title: 4-ok1474-OP50


title: 416_German Mutton sheep DNA

status: Public on May 01 2015

type: genomic

city: Beijing

first: Li

last: Zhang

address: Yuanmingyuan Street

country: China

institute: CAAS

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from sheep blood was genotyped using OvineSNP50 Beadchip (Illumina). Genome wide association studies (GWAS) software TASSEL 3.0 (http://www.maizegenetics.net) and Plink software (v1.07,http://pngu.mgh.harvard.edu/~purcell/plink) were used for data analysis and quality control.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Ovis aries

source_name: German Mutton sheep

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from blood samples using the TIANamp Blood DNA Kit (Tiangen Biotech Co,Ltd., Beijing, China).

tag: gender

value: female

tag: tissue

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 288_German Mutton sheep DNA

value: male


title: Synchronized cells, 160 min, biological replicate E | array yoG_12B

type: RNA

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Medical School

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Mid-log mRNA (unsynchronized)

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and poly A+ mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

tag: Strain

source_name: 160 min

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: 300_German Mutton sheep DNA


title: 281_German Mutton sheep DNA


title: 6-ok1474-OP50

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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: RMA by software Partek

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

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

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: C. elegans  were maintained in a pathogen-free facility  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: genotype

tag: treatment

value: E. coli

tag: developmental stage

value: L4-exposed worms


title: 284_German Mutton sheep DNA

tag: gender


title: 277_German Mutton sheep DNA

tag: tissue


title: 299_German Mutton sheep DNA

tag: birth weight (kg)


title: 283_German Mutton sheep DNA

tag: weaning weight (kg)


title: Synchronized cells, 120 min, biological replicate E | array yoG_10B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 120 min


title: Synchronized cells, 110 min, biological replicate E | array yoG_35B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 110 min


title: Synchronized cells, 90 min, biological replicate E | array yoG_09B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 90 min


title: Synchronized cells, 80 min, biological replicate E | array yoG_35T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 80 min


title: Synchronized cells, 70 min, biological replicate E | array yoG_09T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 70 min


title: 2-km25-OP50


title: Synchronized cells, 100 min, biological replicate E | array yoG_10T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 100 min


title: 268_German Mutton sheep DNA

tag: 6-month weight (kg)


title: 271_German Mutton sheep DNA

tag: fat thickness (cm)


title: 276_German Mutton sheep DNA

tag: eye muscle area (cm2)


title: 269_German Mutton sheep DNA

tag: height at withers (cm)


title: 272_German Mutton sheep DNA

tag: chest girth (cm)


title: Synchronized cells, 50 min, biological replicate E | array yoG_33B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 50 min


title: 267_German Mutton sheep DNA

tag: shin circumference (cm)


title: Synchronized cells, 30 min, biological replicate E | array yoG_06B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 30 min


title: Synchronized cells, 10 min, biological replicate E | array yoG_06T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 10 min


title: 266_German Mutton sheep DNA

tag: pre-weaning gain(kg)


title: Synchronized cells, 20 min, biological replicate E | array yoG_33T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 20 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 20 min


title: Synchronized cells, 60 min, biological replicate E | array yoG_07B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 60 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 60 min


title: Synchronized cells, 40 min, biological replicate E | array yoG_07T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 40 min


title: Synchronized cells, 140 min, biological replicate E | array yoG_36T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 140 min


title: Synchronized cells, 130 min, biological replicate E | array yoG_12T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 130 min


title: Synchronized cells, 0 min, biological replicate E | array yoG_76T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were immediately harvested, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 0 min


title: 264_German Mutton sheep DNA

source_name: German Mutton sheep

tag: post-weaning gain (kg)


title: 263_German Mutton sheep DNA

tag: daily weight gain (kg)


title: 265_German Mutton sheep DNA


title: Synchronized cells, 210 min, biological replicate B | array yofG_32T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 210 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: Mid-log mRNA (unsynchronized)

tag: Strain

source_name: 210 min


title: Synchronized cells, 180 min, biological replicate B | array yofG_30T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 180 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 180 min


title: Synchronized cells, 150 min, biological replicate B | array yofG_28T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 150 min


title: Synchronized cells, 165 min, biological replicate B | array yofG_28B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 165 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 165 min


title: genomic DNA from elderly adult muscle cells 3

city: Paris

first: Stéphanie

last: Duguez

state: France

address: UPMC Univ. Paris 6 / U974

department: Thérapie des maladies du muscle strié

country: France

institute: Institut de Myologie

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation 450 BeadChips using standard Illumina protocol

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

data_processing: Illumina GenomeStudio Software 2011.1

label: Cy5 and Cy3

organism: Homo sapiens

source_name: elderly adult muscle cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from muscle cell pellets using the Gentra Puregene Blood Kit (Qiagen)

tag: age

value: elderly adult

tag: cell type

value: muscle cell


title: Synchronized cells, 195 min, biological replicate B | array yofG_30B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 195 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 195 min


title: genomic DNA from elderly adult muscle cells 2


title: genomic DNA from young adult muscle cells 2

source_name: young adult muscle cells

value: young adult


title: Synchronized cells, 135 min, biological replicate B | array yofG_31B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 135 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 135 min


title: genomic DNA from young adult muscle cells 3


title: 262_German Mutton sheep DNA


title: genomic DNA from young adult muscle cells 1


title: 301_German Mutton sheep DNA


title: 260_German Mutton sheep DNA


title: Synchronized cells, 105 min, biological replicate B | array yofG_27B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 105 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 105 min


title: 256_German Mutton sheep DNA


title: 254_German Mutton sheep DNA


title: 252_German Mutton sheep DNA


title: Synchronized cells, 90 min, biological replicate B | array yofG_27T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 90 min


title: 259_German Mutton sheep DNA


title: 258_German Mutton sheep DNA


title: Ethanol_4_+

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: training

hyb_protocol: hybridized on Agilent human whole genome 44K oligo microarrays that contain more than 41,000 unique human genes and transcripts.  Hybridization and washing was performed according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned with an Agilent DNA microarray scanner.

data_processing:
Feature Extraction (Version 9.1; Agilent) was used to filter, normalize, and calculate the signal intensity and ratios.  Spots flagged as not passing the automated quality control standards were excluded.
The file of normalized values ("Normalized_data.txt") is available on the series level and contains the feature extraction normalized log10 ratio (Cy5/Cy3)

source_name: Control

label_protocol: RNAs were labeled with SuperScript indirect cDNA labeling system (Invitrogen)

growth_protocol: TK6 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum. The cell culture density was maintained at 1-10x10^5 cells/ml, and was tested periodically for mycoplasma contamination

extract_protocol: RNA was extracted using the Trizol protocol (Invitrogen) followed by RNA cleanup with an RNeasy column (Qiagen)

treatment_protocol: Exponentially growing cells were treated at the density of 4-5x10^5 cells/ml. For γ-ray exposure, cells were irradiated at 0.87 Gy/min to a dose of 4 Gy using an γ-ray irradiator. Heat-shock treatment was performed by submerging 35 mL cultures in a T175 flask in a 47 °C circulating water bath with gentle agitation for 20 min, while the control was held in the same volume at 37 °C; we have previously found that this is a maximally tolerated dose for transcriptional analysis at this time (Fornace et al., 1989a). All chemicals were purchased from Sigma-Aldrich, except cadmium chloride and potassium chromate were from J.T. Baker.  Fresh stocks were prepared according to manufacturers’ instruction.  Stock solutions were added to the culture medium and incubated for 4 hr.  Simultaneous controls for each experiments were treated with an equal volume of the vehicle, phosphate buffered saline (PBS) or DMSO.  At the end of the 4 h treatment period, cells were pelleted by centrifugation and subjected to RNA extraction.  Dose-response studies were performed for most agents to determine the dose for the microarray experiments.

tag: cell line

source_name: Ethanol


title: 261_German Mutton sheep DNA

tag: gender


title: Ethanol_4_-

description: training


title: Ethanol_2_+

description: training


title: Ethanol_2_-

description: training


title: Synchronized cells, 60 min, biological replicate B | array yofG_25T

source_name: 60 min


title: Vinblastin_+

description: training

source_name: Vinblastin


title: Synchronized cells, 45 min, biological replicate B | array yofG_24B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 45 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 45 min


title: Synchronized cells, 75 min, biological replicate B | array yofG_25B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 75 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 75 min


title: TSA_+

description: training

source_name: TSA


title: Vinblastin_-

description: training


title: 251_German Mutton sheep DNA

source_name: German Mutton sheep

tag: tissue


title: Synchronized cells, 30 min, biological replicate B | array yofG_24T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: Mid-log mRNA (unsynchronized)

source_name: 30 min


title: TSA_-

description: training


title: Paclitaxol_+

description: training

source_name: Paclitaxol


title: Synchronized cells, 225 min, biological replicate B | array yofG_32B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 225 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 225 min


title: Synchronized cells, 0 min, biological replicate B | array yofG_22T

source_name: 0 min


title: Oxamflatin_+

description: training

source_name: Oxamflatin


title: 244_German Mutton sheep DNA

tag: birth weight (kg)


title: 243_German Mutton sheep DNA

tag: weaning weight (kg)


title: genomic DNA from elderly adult muscle cells 1

source_name: elderly adult muscle cells


title: 248_German Mutton sheep DNA

tag: 6-month weight (kg)


title: Synchronized cells, 15 min, biological replicate B | array yofG_22B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 15 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 15 min


title: Methotrexate_+

description: training

source_name: Methotrexate


title: Paclitaxol_-

description: training

source_name: Control


title: 247_German Mutton sheep DNA

tag: fat thickness (cm)


title: 240_German Mutton sheep DNA

tag: eye muscle area (cm2)


title: Oxamflatin_-

description: training


title: 241_German Mutton sheep DNA

tag: height at withers (cm)


title: Methotrexate_-

description: training


title: 238_German Mutton sheep DNA

tag: chest girth (cm)


title: HC toxin_+

description: training

source_name: HC toxin


title: 239_German Mutton sheep DNA

tag: shin circumference (cm)


title: Synchronized cells, 120 min, biological replicate B | array yofG_31T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 120 min


title: 242_German Mutton sheep DNA

tag: pre-weaning gain(kg)


title: HC toxin_-

description: training


title: 236_German Mutton sheep DNA

tag: post-weaning gain (kg)


title: 237_German Mutton sheep DNA

tag: daily weight gain (kg)


title: Docetaxel_+

description: training

source_name: Docetaxel


title: 233_German Mutton sheep DNA


title: Docetaxel_-

description: training


title: 232_German Mutton sheep DNA


title: Apicidin_+

description: training

source_name: Apicidin


title: Colchicine_+

description: training

source_name: Colchicine


title: Apicidin_-

description: training


title: 231_German Mutton sheep DNA


title: 5-FU_+

description: training


title: 224_German Mutton sheep DNA


title: 229_German Mutton sheep DNA


title: 225_German Mutton sheep DNA


title: Colchicine_-

description: training


title: 5-FU_-

description: training


title: 223_German Mutton sheep DNA


title: RIL_#_153

city: Rishon Le-Zion

first: Ron

last: Ophir

address: Hamacabim St.

department: Fruit Tree Sciences

country: Israel

institute: Agricultural Research Organization - the Volcani Center

description: Raw data - Cy3: AS_253671710010_S01_CGH_107_Sep09_1_4.txt

hyb_protocol: Standard Agilent CGH hybridization protocol

scan_protocol: CGH_107_Sep09 Agilent protocol

data_processing:
1. Quantile normalization was applied between all channels accross all arrays. , 2. Removing spatial slide defects, e.g., scratches, bubbles, etc. was performed as follows: The spatial effect on probe density was identified by the method decribed in Chai et al. [BMC Bioinformatics 2010, 11:356], and probes with spatial effect beyond median ±8mad were considered outliers. If 0.2 or more of the probes within 3 points away from some probe were outliers, the probe in the center was also considred an outlier. , 3. Subtracting each probe by its median to normalize between probes. , 4. Four probes were designed per SNP. Two probes, as replicates, for each allele, one replicate probe designed to detect the forward and the other the reverse DNA strand. We Averaged over allele probe replicates (forward and reverse) by ‘medianpolish’ method on a matrix of replicates x arrays to remove the array effect .
matrix.txt: Average over the plus and minus strand probes normalized value for each SNP allele.

organism: Cucumis sativus

source_name: F7 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14

label_protocol: Standard Agilent CGH label protocol

growth_protocol: growth under standard conditions

extract_protocol: not provided

tag: strain/line


title: 249_German Mutton sheep DNA

source_name: German Mutton sheep


title: RIL_#_154

description: Raw data - Cy5: AS_253671710010_S01_CGH_107_Sep09_1_4.txt

value: F7 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Female_Smoker_rep12

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

description: Gene expression with RBC depleted whole blood RNA

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 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded

source_name: Peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Qucik Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The RNA was prepared using the PerfectPure RNA blood kit (PerfectPure, Gaithersburg, MD) following the manufacturer’s recommendations. This protocol differentially lyses red and white blood cells in whole blood to preferentially deplete   globin mRNA. Remaining globin mRNA was further reduced using GLOBINclear (Ambion Inc., Austin, TX) specifically to remove both a- and b-globin. The RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood (approximately 3.0 ml) from smoker and non-smoker volunteers was drawn into 0.105 mol/l sodium citrate Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ).

value: Whole blood

value: Female

tag: age

tag: other

value: smoker


title: RIL_#_135

description: Raw data - Cy3: AS_253671710010_S01_CGH_107_Sep09_1_3.txt


title: 222_German Mutton sheep DNA


title: 219_German Mutton sheep DNA


title: 216_German Mutton sheep DNA


title: 217_German Mutton sheep DNA


title: RIL_#_145

description: Raw data - Cy5: AS_253671710010_S01_CGH_107_Sep09_1_3.txt


title: 220_German Mutton sheep DNA


title: RIL_#_134

description: Raw data - Cy5: AS_253671710010_S01_CGH_107_Sep09_1_2.txt

source_name: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Female_Smoker_rep10


title: 221_German Mutton sheep DNA


title: 218_German Mutton sheep DNA


title: Female_Smoker_rep9


title: 214_German Mutton sheep DNA


title: Female_Smoker_rep11


title: RIL_#_133

description: Raw data - Cy3: AS_253671710010_S01_CGH_107_Sep09_1_2.txt

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: RIL_#_104

description: Raw data - Cy5: AS_253671710010_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_79

description: Raw data - Cy3: AS_253671710010_S01_CGH_107_Sep09_1_1.txt


title: 212_German Mutton sheep DNA


title: 213_German Mutton sheep DNA


title: Female_Smoker_rep7


title: RIL_#_164

description: Raw data - Cy5: AS_253671710009_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_156

description: Raw data - Cy3: AS_253671710009_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_163

description: Raw data - Cy5: AS_253671710009_S01_CGH_107_Sep09_1_3.txt


title: Female_Smoker_rep6


title: 207_German Mutton sheep DNA


title: Female_Smoker_rep3


title: RIL_#_168

description: Raw data - Cy3: AS_253671710009_S01_CGH_107_Sep09_1_3.txt


title: Female_Smoker_rep8


title: Female_Smoker_rep5


title: RIL_#_162

description: Raw data - Cy5: AS_253671710009_S01_CGH_107_Sep09_1_2.txt


title: 210_German Mutton sheep DNA


title: 206_German Mutton sheep DNA


title: RIL_#_166

description: Raw data - Cy3: AS_253671710009_S01_CGH_107_Sep09_1_2.txt


title: 205_German Mutton sheep DNA


title: Female_Smoker_rep4


title: Female_Smoker_rep1


title: Female_Non-smoker_rep11

value: non-smoker


title: 202_German Mutton sheep DNA


title: 211_German Mutton sheep DNA


title: 203_German Mutton sheep DNA


title: 201_German Mutton sheep DNA


title: 208_German Mutton sheep DNA


title: RIL_#_159

description: Raw data - Cy5: AS_253671710009_S01_CGH_107_Sep09_1_1.txt


title: Female_Non-smoker_rep9


title: RIL_#_151

description: Raw data - Cy5: AS_253671710008_S01_CGH_107_Sep09_1_4.txt


title: 10045_Sunit sheep DNA

source_name: Sunit sheep


title: 204_German Mutton sheep DNA


title: RIL_#_147

description: Raw data - Cy3: AS_253671710008_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_150

description: Raw data - Cy5: AS_253671710008_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_149

description: Raw data - Cy5: AS_253671710008_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_152

description: Raw data - Cy3: AS_253671710009_S01_CGH_107_Sep09_1_1.txt


title: 167_Sunit sheep DNA


title: 227_German Mutton sheep DNA


title: Female_Non-smoker_rep4

description: Gene expression with RBC depleted whole blood RNA


title: Female_Non-smoker_rep6


title: RIL_#_165

description: Raw data - Cy3: AS_253671710008_S01_CGH_107_Sep09_1_3.txt


title: Female_Non-smoker_rep10


title: RIL_#_144

description: Raw data - Cy3: AS_253671710008_S01_CGH_107_Sep09_1_2.txt


title: SW_Basal H3K27me3 ChIP_III

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

description: Biological replicate 3 of 3: H3K27me3 ChIP DNA of untreated SW13 cells

hyb_protocol: According to Agilent hyb protocol

scan_protocol: Scanning two-color NimbleGen arrays was done using GenePix 4000B Scanner

data_processing: ChIP-chip data was processed by the TileMap that used the "quantile normalization".

source_name: H3K27me3 ChIP DNA from SW-13 cells

label_protocol: According to Agilent labelling protocol

extract_protocol: Qiagen kit (QIAEX II Gel Extraction Kit)

tag: cell line

tag: chip antibody

source_name: Input DNA from SW-13 cells

value: none, input DNA


title: Female_Non-smoker_rep5

tag: tissue

tag: gender


title: Female_Non-smoker_rep12


title: Female_Non-smoker_rep8


title: Female_Non-smoker_rep3


title: SW_Basal H3K27me3 ChIP_I

description: Biological replicate 1 of 3: H3K27me3 ChIP DNA of untreated SW13 cells


title: Female_Non-smoker_rep2


title: 10027_Sunit sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 10032_Sunit sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: Female_Non-smoker_rep7


title: RIL_#_148

description: Raw data - Cy5: AS_253671710008_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_143

description: Raw data - Cy3: AS_253671710008_S01_CGH_107_Sep09_1_1.txt


title: 10029_Sunit sheep DNA

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: 168_Sunit sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: 175_Sunit sheep DNA

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 10019_Sunit sheep DNA

tag: daily weight gain (kg)


title: RIL_#_132

description: Raw data - Cy3: AS_253671710007_S01_CGH_107_Sep09_1_4.txt

tag: strain/line


title: 10018_Sunit sheep DNA


title: RIL_#_142

description: Raw data - Cy5: AS_253671710007_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_131

description: Raw data - Cy3: AS_253671710007_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_141

description: Raw data - Cy5: AS_253671710007_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_140

description: Raw data - Cy5: AS_253671710007_S01_CGH_107_Sep09_1_2.txt


title: 10015_Sunit sheep DNA


title: Male_Smoker_rep11

value: Male

tag: age

tag: other


title: RIL_#_130

description: Raw data - Cy3: AS_253671710007_S01_CGH_107_Sep09_1_2.txt


title: 10048_Sunit sheep DNA


title: Male_Smoker_rep10


title: 10011_Sunit sheep DNA


title: Female_Smoker_rep2


title: Male_Smoker_rep7


title: Female_Non-smoker_rep1


title: 10010_Sunit sheep DNA


title: Male_Smoker_rep8


title: RIL_#_127

description: Raw data - Cy3: AS_253671710007_S01_CGH_107_Sep09_1_1.txt


title: SW_Basal H3K27me3 ChIP_II

description: Biological replicate 2 of 3: H3K27me3 ChIP DNA of untreated SW13 cells

tag: cell line

tag: chip antibody


title: 169_Sunit sheep DNA

tag: gender

tag: tissue


title: Male_Smoker_rep12


title: RIL_#_126

description: Raw data - Cy5: AS_253671710006_S01_CGH_107_Sep09_1_4.txt


title: Male_Smoker_rep6


title: Male_Smoker_rep5


title: RIL_#_139

description: Raw data - Cy5: AS_253671710007_S01_CGH_107_Sep09_1_1.txt


title: 10003_Sunit sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: 10008_Sunit sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: RIL_#_121

description: Raw data - Cy3: AS_253671710006_S01_CGH_107_Sep09_1_4.txt


title: Male_Smoker_rep9

description: Gene expression with RBC depleted whole blood RNA


title: 10001_Sunit sheep DNA

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: RIL_#_125

description: Raw data - Cy5: AS_253671710006_S01_CGH_107_Sep09_1_3.txt


title: 3599_Sunit sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: Male_Smoker_rep4


title: RIL_#_120

description: Raw data - Cy3: AS_253671710006_S01_CGH_107_Sep09_1_3.txt


title: Male_Smoker_rep2


title: Male_Smoker_rep1


title: 3598_Sunit sheep DNA

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: Male_Smoker_rep3


title: RIL_#_119

description: Raw data - Cy3: AS_253671710006_S01_CGH_107_Sep09_1_2.txt

tag: strain/line


title: RIL_#_122

description: Raw data - Cy5: AS_253671710006_S01_CGH_107_Sep09_1_1.txt


title: Male_Non-smoker_rep12

tag: age


title: RIL_#_118

description: Raw data - Cy3: AS_253671710006_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_117

description: Raw data - Cy5: AS_253671710005_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_124

description: Raw data - Cy5: AS_253671710006_S01_CGH_107_Sep09_1_2.txt


title: 3595_Sunit sheep DNA

tag: daily weight gain (kg)


title: 3594_Sunit sheep DNA


title: 10043_Sunit sheep DNA


title: RIL_#_112

description: Raw data - Cy3: AS_253671710005_S01_CGH_107_Sep09_1_4.txt


title: 3597_Sunit sheep DNA


title: 3592_Sunit sheep DNA


title: RIL_#_116

description: Raw data - Cy5: AS_253671710005_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_111

description: Raw data - Cy3: AS_253671710005_S01_CGH_107_Sep09_1_3.txt


title: Male_Non-smoker_rep11

tag: other


title: RIL_#_115

description: Raw data - Cy5: AS_253671710005_S01_CGH_107_Sep09_1_2.txt


title: Male_Non-smoker_rep9


title: 3588_Sunit sheep DNA


title: RIL_#_110

description: Raw data - Cy3: AS_253671710005_S01_CGH_107_Sep09_1_2.txt


title: Male_Non-smoker_rep6


title: 3582_Sunit sheep DNA


title: 3589_Sunit sheep DNA


title: Male_Non-smoker_rep2


title: RIL_#_113

description: Raw data - Cy5: AS_253671710005_S01_CGH_107_Sep09_1_1.txt


title: Male_Non-smoker_rep7


title: 3577_Sunit sheep DNA


title: Male_Non-smoker_rep10


title: Male_Non-smoker_rep4


title: Male_Non-smoker_rep5


title: Male_Non-smoker_rep3


title: RIL_#_107

description: Raw data - Cy5: AS_253671710019_S01_CGH_107_Sep09_1_4.txt


title: 3585_Sunit sheep DNA


title: 3570_Sunit sheep DNA


title: 174_Sunit sheep DNA


title: RIL_#_109

description: Raw data - Cy3: AS_253671710005_S01_CGH_107_Sep09_1_1.txt


title: 166_Sunit sheep DNA


title: 3580_Sunit sheep DNA


title: RIL_#_106

description: Raw data - Cy5: AS_253671710019_S01_CGH_107_Sep09_1_3.txt


title: Male_Non-smoker_rep1

description: Gene expression with RBC depleted whole blood RNA


title: 180_Sunit sheep DNA


title: RIL_#_101

description: Raw data - Cy3: AS_253671710019_S01_CGH_107_Sep09_1_3.txt


title: 3566_Sunit sheep DNA


title: 171_Sunit sheep DNA


title: 3557_Sunit sheep DNA


title: RIL_#_105

description: Raw data - Cy5: AS_253671710019_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_100

description: Raw data - Cy3: AS_253671710019_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_102

description: Raw data - Cy3: AS_253671710019_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_99

description: Raw data - Cy3: AS_253671710019_S01_CGH_107_Sep09_1_1.txt


title: Granuloma C. burnetii 8 day 2

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

description: PBMC-derived Granuloma induced by C.burnetii at day 8

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies, G4112F) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing:
Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, correspondence analysis (COA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Supervised analysis was performed using SAM and a multiclass model integrating the experimental design (PBMC or granuloma, day 0 or day 8, unstimulated or BCG/C.burnetii). Genes were considered to be differentially expressed for a false discovery rate below 10% and absolute fold change (FC) above 3 in at least one of the 3 pair combinations.
the normalization was done with the quantile algorithm as mentioned  the dataset was filtered to remove controls, spot below BG, spot not found (Agilent FLAG), and saturated spots (Agilent FLAG). For each probe, the probe ws removed if the FLAG was set TRUE in > 75% of the samples
the dataset was then summarized for replicated (identical) probes (to keep only one)

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: Leukopacks from normal blood donor buffy coats were provided from the Etablissement Français du Sang (Marseille, France). Peripheral blood mononuclear cells were isolated from blood samples after deposition over a Ficoll density cushion. Virulent C. burnetii (Nine Mile strain, VR-615; American Type Culture Collection, Manassas, VA) were injected into mice and 10 days later were recovered from spleens, then cultured in mouse L929 fibroblasts maintained in antibiotic-free MEM supplemented with 4% FCS and 2 mM L-glutamine for two passages. After 1 wk, L929 cells were sonicated then the homogenates were centrifuged and finally bacteria were stored at -80°C.Mycobacterium bovis Bacille Calmette-Guérin (BCG) strain (Institut Pasteur, Paris, France) were cultured on Middlebrook 7H10 agar medium. Bacteria (109 per assay) were sonicated  and protein contents were determined by Bradford's method. Bacterial extracts (0.5 mg proteins) were incubated with 10 mg of CN-Br-activated Sepharose 4B beads overnight. The coupling efficiency of bacterial extracts was determined by measuring the protein content of supernatants then beads were stored at 4 °C for a month.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

treatment_protocol: PBMC (2e6 per assay) were co-cultured with 800 beads coated with C.burnetii or BCG extracts in RMPI 1640 supplemented with 10% FCS, 2mM glutamin, 100 IU/mL penicillin and 100µg/mL streptomycin in 35 mm glass bottom culture Petri dish coated with poly-D-lysine for 8 days

tag: stimulation

value: YES

tag: stimulation type

value: bead coated with C. burnetii extract

tag: time

value: 8 day

tag: cell type

value: PBMC-derived Granuloma

tag: bcg

tag: cb

tag: treatment

value: C. burnetii


title: RIL_#_98

description: Raw data - Cy5: AS_253671710018_S01_CGH_107_Sep09_1_4.txt


title: 3591_Sunit sheep DNA

tag: gender

value: male

tag: tissue

value: blood

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: Granuloma BCG 8 day 1

description: PBMC-derived Granuloma induced by BCG at day 8

value: bead coated with BCG extract

value: BCG


title: Granuloma C. burnetii 8 day 4

source_name: PBMC-derived Granuloma induced by C.burnetii at day 8


title: RIL_#_103

description: Raw data - Cy5: AS_253671710019_S01_CGH_107_Sep09_1_1.txt

tag: strain/line


title: Granuloma C. burnetii 8 day 1


title: Granuloma C. burnetii 8 day 3


title: RIL_#_96

description: Raw data - Cy5: AS_253671710018_S01_CGH_107_Sep09_1_3.txt

value: F7 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Granuloma BCG 8 day 3

description: PBMC-derived Granuloma  induced by BCG at day 8


title: Granuloma BCG 8 day 4

source_name: PBMC-derived Granuloma induced by BCG at day 8


title: Granuloma BCG 8 day 2


title: 3556_Sunit sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: RIL_#_92

description: Raw data - Cy3: AS_253671710018_S01_CGH_107_Sep09_1_4.txt


title: 164_Sunit sheep DNA


title: PBMC 0 day 2

description: Unstimulated PBMC  at day 0

source_name: Unstimulated PBMC  at day 0

tag: stimulation

value: NO

tag: stimulation type

value: Unstimulated

tag: time

value: 0 day

tag: cell type

value: PBMC

tag: bcg


title: PBMC 0 day 3

description: Unstimulated PBMC  at day 0

tag: cb

tag: treatment


title: 176_Sunit sheep DNA

tag: gender

tag: tissue

tag: birth weight (kg)

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: 3546_Sunit sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)


title: 3552_Sunit sheep DNA

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: 173_Sunit sheep DNA


title: 3548_Sunit sheep DNA


title: PBMC 0 day 4

description: Unstimulated PBMC  at day 0

tag: stimulation

tag: stimulation type

tag: time

tag: cell type


title: RIL_#_91

description: Raw data - Cy3: AS_253671710018_S01_CGH_107_Sep09_1_3.txt

tag: strain/line

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: 3542_Sunit sheep DNA

tag: gender

tag: tissue


title: RIL_#_89

description: Raw data - Cy3: AS_253671710018_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_93

description: Raw data - Cy5: AS_253671710018_S01_CGH_107_Sep09_1_1.txt


title: 178_Sunit sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: RIL_#_87

description: Raw data - Cy5: AS_253671710017_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_88

description: Raw data - Cy3: AS_253671710018_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_95

description: Raw data - Cy5: AS_253671710018_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_82

description: Raw data - Cy3: AS_253671710017_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_85

description: Raw data - Cy5: AS_253671710017_S01_CGH_107_Sep09_1_3.txt


title: Dentate gyrus - Fast ripple [B10_S1_E]

city: Boston

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

hyb_protocol: Standard Manufacturer's protocol

scan_protocol: Standard Manufacturer's protocol

data_processing: data was imported into R, data was normalized using the Lumi (v2.2) package using the variance stabilizing transform and robust spline normalization

organism: Rattus norvegicus

source_name: Dentate gyrus_Fast ripple

label_protocol: Direct biotin labeling

extract_protocol: Total mRNA using Qiagen spin column

treatment_protocol: Hippocampal slices obtained from Wistar rats injected with pilocarpine to induce epilepsy after in vitro electrophysiological characterization

tag: strain background

value: Wistar

tag: animal id

value: hippocampus; Dentate gyrus

tag: hippocampal slice id

tag: electrophysiology

value: FR


title: Male_Non-smoker_rep8

description: Gene expression with RBC depleted whole blood RNA

value: Whole blood

value: Male

tag: age

tag: other

value: non-smoker


title: Dentate gyrus - Non-fast ripple [B13_S1_NE]

source_name: Dentate gyrus_Non-fast ripple

value: Non-FR


title: Dentate gyrus - Non-fast ripple [B3_S2_NE]


title: 3538_Sunit sheep DNA

value: male

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 3537_Sunit sheep DNA

tag: gender

tag: tissue

value: blood

tag: daily weight gain (kg)


title: Dentate gyrus - Fast ripple [B10_S2_E]

tag: strain background


title: RIL_#_81

description: Raw data - Cy3: AS_253671710017_S01_CGH_107_Sep09_1_3.txt

tag: strain/line


title: Dentate gyrus - Fast ripple [B13_S1_E]

tag: animal id

tag: hippocampal slice id


title: 3541_Sunit sheep DNA

tag: birth weight (kg)

tag: weaning weight (kg)


title: Dentate gyrus - Non-fast ripple [B10_S1_NE]

tag: electrophysiology


title: 165_Sunit sheep DNA

tag: 6-month weight (kg)

tag: fat thickness (cm)


title: RIL_#_84

description: Raw data - Cy5: AS_253671710017_S01_CGH_107_Sep09_1_2.txt


title: 172_Sunit sheep DNA

tag: eye muscle area (cm2)

tag: height at withers (cm)


title: RIL_#_80

description: Raw data - Cy3: AS_253671710017_S01_CGH_107_Sep09_1_2.txt


title: Dentate gyrus - Fast ripple [B3_S2_E]


title: 181_Sunit sheep DNA

tag: chest girth (cm)

tag: shin circumference (cm)


title: RIL_#_83

description: Raw data - Cy5: AS_253671710017_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_78

description: Raw data - Cy3: AS_253671710017_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_77

description: Raw data - Cy5: AS_253671710016_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_73

description: Raw data - Cy3: AS_253671710016_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_76

description: Raw data - Cy5: AS_253671710016_S01_CGH_107_Sep09_1_3.txt


title: Dentate gyrus - Fast ripple [B1_S1_E]


title: 3530_Sunit sheep DNA

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: 3528_Sunit sheep DNA

tag: gender

tag: tissue


title: RIL_#_75

description: Raw data - Cy5: AS_253671710016_S01_CGH_107_Sep09_1_2.txt


title: Dentate gyrus - Non-fast ripple [B9_S3_NE]

tag: strain background


title: Dentate gyrus - Non-fast ripple [B1_S1_NE]


title: Dentate gyrus - Non-fast ripple [B3_S1_NE]


title: 3523_Sunit sheep DNA

tag: daily weight gain (kg)


title: Dentate gyrus - Fast ripple [B3_S1_E]

tag: animal id


title: Dentate gyrus - Fast ripple [B9_S3_E]

tag: hippocampal slice id


title: 3529_Sunit sheep DNA

tag: birth weight (kg)


title: Dentate gyrus - Non-fast ripple [B9_S2_NE]


title: Dentate gyrus - Non-fast ripple [B9_S1_NE]


title: RIL_#_70

description: Raw data - Cy3: AS_253671710016_S01_CGH_107_Sep09_1_3.txt

tag: strain/line


title: RIL_#_69

description: Raw data - Cy3: AS_253671710016_S01_CGH_107_Sep09_1_2.txt


title: Dentate gyrus - Non-fast ripple [P91_S3_NE]

tag: electrophysiology


title: 3520_Sunit sheep DNA

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: 3519_Sunit sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)


title: 3518_Sunit sheep DNA

tag: height at withers (cm)

tag: chest girth (cm)


title: 170_Sunit sheep DNA

tag: shin circumference (cm)

tag: pre-weaning gain(kg)


title: Dentate gyrus - Fast ripple [B9_S1_E]


title: RIL_#_68

description: Raw data - Cy3: AS_253671710016_S01_CGH_107_Sep09_1_1.txt


title: 3516_Sunit sheep DNA

tag: gender

tag: post-weaning gain (kg)


title: RIL_#_67

description: Raw data - Cy5: AS_253671710026_S01_CGH_107_Sep09_1_4.txt


title: 179_Sunit sheep DNA

tag: tissue


title: RIL_#_63

description: Raw data - Cy3: AS_253671710026_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_74

description: Raw data - Cy5: AS_253671710016_S01_CGH_107_Sep09_1_1.txt


title: 3514_Sunit sheep DNA

tag: daily weight gain (kg)


title: Dentate gyrus - Fast ripple [P91_S3_E]

tag: strain background

tag: animal id


title: RIL_#_66

description: Raw data - Cy5: AS_253671710026_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_62

description: Raw data - Cy3: AS_253671710026_S01_CGH_107_Sep09_1_3.txt


title: 3521_Sunit sheep DNA

tag: birth weight (kg)


title: Dentate gyrus - Non-fast ripple [B10_S2_NE]

tag: hippocampal slice id


title: Dentate gyrus - Non-fast ripple [P91_S1_NE]

tag: electrophysiology


title: RIL_#_61

description: Raw data - Cy3: AS_253671710026_S01_CGH_107_Sep09_1_2.txt

tag: strain/line


title: Genes regulation by sMaf (MafG and MafK) in the lens [C2 (Control sample 2)]

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using rank invariant normalisation method  in R

organism: Mus musculus

source_name: Lens tissue, 2 months

label_protocol: Standard protocol for Illumina arrays

extract_protocol: Standard total RNA isolation protocol by RNeasy mini kit (Qiagen)

tag: age

value: 2 months

tag: strain

value: mixed background (129Sv/J, C57BL/6J, and ICR)

tag: genotype/variation

value: Control lens, MafG+/-:MafK+/-


title: RIL_#_64

description: Raw data - Cy5: AS_253671710026_S01_CGH_107_Sep09_1_1.txt


title: Dentate gyrus - Fast ripple [P91_S1_E]


title: PBMC 0 day 1

description: Unstimulated PBMC  at day 0

tag: stimulation

value: NO

tag: stimulation type

tag: time

tag: cell type

tag: bcg

tag: cb

tag: treatment


title: ROW_RNAi_rep2

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: gene expression from ROW RNAi S2 cells

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Data was quantile normalized and RMA summarized using Bioconductor.

organism: Drosophila melanogaster

source_name: ROW RNAi mutant

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

treatment_protocol: S2 cells at 1x10^6/ml were soaked with dsRNA targeting ROW and were incubated for 96h to get depletion.

tag: group

value: ROW RNAi mutant

tag: date


title: Genes regulation by sMaf (MafG and MafK) in the lens [T2 (Test sample 2)]

value: Mutant lens, MafG-/-:MafK+/-


title: 3506_Sunit sheep DNA

tag: gender

tag: tissue

tag: weaning weight (kg)

tag: 6-month weight (kg)

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)

tag: daily weight gain (kg)


title: mRNA Jasp4

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

description: Primary Cells

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.

label: Biotin Allonamide Triphosphate

source_name: Aortic smooth muscle cells_ jasplakinolide

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

growth_protocol: DMEM 10%FCS

extract_protocol: mRNeasy mini kit

treatment_protocol: 100nM Jasplakinolide for 24h

tag: strain

tag: cell type

value: aortic smooth muscle cells


title: ROW_RNAi_rep1

description: gene expression from ROW RNAi S2 cells


title: RIL_#_60

description: Raw data - Cy3: AS_253671710026_S01_CGH_107_Sep09_1_1.txt

tag: strain/line

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Control_rep3

description: gene expression from wild type S2 cells

source_name: wild type

tag: group

value: wild type


title: 3501_Sunit sheep DNA

tag: birth weight (kg)


title: Control_rep2

description: gene expression from wild type S2 cells

tag: date


title: Genes regulation by sMaf (MafG and MafK) in the lens [T1 (Test sample 1)]

tag: age

tag: genotype/variation


title: RIL_#_65

description: Raw data - Cy5: AS_253671710026_S01_CGH_107_Sep09_1_2.txt


title: Control_rep1

description: gene expression from wild type S2 cells


title: RIL_#_58

description: Raw data - Cy5: AS_253671710025_S01_CGH_107_Sep09_1_4.txt


title: ROW_RNAi_rep3

description: gene expression from ROW RNAi S2 cells


title: mRNA Jasp3

description: Primary Cells


title: RIL_#_52

description: Raw data - Cy3: AS_253671710025_S01_CGH_107_Sep09_1_4.txt


title: 3504_Sunit sheep DNA

tag: gender

tag: tissue

tag: weaning weight (kg)

tag: 6-month weight (kg)


title: RIL_#_56

description: Raw data - Cy5: AS_253671710025_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_50

description: Raw data - Cy3: AS_253671710025_S01_CGH_107_Sep09_1_3.txt


title: Human skeletal muscle at after high fat diet in low responder group_LR5

city: bunkyo-ku

first: saori

last: kakehi

state: Tokyo

address: 2-1-1 hongo

department: Graduated shool of medicine

country: Japan

institute: Juntendo University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ onGeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000（Affymetrix 00-0074）.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) .

source_name: Vastus lateralis muscle after high fat diet

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

extract_protocol: Total RNA extraction was performed with Lipid tissue mini kit（Qiagen) according to the manufacturer's instructions.

tag: subject group

value: low responder group

tag: Sex

tag: time point

value: after (post) 3days high fat diet

value: skeletal muscle


title: RIL_#_54

description: Raw data - Cy5: AS_253671710025_S01_CGH_107_Sep09_1_2.txt


title: mRNA Jasp2

description: Primary Cells


title: RIL_#_49

description: Raw data - Cy3: AS_253671710025_S01_CGH_107_Sep09_1_2.txt


title: Genes regulation by sMaf (MafG and MafK) in the lens [C1 (Control sample 1)]


title: mRNA Ctrl4

description: Primary Cells

source_name: Aortic smooth muscle cells_control


title: Human skeletal muscle at after high fat diet in low responder group_LR4


title: mRNA Jasp1

description: Primary Cells


title: RIL_#_53

description: Raw data - Cy5: AS_253671710025_S01_CGH_107_Sep09_1_1.txt


title: mRNA Ctrl3

description: Primary Cells


title: Human skeletal muscle at before high fat diet in low responder group_LR5

source_name: Vastus lateralis muscle before high fat diet

value: before (pre) 3days high fat diet


title: Human skeletal muscle at before high fat diet in low responder group_LR4


title: Human skeletal muscle at after high fat diet in low responder group_LR3


title: mRNA Ctrl1

description: Primary Cells


title: RIL_#_48

description: Raw data - Cy3: AS_253671710025_S01_CGH_107_Sep09_1_1.txt


title: mRNA Ctrl2

description: Primary Cells


title: RIL_#_47

description: Raw data - Cy5: AS_253671710024_S01_CGH_107_Sep09_1_4.txt


title: 177_Sunit sheep DNA

tag: fat thickness (cm)

tag: eye muscle area (cm2)

tag: height at withers (cm)

tag: chest girth (cm)

tag: shin circumference (cm)

tag: pre-weaning gain(kg)

tag: post-weaning gain (kg)


title: Human skeletal muscle at before high fat diet in low responder group_LR3


title: 263 STAT1_#4_Fat_Pad

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Affymetrix microarray gene expression profiling data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Mouse Gene 1.0 Sense Target (ST) Arrays using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol  FS450_0001

data_processing: Data were processed using GeneSpring GX 12.0 software.  Microarray probe intensity values (CEL files) were background-corrected, summarized, and normalized using the Robust Multi-array Average (RMA16) algorithm (Irizarry et al., 2003) and filtered on raw intensity values for probe sets that exceeded a threshold of >38.  Comparison analysis was performed to identify genes that were differentially expressed (≥1.5-fold) between the #4 fat pads of Stat1 KO and wild-type mice.  Data were processed using GeneSpring GX 12.0 software.

source_name: mammary gland

label_protocol: Biotinylated sense strand DNA targets were prepared from 100 ng total RNA using the Ambion WT Expression and Affymetrix GeneChip WT Terminal Labeling Kits according to the standard manufacturers’ protocols

growth_protocol: Mammary glands from WT or Stat1-null mice were removed and prepared for microarray analysis

extract_protocol: Total RNA was isolated from flash-frozen mammary glands using the TRIzol reagent (Life Technologies) and a modified protocol that incorporates a second extraction with acid phenol/chloroform/isoamyl alcohol (25:24:1, pH 4.3).

treatment_protocol: There was no treatment protocol

tag: strain


title: RIL_#_46

description: Raw data - Cy5: AS_253671710024_S01_CGH_107_Sep09_1_3.txt

source_name: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14

tag: strain/line


title: RIL_#_40

description: Raw data - Cy3: AS_253671710024_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_44

description: Raw data - Cy5: AS_253671710024_S01_CGH_107_Sep09_1_2.txt


title: 129WT_#4_Fat_Pad


title: Human skeletal muscle at before high fat diet in low responder group_LR2


title: RIL_#_43

description: Raw data - Cy5: AS_253671710024_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_39

description: Raw data - Cy3: AS_253671710024_S01_CGH_107_Sep09_1_2.txt

source_name: F7 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Human skeletal muscle at after high fat diet in low responder group_LR2


title: Human skeletal muscle at before high fat diet in high responder group_HR5

value: high responder group


title: RIL_#_42

description: Raw data - Cy3: AS_253671710024_S01_CGH_107_Sep09_1_4.txt


title: 263 STAT1_#2_Fat_Pad


title: 129WT_#2_Fat_Pad


title: RIL_#_37

description: Raw data - Cy3: AS_253671710024_S01_CGH_107_Sep09_1_1.txt


title: Mouse embryonic fibroblast- line B (MEF16), (-)Tamoxifen (PKM2 expressing) [R14-726-WJI 6]

city: East Lansing

first: Sophia

middle: Y

last: Lunt

state: MI

address: Biomed Phys Sci Rm 2120, 567 Wilson Rd

institute: Michigan State University

description: Gene expression data from mouse mammary tumor tissue.

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse 430A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara,

data_processing: The data were analyzed using Stratagene's ArrayAssist Enterprise using Affymetrix default analysis settings.

source_name: Mouse embryonic fibroblast

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

growth_protocol: Animal use and husbandry was in accordance with institutional and federal guidelines.

extract_protocol: Total RNA from mouse mammary tumors was extracted using the Qiagen RNeasy Midi kit.

tag: genotype/variation

value: (-)Tamoxifen (PKM2 expressing)


title: Mouse embryonic fibroblast- line A (MEF10), (+)Tamoxifen (PKM1 expressing) [R14-724-WJI 4]

value: (+)Tamoxifen (PKM1 expressing)


title: Human skeletal muscle at after high fat diet in high responder group_HR3

value: male


title: Human skeletal muscle at after high fat diet in high responder group_HR5


title: Mouse embryonic fibroblast- line B (MEF16), (+)Tamoxifen (PKM1 expressing) [R14-727-WJI 7]


title: Human skeletal muscle at after high fat diet in low responder group_LR1


title: Human skeletal muscle at before high fat diet in low responder group_LR1


title: Human skeletal muscle at after high fat diet in high responder group_HR4


title: Mouse embryonic fibroblast- line B (MEF16), (-)Tamoxifen (PKM2 expressing) [R14-725-WJI 5]


title: Mouse embryonic fibroblast- line A (MEF10), (+)Tamoxifen (PKM1 expressing) [R14-723-WJI 3]


title: Human skeletal muscle at before high fat diet in high responder group_HR4


title: RIL_#_36

description: Raw data - Cy5: AS_253671710023_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_31

description: Raw data - Cy3: AS_253671710023_S01_CGH_107_Sep09_1_3.txt


title: Human skeletal muscle at before high fat diet in high responder group_HR3


title: Human skeletal muscle at after high fat diet in high responder group_HR2


title: RIL_#_29

description: Raw data - Cy3: AS_253671710023_S01_CGH_107_Sep09_1_2.txt

value: F7 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: Human skeletal muscle at before high fat diet in high responder group_HR2


title: RIL_#_34

description: Raw data - Cy5: AS_253671710023_S01_CGH_107_Sep09_1_2.txt


title: Mouse embryonic fibroblast- line A (MEF10), (-)Tamoxifen (PKM2 expressing) [R14-722-WJI 2]


title: RIL_#_33

description: Raw data - Cy5: AS_253671710023_S01_CGH_107_Sep09_1_1.txt


title: Mdr2-KO/IL6-KO BIL206

city: Jerusalem

first: Jonathan

middle: Hillel

last: Axelrod

department: Gene Therapy

institute: Hadassah Medical School

hyb_protocol: Whole genome gene expression profiling of RNA samples was performed using Affymetrix GeneChip® Mouse Gene 1.0 ST (Affymetrix, Santa Clara, CA).

data_processing: The raw data were processed by the Partek® Genomics Suite™ (Partek GS) (Partek Inc., St. Louis, MO) software. RMA algorithm was applied for summarization. Probeset intensities where transformed to logarithmic scale.

source_name: Mouse liver, IL-6 deficient Mdr2-KO tumor free tissue, 14 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: All mice were maintained in an animal facility at a temperature of ~23° C in a 12-hour light-dark cycle, under SPF conditions as assessed by regular microbiological screening. The mice received sterile commercial rodent chow and water ad libitum, and were acclimated for at least 4 days prior to use. Procedures and maintenance were performed in accordance with the Institutional Animal Care and Use Committee approved animal treatment protocols.

extract_protocol: RNA samples were prepared from approximately 100 mg snap-frozen tissue by homogenization in Trizol Reagent (Invitrogen, Carlsbad, California, USA), according to the manufacturer's instructions using a Polytron high-speed homogenizer, followed by treatment with DNA-free Dnase (Applied Biosystems, Foster City, California, USA).

tag: age

value: 14 months

tag: gender

value: female


title: Mouse embryonic fibroblast- line B (MEF16), (+)Tamoxifen (PKM1 expressing) [R14-728-WJI 8]


title: Mdr2-KO/IL6-KO BIL205


title: RIL_#_28

description: Raw data - Cy3: AS_253671710023_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_35

description: Raw data - Cy5: AS_253671710023_S01_CGH_107_Sep09_1_3.txt


title: Human skeletal muscle at before high fat diet in high responder group_HR1

tag: tissue


title: Mdr2-KO/IL6-KO BIL237


title: Human skeletal muscle at after high fat diet in high responder group_HR1


title: Mouse embryonic fibroblast- line A (MEF10), (-)Tamoxifen (PKM2 expressing) [R14-721-WJI 1]


title: IFNG.pos.Treg.expanded.rep5

city: SAN FRANCISCO

first: GAURAV

last: CHOPRA

address: 513 PARNASSUS AVE, HSW 1102

department: DIABETES CENTER

institute: UNIVERSITY OF CALIFORNIA - SAN FRANCISCO (UCSF)

hyb_protocol: GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix) were hybridized by Pfizer to 5 μg labeled, amplified cDNA, washed, stained, and scanned according to the protocol described in the GeneChip Expression analysis manual (Affymetrix).

scan_protocol: Scanning protocol was performed according to the protocol described in the GeneChip Expression analysis manual (Affymetrix).

data_processing:
Gene expression profiling data was extracted from the Affymetrix Microarray Suite 5.0 (MAS 5.0) software and R/Bioconductor package was used for QC of microarray data. The data was processed using MAS5 (Affymetrix) with a trimmed mean value scaled to 100. Fresh samples and expanded samples were then further normalized separately by lowess method, using each group median as the respective baseline reference and a fraction parameter of 10%. A filter was applied to remove the poorly detected probe sets. To be retained for further analysis, a probe set had to be expressed at an average value of 20 or more and have a detection p-value less than 0.065 in 80% of the samples of any one group. This filter resulted in 23,805 retained probe sets.
Lowess normalized expression signal is provided in the sample data table for each sample replicate with MAS5 detection p-value.

label_protocol: For each sample, 25 ng total RNA were amplified using the Ovation® Pico WTA System (NuGen) and labeled  with Encore Biotin Module V2 (NuGen).

growth_protocol: Human Treg and Tconv were FACS isolated from blood samples of five healthy subjects and divided in two groups: first set was treated immediately, second set was subjected to a 14 day expansion protocol before treatment.

extract_protocol: Total RNA was extracted by Pfizer using the RNeasy Micro Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.  RNA quantification was done using a Nanodrop Spectrophotometer 2000 (Thermo Fisher Scientific) and the quality was confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: Both fresh and expanded cells were stimulated for 4 hours with PMA/ionomycin and labeled with the IFNg cytokine capture kit (Miltenyi Biotech) followed by FACS isolation of IFNg- and IFNg+ populations, which were pelleted and flash frozen before RNA isolation and processing.

tag: subject id

tag: subject status

value: healthy

tag: subject age range

value: blood

tag: cell type

value: CD4+CD127-CD25+ Treg

tag: treatment group

value: 14 day expansion

tag: cell subpopulation

value: IFNg positive


title: RIL_#_26

description: Raw data - Cy5: AS_253671710022_S01_CGH_107_Sep09_1_3.txt

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: RIL_#_22

description: Raw data - Cy3: AS_253671710022_S01_CGH_107_Sep09_1_4.txt


title: IFNG.pos.Treg.expanded.rep3


title: Mdr2-KO BIL192

source_name: Mouse liver, Mdr2-KO tumor free tissue, 14 months


title: IFNG.pos.Treg.expanded.rep4


title: Mdr2-KO/IL6-KO BIL200


title: Mdr2-KO BIL170


title: IFNG.pos.Treg.expanded.rep2


title: RIL_#_27

description: Raw data - Cy5: AS_253671710022_S01_CGH_107_Sep09_1_4.txt


title: IFNG.neg.Treg.expanded.rep5

value: IFNg negative


title: RIL_#_170

description: Raw data - Cy5: AS_253671710022_S01_CGH_107_Sep09_1_2.txt


title: IFNG.neg.Treg.expanded.rep4


title: RIL_#_24

description: Raw data - Cy5: AS_253671710022_S01_CGH_107_Sep09_1_1.txt


title: Mdr2-KO/IL6-KO BIL189


title: Mdr2-KO BIL104


title: RIL_#_19

description: Raw data - Cy3: AS_253671710022_S01_CGH_107_Sep09_1_1.txt


title: Wild Type W2

description: Wild Type

source_name: Mouse liver, wild type control, 14 months

value: wild type


title: Mdr2-KO/IL6-KO BIL236


title: IFNG.neg.Treg.expanded.rep2


title: RIL_#_17

description: Raw data - Cy5: WIS_253671710021_S01_CGH_107_Sep09_1_3.txt


title: IFNG.neg.Tconv.expanded.rep3

value: CD4+CD127+CD25- Tconv


title: IFNG.pos.Treg.expanded.rep1


title: RIL_#_21

description: Raw data - Cy3: AS_253671710022_S01_CGH_107_Sep09_1_3.txt


title: IFNG.neg.Treg.expanded.rep3


title: Mdr2-KO BIL112


title: IFNG.neg.Tconv.expanded.rep4


title: Mdr2-KO BIL111


title: IFNG.neg.Tconv.expanded.rep5


title: RIL_#_12

description: Raw data - Cy3: WIS_253671710021_S01_CGH_107_Sep09_1_2.txt


title: RIL_#_16

description: Raw data - Cy5: WIS_253671710021_S01_CGH_107_Sep09_1_2.txt


title: Mdr2-KO/IL6-KO BIL165

hyb_protocol: Whole genome gene expression profiling of RNA samples was performed using Affymetrix GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

value: liver


title: RIL_#_15

description: Raw data - Cy5: WIS_253671710021_S01_CGH_107_Sep09_1_1.txt


title: Wild Type W3

description: Wild Type


title: Mdr2-KO/IL6-KO BIL99


title: RIL_#_11

description: Raw data - Cy3: WIS_253671710021_S01_CGH_107_Sep09_1_1.txt


title: RIL_#_32

description: Raw data - Cy3: AS_253671710023_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_10

description: Raw data - Cy5: WIS_253671710020_S01_CGH_107_Sep09_1_4.txt


title: Mdr2-KO BIL169


title: Mdr2-KO/IL6-KO BIL204


title: Mdr2-KO/IL6-KO BIL101


title: RIL_#_9

description: Raw data - Cy5: WIS_253671710020_S01_CGH_107_Sep09_1_3.txt


title: IFNG.neg.Tconv.expanded.rep1


title: RIL_#_4

description: Raw data - Cy3: WIS_253671710020_S01_CGH_107_Sep09_1_3.txt


title: RIL_#_5

description: Raw data - Cy3: WIS_253671710020_S01_CGH_107_Sep09_1_4.txt


title: RIL_#_8

description: Raw data - Cy5: WIS_253671710020_S01_CGH_107_Sep09_1_2.txt


title: IFNG.neg.Tconv.expanded.rep2


title: IFNG.pos.Tconv.expanded.rep1


title: IFNG.pos.Tconv.expanded.rep3


title: IFNG.neg.Treg.expanded.rep1


title: Wild Type W9


title: Wild Type W7


title: Mdr2-KO BIL154


title: Mdr2-KO BIL168


title: RIL_#_3

description: Raw data - Cy3: WIS_253671710020_S01_CGH_107_Sep09_1_2.txt


title: Wild Type W1

description: Wild Type


title: IFNG.pos.Tconv.fresh.rep4

value: fresh


title: RIL_#_7

description: Raw data - Cy5: WIS_253671710020_S01_CGH_107_Sep09_1_1.txt


title: IFNG.pos.Tconv.fresh.rep2


title: IFNG.pos.Tconv.fresh.rep3


title: Wild Type W10


title: IFNG.pos.Tconv.expanded.rep2


title: RIL_#_1

description: Raw data - Cy3: WIS_253671710020_S01_CGH_107_Sep09_1_1.txt


title: IFNG.pos.Tconv.fresh.rep5


title: shMFNG 49-5

city: Jackson

first: Keli

last: Xu

state: MS

address: 2500 N. State St.

department: Cancer Institute

institute: University of Mississippi Medical Center

description: RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hours at 45°C on HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with gene level RMA sketch default analysis settings as normalization method using Affymetrix Expression Console.

label: Biotin

source_name: shMFNG

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit,  2012, Affymetrix).

growth_protocol: Xenograft tumors were generated by injecting a total of 1 x 10^6 MDA-MB231 cells mixed with Matrigel into the mammary fat pad in ICR/SCID mice at 4 wk of age. Tumors were collected  after 8 wks.

extract_protocol: Total RNA was extracted from xenografts using RNeasy Mini Kit (Qiagen)

value: MDA-MB231 cell xenograft tumor

tag: treatment

value: shMFNG


title: shMFNG 49-2


title: shMFNG 49-1


title: IFNG.pos.Tconv.fresh.rep1


title: IFNG.pos.Tconv.expanded.rep5


title: 9930_rep5

description: Raw data - Cy5: AS_253671710014_S01_CGH_107_Sep09_1_3.txt

source_name: `Chinese Long` inbred line 9930

value: `Chinese Long` inbred line 9930


title: Mdr2-KO BIL76

value: male


title: IFNG.neg.Tconv.fresh.rep4


title: F1_rep5

description: Raw data - Cy5: AS_253671710014_S01_CGH_107_Sep09_1_4.txt

source_name: F1 progeny of a cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: shCtrl 13-4

source_name: shCtrl

value: shCtrl


title: IFNG.neg.Tconv.fresh.rep1


title: GY14_rep5

description: Raw data - Cy3: AS_253671710014_S01_CGH_107_Sep09_1_3.txt

source_name: North American pickling GY14

value: North American pickling GY14


title: CCR2-pos-3

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

hyb_protocol: According to the manufacturer's instructions (Affymetrix)

data_processing: R/Bioconductor, RMA. These six CEL files were normalized as part of a larger batch, so separate normalization may yield slightly different results.

source_name: FACS-sorted CCR2+ HSC

label_protocol: 5 ng of total RNA per sample were used as input to the Ovation Pico WTA System V2 (NuGEN)

extract_protocol: Arcturus PicoPure RNA extraction kit (Applied Biosystems)

value: hematopoietic stem cells (HSC)

tag: cell population

value: CCR2+ HSC


title: IFNG.neg.Tconv.fresh.rep2

value: healthy

value: blood


title: shCtrl 13-1


title: Total 3

first: Christer

last: Larsson

address: Medicon Village, Bldg 404:C3

department: Laboratory Medicine

institute: Lund university

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 47C on GeneChip Human Gene 1.0 ST array in GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

source_name: breast cancer

label_protocol: Biotinylated cDNA were prepared according to the SensationPlus FFPE Affymetrix protocol from approximately 100 ng total RNA (SensationPlus FFPE Amplification and WT labeling kit User guide, 2012, Affymetrix).

extract_protocol: Qiagen AllPrep DNA/RNA FFPE kit

value: Total tumor


title: Stroma 3

value: Stroma


title: CCR2-pos-2

scan_protocol: According to the manufacturer's instructions (Affymetrix)


title: IFNG.neg.Tconv.fresh.rep5

value: IFNg negative


title: 9930_rep6

description: Raw data - Cy3: AS_253671710014_S01_CGH_107_Sep09_1_4.txt

hyb_protocol: Standard Agilent CGH hybridization protocol


title: shCtrl 13-5


title: RIL_#_20

description: Raw data - Cy3: AS_253671710022_S01_CGH_107_Sep09_1_2.txt

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: F1_rep4

description: Raw data - Cy5: AS_253671710014_S01_CGH_107_Sep09_1_2.txt

value: F1 progeny of a cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: IFNG.neg.Tconv.fresh.rep3

value: CD4+CD127+CD25- Tconv


title: IFNG.pos.Treg.fresh.rep5

value: CD4+CD127-CD25+ Treg

value: fresh

value: IFNg positive


title: 9930_rep4

description: Raw data - Cy3: AS_253671710014_S01_CGH_107_Sep09_1_2.txt

value: `Chinese Long` inbred line 9930


title: IFNG.pos.Treg.fresh.rep4


title: CCR2-pos-1


title: GY14_rep4

description: Raw data - Cy5: AS_253671710014_S01_CGH_107_Sep09_1_1.txt


title: 9930_rep3

description: Raw data - Cy5: AS_253671710013_S01_CGH_107_Sep09_1_4.txt


title: F1_rep3

description: Raw data - Cy3: AS_253671710014_S01_CGH_107_Sep09_1_1.txt


title: GY14_rep3

description: Raw data - Cy3: AS_253671710013_S01_CGH_107_Sep09_1_4.txt


title: Cancer Cells 3

value: Cancer cells


title: 9930_rep2

description: Raw data - Cy5: AS_253671710013_S01_CGH_107_Sep09_1_3.txt


title: Total 2


title: IFNG.pos.Treg.fresh.rep3


title: CCR2-neg-3

source_name: FACS-sorted CCR2- HSC

value: CCR2- HSC


title: IFNG.pos.Treg.fresh.rep2


title: CCR2-neg-2


title: GY14_rep2

description: Raw data - Cy3: AS_253671710013_S01_CGH_107_Sep09_1_3.txt

value: North American pickling GY14


title: CCR2-neg-1

value: hematopoietic stem cells (HSC)


title: F1_rep2

description: Raw data - Cy5: AS_253671710013_S01_CGH_107_Sep09_1_2.txt


title: non-Diabetic Foot Skin 03 gene expression profile

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

description: NFS 03

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
The data were analyzed with Affymetrix transcriptome analysis software using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: non-Diabetic Foot skin

label_protocol: standard Affymetrix protocol

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

value: healthy non-diabetic foot skin (NFS)


title: IFNG.pos.Treg.fresh.rep1

value: healthy


title: Cancer Cells 1


title: IFNG.neg.Treg.fresh.rep2

value: blood


title: IFNG.neg.Treg.fresh.rep3


title: Total 1

value: Total tumor


title: scrambled shRNA_3

city: Vienna

first: Robin

last: Ristl

address: Spitalgasse 23

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix, according to manufacturers protocols (Affymetrix, Santa Clara, CA, USA, https://www.affymetrix.com)

scan_protocol: Affymetrix 3000, Software Command Console

data_processing: Statistical analyses were performed with R-Bioconductor. Data was normalized using R-Bioconductor function RMA.

source_name: MEC-1 cell line

label_protocol: Affymetrix WT labeling kit (Biotin)

growth_protocol: RPMI 10%FCS, no phenol red, no antibiotics

extract_protocol: Trizol (Invitrogen) and subsequent RNeasy mini kit (Qiagen)

treatment_protocol: lentiviral shRNA transfection

tag: cell line

value: scrambled shRNA


title: Cancer Cells 2


title: 9930_rep1

city: Rishon Le-Zion

first: Ron

last: Ophir

institute: Agricultural Research Organization - the Volcani Center

description: Raw data - Cy3: AS_253671710013_S01_CGH_107_Sep09_1_2.txt

data_processing:
1. Quantile normalization was applied between all channels accross all arrays. , 2. Removing spatial slide defects, e.g., scratches, bubbles, etc. was performed as follows: The spatial effect on probe density was identified by the method decribed in Chai et al. [BMC Bioinformatics 2010, 11:356], and probes with spatial effect beyond median ±8mad were considered outliers. If 0.2 or more of the probes within 3 points away from some probe were outliers, the probe in the center was also considred an outlier. , 3. Subtracting each probe by its median to normalize between probes. , 4. Four probes were designed per SNP. Two probes, as replicates, for each allele, one replicate probe designed to detect the forward and the other the reverse DNA strand. We Averaged over allele probe replicates (forward and reverse) by ‘medianpolish’ method on a matrix of replicates x arrays to remove the array effect .
matrix.txt: Average over the plus and minus strand probes normalized value for each SNP allele.

label_protocol: Standard Agilent CGH label protocol

extract_protocol: not provided


title: IFNG.pos.Tconv.expanded.rep4

value: 14 day expansion


title: Stroma 2

value: Stroma


title: IFNG.neg.Treg.fresh.rep4

value: IFNg negative


title: GY14_rep1

description: Raw data - Cy5: AS_253671710013_S01_CGH_107_Sep09_1_1.txt


title: Stroma 1


title: scrambled shRNA_2


title: RIL_#_13

description: Raw data - Cy3: WIS_253671710021_S01_CGH_107_Sep09_1_3.txt

value: F8 RIL from the cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: F1_rep1

description: Raw data - Cy3: AS_253671710013_S01_CGH_107_Sep09_1_1.txt

value: F1 progeny of a cross between `Chinese Long` inbred line 9930 and North American pickling GY14


title: IFNG.neg.Treg.fresh.rep5

value: CD4+CD127-CD25+ Treg

value: fresh


title: non-Diabetic Foot Skin 02 gene expression profile

description: NFS 02


title: Diabetic Foot Skin 03 gene expression profile

description: DFS 03

source_name: Diabetic Foot skin

value: non-ulcerated non-neuropathic diabetic foot skin (DFS)


title: T-ALL_1123

status: Public on Apr 30 2015

city: Paris

first: Andre

last: Bortolini Silveira

address: 26 rue d'Ulm

institute: Institut Curie

description: Diagnostic T-ALL sample

hyb_protocol: Samples were hybridized on the GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Inc.), according to the manufacturer's instructions. Arrays were washed and stained with the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000, according to the manufacturer's instructions.

data_processing: Arrays were normalized and expression values were obtained with the default transcript level iterPLIER algorithm of the Affymetrix Expression Console software.

source_name: Bone marrow mononuclear cells obtained from patient with newly diagnosed T-ALL

label_protocol: Samples were processed with the WT Expression Kit (Ambion, Inc., Austin, TX, USA) and GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Inc., Santa Clara, CA, USA), according to the manufacturer's instructions.

growth_protocol: Mononuclear cells were ficoll-isolated from diagnostic bone marrow samples of T-ALL patients.

extract_protocol: RNA was extracted with the Illustra RNAspin Mini RNA Isolation Kit (GE Healthcare, Little Chalfont, UK), according to the manufacturer's instructions.

treatment_protocol: Five million primary T-ALL cells were preserved in 150 µL of thiocyanate solution at -70ºC until use.

value: Bone marrow mononuclear cells

tag: il7r mutational status

value: Wild type

tag: age (years)

value: Male

tag: wbc at diagnosis (cells/mm3)

tag: induction failure

value: Remission

tag: relapse

value: No Relapse


title: T-ALL_1106

description: Diagnostic T-ALL sample


title: T-ALL_1260

description: Diagnostic T-ALL sample


title: IFNG.neg.Treg.fresh.rep1

value: healthy


title: T-ALL_0797

description: Diagnostic T-ALL sample


title: T-ALL_1493

description: Diagnostic T-ALL sample

value: Induction failure


title: non-Diabetic Foot Skin 01 gene expression profile

description: NFS 01

value: healthy non-diabetic foot skin (NFS)