title: CD38low CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep1

first: Anil

middle: K.

last: Rustgi

address: 421 Curie Boulevard

department: Gastroenterology

institute: University of Pennsylvania

description:
2109lo
CD38low MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2109

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. 5.5 micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Exon 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing:
All samples were carried out by doing background subtraction, normalization and summarizing probe sets from Affymetrix expression microarrays using Affymetrix Power tools (APT). The data were processed with RMA (Robust Multichip Average) and Probe Logarithmic Intensity Error (PLIER) Estimation methods in APT.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label_protocol: The cDNA were fragmented, assessed by Bioanalyzer, and biotinylated  using terminal transferase end labeling.

growth_protocol: spleens were extracted from esophageal tumor-bearing mice

extract_protocol: Splenocytes were isolated by FACS sorting (CD38high and CD38low CD11b+Gr1+ cells were collected) into complete RPMI medim, spun for 5min at 500g. Total RNA was isolated from the pellets using the RNAqueous RNA exptraction kit (Ambion). Quality control check of the total RNA samples was performed using Agilent Bioanalyzer and Nanodrop spectrophotometry. All protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA.

treatment_protocol: not applicable

tag: age

value: spleen

tag: genotype

tag: strain

value: mixed C57BL/6x129 background


title: Heart_VEHICLE_VEHICLE_Day4_Rep7

status: Public on Aug 31 2015

type: RNA

city: Dundee

first: Runxuan

last: Zhang

state: Angus

address: Errol Road, Invergowrie

department: Information and Computational Sciences

country: United Kingdom

institute: The James Hutton Institute

description: Heart from mouse treated with vehicle for 4 days (Mouse_7_Heart)

hyb_protocol: Following fragmentation, 3.75ug of cDNA were hybridized for 18 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) normailzation method using Partek (Liver, heart, kidney, and skeletal muscle samples were each normalized independently)

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotinylated cDNA were prepared according to the Nugen protocol from 100ng total RNA using Nugen WT Ovation V2 (cat. 3100-60) and Nugen Encore Biotin (cat. 4200-60)

extract_protocol: Qiagen miRNEasy was used according to maufacturers instruction including DNAse I treatment.

tag: tissue

value: Heart

tag: compound

value: Vehicle

tag: dose

value: N / A

tag: timepoint

value: 4 days


title: AHLCL_VPA_0.2mM_0min_rep2

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors

hyb_protocol: Samples were hybridised using a Nimblegen Hybridisation Kit (05 583 934 001), including Sample Tracking Controls (05 223 512 001)

scan_protocol: Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain

data_processing: Data were extracted using DEVA (Roche Nimblegen) and normalised by robust multichip average in R.

organism: Homo sapiens

source_name: AH LCL, 0.2mM VPA, 0min

label_protocol: Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)

growth_protocol: Immortalized, EBV-transformed lymphoblastoid cell lines (AH LCL) from healthy, karyotypically normal individuals were established in house. GM12878 Lymphoblastoid cells were purchased from the Coriell Institute. Both cell lines were maintained at  37°C, 5% CO2 in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all additives from Gibco).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was converted to double-stranded cDNA using cDNA synthesis kit (Roche Nimblegen, 11 117 831 001)

treatment_protocol: Cells were treated with 0.2mM, 1mM or 5mM valproic acid (VPA) or 0.5, 2.5 or 12.5µM suberoylanilide hydroxamic acid (SAHA) for 0, 30, 60 and 120 minutes

tag: gender

value: Male


title: Heart_VEHICLE_VEHICLE_Day8_Rep8

description: Heart from mouse treated with vehicle for 8 days (Mouse_48_Heart)

value: 8 days


title: CD38low CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep3

city: Philadelphia

state: PA

country: USA

description:
2181lo
CD38low MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2181


title: Heart_VEHICLE_VEHICLE_Day4_Rep3

description: Heart from mouse treated with vehicle for 4 days (Mouse_3_Heart)


title: CD38high CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep3

description:
2181hi
CD38high MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2181


title: Heart_VEHICLE_VEHICLE_Day8_Rep10

description: Heart from mouse treated with vehicle for 8 days (Mouse_50_Heart)


title: Heart_VEHICLE_VEHICLE_Day4_Rep2

description: Heart from mouse treated with vehicle for 4 days (Mouse_2_Heart)


title: CD38high CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep2

description:
2124hi
CD38high MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2124


title: Heart_VEHICLE_VEHICLE_Day4_Rep4

description: Heart from mouse treated with vehicle for 4 days (Mouse_4_Heart)


title: CD38low CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep2

description:
2124lo
CD38low MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2124


title: CD38high CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep1

description:
2109hi
CD38high MDSCs from tumor-bearing L2-Cre;p120f/f mouse #2109


title: Heart_VEHICLE_VEHICLE_Day4_Rep6

description: Heart from mouse treated with vehicle for 4 days (Mouse_6_Heart)


title: Heart_VEHICLE_VEHICLE_Day4_Rep10

description: Heart from mouse treated with vehicle for 4 days (Mouse_10_Heart)


title: Heart_VEHICLE_VEHICLE_Day4_Rep5

description: Heart from mouse treated with vehicle for 4 days (Mouse_5_Heart)


title: CD38low CD11b+Gr1+ splenocytes pooled from 3 tumor-bearing L2-Cre;p120f/f mice

description:
poollo
CD38low MDSCs from tumor-bearing L2-Cre;p120f/f mice

source_name: tumor-bearing L2-Cre;p120f/f mice


title: HMLE-SNAIL cell line KPT-treated relative to vehicle-treated, replicate 4 of 4

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: Whole-genome expression was measured by a 2-color microarray approach using Agilent Human GE 4x44K v2 Microarray

scan_protocol: GE2_1105_Oct12 protocol and Agilent SureScan System

data_processing: Data quality were assessed and data were processed with Agilent Feature Extraction software (version 11.5) producing expression data measures including Log10 Ratio expression levels (background subtracted, lowess normalizd), LogRatioError and PValueLogRatio.

source_name: KPT-treated HMLE-SNAIL cell line, replicate 4 of 4

label_protocol: Labeling reaction used the Low Input Quick Amp Labeling Kit from Agilent Technologies following the recommended protocol to produce cRNA for a two-color microarray experiment

growth_protocol: The human mammary epithelial cell line, HMLE-SNAIL  (HMLE cells previously transduced to stably overexpress SNAI1), was cultured in 1:1 Dulbecco’s Modified Eagle’s Medium (DMEM)/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex), 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (EGF) (PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Sigma).

extract_protocol: Total RNA was isolated from cell pellets using an RNeasy Midi Kit from Qiagen.  Quantity and quality of all mRNA samples was determined by analysis with the NanoDrop 1000, Agilent Bioanalyzer and the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HMLE-SNAIL cell cultures were  treated with KPT (150 nanomolar) or vehicle (DMSO) for 24 hours, in parallel quadruplicates.

tag: cell type

value: immortilized human breast epithelial cell line

tag: treatment

value: KPT

value: vehicle

source_name: vehicle-treated HMLE-SNAIL cell line, replicate 4 of 4


title: Heart_VEHICLE_VEHICLE_Day4_Rep1

description: Heart from mouse treated with vehicle for 4 days (Mouse_1_Heart)


title: HMLE-SNAIL cell line KPT-treated relative to vehicle-treated, replicate 2 of 4

source_name: KPT-treated HMLE-SNAIL cell line, replicate 2 of 4

source_name: vehicle-treated HMLE-SNAIL cell line, replicate 2 of 4


title: Heart_VEHICLE_VEHICLE_Day15_Rep8

description: Heart from mouse treated with vehicle for 15 days (Mouse_88_Heart)

value: 15 days


title: HMLE-SNAIL cell line KPT-treated relative to vehicle-treated, replicate 3 of 4

source_name: KPT-treated HMLE-SNAIL cell line, replicate 3 of 4

source_name: vehicle-treated HMLE-SNAIL cell line, replicate 3 of 4


title: Heart_VEHICLE_VEHICLE_Day15_Rep9

description: Heart from mouse treated with vehicle for 15 days (Mouse_89_Heart)


title: AHLCL_SAHA_0.5µM_0min_rep1

description: Gene expression data following treatment of lymphoblastoid cells with histone deacetylase inhibitors

source_name: AH LCL, 0.5µM SAHA, 0min


title: 177Lu Medulla 120 MBq 8 months 1

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

source_name: Medulla

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

value: Medulla

tag: nuclide

tag: injected activity

tag: time

value: 8 months


title: 177Lu Medulla 120 MBq 8 months 3


title: 177Lu Medulla 90 MBq 8 months 4


title: 177Lu Medulla 120 MBq 8 months 2


title: HMLE-SNAIL cell line KPT-treated relative to vehicle-treated, replicate 1 of 4

source_name: KPT-treated HMLE-SNAIL cell line, replicate 1 of 4

source_name: vehicle-treated HMLE-SNAIL cell line, replicate 1 of 4


title: Heart_VEHICLE_VEHICLE_Day15_Rep6

description: Heart from mouse treated with vehicle for 15 days (Mouse_86_Heart)


title: Heart_VEHICLE_VEHICLE_Day15_Rep7

description: Heart from mouse treated with vehicle for 15 days (Mouse_87_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day8_Rep5

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_80_Heart)

source_name: Heart_ROSIGLITAZONE_10 mg/kg_Day8

value: Rosiglitazone

value: 10 mg/kg


title: Heart_VEHICLE_VEHICLE_Day15_Rep3

description: Heart from mouse treated with vehicle for 15 days (Mouse_83_Heart)


title: 177Lu Medulla 30 MBq 8 months 4


title: 177Lu Medulla 90 MBq 8 months 2


title: 177Lu Medulla 90 MBq 8 months 1


title: Heart_VEHICLE_VEHICLE_Day15_Rep1

description: Heart from mouse treated with vehicle for 15 days (Mouse_81_Heart)


title: 177Lu Medulla 60 MBq 8 months 3


title: 177Lu Medulla 30 MBq 8 months 1


title: Heart_VEHICLE_VEHICLE_Day15_Rep5

description: Heart from mouse treated with vehicle for 15 days (Mouse_85_Heart)


title: Heart_VEHICLE_VEHICLE_Day15_Rep2

description: Heart from mouse treated with vehicle for 15 days (Mouse_82_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day8_Rep4

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_79_Heart)


title: 177Lu Medulla 30 MBq 8 months 3


title: Heart_VEHICLE_VEHICLE_Day15_Rep4

description: Heart from mouse treated with vehicle for 15 days (Mouse_84_Heart)


title: Heart_VEHICLE_VEHICLE_Day15_Rep10

description: Heart from mouse treated with vehicle for 15 days (Mouse_90_Heart)


title: 177Lu Medulla 150 MBq 4 months 3

value: 4 months


title: 177Lu Medulla 60 MBq 8 months 2


title: 177Lu Medulla 60 MBq 8 months 4


title: 177Lu Medulla 120 MBq 4 months 3


title: 177Lu Medulla 150 MBq 4 months 2


title: 177Lu Medulla 120 MBq 4 months 4


title: 177Lu Medulla 120 MBq 4 months 2


title: Heart_ROSIGLITAZONE_10 mg/kg_Day8_Rep1

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_76_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day4_Rep2

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_37_Heart)

source_name: Heart_ROSIGLITAZONE_10 mg/kg_Day4


title: 177Lu Medulla 60 MBq 4 months 3


title: Heart_ROSIGLITAZONE_10 mg/kg_Day4_Rep3

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_38_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day4_Rep4

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_39_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day8_Rep3

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_78_Heart)


title: 177Lu Medulla 150 MBq 4 months 1


title: Heart_ROSIGLITAZONE_10 mg/kg_Day4_Rep5

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_40_Heart)


title: Heart_ROSIGLITAZONE_10 mg/kg_Day15_Rep1

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_116_Heart)

source_name: Heart_ROSIGLITAZONE_10 mg/kg_Day15


title: Heart_ROSIGLITAZONE_10 mg/kg_Day8_Rep2

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days (Mouse_77_Heart)


title: 177Lu Medulla 60 MBq 4 months 2


title: Heart_ROSIGLITAZONE_10 mg/kg_Day4_Rep1

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days (Mouse_36_Heart)


title: 177Lu Medulla 60 MBq 4 months 1


title: Heart_ROSIGLITAZONE_10 mg/kg_Day15_Rep3

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_118_Heart)


title: 177Lu Medulla 30 MBq 4 months 3


title: Heart_GW501516_10 mg/kg_Day8_Rep5

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_70_Heart)

source_name: Heart_GW501516_10 mg/kg_Day8


title: Heart_ROSIGLITAZONE_10 mg/kg_Day15_Rep2

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_117_Heart)


title: 177Lu Medulla 90 MBq 4 months 3


title: 177Lu Medulla 30 MBq 4 months 2


title: 177Lu Medulla 90 MBq 4 months 4


title: Heart_ROSIGLITAZONE_10 mg/kg_Day15_Rep5

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_120_Heart)


title: 177Lu Medulla 30 MBq 4 months 4


title: Heart_ROSIGLITAZONE_10 mg/kg_Day15_Rep4

description: Heart from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days (Mouse_119_Heart)


title: 177Lu Medulla Control 12 months 3

value: Control

value: 12 months


title: 177Lu Medulla Control 12 months 2


title: 177Lu Medulla Control 8 months 1


title: 177Lu Medulla Control 8 months 3


title: 177Lu Medulla Control 8 months 2


title: 177Lu Medulla Control 12 months 1


title: Heart_GW501516_10 mg/kg_Day8_Rep3

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_68_Heart)

value: Heart


title: Heart_GW501516_10 mg/kg_Day8_Rep2

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_67_Heart)


title: Heart_GW501516_10 mg/kg_Day8_Rep1

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_66_Heart)


title: Heart_GW501516_10 mg/kg_Day4_Rep4

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_29_Heart)

source_name: Heart_GW501516_10 mg/kg_Day4


title: Heart_GW501516_10 mg/kg_Day8_Rep4

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days (Mouse_69_Heart)


title: Heart_GW501516_10 mg/kg_Day4_Rep5

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_30_Heart)


title: 177Lu Medulla Control 4 months 3


title: 177Lu Medulla Control 4 months 2


title: Heart_GW501516_10 mg/kg_Day4_Rep3

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_28_Heart)


title: 177Lu Medulla 150 MBq 12 months 6


title: 177Lu Medulla Control 4 months 1


title: 177Lu Medulla 150 MBq 12 months 5+3


title: Heart_GW501516_10 mg/kg_Day4_Rep2

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_27_Heart)


title: Heart_GW501516_10 mg/kg_Day4_Rep1

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days (Mouse_26_Heart)


title: PAA071

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

description: memory CD4+ T-cell subsets were isolated by FACS

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanHT-12 v4 Expression BeadChip

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalisation using Bioconductor

source_name: PBMC

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

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

treatment_protocol: immobilized CD3 and soluble CD28 (1µg/ml) for 3 days

tag: donor

tag: cell population


title: PAA069


title: 177Lu Medulla 150 MBq 12 months 2


title: Heart_GW501516_10 mg/kg_Day15_Rep4

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_109_Heart)

source_name: Heart_GW501516_10 mg/kg_Day15


title: PAA068


title: PAA070


title: Heart_GW501516_10 mg/kg_Day15_Rep5

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_110_Heart)


title: Heart_GW501516_10 mg/kg_Day15_Rep3

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_108_Heart)


title: PAA072


title: 177Lu Medulla 120 MBq 12 months 1


title: PAA067


title: 177Lu Medulla 120 MBq 12 months 4


title: 177Lu Medulla 90 MBq 12 months 2


title: Liver_WY14643_10 mg/kg_Day8_Rep4

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days  (Mouse_ML59_Liver)

source_name: Liver_WY14643_10 mg/kg_Day8

value: Liver

tag: time point


title: CD38high CD11b+Gr1+ splenocytes pooled from 3 tumor-bearing L2-Cre;p120f/f mice

description:
poolhi
CD38high MDSCs from tumor-bearing L2-Cre;p120f/f mice

source_name: tumor-bearing L2-Cre;p120f/f mice

value: spleen

value: mixed C57BL/6x129 background


title: PAA066


title: 177Lu Medulla 90 MBq 12 months 4


title: Heart_GW501516_10 mg/kg_Day15_Rep2

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_107_Heart)


title: Liver_WY14643_10 mg/kg_Day8_Rep5

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days  (Mouse_ML60_Liver)

value: 8 days


title: PAA064


title: Liver_WY14643_10 mg/kg_Day8_Rep3

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days  (Mouse_ML58_Liver)


title: PAA063


title: 177Lu Medulla 120 MBq 12 months 2


title: Liver_WY14643_10 mg/kg_Day4_Rep5

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days  (Mouse_ML20_Liver)

source_name: Liver_WY14643_10 mg/kg_Day4

value: 4 days


title: 177Lu Medulla 90 MBq 12 months 1


title: Heart_GW501516_10 mg/kg_Day15_Rep1

description: Heart from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days (Mouse_106_Heart)


title: Liver_WY14643_10 mg/kg_Day8_Rep2

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days  (Mouse_ML57_Liver)


title: Liver_WY14643_10 mg/kg_Day8_Rep1

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 8 days  (Mouse_ML56_Liver)


title: Liver_WY14643_10 mg/kg_Day4_Rep4

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days  (Mouse_ML19_Liver)


title: 177Lu Medulla 60 MBq 12 months 1


title: PAA065


title: 177Lu Medulla 60 MBq 12 months 4


title: PAA059


title: PAA060


title: Liver_WY14643_10 mg/kg_Day4_Rep3

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days  (Mouse_ML18_Liver)


title: 177Lu Medulla 90 MBq 4 months 2


title: PAA062


title: 177Lu Medulla 30 MBq 12 months 4


title: Liver_WY14643_10 mg/kg_Day4_Rep2

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days  (Mouse_ML17_Liver)


title: PAA054


title: PAA057


title: Liver_WY14643_10 mg/kg_Day15_Rep4

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days  (Mouse_ML99_Liver)

source_name: Liver_WY14643_10 mg/kg_Day15


title: PAA056

description: memory CD4+ T-cell subsets were isolated by FACS


title: 177Lu Medulla 30 MBq 12 months 2


title: PAA055


title: 177Lu Medulla 150 MBq 8 months 2


title: 177Lu Medulla 30 MBq 12 months 3


title: PAA058


title: Liver_WY14643_10 mg/kg_Day15_Rep3

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days  (Mouse_ML98_Liver)


title: 177Lu Medulla 150 MBq 8 months 4


title: 177Lu Medulla 150 MBq 8 months 3


title: PAA053


title: 177Lu Cortex 120 MBq 8 months 3

source_name: Cortex

value: Cortex


title: Liver_WY14643_10 mg/kg_Day4_Rep1

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 4 days  (Mouse_ML16_Liver)


title: NeoB-treated  Huh7.5.1 cells rep1

city: Yokohama

first: Piero

last: Carninci

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanning of the chip was performed using Illumina BeadScan and BeadStudio software packages

data_processing: Expression levels were background-corrected and quantile normalized using the neqc function of the limma package.

source_name: Human Huh7.5.1 cells

label_protocol: Total RNA (500 ng) was amplified and labled using the Ambion Illumina® Total Prep RNA Amprification Kit (Ambion).

extract_protocol: Total RNA was prepared using RNeasy mini kit (QIAGEN).

tag: cell line

value: 20 microM NeoB for 24 h


title: NeoB-treated  Huh7.5.1 cells rep2

description: Replicate 2


title: 177Lu Cortex 120 MBq 8 months 2


title: Liver_VEHICLE_VEHICLE_Day8_Rep9

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML49_Liver)

value: Vehicle

value: N / A


title: Liver_WY14643_10 mg/kg_Day15_Rep2

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days  (Mouse_ML97_Liver)

value: 15 days


title: NeoB-treated  Huh7.5.1 cells rep3

description: Replicate 3


title: ATF7_pMp_Whole_C

type: genomic

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array C of A-G

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing:
We calculated Model-Based Analysis of Tiling-Arrays (MAT) score software implementation in R (rMAT package). Signals were mapped against mouse genome assembly mm8 (NCBI Build 36), and ChIP was normalized against input for both Mouse Tiling 2.0R Arrays and Mouse Promoter 1.0R Arrays. Normalization and MAT score computations were performed using default parameters (Bandwidth = 600; MaxGap = 300; and MinProbe = 8) and the ‘pair-binned’ method for normalization. Enriched regions (peaks) were then detected using a p-value threshold set to 10-10 for both arrays. All detected peaks have a false-discovery rate, as computed by rMAT, lower than 1%.
The resulting BED files are generated by rMAT using default parameters (Bandwidth = 600; MaxGap = 300; and MinProbe = 8). Enriched regions are then detected using a p-value threshold set to 10-10 for both arrays.

molecule: genomic DNA

source_name: Peritoneal macrophages from wild-type mice

label_protocol: DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin‐N11‐ddATP.

growth_protocol: Peritoneal resident macrophages were collected by peritoneal washing, without thioglycollate injection, and were incubated in Macrophage-SFM (Life Tech.) containing 100 U/ml penicillin and 100 µg/ml streptomycin. Before and after overnight incubation, dish surfaces were washed by pipetting with PBS to remove non-adherent cells such as lymphocytes.

extract_protocol: Peritoneal macrophages were crosslinked with 1% formaldehyde for 8 min at RT and after washing with ice-cold PBS prepared for ChIP. Chromatin immunoprecipitation was performed using ATF7 antibody. The lysate was incubated with the antibodies over night at 4 degree, and then protein A dynabeads (Life Tech.) were added and incubated for 3 hours at 4 degree. The beads were washed several times and eluted with elution buffer (50 mM Tris, 10 mM EDTA, 1 % SDS). After reverse cross-linking by overnight incubation at 65 degree, the eluate from the beads was treated with Proteinase K. Contaminating RNA was removed by RNAse treatment. The sample was further purified by phenol-chloroform extraction and using the PCR purification kit (Qiagen).

treatment_protocol: Unterated

value: ChIP using ATF7 Ab

value: wild-type in C57BL/6 background

tag: cell-type

value: peritoneal macrophage


title: 177Lu Cortex 120 MBq 8 months 1

value: Balb/c

value: 8 months


title: ATF7_pMp_Whole_A

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array A of A-G


title: 177Lu Cortex 60 MBq 8 months 3


title: Non-treated (DMSO) Huh7.5.1 cells rep2

description: Replicate 2

value: 0.2% DMSO


title: Liver_VEHICLE_VEHICLE_Day8_Rep4

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML44_Liver)


title: Liver_VEHICLE_VEHICLE_Day8_Rep8

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML48_Liver)


title: Liver_VEHICLE_VEHICLE_Day8_Rep7

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML47_Liver)


title: Liver_VEHICLE_VEHICLE_Day8_Rep2

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML42_Liver)


title: 177Lu Cortex 60 MBq 8 months 2


title: Non-treated (DMSO) Huh7.5.1 cells rep3

description: Replicate 3


title: 177Lu Cortex 90 MBq 8 months 2


title: Liver_VEHICLE_VEHICLE_Day8_Rep6

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML46_Liver)


title: Liver_VEHICLE_VEHICLE_Day8_Rep5

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML45_Liver)


title: myrAKT DBZ rep3

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DBZ
myrAKT_DBZ_3

hyb_protocol: hybridized on Illumina BeadChip Array Mouse WG-6 v2 arrays according to the manufacturer's protocol

scan_protocol: Standard scan according to manufacturer's protocol

data_processing: Expression values were log2 transformed and quantile normalized.

source_name: Pten wild type NOTCH1 induced tumors infected with MSCV Myr-AKT-IRES-mCherry, treated with DBZ

label_protocol: RNA (1 µg)  from Pten-positive mCherry and Pten-positive myr-AKT leukemic cells treated with vehicle or DBZ was amplified and labeled with the Illumina TotalprepRNA kit

growth_protocol: We transplanted leukemia cells from primary recipients into secondary recipients. We monitored the mice until they showed more than 70% of GFP positive cells in peripheral blood

extract_protocol: We isolated RNA from leukemic cells from spleen samples collected from mice acutely treated with Vehicle or DBZ using RNeasy plus mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Mice were treated twice, 16 hours apart, with vehicle only or DBZ (5 mg kg-1). 4 hours after the second treatment, mice were sacrificed and splenic samples were collected and subsequently snap-frozen

value: Leukemia


title: 177Lu Cortex 60 MBq 8 months 4


title: Non-treated (DMSO) Huh7.5.1 cells rep1

description: Replicate 1


title: 177Lu Cortex 90 MBq 8 months 1


title: Liver_VEHICLE_VEHICLE_Day8_Rep3

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML43_Liver)

value: Liver


title: 177Lu Cortex 30 MBq 8 months 4


title: myrAKT DBZ rep1

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DBZ
myrAKT_DBZ_1


title: myrAKT DBZ rep2

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DBZ
myrAKT_DBZ_2


title: Liver_VEHICLE_VEHICLE_Day8_Rep10

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML50_Liver)


title: Liver_VEHICLE_VEHICLE_Day8_Rep1

description: Liver from mouse treated with vehicle for 8 days  (Mouse_ML41_Liver)


title: myrAKT Control rep3

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DMSO
myrAKT_DMSO_3

source_name: Pten wild type NOTCH1 induced tumors infected with MSCV Myr-AKT-IRES-mCherry, treated with DMSO


title: 177Lu Cortex 30 MBq 8 months 3


title: 177Lu Cortex 90 MBq 8 months 4


title: Liver_VEHICLE_VEHICLE_Day4_Rep8

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML01_Liver)


title: Liver_VEHICLE_VEHICLE_Day4_Rep9

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML10_Liver)


title: 177Lu Cortex 30 MBq 8 months 1


title: 177Lu Cortex 120 MBq 4 months 4

value: 4 months


title: 177Lu Cortex 150 MBq 4 months 1


title: 177Lu Cortex 150 MBq 4 months 2


title: Liver_VEHICLE_VEHICLE_Day4_Rep6

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML08_Liver)


title: Liver_VEHICLE_VEHICLE_Day4_Rep7

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML09_Liver)


title: Liver_VEHICLE_VEHICLE_Day4_Rep5

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML07_Liver)


title: myrAKT Control rep1

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DMSO
myrAKT_DMSO_1


title: 177Lu Medulla 60 MBq 12 months 2

source_name: Medulla

value: Medulla

value: 12 months


title: PAA061

description: memory CD4+ T-cell subsets were isolated by FACS


title: myrAKT Control rep2

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV Myr-AKT-IRES-mCherry, treated with DMSO
myrAKT_DMSO_2


title: 177Lu Cortex 120 MBq 4 months 2


title: 177Lu Cortex 150 MBq 4 months 3


title: 177Lu Cortex 120 MBq 4 months 3


title: AKT WT Control rep3

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DMSO
EMPTY_DMSO_3

source_name: Pten wild type NOTCH1 induced tumors infected with MSCV empty-mCherry, treated with DMSO


title: Liver_VEHICLE_VEHICLE_Day4_Rep3

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML05_Liver)

value: 4 days


title: AKT WT DBZ rep3

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DBZ
EMPTY_DBZ_3

source_name: Pten wild type NOTCH1 induced tumors infected with MSCV empty-mCherry, treated with DBZ


title: AKT WT DBZ rep2

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DBZ
EMPTY_DBZ_2


title: AKT WT Control rep2

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DMSO
EMPTY_DMSO_2


title: Liver_VEHICLE_VEHICLE_Day4_Rep4

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML06_Liver)


title: Liver_VEHICLE_VEHICLE_Day4_Rep10

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML02_Liver)


title: AKT WT Control rep1

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DMSO
EMPTY_DMSO_1


title: AKT WT DBZ rep1

description:
gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias infected with MSCV empty-mCherry, treated with DBZ
EMPTY_DBZ_1


title: 177Lu Cortex 90 MBq 4 months 3

value: Cortex


title: 177Lu Cortex 90 MBq 4 months 2


title: Liver_VEHICLE_VEHICLE_Day4_Rep1

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML03_Liver)


title: 177Lu Cortex 60 MBq 4 months 3


title: pMp_BG3w_Rep4

description: peritoneal macrophages from wild-type administrated with BG

hyb_protocol: Samples are hybridized to the Mouse Gene 1.0 ST Array (Affymetrix) according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G　according to the manufacturer's instructions..

data_processing:
The obtained data are analyzed using the Expression Console software (Affymetrix). Normalization was performed using the RMA algorithm.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: wild-type, peritoneal macrophages, BG, 3w

label_protocol: cDNA is labeled using by WT terminal labeling kit (Affymetrix) according to the manufacturer’s instructions.

extract_protocol: RNAs are prepared using Trizol (Life Tech.) from each of four independent samples of peritoneal resident macrophages. Total RNA (100 ng) was amplified using the WT Expression Kit (Ambion).

treatment_protocol: In some experiments, mice were injected intravenously with LPS (E. coli O111:B4, Sigma), PGN (tlrl-pgnbs, InvivoGen), imiquimod (tlrl-imq, InvivoGen), β-glucan (prepared as described in Ishibashi et al.47), or PBS at 7–8 weeks of age, and 3–4 weeks after injection, macrophages collected from the injected mice were analyzed (i.e., when the animals were 10–12 weeks of age).

value: peritoneal macrophages

tag: administration into mice


title: 177Lu Cortex 90 MBq 4 months 4

tag: strain


title: 177Lu Cortex 60 MBq 4 months 2

tag: tissue


title: Liver_WY14643_10 mg/kg_Day15_Rep1

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days  (Mouse_ML96_Liver)

tag: compound

value: 10 mg/kg


title: Liver_VEHICLE_VEHICLE_Day4_Rep2

description: Liver from mouse treated with vehicle for 4 days  (Mouse_ML04_Liver)

value: Vehicle

tag: dose

value: N / A


title: Liver_VEHICLE_VEHICLE_Day15_Rep9

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML89_Liver)

value: 15 days


title: pMp_BG3w_Rep3

value: wild-type in C57BL/6 background


title: 177Lu Cortex 30 MBq 4 months 3


title: Liver_VEHICLE_VEHICLE_Day15_Rep7

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML87_Liver)


title: pMp_BG3w_Rep1


title: pMp_BG3w_Rep2


title: pMp_IMQ3w_Rep4

description: peritoneal macrophages from wild-type administrated with IMQ

source_name: wild-type, peritoneal macrophages, IMQ, 3w


title: Liver_VEHICLE_VEHICLE_Day15_Rep6

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML86_Liver)


title: pMp_IMQ3w_Rep3


title: Liver_WY14643_10 mg/kg_Day15_Rep5

description: Liver from mouse treated with WY14643 at a dose of 10 mg/kg for 15 days  (Mouse_ML100_Liver)


title: pMp_PGN3w_Rep4

description: peritoneal macrophages from wild-type administrated with PGN

source_name: wild-type, peritoneal macrophages, PGN, 3w


title: Liver_VEHICLE_VEHICLE_Day15_Rep8

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML88_Liver)


title: 177Lu Cortex 60 MBq 4 months 1


title: pMp_PGN3w_Rep3


title: pMp_IMQ3w_Rep1


title: 177Lu Cortex 30 MBq 4 months 2


title: Liver_VEHICLE_VEHICLE_Day15_Rep5

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML85_Liver)


title: Liver_VEHICLE_VEHICLE_Day15_Rep3

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML83_Liver)


title: 177Lu Cortex Control 12 months 3

value: Control


title: 177Lu Cortex 30 MBq 4 months 4

value: Balb/c


title: Liver_VEHICLE_VEHICLE_Day15_Rep10

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML90_Liver)


title: 177Lu Cortex Control 12 months 1


title: IVL1 Patient

city: Otsu-shi

first: keiki

last: sugimoto

state: Shiga

address: 1-11-1, Karasaki

department: Fujii Memorial Research Institute

institute: Otsuka Pharmaceutical

hyb_protocol: Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 ºC for 5 minutes and immediately chill on ice for 30 minutes.  Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips.  Set the shaker speed to 300 rpm and incubate slides for 18 h.  Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75× TNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75× TNT, and incubate at 46 °C for exactly 1 h.  Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir into the small reagent reservoir and incubate bioarrays at ambient temperature for 30 minutes. Wash the bioarrays four times with 1× TNT (5 minutes each wash) in large reagent reservoirs. Rinse the bioarrays in 0.1× SSC/0.05% Tween for 30 seconds. Immediately follow the rinse with centrifugation to dry bioarrays.

scan_protocol: The arrays were scanned with GenePix 4000B (Molecular Devices).

data_processing: Signal intensities were quantified with CodeLinh Expression Anlysis Software v5.0 (Applied Microarray, Inc.)

source_name: Primary Lymphoma from Patient

label_protocol: In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5× fragmentation buffer and incubate at 94 ºC for 20 minutes.

extract_protocol: none provided by the submitter

value: Peripheral Blood

tag: age

tag: Sex

value: Male


title: Liver_VEHICLE_VEHICLE_Day15_Rep4

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML84_Liver)


title: 177Lu Cortex Control 12 months 2


title: 177Lu Cortex Control 8 months 1

value: 8 months


title: Liver_VEHICLE_VEHICLE_Day15_Rep1

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML81_Liver)

value: Liver


title: IVL2 PDX

source_name: Primary Lymphoma from PDX mouse


title: pMp_IMQ3w_Rep2


title: 177Lu Cortex Control 8 months  3


title: Liver_VEHICLE_VEHICLE_Day15_Rep2

description: Liver from mouse treated with vehicle for 15 days  (Mouse_ML82_Liver)


title: Liver_ROSIGLITAZONE_10 mg/kg_Day8_Rep4

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days  (Mouse_ML79_Liver)

source_name: Liver_ROSIGLITAZONE_10 mg/kg_Day8

value: Rosiglitazone

value: 8 days


title: 177Lu Cortex Control 4 months 2

value: 4 months


title: 177Lu Cortex Control 8 months 2


title: DLB2 Patient

value: Female


title: DLB2 PDX


title: Liver_ROSIGLITAZONE_10 mg/kg_Day8_Rep5

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days  (Mouse_ML80_Liver)


title: Liver_ROSIGLITAZONE_10 mg/kg_Day8_Rep2

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days  (Mouse_ML77_Liver)


title: pMp_PGN3w_Rep1


title: 177Lu Cortex Control 4 months 3

value: Cortex


title: pMp_LPS3w_Rep3

description: peritoneal macrophages from wild-type administrated with LPS

source_name: wild-type, peritoneal macrophages, LPS, 3w

value: peritoneal macrophages


title: Liver_ROSIGLITAZONE_10 mg/kg_Day8_Rep3

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days  (Mouse_ML78_Liver)

value: 10 mg/kg


title: pMp_LPS3w_Rep1


title: pMp_LPS3w_Rep4


title: pMp_PGN3w_Rep2


title: DLB1 In Vitro

source_name: Lymphoma cells in vitro culture


title: 177Lu Cortex 150 MBq 12 months 6

value: 12 months


title: DLB3 PDX


title: ura3 log phase replicate 3

city: Durham

first: Keely

last: Dulmage

state: NC

address: FFSC3242, 124 Science Drive

department: Biology

institute: Duke University

description: mid-log culture grown at 37C with shaking at 250rpm

hyb_protocol: Labelled cDNA was hybridised to Agilent slides for 18h at 68°C. Arrays were then washed in Agilent Gene Expression Wash Buffer 1 (RT), Agilent Gene Expression Wash Buffer 2 (37C), acetonitrile, and stabilizaiton and drying solution prior to drying and scanning.

scan_protocol: Arrays scanned using an Axon Genepix Scanner and Agilent Feature Extraction v.10.7 software.

data_processing: Data analysis was carried out using the R package Limma (Smyth, G.K.,2005). The median values from each channel were log2 transformed, background was subtracted using the normexp algorithm with an offset of 50, data were normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values, and data were normalized between arrays using the quantile algorithm.  For each gene,the experimental/reference log2 value was calculated as the median value of replicate spots on a given array in addition to the inverted values of the dye-flipped experiment (8-12 data points total).

organism: Halobacterium salinarum NRC-1

source_name: ura3 log phase

label_protocol: Labelled total RNA with Cy3 and Cy5 using the ULS aRNA Fluorescent Labeling Kit (Kreatech) as per manufacturers instructions.

growth_protocol: Cells were grown in CM (250g/L NaCl, 20g/L MgSO4*7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) with uracil supplemented as needed to a final concentration of 50ug/ml.  Cultures were incubated at 42C and 250rpm in erlenmeyer flasks.

extract_protocol: RNA was harvested from midlog (OD600=0.5) and stationary (OD600=1.5) cultures using the Absolutely RNA Miniprep Kit (Agilent) according to manufacturer's instructions.

tag: genotype/variation

source_name: Halobacterium standard reference sample

value: wildtype


title: pMp_LPS3w_Rep2


title: DLB3 Patient


title: 177Lu Cortex 150 MBq 12 months 5+3

source_name: Cortex


title: ura3 stationary phase replicate 2

source_name: ura3 stationary phase


title: Liver_ROSIGLITAZONE_10 mg/kg_Day4_Rep5

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days  (Mouse_ML40_Liver)

source_name: Liver_ROSIGLITAZONE_10 mg/kg_Day4

value: 4 days


title: 177Lu Cortex 150 MBq 12 months 2


title: Liver_ROSIGLITAZONE_10 mg/kg_Day4_Rep4

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days  (Mouse_ML39_Liver)


title: ura3 stationary phase replicate 3


title: DLB1 Patient


title: pMp_PBS3w_Rep4

description: peritoneal macrophages from wild-type administrated with PBS

source_name: wild-type, peritoneal macrophages, PBS, 3w

value: wild-type in C57BL/6 background


title: 177Lu Cortex Control 4 months 1

value: Control


title: Liver_ROSIGLITAZONE_10 mg/kg_Day8_Rep1

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 8 days  (Mouse_ML76_Liver)


title: pMp_PBS3w_Rep3


title: pMp_PBS3w_Rep1


title: pMp_PBS3w_Rep2


title: ura3 log phase replicate 2


title: ura3 log phase replicate 1


title: pMp_KO_Rep4

description: peritoneal macrophages from ATF7 knockout

source_name: ATF7 knockout, peritoneal macrophages, NT

value: ATF7 knockout in C57BL/6 background

value: NT


title: ura3 stationary phase replicate 1


title: 177Lu Cortex 120 MBq 12 months 4

value: Balb/c


title: Liver_ROSIGLITAZONE_10 mg/kg_Day4_Rep3

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days  (Mouse_ML38_Liver)


title: 177Lu Cortex 120 MBq 12 months 1


title: pMp_KO_Rep2


title: 177Lu Cortex 120 MBq 12 months 2


title: hpyA stationary phase replicate 3

source_name: hpyA stationary phase


title: pMp_KO_Rep1


title: Liver_ROSIGLITAZONE_10 mg/kg_Day15_Rep3

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days  (Mouse_ML118_Liver)

source_name: Liver_ROSIGLITAZONE_10 mg/kg_Day15

value: 15 days


title: 177Lu Cortex 90 MBq 12 months 4


title: pMp_KO_Rep3


title: 177Lu Cortex 90 MBq 12 months 2


title: pMp_WT_Rep4

description: peritoneal macrophages from wild-type

source_name: wild-type, peritoneal macrophages, NT


title: 177Lu Cortex 90 MBq 12 months 1


title: Liver_ROSIGLITAZONE_10 mg/kg_Day15_Rep4

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days  (Mouse_ML119_Liver)

value: Liver


title: hpyA stationary phase replicate 2


title: Liver_ROSIGLITAZONE_10 mg/kg_Day15_Rep2

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days  (Mouse_ML117_Liver)

value: Rosiglitazone


title: hpyA log phase replicate 3

source_name: hpyA log phase


title: hpyA stationary phase replicate 1


title: hpyA log phase replicate 2


title: Liver_ROSIGLITAZONE_10 mg/kg_Day15_Rep1

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days  (Mouse_ML116_Liver)


title: 177Lu Cortex 60 MBq 12 months 4


title: 177Lu Cortex 60 MBq 12 months 2


title: pMp_WT_Rep2

description: peritoneal macrophages from wild-type


title: Liver_GW501516_10 mg/kg_Day8_Rep4

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days  (Mouse_ML66_Liver)

source_name: Liver_GW501516_10 mg/kg_Day8

value: 8 days


title: hpyA log phase replicate 1


title: pMp_WT_Rep1

description: peritoneal macrophages from wild-type


title: 177Lu Cortex 60 MBq 12 months 1


title: pMp_WT_Rep3

description: peritoneal macrophages from wild-type


title: MTLa/alpha dig1Δ/dig1Δ vs WT SN148 (replica 4)

city: Montreal

first: Hannah

last: Regan

address: 7141 Sherbrooke Street West

institute: Concordia University

description:
Arrays are organized in 48 sub-arrays containing 280 spots each
dig1 (replica4)

hyb_protocol: Microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice with 1X SSC-0.2% SDS and 3 times with 0.1X SSC.

scan_protocol: Slides were scanned at 5-µm resolution with an Axon GenePix 4000B microarray scanner running GenePix Pro 4.1.

data_processing:
Signal intensity was quantified with GenePix Pro 4.1 software
Normalization and inspection of the data was done with Mev_4_9. Lowess normalization, and log2 ratio dig1(mutant)/WT

organism: Candida albicans

source_name: dig1Δ_YPD 30C

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)23 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Template RNA was then degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

growth_protocol: Single colonies were inoclulated into 50 mL YPD media and grown overnight at 30oC.  Cultures were then diluted to OD600nm = 0.1 in YPD and grown until OD600nm = 0.6-0.8 at 30oC.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Mutant strains were deleted for DIG1, wild type strains were not.

tag: strain background

value: dig1delta/dig1delta homozygous mutant

source_name: wild type_YPD 30C

value: wild type


title: CLL Exosomal RNA 3

city: Liverpool

first: Mosavar

last: Farahani

address: Daulby Street

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

description: a pool of cellular RNA from 23 CLL individuals

hyb_protocol: The Hy3-labelled exosome samples or CLL cell samples and a Hy5-labelled CLL cell samples pool (n=23; common reference sample) were hybridized to the miRCURY LNA array (Exiqon miRCURYTM LNA array v.5).  The hybridization and all steps of the image analysis and normalisation of data were carried out by Exiqon.

data_processing:
Median data for Hy3 and Hy5 was calculated from the replicated measurements on the same slide (SD-values were calculated from 4 replicate spots).
Different normalization methods such as lowess and quantile were performed to see the best method to use to compare the results between the exosomal and the cellular samples.  We were unable to find a suitable normalizing method for both exosomes and cells thus it was found that the best method was to use the raw intensity data from the arrays after background correction.  Other method skewed the data set and provided unreliable results
The supplementary file "LME_background-subtracted_Hy3.txt" contains LogMedianExpression (LME) of Hy3 background-subtracted raw values.

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 3

label_protocol: We used dual colour hybridizations and we used the common reference approach which each sample whether exosomal RNA or cellular RNA was compared to common reference sample (a pool of 23 CLL cells).

growth_protocol: CLL cells were cultured for 48h and media supernatant was harvested. Exosomes were purified from this supernatant.

extract_protocol: Total RNA extractions were performed using the miRNeasy kit (Qiagen).  Briefly, the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.

tag: rna source

value: Exosomal RNA from CLL patient 3

tag: cell type/component

value: isolated exosomes from culture medium of CLL 3

value: blood

source_name: Pooled reference sample

tag: reference type

value: a collection of 23 RNA extracted from 23 CLL cell samples


title: MTLa/alpha dig1Δ/dig1Δ vs WT SN148 (replica 2)

description:
Arrays are organized in 48 sub-arrays containing 280 spots each
dig1 (replica2)


title: 177Lu Cortex 30 MBq 12 months 3

value: Cortex

tag: nuclide

tag: injected activity

tag: time

value: 12 months


title: ATF7_pMp_Whole_G

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array G of A-G

source_name: Peritoneal macrophages from wild-type mice

tag: treatment

value: ChIP using ATF7 Ab

value: wild-type in C57BL/6 background

value: peritoneal macrophage


title: ATF7_pMp_Whole_D

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array D of A-G

tag: cell-type


title: CLL Cellular RNA 2

scan_protocol: The hybridization and all steps of the image analysis and normalisation of data were carried out by Exiqon.

source_name: RNA extracted  from CLL cells patient 2

value: Cellular RNA from CLL patient 2

value: isolated B cells from fresh blood CLL2


title: MTLa/alpha dig1Δ/dig1Δ vs WT SN148 (replica 3)

description:
Arrays are organized in 48 sub-arrays containing 280 spots each
dig1 (replica3)


title: CLL Cellular RNA 3

source_name: RNA extracted  from CLL cells patient 3

value: Cellular RNA from CLL patient 3

value: isolated B cells from fresh blood CLL 3


title: Liver_GW501516_10 mg/kg_Day8_Rep3

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days  (Mouse_ML69_Liver)

value: Liver

value: 10 mg/kg

tag: time point


title: CLL Exosomal RNA 1

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 1

value: Exosomal RNA from CLL patient 1

value: isolated exosomes from culture medium of CLL 1


title: ATF7_pMp_Whole_E

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array E of A-G

tag: strain


title: CLL Exosomal RNA 2

source_name: RNA extracted from exosomes isolated from CLL culture medium patient 2

value: Exosomal RNA from CLL patient 2

value: isolated exosomes from culture medium of CLL 2

tag: tissue


title: MTLa/alpha dig1Δ/dig1Δ vs WT SN148 (replica 1)

description:
Arrays are organized in 48 sub-arrays containing 280 spots each
dig1 (replica1)

value: dig1delta/dig1delta homozygous mutant

value: wild type


title: Liver_GW501516_10 mg/kg_Day8_Rep1

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days  (Mouse_ML67_Liver)

tag: compound

value: 8 days


title: CLL Cellular RNA 1

source_name: RNA extracted  from CLL cells patient 1

value: Cellular RNA from CLL patient 1

value: isolated B cells from fresh blood CLL 1

value: blood

value: a collection of 23 RNA extracted from 23 CLL cell samples


title: Liver_GW501516_10 mg/kg_Day4_Rep2

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days  (Mouse_ML27_Liver)

source_name: Liver_GW501516_10 mg/kg_Day4

tag: dose

value: 4 days


title: ATF7_KO_pMp_promoter

description:
prom_ATF7_MAT_KO_signalNorm.bed
ATF7 distribution in promoter region of KO peritoneal resident macrophage

source_name: Peritoneal macrophages from ATF7 knockout mice

value: ChIP using ATF7 Ab

value: ATF7 knockout in C57BL/6 background

value: peritoneal macrophage


title: 177Lu Cortex 150 MBq 8 months 4

source_name: Cortex

value: Balb/c

value: Cortex

value: 8 months


title: 177Lu Cortex 30 MBq 12 months 4

value: 12 months


title: 177Lu Cortex 150 MBq 8 months 3


title: ATF7_pMp_Whole_F

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array F of A-G

value: wild-type in C57BL/6 background


title: Liver_GW501516_10 mg/kg_Day8_Rep5

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days  (Mouse_ML70_Liver)

value: Liver

value: 10 mg/kg


title: Liver_ROSIGLITAZONE_10 mg/kg_Day4_Rep2

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days  (Mouse_ML37_Liver)

source_name: Liver_ROSIGLITAZONE_10 mg/kg_Day4

value: Rosiglitazone


title: Liver_GW501516_10 mg/kg_Day4_Rep3

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days  (Mouse_ML28_Liver)


title: Liver_GW501516_10 mg/kg_Day4_Rep5

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days  (Mouse_ML30_Liver)


title: ATF7_WT_pMp_promoter

description:
prom_ATF7_MAT_WT_signalNorm.bed
ATF7 distribution in promoter region of WT peritoneal resident macrophage


title: ATF7_pMp_Whole_B

description:
tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array B of A-G


title: DLB1 PDX

source_name: Primary Lymphoma from PDX mouse

tag: age


title: Liver_GW501516_10 mg/kg_Day4_Rep4

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days  (Mouse_ML29_Liver)


title: CK12h

type: SRA

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

description:
Sample 3
small RNAs

library_source: transcriptomic

data_processing:
Raw sequence reads were first trimmed to remove adapter sequences. Sequences with low phred quality scores or shorter than 18 nucleotides were removed. The total number of reads for each data set was normalized to 10 million. Total sequences of the eight data sets were aligned to the rice genomic sequences and miRNA precursor sequences, respectively, using the BLASTN (Altschul et al., 1990) program.
Transposons and repeat regions in the rice genome were identified by the RepeatMasker software.
Target gene prediction for miRNAs and ta-siRNAs was performed as previously described (Zhao et al., 2012).
Statistical analysis and data plotting were carried out using R. Expression comparison of small RNAs was performed at each time point separately. Small RNAs with at least 10 reads in both the Xoo treated and control samples were included in the expression comparison analysis. Differentially expressed small RNAs were selected with at least 2 fold expression increment or decrease in the Xoo treated sample as compared to the control. fold change equal to or more than 2.
Original raw files unavailable:  The *raw_reads.txt files are similar to FASTQ format but without phred quality score. In these files, the sequences with low phred scores have been removed.
Genome_build: rice genomic sequences version 6.1 [http://rice.plantbiology.msu.edu/ (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/)]
Supplementary_files_format_and_content: raw reads and normalized reads

organism: Oryza sativa Japonica Group

source_name: Leaves

growth_protocol: Japonica rice varieties (Oryza sativa, Nipponbare) were grown in the experimental fields in Beijing.

extract_protocol:
Samples were collected from multiple plants and pooled together before use. Total RNAs of each sample were isolated using Trizol reagent (Invitrogen), and small RNAs were collected and sequenced by the Illumina’s sequencing technology.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 40-day-old rice seedling were infected by Xoo PXO99 and water for experimental and control samples, respectively. Leaf tissues at 1 cm below the infected loci were collected at 2, 6, 12, and 24 hpi, respectively.

tag: cultivar

value: Nipponbare

tag: developmental stage

value: 40-day old

value: leaf

tag: infection

value: water


title: CK24h

description:
Sample 4
small RNAs


title: Xoo2h

description:
Sample 5
small RNAs

value: Xoo PXO99


title: CK6h

description:
Sample 2
small RNAs


title: Biofilm_day3_dyjiY

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 1000ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Custom Salmonella GXP, 8X15K (AMADID No: 046639) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: LB w/o NaCl, static, Day3

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using WT primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight culture was subcultured at 1:100 in LB w/o NaCL and grown at static conditions for 3days at room temperature

extract_protocol: RNA isolation was done by using TRIzol method as per the manufacturer’s instructions.

tag: bacteria

value: ygeA knockout

tag: growth mode

value: biofilm


title: CK2h

description:
Sample 1
small RNAs


title: 177Lu Cortex 150 MBq 8 months 2


title: Biofilm_day3_daspR

value: aspR knockout


title: Biofilm_day3_wt

value: wild type


title: Xoo24h

description:
Sample 8
small RNAs


title: 177Lu Cortex 30 MBq 12 months 2

value: Balb/c


title: Liver_GW501516_10 mg/kg_Day15_Rep5

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days  (Mouse_ML110_Liver)

source_name: Liver_GW501516_10 mg/kg_Day15

value: 15 days


title: Liver_GW501516_10 mg/kg_Day8_Rep2

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 8 days  (Mouse_ML68_Liver)

source_name: Liver_GW501516_10 mg/kg_Day8

value: 8 days


title: Liver_GW501516_10 mg/kg_Day15_Rep4

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days  (Mouse_ML109_Liver)


title: Xoo12h

description:
Sample 7
small RNAs


title: LB_late log_wt

description: LB_late log_wt

source_name: LB, shaking, late log phase

growth_protocol: Overnight culture was subcultured at a ratio of 1:33 in LB and grown for 3h at 37°C at 170rpm

value: wildtype

value: planktonic


title: wild type iPSC, biological rep1

first: Jingping

last: Ge

address: 3615 CivicCenter Blvd, ARC 303

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: CHOP_2.2A_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the CHOP Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA (Partek Genomics Suite v6.6).

source_name: wild type iPSC

label_protocol: 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: Human iPSCs grew in the stem cell medium

extract_protocol: All RNA samples  were prepared using Trizol, and then treated with DNase.

tag: subject status

value: DBA patients

tag: cell type

value: induced pluripotent stem cells

tag: genotype/variation

tag: passage

value: Passage 27


title: Liver_GW501516_10 mg/kg_Day4_Rep1

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 4 days  (Mouse_ML26_Liver)

value: Liver

value: 10 mg/kg

value: 4 days


title: Xoo6h

description:
Sample 6
small RNAs

value: Nipponbare

value: 40-day old

value: leaf

tag: time


title: Biofilm_day3_dd

value: double knockout

value: biofilm


title: iPSC with a RPL5 muation, biological rep2

description: 346.1#3C_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

source_name: iPSC with a RPL5 muation

value: DBA patients carrying RPL5 mutation

value: RPL5 mutant

value: Passage 28


title: LB_late log_dyjiY

description: LB_late log_dyjiY

value: ygeA knockout


title: Liver_GW501516_10 mg/kg_Day15_Rep1

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days  (Mouse_ML106_Liver)

value: 15 days


title: Liver_GW501516_10 mg/kg_Day15_Rep2

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days  (Mouse_ML107_Liver)


title: wild type iPSC, biological rep2

description: CHOP_2.2B_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

value: wild type


title: LB_late log_daspR

description: LB_late log_daspR

value: aspR knockout

value: planktonic


title: Liver_GW501516_10 mg/kg_Day15_Rep3

description: Liver from mouse treated with GW501516 at a dose of 10 mg/kg for 15 days  (Mouse_ML108_Liver)


title: LB_late log_dd

description: LB_late log_dd


title: iPSC with a RPL5 muation, biological rep1

description: 346.1#3A_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

value: induced pluripotent stem cells

value: Passage 27


title: iPSC with a RPS19 muation, biological rep1

description: 6.2#4A_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

source_name: iPSC with a RPS19 muation

value: DBA patients carrying RPS19 mutation

value: RPS19 mutant


title: Liver_ROSIGLITAZONE_10 mg/kg_Day4_Rep1

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 4 days  (Mouse_ML36_Liver)

value: Liver

value: Rosiglitazone

value: 10 mg/kg

value: 4 days


title: Liver_ROSIGLITAZONE_10 mg/kg_Day15_Rep5

description: Liver from mouse treated with ROSIGLITAZONE at a dose of 10 mg/kg for 15 days  (Mouse_ML120_Liver)

source_name: Liver_ROSIGLITAZONE_10 mg/kg_Day15


title: control (empty vector OP) -biological replicate -1

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

institute: University of Calcutta

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix Scanner G 300 7G

data_processing: GeneSpring GX12.6

organism: Schizosaccharomyces pombe

source_name: WILDStrain

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

extract_protocol: total RNA extraction using Epicentre yeast RNA extraction kit

value: Wild type


title: cecumdead_3days_4

status: Public on Aug 30 2015

city: kunitachi-si

first: tatsuichiro

last: shima

state: Tokyo

department: basic research

institute: Yakult central institute for microbiological research

description: Gene expression in ex-GF mouse 3days after dead BbrY association

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 °C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarrays (G4122F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent) and 1 minute at room temperature acetonitorile.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cecum,epithelial cell,dead,3days,4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the Spectrophotometer.

extract_protocol: RNA was prepared using the Chloroform and isopropanol and DNase treatment at 37 °C. The total RNA was extracted from TRI-zol reagent buffer of cecal epithelial cells.  RNA was quantified using the spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: GB mouse was prepared from GF mouse by live or dead BbrY. Cecal epithelial cells were collected 3 days or 28 days after live or dead BbrY association. Cecal epithelial cells were released by incubation with HANKS including 4 mM EDTA and 10 mM HEPES at 37 °C and collected by centrifugation after being washed with PBS and filtrated with a filter (100 mesh). The collected epithelial cells were treated with TRI-zol reagents and stored at -80 °C.

tag: agent

value: dead, 3days

value: cecal epithelial cell

tag: gender

value: female


title: cecumGF_28days_3

description: Gene expression in GF mouse 28days after starting of experiment

source_name: cecum,epithelial cell,GF,28days,3

value: GF, 28days


title: cecumlive_28days_3

description: Gene expression in ex-GF mouse 28days after live BbrY association

source_name: cecum,epithelial cell,live,28days,3

value: live, 28days


title: cecumlive_3days_2

description: Gene expression in ex-GF mouse 3days after live BbrY association

source_name: cecum,epithelial cell,live,3days,2

value: live, 3days


title: cecumdead_28days_1

description: Gene expression in ex-GF mouse 28days after dead BbrY association

source_name: cecum,epithelial cell,dead,28days,1

value: dead, 28days


title: cecumdead_28days_4

source_name: cecum,epithelial cell,dead,28days,4


title: cecumGF_3days_4

description: Gene expression in GF mouse 3days after starting of experiment

source_name: cecum,epithelial cell,GF,3days,4

value: GF, 3days


title: cecumlive_28days_2

source_name: cecum,epithelial cell,live,28days,2


title: control (empty vector OP) -biological replicate -2

tag: strain


title: Atf1-OP -biological replicate -1


title: cecumlive_3days_3

source_name: cecum,epithelial cell,live,3days,3

tag: tissue


title: cecumGF_3days_3

source_name: cecum,epithelial cell,GF,3days,3


title: cecumlive_3days_4

source_name: cecum,epithelial cell,live,3days,4


title: cecumlive_28days_4

source_name: cecum,epithelial cell,live,28days,4


title: cecumdead_28days_2

source_name: cecum,epithelial cell,dead,28days,2


title: cecumdead_3days_1

source_name: cecum,epithelial cell,dead,3days,1


title: Atf1-OP -biological replicate -2


title: cecumlive_3days_1

source_name: cecum,epithelial cell,live,3days,1


title: cecumGF_28days_1

source_name: cecum,epithelial cell,GF,28days,1


title: cecumdead_3days_3

source_name: cecum,epithelial cell,dead,3days,3


title: cecumlive_28days_1

source_name: cecum,epithelial cell,live,28days,1


title: cecumdead_3days_2

source_name: cecum,epithelial cell,dead,3days,2


title: iPSC with a RPS19 muation, biological rep2

description: 6.2#4B_043012_(HuEx-1_0-st-v2).rma-gene-core-Signal

source_name: iPSC with a RPS19 muation

value: induced pluripotent stem cells

value: Passage 28


title: cecumdead_28days_3

source_name: cecum,epithelial cell,dead,28days,3


title: cecumGF_28days_2

source_name: cecum,epithelial cell,GF,28days,2


title: cecumGF_28days_4

source_name: cecum,epithelial cell,GF,28days,4


title: DL206-A-T3

city: Sydney

first: Miguel

middle: A

last: Hernández-Prieto

state: NSW

address: Macleay Building A12

department: School of life and environmental sciences

country: Australia

institute: University of Sydney

description: Prochlorococcus strain NATL2A infected with P-TIM40

hyb_protocol: Hybridization was carried out according to Affymetrix protocols for Prokaryotic target RNA (GeneChip Expression Analysis Technical Manual, Prokaryotic; 702232, Rev.3) and was carried out at the Center for Genomic Technologies, Hebrew University of Jerusalem, Israel.

scan_protocol: Scanning was carried out according to Affymetrix protocols for Prokaryotic target RNA (GeneChip Expression Analysis Technical Manual, Prokaryotic; 702232, Rev.3), and was carried out at the Center for Genomic Technologies, Hebrew University of Jerusalem, Israel.

data_processing: Data were analyzed using the probe signal intensities from the CEL files and the probe sets defined in the CDF library file using the R statistical language with Bioconductor add-on packages. Following previous analyses (Lindell et al. 2007), background signal correction, normalization and summarization were performed by Robust Multiarray Averaging (RMA) from the Limma package (Smyth 2005). Differential expression between infected and uninfected controls was statistically evaluated by a linear model comparing the time-resolved signal intensities from the arrays with uninfected hosts to those from arrays with infected hosts. P-values were adjusted for multiple testing and converted to false discovery rates (q-values) by the Benjamini-Hochberg approach.

organism: Prochlorococcus marinus str. NATL2A

source_name: Prochlorococcus strain NATL2A

label_protocol: Labeling was carried out according to Affymetrix protocol for Prokaryotic target RNA (GeneChip Expression Analysis Technical Manual, Prokaryotic; 702232, Rev.3) using 2 µg of total RNA, and was carried out at the Center for Genomic Technologies, Hebrew University of Jerusalem, Israel.

growth_protocol: Prochlorococcus strain NATL2A  was grown in the Pro99 seawater-based medium (Moore et al. 2007) at 22 °C under cool white light with a 14:10 h light:dark cycle at an intensity of 30 μmol photon•m-2•s-1 during the light period.

extract_protocol: Prochlorococcus NATL2A cells (80 ml of each infected or control culture) were collected on 0.45 μm pore-sized supor-450 membranes (Pall, USA) by filtration at a vacuum pressure of 10 inch Hg and snap frozen in liquid nitrogen, after addition of 2 ml PGTX buffer (40 ml liquid phenol 95%, 6.9 ml glycerol, 0.1 g 8-hydroxyquinoline, 0.58 g EDTA, 0.8 g sodium acetate, 0.5 g guanidine thiocyanate and 4.6 g guanidine hydrochloride in a final volume of 100ml) without Triton X-100. Total RNA was extracted using the PGTX 95 method described in Pinto et al. (2009) with some minor modifications. Briefly, the samples were thawed on ice and subjected to a 15-min incubation at 65 °C followed by a further 5-min on ice. The aqueous phase was extracted twice with an equal volume of chloroform:isoamyl alcohol (24:1, vol/vol). RNA was precipitated with 1/10 volume of 3M sodium acetate, 3 volumes 100% ethanol and 0.2 µl glycogen at -20°C overnight. Subsequently, the pelleted RNA was washed in 75% ethanol and resuspended in RNase-free water. Total nucleic acids were quantified based on absorption at 260 nm and RNA integrity was verified by gel electrophoresis. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion). For microarray analysis 15 μg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by inactivation of DNase I with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.

treatment_protocol: Prochlorococcus *NATL2A was infected with the P-TIM40 phage at a multiplicity of infection (MOI) of 2. The experiment was carried out in triplicate.

tag: time point

value: 60 min

value: P-TIM40 phage


title: DL209-B-T2

value: time 240 min


title: DL212-C-T1


title: TFFI3

city: Beijing

first: chan

last: tian

address: Changbai Road, Changping district

country: China

institute: Chinese Center for Disease Control and Prevention, China CDC

description: Gene expression data from FFI patient 3 thalamus

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: FFI patient thalamus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of parietal cortex and thalamus of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

tag: Sex

value: male


title: DL214-C-T3

value: time 120 min


title: DL213-C-T2

value: time 90 min


title: NPL

description: Gene expression data from normal human parietal lobe

source_name: normal human parietal lobe

tag: age


title: DL207-A-T4


title: DL208-B-T1

value: time 180 min


title: cecumGF_3days_1

source_name: cecum,epithelial cell,GF,3days,1


title: DL210-B-T3

value: time 0


title: DL205-A-T2

value: 30 min


title: PLFFI3

description: Gene expression data from FFI patient 3 parietal lobe

source_name: FFI patient parietal lobe


title: TFFI2

description: Gene expression data from FFI patient 2 thalamus

value: 26 year-old

value: female


title: PLFFI2

description: Gene expression data from FFU patient 2 parietal lobe


title: cecumGF_3days_2

source_name: cecum,epithelial cell,GF,3days,2

value: cecal epithelial cell


title: TFFI1

description: Gene expression data from FFI patient 1 thalamus

value: 48 year-old


title: DL211-B-T4


title: NT

description: Gene expression data from normal human thalamus

source_name: normal human thalamus


title: DL161-III-4h-6 (WH8109)

description: Synechococcus sp. Strain WH8109 infected with the broad-host range T4-like myovirus, Syn9

organism: Synechococcus sp. WH 8109

source_name: Synechococcus sp. strain WH8109 infected by Syn9

growth_protocol: Synechococcus sp. strain WH8109 cells were grown in an artificial sea water-based medium (ASW) (Wyman et al. 1985) with modifications as described in Lindell et al. (1998), at 22 °C under cool white light with a 14:10 h light:dark cycle at an intensity of 30 μmol photon•m-2•s-1 during the light period.

extract_protocol: Synechococcus cells (50-75 ml of each infected or control culture) were collected on 0.4 μm pore-sized polycarbonate filters (GE) by filtration at a vacuum pressure of 10 inch Hg and snap frozen at -80 ºC in 2 ml PGTX buffer (40 ml liquid phenol 95%, 6.9 ml glycerol, 0.1 g 8-hydroxyquinoline, 0.58 g EDTA, 0.8 g sodium acetate, 0.5 g guanidine thiocyanate and 4.6 g guanidine hydrochloride at final pH = 4.2 in a final volume of 100ml) as described in Pinto et al (2009) but without Triton X-100. Each culture was sampled a minute apart such that WH8102-infected cells were sampled 1 and 2 minutes after WH8109- and WH8109-infected cells, respectively. Total RNA was extracted by the PGTX 95 method (Pinto et al. 2009) with some minor modifications. Briefly, the samples were thawed on ice and subjected to a 5-min incubation at 95 °C followed by a further 5-min on ice. The aqueous phase was extracted with an equal volume of chloroform:isoamyl alcohol (24:1, vol/vol). RNA was precipitated with 1 volume of isopropanol and washed in 75% ethanol. Total nucleic acids were quantified based on absorption at 260 nm and RNA integrity was verified by gel electrophoresis. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion). For microarray analysis 15 μg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by DNase I inactivation with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.

treatment_protocol: The experimental treatment was repited for three biological replicates at one week intervals. For each replicate the cultures were divided into two, one of which was infected with Syn9 at a multiplicity of infection (MOI) of 2-3, while the other served as an uninfected control.

value: Infected by Syn9

value: 240 min


title: PLFFI1

description: Gene expression data from FFI patient 1 parietal lobe


title: DL204-A-T1


title: DL147-I-4h-6 (WH8109)


title: DL160-III-3h-6 (WH8109)

value: 180 min


title: DL156-III-0.5h-6 (WH8109)


title: DL157-III-1h-6 (WH8109)


title: DL158-III-1.5h-6 (WH8109)

value: 90 min


title: DL159-III-2h-6 (WH8109)

value: 120 min


title: DL145-I-2h-6 (WH8109)


title: DL143-I-1h-6 (WH8109)

value: 60 min


title: DL146-I-3h-6 (WH8109)


title: DL144-I-1.5h-6 (WH8109)


title: DL133-II-4h-6 (WH8109)


title: DL142-I-0.5h-6 (WH8109)


title: DL153-III-3h-3 (WH8109)

description: Synechococcus sp. Strain WH8109 grown in parallel to an infected sample

source_name: Synechococcus sp. strain WH8109

value: Non-infected


title: DL141-I-0h-6 (WH8109)

value: 0 min


title: DL132-II-3h-6 (WH8109)


title: DL139-I-3h-3 (WH8109)


title: DL140-I-4h-3 (WH8109)


title: DL128-II-0h-6 (WH8109)


title: DL130-II-1.5h-6 (WH8109)


title: DL154-III-4h-3 (WH8109)


title: DL150-III-1h-3 (WH8109)


title: DL129-II-1h-6 (WH8109)


title: DL151-III-1.5h-3 (WH8109)


title: DL136-I-1h-3 (WH8109)


title: DL152-III-2h-3 (WH8109)


title: DL137-I-1.5h-3 (WH8109)


title: DL148-III-0h-3 (WH8109)


title: DL131-II-2h-6 (WH8109)


title: DL138-I-2h-3 (WH8109)


title: DL149-III-0.5h-3 (WH8109)


title: DL134-I-0h-3 (WH8109)


title: DL135-I-0.5h-3 (WH8109)


title: DL126-II-3h-3 (WH8109)


title: DL124-II-1.5h-3 (WH8109)


title: DL125-II-2h-3 (WH8109)


title: DL117-III-1.5h-4 (WH8102)

description: Synechococcus sp. Strain WH8102 infected with the broad-host range T4-like myovirus, Syn9

organism: Parasynechococcus marenigrum WH 8102

source_name: Synechococcus sp. strain WH8102 infected by Syn9

growth_protocol: Synechococcus sp. strain WH8102 cells were grown in an artificial sea water-based medium (ASW) (Wyman et al. 1985) with modifications as described in Lindell et al. (1998), at 22 °C under cool white light with a 14:10 h light:dark cycle at an intensity of 30 μmol photon•m-2•s-1 during the light period.

extract_protocol: Synechococcus cells (50-75 ml of each infected or control culture) were collected on 0.4 μm pore-sized polycarbonate filters (GE) by filtration at a vacuum pressure of 10 inch Hg and snap frozen at -80 ºC in 2 ml PGTX buffer (40 ml liquid phenol 95%, 6.9 ml glycerol, 0.1 g 8-hydroxyquinoline, 0.58 g EDTA, 0.8 g sodium acetate, 0.5 g guanidine thiocyanate and 4.6 g guanidine hydrochloride at final pH = 4.2 in a final volume of 100ml) as described in Pinto et al (2009) but without Triton X-100. Each culture was sampled a minute apart such that WH8102-infected cells were sampled 1 and 2 minutes after WH8102- and WH8109-infected cells, respectively. Total RNA was extracted by the PGTX 95 method (Pinto et al. 2009) with some minor modifications. Briefly, the samples were thawed on ice and subjected to a 5-min incubation at 95 °C followed by a further 5-min on ice. The aqueous phase was extracted with an equal volume of chloroform:isoamyl alcohol (24:1, vol/vol). RNA was precipitated with 1 volume of isopropanol and washed in 75% ethanol. Total nucleic acids were quantified based on absorption at 260 nm and RNA integrity was verified by gel electrophoresis. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion). For microarray analysis 15 μg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by DNase I inactivation with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.


title: DL118-III-2h-4 (WH8102)


title: DL127-II-4h-3 (WH8109)


title: DL121-II-0h-3 (WH8109)


title: DL122-II-0.5h-3 (WH8109)


title: DL116-III-1h-4 (WH8102)


title: DL123-II-1h-3 (WH8109)


title: DL119-III-3h-4 (WH8102)


title: DL120-III-4h-4 (WH8102)


title: DL103-II-1.5h-4 (WH8102)


title: DL106-II-4h-4 (WH8102)


title: DL102-II-1h-4 (WH8102)


title: DL114-III-0h-4 (WH8102)


title: DL91-I-3h-4 (WH8102)


title: DL100-II-0h-4 (WH8102)


title: DL104-II-2h-4 (WH8102)


title: DL101-II-0.5h-4 (WH8102)


title: DL105-II-3h-4 (WH8102)


title: DL113-III-4h-1 (WH8102)

description: Synechococcus sp. Strain WH8102 grown in parallel to an infected sample

source_name: Synechococcus sp. strain WH8102


title: DL112-III-3h-1 (WH8102)


title: DL92-I-4h-4 (WH8102)


title: DL110-III-1.5h-1 (WH8102)


title: DL89-I-1h-4 (WH8102)


title: DL115-III-0.5h-4 (WH8102)


title: DL108-III-0.5h-1 (WH8102)


title: DL111-III-2h-1 (WH8102)


title: DL88-I-0.5h-4 (WH8102)


title: DL90-I-1.5h-4 (WH8102)


title: DL97-II-2h-1 (WH8102)


title: DL95-II-1h-1 (WH8102)


title: DL96-II-1.5h-1 (WH8102)


title: DL99-II-4h-1_2 (WH8102)


title: DL109-III-1h-1 (WH8102)


title: DL94-II-0.5h-1 (WH8102)


title: DL87-I-4h-1 (WH8102)


title: DL93-II-0h-1 (WH8102)


title: DL85-I-1.5h-1 (WH8102)


title: DL201-III-2h-5 (WH7803)

description: Synechococcus sp. Strain WH7803 infected with the broad-host range T4-like myovirus, Syn9

organism: Synechococcus sp. WH 7803

source_name: Synechococcus sp. strain WH7803 infected by Syn9

growth_protocol: Synechococcus sp. strain WH7803 cells were grown in an artificial sea water-based medium (ASW) (Wyman et al. 1985) with modifications as described in Lindell et al. (1998), at 22 °C under cool white light with a 14:10 h light:dark cycle at an intensity of 30 μmol photon•m-2•s-1 during the light period.

extract_protocol: Synechococcus cells (50-75 ml of each infected or control culture) were collected on 0.4 μm pore-sized polycarbonate filters (GE) by filtration at a vacuum pressure of 10 inch Hg and snap frozen at -80 ºC in 2 ml PGTX buffer (40 ml liquid phenol 95%, 6.9 ml glycerol, 0.1 g 8-hydroxyquinoline, 0.58 g EDTA, 0.8 g sodium acetate, 0.5 g guanidine thiocyanate and 4.6 g guanidine hydrochloride at final pH = 4.2 in a final volume of 100ml) as described in Pinto et al (2009) but without Triton X-100. Each culture was sampled a minute apart such that WH8102-infected cells were sampled 1 and 2 minutes after WH7803- and WH8109-infected cells, respectively. Total RNA was extracted by the PGTX 95 method (Pinto et al. 2009) with some minor modifications. Briefly, the samples were thawed on ice and subjected to a 5-min incubation at 95 °C followed by a further 5-min on ice. The aqueous phase was extracted with an equal volume of chloroform:isoamyl alcohol (24:1, vol/vol). RNA was precipitated with 1 volume of isopropanol and washed in 75% ethanol. Total nucleic acids were quantified based on absorption at 260 nm and RNA integrity was verified by gel electrophoresis. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion). For microarray analysis 15 μg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by DNase I inactivation with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.


title: DL203-III-4h-5 (WH7803)


title: DL86-I-3h-1 (WH8102)


title: DL202-III-3h-5 (WH7803)


title: DL215-C-T4

value: P-TIM40 phage


title: DL82-I-0h-1 (WH8102)


title: DL200-III-1.5h-5 (WH7803)


title: Schwannoma 31 [re-analysis]

city: Badalona

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

country: Spain

institute: Hospital Universitari Germans Trias i Pujol

description:
1_350
re-analysis of GSM973660

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix Human Gene ST 1.0 arrays were performed following the manufacturer's recommendations

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
RMA signal log2 converted from Expression Console Software 1.1.2800.29167. As samples were processes in three batches, ComBat method was used to remove batch effect.

source_name: Vestibular Schwannoma

label_protocol: library preparation and amplification were performed following the distributor’s (Sigma-Aldrich) recommendations for whole transcriptome amplification (WTA2). Amplification was performed for 17 cycles, and amplified cDNA was purified and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo-Fischer). Some 8 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from a GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: RNA was isolated using RNeasy® Mini Kit (QIAGEN) following instructions. Rnase-Free Dnase Set  (QIAGEN) was used to eliminate DNA contamitations.

treatment_protocol: Samples were frozen in liquid Nitrogen immediately after surgical resection, and then conserved at -80ºC until extraction

tag: sample group

value: Tumor

tag: tissue subtype

value: Vestibular Schwannoma

tag: batch


title: DL98-II-3h-1 (WH8102)

tag: infection


title: DL84-I-1h-1 (WH8102)


title: DL83b-I-0.5h-1 (WH8102)


title: Schwannoma 29 [re-analysis]

description:
1_354
re-analysis of GSM973658


title: DL198-III-0.5h-5 (WH7803)


title: Schwannoma 27 [re-analysis]

description:
1_371
re-analysis of GSM973656


title: Schwannoma 24 [re-analysis]

description:
2_399
re-analysis of GSM973653


title: Schwannoma 22 [re-analysis]

description:
1_417
re-analysis of GSM973651


title: DL197-III-0h-5 (WH7803)


title: Schwannoma 25 [re-analysis]

description:
1_374
re-analysis of GSM973654


title: Schwannoma 28 [re-analysis]

description:
1_369
re-analysis of GSM973657


title: Schwannoma 30 [re-analysis]

description:
1_352
re-analysis of GSM973659


title: DL189-II-4h-5 (WH7803)


title: Schwannoma 20 [re-analysis]

description:
2_437
re-analysis of GSM973649


title: DL188-II-3h-5 (WH7803)


title: Schwannoma 16 [re-analysis]

description:
2_450
re-analysis of GSM973645


title: Schwannoma 23 [re-analysis]

description:
1_407
re-analysis of GSM973652


title: Schwannoma 26 [re-analysis]

description:
2_373
re-analysis of GSM973655


title: DL187-II-2h-5 (WH7803)


title: Schwannoma 14 [re-analysis]

description:
1_467
re-analysis of GSM973643


title: Schwannoma 17 [re-analysis]

description:
2_449
re-analysis of GSM973646


title: Schwannoma 18 [re-analysis]

description:
1_447
re-analysis of GSM973647


title: Schwannoma 21 [re-analysis]

description:
1_422
re-analysis of GSM973650


title: Schwannoma 19 [re-analysis]

description:
2_444
re-analysis of GSM973648


title: Schwannoma 13 [re-analysis]

description:
1_471
re-analysis of GSM973642


title: Schwannoma 11 [re-analysis]

description:
1_474
re-analysis of GSM973640


title: Schwannoma 12 [re-analysis]

description:
1_473
re-analysis of GSM973641


title: DL186-II-1.5h-5 (WH7803)


title: DL185-II-1h-5 (WH7803)


title: DL199-III-1h-5 (WH7803)


title: Schwannoma 15 [re-analysis]

description:
2_458
re-analysis of GSM973644


title: Schwannoma 8 [re-analysis]

description:
2_488
re-analysis of GSM973637


title: Schwannoma 9 [re-analysis]

description:
2_486
re-analysis of GSM973638


title: Schwannoma 7 [re-analysis]

description:
1_490
re-analysis of GSM973636


title: Schwannoma 3 [re-analysis]

description:
2_507
re-analysis of GSM973632


title: DL184-II-0.5h-5 (WH7803)


title: Schwannoma 4 [re-analysis]

description:
2_506
re-analysis of GSM973633


title: Schwannoma 5 [re-analysis]

description:
2_505
re-analysis of GSM973634


title: Schwannoma 6 [re-analysis]

description:
1_491
re-analysis of GSM973635


title: DL174-I-3h-5 (WH7803)


title: DL172-I-1.5h-5 (WH7803)


title: DL183-II-0h-5 (WH7803)


title: Nerve 8 [re-analysis]

description:
2_N_432
re-analysis of GSM973628

source_name: Vestibular Nerve

value: Control

value: Vestibular Nerve


title: Nerve 6 [re-analysis]

description:
1_N_483
re-analysis of GSM973626

source_name: VIII craneal nerve

value: VIII craneal nerve


title: Nerve 7 [re-analysis]

description:
2_N_434
re-analysis of GSM973627

source_name: Facial Nerve

value: Facial Nerve


title: DL173-I-2h-5 (WH7803)


title: DL170-I-0.5h-5 (WH7803)

value: 30 min


title: DL171-I-1h-5 (WH7803)


title: Schwannoma 2 [re-analysis]

description:
2_509
re-analysis of GSM973631


title: Nerve 9 [re-analysis]

description:
1_N_HSC
re-analysis of GSM973629

source_name: Human Schwann Cells

value: Human Schwann Cells


title: DL169-I-0h-5 (WH7803)

value: Infected by Syn9


title: Schwannoma 1 [re-analysis]

description:
2_510
re-analysis of GSM973630


title: Nerve 5 [re-analysis]

description:
2_N_502
re-analysis of GSM973625

source_name: Cervical Nerve

value: Cervical Nerve


title: Nerve 4 [re-analysis]

description:
2_N_504
re-analysis of GSM973624


title: DL196-III-4h-2 (WH7803)

description: Synechococcus sp. Strain WH7803 grown in parallel to an infected sample

source_name: Synechococcus sp. strain WH7803

value: 240 min


title: Nerve 2 [re-analysis]

description:
2_N_511
re-analysis of GSM973622

source_name: Auricular Nerve

value: Auricular Nerve


title: Nerve 3 [re-analysis]

description:
2_N_504HIP
re-analysis of GSM973623

source_name: Hipoglosal Nerve

value: Hipoglosal Nerve


title: Nerve 1 [re-analysis]

description:
2_N_518
re-analysis of GSM973621


title: Meningioma 21

source_name: Meningioma Grade I

value: Meningioma Grade I


title: DL193-III-1.5h-2 (WH7803)

value: Non-infected

value: 90 min


title: Meningioma 22


title: Meningioma 20


title: DL175-I-4h-5 (WH7803)


title: DL195-III-3h-2 (WH7803)

value: 180 min


title: Meningioma 18

value: Tumor


title: S19

hyb_protocol: High quality RNA was reverse transcribed and hybridized on the Illumina HumanWG-6 v3 Expression BeadChip

data_processing: quantile normalisation using Bioconductor

source_name: memory CD4+ T-cell subsets were isolated by FACS

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

tag: donor

value: PBMC

tag: cell population


title: Meningioma 19


title: Meningioma 17


title: DL194-III-2h-2 (WH7803)

value: 120 min


title: Meningioma 15


title: DL191-III-0.5h-2 (WH7803)


title: Meningioma 16


title: DL192-III-1h-2 (WH7803)

value: 60 min


title: DL107-III-0h-1 (WH8102)

value: 0 min


title: DL168-II-4h-2 (WH7803)


title: S16

tag: cell type


title: S18


title: S17


title: Meningioma 13


title: Meningioma 14


title: DL190-III-0h-2 (WH7803)


title: S15


title: Meningioma 12


title: DL167-II-3h-2 (WH7803)


title: DL164-II-1h-2 (WH7803)


title: Meningioma 10


title: DL166-II-2h-2 (WH7803)


title: Meningioma 8


title: S12


title: S14


title: DL163-II-0.5h-2 (WH7803)


title: S9


title: DL162-II-0h-2 (WH7803)


title: Meningioma 9

source_name: Meningioma Grade 2

value: Meningioma Grade 2


title: DL165-II-1.5h-2 (WH7803)


title: S13


title: S10


title: Meningioma 11


title: Meningioma 6


title: S11


title: S8


title: Meningioma 7


title: Meningioma 4


title: DL168-I-4h-2 (WH7803)


title: Meningioma 5


title: S5


title: DL165-I-1.5h-2 (WH7803)


title: S7


title: S4


title: DL167-I-3h-2 (WH7803)


title: DL166-I-2h-2 (WH7803)


title: DL162-I-0h-2 (WH7803)


title: DL163-I-0.5h-2 (WH7803)

value: 30 min


title: DL164-I-1h-2 (WH7803)


title: Meningioma 3


title: S3


title: Healthy Meninge 2

source_name: Meningeal Control

value: Control

value: Meningeal Control

tag: control source

value: BioChain RNA commercial sample

tag: reference cat. #

tag: reference lot #


title: S2


title: Meningioma 1


title: S6


title: BN_Day01h_aorta_rep2

status: Public on Aug 29 2015

city: Tokyo

first: Yi-Ting

middle: Emma

last: Hsieh

address: 2-2Wakamatsu-cho, Shinjuku

institute: Waseda University

description: BN AO replicate 2

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hrs at 45℃ on Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software (AGCC v.2.0) and processed by RMA.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

extract_protocol: Total RNA was extracted from pooled tissues using TRIzol reagent (Invitrogen, La Jolla, CA) as recommended by the manufacturer.

value: Brown-Norway

value: 1hr after birth (Day0, full-term)

value: aorta


title: BN_Day01h_aorta_rep1

description: BN AO replicate 1


title: Meningioma 2


title: Schwannoma 10 [re-analysis]

description:
2_482
re-analysis of GSM973639

value: Vestibular Schwannoma