EGFP Sto organoids_SI med 2

description: full organoids

source_name: Cdx2-/fl / Lgr5-EGFP stomach organoids cultured into SI med_(ENR)

value: Sto_SI med (ENR)_2


title: Cdx2null / Lgr5-EGFP SISCs 2

description: Lgr5 high expression level

source_name: FACS sorted small intestinal stem cells from Cdx2null / Lgr5-EGFP intestinal organoids

value: Cdx2null / Lgr5-EGFP


title: Cdx2null / Lgr5-EGFP SISCs 1

description: Lgr5 high expression level


title: Cdx2-/fl / Lgr5-EGFP SISCs 1

description: Lgr5 high expression level


title: Cdx2-/fl / Lgr5-EGFP SISCs 3

description: Lgr5 high expression level

value: Control SI SCs_1


title: Cdx2-/fl / Lgr5-EGFP StoScs 1

description: Lgr5 high expression level


title: Cdx2-/fl / Lgr5-EGFP Sto organoids_SI med 1

description: full organoids

value: Sto_SI med (ENR)_1


title: Cdx2-/fl / Lgr5-EGFP SI organoids_SI med 1

description: full organoids


title: oxLDL.3

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

hyb_protocol: The fragmented, biotin-labeled cDNA was hybridized to the Affymetrix Mouse Exon Array 1.0 ST GeneChip and the GeneChip was washed and stained using the protocol and reagents in the Affymetrix GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: The stained GeneChip was imaged using the Affymetrix GeneChip Scanner 3000.

data_processing:
Probe-level intensities were quantile-normalized without background adjustment and then summarized for probeset intensities using the Affymetrix PLIER algorithm and for detection above background using the Affymetrix DABG algorithm using probe-to-probeset mappings from the CustomCDF project  version 15, based on the mouse transcripts and mouse exons lists from the Ensembl database release 65.
MoEx10stv1_Mm_ENST.pgf
meta-probeset file n/a (used a transcript-level probe-to-probeset mapping from the CustomCDF project)

source_name: oxLDL

label_protocol: cDNA was synthesized using Affymetrix One-Cycle Eukaryotic Target Labeling Assay protocol and reagents, following the manufacturer's instructions.

growth_protocol: 8-12 week old female C57BL/6J mice were sacrified by CO2 asphyxiation and peritoneal exudate cells were obtained by intraperitoneal lavage with 8 mL of ice-cold PBS, followed by intraperitoneal lavage with an additional 4 mL of ice-cold PBS. Cells were counted, collected, resuspended in macrophage growth medium (RPMI 1640 + L-glutamine, 10% FBS, and 1% pen-strep), plated in a 12-well plate with tissue culture-treated TC plate at 1.65 million cells per well, and incubated at 37 C for 2 h followed by triple wash with warm PBS.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's instructions and RNA samples were assayed for quality using the Agilent 2100 Bioanalyzer.

treatment_protocol: Adherent cells were incubated for 24 h at 37 C with macrophage growth medium with either 25 ug/mL CuSO4-oxidized human LDL (Intracel) or vehicle (PBS). Foam cell formation in the oxLDL-treated cells was verified by light microscopy.

tag: cell type

value: resident peritoneal macrophage

tag: agent

value: oxLDL


title: unstim.3

source_name: unstim


title: unstim.2


title: oxLDL.2


title: oxLDL.1


title: unstim.1


title: Reversa.female.saline.6

data_processing:
GeneChip scan images were processed into probe intensities using the Affymetrix GeneChip Operating Software system and then background-adjusted, quantile-normalized, and probeset-summarized using the Robust Multichip Average feature of Affymetrix Power Tools, with transcript-level probeset definitions from the Version 15 of the CustomCDF Project (Ensembl Transcript-derived probeset definitions). Probe intensities were separately processed into exon-level normalized probeset intensities using the Robust Multichip Average Feature of Affymetrix Power Tools (version 1.10.2), and (separately) using exon-level probeset definitions from the CustomCDF project (Ensembl Exon) and from the Affymetrix Mouse Exon Array 1.0 ST NetAffx Annotations version 29. Exon-level detect-above-background calls were made using the two separate sets of (CustomCDF and NetAffx) exon-level probesets using the Detection Above Background algorithm in Affymetrix Power Tools. For each exon-level probeset, detect-above-background P values were combined for all samples within a sample group using the geometric mean, and then across sample groups by taking the minimum P value, to obtain a single “present” P value for each exon-level probeset. For each Ensembl Transcript corresponding to one of the transcript-level probesets for which at least 75% of the constituent exon-level probesets was interrogated on the array, the transcript was considered to be above background in the sample if at least half of its constituent exons (that were interrogated with probes on the array) were detected above background with a “present” P value of less than or equal to 0.01. For all probesets that passed the filter, log2 probeset intensities across all 24 Reversa samples (see Table S1) were analyzed for differential expression between the Mttp-inactivated and control sample groups using a two-factor model (sex and treatment) with empirical Bayes variance estimates, using the software package Limma.
MoEx10stv1_Mm_ENST.pgf
n/a (used a transcript-level probe-to-probeset mapping from the CustomCDF project)

source_name: Aortic root CD68+ cells

label_protocol: The cDNA was analyzed on the Agilent 2100 Bioanalyzer and then fragmented and biotin-labeled using the NuGEN Encore Biotin Module.

growth_protocol: Four-week-old Reversa mice (Lieu et al., ibid) and two Ldlr-/- mice (as a control group for effect of poly I:C independent of Mttp inactivation) were weaned onto a Western diet (Catalog no. 100244; Dyets Inc., Bethlehem, PA) for 16 weeks (baseline time point) to establish aortic plaque and then switched to a chow diet.

extract_protocol: Seven days after the final injection, animals were sacrified, hearts were dissected and frozen-embedded, and aortic roots were serial-sectioned at 6 um thickness. Every seventh section was immunostained with a CD68-specific (AbD Serotec, MCA 1957) antibody as previously described (Trogan et al., 2006. Proc Natl Acad Sci U S A. v.103, pp.3781-6) and used as a guide slide for laser-capture microdissection for the next six serial sections. Laser-capture microdissection (LCM) was performed with the PixCell II instrument (Arcturus Bioscience), under RNase-free conditions, using the CD68-stained guide slides (two caps per animal). RNA was isolated from LCM caps using the Arcturus PicoPure RNA Isolation Kit following the manufacturer’s instructions. Total RNA was quantitated using the NanoDrop spectrophotometer and assayed for quality using the Agilent Bioanalyzer 2100. From the RNA template, single-stranded cDNA was produced in microgram quantities using the NuGEN Ovation Pico WTA System v2, with the QIAGEN QIAquick PCR Purification Kit used for cDNA purification.

treatment_protocol: Mice were injected (i.p.) every other day, for a total of four injections, with either 500 µg polyinosinic:polycytidylic acid (poly I:C) (Sigma-Aldrich) or vehicle (saline, Reversa mice only).

value: Reversa

value: Aortic root CD68+ cells

value: female

tag: treatment

value: saline


title: Chicken mock-infected control, biological rep1

city: Sutton Bonington

first: Suresh

middle: Varma

last: Kuchipudi

address: College Road

department: School of Veterinary Medicine and Science

country: United Kingdom

institute: University of Nottingham

description:
Chicken_Control-mock infected_1
Gene expression data from mock-infected chicken lung cells at 24h post-infection.

hyb_protocol: 12.5µg of labeled and fragmented aRNA were hybridized to a  GeneChip® Chicken Genome Array (Affymetrix) for 16hrs at  45 °C.

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 with AGCC scan control software (Affymetrix).

data_processing: Gene expression analysis was carried out using the GeneSpring GX10 expression analysis software (Agilent Technologies). Probe summarization was carried out by the Robust Multichip Averaging (RMA) summarization algorithm, followed by baseline transformation using baseline to median of all samples. Statistical analysis was carried out by analysis of variance (ANOVA) with a p value cut-off of 0.05 by asymptotic p-value computation algorithm with no multiple testing correction.

organism: Gallus gallus

source_name: Primary lung cells derived from 4-week-old broiler chicken, mock infection

label_protocol: Biotinylated cRNA were prepared with 100ng of total RNA using the GeneChip® 3′ IVT Express Kit (Affymetrix) following the manufacturer’s instructions.

growth_protocol: Cells were grown in collagen-coated cell culture flasks (Costar) in DMEM and Ham’s F12 (1:1) supplemented with 2% chicken embryo extract (Biosera), 5% fetal calf serum, 1% insulin-transferrin selenium (Invitrogen) and antibiotics.

extract_protocol: Twenty-four hours following infection, total RNA from each well was extracted using the RNeasy Mini - QIAshredder Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Monolayers of primary cells in 6-well cell culture plates (Costar) were infected with LPAI and HPAI viruses at multiplicity of infection (MOI) of 1.0. Three wells of each cell type were used for each of the three viruses. Negative controls were performed in triplicate wells for each cell type without virus infection.

value: 4 weeks

value: primary lung cells

value: mock infection

tag: treatment duration

value: 24 hrs


title: Duck H2N3 infected, biological rep2

description:
Duck_AI-H2N3-Infected_2
Gene expression data from duck lung cells at 24h post-infection with H2N3 (LPAI) influenza virus.

organism: Anas platyrhynchos

source_name: Primary lung cells derived from 6-week-old Pekin ducks, H2N3 influenza virus infection

value: 6 weeks

value: H2N3 influenza virus infection


title: Duck mock-infected control, biological rep2

description:
Duck_Control-mock infected_2
Gene expression data from mock-infected duck lung cells at 24h post-infection.

source_name: Primary lung cells derived from 6-week-old Pekin ducks, mock infection


title: Duck H5N1 ty-Ty infected, biological rep1

description:
Duck_AI-ty-TY-Infected_1
Gene expression data from duck lung cells at 24h post-infection with H5N1 ty-Ty (HPAI) influenza virus.

source_name: Primary lung cells derived from 6-week-old Pekin ducks, H5N1 ty-Ty influenza virus infection

value: H5N1 ty-Ty influenza virus infection


title: Chicken H5N1 ty-Ty infected, biological rep2

description:
Chicken_AI-ty-TY-Infected_2
Gene expression data from chicken lung cells at 24h post-infection with H5N1 ty-Ty (HPAI) influenza virus.

source_name: Primary lung cells derived from 4-week-old broiler chicken, H5N1 ty-Ty influenza virus infection


title: Duck H5N1 ty-Ty infected, biological rep2

description:
Duck_AI-ty-TY-Infected_2
Gene expression data from duck lung cells at 24h post-infection with H5N1 ty-Ty (HPAI) influenza virus.


title: Chicken mock-infected control, biological rep2

description:
Chicken_Control-mock infected_2
Gene expression data from mock-infected chicken lung cells at 24h post-infection.


title: Duck H5N1 50-92 infected, biological rep1

description:
Duck_AI-50-92-Infected_1
Gene expression data from duck lung cells at 24h post-infection with H5N1 50-92 (HPAI) influenza virus.

source_name: Primary lung cells derived from 6-week-old Pekin ducks, H5N1 50-92 influenza virus infection

value: H5N1 50-92 influenza virus infection


title: Reversa.female.saline.5


title: Chicken H5N1 50-92 infected, biological rep1

description:
Chicken_AI-50-92-Infected_1
Gene expression data from chicken lung cells at 24h post-infection with H5N1 50-92 (HPAI) influenza virus.

source_name: Primary lung cells derived from 4-week-old broiler chicken, H5N1 50-92 influenza virus infection


title: rpb2-10, biological rep. 1

city: Seville

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 2-fold expression change compared to wild-type strain with a p-value FDR < 0.05, were considered as altered. Expression values were obtained with the anti-log of RMA values

organism: Saccharomyces cerevisiae

source_name: Total RNA from W303 rpb2-10 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)


title: Duck H2N3 infected, biological rep1

description:
Duck_AI-H2N3-Infected_1
Gene expression data from duck lung cells at 24h post-infection with H2N3 (LPAI) influenza virus.


title: rpb2-10, biological rep. 3


title: rpb2-10, biological rep. 2


title: Duck mock-infected control, biological rep1

description:
Duck_Control-mock infected_1
Gene expression data from mock-infected duck lung cells at 24h post-infection.


title: Chicken H5N1 50-92 infected, biological rep2

description:
Chicken_AI-50-92-Infected_2
Gene expression data from chicken lung cells at 24h post-infection with H5N1 50-92 (HPAI) influenza virus.


title: Duck H5N1 50-92 infected, biological rep2

description:
Duck_AI-50-92-Infected_2
Gene expression data from duck lung cells at 24h post-infection with H5N1 50-92 (HPAI) influenza virus.


title: WT1A, biological rep. 2

source_name: Total RNA from W303 cells


title: Reversa.male.saline.6

value: male


title: Chicken H2N3 infected, biological rep2

description:
Chicken_AI-H2N3-Infected_2
Gene expression data from chicken lung cells at 24h post-infection with H2N3 (LPAI) influenza virus.

source_name: Primary lung cells derived from 4-week-old broiler chicken, H2N3 influenza virus infection


title: WT1A, biological rep. 1


title: Chicken H5N1 ty-Ty infected, biological rep1

description:
Chicken_AI-ty-TY-Infected_1
Gene expression data from chicken lung cells at 24h post-infection with H5N1 ty-Ty (HPAI) influenza virus.


title: Chicken H2N3 infected, biological rep1

description:
Chicken_AI-H2N3-Infected_1
Gene expression data from chicken lung cells at 24h post-infection with H2N3 (LPAI) influenza virus.


title: WT1A, biological rep. 3


title: Reversa.female.saline.4


title: Reversa.male.polyic.5

value: polyic


title: Reversa.male.polyic.6


title: rpb1-1, biological rep. 3

source_name: Total RNA from W303 rpb1-1 cells

value: WRP1- 12A


title: rpb1S751F, biological rep. 1

source_name: Total RNA from W303 rpb1S751Fcells


title: Reversa.male.polyic.4


title: rpb1-1, biological rep. 1


title: Reversa.female.polyic.6


title: Reversa.male.polyic.3


title: WT1B, biological rep. 1


title: rpb1S751F, biological rep. 3

source_name: Total RNA from W303 rpb1S751F cells


title: rpb1S751F, biological rep. 2


title: rpb1-1, biological rep. 2


title: SUM159-mir100, ALDH- flow-sorted cells, Doxycycline(DOX), 10hrs

city: Hefei

first: Suling

last: Liu

state: Anhui

address: 96 Jin Zai Road

department: School of Life Sciences and Medical Center

country: China

institute: University of Science & Technology of China

description: flow sorted ALDH- cells from SUM159 cell lines were treated by Doxorubicin for 13 hours

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Expression data were analyzed by the Robust Multi-array Average method (RMA) in R using Bioconductor and associated packages.

source_name: SUM159-mir100, ALDH-, DOX, 10hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: ALDH-positive and -negative populations of pTRIPZ-SUM159-mir-100 cells were separated and cultured in suspension for ten hours in the presence or absence of DOXYCYLINE(DOX)

tag: cell line

tag: aldh status

value: ALDH-

value: Doxycycline(DOX), 10hrs


title: SUM159-mir100, ALDH- flow-sorted cells, control

description: flow sorted ALDH- cells from SUM159 cell lines were cultured for 13 hours, used as control to compare with those treated by Doxorubicin for 13 hours

source_name: SUM159-mir100, ALDH-, CTRL, 10hrs

value: control


title: WT1B, biological rep. 2

tag: genotype


title: Reversa.female.saline.2

tag: strain

value: Reversa

value: Aortic root CD68+ cells


title: Reversa.female.saline.3

tag: gender

value: female

value: saline


title: Reversa.female.polyic.5


title: SUM159-mir100, ALDH+ flow-sorted cells, Doxycycline(DOX), 10hrs

description: flow sorted ALDH+ cells from SUM159 cell lines were treated by Doxorubicin for 13 hours

source_name: SUM159-mir100, ALDH+, DOX, 10hrs

value: ALDH+


title: SUM159-mir100, ALDH+ flow-sorted cells, control

description: flow sorted ALDH+ cells from SUM159 cell lines were cultured for 13 hours, used as control to compare with those treated by Doxorubicin for 13 hours

source_name: SUM159-mir100, ALDH+, CTRL, 10hrs


title: GP66-specific CD4, LMgp61, mouse #3

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

institute: University of Oxford

hyb_protocol: 5 ug was hybridized following standard Nugen/Affymetrix protocols

scan_protocol: Scanned with Affymetrix using AGCC v. 1.1

data_processing: Analyzed on Affymetrix Expression Console v. 1.1 using a GC-RMA normalization algorithm producing log base 2 results

source_name: GP66-specific CD4 T cell from LMgp61 immunized mouse challenged with LCMV cl-13, mouse #3

label_protocol: 1st and 2nd strand synthesis, followed by Spia amplification using the Nugen WT pico kit to generate cDNA. Fragmentation and biotinylation using Nugen cat# 4200 following standard Nugen/Affymetrix protocols

growth_protocol: Mice were immunized with either Listeria monocytogenes WT (LMwt) or Listeria monocytogenes expressing LCMV GP61 epitope (LMgp61) and subsequently infected with LCMV Cl-13

extract_protocol: GP66-specific CD4 T cells were isolated using a BD Biosciences Aria cell sorter. RNA extraction was performed by Phenol/Chloroform followed by Agilent RNA extraction proctol with optional DNase treatment.

treatment_protocol: Day 8 post-infection, splenic CD4 T cells were enriched by negative selection (MACS), stained for CD4, CD44, and I-Ab/GP66 and sort purified on a BD Biosciences Aria cell sorter.

value: spleen

value: CD4 T cell

tag: vaccine

tag: timepoint

value: day 8 post-LCMV Cl-13


title: GP66-specific CD4, LMgp61, mouse #2

source_name: GP66-specific CD4 T cell from LMgp61 immunized mouse challenged with LCMV cl-13, mouse #2


title: GP66-specific CD4, LMgp61, mouse #4

source_name: GP66-specific CD4 T cell from LMgp61 immunized mouse challenged with LCMV cl-13, mouse #4


title: Reversa.male.saline.5

source_name: Aortic root CD68+ cells


title: GP66-specific CD4, LMwt, mouse #3

source_name: GP66-specific CD4 T cell from LMwt immunized mouse challenged with LCMV cl-13, mouse #3

value: LMwt


title: WT1B, biological rep. 3


title: GP66-specific CD4, LMgp61, mouse #1

source_name: GP66-specific CD4 T cell from LMgp61 immunized mouse challenged with LCMV cl-13, mouse #1


title: Reversa.female.polyic.4


title: Reversa.female.polyic.3


title: Reversa.male.saline.3


title: Reversa.female.polyic.2


title: 7 days postpartum, biological rep 2

city: Chicago

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

description: CYP2D6-humanized mouse livers. Transgenic mice harboring CYP2D6 (PMID:16033950).

hyb_protocol: 12 µg of biotin-labeled and fragmented target cRNA was hybridized to MG 430 2.0 expression array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. After hybridization, arrays were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G to extract CEL files. Intensity expression data by GeneChip Operating Software v. 1.4 (MicroArray Suite 5.0).

data_processing: The raw data were then summarized with RMA and quantile normalization using Affymetrix Power Tools.

source_name: liver at 7 days postpartum

label_protocol: 250 ng of total RNA was processed for biotin-labeled target preparation according to the GeneChip 3' IVT Express protocol (Affymetrix, Inc).

tag: strain/background

value: CYP2D6 transgenic

value: liver

tag: stage of pregnancy

value: 7 days postpartum


title: 21 days pregnancy, biological rep 1

source_name: liver at 21 days of pregnancy

tag: tissue

value: 21 days of pregnancy


title: Reversa.male.saline.4

value: male


title: Reversa.female.polyic.1

value: polyic


title: 21 days pregnancy, biological rep 2


title: 7 days postpartum, biological rep 1


title: Pre-pregnancy, biological rep 2

source_name: liver at pre-pregnancy

value: pre-pregnancy


title: Pre-pregnancy, biological rep 1


title: Reversa.male.saline.2


title: GP66-specific CD4, LMwt, mouse #2

source_name: GP66-specific CD4 T cell from LMwt immunized mouse challenged with LCMV cl-13, mouse #2


title: sorafenib_rep4

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

description: Gene expression in heart of zebrafish exposed to sorafenib

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacture's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction 100 uL was hybridized to an Agilent Zebrafish DNA Oligo Microarray (GPL14688) for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using Agi4x44PreProcess in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.

organism: Danio rerio

source_name: Sorafenib

label_protocol: Cy3 labeled cRNA was prepared from 0.7 ug RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Zebrafish was maintained in egg water.

extract_protocol: Total RNA was extracted from zebrafish heart using RNAqueous-Micro Kit (Life Technologies, Carlsbad, CA), qualified by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and quantified using using Nano Drop ND-100 (Wilmington, DE, USA).

treatment_protocol: Zebrafish was exposed to sorafenib (1 uM) or the vehicle from 72 to 96 hpf.

value: Sorafenib

value: heart

tag: age

value: 4 dpf


title: sorafenib_rep2


title: LdlrKO.male.polyic.2

value: Ldlr-/-

value: Aortic root CD68+ cells


title: Reversa.male.polyic.2

value: Reversa


title: Reversa.male.polyic.1


title: GP66-specific CD4, LMwt, mouse #1

source_name: GP66-specific CD4 T cell from LMwt immunized mouse challenged with LCMV cl-13, mouse #1

value: spleen


title: Rrm3-Flag rpb1-1 exp2

description:
Rrm3-rpb1-1_signal.bar
Rrm3-rpb1-1_pvalue.bar
Asynchronous cultures growing in rich YPD medium

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

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

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run. 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

source_name: Rrm3-Flag ChIP DNA from RRBB-21D, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 30°C

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-c-Myc monoclonal antibody (Clontech) was used for ChIP.

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 bar1Δ::RAD5 RRM3::FLAG::KAN rpb1-1 ura3::URA3/GDP-TK(7X)

tag: cell cycle stage

value: asynchronous

tag: chip antibody

value: anti-Flag

source_name: Input DNA from N3RBb-4B


title: LdlrKO.male.polyic.1

tag: cell type


title: Reversa.male.saline.1

value: saline


title: Rrm3-Flag rpb1-1 exp1

source_name: Rrm3-Flag ChIP DNA from RRBB-21D asynchronous culture


title: Rrm3-Flag WT exp2

description:
Rrm3-WT_signal.bar
Rrm3-WT_pvalue.bar
Asynchronous cultures growing in rich YPD medium

source_name: Rrm3-Flag ChIP DNA from WRBb-9D, asynchronous culture

value: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 bar1Δ::RAD5 RRM3::FLAG::KAN ura3::URA3/GDP-TK(7X)

source_name: Input DNA from WRBb-9B


title: sorafenib_rep1


title: Reversa.female.saline.1

value: female


title: Rrm3-Flag WT exp1


title: control_rep4

description: Gene expression in heart of zebrafish without exposure to sorafenib

source_name: control

value: control


title: control_rep2


title: sorafenib_rep3


title: control_rep1


title: control_rep3


title: Testis_HybZoneMale_indFP144

city: Ploen

first: Leslie

middle: M

last: Turner

address: August-Thienemann Str 2

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Biology

description: testis

hyb_protocol: Hybridization was performed following the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol from Agilent.

scan_protocol: Arrays were scanned using a High Resolution Microarray Scanner (Agilent) and raw images processed using Feature Extraction Software (Agilent). Raw images and the distribution of non-uniformity outliers were visually inspected for large spatial artifacts (e.g. caused by buffer leakage or dust particles). We used quality control metrics from Feature Extraction protocol GE1_QCMT_Dec08.

data_processing: We mapped the 41,174 non-control probe sequences from the Whole Mouse Genome Microarray to the mouse reference genome (NCBI37, downloaded March 2011) using BLAT (minScore = 55, default settings for all other options).  We excluded probes with multiple perfect matches, more than nine matches, matches to non-coding/intergenic regions only, and matches to more than one gene. A total of 36,323 probes (covering 19,742 Entrez Genes) were retained. Preprocessing of microarray data was performed using the BioConductor package Agi4x44PreProcess. We used the “half” setting, which sets intensities below 0.5 to 0.5 following background subtraction, and an offset value of 50. The background signal was computed in Feature Extraction. During preprocessing, we filtered probes based on flags from Feature Extraction. Probes with signal above background in at least 10% of samples were retained (settings: wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE). We used default settings for quality-control flags. Following preprocessing, we removed probes for which the 98th percentile was <2-fold greater than background. The final data set includes 24,218 probes.

organism: Mus musculus musculus x M. m. domesticus

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP144

label_protocol: We used single-color Quick-Amp Labeling Kits (Agilent) to amplify and label RNA. The yield (>2 μg) and specific activity (>9.0 pmol Cy3/μg cRNA) of labeling reactions was verified using a NanoDrop ND-1000 UV-VIS Spectrophotometer (NanoDrop, Wilmington, DE, USA).

growth_protocol: Pups were weaned at 28 days, and males were separated into individual cages. Males were killed for phenotyping at 62-86 days of age using carbon dioxide.

extract_protocol: We extracted RNA from testis using RNeasy kits (Qiagen, Hilden, Germany). RNA quality (RIN > 8) was verified using RNA 6000 Nano kits (Agilent) on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Freshly dissected right testes were stored in RNAlater (Qiagen) at 4° overnight, then transferred to -20° until processed.

value: testis


title: Testis_HybZoneMale_indFP191

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP191


title: Testis_HybZoneMale_indFP037

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP037


title: Testis_HybZoneMale_indFP038

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP038


title: Testis_HybZoneMale_indFP186

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP186


title: Testis_HybZoneMale_indFP233

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP233


title: Testis_HybZoneMale_indFP126

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP126


title: Testis_HybZoneMale_indFP165

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP165


title: Testis_HybZoneMale_indFP230

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP230


title: Testis_HybZoneMale_indFP121

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP121


title: Testis_HybZoneMale_indFP240

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP240


title: Testis_HybZoneMale_indFP140

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP140


title: Testis_HybZoneMale_indFP149

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP149


title: Testis_HybZoneMale_indFP193

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP193


title: Testis_HybZoneMale_indFP115

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP115


title: Testis_HybZoneMale_indFP215

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP215


title: Testis_HybZoneMale_indFP032

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP032


title: Testis_HybZoneMale_indFP143

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP143


title: Testis_HybZoneMale_indFP225

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP225


title: Testis_HybZoneMale_indFP245

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP245


title: Testis_HybZoneMale_indFP211

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP211


title: Testis_HybZoneMale_indFP250

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP250


title: Testis_HybZoneMale_indFP119

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP119


title: Testis_HybZoneMale_indFP214

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP214


title: Testis_HybZoneMale_indFP111

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP111


title: Testis_HybZoneMale_indFP236

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP236


title: Testis_HybZoneMale_indFP103

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP103


title: Testis_HybZoneMale_indFP102

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP102


title: MK3619_SM

city: Uji

first: Shigeyuki

last: Kawai

state: Kyoto

address: Gokasyo

institute: Kyoto University

description: This sample is of MK3619 strain cultured in SM medium for 24 h. MK3619 strain is derived from BY4742 cells cultured on mannitol plate for long-period.

hyb_protocol: Hybridization was performed by NimbleGen Systems according to the standard NimbleGen operating protocol.

scan_protocol: Scanning was performed using NimbleGen MS200 microarray scanner.

data_processing: The data were analyzed by quantile normalization and RMA algorithm (NimbleScan version 2.6 software).

source_name: Saccharomyces cerevisiae MK3619 cells cultured in SM medium

label_protocol: Labeling was performed by NimbleGen Systems according to the standard NimbleGen operating protocol.

growth_protocol: Saccharomyces cerevisiae cells were grown to the logarithmic phase at 30°C in SC or SM media.

extract_protocol: Total RNA was extracted using hot phenol (McEntee and Hudson Anal. Biochem. 176(2):303), treated with DNase I to digest genomic DNA, and purified on RNeasy column (Qiagen).

value: Derived from BY4742

tag: growth culture

value: SM medium


title: BY4742_SC

description: This sample is of BY4742 strain cultured in SC medium for 24 h.

source_name: Saccharomyces cerevisiae BY4742 cells cultured in SC medium

value: MATalpha, his3delta1, leu2delta0, lys2delta0, ura3delta0

value: SC medium


title: MK3683_SM

description: This sample is of MK3683 strain cultured in SM medium for 24 h. MK3683 strain is derived from BY4742 cells cultured on mannitol plate for long-period.

source_name: Saccharomyces cerevisiae MK3683 cells cultured in SM medium


title: Testis_HybZoneMale_indFP098

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP098


title: Testis_HybZoneMale_indFP244

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP244


title: Testis_HybZoneMale_indFP100

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP100


title: Testis_HybZoneMale_indFP095

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP095


title: Testis_HybZoneMale_indFP083

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP083


title: Testis_HybZoneMale_indFP090

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP090


title: Splenic NK1.1+ cells of TLR7tg mouse A2205

city: Rockville

first: Silvia

last: Bolland

state: MD

address: 12441 Parklawn Drive

department: AFGS

institute: NIAID

description: Unique biological replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on Illumina HiScan-SQ scanner

data_processing: Data were quanitile normalized in R

source_name: Mouse splenic NK1.1+ cells

label_protocol: Biotinylated cRNA were prepared using Ambion Illumina TotalPrep RNA amplification kit

extract_protocol: RNA was extracted with Trizol reagent.  Quality was tested using Experion RNA StdSens electrophoresis machine

value: splenic NK1.1+ cells

tag: mouseid


title: Testis_HybZoneMale_indFP094

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP094


title: Splenic NK1.1+ cells of TLR7tg mouse A2400

description: Unique biological replicate


title: Testis_HybZoneMale_indFP075

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP075


title: Testis_HybZoneMale_indFP071

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP071


title: Testis_HybZoneMale_indFP067

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP067


title: Testis_HybZoneMale_indFP096

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP096


title: Splenic NK cells of B6 WT mouse A2398

description: Unique biological replicate

source_name: Mouse splenic NK cells

value: splenic NK cells


title: MK3683_SC

description: This sample is of MK3683 strain cultured in SC medium for 28 h. MK3683 strain is derived from BY4742 cells cultured on mannitol plate for long-period.

source_name: Saccharomyces cerevisiae MK3683 cells cultured in SC medium


title: Splenic NK cells of B6 WT mouse A2204

description: Unique biological replicate


title: Testis_HybZoneMale_indFP065

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP065


title: Stimulation for 12 hr-1

city: Seoul

first: Myunghwan

last: Jung

address: 1 Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 12 h-1

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R 3.0.2

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

growth_protocol: 8.0 × 10^4 cells/cm2 in T75 flasks with 20 mL of RPMI containing 2 % FBS

extract_protocol: Total RNA was isolated from the cells using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were incubated with 100 µg/mL of mica fine particle and collected at 0, 12, and 48 h post-stimulation

value: Leukemic monocyte macrophage

tag: culture media

value: RPMI

tag: cell culture condition

value: 8.0 × 10^4 cells/cm2 in T75 flasks with 20 mL of media containing 2 % FBS


title: Stimulation for 48 hr-1

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 48 h-1

tag: cell line


title: Testis_HybZoneMale_indFP061

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP061


title: Average of two technical replicates from splenic NK1.1+ cells of TLR7tg mouse A2077

description: Average of two Tg 2078 technical replicates 7011D+7011E


title: Testis_HybZoneMale_indFP056

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP056


title: Stimulation for 12 hr-2

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 12 h-2


title: Testis_HybZoneMale_indFP055

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP055


title: Stimulation for 0 hr-2

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 0 h-2


title: Testis_HybZoneMale_indFP053

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP053


title: Testis_HybZoneMale_indFP060

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP060


title: Testis_HybZoneMale_indFP054

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP054


title: Average of two technical replicates from splenic NK cells of B6 WT mouse A2077

description: Average of two B6 2077 technical replicates 7011A+7011C


title: Stimulation for 0 hr-1

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 0 h-1


title: Stimulation for 48 hr-2

description: Gene expression in RAW 264.7 cell treated 100 µg/mL of mica nanoparticles for 48 h-2


title: Testis_HybZoneMale_indFP044

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP044


title: Testis_HybZoneMale_indFP026

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP026


title: WT_RAD51_shRNA_2

first: Ana

middle: Rita

last: Carlos

address: Old Road Campus Research Building

department: The CR-UK/MRC Gray Institute for Radiation Oncology and Biology

description: replicate 3

data_processing:
Data was normalized with quantile normalization and further analysed with the EXPANDER package. Background correction was carried out by variance-stabilizing transformation (VST) available in Bioconductor’s lumi package
To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction. Those genes with FDR <0.1 were selected as differentially expressed.

source_name: embryonic fibroblasts

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: Mouse embryonic fibroblast (MEFs) were grown in DMEM supplemented with 10% foetal bovine serum, penicillin and streptomycin in a low oxygen (3%) incubator.

extract_protocol: Total RNA was extracted from cells collected 4 days after infection using Trizol reagent.

treatment_protocol: MEFs were then infected with retrovirus containing GFP and RAD51 shRNAs.

tag: genotype

value: WT

tag: treatment

value: RAD51 shRNA

value: embryonic fibroblasts

tag: genetic background


title: Testis_HybZoneMale_indFP042

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP042


title: Testis_HybZoneMale_indFP039

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP039


title: Testis_HybZoneMale_indFP041

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP041


title: Testis_HybZoneMale_indFP015

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP015


title: WT_GFP_shRNA_2

description: replicate 3

value: GFP shRNA


title: WT_RAD51_shRNA

description: replicate 1


title: ARF_RAD51_shRNA

description: replicate 1

value: ARF negative


title: Testis_HybZoneMale_indFP019

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP019


title: WT_RAD51_shRNA_1

description: replicate 2


title: ARF_RAD51_shRNA_2

description: replicate 3


title: Testis_HybZoneMale_indFP013

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP013


title: Testis_HybZoneMale_indFP033

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP033


title: 194.125

city: Philadelphia

first: Hongzhe

last: Li

state: Pennsylvania

address: 415  Curie Blvd

department: Biostatistics and Epidemiology

institute: University of Pennsylvania

hyb_protocol: RNA were reverse transcribed into cDNAs followed by fragmentation

scan_protocol: After hybridization to the GeneChip Human Gene 1.0 ST Arrays, the chips were labeled with a WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA) and scanned on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: Data were normalized using the Robust Multi-Chip Average (RMA) method and Log2 transformed using Partek Genomics Suite 6.4 (Partek Inc., St. Louis, MO).

source_name: ovary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Qiagen miRNeasy Mini kit

value: ovary

tag: tumor stage

value: III-IV


title: ARF_RAD51_shRNA_1

description: replicate 2


title: 7.178


title: ARF_GFP_shRNA_2

description: replicate 3


title: 100.352


title: Testis_HybZoneMale_indFP007

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP007

value: testis


title: Testis_HybZoneMale_indFP020

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP020


title: WT_GFP_shRNA_1

description: replicate 2


title: ARF_GFP_shRNA_1

description: replicate 2


title: ARF_GFP_shRNA

description: replicate 1


title: Testis_HybZoneMale_indFP006

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP006


title: Testis_HybZoneMale_indFP012

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP012


title: WT_GFP_shRNA

description: replicate 1


title: Testis_HybZoneMale_indFP005

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP005


title: 110.462


title: Testis_HybZoneMale_indFP004

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP004


title: Testis_HybZoneMale_indFP002

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP002


title: 127r.170


title: 135r.382


title: 130r.278


title: Testis_HybZoneMale_indFP125

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP125


title: 186.296


title: Testis_HybZoneMale_indFP195

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP195


title: Testis_HybZoneMale_indFP196

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP196


title: 77.386


title: Testis_HybZoneMale_indFP249

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP249


title: Testis_HybZoneMale_indFP182

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP182


title: 129r.250


title: 63.96


title: Testis_HybZoneMale_indFP175

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP175


title: 133r.353


title: 116.612


title: Testis_HybZoneMale_indFP167

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP167


title: Testis_HybZoneMale_indFP194

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP194


title: Testis_HybZoneMale_indFP017

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP017


title: Testis_HybZoneMale_indFP128

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP128


title: 145r.533

source_name: ovary


title: 119.631


title: 134r.378


title: Testis_HybZoneMale_indFP163

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP163


title: Testis_HybZoneMale_indFP141

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP141


title: Testis_HybZoneMale_indFP072

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP072


title: 193.221


title: 144r.520


title: Testis_HybZoneMale_indFP161

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP161


title: Testis_HybZoneMale_indFP138

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP138


title: 6.146


title: 131r.283


title: 21.325


title: Testis_HybZoneMale_indFP104

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP104


title: Testis_HybZoneMale_indFP084

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP084


title: Testis_HybZoneMale_indFP078

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP078


title: 1.103


title: 128r.246


title: Testis_HybZoneMale_indFP066

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP066


title: 146r.539


title: 125r.134


title: Testis_HybZoneMale_indFP076

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP076


title: 140r.450


title: 102.368


title: Testis_HybZoneMale_indFP047

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP047


title: 113.584


title: 147r.543


title: 132r.301


title: Testis_HybZoneMale_indFP051

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP051


title: Testis_HybZoneMale_indFP050

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP050


title: 17.292


title: 49.448


title: Testis_HybZoneMale_indFP021

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP021


title: Testis_HybZoneMale_indFP188

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP188


title: Testis_HybZoneMale_indFP183

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP183


title: Testis_HybZoneMale_indFP198

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP198


title: Testis_HybZoneMale_indFP113

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP113


title: Testis_HybZoneMale_indFP155

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP155


title: 42.356

description: nobatch

source_name: ovary


title: 5.144


title: Testis_HybZoneMale_indFP154

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP154


title: Testis_HybZoneMale_indFP045

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP045


title: 9.236


title: Testis_HybZoneMale_indFP142

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP142


title: 137r.400


title: Testis_HybZoneMale_indFP185

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP185


title: Testis_HybZoneMale_indFP034

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP034


title: Testis_HybZoneMale_indFP063

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP063


title: 136r.396


title: 103.377


title: 114.606


title: 179.597


title: Testis_HybZoneMale_indFP028

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP028


title: Testis_HybZoneMale_indFP036

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP036


title: 190.553

description: nobatch


title: 101.357


title: 3.117


title: 124.115


title: 157.135


title: 176.538


title: 182.656


title: 115.607


title: Testis_HybZoneMale_indFP145

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP145


title: Testis_HybZoneMale_indFP169

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP169


title: Testis_HybZoneMale_indFP177

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP177


title: Testis_HybZoneMale_indFP016

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP016


title: Testis_HybZoneMale_indFP011

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP011


title: 58.604


title: Testis_HybZoneMale_indFP091

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP091


title: Testis_HybZoneMale_indFP200

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP200


title: Testis_HybZoneMale_indFP130

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP130


title: 148r.556

source_name: ovary


title: Testis_HybZoneMale_indFP114

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP114


title: 86.594


title: 52.461


title: 177.541


title: 122.65


title: 53.463


title: 97.244


title: 141r.464


title: 197.223


title: 143r.501


title: 149.558


title: 152.651


title: Testis_HybZoneMale_indFP086

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP086


title: Testis_HybZoneMale_indFP123

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP123


title: Testis_HybZoneMale_indFP082

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP082


title: Testis_HybZoneMale_indFP109

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP109


title: Testis_HybZoneMale_indFP135

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP135


title: Testis_HybZoneMale_indFP172

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP172


title: Testis_HybZoneMale_indFP112

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP112


title: Testis_HybZoneMale_indFP087

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP087


title: Testis_HybZoneMale_indFP108

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP108


title: Testis_HybZoneMale_indFP162

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP162


title: Testis_HybZoneMale_indFP089

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP089


title: Testis_HybZoneMale_indFP184

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP184


title: Testis_HybZoneMale_indFP022

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP022


title: Testis_HybZoneMale_indFP049

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP049


title: Testis_HybZoneMale_indFP107

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP107


title: Testis_HybZoneMale_indFP093

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP093


title: Testis_HybZoneMale_indFP171

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP171


title: 150.563

source_name: ovary


title: Testis_HybZoneMale_indFP199

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP199


title: Testis_HybZoneMale_indFP158

description: testis

source_name: Testis, 1st generation lab-bred offspring of wild-caught hybrid zone mice, indiv FP158