title: Red_13428208_S01_FlippedLLtoURr

status: Public on Feb 28 2013

type: RNA

city: Stockholm

first: Daniel

last: Klevebring

address: Nobels väg 12A

department: Medical Epidemiology and Biostatistics

country: Sweden

institute: Karolinska Institutet

description: Control 36h vs. knockdown 36h.

hyb_protocol: Slide preparation: Slides were pre-hybridised at 42°C for 45 min in the GeneTac hybridisation station. The pre-hybridisation mix consisted of 5x SSC, 1% BSA (Sigma-Aldrich), 0.1% SDS, 40 µg poly(dA) (Sigma-Aldrich) and 20 µg tRNA (Sigma-Aldrich). Target preparation: Purified targets were pooled for each hybridisation. Hybridisation mixture was added to a final hybridisation composition of 5x SSC, 25% formamide, 0.1% SDS, 40 µg poly(dA) and 20 µg tRNA. The mixture was denaturated at 95 °C for 2 minutes and stored on ice. Hybridisation: Hybridisation in a total volume of 110 µl was carried out for 16-18 hours at 42 °C using continuous agitation. Wash: Hybridised slides were washed for five minutes with 2x SSC and 0.1% SDS at 42°C, followed by 0.1x SSC and 0.1% SDS at room temperature (five minutes) and finally by three one-minute washes with 0.1x SSC at room temperature. Washed slides were immediately dried using a slide centrifuge (Telechem).

scan_protocol: Slides were scanned at 10-µm resolution immediately after washing. The photomultiplier tube setting was kept at 100 for all scans. Obtained images were rotated and the mirror image created using the provided software.

data_processing: Raw data files were imported into R using the KTH package for microarray analysis. Spots that were either saturated, flagged or had a foreground signal within two standard deviations from that spot's background were removed from further analysis. Individual channel data was converted into MA-format (M=log2 [Cy5/Cy3] ratio, A=log intensity) and within-slide print-tip normalisation was carried out. After manual evaluation of the distrubtion of M- and A-values across arrays, no between-slide normalisation was performed.

molecule: total RNA

organism: Homo sapiens

source_name: SiControl, 36h

label_protocol:
RNA priming: To 20 ug total RNA, add 10 ug 20(T)VN primer (MWG Biotech AG), adjust total volume to 18.4 µl, 70C 10 min , ice > 2 min, Prepare 1x RT-mixture (all reagents from Invitrogen): 5x RT-buff 6 µl, 50x aa-dNTP* 0.6 µl, DTT (0.1M) 3 µl, SuperScript II (200 U/µl) 2 µl.
cDNA synthesis: To primed RNA, add 11.6 µl RT-mix, add 42C 1 h 45 min.
RNA degradation: Add 3 µl 200 mM EDTA, add 4.5 µl 1 M NaOH, 70 C 15 min.
Neutralisation: Add 3 µl 1 M HCl.
Cleanup 1: Add 70 µl H20 + 500 µl PB, transfer to MinElute column (Qiagen), 13000 rpm 60 s, reapply flow-though, 13000 rpm 1 min, discard flow-through, add 600 µl 80% EtOH, 13000 rpm 60 s, repeat EtOH wash, spin column dry, 13000 rpm 60 s, transfer column to new microtube, add 10 µl 0.1 M NaCO3 pH 9.0, incubate 2 min, 13000 rpm 60 s, add 10 µl 0.1 M NaCO3 pH 9.0, 13000 rpm 60 s, transfer elution to aliquot of Cy3-dye (Amersham)**, mix with pipette, briefly centrifuge, incubate 1.5 h in dark at room temperature, add 4.5 µl 1 M hydroxylamine Cleanup 2 add 60 µl H20 to cDNA, add 500 µl Buffer PB, apply to MinElute column, 13000 rpm 1 min, re-apply flow-though, 13000 rpm 1 min, discard flow-through, add 650 mL Buffer PE, 13000 rpm 1 min, dscard flow-through, repeat wash, spin column dry, 13000 rpm 60 s, transfer to fresh microtube, add 10 µl Buffer EB to center of filter, 2 minutes at RT, 13000 rpm 1 min, repeat elution with another 10 µl EB.
*50x aadNTP (4:1 aadUTP:dTTP): 10 µl each 100 mM dATP, dGTP, dCTP (Pharmacia), 8 µl 100 mM aminoallyl-dUTP (Sigma, #A0410), 2 µl 100 mM dTTP.
**Aliquot Cy3 dye: Dissolve 1 tube in 50 µl DMSO, add 5 µl to 8 tubes. Speed vac dry, store tubes in a dessicator in fridge.

growth_protocol: See Cepeda et al. The ubiquitin ligase SCFFBXO28 regulates Myc-driven transcription through non-proteolytic ubiquitylation and is required for cell proliferation.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

tag: cell line

tag: cell type

value: colorectal carcinoma cells

tag: genotype

value: control

tag: time point

source_name: SiFbxo28, 36h

value: FBXO28 knockdown


title: Red_13433525_S01_FlippedLLtoURr

description: Control 16h vs. knockdown 16h.

source_name: SiControl, 16h

treatment_protocol: See Cepeda et al. The ubiquitin ligase SCFFBXO28 regulates Myc-driven transcription through non-proteolytic ubiquitylation and is required for cell proliferation.

source_name: SiFbxo28, 16h


title: Red_13433526_S01_FlippedLLtoURr

description: Control 16h vs. knockdown 16h.


title: Red_13428214_S01_FlippedLLtoURr

description: Knockdown 36h vs. control 36h.


title: Red_13428213_S01_FlippedLLtoURr

description: Control 36h vs. knockdown 36h.


title: Red_13433522_S01_FlippedLLtoURr

description: Knockdown 36h vs. control 36h.


title: Guard cell protoplast_scap1_rep1

city: Fukuoka

first: Juntaro

last: Negi

address: 6-10-1 Hakozaki, Higashi-ku

department: Biology

country: Japan

institute: Kyushu University

description: Gene expression data from guard cell protoplasts of scap1

hyb_protocol: Labelled cRNA probes (1.65 µg) were fragmented using fragmentation buffer (Agilent) and hybridised to the whole Arabidopsis Gene Expression Microarray (V4, design ID 21169; Agilent Technologies) for 17 h at 65°C in a hybridization oven.

scan_protocol: The arrays were air-dried and scanned using the high-resolution array scanner (Agilent) with the appropriate settings for one-color gene expression arrays.

data_processing: Raw data files were imported into GeneSpring 12 software (Agilent) and normalised using the intra-array percentile shift normalisation (threshold of 75 and above).

organism: Arabidopsis thaliana

source_name: Guard cell protoplast, scap1, replicate 1

label_protocol: Total RNA (200 ng) was used to prepare Cyanine-3 (Cy3) labelled probes using a low RNA input linear amplification/labeling kit (Agilent)

growth_protocol: Arabidopsis plants were grown on Jiffy-7 peat pellets (Jiffy Products International AS) under continuous light in a growth chamber at 23°C.

extract_protocol: QIAGEN Rneasy Plant Mini Kit used for total RNA isolation

treatment_protocol: Detached leaves were blended for 2 min and filtered through a 100 μm nylon mesh. Harvested epidermal peels were transferred to digestion solution 1 (0.5% (w/v) cellulase R-10 (Yakult Pharmaceutical Industry Co., Tokyo, Japan), 0.002% (w/v) pectolyase Y-23 (Seishin Pharmaceutical, Tokyo, Japan), 0.1% (w/v) polyvinylpyrrolidone K-30, 0.2% (w/v) bovine serum albumin (BSA), 0.25 M mannitol, 0.5 mM CaCl2, 0.5 mM MgCl2 and 10 mM MES-KOH, pH 5.5) and incubated at 25 °C for 3 h in a vigorously shaking water bath. After checking that mesophyll cell layers had been dissociated, the peels were transferred to digestion solution 2 (1.3% (w/v) cellulase RS, 0.0075% (w/v) pectolyase Y-23, 0.2% (w/v) BSA, 0.4 M mannitol, 0.5 mM CaCl2 and 0.5 mM MgCl2, pH 5.5) and incubated at 19 °C for 2 h. Protoplasts were filtered through four layers of 10 μm nylon mesh and collected by centrifugation at 1000 x g for 10 min. To remove mesophyll cell fragments and other contaminants, the protoplasts were subjected to density gradient centrifugation using Histopaque-1077 (Sigma-Aldrich, MO)

tag: ecotype

tag: tissue

value: Guard cell protoplast


title: CaSki-RYBP siRNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

label: biotin

source_name: Uterine cervical cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mock cells received only transfection reagent, control cells were transfected with 100nM siGENOME non-targeting siRNA Pool#1 (Dharmacon, Chicago, IL) mixed with Oligofectamine transfection reagent (Invitrogen, Carlsbad, CA), siRNA treated cells were transfected with 100nM siGENOME SMARTpool (Dharmacon, Chicago, IL) with four siRNAs of the gene of interest mixed with Oligofectamine transfection reagent (Invitrogen, Carlsbad, CA).

value: CaSki

value: Uterine cervical cancer

tag: histology

value: Squamous cell carcinoma

tag: transfected with

value: 100nM siGENOME SMARTpool with RYBP siRNA


title: CaSki-control

value: 100nM siGENOME non-targeting siRNA Pool


title: SiHa-TMF1 siRNA

value: SiHa

value: 100nM siGENOME SMARTpool with TMF1 siRNA


title: CaSki-mock

value: only transfection reagent (untreated)


title: Guard cell protoplast_scap1_rep2

source_name: Guard cell protoplast, scap1, replicate 2


title: CaSki-TMF1 siRNA


title: uninfected-rep-5

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with Expression Console

organism: Chlamydia trachomatis

source_name: McCoy cells uninfected (mock-infected)

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

growth_protocol: Six 6-well plates containing McCoy cells (1.5×10^6 cells per well) were infected with L2, L2R, L2Rp+, L2RpΔpgp4, L2RpΔpgp5 (MOI of 1.5) or mock infected and grown for 24 h at 37°C with 5% CO2.  Each infection group consisted of six replicates.  The medium was removed by aspiration.

extract_protocol: RNA and genomic DNA were extracted in randomized order using Trizol LS (Life Technologies, Carlsbad, CA) according to manufacturer's recommendation.

tag: strain

value: uninfected


title: Guard cell protoplast_WT_rep2

description: Gene expression data from guard cell protoplasts of Col-0

source_name: Guard cell protoplast, WT, replicate 2


title: Guard cell protoplast_scap1_rep3

source_name: Guard cell protoplast, scap1, replicate 3


title: uninfected-rep-6


title: Guard cell protoplast_WT_rep4

source_name: Guard cell protoplast, WT, replicate 4


title: SiHa-control


title: Guard cell protoplast_WT_rep3

source_name: Guard cell protoplast, WT, replicate 3


title: strain-L2RpBRC∆pgp5-rep 5

description: 4720_HC_6_Ct_29_L2RpBRCTDpgp5-5-F05-5980_01_0503

source_name: McCoy cells infected with L2RpBRC∆pgp5


title: Guard cell protoplast_WT_rep1

source_name: Guard cell protoplast, WT, replicate 1


title: strain-L2RpBRC∆pgp5-rep 6

description: 4721_HC_6_Ct_30_L2RpBRCTDpgp5-6-F09-5987_01_0474


title: SiHa-PSMD6 siRNA

value: 100nM siGENOME SMARTpool with PSMD6 siRNA


title: strain-L2RpBRC∆pgp5-rep 4

description: 4719_HC_6_Ct_28_L2RpBRCTDpgp5-4-E04-5973_01_0478


title: uninfected-rep-1


title: strain-L2RpBRC∆pgp5-rep 3

description: 4718_HC_6_Ct_27_L2RpBRCTDpgp5-3-C09-5966_01_0498


title: Red_13433524_S01_FlippedLLtoURr

description: Knockdown 16h vs. control 16h.


title: SiHa-RYBP siRNA


title: SiHa-mock


title: uninfected-rep-4


title: uninfected-rep-3


title: strain-L2RpBRC∆pgp5-rep 2

description: 4717_HC_6_Ct_26_L2RpBRCTDpgp5-2-C05-5959_01_0465


title: Guard cell protoplast_scap1_rep4

source_name: Guard cell protoplast, scap1, replicate 4


title: uninfected-rep-2


title: Red_13433527_S01_FlippedLLtoURr

description: Knockdown 16h vs. control 16h.


title: RNA pol GD15 treated rep1

type: genomic

city: Newort on tay

first: Simon

last: Plummer

address: 23 Wellgate Street

country: United Kingdom

institute: Micromatrices Associates ltd

hyb_protocol: The hybridisation were set up using the Agilent Oligo aCGH Hybridization Kit acording to the manufacturers instructions

scan_protocol: Agilent FE 8.5.1.1 software, GE2 scan protocol, Agilent G2565B scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: RNA pol GD15 treated Cy5

label_protocol: 1.3µg (13µl) of the amplified IP and Input DNA will be used for the fluorescent labeling using a Genomic DNA Labeling kit plus (Agilent# 5188-5309) according to the “Agilent Chip on chip protocol 10th May 2008 part number G4481-90010”

extract_protocol: 8 testes taken from each of four different litters were used to prepare a sample for chromatin fragmentation for each treatment (control and DBP treated) at each time point (GD-15 and GD-19)  4 biological replicates per treatment per time

tag: antibody

value: RNA Pol II (Active motif-39097)

value: testes

tag: agent

value: DBP 500mg/Kg

source_name: RNA pol GD15 treated Cy3

tag: fraction

value: input


title: RNA pol GD15 treated rep4


title: RNA pol GD15 control rep4

source_name: RNA pol GD15 control Cy5

value: control

source_name: RNA pol GD15 control Cy3


title: RNA pol GD15 control rep3


title: strain-L2RpBRC∆pgp5-rep 1

description: 4716_HC_6_Ct_25_L2RpBRCTDpgp5-1-D04-5958_01_0508


title: RNA pol GD15 treated rep3


title: strain-L2RpBRC∆pgp4-rep 6

description: 4715_HC_6_Ct_24_L2RpBRCTDpgp4-6-F08-5986_01_0469

source_name: McCoy cells infected with L2RpBRC∆pgp4


title: RNA pol GD15 treated rep2


title: strain-L2RpBRC∆pgp4-rep 3

description: 4712_HC_6_Ct_21_L2RpBRCTDpgp4-3-C08-5965_01_0476


title: RNA pol GD15 control rep1


title: strain-L2RpBRC∆pgp4-rep 4

description: 4713_HC_6_Ct_22_L2RpBRCTDpgp4-4-E03-5972_01_0507


title: RNA pol GD15 control rep2


title: PPARA GD15 treated rep4

source_name: PPARA GD15 treated Cy5

value: PPARalpha (Sigma PO869-100UG)

source_name: PPARA GD15 treated Cy3


title: PPARA GD15 treated rep1


title: PPARA GD15 control rep4

source_name: PPARA GD15 control Cy5

source_name: PPARA GD15 control Cy3


title: strain-L2RpBRCT-rep 6

description: 4709_HC_6_Ct_18_L2RpBRCT-6-E10-5985_01_5828

source_name: McCoy cells infected with L2RpBRCT

tag: equivalent strain name

value: L2Rp+; L2R transformed with the shuttle vector pBRCT


title: PPARA GD15 treated rep3


title: strain-L2RpBRCT-rep 2

description: 4705_HC_6_Ct_14_L2RpBRCT-2-D06-5963_01_0470


title: strain-L2RpBRCT-rep 1

description: 4704_HC_6_Ct_13_L2RpBRCT-1-D02-5956_01_0471


title: PPARA GD15 treated rep2


title: strain-L2RpBRC∆pgp4-rep 2

description: 4711_HC_6_Ct_20_L2RpBRCTDpgp4-2-D07-5964_01_0467


title: PPARA GD15 control rep3


title: PPARA GD15 control rep2


title: strain-L2RpBRC∆pgp4-rep 5

description: 4714_HC_6_Ct_23_L2RpBRCTDpgp4-5-E07-5979_01_0477


title: strain-L2R-rep 6

source_name: McCoy cells infected with L2R

value: L2R (25667R); natural plasmid-less strain


title: strain-L2RpBRCT-rep 5

description: 4708_HC_6_Ct_17_L2RpBRCT-5-E06-5978_01_5805


title: strain-L2R-rep 5


title: strain-L2RpBRCT-rep 4

description: 4707_HC_6_Ct_16_L2RpBRCT-4-E02-5971_01_0462


title: strain-L2RpBRCT-rep 3

description: 4706_HC_6_Ct_15_L2RpBRCT-3-D10-5970_01_0491


title: PPARA GD15 control rep1


title: CBP GD15 treated rep3

source_name: CBP GD15 treated DNA Cy5

value: CBP (Santa Cruz Biotechnology Ltd # SC-369)

source_name: CBP GD15 treated DNA Cy3


title: CBP GD15 treated rep2


title: CBP GD15 treated rep1


title: CBP GD15 control rep4

source_name: CBP GD15 control DNA Cy5

source_name: CBP GD15 control DNA Cy3


title: strain-L2R-rep 3


title: SF1 GD15 treated rep4

source_name: SF1 GD15 treated DNA Cy5

value: SF1 (Upstate Millipore 07-618)

source_name: SF1 GD15 treated DNA Cy3


title: strain-L2R-rep 2


title: CBP GD15 control rep1


title: strain-L2R-rep 1


title: strain-L2434-rep 4

description: 4695_HC_6_Ct_04_L2434-4-F03-5975_01_0466

source_name: McCoy cells infected with L2(434)

value: L2(434) Bu; plasmid bearing strain


title: strain-L2434-rep 6

description: 4697_HC_6_Ct_06_L2434-6-E08-5983_01_0484


title: SF1 GD15 treated rep3


title: CBP GD15 control rep3


title: CBP GD15 control rep2


title: strain-L2434-rep 2

description: 4693_HC_6_Ct_02_L2434-2-C07-5961_01_0501


title: strain-L2R-rep 4


title: SF1 GD15 treated rep2


title: strain-L2434-rep 1

description: 4692_HC_6_Ct_01_L2434-1-C03-5954_01_0482


title: SF1 GD15 treated rep1


title: SF1 GD15 control rep4

source_name: SF1 GD15 control DNA Cy5

source_name: SF1 GD15 control DNA Cy3


title: strain-L2434-rep 3

description: 4694_HC_6_Ct_03_L2434-3-D08-5968_01_0494


title: strain-L2434-rep 5

description: 4696_HC_6_Ct_05_L2434-5-F07-5982_01_0488


title: als_7

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

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

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on HG 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: The data were analyzed with oneChannelGui using rma as probeset summarization algoritm

source_name: quadriceps

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Tot RNA was further purified using the RNAeasy mini purification kit (QIAGEN) according to the RNA cleanup protocol

tag: Sex

value: male

value: quadriceps

tag: disease status

value: ALS


title: SF1 GD15 control rep3


title: SF1 GD15 control rep2


title: als_6

source_name: deltoid

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

value: female

value: deltoid


title: als_5


title: Nup170-myc ChIP from sir4∆ cells

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

country: China

institute: Southeast University

description: Genome-wide localization of Nup170-9xMyc in sir4∆ cells

hyb_protocol: Agilent yeast ChIP protocol

scan_protocol: Agilent yeast ChIP protocol

data_processing: Data extraction was performed using the Agilent Feature Extraction software.  Bound probes were analyzed by the Agilent ChIP Analytics software according to the neighborhood model.  In the neighborhood model, a probe to be considered as significantly bound was required to pass the following filters: 1) the candidate bound probe has a p-value ≤ 0.05, and 2) the central probe has a p-value ≤ 0.05 or at least one neighboring probe has a p-value ≤ 0.25.  The purpose of neighborhood model is to identify which probes are most representative of binding events.

organism: Saccharomyces cerevisiae

source_name: Nup170-myc ChIP from sir4∆ cells, ChIP

label_protocol: Agilent yeast ChIP protocol

growth_protocol: Yeast strains were cultured at 30˚C in YPD medium to an OD600 of 1.0 and proteins were cross-linked to their respective DNA binding sites with 1% formaldehyde for 1 h at room temperature and the cross-linking reaction was quenched by incubation with 125 mM glycine for 5 min prior to harvesting of cells.

extract_protocol: Chromatin immunoprecipitations were performed as described by Smith et al., 2007 with modifications according to Wan et al., 2009.  Cells were disrupted by glass bead lysis and chromatin was sheared to an average size of 400 bp.  Myc-tagged fusion proteins were purified using 2 μg of α-Myc antibody (9E10; Roche) prebound to 50 μl of Dynabead Pan Mouse IgG magnetic beads (Invitrogen) and incubated with sheared chromatin lysate containing 1 mg of protein overnight at 4˚C.  Crosslinks were reversed in ChIP and whole cell lysate fractions and purified samples were analyzed by DNA microarrays.

tag: chip antibody

value: anti-Myc monoclonal antibody (cat# 9E10; Roche)

value: YWY1501 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP170-9xMYC::hphR sir4∆::natR)

source_name: Whole cell extractof Nup170-9xMyc in sir4∆ cells

value: none (whole cell extract)


title: Nup157-myc ChIP from wild type cells

description: Genome-wide localization of Nup157-9xMyc

source_name: Nup157-myc ChIP from wild type cells, ChIP

value: YWY953 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP157-9xMYC::hphR)

source_name: Whole cell extractof Nup157-9xMyc


title: Nup170-myc ChIP from wild type cells

description: Genome-wide localization of Nup170-9xMyc

source_name: Nup170-myc ChIP from wild type cells, ChIP

value: YWY655 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP170-9xMYC::hphR)

source_name: Whole cell extractof Nup170-9xMyc


title: Nup170-myc ChIP from yku70∆ cells

description: Genome-wide localization of Nup170-9xMyc in yku70∆ cells

source_name: Nup170-myc ChIP from yku70∆ cells, ChIP

value: YWY1502 (MATa  his3∆1 leu2∆0 ura3∆0 lys2∆0 NUP170-9xMYC::hphR yku70∆::natR)

source_name: Whole cell extractof Nup170-9xMyc in yku70∆ cells


title: als_4


title: als_3


title: RNA pol GD19 treated rep3

source_name: RNA pol GD19 treated Cy5

value: RNA Pol II (Active motif-39097)

value: testes

value: DBP 500mg/Kg

source_name: RNA pol GD19 treated Cy3

value: input


title: RNA pol GD19 treated rep4


title: als_2


title: RNA pol GD19 control rep4

source_name: RNA pol GD19 control Cy5

value: control

source_name: RNA pol GD19 control Cy3


title: control_3


title: SF1 GD15 control rep1

value: SF1 (Upstate Millipore 07-618)


title: control_4


title: RNA pol GD19 control rep1


title: control_5


title: PPARA GD19 treated rep4

source_name: PPARA GD19 treated Cy5

value: PPARalpha (Sigma PO869-100UG)

source_name: PPARA GD19 treated Cy3


title: RNA pol GD19 treated rep1


title: als_1

value: male

value: quadriceps


title: control_6

value: female


title: RNA pol GD19 control rep3


title: control_7

value: deltoid


title: RNA pol GD19 treated rep2


title: control_2


title: PPARA GD19 treated rep3


title: RNA pol GD19 control rep2


title: PPARA GD19 treated rep2


title: PPARA GD19 control rep3

source_name: PPARA GD19 control Cy5

source_name: PPARA GD19 control Cy3


title: PPARA GD19 treated rep1


title: PPARA GD19 control rep4


title: control_1

source_name: deltoid


title: PPARA GD19 control rep2


title: CBP GD19 treated rep3

source_name: CBP GD19 treated DNA Cy5

value: CBP (Santa Cruz Biotechnology Ltd # SC-369)

source_name: CBP GD19 treated DNA Cy3


title: PPARA GD19 control rep1


title: CBP GD19 treated rep4


title: CBP GD19 control rep4

source_name: CBP GD19 control DNA Cy5

source_name: CBP GD19 control DNA Cy3


title: CBP GD19 treated rep1


title: CBP GD19 treated rep2


title: CBP GD19 control rep2


title: CBP GD19 control rep3


title: CBP GD19 control rep1


title: 6hr asyn 3

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: The primary rat microglia incubated with aSCM for 6 hours.

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1).

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: Differentiated SH-SY5Y cells were infected with adenoviral vectors expressing a-synuclein, mychis-tagged a-synuclein, and LacZ at multiplicity of infection of 100. On day two post-infection, media were replaced with serum-free DMEM. After 18 hours of incubation, media were centrifuged at 1,000 x g for 10 min and subsequently at 10,000 x g for 10 min to remove cell debris and dead cells. The recovered supernatants were concentrated by using 10,000 molecular weight cut-off centrifugal filters (Millipore, Carrighwohill, Cork, Ireland). For treatment to the cells, 5x concentrates were used, except for the pull-down experiments in which 1/10 diluted conditioned media were used.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The primary rat microglia incubated with LZCM or a SCM for 6 hours and 24 hours.

value: primary rat microglia

tag: transfection genes


title: strain-L2RpBRC∆pgp4-rep 1

description: 4710_HC_6_Ct_19_L2RpBRCTDpgp4-1-D03-5957_01_0496

source_name: McCoy cells infected with L2RpBRC∆pgp4


title: 24hr asyn 2

description: The primary rat microglia incubated with aSCM for 24 hours.


title: 6hr LacZ 3

description: The primary rat microglia incubated with LZCM for 6 hours.


title: 24hr LacZ 3

description: The primary rat microglia incubated with LZCM for 24 hours.


title: 6hr LacZ 1

source_name: primary rat microglia incubated with LZCM for 6 hours


title: 24hr LacZ 2

source_name: primary rat microglia incubated with LZCM for 24 hours


title: 6hr asyn 1

source_name: primary rat microglia incubated with aSCM for 6 hours


title: 24hr asyn 3

source_name: primary rat microglia incubated with aSCM for 24 hours


title: 6hr asyn 2


title: 24hr asyn 1


title: SF1 GD19 treated rep4

source_name: SF1 GD19 treated DNA Cy5

source_name: SF1 GD19 treated DNA Cy3


title: SF1 GD19 treated rep3


title: 24hr LacZ 1


title: SF1 GD19 treated rep2


title: 6hr LacZ 2


title: SF1 GD19 treated rep1


title: Mouse_cortex_184_days

city: Shanghai

first: Zhao

last: Guodong

address: Yueyang Road

institute: PICB

description: Gene expression of Mice cortex 184 days

hyb_protocol: Hybridization to Affymetrix® Mouse Gene 1.0 ST Arrays was carried out following standard Affymetrix protocols.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
To exclude those probes with signal intensities below background noise, we compared each probe’s intensity to the distribution of anti-genomic probes’ intensities with the same GC content (the latter are designed to detect non-specific hybridization). A “detectable” probe was defined as one with intensity larger than 95% percentile of the anti-genomic probes’ intensities (comparing only to those anti-genomic probes with the same GC content). Detectable probe intensity values were log2 transformed and quantile normalized. If a transcript had both more than 80% probes and more than 7 probes detected, we likewise called this a detectable transcript.
probe group file: MoGene-1_0-st-v1.r2.pgf
meta-probeset file: MoGene-1_0-st-v1.r2.all.ps

organism: Mus musculus

source_name: Dissected mouse prefrontal cortex

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: Mouse samples were provided by the animal housing center at the Max Planck Institute for Evolutionary Anthropology (Germany). All subjects had unrestricted access to food, none were obese, and none suffered from acute metabolic disorders.

value: prefrontal cortex of the brain

tag: age

value: 184 days


title: Mouse_cortex_365_days

description: Gene expression of Mice cortex 365 days

value: 365 days


title: Mouse_cortex_649_days

description: Gene expression of Mice cortex 649 days

value: 649 days


title: Mouse_cortex_904_days

description: Gene expression of Mice cortex 904 days

value: 904 days


title: Mouse_cortex_61_days

description: Gene expression of Mice cortex 61 days

value: 61 days


title: Mouse_cortex_122_days

description: Gene expression of Mice cortex 122 days

value: 122 days


title: Mouse_cortex_32_days

description: Gene expression of Mice cortex 32 days

value: 32 days


title: Mouse_cortex_11_days

description: Gene expression of Mice cortex 11 days

value: 11 days


title: SF1 GD19 control rep3

source_name: SF1 GD19 control DNA Cy5

value: SF1 (Upstate Millipore 07-618)

value: testes

value: control

source_name: SF1 GD19 control DNA Cy3

value: input


title: SF1 GD19 control rep4


title: SF1 GD19 control rep2


title: Mouse_cortex_20_days

description: Gene expression of Mice cortex 20 days

value: 20 days


title: Mouse_cortex_2_days_rep2

description: Gene expression of Mice cortex 2 days

value: 2 days


title: Mouse_cortex_5_days

description: Gene expression of Mice cortex 5 days

value: 5 days


title: CBP GD15 treated rep4

source_name: CBP GD15 treated DNA Cy5

value: CBP (Santa Cruz Biotechnology Ltd # SC-369)

value: DBP 500mg/Kg

source_name: CBP GD15 treated DNA Cy3


title: SF1 GD19 control rep1


title: Mouse_cortex_2_days_rep1

description: Gene expression of Mice cortex 2 days

value: prefrontal cortex of the brain


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP5

city: Campus de Cantoblanco

first: Pilar

last: Cubas

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

country: Spain

institute: CNB-CSIC

description:
Biological replicate 5 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911150 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 4.gpr

hyb_protocol: Equal amounts of dye of each aRNA labeled with either Cy3 or Cy5, ranging from 200 to 300 pmol, were mixed with 20 ug of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 9 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were then drained with a 2000-rpm spin for 2 min. The slides were stored in darkness until they were scanned.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenPix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

source_name: Rosette brc1-WL [reference]

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

growth_protocol: Plants were grown in a growth chamber at 22ºC with a 16-h photoperiod (long days).

extract_protocol: RNA from dissected flowering rosettes comprising axillary buds but not rosette leaves were obtained using TRIzol (Invitrogen). The RNA fraction was cleaned using RNeasy midi columns (Qiagen) following manufacturer's protocol.

treatment_protocol: When the bolt was ~2cm long, plants were treated with 8 hours of white-light (control, Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) or white light supplemented with far-red light (treatment, Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1). After the treatment, samples were collected in N2.

tag: genotype/variation

value: brc1 mutant

tag: light

value: WL

value: Flowering rosettes comprising axillary buds but not rosette leaves

source_name: Rosette brc1-FR [test]

value: FR


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP2

description:
Biological replicate 2 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911151 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 3.gpr


title: Rosette-WT-FR vs Rosette-WT-WL-REP5

description:
Biological replicate 5 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911151 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 1.gpr

source_name: Rosette WT-WL [reference]

value: WT

source_name: Rosette WT-FR [test]


title: Rosette-WT-FR vs Rosette-WT-WL-REP3

description:
Biological replicate 3 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911150 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 1.gpr


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP6

description:
Biological replicate 6 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911150 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 3.gpr


title: Rosette-WT-FR vs Rosette-WT-WL-REP4

description:
Biological replicate 4 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911149 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 2.gpr


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP3

description:
Biological replicate 3 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911151 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 4.gpr


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP4

description:
Biological replicate 4 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911149 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 4.gpr


title: Rosette-WT-FR vs Rosette-WT-WL-REP6

description:
Biological replicate 6 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911150 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 2.gpr


title: Rosette-brc1-FR vs Rosette-brc1-WL-REP1

description:
Biological replicate 1 of 6: brc1 type plants illuminated with red and far-red light versus brc1 type plants illuminated with cool white fluorescent light
252116911149 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 3.gpr


title: Patient 29 (PA)_AV80

city: Liverpool

first: Bahram

last: Ebrahimi

address: Crown Street

institute: Liverpool University

description: Gene expression data from low passage cultured gastric myofibroblasts

hyb_protocol: Following labelling and fragmentation, 10ug of aRNA was hybridised for 16 hours at 450C on GeneChip Human U133 Plus 2.0 arrays in the GeneChip hybridisation oven 640. The arrays were washed and stained using the GeneChip Hybridisation wash and stain kit on the Affymetrix Fluidics station 450 using protocol FS450_0001

scan_protocol: Genechips were scanned using the Affymetrix GeneChip scanner 3000 or 3000 7G

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 100.

label: Biotin

source_name: gastric myofibroblasts from pernicious anaemia patient

label_protocol: Biotinylated aRNA was prepared according to standard Affymetrix protocols from either 4ug total RNA (GeneChip One-Cycle Target Labelling kit) or 100ng total RNA (GeneChip 3'IVT Express kit)

growth_protocol: Early passage gastric myofibroblasts were grown in  DMEM (Sigma) containing 10% FBS (Pierce), 2% anti-mycotic/anti-biotic (Sigma), 1% penicillin/streptomycin (Sigma) and 1% non-essential amino acids (Sigma)

extract_protocol: Early passage gastric myofibroblasts were grown in culture to 80–90% confluency, trysenized and total RNA extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

tag: cell type

value: gastric myofibroblast

tag: igf response

value: Responder

tag: myofibroblast source

value: pernicious anaemia patient


title: Patient 20 (NTM)_AV49

source_name: normal tissue gastric myofibroblasts

value: normal tissue


title: Patient 28 (PA)_AV81

value: Non-responder


title: SLAM Project Data: Synthetic Lethality with yor121c

city: Baltimore

first: Jef

last: Boeke

address: 733 N BROADWAY # 339

institute: Johns Hopkins U

description:
Internal identifier for dataset: SL/091105/8
Original datafile name: 091105NG264530A04_532.pair
Original datafile2 name: 091105NG264530A04_635.pair
SD of values from reference genes: 0.285
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.01 2.47 3.04
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

hyb_protocol: Labeled extracts were hybridized overnight to NimbleGen 72k 4-plex microarray slides at 42 degrees C.

scan_protocol: Images were acquired with a GenePix 4200AL scanner at 5 um resolution or an Agilent G2505C scanner at 2 um resolution

data_processing: Two-channel image files were analyzed with the NimbleScan software package (Roche NimbleGen, version 2.3.78 or higher). Annotations were reconstructed from data downloaded from the Saccharomyces Genome Database on 2008-11-15. Numerical data were obtained as the mean of the central pixels. Background signal intensities were not used. Custom R packages (hoptag v3.9-7; hoptagInfo07A v3.9-6) were used with their default options. See the software and PDF documentation included with this GEO Series submission for details. The VALUE column represents a dynamically weighted sum of data from the UpTag and DnTag probes for each gene.

source_name: Reference

label_protocol: UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers.

growth_protocol: Cells were grown at 30 degrees C for approximately eight doublings using "Magic Marker" selectable medium supplemented with uracil.

extract_protocol: Genomic DNA was extracted by phenol extraction or by use of proprietary kits (e.g., Epicentre, Norgen).

tag: query gene

tag: knockout clone

value: Plate 223 well D09 (strain 22377)

tag: genetic background

tag: pool genotype

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX

source_name: Test

growth_protocol: Cells were grown without added uracil, using materials and procedures that were otherwise the same as those for Channel 1.


title: SLAM Project Data: Synthetic Lethality with yor111w

description:
Internal identifier for dataset: SL/091105/4
Original datafile name: 091105NG301654A04_532.pair
Original datafile2 name: 091105NG301654A04_635.pair
SD of values from reference genes: 0.387
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.25 2.27 2.57
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 223 well D01 (strain 22367)


title: Patient 19 (NTM)_AV48


title: SLAM Project Data: Synthetic Lethality with yor139c

description:
Internal identifier for dataset: SL/091118/6
Original datafile name: 091118NG300159A02_532.pair
Original datafile2 name: 091118NG300159A02_635.pair
SD of values from reference genes: 0.307
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.71 2.45 2.84
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 223 well F01 (strain 22395)


title: SLAM Project Data: Synthetic Lethality with yol118c

description:
Internal identifier for dataset: SL/100603/12
Original datafile name: 310225A04_532.pair
Original datafile2 name: 310225A04_635.pair
SD of values from reference genes: 0.261
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.76 2.89 3.10
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well H03 (strain 26268)


title: Rosette-WT-FR vs Rosette-WT-WL-REP2

description:
Biological replicate 2 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911151 Arabidopsis V4 (Ct-Cy3_Exp-Hyper5) Cuadrante 2.gpr

tag: tissue


title: SLAM Project Data: Synthetic Lethality with yol114c

description:
Internal identifier for dataset: SL/100603/8
Original datafile name: 310200A04_532.pair
Original datafile2 name: 310200A04_635.pair
SD of values from reference genes: 0.293
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.60 2.24 2.70
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well G11 (strain 26264)


title: Rosette-WT-FR vs Rosette-WT-WL-REP1

description:
Biological replicate 1 of 6: wild type plants illuminated with red and far-red light versus wild type plants illuminated with cool white fluorescent light
252116911149 Arabidopsis V4 (Ct-Hyper5_Exp-Cy3) Cuadrante 1.gpr


title: Patient 15 (ATM)_AV216

source_name: adjacent tissue gastric myofibroblasts

value: adjacent tissue


title: Patient 13 (CAM)_AV182

source_name: cancer associated gastric myofibroblasts

value: cancer associated


title: SLAM Project Data: Synthetic Lethality with yol106w

description:
Internal identifier for dataset: SL/100604/14
Original datafile name: 308122A02_532.pair
Original datafile2 name: 308122A02_635.pair
SD of values from reference genes: 0.248
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.38 2.21 3.06
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well G03 (strain 26256)


title: SLAM Project Data: Synthetic Lethality with yor152c

description:
Internal identifier for dataset: SL/091201/3
Original datafile name: 091201NG301593A03_532.pair
Original datafile2 name: 091201NG301593A03_635.pair
SD of values from reference genes: 0.344
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.59 2.14 2.67
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 223 well G01 (strain 22408)


title: Patient 19 (NTM)_AV47


title: Patient 14 (CAM)_AV183


title: SLAM Project Data: Synthetic Lethality with yol107w

description:
Internal identifier for dataset: SL/100604/15
Original datafile name: 308122A03_532.pair
Original datafile2 name: 308122A03_635.pair
SD of values from reference genes: 0.340
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.06 1.62 2.14
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well G04 (strain 26257)


title: Patient 12 (ATM)_AV190


title: SLAM Project Data: Synthetic Lethality with yol087c

description:
Internal identifier for dataset: SL/100604/6
Original datafile name: 308117A02_532.pair
Original datafile2 name: 308117A02_635.pair
SD of values from reference genes: 0.379
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.28 1.51 2.07
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well E10 (strain 26237)


title: SLAM Project Data: Synthetic Lethality with yol092w

description:
Internal identifier for dataset: SL/100604/10
Original datafile name: 308120A02_532.pair
Original datafile2 name: 308120A02_635.pair
SD of values from reference genes: 0.298
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.34 1.56 2.28
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well F03 (strain 26242)


title: SLAM Project Data: Synthetic Lethality with yol098c

description:
Internal identifier for dataset: SL/100604/12
Original datafile name: 308120A04_532.pair
Original datafile2 name: 308120A04_635.pair
SD of values from reference genes: 0.349
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.94 1.88 2.17
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well F09 (strain 26248)


title: SLAM Project Data: Synthetic Lethality with yol099c

description:
Internal identifier for dataset: SL/100604/13
Original datafile name: 308122A01_532.pair
Original datafile2 name: 308122A01_635.pair
SD of values from reference genes: 0.361
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.46 1.62 1.60
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well F10 (strain 26249)


title: Patient 12 (CAM)_AV189

value: gastric myofibroblast


title: SLAM Project Data: Synthetic Lethality with yol073c

description:
Internal identifier for dataset: SL/090728/12
Original datafile name: 090728NG129573A04_532.pair
Original datafile2 name: 090728NG129573A04_635.pair
SD of values from reference genes: 0.249
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.13 4.11 4.22
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate  well  (strain 27824)


title: SLAM Project Data: Synthetic Lethality with yol073c-rep3

description:
Internal identifier for dataset: SL/100115/12
Original datafile name: 100115NG252136A04_532.pair
Original datafile2 name: 100115NG252136A04_635.pair
SD of values from reference genes: 0.530
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.71 1.59 1.93
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).


title: Patient 11 (CAM)_AV33

description: Gene expression data from low passage cultured gastric myofibroblasts

value: Non-responder


title: SLAM Project Data: Synthetic Lethality with yol073c-rep2

description:
Internal identifier for dataset: SL/100122/12
Original datafile name: 100122NG258957A04_532.pair
Original datafile2 name: 100122NG258957A04_635.pair
SD of values from reference genes: 0.215
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.37 3.86 4.19
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Patient 10 (ATM)_AV38

value: Responder


title: SLAM Project Data: Synthetic Lethality with ynr073c

description:
Internal identifier for dataset: SL/100616/21
Original datafile name: 308147A01_532.pair
Original datafile2 name: 308147A01_635.pair
SD of values from reference genes: 0.454
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.81 1.47 1.85
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well E05 (strain 26232)


title: Patient 11 (ATM)_AV34


title: Patient 10 (CAM)_AV36


title: SLAM Project Data: Synthetic Lethality with yol013w-a

description:
Internal identifier for dataset: SL/100604/5
Original datafile name: 308117A01_532.pair
Original datafile2 name: 308117A01_635.pair
SD of values from reference genes: 0.418
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.77 1.24 1.76
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well E08 (strain 26235)


title: SLAM Project Data: Synthetic Lethality with ynr070w

description:
Internal identifier for dataset: SL/100604/3
Original datafile name: 308116A03_532.pair
Original datafile2 name: 308116A03_635.pair
SD of values from reference genes: 0.586
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.15 1.11 1.36
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well E02 (strain 26229)


title: Patient 9 (CAM)_AV29


title: Patient 9 (ATM)_AV31

value: adjacent tissue


title: Patient 8 (CAM)_AV24

value: cancer associated


title: CGH: HiPro_v_LoPro

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: CGH: HiPro_v_LoPro

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: DNA from HiPro

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

tag: line/genotype

value: HiPro

value: single plant leaf tissue

tag: seed protein content

value: high

source_name: DNA from LoPro

tag: line/genotype/variation

value: LoPro

value: single plant leaf

value: low


title: Patient 9 (ATM)_AV30


title: Patient 8 (ATM)_AV25


title: SLAM Project Data: Synthetic Lethality with ynk1

description:
Internal identifier for dataset: SL/090814/10
Original datafile name: 090814NG300366A02_532.pair
Original datafile2 name: 090814NG300366A02_635.pair
SD of values from reference genes: 0.328
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.89 2.39 2.33
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 222 well A10 (strain 24916)


title: SLAM Project Data: Synthetic Lethality with ymr316c-b

description:
Internal identifier for dataset: SL/100622/17
Original datafile name: 308399A01_532.pair
Original datafile2 name: 308399A01_635.pair
SD of values from reference genes: 0.287
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.17 2.80 3.26
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well G06 (strain 26457)


title: SLAM Project Data: Synthetic Lethality with ymr316c-a

description:
Internal identifier for dataset: SL/100622/10
Original datafile name: 308396A02_532.pair
Original datafile2 name: 308396A02_635.pair
SD of values from reference genes: 0.218
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.81 2.88 3.30
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well G05 (strain 26456)


title: Patient 3 (CAM)_AV1

value: gastric myofibroblast

value: Non-responder


title: SLAM Project Data: Synthetic Lethality with ymr315w

description:
Internal identifier for dataset: SL/100622/9
Original datafile name: 308396A01_532.pair
Original datafile2 name: 308396A01_635.pair
SD of values from reference genes: 0.277
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.79 1.85 2.72
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well G04 (strain 26455)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Patient 7 (ATM)_AV28

value: Responder


title: SLAM Project Data: Synthetic Lethality with ymr31

description:
Internal identifier for dataset: SL/100421/20
Original datafile name: 310113A04_532.pair
Original datafile2 name: 310113A04_635.pair
SD of values from reference genes: 0.359
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.86 1.79 1.98
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 232 well A08 (strain 25863)


title: Patient 5 (CAM)_AV22


title: Patient 7 (CAM)_AV26


title: Patient 1 (CAM)_AV18


title: Patient 3 (ATM)_AV2

value: adjacent tissue


title: SLAM Project Data: Synthetic Lethality with ymr181c

description:
Internal identifier for dataset: SL/100622/2
Original datafile name: 308393A02_532.pair
Original datafile2 name: 308393A02_635.pair
SD of values from reference genes: 0.251
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.25 2.47 3.25
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well F07 (strain 26446)


title: SLAM Project Data: Synthetic Lethality with ymr103c

description:
Internal identifier for dataset: SL/100625/20
Original datafile name: 255894A04_532.pair
Original datafile2 name: 255894A04_635.pair
SD of values from reference genes: 0.306
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.02 1.95 2.27
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well F05 (strain 26543)


title: SLAM Project Data: Synthetic Lethality with ymr279c

description:
Internal identifier for dataset: SL/100622/5
Original datafile name: 308394A01_532.pair
Original datafile2 name: 308394A01_635.pair
SD of values from reference genes: 0.297
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.58 2.23 3.07
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well F10 (strain 26449)


title: Patient 2 (CAM)_AV4

value: cancer associated


title: SLAM Project Data: Synthetic Lethality with ymr209c

description:
Internal identifier for dataset: SL/100622/3
Original datafile name: 308393A03_532.pair
Original datafile2 name: 308393A03_635.pair
SD of values from reference genes: 0.272
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.93 2.18 2.85
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 240 well F08 (strain 26447)


title: SLAM Project Data: Synthetic Lethality with ymr099c

description:
Internal identifier for dataset: SL/100625/16
Original datafile name: 255893A04_532.pair
Original datafile2 name: 255893A04_635.pair
SD of values from reference genes: 0.267
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.69 2.11 2.68
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well F01 (strain 26539)


title: SLAM Project Data: Synthetic Lethality with ymr102c

description:
Internal identifier for dataset: SL/100625/19
Original datafile name: 255894A03_532.pair
Original datafile2 name: 255894A03_635.pair
SD of values from reference genes: 0.536
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.25 0.92 1.20
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well F04 (strain 26542)


title: SLAM Project Data: Synthetic Lethality with ymr086w

description:
Internal identifier for dataset: SL/100616/7
Original datafile name: 308132A03_532.pair
Original datafile2 name: 308132A03_635.pair
SD of values from reference genes: 0.456
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.70 1.73 1.90
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well D07 (strain 26221)


title: SLAM Project Data: Synthetic Lethality with ymr085w

description:
Internal identifier for dataset: SL/100616/5
Original datafile name: 308132A01_532.pair
Original datafile2 name: 308132A01_635.pair
SD of values from reference genes: 0.441
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.53 2.03 1.99
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well D05 (strain 26219)


title: Non-migratory hiPSCs-NSCs towards 4T1, biological rep1

city: Singapore

first: Can

last: Chen

address: Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Gene expression data from non-migratory hiPSCs derived NSCs towards 4T1

hyb_protocol: Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.

data_processing: Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.

source_name: hiPSCs-NSCs not migrating towards 4T1

label_protocol: One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).

growth_protocol: hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine,  20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin.  These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.

extract_protocol: Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)

treatment_protocol: Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.

value: human induced pluripotent stem cell-derived neural stem cells


title: SLAM Project Data: Synthetic Lethality with ymr086c-a

description:
Internal identifier for dataset: SL/100616/6
Original datafile name: 308132A02_532.pair
Original datafile2 name: 308132A02_635.pair
SD of values from reference genes: 0.430
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.93 1.48 1.98
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well D06 (strain 26220)


title: Migratory hiPSCs-NSCs towards 4T1, biological rep3

description: Gene expression data from migratory hiPSCs derived NSCs towards 4T1

source_name: hiPSCs-NSCs migrating towards 4T1


title: Non-migratory hiPSCs-NSCs towards 4T1, biological rep2


title: Non-migratory hiPSCs-NSCs towards 4T1, biological rep3


title: Migratory hiPSCs-NSCs towards 4T1, biological rep2


title: SLAM Project Data: Synthetic Lethality with ymr075c-a

description:
Internal identifier for dataset: SL/100603/24
Original datafile name: 308113A04_532.pair
Original datafile2 name: 308113A04_635.pair
SD of values from reference genes: 0.473
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): NA 1.53 1.58
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well C06 (strain 26208)


title: Non-migratory hiPSCs-NSCs towards U87, biological rep3

description: Gene expression data from non-migratory hiPSCs derived NSCs towards U87

source_name: hiPSCs-NSCs not migrating towards U87

treatment_protocol: Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.


title: SLAM Project Data: Synthetic Lethality with ymr082c

description:
Internal identifier for dataset: SL/100604/1
Original datafile name: 308116A01_532.pair
Original datafile2 name: 308116A01_635.pair
SD of values from reference genes: 0.336
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): NA 1.84 1.99
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 239 well D01 (strain 26216)


title: SLAM Project Data: Synthetic Lethality with yml119w

description:
Internal identifier for dataset: SL/100623/19
Original datafile name: 255846A03_532.pair
Original datafile2 name: 255846A03_635.pair
SD of values from reference genes: 0.625
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.43 1.28 1.45
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well D06 (strain 26520)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: SLAM Project Data: Synthetic Lethality with yml131w

description:
Internal identifier for dataset: SL/100623/24
Original datafile name: 255849A04_532.pair
Original datafile2 name: 255849A04_635.pair
SD of values from reference genes: 0.286
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.65 2.80 3.14
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well E06 (strain 26532)


title: Non-migratory hiPSCs-NSCs towards U87, biological rep1


title: Migratory hiPSCs-NSCs towards U87, biological rep2

description: Gene expression data from migratory hiPSCs derived NSCs towards U87

source_name: hiPSCs-NSCs migrating towards U87


title: Non-migratory hiPSCs-NSCs towards U87, biological rep2


title: SLAM Project Data: Synthetic Lethality with yml122c

description:
Internal identifier for dataset: SL/100623/21
Original datafile name: 255849A01_532.pair
Original datafile2 name: 255849A01_635.pair
SD of values from reference genes: 0.415
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.71 1.51 1.86
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well D09 (strain 26523)


title: Migratory hiPSCs-NSCs towards 4T1, biological rep1


title: Migratory hiPSCs-NSCs towards U87, biological rep3


title: SLAM Project Data: Synthetic Lethality with yml100w-a

description:
Internal identifier for dataset: SL/100623/9
Original datafile name: 255796A01_532.pair
Original datafile2 name: 255796A01_635.pair
SD of values from reference genes: 0.331
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.24 2.47 2.73
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well B09 (strain 26499)


title: SLAM Project Data: Synthetic Lethality with yml116w-a

description:
Internal identifier for dataset: SL/100623/17
Original datafile name: 255846A01_532.pair
Original datafile2 name: 255846A01_635.pair
SD of values from reference genes: 0.280
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.16 2.36 3.39
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well D03 (strain 26518)


title: SLAM Project Data: Synthetic Lethality with yml101c-a

description:
Internal identifier for dataset: SL/100623/11
Original datafile name: 255796A03_532.pair
Original datafile2 name: 255796A03_635.pair
SD of values from reference genes: 0.314
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.38 2.00 2.37
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well B11 (strain 26501)


title: Muscle_Old Men_Rep4

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

description: Gene expression data from older healthy human subject

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays (Santa Clara, CA) according to manufacturer's instructions. Following hybridization, the probe arrays were washed and stained.

scan_protocol: The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray Scanner, Agilent), and the stored images were analyzed using the GeneChip software Microarray Analysis Suite (MAS) 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Raw intensity values of all samples were preprocessed and normalized by RMA using Bioconductor. Differentially expressed genes were tested by using an intensity-based Bayesian moderated t-statistic.

source_name: Older men resting biceps

label_protocol: Total RNA was used as a template for double-stranded cDNA synthesis (Superscript Double-Stranded cDNA synthesis kit, Invitrogen, Carlsbad, CA). Biotin-labeledcDNA was synthesized (EnzoBioarray High Yield RNA transcription Labeling Kit, Affymetrix).

extract_protocol: Total RNA was extracted from frozen tissue with a polytron homogenizer (Brinkman, Westbury, NY) and Trizol reagent (Invitrogen, Rockville, MD) and purified with an RNAse kit (Qiagen, Santa Clara, CA).

tag: gender

value: Male

tag: age group

value: Older


title: Migratory hiPSCs-NSCs towards U87, biological rep1


title: Muscle_Old Men_Rep2


title: SLAM Project Data: Synthetic Lethality with yml096w

description:
Internal identifier for dataset: SL/100623/5
Original datafile name: 255795A01_532.pair
Original datafile2 name: 255795A01_635.pair
SD of values from reference genes: 0.353
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.37 1.82 2.29
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well B04 (strain 26494)


title: Muscle_Old Men_Rep3


title: SLAM Project Data: Synthetic Lethality with yml108w

description:
Internal identifier for dataset: SL/100623/12
Original datafile name: 255796A04_532.pair
Original datafile2 name: 255796A04_635.pair
SD of values from reference genes: 0.286
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.47 2.59 2.88
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well C06 (strain 26508)


title: Muscle_Old Women_Rep2

source_name: Older women resting biceps

value: Female


title: Muscle_Old Men_Rep1


title: SLAM Project Data: Synthetic Lethality with ylr416c

description:
Internal identifier for dataset: SL/100331/8
Original datafile name: 308070A04_532.pair
Original datafile2 name: 308070A04_635.pair
SD of values from reference genes: 0.623
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.66 1.41 1.71
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well G02 (strain 25324)


title: SLAM Project Data: Synthetic Lethality with ylr414c

description:
Internal identifier for dataset: SL/100331/7
Original datafile name: 308070A03_532.pair
Original datafile2 name: 308070A03_635.pair
SD of values from reference genes: 0.340
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.64 2.27 2.48
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well F12 (strain 25322)


title: Muscle_Old Women_Rep3


title: SLAM Project Data: Synthetic Lethality with yml090w

description:
Internal identifier for dataset: SL/100623/3
Original datafile name: 255770A03_532.pair
Original datafile2 name: 255770A03_635.pair
SD of values from reference genes: 0.377
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.02 1.70 2.06
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 241 well A09 (strain 26487)


title: Muscle_Old Women_Rep4


title: Muscle_Young Men_Rep7

description: Gene expression data from young healthy human subject

source_name: Young men resting biceps

value: Young


title: Muscle_Old Women_Rep1


title: SLAM Project Data: Synthetic Lethality with ylr407w

description:
Internal identifier for dataset: SL/100331/5
Original datafile name: 308070A01_532.pair
Original datafile2 name: 308070A01_635.pair
SD of values from reference genes: 0.378
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.17 1.97 2.47
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well F06 (strain 25316)


title: SLAM Project Data: Synthetic Lethality with ylr408c

description:
Internal identifier for dataset: SL/100331/6
Original datafile name: 308070A02_532.pair
Original datafile2 name: 308070A02_635.pair
SD of values from reference genes: 0.392
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.40 1.87 2.43
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well F07 (strain 25317)


title: Muscle_Young Men_Rep6


title: Muscle_Young Men_Rep5


title: Muscle_Young Men_Rep2


title: Muscle_Young Men_Rep3


title: Muscle_Young Men_Rep4


title: SLAM Project Data: Synthetic Lethality with ylr400w

description:
Internal identifier for dataset: SL/100330/20
Original datafile name: 308036A04_532.pair
Original datafile2 name: 308036A04_635.pair
SD of values from reference genes: 0.318
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.68 2.07 2.31
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well E12 (strain 25309)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: SLAM Project Data: Synthetic Lethality with ylr352w

description:
Internal identifier for dataset: SL/090624/1
Original datafile name: 090624NG129648BA01_532.pair
Original datafile2 name: 090624NG129648BA01_635.pair
SD of values from reference genes: 0.349
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.88 2.76 3.00
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well B05 (strain 25261)


title: SLAM Project Data: Synthetic Lethality with ylr392c

description:
Internal identifier for dataset: SL/100330/16
Original datafile name: 308032A04_532.pair
Original datafile2 name: 308032A04_635.pair
SD of values from reference genes: 0.316
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.23 1.99 2.43
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 227 well E05 (strain 25301)


title: SLAM Project Data: Synthetic Lethality with ylr296w

description:
Internal identifier for dataset: SL/100324/1
Original datafile name: 100324NG300347A01_532.pair
Original datafile2 name: 100324NG300347A01_635.pair
SD of values from reference genes: 0.310
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.56 2.65 3.21
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well D04 (strain 25206)


title: SLAM Project Data: Synthetic Lethality with ylr312c

description:
Internal identifier for dataset: SL/100324/11
Original datafile name: 100324NG300491A03_532.pair
Original datafile2 name: 100324NG300491A03_635.pair
SD of values from reference genes: 0.353
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.31 2.30 2.65
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well E06 (strain 25220)


title: SLAM Project Data: Synthetic Lethality with ylr311c

description:
Internal identifier for dataset: SL/100324/10
Original datafile name: 100324NG300491A02_532.pair
Original datafile2 name: 100324NG300491A02_635.pair
SD of values from reference genes: 0.295
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.65 2.61 3.16
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well E05 (strain 25219)


title: Muscle_Young Women_Rep6

source_name: Young women resting biceps


title: SLAM Project Data: Synthetic Lethality with ylr290c

description:
Internal identifier for dataset: SL/100323/18
Original datafile name: 100323NG300343A02_532.pair
Original datafile2 name: 100323NG300343A02_635.pair
SD of values from reference genes: 0.344
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.76 2.52 3.08
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well C10 (strain 25200)


title: Muscle_Young Men_Rep1

value: Male


title: Muscle_Young Women_Rep7


title: SLAM Project Data: Synthetic Lethality with ylr297w

description:
Internal identifier for dataset: SL/100324/2
Original datafile name: 100324NG300347A02_532.pair
Original datafile2 name: 100324NG300347A02_635.pair
SD of values from reference genes: 0.356
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.75 2.18 2.89
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well D05 (strain 25207)


title: SLAM Project Data: Synthetic Lethality with ylr294c

description:
Internal identifier for dataset: SL/100323/20
Original datafile name: 100323NG300343A04_532.pair
Original datafile2 name: 100323NG300343A04_635.pair
SD of values from reference genes: 0.301
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 3.46 3.01 3.61
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well D02 (strain 25204)


title: Muscle_Young Women_Rep4

value: Female


title: SLAM Project Data: Synthetic Lethality with ylr287c

description:
Internal identifier for dataset: SL/100323/15
Original datafile name: 100323NG300346A03_532.pair
Original datafile2 name: 100323NG300346A03_635.pair
SD of values from reference genes: 0.329
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.81 2.31 2.95
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well C06 (strain 25196)


title: SLAM Project Data: Synthetic Lethality with ylr283w

description:
Internal identifier for dataset: SL/100323/12
Original datafile name: 100323NG300342A04_532.pair
Original datafile2 name: 100323NG300342A04_635.pair
SD of values from reference genes: 0.469
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.55 1.69 1.85
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well C03 (strain 25192)


title: Muscle_Young Women_Rep3

value: Young


title: Muscle_Young Women_Rep5


title: SLAM Project Data: Synthetic Lethality with ylr271w

description:
Internal identifier for dataset: SL/100323/6
Original datafile name: 100323NG300341A02_532.pair
Original datafile2 name: 100323NG300341A02_635.pair
SD of values from reference genes: 0.397
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 2.20 1.61 2.11
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well B02 (strain 25180)


title: RNA pool 3, treated allergic group, post-polinization period

city: Madrid

first: Miriam

last: Aguerri

address: avd/Reyes Católicos, 2

department: Immunology

institute: IIS-Fundación Jiménez Díaz

description: GROUP 5 POOL 3 POST

hyb_protocol: Following fragmentation, 10 µg of cDNA were hybridized for 16 hr at 45C on the GeneChip HuGe U133 plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000, enabled for High-Resolution Scanning

data_processing: Preliminary microarray analysis included assessment of data quality by standard quality checks and principal component assays. First-line check, background corrections, and quantile normalization of the data were performed by Robust Multiarray Averaging (RMA) method. Data analysis was performed using Partek Genomics Suite software. Affymetrix raw data files (CEL files) where background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. Further analyses where carried out using Babelomics web suite.

source_name: RNA from PBMCs of 2 treated allergic subjects outside polinization

label_protocol: Microarray targets were prepared from 200 ng of total RNA using the Affymetrix (Santa Clara, CA, USA) kit for reverse transcription and a double round of in vitro transcription. Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 µg of cDNA.

growth_protocol: PBMCs isolated from peripheral blood by density gradient

extract_protocol: Total RNA was isolated from PBMCs (106 cells) using Trizol (Invitrogen, Carlsbad, CA, USA) extraction and isopropyl alcohol precipitation. RNA was quantified by spectrophotometry in a nanodrop, and integrity was confirmed with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).We utilized an RNA-pooling strategy to maximize the number of individuals in the microarray study to increase statistical power and representation of intra-individual variability in gene expression.Three independent pools were created for each clinical group of study (non-allergic, asymptomatic, allergic non-related to olive pollen, allergic to olive pollen without treatment and allergic to olive pollen with specific treatment) and there were two different pollen exposition condition (during and outside pollen season). Total number of RNAs analyzed by microarrays was of 28 samples.

tag: period

value: Post- polinization period

tag: clinical group

value: Treated allergic group


title: SLAM Project Data: Synthetic Lethality with ylr269c

description:
Internal identifier for dataset: SL/100323/4
Original datafile name: 100323NG300340A04_532.pair
Original datafile2 name: 100323NG300340A04_635.pair
SD of values from reference genes: 0.734
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.35 1.17 1.38
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well A12 (strain 25178)

value: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX


title: Muscle_Young Women_Rep2


title: RNA pool 1, treated allergic group, post-polinization period

description: GROUP 5 POOL 1 POST


title: SLAM Project Data: Synthetic Lethality with ylr278c

description:
Internal identifier for dataset: SL/100323/7
Original datafile name: 100323NG300341A03_532.pair
Original datafile2 name: 100323NG300341A03_635.pair
SD of values from reference genes: 0.357
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.44 1.67 2.00
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well B09 (strain 25187)


title: SLAM Project Data: Synthetic Lethality with ylr282c

description:
Internal identifier for dataset: SL/100323/11
Original datafile name: 100323NG300342A03_532.pair
Original datafile2 name: 100323NG300342A03_635.pair
SD of values from reference genes: 0.351
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.74 2.11 2.42
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 226 well C01 (strain 25191)


title: RNA pool 3, non-treated allergic group, post-polinization period

description: GROUP 4 POOL 3 POST

source_name: RNA from PBMCs of 2 non-treated allergic subjects outside polinization

value: Untreated allergic group


title: RNA pool 2, treated allergic group, post-polinization period

description: GROUP 5 POOL 2 POST


title: SLAM Project Data: Synthetic Lethality with ylr217w

description:
Internal identifier for dataset: SL/090505/18
Original datafile name: 090505NG142907BA02_532.pair
Original datafile2 name: 090505NG142907BA02_635.pair
SD of values from reference genes: 0.326
QueryDeletion::URA3 selection scores (want >> 1; UpTag|DnTag|combined): 1.93 3.17 3.31
For methodological details, please see the following PubMed IDs: 9483801 (BY4743 strain background), 10436161 (Yeast Knockout strain collection), 11743205 (mating-type-specific selection), 15525520 (the "dSLAM" selection scheme), 15994458 (asymmetric PCR), 17060357 (spatial normalization), 17189863 (Methods paper), 18392971 (Methods Mol. Biol. chapter).

value: Plate 220 well C11 (strain 24166)