title: Rrm3 binding wild type 150mM HU 90 minutes from G1 release (related to Figure 1A)

description: RRM3-MYC cells were arrested in G1 and released in 150 mM of HU.Rrm3 binding profiles have been determined at 90 minutes from the G1  release.

source_name: WT Rrm3 binding 90 min 150mM HU

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, RRM3-13MYC-KANMX6 (W303 derivative RAD5 locus wild type)


title: Control neutrophil rep3

status: Public on Sep 24 2015

type: RNA

city: Bronx

first: Dachuan

last: Zhang

state: NY

address: 1301 Morris Park Avenue, Price Center 113

department: Cell Biology

country: USA

institute: Albert Einstein College of Medicine

description: gene expression data from neutrophils with CD45.1 allele

hyb_protocol: Labeled cRNA was hybridized to Mouse Gene ST 1.0 microarrays (Affymetrix).

scan_protocol: Gene chips were scanned by GeneChip Scanner 3000 7G system (Affymetrix).

data_processing: Raw data were normalized by RMA algorithm and analysed using the Gene Pattern analysis platform (Broad Institute).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: neutrophils 10 min after adoptive transfer

label_protocol: Amplified cRNA was labelled with the GeneChip WT terminal labelling kit (Affymetrix).

growth_protocol: Control and aged neutrophils were derived by adoptive transfer for 10 min and 6 h, respectively. Activated neutrophils were harvested from mice injected with 0.5 μg TNF-α for 2 hours.

extract_protocol: Total RNA from sorted neutrophils was extracted using RNeasy Plus Micro Kit (Qiagen). RNA was amplified using Ovation One-Direct System (NuGEN).

treatment_protocol: 2000 neutrophils were directly sorted from mouse blood using fluorescence-activated cell sorting (FACS).

tag: tissue

value: Blood

tag: cell type

value: neutrophil

tag: treatment

value: control


title: STANB7pol

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description:
mRNA profiling
STANB7pol
polysomal gene expression profiling

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2565BA

data_processing: The scanned images were analyzed with FeatureExtractor. Intensity values were then processed with Agi4x44PreProcess using default parameters to remove low-quality probes. Signals where then normalized by means of the quantile normalization method.

organism: Homo sapiens

source_name: Cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: Total RNA was isolated according to the manufacturer protocol by using the RNeasy Mini Kit (Qiagen), then quantified and quality assessed using the RNA 6000 Nano assay on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, United States): a RIN threshold of 7 was used to select samples for the study.  For polysomal profiling, Cells were incubated for 3 min with 0.01 mg/ml cycloheximide at 37°C, then plates were put on ice; media was removed, and cells were washed twice with PBS and cycloheximide 0.01 mg/ml. Cells were lysed with 300 µl of cold lysis buffer (10 mM MgCl2, 10 mM NaCl, 10 mM Tris–HCl pH 7.5,  0.2 U/ml RNase inhibitor (Fermentas, Burlington, CA, United States), 1 mM dithiothreitol, 1% Triton X-100, 1% sodium deoxycholate and 0.01 mg/ml cycloheximide) and scraped. Extracts were centrifuged for 5 min at 12 000g and 4°C. The supernatant was loaded on a 15–50% linear sucrose gradient containing 30 mM Tris–HCl, pH 7.5, 100 mM NaCl and 10 mM MgCl2, and centrifuged on an SW41 rotor for 100 min at 180 000g. Fractions were collected by monitoring absorbance at 254 nm and treated with 0.1 mg/ml proteinase K for 2 hrs at 37°C. RNA was extracted with phenol–chloroform and isopropanol precipitation, suspended in 30 µl of RNAse-free water and purified using the RNeasy kit (Qiagen).

value: Neuroblastoma

tag: cell line

tag: rna fraction

value: polysomal


title: Activated neutrophil rep1

source_name: neutrophils 2 hours after TNF-α injection

value: activated


title: Control neutrophil rep1


title: SKNDZpol

description:
mRNA profiling
SKNDZpol
polysomal gene expression profiling

value: SKNDZ


title: Pol1 binding wild type 150mM HU 90 minutes from G1 release (related to Figure 1A)

type: genomic

city: Milano

first: Michele

last: Giannattasio

state: Italy

address: Via Adamello, 16

department: Genome stability

institute: IFOM

description: POL1-MYC cells were arrested in G1 and released in 150 mM of HU.Pol1 binding profiles have been determined at 90 minutes from the G1  release.

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT Pol1 binding 90 min 150mM HU

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YP+glucose 2% at 28°C

extract_protocol: ssDNA-BrdU-IP on chip profiles were determined as described in (Katou et al 2003). Binding profiles by ChIP on chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G1 synchronization was performed in YP+glucose 2% at 28°C with 4 μg/ml final alpha facfor concentration.G1-arrested cells were released in YP+glucose 2% supplemented either with 150 mM or 25 mM of hydroxyurea (HU).For ChIP on chip binding profiles cells were fixed with 1% Formaldehyde for 30 minutes. For BrdU incorporation profiles cells were released in HU with 200 ug/ml of BrdU and fixed with 0.1% Sodium Azide on ice for 30 minutes at the indicated times.

tag: antibody

value: anti-MYC antibody

tag: strain

tag: genotype

value: MAT a, ade2-1, ura3-1, his3-11,15, leu2-3,112, trp1-1, can1-100, GAL, PSI+, POL1-9MYC-TRP1 (W303 derivative RAD5 locus wild type)

tag: growth protocol

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU).

value: 150 mM hydroxyurea (HU) 90 minutes. Cell were fixed with 1% Formaldehyde for 30 minutes.

source_name: input DNA

tag: sample type

value: input DNA


title: BrdU incorporation rad53-k227a 150mM HU 90 minutes from G1 release (related to Figure 1A)

description: rad53-k227a  cells carrying the TK repeats were arrested in G1 and released in 150 mM of HU with 200 ug/ml of BrdU. BrdU incorporation profiles were determined at 90 minutes from the G1  release.

source_name: rad53-k227a BrdU 90 min 150mM HU

value: anti-BrdU MI-11-3 (MBL)

value: MAT a ade2-1, ura3-1, his3-11,15 leu2-3,112, trp1-1, CAN1, rad53-K227A-KANMX4, ura3::7x-TKs-URA3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU)  and 200ug/ml BrdU.

value: 150 mM hydroxyurea (HU) 90 minutes with 200ug/ml BrdU. Cell were fixed with 0.1% sodium azide 40 minutes in ice.


title: BrdU incorporation wild type 150mM HU 90 minutes from G1 release (related to Figure 1A)

description: wild type cells carrying the TK repeats were arrested in G1 and released in 150 mM of HU with 200 ug/ml of BrdU. BrdU incorporation profiles were determined at 90 minutes from the G1  release.

source_name: WT BrdU 90 min 150mM HU

value: MAT a ade2-1, ura3-1, his3-11,15 leu2-3,112, trp1-1, CAN1, GAL, PSI+, ura3::7x-TKs-URA3 (W303 derivative RAD5 locus wild type)

value: cells were grown in YP+2% glucose, arrested in alpha factor (4ug/ml) for 2h and 15 minutes and released in YP+2% glucose with 150 mM hydroxyurea (HU) and 200ug/ml BrdU.


title: SIMApol

description:
mRNA profiling
SIMApol
polysomal gene expression profiling

value: SIMA


title: STANB1pol

description:
mRNA profiling
STANB1pol
polysomal gene expression profiling


title: STANB10aCGH

description: array-CGH

hyb_protocol: not provided

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2565BA.

data_processing: The scanned images were analyzed with FeatureExtractor  (protocol GE1_107_Sep09 and Grid: 014868_D_F_20120131) . Probes were then processed with limma and MANOR using default parameters to remove low-quality probes. Log2 ratios where then median-centered.

label_protocol: not provided

extract_protocol: Total DNA was isolated according to the manufacturer protocol by using the DNA Blood and Tissue Extraction Kit (Qiagen, Hilde, Germany);


title: LAN1pol

description:
mRNA profiling
LAN1pol
polysomal gene expression profiling


title: SKNBE2pol

description:
mRNA profiling
SKNBE2pol
polysomal gene expression profiling


title: CHP212pol

description:
mRNA profiling
CHP212pol
polysomal gene expression profiling


title: KELLYpol

description:
mRNA profiling
KELLYpol
polysomal gene expression profiling

value: KELLY


title: STANB10pol

description:
mRNA profiling
STANB10pol
polysomal gene expression profiling

value: Neuroblastoma


title: MHHNB11pol

description:
mRNA profiling
MHHNB11pol
polysomal gene expression profiling

value: polysomal


title: 2446WT

city: Hanover

first: Michael

last: Whitfield

state: New Hampshire

address: 710 Remsen 74 College Street

department: Genetics

institute: Geisel School of Medicine at Dartmouth

description: 4-week old female WT mouse

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Mouse Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro

source_name: UMR

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy5

growth_protocol: Fibroblast was maintained in cultural media; skin samples were stored in RNALater prior to RNA extraction

extract_protocol: Fibroblast total RNA was extracted using Clonetech RNA Purification kit; skin total RNA was extracted using Qiagen Rneasy mini fibrous kit

treatment_protocol: Col3a1 knockout mice fibroblast transfected with either WT Col3a1 or Tsk2 Col3a1

value: UMR (universal mouse reference)

source_name: Skin

value: Skin

value: 4-week old female WT mouse

value: WT mouse


title: 2432WT

description: 4-week old female WT mouse


title: 2431WT

description: 4-week old female WT mouse


title: STANB1aCGH

description: array-CGH


title: SKNDZaCGH

description: array-CGH

value: SKNDZ


title: SKNBE2aCGH

description: array-CGH


title: SIMAaCGH

description: array-CGH


title: IMR32pol

description:
mRNA profiling
IMR32pol
polysomal gene expression profiling


title: STANB7aCGH

description: array-CGH


title: CHP134pol

description:
mRNA profiling
CHP134pol
polysomal gene expression profiling


title: CHP126pol

description:
mRNA profiling
CHP126pol
polysomal gene expression profiling


title: 2468Tsk2

description: 4-week old female Tsk2 mouse

value: 4-week old female Tsk2 mouse

value: Tsk2 mouse


title: LAN1aCGH

description: array-CGH


title: STANB10tot

description:
mRNA profiling
STANB10tot
total gene expression profiling

value: total


title: MHHNB11aCGH

description: array-CGH


title: 2465Tsk2

description: 4-week old female Tsk2 mouse


title: 2429WT

description: 4-week old female WT mouse


title: STANB1tot

description:
mRNA profiling
STANB1tot
total gene expression profiling


title: SKNDZtot

description:
mRNA profiling
SKNDZtot
total gene expression profiling


title: STANB7tot

description:
mRNA profiling
STANB7tot
total gene expression profiling


title: 2408Tsk2

description: 4-week old female Tsk2 mouse


title: 2409Tsk2

description: 4-week old female Tsk2 mouse


title: SKNBE2tot

description:
mRNA profiling
SKNBE2tot
total gene expression profiling


title: SIMAtot

description:
mRNA profiling
SIMAtot
total gene expression profiling


title: CHP134aCGH

description: array-CGH


title: Wild Type TF3B

description: Col3a1 knockout fibroblast transfected with WT Col3a1

source_name: Fibroblast

value: Fibroblast

value: Col3a1 knockout

value: transfected with WT Col3a1


title: KELLYtot

description:
mRNA profiling
KELLYtot
total gene expression profiling


title: Tsk2 TF2

description: Col3a1 knockout fibroblast transfected with Tsk2 Col3a1

value: transfected with Tsk2 Col3a1


title: White Sector of red/white sectored colony 34 from KO_132_29

status: Public on Sep 23 2015

city: Durham

first: Karen

middle: Eileen

last: O'Connell

state: NC

address: Box 3054 DUMC

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing:
The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes.”
In the labels of the oligonucleotides “SF”, “SR”, “YF” and “YR” refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. “S” and “Y” indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. “F” and “R” indicate whether the orientation (5’ to 3’) is identical to the orientation in SGD (“F” standing for forward) or opposite to that shown in SGD (“R” for reverse). Thus, “F” and “R” have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the “F” orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830). The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

label_protocol: The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC23) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Two different growth protocols were used. For sub-cultured strains, single colonies were struck to singles on YPD and grown at 300 for two days. In all mutant strain a single colony was the re-struck to singles again until sub-cultured for 20 cycles. Wild type strains were assayed after 10 cycles.

extract_protocol: We purified single colonies derived from each sector or a single colony from the sub-cultured strain and prepared DNA by standard procedures (St. Charles et al., 2012).

treatment_protocol: No treatment was applied to these cells. Spontaneous events were assayed.

tag: colony color

value: White

tag: growth condition

value: Spontaneous red/white sector

source_name: JSC23 grown at 30 degrees

value: pink


title: Red Sector of red/white sectored colony 34 from KO_132_29

value: Red


title: Wild Type TF3A

value: Col3a1 knockout fibroblast transfected with WT Col3a1


title: IMR32aCGH

description: array-CGH

value: Neuroblastoma


title: KELLYaCGH

description: array-CGH

value: KELLY


title: White Sector of red/white sectored colony 24 from KO_132_29


title: IMR32tot

description:
mRNA profiling
IMR32tot
total gene expression profiling


title: LAN1tot

description:
mRNA profiling
LAN1tot
total gene expression profiling


title: MHHNB11tot

description:
mRNA profiling
MHHNB11tot
total gene expression profiling


title: Red Sector of red/white sectored colony 24 from KO_132_29


title: Red Sector of red/white sectored colony 18 from KO_132_29


title: White Sector of red/white sectored colony 18 from KO_132_29


title: White Sector of red/white sectored colony 3 from KO_132_29


title: Red Sector of red/white sectored colony 7 from KO_132_29


title: White Sector of red/white sectored colony 7 from KO_132_29


title: CHP212tot

description:
mRNA profiling
CHP212tot
total gene expression profiling


title: Wild Type TF1

value: UMR (universal mouse reference)


title: White Sector of red/white sectored colony 24 from KO_132_31


title: Red Sector of red/white sectored colony 3 from KO_132_29


title: Red Sector of red/white sectored colony 24 from KO_132_31


title: Tsk2 TF1

value: Col3a1 knockout fibroblast transfected with Tsk2 Col3a1


title: CHP126tot

description:
mRNA profiling
CHP126tot
total gene expression profiling


title: CHP134tot

description:
mRNA profiling
CHP134tot
total gene expression profiling


title: CHP212aCGH

description: array-CGH


title: Red Sector of red/white sectored colony 22 from KO_132_31


title: White Sector of red/white sectored colony 22 from KO_132_31


title: Red Sector of red/white sectored colony 21 from KO_132_31


title: White Sector of red/white sectored colony 15 from KO_132_31


title: White Sector of red/white sectored colony 21 from KO_132_31


title: Red Sector of red/white sectored colony 17 from KO_132_31


title: White Sector of red/white sectored colony 17 from KO_132_31


title: Red Sector of red/white sectored colony 15 from KO_132_31


title: White Sector of red/white sectored colony 6 from KO_132_31


title: Red Sector of red/white sectored colony 2 from KO_132_31


title: White Sector of red/white sectored colony 8 from KO_132_31


title: Red Sector of red/white sectored colony 6 from KO_132_31


title: Colony of sub-cultured KO_5_9_J rnh1Δ rnh201Δ mutant strain after ~500 cell divisions

source_name: KO_5_9 subcutlured twenty times

value: Subcultured for ~500 cell divisions


title: Colony of sub-cultured KO_5_9_E rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_I rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_H rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_L rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Red Sector of red/white sectored colony 8 from KO_132_31


title: Colony of sub-cultured KO_5_9_a rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_D rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_c rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_b rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_K rnh1Δ rnh201Δ mutant strain after ~500 cell divisions

source_name: KO_5_6 subcultured twenty times


title: Colony of sub-cultured KO_5_9_G rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_L rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_J rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: White Sector of red/white sectored colony 2 from KO_132_31


title: Colony of sub-cultured KO_5_6_H rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_G rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_F rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_E rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_c rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_b rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_9_F rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_a rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_G rnh201Δ pol2-M644L mutant strain after ~500 cell divisions

source_name: KO_244_2 subcultured twenty times


title: Colony of sub-cultured KO_244_2_XX_D rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_E rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_I rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_C rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_B rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_I rnh201Δ pol2-M644L mutant strain after ~500 cell divisions

source_name: KO_244_1 subcultured twenty times


title: Colony of sub-cultured KO_244_1_XX_J rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_A rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_5_6_D rnh1Δ rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_F rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_C rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_E rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_G rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_2_XX_H rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_D rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_B rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_2_XX_K rnh201Δ mutant strain after ~500 cell divisions

source_name: KO_75_2 subcultured twenty times


title: Colony of sub-cultured KO_75_2_XX_J rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_244_1_XX_H rnh201Δ pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_2_XX_G rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_2_XX_I rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_2_XX_E rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_M rnh201Δ mutant strain after ~500 cell divisions

source_name: KO_75_1 subcultured twenty times


title: Colony of sub-cultured KO_75_2_XX_C rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_2_XX_D rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_K rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_I rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_H rnh201Δ mutant strain after ~500 cell divisions


title: Human KBM7 LaminB1, replicate 2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 50 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. The score was calculated as the log2 Dam-LaminB1: Dam ratio of the normalized data.

source_name: Dam-only DamID DNA

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing Dam or Dam-Lamin B1. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

value: Human KBM7

tag: trasduced with

value: Dam-only contruct

source_name: Dam-LaminB1 DamID DNA

tag: transduced with

value: Dam-Lamn B1 construct


title: Colony of sub-cultured KO_75_1_XX_J rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_136_XX_D pol2-M644L mutant strain after ~500 cell divisions

source_name: KO_234_136 subcultured twenty times


title: Colony of sub-cultured KO_75_1_XX_C rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_E rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_D rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_136_XX_A pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_136_XX_C pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_136_XX_B pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_106_XX_D pol2-M644L mutant strain after ~500 cell divisions

source_name: KO_234_106 subcultured twenty times


title: Colony of sub-cultured KO_75_2_XX_F rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_106_XX_C pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_106_XX_B pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_L rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_44_XX_D pol2-M644L mutant strain after ~500 cell divisions

source_name: KO_234_44 subcultured twenty times


title: Colony of sub-cultured KO_234_44_XX_C pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_44_XX_A pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_234_44_XX_B pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_L rnh1Δ mutant strain after ~500 cell divisions

source_name: KO_73_2 subcultured twenty times


title: Colony of sub-cultured KO_73_2_XX_K rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_75_1_XX_G rnh201Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_I rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_J rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_H rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_F rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_G rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_E rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_73_2_XX_D rnh1Δ mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_198_3_X_I wild type after ~250 cell divisions

source_name: KO_198_3 subcultured ten times


title: Colony of sub-cultured KO_198_3_X_H wild type after ~250 cell divisions


title: Colony of sub-cultured KO_198_2_X_J wild type after ~250 cell divisions

source_name: KO_198_2 subcultured ten times


title: CHP126aCGH

description: array-CGH

source_name: Cell line


title: Colony of sub-cultured KO_198_2_X_I wild type after ~250 cell divisions


title: Colony of sub-cultured KO_234_106_XX_A pol2-M644L mutant strain after ~500 cell divisions


title: Colony of sub-cultured KO_198_2_X_H wild type after ~250 cell divisions


title: Colony of sub-cultured KO_198_2_X_G wild type after ~250 cell divisions


title: Colony of sub-cultured KO_198_1_X_I wild type after ~250 cell divisions

source_name: KO_198_1 subcultured ten times


title: Colony of sub-cultured KO_198_1_X_H wild type after ~250 cell divisions

source_name: JSC23 grown at 30 degrees


title: Colony of sub-cultured KO_198_1_X_G wild type after ~250 cell divisions


title: Colony of sub-cultured KO_73_2_XX_C rnh1Δ mutant strain after ~500 cell divisions


title: Human KBM7 LaminB1, replicate 1


title: Tsk2 TF3

source_name: UMR

source_name: Fibroblast

value: Fibroblast


title: Colony of sub-cultured KO_198_3_X_G wild type after ~250 cell divisions


title: cell line R7 at P19

city: Boston

first: Mary-Lee

last: Dequeant

email: mdequeant@genetics.med.harvard.edu, fagegalt@cshl.edu, Greg.Hannon@cruk.cam.ac.uk, perrimon@receptor.med.harvard.edu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: Gene expression data from cell line R7 at Passage 19

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to the Affymetrix Drosophila Genome 2.0 Array according to the protocols provided by the manufacturer.

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

data_processing: The data were analyzed using dCHIP

organism: Drosophila melanogaster

source_name: Drosophila cell line R7 at Passage 19

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: cells cultured in Schneider's media supplemented with 10% FBS (fetal bovine serum) and antibiotics.

extract_protocol: RNA isolation using All Prep RNA Qiagen.

treatment_protocol: samples were collected from cells cultured in 25 cm2 T flasks

tag: passage


title: cell line R7 at P3

description: Gene expression data from cell line R7 at Passage 3

source_name: Drosophila cell line R7 at Passage 3


title: Huh1_RDBP1

city: Bethesda

first: Hien

middle: T

last: Dang

state: MD

address: 37 Convent Drive

department: CCR

institute: National Insitutes of Health/NCI

description: Gene expression data from HCC Huh1 cells treated with RDBP siRNA for 48hrs

hyb_protocol: Biotin-labeled cDNAs were hybridized overnight to Human HTA 2.0 arrays. Wash and stain of these GeneChip microarrays was carried out under strictly controlled conditions with the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix Scanner.

data_processing: The data were analyzed with Affymetrix® Expression Console™ software version 1.1 using Affymetrix default analysis settings with RMA normalization and general background correction.

source_name: Human HCC Huh1 cells treated with RDBP siRNA for 48hrs

label_protocol: Approximately 100 ng of total RNA were reverse transcribed and labeled by biotin (biotin-labeled cDNA) according to standard Affymetrix protocols used by NCI core facility (LMT/Affymetrix Group, Frederick National Laboratory for Cancer Research, http://atp.ncifcrf.gov/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/microarray/service-details/).

growth_protocol: Hep3B cells were cultured in Minimum Essential Medium (Life Technologies) supplemented with 10% FBS, penicillin, streptomycin and L-glutamine, non-essential amino acids and sodium pyruvate. Huh1 cells were cultured in Dulbecco’s modified Eagle Medium (Life Technologies) supplemented with 10% fetal bovine serum (FBS), penicillin, streptomycin and L-glutamine.

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

treatment_protocol: 3x105 Hep3B cells are plated in quadrupplicates on 6 cm plates and transfected with scr or RDBP siRNA for 48 hours.

value: primary HCC cells


title: Huh1_RDBP3


title: Huh1_scr3

description: Gene expression data from HCC Huh1 cells treated with scrambled siRNA for 48hrs

source_name: Human HCC Huh1 cells treated with scrambled siRNA for 48hrs


title: cell line R7 at P17

description: Gene expression data from cell line R7 at Passage 17

source_name: Drosophila cell line R7 at Passage 17


title: cell line R7 at P8

description: Gene expression data from cell line R7 at Passage 8

source_name: Drosophila cell line R7 at Passage 8


title: Huh1_RDBP2


title: Hep3B_RDBP2

description: Gene expression data from HCC Hep3B cells treated with RDBP siRNA for 48hrs

source_name: Human HCC Hep3B cells treated with RDBP siRNA for 48hrs


title: cell line R7 at P2 rep2

description: Gene expression data from cell line R7 at Passage 2

source_name: Drosophila cell line R7 at Passage 2


title: iRPE_46

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Retinal Pigment Epithelium-like Cells from Human Fibroblasts Clone 46

hyb_protocol: Biotinylated cRNA was hybridized at the Whitehead Institute Genome Technology Core, according to standard Affymetrix protocols.

scan_protocol: Arrays were stained, scanned, and quantified according to standard Affymetrix protocols.

data_processing: A CDF hgu133plus2cdf was used to process the CLE files. The data were analyzed with Bioconductor using the MAS5 normalization method.

source_name: Retinal Pigment Epithelium-like Cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3' IVT Express Kit manual.

growth_protocol: iRPE cells were grown Minimum Essential Medium Eagle Alpha Modification (Sigma Aldrich, # M4526-500ML) base media containing 5% of Tet System Approved Fetal bovine serum (Clontech, # 631101), 1X N1 Medium Supplement (Sigma Aldrich, # N6530), 1% Sodium Pyruvate (Life Technologies, # 11360070), 2mM L-Glutamine (Life Technologies, # 25030-081), 1X MEM Non-Essential Amino Acids (Life Technologies, #11140), 1 mg/ml Geneticin® Selective Antibiotic (Life Technologies, # 10131035), 1/100 Penicillin-Streptomycin (Life Technologies, # 15140163) and THT composed of  20 μg/L hydrocortisone (Sigma Aldrich, # H6909), 250 mg/L taurine (Sigma Aldrich, # T0625), and 0.013 μg/L triiodo-thyronin (Sigma Aldrich, # T2877). Cells were incubated in a 37°C, 5% CO2 humidified incubator.

tag: source cell type

value: Human Fibroblasts Clone 46

value: induced retinal pigment epithelium-like cells


title: iRPE_42

description: Retinal Pigment Epithelium-like Cells from Human Fibroblasts Clone 42

value: Human Fibroblasts Clone 42


title: Hep3B_RDBP1


title: Hep3B_scr2

description: Gene expression data from HCC Hep3B cells treated with scrambled siRNA for 48hrs

source_name: Human HCC Hep3B cells treated with scrambled siRNA for 48hrs


title: cell line R7 at P7

description: Gene expression data from cell line R7 at Passage 7

source_name: Drosophila cell line R7 at Passage 7


title: cell line R7 at P16

description: Gene expression data from cell line R7 at Passage 16

source_name: Drosophila cell line R7 at Passage 16


title: cell line R7 at P4

description: Gene expression data from cell line R7 at Passage 4

source_name: Drosophila cell line R7 at Passage 4


title: Huh1_scr1


title: cell line R7 at P2 rep1


title: MDAMB231.miR_183_5p_plus2_plus2.Replicate3

city: Philadelphia

first: Isidore

last: Rigoutsos

state: PA

address: 1020 Locust Street, Suite M81

department: Sidney Kimmel Medical College

institute: Thomas Jefferson University

description: Gene expression of MDA-MB-231 breast cancer cells after treatment with the miR-183-5p|+2|+2| isomiR

hyb_protocol: Affymetrix gene chips, Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA), were hybridized with 5 μg fragmented and biotin-labeled cDNA in 200 μl of hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Data processing and normalization was performed by Expression Console Software v 1.4.1 using the SST-RMA algorithm.

source_name: MDA-MB-231 breast cancer cells, treatment with the miR-183-5p|+2|+2| isomiR

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was prepared using the GeneChip WT Plus Kit (Affymetrix, Santa Clara, CA) according to manufacturer's in-structions.

growth_protocol: MDA-MB-231 cells were grown in DMEM medium (Fisher Scientific) supplemented with 10% fetal bovine serum (Life Technologies), 1% Penicillin and Strep (Fisher Scien-tific), and 1% glutamine (Fisher Scientific), at 37oC in a humidified atmosphere contain-ing 5% CO2.

extract_protocol: RNA was extracted from the cells using the TRizol reagent (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: The mirVana miRNA mimic for miR-183-5p, the Negative Control #1,  or the two miRVana customized miRNA mimics for the two isomiRs (miR-183-5p|-2|-2|, 5'-TGTATGGCACTGGTAGAATTCA-3' and miR-183-5p|+2|+2|, 5'-TGGCACTGGTAGAATTCACTGT-3')  (Life Technologies) were transfected at a final concentration of 50nM using the Lipofectamine RNAiMAX transfection Reagent (Life Technologies). Transfection was performed for 48h.


title: Hep3B_RDBP3


title: Hep3B_scr3


title: Huh1_scr2


title: Hep3B_scr1


title: MDAMB231.miR_183_5p_plus2_plus2.Replicate1


title: MDAMB231.miR_183_5p_minus2_minus2.Replicate3

description: Gene expression of MDA-MB-231 breast cancer cells after treatment with the miR-183-5p|-2|-2| isomiR

source_name: MDA-MB-231 breast cancer cells, treatment with the miR-183-5p|-2|-2| isomiR


title: MDAMB231.miR_183_5p_minus2_minus2.Replicate1


title: MDAMB231.miR_183_5p_plus2_plus2.Replicate2


title: MDAMB231.miR_183_5p_minus2_minus2.Replicate2


title: cell line R3 at P19

description: Gene expression data from cell line R3 at Passage 19

source_name: Drosophila cell line R3 at Passage 19


title: Red Sector of red/white sectored colony 1 from KO_132_31

value: Spontaneous red/white sector

source_name: JSC23 grown at 30 degrees


title: White Sector of red/white sectored colony 1 from KO_132_31

value: White

value: pink


title: White Sector of red/white sectored colony 17 from KO_135_6


title: Red Sector of red/white sectored colony 17 from KO_135_6

value: Red


title: White Sector of red/white sectored colony 13 from KO_135_6


title: Red Sector of red/white sectored colony 13 from KO_135_6


title: cell line R3 at P16

description: Gene expression data from cell line R3 at Passage 16

source_name: Drosophila cell line R3 at Passage 16


title: cell line R3 at P7

description: Gene expression data from cell line R3 at Passage 7

source_name: Drosophila cell line R3 at Passage 7


title: cell line R3 at P2 rep2

description: Gene expression data from cell line R3 at Passage 2

source_name: Drosophila cell line R3 at Passage 2


title: cell line R3 at P2 rep1


title: cell line R3 at P5

description: Gene expression data from cell line R3 at Passage 5

source_name: Drosophila cell line R3 at Passage 5


title: Red Sector of red/white sectored colony 11 from KO_135_6


title: White Sector of red/white sectored colony 11 from KO_135_6


title: MDAMB231.Control.Replicate1

description: Gene expression of MDA-MB-231 breast cancer cells after control treatment

source_name: MDA-MB-231 breast cancer cells, control treatment

value: control


title: White Sector of red/white sectored colony 9 from KO_135_6


title: cell line R3 at P17

description: Gene expression data from cell line R3 at Passage 17

source_name: Drosophila cell line R3 at Passage 17


title: cell line R3 at P6

description: Gene expression data from cell line R3 at Passage 6

source_name: Drosophila cell line R3 at Passage 6


title: Red Sector of red/white sectored colony 9 from KO_135_6


title: cell line R3 at P8

description: Gene expression data from cell line R3 at Passage 8

source_name: Drosophila cell line R3 at Passage 8


title: MDAMB231.Control.Replicate2


title: MDAMB231.miR_183_5p_0_0.Replicate3

description: Gene expression of MDA-MB-231 breast cancer cells after treatment with the miR-183-5p|0|0| isomiR

source_name: MDA-MB-231 breast cancer cells, treatment with the miR-183-5p|0|0| isomiR


title: MDAMB231.miR_183_5p_0_0.Replicate2


title: MDAMB231.Control.Replicate3


title: No.4 KO pMf(+)

city: Tsukuba

first: Asuka

last: Inoue

state: IBARAKI

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: KO peritoneal macrophage no.1-3 TNFalpha+

hyb_protocol: Cy3-labelled cRNA hybridized to Agilent SuperPrint G3 Mouse GE Microarray (8x60K)  for 17 hrs in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1min at room temperature with GE Wash Buffer 1(Agilent) and 1 min with GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scaned immediately after washing on the Ailent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scaned images were analyzed with Feature Extraction SoftWare (v.10.7.3.1, Agilent).

source_name: peritoneal macrophage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from cRNA using the Genomic Enzymatic Labeling Kit (Agilent) according to the manufacture's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extracted using Rneasy Plus Kit (Quiagen) according to the instructions supplied by the manufacture.

value: TIARP-/-

value: peritoneal cavity


title: No.1 WT pMf

description: WT peritoneal macrophage no.1-3

value: TIARP+/+


title: White Sector of red/white sectored colony 13 from KO_135_5


title: White Sector of red/white sectored colony 12 from KO_135_5


title: Red Sector of red/white sectored colony 5 from KO_135_5


title: White Sector of red/white sectored colony 5 from KO_135_5


title: Red Sector of red/white sectored colony 12 from KO_135_5


title: Red Sector of red/white sectored colony 13 from KO_135_5


title: No.5 WT Ly6G

description: WT neutrophil no.1-3

source_name: splenic neutrophil

value: spleen


title: No.6 KO Ly6G

description: KO neutrophil no.1-3


title: Red Sector of red/white sectored colony 4 from KO_135_5


title: MDAMB231.miR_183_5p_0_0.Replicate1


title: White Sector of red/white sectored colony 4 from KO_135_5


title: No.3 WT pMF(+)

description: WT peritoneal macrophage no.1-3 TNFalpha+


title: Red Sector of red/white sectored colony 1 from KO_135_5


title: Red Sector of red/white sectored colony 2 from KO_135_5


title: White Sector of red/white sectored colony 1 from KO_135_5


title: water-treated ugt76b1, biological replicate 1

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

description:
ugt76b1-Ctrl-R1_ATH1
ugt76b1 mutant expression in the absence of infection

hyb_protocol: Operated by the NASC's International Affymetrix Service

data_processing: Background adjustment, quantile normalization, and summarization of raw data were performed with the Affymetrix Power Tools APT1.14.4 software package.

organism: Arabidopsis thaliana

source_name: A. thaliana ugt76b1 treated with water

growth_protocol: A. thaliana seeds were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.

extract_protocol: In two independent experiments for each line, cotyledons were treated with water, or inoculated with Hpa to establish a compatible interaction. Total RNA was extracted from about 100 mg of these tissues according to a procedure described (Laroche-Raynal et al., Plant Science Letters 35, 139-146,1984).

treatment_protocol: For infection, 10-day-old plants were spray-inoculated to saturation with a spore suspension of 40,000 spores/ml (strain Emwa1)

value: Cotyledons

tag: genetic background

tag: infection

tag: time


title: No.2 KO pMf

description: KO peritoneal macrophage no.1-3

tag: tissue


title: water-treated ugt76b1, biological replicate 2

description:
ugt76b1-Ctrl-R2_ATH1
ugt76b1 mutant expression in the absence of infection

scan_protocol: Operated by the NASC's International Affymetrix Service


title: White Sector of red/white sectored colony 2 from KO_135_5


title: Emwa1 inoculated ugt76b1 at 3 dpi, biological replicate 1

description:
ugt76b1-Hpa-R1_ATH1
ugt76b1 mutant expression after infection

source_name: A. thaliana ugt76b1 Hpa-inoculated

label_protocol: Operated by the NASC's International Affymetrix Service

value: biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis strain Emwa1

value: 3 dpi


title: Emwa1 inoculated ugt76b1 at 3 dpi, biological replicate 2

description:
ugt76b1-Hpa-R2_ATH1
ugt76b1 mutant expression after infection


title: water-treated map65-3, biological replicate 1

description:
map65-3-Ctrl-R1_ATH1
map65-3 mutant expression in the absence of infection

source_name: A. thaliana map65-3 treated with water


title: Emwa1 inoculated map65-3 at 3 dpi, biological replicate 1

description:
map65-3-Hpa-R1_ATH1
map65-3 mutant expression after infection

source_name: A. thaliana map65-3 Hpa-inoculated


title: Emwa1 inoculated map65-3 at 3 dpi, biological replicate 2

description:
map65-3-Hpa-R2_ATH1
map65-3 mutant expression after infection


title: water-treated map65-3, biological replicate 2

description:
map65-3-Ctrl-R2_ATH1
map65-3 mutant expression in the absence of infection


title: Liver from 1.5 month Abcb11-/- mouse, replicate 2

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description:
zyy010
Female C57BL/6 Abcb11-/-.

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5. Lung and liver tissues were summarized as independent groups.

label: Biotin

source_name: liver tissue, Abcb11-/-, 1.5 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).

extract_protocol: RNA was isolated using RNeasy Kit (Qiagen) according to the manufacturer’s protocol.

tag: strain/background

tag: genotype/variation

tag: age

value: 1.5 months

tag: gender

value: female

value: liver


title: Liver from 1.5 month wild-type mouse, replicate 3

description:
zyy003
Female C57BL/6 wild-type.

source_name: liver tissue, wild-type, 1.5 months

value: wild-type


title: NTHi375 infected A549 cells_2hr_rep4

city: Pamplona

first: Junkal

last: Garmendia

address: Avda de Pamplona, 123

department: Sanidad Animal

country: Spain

description: Gene expression analysis of A549 human type II pneumocyte infected with Haemophilus influenzae strain NTHi375 for 2 h post-infection.

hyb_protocol: Cy3 fluorescently labeled samples were hybridized to “Agilent (012097) Human 1A Microarrays” according to manufacturer recommendations (Agilent Technologies, Santa Clara, CA, USA) recommendations.

scan_protocol: Slides were scanned using a Gene Pix 4100A scanner (Axon Instruments, Union City, CA, USA) at 5µ resolution. Image analysis was performed using associated software GenePiX Pro.

data_processing: The data were normalized with Bioconductor software using quantiles.

source_name: NTHi375 infected A549 cells_2hr_rep4

label_protocol: Samples Labeling was performed using the “Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion)” following manufacturer recommendations. Each sample was fluorescently labeled with Cy3-fluorescent dye.

growth_protocol: A549 cells were grown for 32 h with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37ºC in a humidified incubator with 5% CO2 to reach 90% confluency; at this point, cells were serum starved for 16 h.

extract_protocol: Total RNA was isolated using a Nucleospin RNAII kit (Macherey-Nagel) as recommended by the manufacturer, including an on column DNase treatment step. Total RNA quality was evaluated using RNA 6000 Nano LabChips (Agilent 2100 Bioanalyzer, Santa Clara, CA). All samples had intact 18S and 28S ribosomal RNA bands with RNA integrity numbers (RIN) between 9.3 to 9.7, and RNA A260/280 ratios of 2.1.

treatment_protocol: A freshly grown A549 cell monolayer was infected in EBSS medium with Haemophilus influenzae strain NTHi375, using a multiplicity of infection of 100:1, for 2 h at 37 ºC in a humidified incubator with 5% CO2. As a control, a freshly grown A549 cell monolayer was left untreated.

tag: agent

value: Haemophilus influenzae strain NTHi375

tag: cell line


title: Liver from 1.5 month Abcb11-/- mouse, replicate 3

description:
zyy011
Female C57BL/6 Abcb11-/-.


title: Liver from 1.5 month Abcb11-/- mouse, replicate 1

description:
zyy009
Female C57BL/6 Abcb11-/-.


title: NTHi375 infected A549 cells_2hr_rep3

source_name: NTHi375 infected A549 cells_2hr_rep3


title: A549 control non-infected cells_2hr_rep4

description: Gene expression analysis of A549 human type II pneumocytes, grown in monolayer and incubated in EBSS medium for 2 h.

source_name: A549 cells_2hr_rep4


title: NTHi375 infected A549 cells_2hr_rep1

source_name: NTHi375 infected A549 cells_2hr_rep1


title: Liver from 1.5 month wild-type mouse, replicate 2

description:
zyy002
Female C57BL/6 wild-type.


title: NTHi375 infected A549 cells_2hr_rep2

source_name: NTHi375 infected A549 cells_2hr_rep2


title: E17.5 lung from Abcb11-/+ mouse, wildtype mother

description:
rds023
Embryonic day 17.5 offspring from female C57BL/6 wild-type crossed with male C57BL/6 Abcb11-/- mouse.

source_name: lung tissue, Abcb11+/-, wild-type mother, E17.5

tag: genotype/variation of mother

value: embryonic day 17.5 (E17.5)

value: lung


title: A549 control non-infected cells_2hr_rep3

source_name: A549 cells_2hr_rep3


title: E18.5 lung from Abcb11-/+ mouse, Abcb11-/- mother

description:
rds026
Embryonic day 18.5 offspring from female C57BL/6 Abcb11-/- crossed with male C57BL/6 wild-type mouse.

source_name: lung tissue, Abcb11+/-, Abcb11-/- mother, E18.5

value: embryonic day 18.5 (E18.5)


title: E18.5 lung from Abcb11-/+ mouse, wildtype mother

description:
rds025
Embryonic day 18.5 offspring from female C57BL/6 wild-type crossed with male C57BL/6 Abcb11-/- mouse.

source_name: lung tissue, Abcb11+/-, wild-type mother, E18.5


title: A549 control non-infected cells_2hr_rep2

source_name: A549 cells_2hr_rep2


title: Neonatal lung from Abcb11-/+ mouse, wildtype mother

description:
rds027
Neonatal day 0 offspring from female C57BL/6 wild-type crossed with male C57BL/6 Abcb11-/- mouse.

source_name: lung tissue, Abcb11+/-, wild-type mother, N0

value: neonatal day 0 (N0)


title: Bs_ylbM_rep2

city: Jouy-en-Josas

first: Etienne

last: Dervyn

address: domaine de Vilvert

department: Microbiologie

description: strain CB167 replicate2

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) or by PartnerChip (Evry, France) following their standard operating protocol.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) or by PartnerChip (Evry, France) following their standard operating protocol.

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region as described in (Nicolas et al., 2012 PMID: 22383849).
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).           10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).           10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: B. subtilis strains (wild-type and mutants) were grown in LB medium at 37°C and harvested by centrifigution during the exponential phase of growth.

extract_protocol: Total RNA was extracted as described in Nicolas et al (2012) (PMID:22383849)

tag: strain

tag: genotype

value: ylbM


title: Bs_ylbM_rep1

description: strain CB167 replicate1


title: E17.5 lung from Abcb11-/+ mouse, Abcb11-/- mother

description:
rds024
Embryonic day 17.5 offspring from female C57BL/6 Abcb11-/- crossed with male C57BL/6 wild-type mouse.

source_name: lung tissue, Abcb11+/-, Abcb11-/- mother, E17.5


title: Neonatal lung from Abcb11-/+ mouse, Abcb11-/- mother

description:
rds028
Neonatal day 0 offspring from female C57BL/6 Abcb11-/- crossed with male C57BL/6 wild-type mouse.

source_name: lung tissue, Abcb11+/-, Abcb11-/- mother, N0


title: Bs_WT_rep3

description: wild-type strain replicate 3

value: wildtype


title: Bs_ywlC_rep2

description: strain CB169 replicate2

value: ywlC


title: Bs_ywlC_rep1

description: strain CB169 replicate1


title: A549 control non-infected cells_2hr_rep1

source_name: A549 cells_2hr_rep1


title: RPE_shZNF92_2

description: RPE sh KD ZNF92 2

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the ribosomal genes. See manuscript for additional details.

source_name: Retinal Pigment Epithelial Cells

label_protocol: Biotinylated RNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Human retinal pigment epithelial (hRPE) cells used for knockdown experiments were purchased from ScienCell (ScienCell, cat. #6540). hRPE cells were maintained in epithelial cell medium (EpiCM) (ScienCell, cat. #4101) supplemented with 2% fetal bovine serum (ScienCell, cat. #0010), 1x epithelial cell growth supplement (EpiCGS) (ScienCell, cat. #4152), and 1x penicillin/streptomycin solution (ScienCell, cat. #0503). Human foreskin fibroblasts (HFF) were purchased from GlobalStem (GlobalStem, cat. #GSC-3002) and maintained in DMEM (Life Technologies, cat. #11965-092) supplemented with 15% of Tet System Approved fetal bovine serum (Clontech, cat. #631101), 2mM L-Glutamine (Life Technologies, cat. #25030-081) and 100 U/ml penicillin-streptomycin (Life Technologies, cat. #15140-163).

extract_protocol: Total RNA was harvested and used for library preparation. For each transcription factor, total RNA was harvested from two different lines, each harboring a different shRNAmir construct. 100 ng of total RNA was used to prepare biotinylated cRNA (cRNA) using the 3’ IVT Express Kit (Affymetrix, cat. #901228), following the manufacturer’s suggested protocol.

treatment_protocol: shRNAmir lentiviral vectors were obtained from Thermo Scientific. High-titer lentiviral particles for each plasmid were used to transduce hRPE cells (ScienCell, cat. #6540). Twenty-four hours after infection, epithelial cell medium was replaced and selection with 1 μg/ml puromycin (Life Technologies, cat. #A1113803) was carried out. Puromycin-resistant cells were harvested for future analysis five days after transduction.  Additional details are provided in the Extended Experimental Procedures.

tag: cell type

value: Human retinal pigment epithelial (hRPE)

tag: lentivirus


title: Bs_WT_rep1

description: wild-type strain replicate 1


title: Bs_WT_rep2

description: wild-type strain replicate 2


title: Red Sector of red/white sectored colony 12 from KO_188_2

tag: colony color

value: Red

tag: growth condition

value: Spontaneous red/white sector

source_name: JSC23 grown at 30 degrees

value: pink


title: White Sector of red/white sectored colony 11 from KO_188_2

value: White


title: RPE_shSOX9_1

description: RPE sh KD SOX9 1


title: RPE_shZNF92_1

description: RPE sh KD ZNF92 1


title: RPE_shSOX9_2

description: RPE sh KD SOX9 2


title: RPE_shGLIS3_2

description: RPE sh KD GLIS3 2


title: RPE_shGLIS3_1

description: RPE sh KD GLIS3 1


title: RPE_shFOXD1_2

description: RPE sh KD FOXD1 2


title: White Sector of red/white sectored colony 12 from KO_188_2


title: Liver from 1.5 month wild-type mouse, replicate 1

description:
zyy001
Female C57BL/6 wild-type.

source_name: liver tissue, wild-type, 1.5 months

value: 1.5 months


title: RPE_shSIX3_2

description: RPE sh KD  SIX3 2


title: Red Sector of red/white sectored colony 7 from KO_188_2


title: MCMV Inflating d50_replicate 3a

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

description:
S24_M38_50
replicate 3
5785978001_F.idat

hyb_protocol: Samples were hybridized following protocols for Illumina MouseWG-6 v2.0 beadchip.

scan_protocol: Illumina GenomeStudio software (v1.0.6) was used to process scanner images and produce raw microarray outputs

data_processing: Probe intensity levels were generated from Illumina GenomeStudio software outputs and normalised using R/Bioconductor tools (vsn normalisation)

source_name: Organ (spleen) CD8+ T cells

label_protocol: cDNA was synthesized and cRNA made using Illumina Total Prep RNA amplification Kit (Ambion)

extract_protocol: Total RNA was isolated from sorted cells according to manufactures instructions using the mirVana Kit (Ambion). RNA integrity was checked using Agilent 2100 Bioanalyzer, samples with a RIN value of 8 or more were used for amplification

treatment_protocol: MCMV was propagated and titrated on NIH 3T3 cells (ECACC, UK), stored at -80°C and injected intravenously at a dose of 2x106 pfu; Recombinant adenovirus expressing the βgal protein under the control of the human CMV promoter (Ad-LacZ) lacking E1 and E3 genes was used (Krebs et al., 2005). Ad-LacZ was propagated on permissive HER-911 cells and purified with the Vivapure AdenoPack 20 (Sartorius, Stedim biotech, 13781 Aubagne Cedex, France) according to manufacturer’s specifications. Virus titer was determined in a cytopathic effect assay (Krebs et al., 2005). Ad-LacZ was stored at -80°C in PBS and injected intravenously at a dose of 2x109 pfu.

value: spleen

value: CD8+ T cells

tag: Stage

value: 50 days post infection


title: MCMV non Inflating d7_replicate 3

description:
S20_M45_7
replicate 3
5785978001_E.idat

value: 7 days post infection


title: Adeno Inflating d21_replicate 3

description:
S12_D8V_21
replicate 3
5785978001_C.idat

value: 21 days post infection


title: MCMV Inflating d50_replicate 3b

description:
S28_M38_50
replicate 3
5785978001_G.idat


title: White Sector of red/white sectored colony 6 from KO_188_2


title: RPE_shSIX3_1

description: RPE sh KD  SIX3 1


title: Adeno non Inflating d21_replicate 3

description:
S4_I8V_21
replicate 3
5785978001_A.idat


title: RPE_shOTX2_2

description: RPE sh KD  OTX2 2


title: RPE_shFOXD1_1

description: RPE sh KD FOXD1 1


title: Adeno non Inflating d100_replicate 3

description:
S8_I8V_100
replicate 3
5785978001_B.idat

value: 100 days post infection


title: RPE_shMITF_2

description: RPE sh KD  MITF 2

value: shMITF


title: Red Sector of red/white sectored colony 11 from KO_188_2


title: RPE_shMITF_1

description: RPE sh KD  MITF 1


title: Red Sector of red/white sectored colony 6 from KO_188_2


title: MCMV Inflating d7_replicate 3

description:
S16_M38_7
replicate 3
5785978001_D.idat


title: RPE_shOTX2_1

description: RPE sh KD  OTX2 1


title: White Sector of red/white sectored colony 7 from KO_188_2


title: White Sector of red/white sectored colony 4 from KO_188_1


title: Red Sector of red/white sectored colony 4 from KO_188_1


title: White Sector of red/white sectored colony 2 from KO_188_1


title: Red Sector of red/white sectored colony 2 from KO_188_1


title: MCMV non Inflating d50_replicate 3

description:
S27_M45_50
replicate 3
5773660153_G.idat


title: White Sector of red/white sectored colony 7 from KO_135_6


title: MCMV Inflating d50_replicate 2

description:
S23_M38_50
replicate 2
5773660153_F.idat


title: Red Sector of red/white sectored colony 7 from KO_135_6


title: Adeno Inflating d21_replicate 2

description:
S11_D8V_21
replicate 2
5773660153_C.idat


title: RPE_shPAX6_2

description: RPE sh KD  PAX6 2


title: RPE_shPAX6_1

description: RPE sh KD  PAX6 1


title: Cultured Monocytes 3

city: Louisville

first: Kavitha

last: Yaddanapudi

state: KY

address: 505 South Hancock Street

department: Medicine

institute: University of Louisville

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Primeview Human arrays according to the GeneChip 3' Array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization.

source_name: Monocytes cultured for 64 hours

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Plus Reagent Kit from 100 ng total RNA

growth_protocol: A375 co-cultured monocytes (both untreated and 4-IPP treated) and control monocytes were cultured for 64 hours in 6 well plates in IMDM medium supplemented with 10% human serum.

extract_protocol: Total RNA from cultured monocytes, vehicle-treated and 4-IPP-treated A375-MDSCs were isolated. For RNA extraction, cells were lysed in buffer RLT (Qiagen, Valencia, CA), homogenized and purified using RNeasy mini kit (Qiagen) following manufacturer’s instructions. Integrity of RNA was checked using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: A375 co-cultured monocytes (both untreated and 4-IPP treated) and control monocytes cultured without tumor cells were harvested by gently scraping after 64-68 hours of culture and CD11b+ A375-MDSCs were purified with anti-CD11b+ microbeads and autoMACS separator (Miltenyi Biotec).

value: PBMC

value: Monocyte


title: Adeno Inflating d100_replicate 3

description:
S15_D8V_100
replicate 3
5773660153_D.idat


title: RPE_shControl_1

description: RPE sh KD control 1

value: shControl


title: Red Sector of red/white sectored colony 1 from KO_188_1


title: Cultured Monocytes 1


title: MDSC+4-IPP 2

source_name: MDSC treated with MIF inhibitor

value: myeloid-derived suppressor cell (MDSC)


title: MDSC+4-IPP 3


title: Naïve CD8 cell_replicate 3

description:
S3_NAIVE
replicate 3
5773660153_A.idat

value: Naïve


title: MCMV Inflating d50_replicate 2b

description:
S30_M38_50
replicate 2
5665159050_H.idat


title: MCMV Inflating d7_replicate 2

description:
S18_M38_7
replicate 2
5665159050_E.idat


title: White Sector of red/white sectored colony 1 from KO_188_1


title: MCMV non Inflating d7_replicate 2

description:
S19_M45_7
replicate 2
5773660153_E.idat


title: MDSC+4-IPP 1


title: MCMV Inflating d50_replicate 2a

description:
S22_M38_50
replicate 2
5665159050_F.idat


title: Adeno Inflating d100_replicate 2

description:
S14_D8V_100
replicate 2
5665159050_D.idat


title: Cultured Monocytes 2


title: RPE_shControl_2

description: RPE sh KD control 2

value: Human retinal pigment epithelial (hRPE)


title: Red Sector of red/white sectored colony 5 from KO_135_6

value: Red

value: Spontaneous red/white sector


title: A375-MDSC 2

source_name: melanoma cell line induced MDSC


title: A375-MDSC 3


title: MCMV non Inflating d50_replicate 2

description:
S26_M45_50
replicate 2
5665159050_G.idat


title: Adeno non Inflating d100_replicate 2

description:
S7_I8V_100
replicate 2
5773660153_B.idat


title: White Sector of red/white sectored colony 5 from KO_135_6

value: White

value: pink


title: Red Sector of red/white sectored colony 4 from KO_135_6


title: White Sector of red/white sectored colony 1 from KO_135_6


title: Red Sector of red/white sectored colony 1 from KO_135_6


title: White Sector of red/white sectored colony 4 from KO_135_6


title: Adeno Inflating d21_replicate 1

description:
S10_D8V_21
replicate 1
5665159050_C.idat

value: spleen


title: A375-MDSC 1


title: Adeno non Inflating d21_replicate 2

description:
S6_I8V_21
replicate 2
5665159050_B.idat

value: CD8+ T cells


title: Naïve CD8 cell_replicate 2

description:
S2_NAIVE
replicate 2
5665159050_A.idat


title: MCMV non Inflating d7_replicate 1

description:
S21_M45_7
replicate 1
5511168047_F.idat


title: MCMV Inflating d7_replicate 1

description:
S17_M38_7
replicate 1
5511168047_E.idat


title: MCMV non Inflating d50_replicate 1

description:
S25_M45_50
replicate 1
5511168047_G.idat

value: 50 days post infection


title: Adeno non Inflating d100_replicate 1

description:
S9_I8V_100
replicate 1
5511168047_C.idat


title: SCC Sample S96

status: Public on Sep 22 2015

city: Beijing

first: Dongmei

last: Lin

address: Panjiayuannanli 17, Chaoyang District

department: Pathology

country: China

institute: Cancer Hospital, CAMS

hyb_protocol: A total of 500ng of both gDNA samples and human Cot-I DNA was dissolved in the hybridization mixture supplied within the Agilent Oligo array-CGH Hybridization Kit (Agilent Technologies).  After denaturation at 95℃ for 3 minutes and incubation at 37℃ for 30 minutes, the mixtures were slowly dispensed onto the gasket.  A microarray slide was then placed onto the gasket slide.  The samples were hybridized in a hybridization oven at 65℃ and 20 rpm for 40 hours.

scan_protocol: Slides were scanned with the Agilent Scanner System, and the Feature Extraction 12.0 (Agilent Technologies) was used for data extraction.

data_processing: Data were normalized with quantile method with limma package in R (version 2.12.0).

source_name: Lung Squamous Cell Carcinoma

label_protocol: Tumor and reference gDNA (Promega Inc., WI) were labeled with Cy5 and Cy3, respectively, using the Agilent Genomic DNA USL Labeling Kit (Agilent Technologies) for FFPE Samples according to the manufacturer's instructions.

extract_protocol: Genomic DNA (gDNA) was extracted from the tumor cells using a DNeasy Blood & Tissue Kit (Qiagen Inc., Hilden, Germany).

treatment_protocol: Tumor cells were scraped using a scalpel and then collected under the direction of pathologists from ten 10-μm thick FFPE slides for each histological lesion.

value: M

tag: time (month)

tag: event (1=dead; 0=alive)

value: squamous cell carcinoma

tag: tissue type

value: lung

source_name: Human genomic DNA: Male (Promega)

tag: reference

value: Male (Promega)


title: SCC Sample S98


title: SCC Sample S94


title: Adeno Inflating d100_replicate 1

description:
S13_D8V_100
replicate 1
5511168047_D.idat

tag: tissue

value: 100 days post infection


title: MCMV Inflating d50_replicate 1

description:
S29_M38_50
replicate 1
5511168047_H.idat


title: SCC Sample S91

tag: age


title: SCC Sample S100

tag: gender


title: SCC Sample S95


title: SCC Sample S89


title: SCC Sample S90


title: Naïve CD8 cell_replicate 1

description:
S1_NAIVE
replicate 1
5511168047_A.idat


title: Adeno non Inflating d21_replicate 1

description:
S5_I8V_21
replicate 1
5511168047_B.idat

value: 21 days post infection


title: SCC Sample S97


title: SCC Sample S93


title: SCC Sample S99


title: SCC Sample S85


title: SCC Sample S92


title: SCC Sample S87


title: SCC Sample S77


title: SCC Sample S76


title: SCC Sample S84


title: SCC Sample S82


title: SCC Sample S66


title: SCC Sample S79


title: SCC Sample S86

value: F

source_name: Human genomic DNA: Female (Promega)

value: Female (Promega)


title: SCC Sample S83


title: SCC Sample S88


title: SCC Sample S80


title: SCC Sample S67


title: SCC Sample S64


title: SCC Sample S78


title: SCC Sample S81


title: SCC Sample S58


title: SCC Sample S74


title: SCC Sample S68


title: SCC Sample S75


title: SCC Sample S71


title: SCC Sample S73


title: SCC Sample S63


title: SCC Sample S69


title: SCC Sample S70


title: SCC Sample S61


title: SCC Sample S56


title: SCC Sample S72


title: SCC Sample S57


title: SCC Sample S65


title: SCC Sample S62


title: SCC Sample S55


title: SCC Sample S60


title: SCC Sample S59


title: SCC Sample S53


title: SCC Sample S52


title: SCC Sample S46


title: SCC Sample S54


title: SCC Sample S50


title: SCC Sample S49


title: SCC Sample S48


title: SCC Sample S43


title: SCC Sample S51


title: SCC Sample S47


title: SCC Sample S42


title: SCC Sample S44


title: SCC Sample S40


title: SCC Sample S45


title: SCC Sample S41


title: SAMPLE 11_Control

first: Kensuke

last: Tateishi

state: Massachusetts

address: 185 cambridge street

department: Neurosurgery

institute: Massachusetts General Hospital

description: SAMPLE 11

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio analysis software ver2011.1 and methylation module 1.9.0
the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Control DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Glioblastoma tumorsphere lines were treated with serum free neurosphere culture medium. HT1080 was cultured using EMEM medium supplemented with 10%FBS.

extract_protocol: genomic DNA was extracted  using Zymo EZ-96 DNA Methylation kit  according to standard instructions

treatment_protocol: Samples 2-4 were treated with DMSO (0.1%) or IDH1i (5uM) for 10 months.

tag: sample type

value: Control DNA (CEPH Individual 1347-02) from Life Technologies Cat# 403062

tag: tissue/cell type

value: control

value: wild-type


title: SCC Sample S39


title: SCC Sample S38


title: SAMPLE 9_HT1080

description: SAMPLE 9

source_name: fibrosarcoma

tag: cell lie

value: glioblastoma tumorsphere

value: mutant


title: SCC Sample S37


title: SAMPLE 10_MGG119

description: SAMPLE 10

source_name: glioblastoma tumorsphere

value: fibrosarcoma


title: SAMPLE 6_MGG23

description: SAMPLE 6


title: SCC Sample S35


title: SAMPLE 8_MGG91

description: SAMPLE 8


title: SCC Sample S36


title: SCC Sample S33


title: SAMPLE 2_MGG152 cultured with DMSO for 10month

description: SAMPLE 2

tag: treated with

value: DMSO (0.1%) for 10 months


title: SAMPLE 4_MGG152 with IDH1i for 10 months

description: SAMPLE 4

value: IDH1i (5uM) for 10 months


title: SCC Sample S32


title: SAMPLE 7_MGG85

description: SAMPLE 7


title: E1014622_Pancreas

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing:
DNA methylation data was corrected for background and color bias and the data was quantile normalized using lumi. Probes were discarded if they had a low bead count (< 3), high detection P value  (> 0.01), or  a low success rate (< 95%).
The 'raw_signal_intensities.txt' contains unmethylated and methylated signal intensities

label_protocol: According to Illumina protocol

extract_protocol: Chlorophorm/isoamylalcohol protocol

tag: time point

value: 22 weeks of gestation

value: Pancreas


title: E1014618-_Pancreas

value: 18 weeks of gestation


title: SAMPLE 1_MGG152

description: SAMPLE 1


title: E1011321_Pancreas


title: SCC Sample S31

value: M

tag: cell type

value: squamous cell carcinoma

value: lung


title: miR-27bKD_rep3

city: Singapore

first: Vivian

middle: Y

last: Poon

state: SINGAPORE

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description: SAMPLE 6

hyb_protocol: 1.5ug of biotin-labeled cRNA were hybridized on the Illumina Mouse WG-6 version 2 beadchip according to Manufacturer’s instruction (Illumina, Inc., San Diego, CA)

scan_protocol: Beadchips were washed and stained according to Manufacturer’s instruction and scanned using Illumina BeadArray Reader (Illumina, Inc., San Diego, CA)

data_processing: The data were normalized using quantile normalization with R according to 'Analyzing An Illumina Microarray Dataset Using R and Bioconductor' by Giovanni Coppola, August 2010

source_name: cortical neurons transduced with lentivirus to knock down miR-27b

label_protocol: Biotin-labeled cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion Inc.) from 500ng of total RNA.

growth_protocol: 500,000 neurons were seeded on 12-well poly-L-lysine-coated tissue culture dishes and cultured in Neurobasal media with B27 supplement for two weeks.

extract_protocol: RNA was extracted with RLT buffer, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Lentivirus (MOI=5) was introduced to neurons after they had attached on the dish

tag: strain

value: cortical neuron

tag: genotype

value: Dicerflox/flox

tag: treatment

value: miR-27b knockdown


title: CTKD_rep3

description: SAMPLE 5

source_name: cortical neurons transduced with control lentivirus


title: SAMPLE 5_MGG18

description: SAMPLE 5


title: E1011321_Adrenal

value: Adrenal


title: E1032118+_Pancreas


title: E1014622_Adrenal


title: E101539.4_Pancreas

value: 9 weeks of gestation


title: miR-27bKD_rep1

description: SAMPLE 2


title: miR-27bKD_rep2

description: SAMPLE 4


title: E1032118+_Adrenal


title: CTKD_rep1

description: SAMPLE 1

value: control


title: E1014318_Pancreas


title: SCC Sample S29

value: Male (Promega)


title: CTKD_rep2

description: SAMPLE 3


title: SCC Sample S28


title: E101559_Pancreas


title: listeria infected control flies, 72hpi, rep1

city: Miami

first: Glen

middle: N.

last: Barber

state: FL

address: 1550 NW 10th Ave

department: Cell Biology

institute: University of Miami

description:
Gene expression data following inoculation'
control_listeria_72h_1

hyb_protocol: Affynetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus

data_processing: GeneSpring GX 12.0 using the default summarization/scaling/normalization algorithms. Pathogen-inoculated samples were normalized to mock(PBS)-inoculated samples and used for Gene Set Enrichment Analysis

source_name: whole flies listeria infected control flies, 72hpi

label_protocol: Affymetrix GeneChip 3' IVT Express Kit

growth_protocol:
F1 generation flies were raised on standard cornmeal and used for all experiments
Parental flies (y1v1;P{TRiP.JF01138}attP2 and y1w*;P{Act5C-GAL4}25FO1/CyO,y+) were mated and 4-7 day old flies were used for all subsequent experiments. dSTING RNAi flies expressed the dsRNA hairpin targeting dSTING and had straight wings, while sibling flies not expressing dSTING dsRNA had curly wings.

extract_protocol: Flies were homogenized and total RNA was extracted using Qiagen RNeasy kit. RNA QC was performed using Agilent RNA 6000 Nano chip kit and Agilent Bioanalyzer 2100

treatment_protocol:
Intrathoracic inoculation with a finely pulled glass capillary needle dipped in specified pathogen
Pathogens used for inoculation were Listeria monocytogenes, Drosophila C Virus (DCV), and Insect Iridescent virus 6 (IIV6), at the following concentrations: 1e7 CFU/ml, 5e7 TCID50/ml, 5e6 TCID50/ml. Mock inoculation was performed with PBS. Whole flies were homogenized 24 or 72 h post-infection.

value: whole adult flies

tag: pathogen

value: listeria

tag: hours post-infection


title: listeria infected control flies, 72hpi, rep2

description:
Gene expression data following inoculation'
control_listeria_72h_2


title: listeria infected knockdown flies, 72hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_listeria_72h_1

source_name: whole flies listeria infected knockdown flies, 72hpi

value: dSTING RNAi


title: SAMPLE 3_MGG152 cultured with DMSO for 10month following DMSO for 2days

description: SAMPLE 3

value: mutant

value: DMSO (0.1%) for 10 months + 2 days


title: E101149.1_Pancreas

value: Pancreas


title: SCC Sample S27

tag: time (month)

tag: event (1=dead; 0=alive)


title: E1020922_Adrenal

value: 22 weeks of gestation


title: listeria infected knockdown flies, 72hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_listeria_72h_2


title: SCC Sample S24

value: M

tag: tissue type

tag: reference


title: listeria infected control flies, 24hpi, rep1

description:
Gene expression data following inoculation'
control_listeria_24h_1

source_name: whole flies listeria infected control flies, 24hpi

tag: tissue


title: SCC Sample S25

tag: age

tag: gender

value: F

value: squamous cell carcinoma

value: Female (Promega)


title: SCC Sample S34

value: lung


title: listeria infected control flies, 24hpi, rep2

description:
Gene expression data following inoculation'
control_listeria_24h_2


title: DCV infected knockdown flies, 72hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_DCV_72h_2

source_name: whole flies DCV infected knockdown flies, 72hpi

value: DCV


title: SCC Sample S26


title: listeria infected knockdown flies, 24hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_listeria_24h_1

source_name: whole flies listeria infected knockdown flies, 24hpi


title: E101149.1_Adrenal

value: Adrenal


title: listeria infected knockdown flies, 24hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_listeria_24h_2


title: E1014618-_Adrenal

value: 18 weeks of gestation


title: SCC Sample S23


title: E1014318_Adrenal


title: DCV infected control flies, 24hpi, rep1

description:
Gene expression data following inoculation'
control_DCV_24h_1

source_name: whole flies DCV infected control flies, 24hpi

value: control


title: DCV infected control flies, 24hpi, rep2

description:
Gene expression data following inoculation'
control_DCV_24h_2


title: SCC Sample S22

value: Male (Promega)


title: DCV infected knockdown flies, 72hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_DCV_72h_1

value: whole adult flies


title: DCV infected control flies, 72hpi, rep2

description:
Gene expression data following inoculation'
control_DCV_72h_2

source_name: whole flies DCV infected control flies, 72hpi


title: DCV infected knockdown flies, 24hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_DCV_24h_2

source_name: whole flies DCV infected knockdown flies, 24hpi


title: E101539.4_Adrenal

value: 9 weeks of gestation


title: E101559_Adrenal


title: IIV6 infected control flies, 72hpi, rep1

description:
Gene expression data following inoculation'
control_IIV6_72h_1

source_name: whole flies IIV6 infected control flies, 72hpi


title: IIV6 infected control flies, 24hpi, rep2

description:
Gene expression data following inoculation'
control_IIV6_24h_2

source_name: whole flies IIV6 infected control flies, 24hpi


title: DCV infected knockdown flies, 24hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_DCV_24h_1

value: dSTING RNAi


title: IIV6 infected knockdown flies, 72hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_IIV6_72h_2

source_name: whole flies IIV6 infected knockdown flies, 72hpi


title: E1014622_Muscle

value: Muscle


title: SCC Sample S21

source_name: Lung Squamous Cell Carcinoma

source_name: Human genomic DNA: Male (Promega)


title: E1020922_Muscle


title: IIV6 infected control flies, 72hpi, rep2

description:
Gene expression data following inoculation'
control_IIV6_72h_2


title: IIV6 infected knockdown flies, 24hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_IIV6_24h_1

source_name: whole flies IIV6 infected knockdown flies, 24hpi


title: SCC Sample S19


title: SCC Sample S20


title: IIV6 infected knockdown flies, 72hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_IIV6_72h_1


title: IIV6 infected control flies, 24hpi, rep1

description:
Gene expression data following inoculation'
control_IIV6_24h_1


title: IIV6 infected knockdown flies, 24hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_IIV6_24h_2


title: E1011321_Muscle


title: SCC Sample S30

source_name: Human genomic DNA: Female (Promega)


title: SCC Sample S17


title: SCC Sample S18


title: SCC Sample S16


title: mock infected control flies, 72hpi, rep4

description:
Gene expression data following inoculation'
control_mock (PBS)_72h_4

source_name: whole flies mock infected control flies, 72hpi

value: PBS-control


title: E1032118+_Muscle


title: E1014318_Muscle


title: mock infected control flies, 72hpi, rep3

description:
Gene expression data following inoculation'
control_mock (PBS)_72h_3


title: mock infected control flies, 72hpi, rep2

description:
Gene expression data following inoculation'
control_mock (PBS)_72h_2


title: E1014618-_Muscle


title: DCV infected control flies, 72hpi, rep1

description:
Gene expression data following inoculation'
control_DCV_72h_1


title: SCC Sample S14


title: mock infected knockdown flies, 72hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_72h_1

source_name: whole flies mock infected knockdown flies, 72hpi


title: E101149.1_Muscle


title: mock infected control flies, 24hpi, rep3

description:
Gene expression data following inoculation'
control_mock (PBS)_24h_3


title: SCC Sample S15


title: SCC Sample S11


title: mock infected knockdown flies, 72hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_72h_2


title: mock infected control flies, 24hpi, rep4

description:
Gene expression data following inoculation'
control_mock (PBS)_24h_4


title: E101539.4_Muscle


title: mock infected knockdown flies, 72hpi, rep3

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_72h_3

source_name: whole flies mock infected control flies, 24hpi


title: mock infected knockdown flies, 72hpi, rep4

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_72h_4


title: E103198.6_Muscle


title: SCC Sample S10


title: mock infected control flies, 24hpi, rep2

description:
Gene expression data following inoculation'
control_mock (PBS)_24h_2


title: SCC Sample S13


title: mock infected control flies, 24hpi, rep1

description:
Gene expression data following inoculation'
control_mock (PBS)_24h_1


title: SCC Sample S12


title: mock infected control flies, 72hpi, rep1

description:
Gene expression data following inoculation'
control_mock (PBS)_72h_1


title: E1011321_Amnion

value: Amnion


title: mock infected knockdown flies, 24hpi, rep4

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_24h_4

source_name: whole flies mock infected knockdown flies, 24hpi


title: mock infected knockdown flies, 24hpi, rep3

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_24h_3


title: E1014622_Amnion

value: 22 weeks of gestation


title: E1032118+_Amnion


title: mock infected knockdown flies, 24hpi, rep2

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_24h_2


title: mock infected knockdown flies, 24hpi, rep1

description:
Gene expression data following inoculation'
dSTING RNAi_mock (PBS)_24h_1


title: control cells, dsDNA treated, rep2

description:
Gene expression data following inoculation'
dsDNA90

source_name: S2 control cells, dsDNA treated

growth_protocol: S2 cells were grown in Schneider's media containing 10% FBS and antibiotics

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit. RNA QC was performed using Agilent RNA 6000 Nano chip kit and Agilent Bioanalyzer 2100

treatment_protocol: S2 cells were first transfected with non-specific dsRNA or dsRNA targeting dSTING, using Invitrogen CellfectinII following manufacturer's instructions.  3 days post-transfection, cells were transfected with a 90-mer dsDNA or mock transfected. Cells were lysed 24h later.


title: dSTING RNAi cells, dsDNA treated, rep2

source_name: S2 dSTING RNAi cells, dsDNA treated


title: SCC Sample S9

value: M


title: SCC Sample S8


title: dSTING RNAi cells, dsDNA treated, rep1


title: dSTING RNAi cells, mock treated, rep2

description:
Gene expression data following inoculation'
mock (lipofectamine only)

source_name: S2 dSTING RNAi cells, mock treated


title: E1014318_Amnion


title: E101539.4_Amnion


title: control cells, mock treated, rep1

source_name: S2 control cells, mock treated


title: E1014618-_Amnion


title: control cells, mock treated, rep2


title: dSTING RNAi cells, mock treated, rep1


title: SCC Sample S7

value: F


title: SCC Sample S6

value: squamous cell carcinoma


title: control cells, dsDNA treated, rep1


title: SCC Sample S3


title: SCC Sample S5


title: L-Hyp_01

city: ATLANTA

first: GUOQING

last: LI

state: GEORGIA

address: 161 Jessie Hill Jr. Drive

department: BIOLOGY

institute: GEORGIA STATE UNIVERSITY

description: Gene expression data from PAO1 at 5mM L-Hyp

scan_protocol: Affymetrix Protocol:Scan-M10

data_processing:
GCOS 1.4.0
Algorithm: ExpressionStat 5.0

organism: Pseudomonas aeruginosa

source_name: PAO1 in MMP+Glutamate+L-Hyp

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 10 ug total RNA

growth_protocol: Overnight grown cultures of P. aeruginosa PAO1 were used to inoculate 10 ml minimal medium P and grown at 37ºC with shaking at 300rpm. Cells were harvested when the optical density at 600 nm reached 0.4~0.6 by centrifugation for 5 minutes at 4C.

extract_protocol: Total RNA samples were isolated by RNeasy Plus Micro Kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis and fragmentation by DNase I treatment were performed according to the instructions of GeneChip manufacturer (Affymetrix).

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-Glutamate at 10 mM and Hyp at 5mM.

tag: culture media

value: minimal medium P supplemented with 10 mM L-Glutamate and 5mM L-Hyp


title: SCC Sample S4

value: lung

value: Female (Promega)


title: D-Hyp_01

description: Gene expression data from PAO1 at 5mM D-Hyp

source_name: PAO1 in MMP+Glutamate+D-Hyp

value: minimal medium P supplemented with 10 mM L-Glutamate and 5mM D-Hyp


title: L-Hyp_02


title: D-Hyp_02


title: E101559_Amnion


title: E101578.2_Amnion


title: SCC Sample S2


title: 815_PTEN_SP_HSC

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description: Gene expression in HSCs

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: Pten deficient spleen HSCs

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

growth_protocol: HSCs harvested directly from mouse by flow cytometry

extract_protocol: RNA was prepared using the nucelospin RNA isolation kit (Machery-Nagel)

treatment_protocol: HSCs from control mice or after 7 days of G-CSF treatment or 14 days after Pten deletion

value: spleen

value: Pten deficient

value: CD150+CD48-Lin-kit+Sca1+ HSCs

value: 8-10 week


title: SCC Sample S1

value: Male (Promega)


title: PTEN_HSC_720

description: Gene expression in HSCs


title: 814_PTEN_SP_HSC

description: Gene expression in HSCs


title: G_Spl4

description: Gene expression in HSCs

source_name: G-CSF mobilized spleen HSCs

value: G-CSF treated/mobilized


title: PTEN_HSC_T11

description: Gene expression in HSCs


title: G_Spl3

description: Gene expression in HSCs


title: 4T1_shCtrl_c5.2

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

hyb_protocol: per manufacturer protocol

scan_protocol: per manufacturer protocol

data_processing: The data was normalized by using the rma function/algorithm of package oligo of bioconductor.

source_name: 4T1 mammary tumor cell line

label_protocol: per manufacturer protocol

growth_protocol: DMEM + 10% FBS + PS

extract_protocol: Trizol, following manufacturers protocol

tag: cell line

value: 4T1 mammary tumor cell line

value: shScramble control


title: 4T1_shCtrl_c4.1


title: G_Spl2

description: Gene expression in HSCs


title: 817_WT_BM_HSC

description: Gene expression in HSCs

source_name: Bone marrow HSCs

value: bone marrow

value: control


title: 4T1_sh75_c5.2

value: Cnot shRNA75


title: 4T1_sh75_c4.2


title: WT_HSC_7000

description: Gene expression in HSCs


title: G_Spl1

description: Gene expression in HSCs


title: 4T1_sh74_c1.2

value: Cnot shRNA74


title: 4T1_sh74_c7.2


title: 4T1_sh75_c5.1


title: 4T1_shCtrl_c2.2


title: 4T1_Cnot7_c5.2

value: Cnot over-expression


title: 4T1_Cnot7_c5.1


title: Ctrl_BM3

description: Gene expression in HSCs


title: Ctrl_BM1

description: Gene expression in HSCs


title: Ctrl_BM4

description: Gene expression in HSCs


title: 4T1_Cnot7_c4.2


title: 4T1_8166_c7.2


title: Ctrl_BM2

description: Gene expression in HSCs


title: 4T1_8166_c1.1


title: 4T1_8166_c6.2


title: Mouse with RAS - replication 2

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Hybriddized biotinylated-aRNA accordig to the manufacturer prorocol.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software. Data processing and analysis were done by affy, limma, xps, et al R/Bioconductor packages.

source_name: RAS - replication 2

label_protocol: Biotin labelled accordig to the manufacturer prorocol.

extract_protocol: Total RNA from thyroids was isolated using TRIzol (Invitrogen, Carlsbad, CA) as indicated by the protocol of the manufacturer.

tag: background strain

value: mixed background of C57Bl/6n, C129 and FVB strains

tag: genotype/variation

value: RAS mutation (KrasG12D)


title: N2_3

city: Goettingen

first: Michal

last: Turek

address: Am Fassberg 11

department: Sleep and Waking

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

description: Gene expression in N2 wild type sleeping L4 larvae

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65uC in the Hybridization Oven (Agilent).

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B).

data_processing: Intensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor.

organism: Caenorhabditis elegans

source_name: N2, replicate 3

label_protocol: 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer’s recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 21.5°C. For each sample 200 L4 sleeping animals were picked individually with a platinum wire pick and were immediately placed into a tube containing one ml of Trizol (Invitrogene).

extract_protocol: RNA was extracted from the Trizol using standard procedure.

treatment_protocol: For performing the experiment ‘‘Low RNA Input linear Amplification Kit Plus, One Color’’ protocol (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. Nu: 5188–5282)were used following the manufacturer’s standard protocol.

value: whole animal

value: hermaphrodite

value: L4 sleep

value: N2 wild type sleeping L4 larvae