title: Pb01_M-to-Y_Control-ethanol-treated_4 h_flask1_rep2

description:
13237558_OH_4_F1
Flask1_rep2. Control, Pb01  M-to-Y, 4 h

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m


title: Day 70 T3 Ethanol, Biological Rep2

status: Public on Dec 14 2011

type: RNA

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

country: USA

institute: Genentech

description: miRNA expression data from day 70 males exposed prenatally to alcohol during Trimester 3 (PND 3 and 7) via injections of  20% ethanol in 0.15M saline with a dosage of 2.5g/kg. Ethanol was administered twice separated by two hours.

hyb_protocol: Samples were then hybridized to Affymetrix miRNA 2.0 arrays for 16 hours at 45°C

scan_protocol: Probe level (.CEL file) data was generated using Affymetrix Command Console v1.1.

data_processing: Probes were summarized to gene level data in Partek Genomics Suite v6.6 (Partek, St. Louis, MO, USA) using the RMA algorithm. Partek software was used to determine ANOVA p-values and fold changes.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Day 70 T3 Ethanol

label_protocol: One microgram of total RNA was labeled using the Flash Tag Biotin HSR kit (Genisphere)

growth_protocol: C57BL/6J mice were prenatally exposed to ethanol either via Trimister 1,2, or 3, injections or continous preference drinking (Labelled T1, T2, T3, or CPD, respectively).

extract_protocol: TRIzol according to manufacturers protocol

treatment_protocol: Day 70 male mice were subjected to CO2 asphyxiation followed by cervical disolaction. Whole brain tissue was dissected in under five minutes and flash frozen liquid nitrogen.

tag: strain

tag: gender

value: Male

tag: tissue

value: Whole Brain (without olfactory bulb)

tag: treament

value: Fetal alcohol exposed

tag: model

tag: # samples pooled


title: Dif 96 Cl 1

city: Montpellier

first: Jean-Marc

last: Lemaitre

address: 141 rue de la cardonille

country: France

institute: INSERM

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

organism: Homo sapiens

source_name: Differentiated iPSC 96 Cl1

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

growth_protocol: Human iPSC line derived from a 96 year old donor proliferative fibroblasts, re-differentiated into fibroblasts

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer

tag: cell line

value: Dif 96 Cl1

tag: cell type

value: fibroblast


title: HeyA8 Norepinephrine Rep2

city: Houston

first: Guillermo

middle: N

last: Armaiz-Pena

state: Texas

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Affymetrix U133A

hyb_protocol: Standard Affymetrix hybridization protocol for gen expression profiling (carried out in UCLA DNA Microarray Core).

scan_protocol: Standard Affymetrixscan protocol for gene expression profiling (carried out in UCLA DNA Microarray Core).

data_processing: MAS 5.0

label: biotin

label_protocol: Standard Affymetrix probe synthesis for gene expression profiling (carried out in UCLA DNA Microarray Core).

extract_protocol: Total RNA was extracted using Qiagen RNEasy.

tag: treatment

value: Norepinephrine


title: Pb01_M-to-Y_Control-untreated_4 h_flask2_rep1

city: San Jose

first: Jata

last: Shankar

state: CA

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description:
13238064_C_4_F2
Flask2_rep1. Control, Pb01  M-to-Y, 4 h

hyb_protocol: Cy3-labeled samples were competitively hybridized against the Cy5-labeled reference sample on a pre-hybridized microarray slide (random shear gDNA microarray (Monteiro, Clemons et al. 2009)). cDNA labeling and pre-hybridization procedures were followed as previously described (Monteiro, Clemons et al. 2009). Samples of labeled cDNA for hybridization were concentrated using a Microcon® YM-30 Centrifugal Filter Device (Millipore) and suspended to 40 μl with 3X saline-sodium citrate buffer (SSC; Sigma-Aldrich, St. Louis, MO), 0.1% sodium dodecyl sulfate (SDS; Sigma-Aldrich).  These samples were preincubated at 100o C for 2 minutes, 37oC for 15-25 minutes, transferred onto a microarray slide, covered with a cover glass and placed in hybridization chambers. Hybridization was carried out at 50o C for 14 to 18 hours followed by washing, in order, with 2X SSC with 0.03%SDS, 2X SSC, 1X SSC and 0.2X SSC for 2-5 minutes in each solution. Slides were dried by centrifugation and scanned within 24 hours. All hybridization experiments were done in duplicate using samples from each of two independent cultures.

scan_protocol: Scanner settings used 10 µm pixel size and photomultiplier tube gains for both detection channels, 635 nm (Cy5-red color) and 532 nm (Cy3-green color), were 540 and 500, respectively (GenePix® 4000B Microarray Scanner, Axon Instruments, Union City, CA).

data_processing:
Cited Bibliography: Stover, E. P., G. Schar, et al. (1986). Estradiol-binding proteins from mycelial and yeast-form cultures of Paracoccidioides brasiliensis. Infect. Immun. 51(1): 199-203. Clemons, K. V., D. Feldman, et al. (1989). Influence of oestradiol on protein expression and methionine utilization during morphogenesis of Paracoccidioides brasiliensis. J Gen Microbiol 135(6): 1607-17.                                                                                Monteiro, J. P., K. V. Clemons, et al. (2009). Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro. Microbiology 155(Pt 8): 2795-808.                                                                                Gentleman, R. C., V. J. Carey, et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10): R80.         Smyth, G. K. and T. Speed (2003). Normalization of cDNA microarray data. Methods 31(4): 265-73.                                                                                Ritchie, M. E., J. Silver, et al. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23(20): 2700-7. Kauffmann, A., R. Gentleman, et al. (2009). arrayQualityMetrics--a bioconductor package for quality assessment of microarray data. Bioinformatics 25(3): 415-6.  Huber, W., A. von Heydebreck, et al. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl 1: S96-104.
Microarray hybridizations were imaged using a GenePix scanner and images were processed using GenePix Pro 6.1.0.4 software.  GenePix files were imported into R/Bioconductor (Gentleman, Carey et al. 2004), using the limma package (Smyth and Speed 2003), removing spots having quality flags of -50 or less. Analysis of array backgrounds revealed evidence of spatial gradients, so background correction was applied to each array using the normexp method with an offset of 50 (Ritchie, Silver et al. 2007). We applied the arrayQualityMetrics package  (Kauffmann, Gentleman et al. 2009).  We normalized between arrays using variance stabilization from the vsn package (Huber, von Heydebreck et al. 2002), allowing for 20 percent outliers. We then normalized within arrays using loess to remove non-linearity from the MA curves (M and A are defined as: M = log2 (I1) - log2 (I2), A = 1/2 (log2 (I1) + log2 (I2)), where I1 and I2 are the intensities of the two channels).
We obtained standardized log2 ratios by dividing the log2 ratios of each array by its median absolute deviation (Cy3/Cy5=test/reference).

organism: Paracoccidioides lutzii Pb01

source_name: Pb01  M-to-Y, 4 h

label_protocol: Total RNA (48 µg) was used for cDNA synthesis using anchored oligo-dT (5’ TTT TTT TTT TTT TTT TTT TTV N 3’). Fluorescently labeled cDNA was made by incorporating Cy5 or Cy3 labeled dUTP during reverse transcription of poly-adenylated (PolyA) mRNA. An equal amount of total RNA from untreated controls from each time-point was pooled to generate a Cy5-labeled cDNA reference sample.  Samples from each time point were individually labeled with Cy3.

growth_protocol: Mycelial (M) culture filtrate was filter sterilized from MVM broth cultures (Pb01) after 2-4 weeks of growth at 25°C on a gyrator shaker at 150 r.p.m. and stored at 4°C for use as a growth supplement. M spent culture medium used as growth supplement (2:1 ratio of fresh liquid MVM to spent culture filtrate) as described previously for the growth of M liquid cultures (Stover, Schar et al. 1986; Clemons, Feldman et al. 1989). Two-week-old M slants were used to inoculate 300 ml of supplemented liquid MVM media and liquid cultures were grown for 8 d on a gyratory shaker at 150 r.p.m. at 25°C.

extract_protocol: Fungal cells were thawed in TRIzol reagent (Invitrogen, Carlsbad, CA) followed by cell disruption with 0.5 mm zirconia/silica beads (Biospec) using a BeadBeater apparatus (Biospec Products, Inc., Bartlesville, OK) using a high speed setting (3 pulses of 12-15 sec). Total RNA was extracted using TRIzol reagent per the manufacturer’s instructions. Contaminating gDNA was removed per the manufacturer’s instructions using an RNeasy mini spin column (RNeasy mini kit, Qiagen Science, MD, USA) and an RNase-free DNase set (50) (Qiagen, GmbH, Hilden). The quantity and quality of the extracted RNA were assessed by A260nm/A280nm ratio as well as by electrophoresis through a 1.5% agarose gel stained with ethidium bromide for the presence of intact 18S and 28S ribosomal RNA bands, visualized by UV transillumination at 302 nm.

treatment_protocol: After the 8 d growth period, E2 (17β-estradiol; Steraloids, Newport, RI, USA) at a final concentration of 2.6×10-7 M in 0.1% absolute ethanol or ethanol alone (final concentration 0.1%) was added to M-phase cultures.  Morphological transition from M-to-Y was induced by increasing the incubation temperature from 25°C to 37°C. Samples from 8 d old M cultures were collected, before adding E2 or ethanol alone and served as the 0 h time point. After temperature switch, samples were harvested from untreated controls, ethanol alone-treated controls or E2-treated cultures at 4 h, 12 h, 24 h, 72 h, 144 h, or 216 h time points by centrifugation at 1500 r.p.m. for 10 minutes followed by snap-freezing of the fungal mass in liquid nitrogen. These samples were stored at -80°C until RNA extraction was performed.

tag: isolate

value: Pb01 (ATCC:MYA-826)

tag: morphologic form

value: M-to-Y

tag: sample

value: M-to-Y, 4 h, Untreated-Control

tag: growth

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C

source_name: Pb01 (Mycelial form plus M-to-Y transition form)

tag: morphology

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h

tag: rna source

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: Fib IMR90 P

source_name: Embryonic Fibroblasts

growth_protocol: Human embryonic  fibroblasts

treatment_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer


title: Day 70 T2 Ethanol, Biological Rep2

description: miRNA expression data from day 70 males exposed prenatally to alcohol during Trimester 2 (GD 14 and 16)l via maternal injections of  20% ethanol in 0.15M saline with a dosage of 2.5g/kg. Saline was administered twice separated by two hours.

source_name: Day 70 T2 Ethanol

value: Whole Brain (with olfactory bulb)


title: HeyA8 Control Rep3

description: Affymetrix U133A

value: Control


title: Day 70 T3 Ethanol, Biological Rep1


title: hHFF SM3

source_name: Post natal fibroblast

growth_protocol: Human post-natal fibroblasts from a 4 year old donor


title: HeyA8 Norepinephrine Rep3

description: Affymetrix U133A


title: Day 70 CPD Control, Biological Rep3

description: miRNA expression data from Day 70 males that are matched controls for CPD mice

source_name: Day 70 CPD Control

value: Matched Control

value: CPD


title: Pb01_M-to-Y_Control-ethanol-treated_4 h_flask1_rep1

description:
13237557_OH_4_F1
Flask1_rep1. Control, Pb01  M-to-Y, 4 h

source_name: Pb01 M-to-Y, 4 h

value: M-to-Y, 4 h, ethanol-treated-Control

source_name: Pb01 (Mycelial form plus M-to-Y transition forms)

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m


title: HeyA8 Norepinephrine Rep1

description: Affymetrix U133A


title: Pb01_M-to-Y_Control-untreated_4 h_flask1_rep2

description:
13235549_C_4_F1
Flask1_rep2. Control, Pb01  M-to-Y, 4 h


title: 74S

growth_protocol: 74 year old donor senescent fibroblasts

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.


title: HeyA8 Control Rep2

description: Affymetrix U133A


title: Dif 74S Cl F

source_name: Differentiated iPSC 74S Cl F

growth_protocol: Human iPSC line derived from a 74 year old donor senescent fibroblasts, re-differentiated into fibroblasts.

value: Dif 74S F


title: Pb01_mycelia form_Control_0 h_flask2_rep2

description:
13235322_0_MYCELIA_C_F2
Flask2_rep2. Control, Pb01 mycelial form, 0 h

source_name: Pb01 mycelial form, 0 h

value: Mycelia

value: mycelial form, 0 h untreated control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C


title: Pb01 mycelia form_Control_0 h_flask2_rep1

description:
13235321_0_MYCELIA_C_F2
Flask2_rep1. Control, Pb01 mycelial form, 0 h

value: Pb01 (ATCC:MYA-826)


title: Day 70 CPD Control, Biological Rep1

value: Male

value: Whole Brain (without olfactory bulb)


title: Pb01_mycelia form_Control_0 h_flask1_rep2

description:
13235546_0_MYCELIA_C_F1
Flask1_rep2. Control, P. brasiliensis mycelial form, 0 h


title: Pb01_M-to-Y_Control-untreated_12 h_flask2_rep2

description:
13235604_C_12_F2
Flask2_rep2. Control, Pb01  M-to-Y, 12 h

source_name: P. brasiliensis M-to-Y,12 h

value: M-to-Y

value: M-to-Y, 12 h, Untreated-Control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C


title: 74P

source_name: fibroblasts 74

growth_protocol: 74 year old donor proliferative fibroblasts

value: fibroblast


title: Day 70 CPD Control, Biological Rep2


title: 96

source_name: fibroblasts 96 M

growth_protocol: 96 year old donor proliferative fibroblasts


title: Day 70 CPD Ethanol, Biological Rep2

description: miRNA Expression data from Day 70 males exposed prenatally to alcohol via mothers given free access to 10% ethanol and water as source of liquid from gestation day 0 (G0) to postnatal day 10 (P10).

source_name: Day 70 CPD Ethanol

value: Fetal alcohol exposed


title: Rif1ChIP_M-phase

status: Public on Dec 13 2011

type: genomic

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 6µg of DNA was hybridized to Affymetrix S. pombe Tiling 1.0FR Array using Affymetrix recommend component. The arrays were hybridized for 16 hours at 42ºC at 60 rpm using an Affymetrix hybridization oven.

scan_protocol: Standard protocol by Affymetrix

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Input fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.001 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction or BrdU-incorporation region will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Flag ChIPed from the strain expressing 13Myc-fused Rif1

label_protocol: About 10µg amplified DNA was fragmented to 50bp with DNase I, and the ends of the fragments were labeled with biotin-6N-ddATP by terminal transferase.

growth_protocol:
Protocol 1: The stains were grown to early exponential phase in YES medium and arrested at Metaphase at 20ºC for 5h. The arrested cells were released into subsequential phase at 30ºC for 60min.
Protocol 2: The stains were grown to early exponential phase in YES medium at 25ºC and arrested at late G2-phase at 36ºC for 3h. The arrested cells were released into subsequential phase at 25ºC for 90min and then the cells were around G1/S boundary.

extract_protocol:
The cells (1.0 x 10E9 cells) which were synchronized at appropriate cell cycle were cross-linked with 1% formaldehyde for 15 minutes and were homogenized by Multi-beads Shocker (Yasui-kikai Co., Osaka). DNA was sheared to 600 bp by sonication. Immunoprecipitation was performed by using monoclonal anti-Myc antibody (nacalai). After incubation of lysate with antibody and protein G beads (Dynal) for 4 h, beads were washed 6 times with the lysis buffer. Co-immunoprecipitated DNA was reverse-crosslinked and purified by QIAquick PCR Purification Kit (QIAGEN).
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

treatment_protocol: The stains were treated with 200µM BrdU and 25mM Hydroxyurea after Metaphase arrest.

tag: cell cycle

value: Metaphase arrested in nda3-KM311 mutant

tag: molecule tag

value: c-Myc

tag: antibody

value: Anti-c-Myc Monoclonal (nacalai), Subclass; mouse lgG1-κ), Clone; MC045; Cat No.; 04362-34


title: Cdc45ChIP_rif1∆_60minHU

source_name: Flag ChIPed from the strain expressing 3Flag-fused Cdc45 in rif1∆

extract_protocol:
The cells (1.0 x 10E9 cells) which were synchronized at appropriate cell cycle were cross-linked with 1% formaldehyde for 15 minutes and were homogenized by Multi-beads Shocker (Yasui-kikai Co., Osaka). DNA was sheared to 600 bp by sonication. Immunoprecipitation was performed by using monoclonal anti-FLAG M2 antibody (SIGMA). After incubation of lysate with antibody and protein G beads (Dynal) for 4 h, beads were washed 6 times with the lysis buffer. Co-immunoprecipitated DNA was reverse-crosslinked and purified by QIAquick PCR Purification Kit (QIAGEN).
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

value: Early S-phase in HU at 60min after release from metaphase arrest

value: FLAG

value: Monoclonal ANTI-FLAG M2 antibody(Sigma), Subclass; IgG1, Clone; M2, Cat No.; F1804


title: Rif1ChIP_G1/S_ boudnary

source_name: Flag ChIPed from the strain expressing 10Flag-fused Rif1

value: Around G1/S bundary at 90min after release from late G2-phase arrest in cdc25-22 mutant


title: Mcm4ChIP_rif1∆_60minHU

source_name: Flag ChIPed from the strain expressing 3Flag-fused Mcm4 in rif1∆


title: Input DNA from Metaphase arrested cells

source_name: Input DNA from Metaphase arrested cells

extract_protocol:
The genomic DNA was extracted and purified from the arrested at M-phase in nda-KM311 cells. The genomic DNA was sheared by sonication.
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).


title: Cdc45ChIP_Wild_60minHU

source_name: Flag ChIPed from the strain expressing 3Flag-fused Cdc45


title: Normal Ovary Control Rep3

description: Affymetrix U133A

source_name: Normal Ovary

value: Control

value: ovary


title: Pb01_M-to-Y_Control-untreated_4 h_flask1_rep1

description:
13235547_C_4_F1
Flask1_rep1. Control, Pb01 M-to-Y, 4 h

value: Pb01 (ATCC:MYA-826)

value: M-to-Y, 4 h, Untreated-Control

source_name: Pb01(Mycelial form plus M-to-Y transition form)

value: Mycelia plus M-to-Y

value: Untreated mycelial form at 0 h plus untreated M-to-Y transition form at 4, 12 24, 72, 144 and 216h

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C Plus Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m, then swtich to 37°C with 150 r.p.m

value: Total RNA (Pooled from untreated sample of 0, 4, 12, 24, 72, 144, and 216h)


title: BrdUIP_rif1∆_60minHU

source_name: BrdU IPed from BrdU-incorporated DNA

extract_protocol:
Growing nda3-KM311 cells (1.0 x 10E9 cells) expressing Thymidine Kinase under control by Adh1 promoter and rif1∆ were arrested at metaphase and release in the presence of 200µM BrdU and 25mM HU at 30ºC for 60min. BrdU was incorporated into nascent DNA during the sub-sequential S-phase. The genomic DNA was extracted and purified by Qiagen Genomic DNA Buffer Set and Genomic-tip. BrdU-incorporated DNA after shearing and denature was immuno-precipitated by anti-bromodeoxyuridine (MBL) and purified by QIAquick PCR Purification Kit (QIAGEN).
The purified Input, BrdUIP DNA were amplified by IVT as described previously (Liu, C. et al., 2003, BMC Genomics).

value: BrdU

value: Anti-bromodeoxyuridine (MBL), Subclass; mouse IgG1, Clone; 2B1, Cat No.; MI-11-3,


title: Day 70 CPD Ethanol, Biological Rep3

tag: strain

tag: gender

value: Male

value: Whole Brain (without olfactory bulb)

value: Fetal alcohol exposed

value: CPD


title: Pb01_mycelia form_Control_0 h_flask1_rep1

description:
13235545_0_MYCELIA_C_F1
Flask1_rep1. Control, Pb01 mycelial form, 0 h

value: Mycelia

value: mycelial form, 0 h untreated control

value: Modified McVeigh/Morton liquid media for 8 days at 150 r.p.m at 25°C

source_name: Pb01 (Mycelial form plus M-to-Y transition form)


title: HeyA8 Control Rep1

description: Affymetrix U133A

value: Control


title: iPSC 74P Cl H

source_name: Reprogrammed fibroblast into iPSC

growth_protocol: Human iPSC line derived from a 74 year old donor proliferative fibroblasts

value: iPSC 74P Cl H

value: induced pluripotent stem cell


title: Normal Ovary Control Rep1

description: Affymetrix U133A

tag: tissue

value: ovary


title: Normal Ovary Control Rep2

description: Affymetrix U133A


title: Day 70 CPD Ethanol, Biological Rep1

tag: treament

tag: model


title: iPSC 74S Cl F

growth_protocol: Human iPSC line derived from a 74 year old donor replicative senescent fibroblast

tag: cell line

value: iPSC 74S Cl F


title: 05 MINUS OHT 3

city: New York

first: Danae

last: Schulz

state: NY

address: 1230 York Ave.

institute: Rockefeller University

description: AMuLV pro-B cell line expressing Gfi1b-estrogen receptor fusion protein

hyb_protocol: done by UCSF core facility

scan_protocol: done by UCSF core facility

data_processing: Partek software 2008

source_name: Wt

label_protocol: done by UCSF core facility

growth_protocol: cell lines were grown in RPMI supplemented with 10%FCS

extract_protocol: trizol followed by Rneasy

treatment_protocol: cels were treated for 12 hours with tamoxifen to induce overexpression of Gfi1b (Gfi1b fused to estrogen receptor domain)

value: Abelson B cell line


title: 06 PLUS OHT 3

source_name: Gfi1b overexpressed


title: 03 MINUS OHT 2


title: R11_786_Pipes8

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Gene 1.0 ST arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.

data_processing: Data processing was done using Partek Genomics Suite 6.5 software. RMA was used to summarize and quantile normalize and the probe data into probe set expression values using the adjust for GC content and background correction options.

source_name: Tumor cells alone

label_protocol: Nugen Applause® WT-Amp Plus ST System

growth_protocol: Ep5 cells cultured in DMEM 10% FCS, 1% Penicillin/Streptomycin and 2 mM L-Glutamine

extract_protocol: RNA was extracted using Qiagen RNAeasy

tag: background strain

value: Ep5 (EpRas) cells

tag: platelet description

value: Wild-type C57BL/6 platelets isolated by centrifugation

tag: treatment protocol

value: Sub-confluent EP cells alone


title: FTL-CB1

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Bisulfite Converted and hybridized to Illumina Infinium HumanMethylation27 Arrays

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

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

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: normal cerebella

label_protocol: Standard Illumina Protocol

extract_protocol: High molecular weight genomic DNA was extracted using standard SDS/Proteinase K digestion, followed by phenol extraction and ethanol precipitation.

tag: sentrix position

tag: tumor type

tag: tumor source

tag: patient gender

value: Female

tag: patient age at diagnosis

tag: medulloblastoma subgroup


title: FTL-CB2

value: Male


title: R11_790_Sup9

source_name: Tumor cells and centrifuged platelet releasate co-culture

value: Wild-type C57BL/6 platelets releasate

value: Thrombin treated platelets were centrifuged, releasate was added to EP5 culture for 24 hours followed by RNA isolation


title: ADT-CB4


title: R11_785_Sup7


title: 01 MINUS OHT 1A


title: R11_788_Pellet9

source_name: Tumor cells and centrifuged platelet pellet co-culture

value: Wild-type C57BL/6 pelleted platelets

value: Thrombin treated platelets were centrifuged, pellet was resuspended and added to EP5 culture for 24 hours followed by RNA isolation


title: 02 PLUS OHT 1


title: ADT-CB5


title: MB-1395

source_name: brain tumor

value: medulloblastoma

value: metastatic tumor


title: MB-1324

value: Group D


title: MB-321

value: primary tumor


title: MB-1399


title: MB-1323


title: MB-1394


title: Dif 74P Cl H

source_name: Differentiated iPSC 74P Cl H

growth_protocol: Human iPSC line derived from a 74 year old donor proliferative fibroblasts, re-differentiated into fibroblasts

value: Dif iPSC 74P Cl H

tag: cell type

value: fibroblast


title: R11_789_PLT9

source_name: Tumor cells and platelet co-culture

value: roughly 1000:1 Platelet-Ep5 ratio cultured together for 24 hours


title: PHBuf6

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.

data_processing:
Data processing was done using Partek Genomics Suite 6.4 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
probeSet list file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.ps
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps

source_name: Tumor cells and platelets combined just prior to RNA isolation

label_protocol: Affymetrix GeneChip® WT Sense Target Labeling

value: roughly 1000:1 Platelet-cell ratio combined immediately prior to RNA isolation


title: R11_784_Pellet7

value: Ep5 (EpRas) cells


title: 04 PLUS OHT 2A

value: Abelson B cell line


title: IPSC 96 Cl 1

growth_protocol: Human iPSC line derived from a 96 year old donor proliferative fibroblasts

value: iPSC 96

value: induced pluripotent stem cell


title: MB-525

value: Group C


title: MB-1398

value: Male


title: R11_787_Pipes9

value: Sub-confluent EP cells alone


title: R11_783_PLT7

value: Wild-type C57BL/6 platelets isolated by centrifugation


title: MB-579

value: Female


title: R11_721_PLT8


title: MB-529

value: medulloblastoma


title: PHBuf4


title: MB-524

value: metastatic tumor


title: PLT2


title: PLT5


title: MB-528

value: Group D


title: PHBuf5


title: MB-522

value: primary tumor


title: Pipes3


title: PLT3


title: Pipes5


title: PLT1


title: R11_722_Pellet8

value: Wild-type C57BL/6 pelleted platelets

value: Thrombin treated platelets were centrifuged, pellet was resuspended and added to EP5 culture for 24 hours followed by RNA isolation


title: R11_723_Sup8

value: Wild-type C57BL/6 platelets releasate

value: Thrombin treated platelets were centrifuged, releasate was added to EP5 culture for 24 hours followed by RNA isolation


title: Pipes1

value: Ep5 (EpRas) cells


title: PLT4

value: roughly 1000:1 Platelet-Ep5 ratio cultured together for 24 hours


title: MB-523


title: MB-527


title: R11_782_Pipes7


title: Pipes4


title: CUS2_delete (Cy5) vs. CUS2 (Cy3) at 30C

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

description: A complete description of the protocols used can be found in the accompanying manuscript.

hyb_protocol: Competitive hybridization at 60C for 16 hours

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 6.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global LOWESS regression implemented in the Bioconductor marray package.

organism: Saccharomyces cerevisiae

label_protocol: Aminoallyl dUTP incorporation in cDNA reaction, followed by coupling to NHS-ester

extract_protocol: Phenol extraction

tag: genotype/variation

value: CUS2 deletion

tag: environmental factor

value: growth at 30C


title: pSAP2 biological rep3

first: Kumiko

last: Nakada-Tsukui

address: 1-23-1, Toyama, Shinjyuku-ku

institute: National Institute of Infectious Diseases

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 °C on GeneChip Eh_Eia520620F_Ei Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing: Raw probe intensities were generated by the GeneChip Operating Software (GCOS) and GeneTitan Instrument. Resulting expression values were analyzed by Genespring GX 10.0.2 to identify differentially expressed genes

organism: Entamoeba histolytica

source_name: mock vector control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: pSAP2, pSAP2-CPBF1 transfected cells were cultured at 35.5C in BIS medium supplied with 10mg/mL G418.

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

tag: strain

tag: transfected with

value: pSAP2 vector

value: vector transformed control


title: TP06-612

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: End Ca_frozen_LCM

hyb_protocol: Labeled RNAs were hybridized according to manufacterer's specifications (Affymetrix) for the HG-U133 plus 2.0 Gene Chip system, see Chapter 3 of Gene Chip® Expression Technical Manual (2005-2009 Affymetrix, Inc) for protocol.

scan_protocol: Hybridized samples were washed, stained and scanned according to manufacterer's specifications (Affymetrix) for the HG-U133 plus 2.0 Gene Chip system, see protocol in GeneChip® Expression Wash, Stain and Scan User Manual.

data_processing: All expression data were normalized to a target intensity of 500 using Affymetrix's MAS5.0 algorithm. Affymetrix .CEL files were processed with the program GCOS to generate signal valuses. All .CEL files were scaled to a global median intensity target intensity of 500. Hieracrchical clustering of samples was performed with Cluster 3.0 and the dendograms were visualized with Tree View (Eisen Lab, University of California, Berkeley). Clustering was performed with the entire gene list (unsupervised) to determine wheter there are groupings of samples and the same software was used to generate heat maps of the most differentially expressed genes. Differential gene expression betweeen groups of samples was performed using BRB array tools from the National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html). The biological annotation of differentially expressed gene lists were carried out by a number of methods including DAVID (http://david.abcc.ncifcrf.gov/), IPA (Ingenuity Systems, Redwood City, CA) and MetaCore (GeneGo, San Diego, CA).

label_protocol: Extracted RNA was processed using the GeneChip two cycle cDNA synthesis kit (Affymetrix), see Chapter 2 of Gene Chip® Expression Technical Manual (2005-2009 Affymetrix, Inc.) for protocol.

growth_protocol: Fresh frozen cancer specimens from 91 stage I endometrial patients were examined. Normal endometrial samples from twelve age matched postmenopausal women were used for comparison. All tissues were collected under an IRB approved protocol at the corresponding institutions. Specimens were harvested by pathologists and frozen within one hour of excision and each uterine tumor was frozen until the time of analysis. Tissue specimens were evaluated by one of two board certified gynecologic pathologists using H&E staining to confirm the diagnosis.

extract_protocol: Approximately 50ng of Total RNA was extracted from each sample with the Qiagen RNeasy® Micro Kit (Qiagen, 2003) by the manufacters suggested protocol for Total RNA Isolation from Microdissected Cryosections. See Rneasy® Micro Handbook Qiagen 4/2003.

treatment_protocol: Laser Capture microscopy was used to dissect cancer cell from tumors or epithelium from normal endometria to provide material for RNA extractions. Approximately 5-8 slides (with tissue samples 10 microns thick) of LCM microdissection were required for each cancer case and 20 slides of LCM were required for each normal. Cancer samples were microdissected to provide >95% purity of cancer. Normal endometria were dissected to provide >95% purity of normal epithelial cells.

tag: race

value: african america

tag: age (years)

tag: stage

tag: grade

tag: histology

value: inactive endometrium


title: LSM6_delete (Cy5) vs. LSM6 (Cy3) at 30C

hyb_protocol: Competitive hybridization at 60C for 16 hours.

tag: phenotype/variation

value: LSM6 deletion


title: TP06-998

description: End Ca_frozen_LCM

value: caucasian

value: atrophic endometrium


title: Bdf1_delete (Cy5) vs. BDF1 (Cy3) at 30C

value: Bdf1 deletion


title: CPBF1gs biological rep1

source_name: CPBF1 gene silenced strain

value: pSAP2-CPBF1 plasmid

value: CPBF1-gene silenced


title: TP06-708

description: End Ca_frozen_LCM


title: CFT2-ts (Cy5) vs. CFT2 (Cy3) at 37C

value: growth at 25C, shift at 37C for 15 minutes


title: CPBF1gs biological rep2

description: 090406 CPBF1gs_(Eh_Eia520620F_Eh)


title: Pipes2

tag: background strain

tag: cell line

tag: platelet description

tag: treatment protocol

value: Sub-confluent EP cells alone


title: VPS72_delete (Cy5) vs. VPS72 (Cy3) at 30C

value: VPS72 deletion


title: YTH1-ts (Cy5) vs. YTH1 (Cy3) at 16C

value: growth at 25C, shift at 16C for 15 minutes


title: 3007-ls

description: End Ca_frozen_LCM

value: african american

value: IB

value: papillary serous


title: TP06-872-lcm

description: End Ca_frozen_LCM

value: weakly proliferative w/cystic changes


title: TP07-152

description: End Ca_frozen_LCM

value: secretory endometrium


title: MUD2_delete (Cy5) vs. MUD2 (Cy3) at 30C

value: MUD2 deletion

value: growth at 30C


title: CPBF1gs biological rep3


title: TP06-727-993

description: End Ca_frozen_LCM

value: inactive endometrium


title: TP07-726B

description: End Ca_frozen_LCM


title: YTH1-ts (Cy5) vs. YTH1 (Cy3) at 37C


title: TP06-963

description: End Ca_frozen_LCM

value: caucasian

value: cystic atrophy with sessile polyp


title: TP02-402

description: End Ca_frozen_LCM

value: atrophic endometrium


title: RSC9-ts (Cy5) vs. RSC9 (Cy3) at 25C

value: growth at 25C


title: 3416-lcm

description: End Ca_frozen_LCM


title: Bdf2_delete (Cy5) vs. BDF2 (Cy3) at 30C

value: Bdf2 deletion

value: BDF2 (WT)


title: FIP1-ts (Cy5) vs. FIP1 (Cy3) at 37C

value: growth at 25C, shift at 37C for 15 minutes


title: G609-lcm

description: End Ca_frozen_LCM

value: unknown


title: G029-lcm

description: End Ca_frozen_LCM

value: IA


title: G519-lcm

description: End Ca_frozen_LCM

value: african american


title: G929-lcm

description: End Ca_frozen_LCM

value: american indian

value: I


title: Metastatic acral melanoma

city: London

first: Simon

last: Furney

address: 237 Fulham Road

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: Labelled cRNA was subsequently hybri- dised to Illumina Sentrix-human 6 version 2 expression bead-chips

scan_protocol: Standard Illumina scanning protocol

data_processing: Samples were variance stabilising transformed and quantile normalised along with 4 other samples in the batch (other samples not included in this series)

source_name: lymph node

label_protocol: 200 ng of each RNA sample was amplified using the Illumina Totalprep RNA amplification kit following the manufacturer’s instructions (Ambion, UK).

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and eluted in RNAse-free water.

tag: gender

value: Male

tag: tissue

value: lymph node


title: pSAP2 biological rep2

description: 090406 pSAP2_(Eh_Eia520620F_Eh)

value: pSAP2 vector

value: vector transformed control


title: 5278-lcm

description: End Ca_frozen_LCM

value: endometrioid


title: G206-lcm

description: End Ca_frozen_LCM

value: asian

value: IB

value: papillary serous


title: G668-lcm

description: End Ca_frozen_LCM

value: caucasian


title: SNT309_delete (Cy5) vs. SNT309 (Cy3) at 30C

data_processing: Spot ratio data were log2 transformed and normalized within each array using global LOWESS regression implemented in the Bioconductor marray package

value: SNT309 deletion

value: growth at 30C


title: G710-lcm

description: End Ca_frozen_LCM


title: 2880 min (late-stationary LSP)_biol4_tech1

type: mixed

city: Western Bank

first: Matthew

middle: D

last: Rolfe

state: Sheffield

address: Firth Court

department: Department of Molecular Biology and Biotechnology

institute: University of Sheffield

hyb_protocol: Slides blocked with DCE according to protocol in PMID 11266573. Hybridization and washing: 1) Dry down the 120 ul of labelled cDNA/gDNA to 10 ul in a speed-vacuum concentrator.  2) To 10 μl of dried down labelling reactions add:  a) 1.5 μl of 50X Denhardts solution  b) 2.25 μl of 20X SSC  c) 1.125 μl of E. coli tRNA (10 μg/μl) (Sigma, Cat: R8759)  d) 0.375 μl of 1M HEPES, pH 7.0.  3) Add 0.375 μl of 10% SDS to the mixture.  4) Incubate 100 °C for 2 min. Let stand on the bench at room temperature for 5-10 min.  5) Spin in a microfuge at full speed for 5 min, transfer supernatant to clean tube and repeat spin.  6) Place a microarray slide in a hybridisation chamber and apply the hybridisation mixture under a glass coverslip.  7) Humidify the chamber with a few drops of 3x SSC.  8) Screw the lid onto the chamber and place at the bottom of a water bath at 63°C overnight.  9) Remove the slides from the hybridisation chambers and immediately place them in a plastic slide rack in wash buffer.  10) Wash in the following washes:  a) Twice at 63°C wash in 2 X SSC, 0.1% SDS with agitation for 5 mins.  b) Twice at room temperature in 1 X SSC with agitation for 5 min.  c) Twice at room temperature in 0.2 X SSC with agitation for 5 min.  11) Spin dry in a centrifuge at 1200 rpm for 5 min at room temp in an enclosed slide chamber (with blotting paper lining the bottom of the chamber).  12) Store in the dark awaiting scanning.

scan_protocol: Axon GenePix4000A, 10nm resolution scan (see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols).

data_processing:
Feature extraction was carried out within BlueFuse forMicroarrays v3.1 following manufacturer's instructions. Raw data files were generated, which are attached. The raw data files were then post-processed using block-by-block median shifting within BlueFuse. This brought the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. All ratios were then transformed such that the ratios shown are relative to the inoculum (Inoc). For early timepoints (Inoc to 120 minutes), this involved dividing the normalised ratio for each replicate by the median of the Inoculum profiles from the same biological replicate; for later timepoints (ME to LSP), each replicate was divided by the median of all inoculum profiles. Data were processed for microarray features corresponding to Salmonella Typhimurium LT2 or SL1344 only.

The block-by-block median-shifted un-logged ratios showing expression relative to the 0 minute timepoint are available in 'GSE22294_ratios__relative_to_0min.txt', which is linked to the Series GSE22294 record as a supplementary file.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Reference genomic DNA

label_protocol: 1) In a sterile microfuge tube add 2 ug of chromosomal DNA and bring volume to 21 ul with RNase-free water.  2) Add 20 ul of 2.5X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labeling System (18094011). Boil 5 min, then put on ice for 5 min.  3) On ice, add:    5 μl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH8.0; 1 mM EDTA);    3 μl of Cy3-dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321);    1 μl of Klenow enzyme from the kit.  4) Spin briefly and incubate the reaction mixture at 37°C overnight.  5) Use a Qia-quick PCR purification kit (Qiagen Cat: 28104) to remove unincorporated/quenched Cy dyes. Elute into 100 ul of RNase-free water.  6) This protocol supplies sufficient labelled DNA for five hybridisations. Mix a 1/5 volume (i.e. 20 μl) of the labelled DNA with each labelled cDNA.

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 grown to stationary phase at 37°C.

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).

tag: sample type

value: reference

source_name: late-stationary phase culture

label_protocol: Two-step labelling of RNA protocol: 1) Set up random priming reactions in 1.5 ml microfuge tubes. Add 2 ug total RNA and 5 ug of random hexamers (Invitrogen, Cat: 48190011) and make up to 15 ul with RNase-free water. 2) Incubate 72°C for 10 min then chill on ice for 10 min.   3) Using reagents from SuperScript III reverse transcriptase (Stratagene) add the following to each tube: 3.0 ul of 10 X RT buffer; 3.0 ul of 0.1M DTT; 0.6 ul of 50x dNTP's (25mM each dCTP, dATP, dGTP, dTTP); 4.4 ul RNase-free water.  4) Add 4 μl of 50U/ul SuperScript III reverse transcriptase.   5) Incubate overnight at 37°C.   6) Add 15 μl of freshly prepared 0.1M NaOH and hydrolyse the RNA at 70°C for 10 minutes. Add 15 μl of 0.1M HCl to neutralise the alkali.   7) Clean up using Qia-quick PCR purification kit (Qiagen, Cat: 28104), eluting into 100 μl RNase-free water and dry-down in a speed-vac to 21 ul.  8) Add 20 ul of 2.5X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labeling System (18094011). Boil 5 min, then put on ice for 5 min.  9) On ice, add:    5 μl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH8.0; 1 mM EDTA);    3 μl of Cy5-dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321);    1 μl of Klenow enzyme from the kit.   10) Spin briefly and incubate the reaction mixture at 37°C overnight.  11) Use a Qia-quick PCR purification kit (Qiagen Cat: 28104) to remove unincorporated/quenched Cy dyes. Elute into 100 ul of RNase-free water. 12) Add 20 ul of Cy3-labelled gDNA to the 100 ul cDNA and use for hybridisation.

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 grown in LB pH 7.0 at 25°C.

extract_protocol: 1) For each sample harvest 2.0 OD600 units of bacterial culture (for example 4 ml of a culture with an OD600 of 0.5).  1a) For exponential and stationary phase cultures: prepare a 50 ml Falcon tube containing 1/4 of the culture volume of ice-cold 5% (v/v) phenol pH 4.3, 95% (v/v) ethanol. Add the appropriate volume of culture e.g. add 4 ml culture to 1 ml of phenol/ethanol. Stand on ice for at least 30 min but no longer than 2 hours to stabilise the RNA and prevent degradation.  1b) For lag phase samples: add 187 ml ice-cold 5% (v/v) phenol pH 4.3, 95% (v/v) ethanol directly to the 750 ml lag phase culture volume. Mix well and stand on ice for at least 30 min but no longer than 2 hours to stabilise the RNA and prevent degradation.  2) Centrifuge samples at 3220 x g at 4°C for 10 min. Discard supernatant, resuspend bacterial pellets using residual liquid in tubes and transfer to 1.5 ml microcentrifuge tubes.  3) Spin tubes 60 secs at maximum speed in a microfuge and discard remaining liquid.  4) Store pellets by freezing at -80°C. Pellets can be kept for up to 1 month before continuing with RNA prep.  5) Resuspend pellets in 100 μl TE buffer containing 50 mg/ml lysozyme. Incubate at room temperature for 5 min.  6) Carry out RNA extraction using the SV Total RNA Purification kit (Promega; Z3100) following manufacturer's instructions, including the DNAse incubation step.  7) Elute RNA from the columns into 100 ul RNAse-free distilled water and allow to stand for 1 min before eluting at 4500 x g for 2 min.   8) Check the RNA concentration using a spectrophotometer and check for degradation using the Aligent Bioanalyzer.

tag: time

value: 2880 minutes

tag: growth phase

value: late stationary

tag: biological replicate


title: Primary acral melanoma

source_name: Toe nail bed

value: Toe nail bed


title: 2880 min (late-stationary LSP)_biol3_tech2

tag: strain


title: pSAP2 biological rep1

tag: transfected with

tag: genotype/variation


title: TP02-478

description: End Ca_frozen_LCM

tag: race

tag: age (years)

tag: stage

value: inactive endometrium


title: G026-lcm

description: End Ca_frozen_LCM

value: african american

value: unknown

tag: grade

tag: histology


title: TP06-987

description: End Ca_frozen_LCM

value: secretory endometrium


title: TP06-855

description: End Ca_frozen_LCM

value: atrophic endometrium


title: 5113-scrape

description: End Ca_frozen_LCM

value: IA


title: 2880 min (late-stationary LSP)_biol3_tech1


title: 5072-scrape

description: End Ca_frozen_LCM

value: endometrioid


title: 2880 min (late-stationary LSP)_biol4_tech2


title: G425

description: End Ca_frozen_LCM


title: 3386-scrape

description: End Ca_frozen_LCM


title: 2907-lcm

description: End Ca_frozen_LCM


title: preCC_OR3515_f57_Flu_D4_2

city: Portland

first: Daniel

last: Bottomly

address: 3181 Sam Jackson Park Rd.

institute: OHSU

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3515f57

hyb_protocol: Individual cRNA samples were hybridized to Agilent mouse whole-genome oligonucleotide 4 × 44 microarrays according to manufacturer instructions.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor (AFE) version 8.1.1.1. The AFE software was used to perform image analysis including significance of signal and spatial detrending and to apply a universal error model.

data_processing: The Agilent arrays were background corrected using the Normal-Exponential convolution model and normalized using quantile normalization

source_name: lung tissue; 4 DPI; animal OR3515f57

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA).  Only a single color was used (Cy3).

extract_protocol: At 4 days post-infection, mice were sacrificed and lung tissue harvested and placed in RNAlater (Applied Biosystems/Ambion, Austin, Tx)  and stored at -80o C.  The tissues were subsequently homogenized, and total RNA extracted

tag: animal

value: lung

tag: group

value: low response


title: 5046-lcm

description: End Ca_frozen_LCM


title: 3381-scrape

description: End Ca_frozen_LCM

value: IB

value: papillary serous


title: 3526-lcm

description: End Ca_frozen_LCM

value: caucasian


title: 900 min (early-stationary ESP)_biol4_tech2

source_name: early-stationary phase culture

value: 900 minutes

value: early stationary


title: preCC_OR3011_f47_Flu_D4_2

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3011f47

source_name: lung tissue; 4 DPI; animal OR3011f47

value: high response


title: 900 min (early-stationary ESP)_biol4_tech1

value: reference


title: 3278-scrape

description: End Ca_frozen_LCM


title: 3765-ls

description: End Ca_frozen_LCM


title: 3598

description: End Ca_frozen_LCM


title: 900 min (early-stationary ESP)_biol3_tech1


title: 900 min (early-stationary ESP)_biol3_tech2


title: preCC_OR555_f58_Flu_D4_2

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR555f58

source_name: lung tissue; 4 DPI; animal OR555f58


title: preCC_OR3415_f49_Flu_D4_2

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3415f49

source_name: lung tissue; 4 DPI; animal OR3415f49


title: 630 min (late-exponential LE)_biol4_tech2

source_name: late-exponential phase culture

value: 630 minutes

value: late exponential


title: preCC_OR3389_f49_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3389f49

source_name: lung tissue; 4 DPI; animal OR3389f49


title: 3094-lcm

description: End Ca_frozen_LCM


title: 630 min (late-exponential LE)_biol4_tech1


title: 3112-lcm

description: End Ca_frozen_LCM


title: 3510-lcm

description: End Ca_frozen_LCM


title: preCC_OR3207_f45_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3207f45

source_name: lung tissue; 4 DPI; animal OR3207f45


title: 3748-lcm

description: End Ca_frozen_LCM


title: 630 min (late-exponential LE)_biol3_tech2


title: 3514-lcm

description: End Ca_frozen_LCM


title: 630 min (late-exponential LE)_biol3_tech1


title: 3010-lcm

description: End Ca_frozen_LCM


title: preCC_OR5515_f122_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5515f122

source_name: lung tissue; 4 DPI; animal OR5515f122


title: preCC_OR3426_f49_Flu_D4_2

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3426f49

source_name: lung tissue; 4 DPI; animal OR3426f49


title: 3348-scrape

description: End Ca_frozen_LCM


title: 3799-lcm

description: End Ca_frozen_LCM


title: 3527-lcm

description: End Ca_frozen_LCM


title: 3557-ls

description: End Ca_frozen_LCM


title: preCC_OR5308_f138_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5308f138

source_name: lung tissue; 4 DPI; animal OR5308f138


title: G643-lcm

description: End Ca_frozen_LCM

value: IC


title: preCC_OR820_f53_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR820f53

source_name: lung tissue; 4 DPI; animal OR820f53


title: preCC_OR559_f156_Flu_D4_2

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR559f156

source_name: lung tissue; 4 DPI; animal OR559f156


title: 3789-scrape

description: End Ca_frozen_LCM

value: hispanic


title: 3749-lcm

description: End Ca_frozen_LCM


title: G016

description: End Ca_frozen_LCM

value: unknown


title: 380 min (mid-exponential ME)_biol4_tech2

source_name: mid-exponential phase culture

value: 380 minutes

value: mid-exponential


title: G205

description: End Ca_frozen_LCM

value: endometrioid


title: 380 min (mid-exponential ME)_biol4_tech1

source_name: Reference genomic DNA


title: 3735-lcm

description: End Ca_frozen_LCM


title: 380 min (mid-exponential ME)_biol3_tech2


title: preCC_OR1516_f60_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR1516f60

source_name: lung tissue; 4 DPI; animal OR1516f60

value: lung


title: G039-lcm

description: End Ca_frozen_LCM


title: 380 min (mid-exponential ME)_biol3_tech1


title: 5062-scrape

description: End Ca_frozen_LCM


title: 3638-lcm

description: End Ca_frozen_LCM


title: preCC_OR5130_f134_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5130f134

source_name: lung tissue; 4 DPI; animal OR5130f134

value: low response


title: preCC_OR1639_f140_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR1639f140

source_name: lung tissue; 4 DPI; animal OR1639f140


title: 3716-lcm

description: End Ca_frozen_LCM


title: 120 min (lag phase)_biol1_tech1

source_name: 120 minute lag phase culture

value: 120 minutes

value: lag phase


title: preCC_OR3564_f38_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3564f38

source_name: lung tissue; 4 DPI; animal OR3564f38


title: 5178-scrape

description: End Ca_frozen_LCM

value: african american

value: IA


title: DNA from Metastatic acral melanoma

description: Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Affymetrix Power Tools apt-probeset-genotype implementing birdseed-v2.models

source_name: lymph node

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tumour DNA was extracted using the DNAaesy Blood and Tissue Kit (Qiagen Ltd, Crawley, UK) according to the manufacturer’s recommendations. Germline DNA was extracted from peripheral blood mononclear cells using the DNAaesy Blood and Tissue Kit (QIAGEN).

value: lymph node

value: Male


title: 5410-lcm

description: End Ca_frozen_LCM

value: caucasian


title: G518

description: End Ca_frozen_LCM


title: preCC_OR219_f64_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR219f64

source_name: lung tissue; 4 DPI; animal OR219f64


title: 3172-scrape

description: End Ca_frozen_LCM


title: 120 min (lag phase)_biol1_tech2

value: reference


title: 120 min (lag phase)_biol2_tech2


title: 3986-lcm

description: End Ca_frozen_LCM


title: 3339-lcm

description: End Ca_frozen_LCM


title: preCC_OR4285_f149_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR4285f149

source_name: lung tissue; 4 DPI; animal OR4285f149

value: high response


title: 3269-lcm

description: End Ca_frozen_LCM


title: 3217-lcm

description: End Ca_frozen_LCM


title: preCC_OR5389_f125_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5389f125

source_name: lung tissue; 4 DPI; animal OR5389f125


title: 3496-lcm

description: End Ca_frozen_LCM


title: 3409-lcm

description: End Ca_frozen_LCM


title: preCC_OR157_f52_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR157f52

source_name: lung tissue; 4 DPI; animal OR157f52


title: 120 min (lag phase)_biol2_tech1


title: 90 min (lag phase)_biol2_tech1

source_name: 90 minute lag phase culture

value: 90 minutes


title: 3769

description: End Ca_frozen_LCM


title: preCC_OR3370_f40_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3370f40

source_name: lung tissue; 4 DPI; animal OR3370f40


title: Germline DNA from blood

source_name: blood

value: blood


title: 3125-lcm

description: End Ca_frozen_LCM


title: 3406-lcm

description: End Ca_frozen_LCM

value: IB


title: 90 min (lag phase)_biol1_tech2


title: DNA from Primary acral melanoma

source_name: Toe nail bed

value: Toe nail bed


title: 3024-lcm

description: End Ca_frozen_LCM

value: unknown


title: 3379-scrape

description: End Ca_frozen_LCM

value: endometrioid


title: preCC_OR3410_f46_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3410f46

source_name: lung tissue; 4 DPI; animal OR3410f46

value: lung


title: 60 min (lag phase)_biol2_tech2

source_name: 60 minute lag phase culture

value: 60 minutes


title: 90 min (lag phase)_biol1_tech1

source_name: Reference genomic DNA


title: 5258-lcm

description: End Ca_frozen_LCM


title: 3080-lcm

description: End Ca_frozen_LCM


title: preCC_OR5454_f133_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5454f133

source_name: lung tissue; 4 DPI; animal OR5454f133


title: 60 min (lag phase)_biol1_tech2


title: 60 min (lag phase)_biol2_tech1


title: 3116-scrape

description: End Ca_frozen_LCM


title: preCC_OR4010_f145_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR4010f145

source_name: lung tissue; 4 DPI; animal OR4010f145


title: 60 min (lag phase)_biol1_tech1


title: 3587-ls

description: End Ca_frozen_LCM


title: preCC_OR3232_f38_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3232f38

source_name: lung tissue; 4 DPI; animal OR3232f38


title: 3783-lcm

description: End Ca_frozen_LCM


title: preCC_OR2291_f89_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR2291f89

source_name: lung tissue; 4 DPI; animal OR2291f89

value: low response


title: 3461

description: End Ca_frozen_LCM


title: G007

description: End Ca_frozen_LCM

value: IC


title: 3583-lcm

description: End Ca_frozen_LCM


title: preCC_OR5168_f148_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5168f148

source_name: lung tissue; 4 DPI; animal OR5168f148


title: 40 min (lag phase)_biol2_tech1

source_name: 40 minute lag phase culture

value: 40 minutes

value: lag phase


title: 40 min (lag phase)_biol2_tech2


title: 3729-lcm

description: End Ca_frozen_LCM


title: 90 min (lag phase)_biol2_tech2


title: 5192-scrape

description: End Ca_frozen_LCM

value: american indian


title: 40 min (lag phase)_biol1_tech1


title: 2795-lcm

description: End Ca_frozen_LCM


title: preCC_OR2417_f56_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR2417f56

source_name: lung tissue; 4 DPI; animal OR2417f56


title: preCC_OR5140_f131_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5140f131

source_name: lung tissue; 4 DPI; animal OR5140f131


title: 2861-scrape

description: End Ca_frozen_LCM


title: 5320-scrape

description: End Ca_frozen_LCM


title: preCC_OR1114_f62_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR1114f62

source_name: lung tissue; 4 DPI; animal OR1114f62


title: 40 min (lag phase)_biol1_tech2


title: 20 min (lag phase)_biol2_tech2

source_name: 20 minute lag phase culture

value: 20 minutes


title: 5021-lcm

description: End Ca_frozen_LCM

value: caucasian


title: 2933-ls

description: End Ca_frozen_LCM

value: african american


title: 5025-scrape

description: End Ca_frozen_LCM


title: 20 min (lag phase)_biol2_tech1

value: reference


title: 20 min (lag phase)_biol1_tech1


title: preCC_OR3009_f40_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3009f40

source_name: lung tissue; 4 DPI; animal OR3009f40

value: high response


title: 3068-scrape

description: End Ca_frozen_LCM


title: 3509-scrape

description: End Ca_frozen_LCM


title: 20 min (lag phase)_biol1_tech2


title: 3025-lcm

description: End Ca_frozen_LCM

value: IA


title: preCC_OR3007_f48_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3007f48

source_name: lung tissue; 4 DPI; animal OR3007f48


title: 2944-lcm

description: End Ca_frozen_LCM


title: 5008-scrape

description: End Ca_frozen_LCM

value: IB


title: G501

description: End Ca_frozen_LCM


title: G630

description: End Ca_frozen_LCM


title: preCC_OR167_f171_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR167f171

source_name: lung tissue; 4 DPI; animal OR167f171


title: 4 min (lag phase)_biol2_tech1

source_name: 4 minute lag phase culture

value: 4 minutes


title: 4 min (lag phase)_biol1_tech2


title: 5407-lcm

description: End Ca_frozen_LCM


title: 2946-scrape

description: End Ca_frozen_LCM


title: preCC_OR5030_f127_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5030f127

source_name: lung tissue; 4 DPI; animal OR5030f127


title: 3458-scrape

description: End Ca_frozen_LCM


title: Healthy controls-plasma

city: Shenzhen

first: Honglei

last: Wang

state: Guangdong

address: No 1017, dongmen north road

department: Clinical Medical Research Center of The Second Clinical Medical College (Shenzhen People’s Hospital)

country: China

institute: Jinan Univesity

description: healthy control (HCs)

hyb_protocol: Hybirdization mixture was assembled according to the protocols provided by the manufacturer. Assembled slide chamber in rotisserie was placed in a hybridization oven set to 55C.  hybridization rotator was set to to rotate at 20 rpm. Hybridization at 55 for 20 hours.

scan_protocol: Slides were scanned immediately after washing on the Microarray Scanner (Agilent p/nG2565BA) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software version 9.5.3 using default miRNA protocol to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: healthy control (HCs)

label_protocol: Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) generates fluorescent miRNA with a sample input of 100ng of total RNA. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule with greater than 90%efficiency. The Agilent miRNA Complete Labeling and Hyb Kit provides all the needed components for sample labeling and hybridization preparation.Dephosphorylate the sample by incubating the reaction at 37℃ in a circulating water bath or heat block for 30 minutes.Add DMSO to each sample.then heat,ice,assemble labeling reaction,incubate 2 hour,16℃,according to the protocols provided by the manufacturer.Completely dry the samples. Use a vacuum concentrator at 45 to 55°C or on the medium-high heat setting. This step may take up to 2 hours.

extract_protocol: Plasma was thawed on ice. The mirVana PARIS kit (Ambion) was used to isolate RNA with EDTA-plasma from 10 SLE patients, 10 RA patients,10 healthy control.  All RNAs were mix together in each sample group respectively, with equal amount (100ng) of RNA ensured from each pooling sample.

treatment_protocol: Whole blood (2.5 ml) of subjects was collected via a direct venous puncture into tubes, containing sodium citrate (BD Biosciences 363048). All blood was processed for isolation of plasma with 4 hours of collection. Blood was procession by spinning at 2000×g for 10 minutes at room temperature. Then plasma was transferred to a freshRNase-free tuber and stored at -80C.

tag: patient condition

value: healthy subjects without evidence for SLE or RA

value: blood plasma

tag: f

value: M ratio:9:1

tag: tag


title: SLE-plasma

description: system lupus erythematosus (SLE)

source_name: system lupus erythematosus (SLE) patient

value: patients never been treated with disease-modifying antirheumatic drugs (DMARDs) or other immunosuppressive drugs

tag: tissue


title: preCC_OR2075_f6_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR2075f6

source_name: lung tissue; 4 DPI; animal OR2075f6

value: lung

value: low response


title: RA-plasma

description: rheumatoid arthritis (RA)

source_name: rheumatoid arthritis (RA) patient


title: preCC_OR3181_f47_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3181f47

source_name: lung tissue; 4 DPI; animal OR3181f47


title: 4 min (lag phase)_biol1_tech1

source_name: Reference genomic DNA

tag: sample type

tag: time


title: preCC_OR3_f78_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3f78

source_name: lung tissue; 4 DPI; animal OR3f78


title: 4 min (lag phase)_biol2_tech2

tag: growth phase

tag: biological replicate


title: 0 min (Standardized inoculum)_biol2_tech2

tag: strain

source_name: 48-hour-old standardized inoculum culture

value: 0 minutes


title: 3433-lcm

description: End Ca_frozen_LCM

value: endometrioid


title: 0 min (Standardized inoculum)_biol2_tech1


title: preCC_OR381_f71_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR381f71

source_name: lung tissue; 4 DPI; animal OR381f71


title: preCC_OR3154_f39_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3154f39

source_name: lung tissue; 4 DPI; animal OR3154f39


title: 0 min (Standardized inoculum)_biol1_tech4


title: 0 min (Standardized inoculum)_biol1_tech3


title: 3285-lcm

description: End Ca_frozen_LCM

value: IC


title: 3415-scrape

description: End Ca_frozen_LCM


title: preCC_OR5232_f130_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5232f130

source_name: lung tissue; 4 DPI; animal OR5232f130


title: 0 min (Standardized inoculum)_biol1_tech1


title: preCC_OR3358_f52_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3358f52

source_name: lung tissue; 4 DPI; animal OR3358f52


title: High dosage of LECT2 vs control,  3.5 hours, biological replicate 2 of 2

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

description: Biological replicate 2 of 2, 5 μg/ml of LECT2 for 3.5 hours vs  0 μg/ml of LECT2 for 3.5 hours

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner.Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software  (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Mouse peritoneal macrophages exposed to 0 μg/ml of LECT2 for 3 hours

label_protocol: 1μg of total RNA was used to synthesize the double strand cDNA. RNA was amplified by in vitro transcription using Ambion’s MessageAmp™ II aRNA Amplification Kits (Life Technologies, Austin, TX, USA). Then, aRNA was reverse transcribed into cDNA and further labeled with cy3-dCTP with Klenow enzyme.

growth_protocol: Mouse peritoneal macrophages were isolated from mouse peritonaeum. After washed with phosphate-buffered saline (PBS) twice,  peritoneal macrophages were plated and cultivated in Dulbecco’s modified Eagle’s medium-low glucose supplemented with 20% FBS.

extract_protocol: Total RNA from different cultured cells was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Mouse peritoneal macrophages  were plated at 1×105 cells/cm2 in complete culture medium and incubated with  0,0.5 or 5 μg/ml LECT2 for 3.5 or 48 hours

value: mouse peritonaeum

tag: treatment

value: exposed to 0 μg/ml of LECT2 for 3 hours

source_name: Mouse peritoneal macrophages exposed to 5 μg/ml of LECT2 for 3 hours

value: exposed to 5 μg/ml of LECT2 for 3 hours


title: 3507-scrape

description: End Ca_frozen_LCM

tag: race

value: caucasian


title: 3264-lcm

description: End Ca_frozen_LCM

tag: age (years)


title: Low dosage of LECT2 vs control, 48 hours, biological replicate 2 of 2

description: Biological replicate 2 of 2, 0.5 μg/ml of LECT2 for 48 hours vs  0 μg/ml of LECT2 for 48 hours

source_name: Mouse peritoneal macrophages exposed to 0 μg/ml of LECT2 for 48 hours

source_name: Mouse peritoneal macrophages exposed to 0.5 μg/ml of LECT2 for 48 hours


title: 3492-ls

description: End Ca_frozen_LCM

tag: stage


title: Low dosage of LECT2 vs control,  3.5 hours, biological replicate 2 of 2

description: Biological replicate 2 of 2, 0.5 μg/ml of LECT2 for 3.5 hours vs  0 μg/ml of LECT2 for 3.5 hours

source_name: Mouse peritoneal macrophages exposed to 0.5 μg/ml of LECT2 for 3 hours


title: High dosage of LECT2 vs control,  3.5 hours, biological replicate 1 of 2

description: Biological replicate 1 of 2, 5 μg/ml of LECT2 for 3.5 hours vs  0 μg/ml of LECT2 for 3.5 hours


title: 0 min (Standardized inoculum)_biol1_tech2

value: reference


title: preCC_OR220_f56_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR220f56

source_name: lung tissue; 4 DPI; animal OR220f56

value: high response


title: Low dosage of LECT2 vs control, 48 hours, biological replicate 1 of 2

description: Biological replicate 1 of 2, 0.5 μg/ml of LECT2 for 48 hours vs  0 μg/ml of LECT2 for 48 hours

value: exposed to 0 μg/ml of LECT2 for 48 hours

value: exposed to 0.5 μg/ml of LECT2 for 48 hours


title: preCC_OR3018_f46_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR3018f46

source_name: lung tissue; 4 DPI; animal OR3018f46


title: High dosage of LECT2 vs control, 48 hours, biological replicate 2 of 2

description: Biological replicate 2 of 2, 5 μg/ml of LECT2 for 48 hours vs  0 μg/ml of LECT2 for 48 hours

source_name: Mouse peritoneal macrophages exposed to 5 μg/ml of LECT2 for 48 hours


title: 3210-lcm

description: End Ca_frozen_LCM

tag: grade


title: preCC_OR5181_f127_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR5181f127

source_name: lung tissue; 4 DPI; animal OR5181f127


title: 2908-lcm

description: End Ca_frozen_LCM

tag: histology


title: High dosage of LECT2 vs control, 48 hours, biological replicate 1 of 2

description: Biological replicate 1 of 2, 5 μg/ml of LECT2 for 48 hours vs  0 μg/ml of LECT2 for 48 hours

value: exposed to 5 μg/ml of LECT2 for 48 hours


title: Low dosage of LECT2 vs control,  3.5 hours, biological replicate 1 of 2

description: Biological replicate 1 of 2, 0.5 μg/ml of LECT2 for 3.5 hours vs  0 μg/ml of LECT2 for 3.5 hours

value: exposed to 0.5 μg/ml of LECT2 for 3 hours


title: Gut_CKPF/BP_replicate 4 (Cy5)

status: Public on Dec 12 2011

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

country: Sweden

institute: Stockholm University

description:
Har G BP vs CKPF-rep4 (Cy5)
pooled from 10 animals
Raw data file: BPd vs CKPFd.txt

hyb_protocol: 825 ng of each cyanine 3 and cy5 labeled cRNA was used for each array and hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent microarray scanner.

data_processing: Note that each sample was labelled once with Cy3 and once with Cy5. Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data for both dye channels from output files were analyzed using GeneSifter microarray analysis software. The matrix includes the log base 2 transformed normalized to median data.

organism: Helicoverpa armigera

source_name: Gut chick pea fruit (CKPF)

label_protocol: Agilent Technologies spike-in RNA was added to 500 ng of total RNA and labeled using a combination of the QuickAmp Labeling kit (Agilent Technologies) for two-color arrays following the manufacturer´s instructions. Labeled amplified cRNA samples were purified using Qiagen RNeasy MinElute columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >825 ng and the specific activity >8.0 pmol Cy3 or Cy5 per ug cRNA

growth_protocol: Helicoverpa armigera larvae was acquired from Bayer CropScience (Leverkusen, Germany) in 2008 and reared under laboratory conditions (26 °C, 55% RH, 16:8 hr = L:D) in Jena, Germany on artificial diet. The artificial diets used in the experiment are the general Lepidoptera wheat-based diet purchased from Bio-Serv (F9772, Frenchtown, NJ, USA) and the pinto bean-based diet (following recipe as reported by Perkins et al., 1973).Cotton (Gossypium hirsutum DP 90) was cultivated under controlled climate chamber conditions (28°C day, 23°C night, 65% RH, L:D =15:9) and all the other host plants i. e. chick pea (Cicer arietinum Didvijay) bean (Phaseolus vulgaris ‘Admires’), and tobacco (Nicotiana tabacum SR1) were reared under greenhouse conditions (21-25°C day, 19-23°C night, 45-60% RH, L:D = 14:10 chick pea, L:D = 16:8 bean and tobacco).

extract_protocol: Gut tissue (without peritrophic membrane and gut contents) were snap-frozen in liquid nitrogen. The frozen tissue was transferred to a liquid nitrogen cooled mortar and ground. The homogenate was covered with 1 ml Trizol reagent (Sigma-Aldrich, St. Louis, MIS). Further steps were performed according to the manufacturers instruction, replacing choloroform with 1-bromo-3-chloro-propane. Also, an additional DNAse (Turbo DNAse, Ambion, Austin, TX) treatment was included to eliminate any contaminating DNA. TotalRNA was dissolved in RNA Storage Solution (Ambion) and RNA content and quality was measured photometrically.

treatment_protocol: Larvae were ice-cold anesthesized prior to dissection which took place under phosphate-buffered saline.

tag: colony/larval stage

value: Bayer 5th instar

tag: diet

value: chick pea fruit (CKPF)

value: gut


title: Gut_CKPF/BP_replicate 3 (Cy5)

description:
Har G BP vs CKPF-rep3 (Cy5)
pooled from 10 animals
Raw data file: BPc vs CKPFc.txt


title: preCC_OR489_f90_Flu_D4

description: Gene expression after 4 DPI (influenza) in the mouse lung for sample OR489f90

source_name: lung tissue; 4 DPI; animal OR489f90

tag: animal

value: lung

tag: group


title: Gut_B/CKPF_replicate 2 (Cy5)

description:
Har G CKPF vs B-rep2 (Cy5)
pooled from 10 animals
Raw data file: CKPFb vs Bb.txt

source_name: Gut cotton fruit (B)

value: cotton fruit (B)


title: Gut_B/CKPF_replicate 4 (Cy5)

description:
Har G CKPF vs B-rep4 (Cy5)
pooled from 10 animals
Raw data file: CKPFd vs Bd.txt


title: Gut_B/CKPF_replicate 3 (Cy5)

description:
Har G CKPF vs B-rep3 (Cy5)
pooled from 10 animals
Raw data file: CKPFc vs Bc.txt


title: Gut_B/CKPF_replicate 1 (Cy5)

description:
Har G CKPF vs B-rep1 (Cy5)
pooled from 10 animals
Raw data file: CKPFa vs Ba.txt


title: Gut_BP/TFB_replicate 4 (Cy5)

description:
Har G TFB vs BP-rep4 (Cy5)
pooled from 10 animals
Raw data file: TFBd vs BPd.txt

source_name: Gut bean pod (BP)

value: bean pod (BP)


title: Gut_BP/TFB_replicate 1 (Cy5)

description:
Har G TFB vs BP-rep1 (Cy5)
pooled from 10 animals
Raw data file: TFBa vs BPa.txt


title: Gut_BP/TFB_replicate 3 (Cy5)

description:
Har G TFB vs BP-rep3 (Cy5)
pooled from 10 animals
Raw data file: TFBc vs BPc.txt


title: Gut_CKPF/BP_replicate 1 (Cy5)

description:
Har G BP vs CKPF-rep1 (Cy5)
pooled from 10 animals
Raw data file: BPa vs CKPFa.txt


title: Gut_BP/TFB_replicate 2 (Cy5)

description:
Har G TFB vs BP-rep2 (Cy5)
pooled from 10 animals
Raw data file: TFBb vs BPb.txt


title: Gut_CKPF/BP_replicate 2 (Cy5)

description:
Har G BP vs CKPF-rep2 (Cy5)
pooled from 10 animals
Raw data file: BPb vs CKPFb.txt


title: Gut_TFB/BIO_replicate 4 (Cy5)

description:
Har G BIO vs TFB-rep4 (Cy5)
pooled from 10 animals
Raw data file: BIOd vs TFBd.txt

source_name: Gut tobacco flower bud (TFB)

value: tobacco flower bud (TFB)


title: Gut_TFB/BIO_replicate 3 (Cy5)

description:
Har G BIO vs TFB-rep3 (Cy5)
pooled from 10 animals
Raw data file: BIOc vs TFBc.txt


title: Gut_TFB/BIO_replicate 1 (Cy5)

description:
Har G BIO vs TFB-rep1 (Cy5)
pooled from 10 animals
Raw data file: BIOa vs TFBa.txt


title: Gut_TFB/BIO_replicate 2 (Cy5)

description:
Har G BIO vs TFB-rep2 (Cy5)
pooled from 10 animals
Raw data file: BIOb vs TFBb.txt


title: Gut_CKPF/B_replicate 4 (Cy3)

description:
Har G CKPF vs B-rep4 (Cy3)
pooled from 10 animals
Raw data file: CKPFd vs Bd.txt


title: Gut_CKPF/B_replicate 1 (Cy3)

description:
Har G CKPF vs B-rep1 (Cy3)
pooled from 10 animals
Raw data file: CKPFa vs Ba.txt


title: Gut_CKPF/B_replicate 3 (Cy3)

description:
Har G CKPF vs B-rep3 (Cy3)
pooled from 10 animals
Raw data file: CKPFc vs Bc.txt


title: Gut_CKPF/B_replicate 2 (Cy3)

description:
Har G CKPF vs B-rep2 (Cy3)
pooled from 10 animals
Raw data file: CKPFb vs Bb.txt


title: Gut_BP/CKPF_replicate 2 (Cy3)

description:
Har G BP vs CKPF-rep2 (Cy3)
pooled from 10 animals
Raw data file: BPb vs CKPFb.txt


title: Gut_BP/CKPF_replicate 1 (Cy3)

description:
Har G BP vs CKPF-rep1 (Cy3)
pooled from 10 animals
Raw data file: BPa vs CKPFa.txt


title: Gut_TFB/BP_replicate 4 (Cy3)

description:
Har G TFB vs BP-rep4 (Cy3)
pooled from 10 animals
Raw data file: TFBd vs BPd.txt


title: Gut_BP/CKPF_replicate 3 (Cy3)

description:
Har G BP vs CKPF-rep3 (Cy3)
pooled from 10 animals
Raw data file: BPc vs CKPFc.txt


title: Gut_TFB/BP_replicate 2 (Cy3)

description:
Har G TFB vs BP-rep2 (Cy3)
pooled from 10 animals
Raw data file: TFBb vs BPb.txt


title: Gut_BIO/TFB_replicate 3 (Cy3)

description:
Har G BIO vs TFB-rep3 (Cy3)
pooled from 10 animals
Raw data file: BIOc vs TFBc.txt

source_name: Gut wheat-based diet (BIO)

value: wheat-based diet (BIO)


title: Gut_BP/CKPF_replicate 4 (Cy3)

description:
Har G BP vs CKPF-rep4 (Cy3)
pooled from 10 animals
Raw data file: BPd vs CKPFd.txt


title: Gut_TFB/BP_replicate 3 (Cy3)

description:
Har G TFB vs BP-rep3 (Cy3)
pooled from 10 animals
Raw data file: TFBc vs BPc.txt


title: Gut_BIO/TFB_replicate 2 (Cy3)

description:
Har G BIO vs TFB-rep2 (Cy3)
pooled from 10 animals
Raw data file: BIOb vs TFBb.txt


title: Gut_BIO/TFB_replicate 4 (Cy3)

description:
Har G BIO vs TFB-rep4 (Cy3)
pooled from 10 animals
Raw data file: BIOd vs TFBd.txt


title: Gut_PB/BIO_replicate 3 (Cy5)

description:
Har G PB vs BIO-rep3 (Cy5)
pooled from 10 animals
Raw data file: PBc vs BIOc.txt

growth_protocol: Helicoverpa armigera larvae was acquired from Bayer CropScience (Leverkusen, Germany) in 2008 and reared under laboratory conditions (26 °C, 55% RH, 16:8 hr = L:D) in Jena, Germany on artificial diet. The artificial diets used in the experiment are the general Lepidoptera wheat-based diet purchased from Bio-Serv (F9772, Frenchtown, NJ, USA) and the pinto bean-based diet (following recipe as reported by Perkins et al., 1973). Cotton (Gossypium hirsutum DP 90) was cultivated under controlled climate chamber conditions (28°C day, 23°C night, 65% RH, L:D =15:9)  until setting fruit.


title: Gut_PB/B_replicate 4 (Cy5)

description:
Har G B vs PB-rep4 (Cy5)
pooled from 10 animals
Raw data file: Bd vs PBd.txt

source_name: Gut pinto bean-based diet (PB)

value: pinto bean-based diet (PB)


title: Gut_PB/BIO_replicate 2 (Cy5)

description:
Har G PB vs BIO-rep2 (Cy5)
pooled from 10 animals
Raw data file: PBb vs BIOb.txt


title: Gut_PB/BIO_replicate 1 (Cy5)

description:
Har G PB vs BIO-rep1 (Cy5)
pooled from 10 animals
Raw data file: PBa vs BIOa.txt


title: Gut_PB/B_replicate 3 (Cy5)

description:
Har G B vs PB-rep3 (Cy5)
pooled from 10 animals
Raw data file: Bc vs PBc.txt


title: Gut_PB/BIO_replicate 4 (Cy5)

description:
Har G PB vs BIO-rep4 (Cy5)
pooled from 10 animals
Raw data file: PBd vs BIOd.txt


title: Gut_B/SQ_replicate 1 (Cy5)

description:
Har G SQ vs B-rep1 (Cy5)
pooled from 10 animals
Raw data file: SQa vs Ba.txt


title: Gut_B/SQ_replicate 4 (Cy5)

description:
Har G SQ vs B-rep4 (Cy5)
pooled from 10 animals
Raw data file: SQd vs Bd.txt


title: Gut_PB/B_replicate 2 (Cy5)

description:
Har G B vs PB-rep2 (Cy5)
pooled from 10 animals
Raw data file: Bb vs PBb.txt


title: Gut_SQ/L_replicate 4 (Cy5)

description:
Har G L vs SQ-rep4 (Cy5)
pooled from 10 animals
Raw data file: Ld vs SQd.txt

source_name: Gut cotton flower bud (SQ)

value: cotton flower bud (SQ)


title: Gut_BIO/TFB_replicate 1 (Cy3)

description:
Har G BIO vs TFB-rep1 (Cy3)
pooled from 10 animals
Raw data file: BIOa vs TFBa.txt


title: Gut_PB/B_replicate 1 (Cy5)

description:
Har G B vs PB-rep1 (Cy5)
pooled from 10 animals
Raw data file: Ba vs PBa.txt


title: Gut_B/SQ_replicate 3 (Cy5)

description:
Har G SQ vs B-rep3 (Cy5)
pooled from 10 animals
Raw data file: SQc vs Bc.txt


title: Gut_L/BIO_replicate 2 (Cy5)

description:
Har G BIO vs L-rep2 (Cy5)
pooled from 10 animals
Raw data file: BIOb vs Lb.txt

source_name: Gut cotton leaf (L)

value: cotton leaf (L)


title: Gut_SQ/L_replicate 2 (Cy5)

description:
Har G L vs SQ-rep2 (Cy5)
pooled from 10 animals
Raw data file: Lb vs SQb.txt


title: Gut_B/SQ_replicate 2 (Cy5)

description:
Har G SQ vs B-rep2 (Cy5)
pooled from 10 animals
Raw data file: SQb vs Bb.txt


title: Gut_SQ/L_replicate 3 (Cy5)

description:
Har G L vs SQ-rep3 (Cy5)
pooled from 10 animals
Raw data file: Lc vs SQc.txt


title: Gut_PB/BIO_replicate 2 (Cy3)

description:
Har G PB vs BIO-rep2 (Cy3)
pooled from 10 animals
Raw data file: PBb vs BIOb.txt


title: Gut_L/BIO_replicate 4 (Cy5)

description:
Har G BIO vs L-rep4 (Cy5)
pooled from 10 animals
Raw data file: BIOd vs Ld.txt


title: Gut_L/BIO_replicate 3 (Cy5)

description:
Har G BIO vs L-rep3 (Cy5)
pooled from 10 animals
Raw data file: BIOc vs Lc.txt


title: Gut_B/PB_replicate 3 (Cy3)

description:
Har G B vs PB-rep3 (Cy3)
pooled from 10 animals
Raw data file: Bc vs PBc.txt


title: Gut_TFB/BP_replicate 1 (Cy3)

description:
Har G TFB vs BP-rep1 (Cy3)
pooled from 10 animals
Raw data file: TFBa vs BPa.txt


title: Gut_SQ/L_replicate 1 (Cy5)

description:
Har G L vs SQ-rep1 (Cy5)
pooled from 10 animals
Raw data file: La vs SQa.txt


title: Gut_L/BIO_replicate 1 (Cy5)

description:
Har G BIO vs L-rep1 (Cy5)
pooled from 10 animals
Raw data file: BIOa vs La.txt


title: Gut_PB/BIO_replicate 3 (Cy3)

description:
Har G PB vs BIO-rep3 (Cy3)
pooled from 10 animals
Raw data file: PBc vs BIOc.txt


title: Gut_B/PB_replicate 4 (Cy3)

description:
Har G B vs PB-rep4 (Cy3)
pooled from 10 animals
Raw data file: Bd vs PBd.txt


title: Gut_PB/BIO_replicate 4 (Cy3)

description:
Har G PB vs BIO-rep4 (Cy3)
pooled from 10 animals
Raw data file: PBd vs BIOd.txt


title: Gut_PB/BIO_replicate 1 (Cy3)

description:
Har G PB vs BIO-rep1 (Cy3)
pooled from 10 animals
Raw data file: PBa vs BIOa.txt


title: Gut_B/PB_replicate 1 (Cy3)

description:
Har G B vs PB-rep1 (Cy3)
pooled from 10 animals
Raw data file: Ba vs PBa.txt


title: Gut_B/PB_replicate 2 (Cy3)

description:
Har G B vs PB-rep2 (Cy3)
pooled from 10 animals
Raw data file: Bb vs PBb.txt


title: Gut_SQ/B_replicate 4 (Cy3)

description:
Har G SQ vs B-rep4 (Cy3)
pooled from 10 animals
Raw data file: SQd vs Bd.txt


title: Gut_SQ/B_replicate 1 (Cy3)

description:
Har G SQ vs B-rep1 (Cy3)
pooled from 10 animals
Raw data file: SQa vs Ba.txt


title: Gut_SQ/B_replicate 2 (Cy3)

description:
Har G SQ vs B-rep2 (Cy3)
pooled from 10 animals
Raw data file: SQb vs Bb.txt


title: Gut_L/SQ_replicate 2 (Cy3)

description:
Har G L vs SQ-rep2 (Cy3)
pooled from 10 animals
Raw data file: Lb vs SQb.txt


title: TEL-AML1-SNP-#29

city: Memphis

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

hyb_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: ETV6-RUNX1 B-precursor ALL

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases at diagnosis.

extract_protocol: Total RNA extraction (Trizol)

value: leukemic cells obtained from bone marrow or blood at diagnosis

tag: cell type

value: ETV6-RUNX1 B-precursor ALL


title: TEL-AML1-SNP-#44

scan_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/

tag: tissue


title: Gut_BIO/L_replicate 2 (Cy3)

description:
Har G BIO vs L-rep2 (Cy3)
pooled from 10 animals
Raw data file: BIOb vs Lb.txt


title: TEL-AML1-SNP-#24

label_protocol: Detailed protocols are as described at http://www.stjuderesearch.org/data/ALL3/


title: TEL-AML1-SNP-#32


title: TEL-AML1-SNP-#21


title: TEL-AML1-SNP-#33


title: Gut_BIO/L_replicate 3 (Cy3)

description:
Har G BIO vs L-rep3 (Cy3)
pooled from 10 animals
Raw data file: BIOc vs Lc.txt


title: Gut_L/SQ_replicate 3 (Cy3)

description:
Har G L vs SQ-rep3 (Cy3)
pooled from 10 animals
Raw data file: Lc vs SQc.txt


title: TEL-AML1-SNP-#37


title: TEL-AML1-SNP-#28


title: Gut_BIO/L_replicate 4 (Cy3)

description:
Har G BIO vs L-rep4 (Cy3)
pooled from 10 animals
Raw data file: BIOd vs Ld.txt


title: TEL-AML1-SNP-#15


title: TEL-AML1-SNP-#12


title: TEL-AML1-SNP-#26


title: Gut_BIO/L_replicate 1 (Cy3)

description:
Har G BIO vs L-rep1 (Cy3)
pooled from 10 animals
Raw data file: BIOa vs La.txt


title: TEL-AML1-SNP-#09


title: TEL-AML1-SNP-#08


title: TEL-AML1-SNP-#22


title: TEL-AML1-SNP-#31


title: TEL-AML1-SNP-#07


title: TEL-AML1-SNP-#04


title: Gut_SQ/B_replicate 3 (Cy3)

description:
Har G SQ vs B-rep3 (Cy3)
pooled from 10 animals
Raw data file: SQc vs Bc.txt


title: TEL-AML1-SNP-#16


title: T-ALL-SNP-#46

source_name: T-lineage ALL

value: T-lineage ALL


title: TEL-AML1-SNP-#10


title: TEL-AML1-SNP-#01


title: T-ALL-SNP-#44


title: T-ALL-SNP-#37


title: T-ALL-SNP-#21


title: T-ALL-SNP-#07


title: T-ALL-SNP-#14


title: T-ALL-SNP-#13


title: T-ALL-SNP-#43


title: T-ALL-SNP-#24


title: T-ALL-SNP-#17


title: T-ALL-SNP-#16


title: T-ALL-SNP-#23


title: T-ALL-SNP-#09


title: T-ALL-SNP-#11


title: T-ALL-SNP-#18


title: T-ALL-SNP-#12


title: T-ALL-SNP-#34


title: T-ALL-SNP-#01


title: T-ALL-SNP-#05


title: T-ALL-SNP-#02


title: T-ALL-SNP-#06


title: Pseudodip-SNP-#23

source_name: B-precursor ALL with miscellaneous karyotype


title: Pseudodip-SNP-#24

value: B-precursor ALL with miscellaneous karyotype


title: T-ALL-SNP-#35


title: T-ALL-SNP-#20


title: T-ALL-SNP-#03


title: Other-SNP-#25


title: Other-SNP-#26


title: Pseudodip-SNP-#06


title: Pseudodip-SNP-#05


title: Pseudodip-SNP-#22


title: Other-SNP-#14


title: Other-SNP-#20


title: Other-SNP-#05


title: Gut_L/SQ_replicate 4 (Cy3)

description:
Har G L vs SQ-rep4 (Cy3)
pooled from 10 animals
Raw data file: Ld vs SQd.txt


title: Gut_L/SQ_replicate 1 (Cy3)

description:
Har G L vs SQ-rep1 (Cy3)
pooled from 10 animals
Raw data file: La vs SQa.txt


title: larvae 3d instar FAIRE-chip

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

description:
FAIRE larvae 3d instar Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

hyb_protocol: according to the manufacturer protocols

scan_protocol: according to the manufacturer protocols

data_processing:
Raw ChIP-chip and FAIRE-chip hybridization intensities were analyzed using R and R/Bioconductor packages. In brief, genome-wide ChIP-chip enrichment was estimated as following: 1) log2-scaled hybridization intensities from the input genomic DNA (5 replicas) were normalized by quantile normalization using Bioconductor package preprocessCore and averaged. 2) log2 – scaled ratios of ChIP hybridization intensities to averaged input were taken and quantile normalized independently for each antibodies giving log2(ChIP/Input) values. 3) The same was done for the Mock ChIP hybridization intensities giving log2(Mock/Input) values. 4) Averaged log2(ChIP/Input) and log2(Mock/Input) ratios were scaled by the median and the log2(Mock/Input)average ratio was subtracted from the log2(ChIP/Input)average ratio giving ChIP-chip enrichment score. For FAIRE-chip, enrichment score was calculated as averaged log2(FAIRE/Input) ratio, as this assay does not rely on antibodies. For histone H3 and H2B ChIP-chip and FAIRE-chip, the resulting enrichment scores were smoothened by running mean on the window of 250 bp. For FAIRE-chip, the results were centered by the mean. Binding sites of ATP-dependent chromatin remodelers were selected based on false discovery rate (FDR) estimation using modified procedure described by (Simonis et al., 2006) as following: 1) ChIP-chip enrichment scores were randomly permutated and a running mean with a window of 500 bp was applied. This provides a "null" distribution for FDR estimation 2) FDR was set at < 0.05 by taking the value from the "null" distribution above 95% this distribution. 3) Finally, a running mean with a window of 500 bp was applied to original data and signals (peaks) above the FDR threshold were taken. In addition, we discarded the peaks represented by less than 5 probes. For each remodeler two different antibodies were used and only sites which met the threshold for both antibodies were considered as positive remodeler-bound regions. The INO80 binding sites were selected at FDR <0.01.  Remodeler binding sites were derived by intersecting the sets of significant ChIP-chip peaks for each antibody (see  the additional results files: (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed files, which are linked as supplementary files on the Series record)
Results file descriptions:
1) raw.bar files contain ChIP.score calculated for each antibody.
2) raw.sgr files contain chromosome, position and ChIP.score.
3) bed files contain binding sites selected at false discovery rate (FDR) of < 0.05 per individual antibody against remodelers subunits. The INO80 sites were selected at FDR < 0.01.
4) Files (P)BAP_sites.bed, NURD_sites.bed, ISWI_sites.bed contain remodeler binding sites, which were derived by intersecting the sets of significant ChIP-chip peaks for each antibody. INO80_sites.bed contains INO80 sites filtered at FDR < 0.01. These bed files are linked as supplementary files on the Series record.

organism: Drosophila melanogaster

source_name: larvae 3d  FAIRE DNA

label_protocol: according to the manufacturer protocols

growth_protocol: Drosophila S2 cells were cultured in Schneider's media (Invitrogen 21720-024) supplied with 10% FBS and Penicillin/Streptomycin mixture at 25°C

extract_protocol: The following antibodies were used: anti-H3 (ab1791, Abcam), anti-H2B (raised against purified Drosophila core histones), anti-BAP111 and anti-BRM (Chalkley et al., 2008), anti-ISWI Ab14 (584-598aa), anti-ISWI Ab18 (1012-1027aa), anti-MI2 anti-MEP1 (Reddy et al., 2010) and anti-INO8016-310 (Klymenko et al., 2006). Log-phase S2 cells were fixed for 10 min with 1% formaldehyde. Fixation was stopped by 125 mM glycine, cells were washed with PBS and resuspended in ice-cold L buffer (1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 0.5 mM phenylmethylsulfonyl fluoride - PMSF, and 100 ng/ml of leupeptin and aprotinin). Cross-linked chromatin was sonicated to an apparent length of ~300-500 bp (corresponding to ~200-300 bp of free DNA). For Drosophila chromatin, 2 g of embryos, or larvae, were homogenized and fixed for 15’ in H buffer (30 mM KCl, 15 mM NaCl, 2 mM MgCl2, 7.5 mM HEPES pH 7.6, 0.5% Triton X-100 and 0.5 mM DTT) containing 2% formaldehyde. After blocking with 0.125 M glycine, the lysate was filtered through miracloth. Nuclei were purified by centrifugation through buffer H, containing 0.15 M sucrose and resuspended in ice-cold buffer L and sonicated as described above. 100 mkg of cross-linked chromatin was diluted with 9 volumes of buffer D (150 mM NaCl, 20 mM Tris-HCl pH8.1, 2 mM EDTA pH8.0, 1% Triton-X100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin), pre-cleared with 10 mkl (bed volume) protein A agarose blocked with salmon sperm DNA (16-157, Upstate), incubated ON at 4°C with ~10 mkl of appropriate antibodies, followed by 1 hr incubation with 20 mkl of pre-blocked protein A agarose. For Mock ChIP, chromatin was incubated with either 10 mkl of preimmune serum (4 replicas) or directly with 20 mkl of pre-blocked protein A agarose (6 replicas). Beads were washed 5x with buffer W (20 mM Tris-HCl pH 8.1, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin) containing 150 mM NaCl, and 1 x with buffer W/500 mM NaCl. DNA was eluted with 250 mkl buffer E (1% SDS, 0.1 M NaHCO3, 500 mkg/ml Proteinase K) for 2 hrs at 37°C and overnight at 65°C. DNA was then extracted with QIAquick PCR purification kit (Qiagen Cat. 28106). For FAIRE, 100 mkg of cross-linked chromatin was diluted 9x with buffer D, phenol-chloroform extracted followed by RNase A treatment (1 mkg/ml) for 2 hours at 37°C. Isolated DNA was amplified with REPLI-g (Qiagen Cat. 150025), digested with DNase, labeled and hybridized on Affymetrix Drosophila tiling 2.0R arrays.

treatment_protocol: Drosophila S2 cells were treated with double-stranded RNA (dsRNA) for 4 days as described (Worby, C. A., N. Simonson-Leff, and J. E. Dixon. 2001. RNA interference of gene expression (RNAi) in cultured Drosophila cells. Sci. STKE 2001:PL1). Double-stranded RNA was synthesized using an Ambion Megascript T7 kit according to the manufacturer's protocol.

value: larvae 3d instar

tag: antibody

value: None - FAIRE assay

source_name: Input DNA

value: S2 cells


title: Kc FAIRE FAIRE-chip

description:
FAIRE Kc cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: Kc FAIRE DNA

value: Kc cells


title: Kc H3 ChIP-chip

description:
H3 ChIP Kc cells Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: Kc H3 ChIP DNA

value: H3 rabbit polyclonal (ab1791, Abcam)

source_name: Input/Mock-ChIP DNA

value: Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA)


title: Other-SNP-#24


title: Pseudodip-SNP-#03


title: Other-SNP-#19


title: Other-SNP-#21


title: Other-SNP-#06


title: Other-SNP-#15


title: embryo 2-12h FAIRE-chip

description:
FAIRE embryo 2-12h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: embryo 2-12h FAIRE DNA

value: embryo 2-12h


title: embryo 0-1h FAIRE-chip

description:
FAIRE embryo 0-1h Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL

source_name: embryo 0-1h FAIRE DNA

value: embryo 0-1h


title: Other-SNP-#08


title: Other-SNP-#17


title: Other-SNP-#01


title: larvae 3d  instar H3 ChIP-chip

description:
H3 ChIP larvae 3d instar Biological Rep 1-3
Test CEL files linked below. Control CEL files listed below are linked to Series record.
Control CEL file: S2_input_1.CEL
Control CEL file: S2_input_2.CEL
Control CEL file: S2_input_3.CEL
Control CEL file: S2_input_4.CEL
Control CEL file: S2_input_5.CEL
Control CEL file: S2_mock_preimmune_1.CEL
Control CEL file: S2_mock_preimmune_2.CEL
Control CEL file: S2_mock_preimmune_3.CEL
Control CEL file: S2_mock_preimmune_4.CEL
Control CEL file: S2_mock_protA_1.CEL
Control CEL file: S2_mock_protA_2.CEL
Control CEL file: S2_mock_protA_3.CEL
Control CEL file: S2_mock_protA_4.CEL
Control CEL file: S2_mock_protA_5.CEL
Control CEL file: S2_mock_protA_6.CEL

source_name: larvae 3d  H3 ChIP DNA


title: Pseudodip-SNP-#01


title: Other-SNP-#22


title: Pseudodip-SNP-#16