title: Chuvash polycythemia Cohort, VHL wildtype_CP57


title: SoxNDam vs βgal rep2

status: Public on Apr 23 2014

type: genomic

city: Cambridge

first: Enrico

last: Ferrero

address: Downing Street

department: Genetics

country: United Kingdom

institute: University of Cambridge

description:
Sample 2
Biological replicate 2 of 3, SoxNDam

hyb_protocol: Resuspend samples in 12.3 µl water.  For each hybridisation, combine 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) and add 31.7µl to each hybridisation sample. Incubate samples at 95°C for 5 minutes, 42°C for 5 minutes and load 41 µl onto the array. The hybridisation is performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 16 hours. Perform post hybridisation washes according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains. Signal for Cy3 and Cy5 channels are balanced using the histogram view in the GenePix software. Images are saved as Single-image TIFF.

data_processing:
Images are processed with NimbleScan software (v.2.6, Roche-Nimblegen) as per manufacturer instructions. Raw data files (*.pair) are created for each channel. Perform Nimblescan loess spatial correction and quantile normalise the raw data.
Supplemetary processed data *quant-all.sgr file description: the first field is the chromosome ("chr"), the second field is the starting nucleotide position of the oligo on the array ("nt"), and the third is a score representing the log2 ratio of sample intensity over control intensity for that oligo, aka M-value ("score"). "quant-all" refers to the fact that scores/M-values/log2 ratios have been quantile normalised.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: SoxNDam

label_protocol: In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

growth_protocol: Grow flies at 25°C; collect and age embryos on grape agar juice plates supplemented with yeast paste, at 25°C

extract_protocol: Extract genomic DNA from dechorionated embryos with the Qiagen DNeasy blood and tissue kit and precipitate with ethanol. Digest DNA overnight at 37°C with DpnI to cut methylated GATC sequences and ligate the fragments to a double-stranded adapter oligonucleotide. Digest ligation products with DpnII to remove unmethylated GATC sequences and PCR amplify. See Vogel et al., 2007 for a detailed protocol.

tag: strain

value: SoxNDam

tag: tissue

value: whole embryos

tag: developmental stage

value: stage 8-11

source_name: Dam


title: SoxND2 vs βgal rep3

description:
Sample 9
Biological replicate 3 of 3, SoxND2

source_name: βgal

extract_protocol: Crosslink dechorionated embryos with formaldehyde, isolate and lyse nuclei to extract protein-DNA complexes. Incubate chromatin overnight poth protein A agarose beads / salmon sperm DNA and anti-βgal or anti-SoxN antibodies. After extensive washes, reverse crosslinking by incubating at 65°C for 6 hours and purify DNA trough phenol-chloroform extraction. Amplify DNA with two rounds of ligation-mediated PCR. See Sandmann et al., 2007 for a detailed protocol.

value: Oregon R


title: SoxNPA179 Late vs βgal rep3

description:
Sample 15
Biological replicate 3 of 3, SoxNPA179 Late

value: stage 11-13

source_name: SoxNPA179 Late


title: SoxNDam vs βgal rep1

description:
Sample 1
Biological replicate 1 of 3, SoxNDam


title: HCT-116 cells/6S  replicate 4

type: RNA

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

country: USA

institute: Coriell Institute for Medical Research

description:
Sample name: 8
Biological replicate 4 of 4 HCT-116 cell cultures treated with [6]-shogaol 20 uM for 24h

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA Agilent Feature Extraction Software 9.1

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Homo sapiens

source_name: HCT-116 cells treated with [6]-shogaol 20 uM for 24h

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color( Agilent p/n 5188-5340) according to the provided protocol.

extract_protocol: Cells were harvested and total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. The quantity of RNA was measured using a spectrophotometer (NanoDrop 2000c; Thermo Scientific). RNA quality was determined by gel electrophoresis and Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HCT-116 cells were plated in 150 × 150 mm culture plates and were allowed to attach overnight at 37 °C. Cells were treated with 20 μM 6S or DMSO control and incubated for 24 h.

tag: cell line

value: Cultured colon cells HCT-116

tag: agent

source_name: Agilent's Universal human Reference RNA

tag: reference

value: 10 human cell lines (Universal human Reference RNA)


title: Chuvash polycythemia Cohort, VHL wildtype_CP60

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix GeneChip Expression Wash, Stain and Scan protocol

data_processing:
Raw probe intensity was log2 transformed, background corrected, quantile normalized, subtracted by probe mean across samples, and summarized as mean probe intensity of transcript cluster. Signals were read by affxparser, other processing/normalization procedures were carried out custom R codes.
HuEx-1_0-st-v2.r2.pgf, HuEx-1_0-st-v2.r2.clf, HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay

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

tag: cell type

value: Peripheral blood mononuclear cells

tag: gender

value: female


title: HCT-116 cells/6S  replicate 3

description:
Sample name: 7
Biological replicate 3 of 4 HCT-116 cell cultures treated with [6]-shogaol 20 uM for 24h


title: HUVEC_Control_1 hour_rep1

city: Suita

first: Takashi

last: Nojiri

state: Osaka

address: 5-7-1, Fujishirodai

department: Biochemistry

country: Japan

institute: National Cerebral and Cardiovascular Center Research Institute

description: Gene expression data from untreated HUVEC for 1 hour

hyb_protocol: 1.65ug 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 55ul containing 25x Agilent GE fragmentation buffer and 10x AgilentGE  blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent GE hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent).

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

data_processing: Intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Data analyses were conducted with Agilent GeneSpring GX software ver.12.5.

source_name: HUVEC, Control, 1 hour, replicate 1

label_protocol: Cy3 labeled cRNA was prepared from 200 ng RNA using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions, followed by Qiagen RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HUVEC was purchased from Lonza (Walkersville, MD, USA), then maintained in EGM-2 according to the manufacturer's instructions at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA are extracted from HUVEC using the Qiagen RNeasy Mini Kit.

treatment_protocol: HUVECs are incubated with 0.1μM ANP or vehicle for 0, 1 and 6 hours.

value: Human Umbilical Vein Endothelial Cells (HUVEC)

tag: treatment

value: vehicle

tag: time point

value: 1 hour


title: Chuvash polycythemia Cohort, VHL wildtype_CP55

value: male


title: SoxN-DDam vs Dam rep1

description: biological replicate 1 of 3 SoxN-DDam

source_name: Dam (control)

value: Dam

value: stage 12-17

source_name: SoxN-DDam

value: SoxN[U6-35]; DDam


title: HUVEC_ANP_6 hours _rep1

description: Gene expression data from HUVEC treated with ANP for 6 hours

source_name: HUVEC, ANP, 6 hours, replicate 1

value: 0.1uM ANP

value: 6 hours


title: Chuvash polycythemia Cohort, VHL wildtype_CP53


title: SoxN-DDam vs Dam rep3

description: biological replicate 3 of 3 SoxN-DDam

value: whole embryos


title: SoxNPA179 Early vs βgal rep1

description:
Sample 10
Biological replicate 1 of 3, SoxNPA179 Early

value: stage 7-10

source_name: SoxNPA179 Early


title: SoxN-DDam vs Dam rep2

description: biological replicate 2 of 3 SoxN-DDam


title: SoxNDam vs βgal rep3

description:
Sample 3
Biological replicate 3 of 3, SoxNDam

value: SoxNDam

value: stage 8-11


title: Chuvash polycythemia Cohort, VHL wildtype_CP54


title: HCT-116 cells/6S  replicate 2

description:
Sample name: 6
Biological replicate 2 of 4 HCT-116 cell cultures treated with [6]-shogaol 20 uM for 24h

value: Cultured colon cells HCT-116


title: SoxND1 vs βgal rep3

description:
Sample 6
Biological replicate 3 of 3, SoxND1

value: Oregon R


title: Chuvash polycythemia Cohort, VHL wildtype_CP51

value: Peripheral blood mononuclear cells


title: HCT-116 cells/6S  replicate 1

description:
Sample name: 5
Biological replicate 1 of 4 HCT-116 cell cultures treated with [6]-shogaol 20 uM for 24h

value: 10 human cell lines (Universal human Reference RNA)


title: HUVEC_Control_0 hour_rep1

description: Gene expression data from untreated HUVEC for 0 hour

source_name: HUVEC, Control, 0 hour, replicate 1

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: 0 hour


title: D-SoxNDam vs Dam rep3

description: biological replicate 3 of 3 D-SoxNDam

source_name: D-SoxNDam

value: SoxNDam; D[r72]


title: Chuvash polycythemia Cohort, VHL wildtype_CP52

value: female


title: HUVEC_ANP_1 hour_rep1

description: Gene expression data from HUVEC treated with ANP for 1 hour

source_name: HUVEC, ANP, 1 hour, replicate 1

value: 1 hour


title: HCT-116 cells/DMSO replicate 4

description:
Sample name: 4
Biological replicate 4 of 4 HCT-116 cell cultures treated with DMSO

source_name: HCT-116 cells treated with DMSO as control

value: control


title: Chuvash polycythemia Cohort, VHL wildtype_CP50

value: male


title: D-SoxNDam vs Dam rep2

description: biological replicate 2 of 3 D-SoxNDam

value: stage 12-17

value: Dam


title: HCT-116 cells/DMSO replicate 3

description:
Sample name: 3
Biological replicate 3 of 4 HCT-116 cell cultures treated with DMSO


title: Chuvash polycythemia Cohort, VHL wildtype_CP48


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP45


title: DDam vs Dam rep3

description: biological replicate 3 of 3 DDam

value: whole embryos

source_name: DDam

value: DDam


title: SoxND2 vs βgal rep1

description:
Sample 7
Biological replicate 1 of 3, SoxND2


title: HCT-116 cells/DMSO replicate 1

description:
Sample name: 1
Biological replicate 1 of 4 HCT-116 cell cultures treated with DMSO


title: HCT-116 cells/DMSO replicate 2

description:
Sample name: 2
Biological replicate 2 of 4 HCT-116 cell cultures treated with DMSO


title: Wildtype mouse Kidney rep1

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

description:
replicate 1
WT_KID_REF5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the default quantile normalisation with R/bioconductor package lumi

organism: Mus musculus

source_name: 12 m old Wildtype mouse Kidney

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

growth_protocol: PAI-1 knockout (PAI-1KO) and wild-type (WT) mice on a C57BL/6 background were purchased from Jackson laboratory (Bar Harbor, ME) and were maintained for 12 months. All mouse protocols were approved by the Animal Care and Use Committee of Northwestern University (Chicago, IL).

extract_protocol: Total RNA was extracted from hearts and kidneys derived from three PAI-1 knockout (12- month old) and three wild-type mice (12-month old) using RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions. The quality of RNA (RNA Integrity, RIN) in all 12 samples (3 wildtype hearts; 3 PAI-1 KO hearts; 3 wildtype kidneys; and 3 PAI-1 KO kidneys) was checked using the bioanalyzer.

treatment_protocol: All heart and kidney tissue samples were collected from 12 months old wild type and PAI-1 knockout mice. The hearts and kidneys were snap frozen and stored at -80oC for RNA and biochemical analysis.

tag: genotype/variation

value: wildtype

tag: age

value: 12 months

value: Kidney


title: HUVEC_ANP_0 hour _rep1

description: Gene expression data from HUVEC treated with ANP for 0 hour

source_name: HUVEC, ANP, 0 hour, replicate 1

value: 0.1uM ANP


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP43

value: Peripheral blood mononuclear cells


title: Wildtype mouse Kidney rep2

description:
replicate 2
WT_KID_REF1


title: Wildtype mouse heart rep3

description:
replicate 3
WT_HT2

source_name: 12 m old Wildtype mouse heart

value: Heart


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP42

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP42


title: SoxNDam vs Dam rep1

description: biological replicate 1 of 3 SoxNDam

source_name: SoxNDam

value: SoxNDam


title: SoxNDam vs Dam rep3

description: biological replicate 3 of 3 SoxNDam


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP41

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP41


title: Wildtype mouse heart rep2

description:
replicate 2
WT_HT1


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP37


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP40


title: Chuvash polycythemia Cohort, VHL wildtype_CP49


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP39

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP39


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP36

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP36


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP34

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP34


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP46


title: D-SoxNDam vs Dam rep1

description: biological replicate 1 of 3 D-SoxNDam

source_name: Dam (control)


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP32

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP32


title: Wildtype mouse heart rep1

description:
replicate 1
WT_HT5


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP35

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP35


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP47

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP47


title: PAI-1 knockout mouse Kidney rep3

description:
replicate 3
KO_KID_REF2

source_name: 12 m old PAI-1 knockout mouse Kidney

value: PAI-1 KO


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP31

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP31


title: PAI-1 knockout mouse Kidney rep2

description:
replicate 2
KO_KID_REF1


title: Wild type feet, Day 7 post Chikungunya infection

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description: Gene expression data for wild type feet day 7  post chikungunya infection

hyb_protocol: As per Affymetrix protocols

scan_protocol: As per Affymetrix protocols

data_processing: RMA normalization using Affymetrix Expression Console

source_name: wild-type C57BL/6 mice

label_protocol: All microarray labelling, hybridisation and scanning was performed by the Ramaciotti Centre for Genomics at the University of New South Wales, Australia. The Ramaciotti Centre for Genomics  uses standard reagents, kits and protocols as recommended by Affymetrix.  Array were performed using Mouse Gene 1.0ST arrays (Affymetrix).

extract_protocol: Feet were homogenised in TRIzol reagent using a Qiagen Tissue lyser and stainless steel beads. RNA was extracted using the standard TRIzol reagent protocol. RNA quality was assessed using a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.  Equal amounts of RNA from 4-6 feet were pooled for each sample.

treatment_protocol: Female 6-10 week old mice were inoculated s.c. into each hind foot with CHIKV (LR2006-OPY1). At day 0 and day 7 post infection, feet were cut lengthways, placed into RNAlater solution for 24 h at 4°C, and frozen at  70°C.

value: feet

value: Female

value: 6-10 week


title: PAI-1 knockout mouse Kidney rep1

description:
replicate 1
KO_KID_REF5


title: PAI-1 knockout mouse heart rep2

description:
replicate 2
KO_HT1

source_name: 12 m old PAI-1 knockout mouse heart


title: Wild type feet, Day 0 post Chikungunya infection

description: Gene expression data for wild type feet day 0  post chikungunya infection


title: DDam vs Dam rep2

description: biological replicate 2 of 3 DDam

source_name: DDam


title: PAI-1 knockout mouse heart rep3

description:
replicate 3
KO_HT2


title: CCR2 knockout feet, Day 0 post Chikungunya infection

description: Gene expression data for CCR2-/- feet day 0 post chikungunya infection

source_name: CCR2 knockout mice C57BL/6 background


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP22

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP22

value: female


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP30

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP30


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP29

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP29

value: male


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP44

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP44


title: T47D_siRAD51B_HU_rep1

status: Public on Apr 22 2014

city: Bethesda

first: Lea

last: Jessop

state: MD

address: 8717 Grovemont Circle 127

department: DCEG

institute: NCI

description: Gene expression post DNA damages without RAD51B

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Background subtracted, quantile normalized data were analyzed using GenomeStudio.

source_name: T47D cells transfected with experimental siRNA and then treated with HU

label_protocol: Affymetric GeneChip 3' IVT Express Kit according to manufacturers instructions

growth_protocol: standard growth condition using RPMI+10% FBS

extract_protocol: Extraction of total RNA was performed using RNeasey Mini Kit according to the manufacturer's instructions.

treatment_protocol: transfected cells were treated with 2mM HU for 24 hrs

value: siRAD51B and hydroxyurea

tag: genotype

value: heterozygous for rs999737


title: T47D_siRAD51B_HU_rep2


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP21


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP26_2


title: DDam vs Dam rep1

description: biological replicate 1 of 3 DDam

value: Dam

value: whole embryos

value: stage 12-17


title: T47D_siCON_HU_rep1

description: Gene expression post DNA damages with RAD51B

source_name: T47D cells transfected with control siRNA and then treated with HU

value: control and hydroxyurea


title: PAI-1 knockout mouse heart rep1

description:
replicate 1
KO_HT5

value: 12 months


title: CCR2 knockout feet, Day 7 post Chikungunya infection

description: Gene expression data for CCR2-/- feet day 7  post chikungunya infection


title: Wildtype mouse Kidney rep3

description:
replicate 3
WT_KID_REF2

source_name: 12 m old Wildtype mouse Kidney

value: wildtype

value: Kidney


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP24

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP24

value: Peripheral blood mononuclear cells


title: T47D_siRAD51B_HU_rep3


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP25

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP25


title: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin_CP28

source_name: Chuvash polycythemia Cohort, VHLR200W homozygous with low ferritin _CP28


title: T47D_siCON_HU_rep2


title: T47D_siCON_HU_rep3


title: Chuvash polycythemia Cohort, VHLR200W homozygous_CP23


title: PT_PANC047

city: Madrid

first: Manuel

last: Hidalgo

state: Madrid

address: C/Melchor Fernandez Almagro 3

department: Clinical Research Programme

country: Spain

institute: CNIO

description: Gene expression data from human pancreatic tumor

hyb_protocol: Following fragmentation, cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array.

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

data_processing: The data were analyzed with frozenRMA (fRMA) using rma and quantile as background correction and normalization methods.

source_name: Human pancreatic tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Extraction of total RNA was performed by using Qiagen mini- RNA kit according to the manufacturer's instructions.

value: Human pancreatic tumor


title: SoxNDam vs Dam rep2

description: biological replicate 2 of 3 SoxNDam

source_name: SoxNDam

value: SoxNDam

source_name: Dam (control)


title: PT_PANC042


title: PDX_PANC421

description: Gene expression data from patient derived xenografts from pancreatic tumor

source_name: Patient derived xenografts from pancreatic tumor

value: Human pancreatic tumor xenografted in six-week-old female athymic nude mice


title: PDX_PANC374


title: PDX_PANC023


title: PDX_PANC028


title: PDX_JH161


title: PDX_JH102


title: PDX_PANC008


title: PDX_PANC017


title: PDX_JH128


title: PDX_PANC266


title: PDX_JH034


title: PDX_PANC014


title: PDX_JH090


title: PDX_JH094


title: PDX_JH112


title: PDX_JH069


title: PDX_JH088


title: PDX_JH032


title: PDX_PANC007


title: PDX_JH041


title: PDX_JH051


title: PDX_JH097


title: PDX_JH171


title: PDX_JH109


title: PDX_JH033


title: PDX_PANC291


title: PDX_JH127


title: PDX_JH131


title: PDX_JH027


title: Rheumatoid Arthritis HF-306412

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

state: CA

address: 1 DNA Way

institute: Genentech

description: Gene expression from Rheumatoid Arthritis synovial tissue samples

hyb_protocol: Samples were hybridized to GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Inc.).  Arrays were washed and stained in the Affymetrix Fluidics station and scanned on a GeneChip® scanner 3000.

scan_protocol: GeneChip® scanner 3000

data_processing: Expression signals were obtained using the Affymetrix GeneChip® operating system and analysis software. The data was normalized using RMA and probesets that failed to meet the affymetrix A-classification were removed.

source_name: Rheumatoid Arthritis patient

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

extract_protocol: RNeasy minikit (Qiagen Inc., Valencia, CA)

treatment_protocol: No treatment

tag: individual

value: Rheumatoid Arthritis patient

value: Synovial tissue

value: unknown

tag: joint location

tag: inflammation

tag: batch


title: Rheumatoid Arthritis HF-270692


title: Rheumatoid Arthritis HF-306262


title: Rheumatoid Arthritis HF-214942


title: PDX_JH011


title: PDX_JH021


title: Rheumatoid Arthritis HF-306462


title: PDX_JH010


title: Rheumatoid Arthritis HF-306342


title: Rheumatoid Arthritis HF-214862


title: Rheumatoid Arthritis HF-306402


title: Rheumatoid Arthritis HF-306212


title: Rheumatoid Arthritis HF-306322


title: Rheumatoid Arthritis HF-306252


title: PDX_JH029


title: Rheumatoid Arthritis HF-306392


title: Rheumatoid Arthritis HF-215012


title: Rheumatoid Arthritis HF-306442


title: Rheumatoid Arthritis HF-214752


title: PDX_JH024


title: Rheumatoid Arthritis HF-306332


title: Rheumatoid Arthritis HF-306242


title: Rheumatoid Arthritis HF-306372


title: Rheumatoid Arthritis HF-306362


title: Rheumatoid Arthritis HF-270622


title: PDX_JH015


title: Rheumatoid Arthritis HF-306382


title: Rheumatoid Arthritis HF-306312


title: Rheumatoid Arthritis HF-306202


title: Rheumatoid Arthritis HF-305792


title: Rheumatoid Arthritis HF-305492


title: Rheumatoid Arthritis HF-305122


title: Rheumatoid Arthritis HF-27009

value: female

value: flexortenosynovium


title: Rheumatoid Arthritis HF-305262


title: Rheumatoid Arthritis HF-27064

value: wrist

value: Non-inf


title: Rheumatoid Arthritis HF-305282


title: Rheumatoid Arthritis HF-21492

value: Inf


title: Rheumatoid Arthritis HF-21485

value: knee


title: Rheumatoid Arthritis HF-21512


title: Rheumatoid Arthritis HF-21479

value: hand


title: Rheumatoid Arthritis HF-27036


title: Rheumatoid Arthritis HF-27060


title: Rheumatoid Arthritis HF-21495


title: Rheumatoid Arthritis HF-305272


title: Rheumatoid Arthritis HF-309482


title: Rheumatoid Arthritis HF-21487


title: Rheumatoid Arthritis HF-21476


title: Rheumatoid Arthritis HF-27087


title: Rheumatoid Arthritis HF-21509


title: Rheumatoid Arthritis HF-21508


title: Rheumatoid Arthritis HF-27033


title: Rheumatoid Arthritis HF-305782


title: Rheumatoid Arthritis HF-21362

value: thumb


title: Rheumatoid Arthritis HF-21424

value: male


title: Rheumatoid Arthritis HF-21506


title: Rheumatoid Arthritis HF-21493


title: Rheumatoid Arthritis HF-305482


title: Rheumatoid Arthritis HF-21496


title: Rheumatoid Arthritis HF-21475


title: Rheumatoid Arthritis HF-27076


title: Rheumatoid Arthritis HF-21484

value: foot


title: Rheumatoid Arthritis HF-21354


title: Rheumatoid Arthritis HF-305132


title: Rheumatoid Arthritis HF-21435


title: Rheumatoid Arthritis HF-21368

value: hip


title: Rheumatoid Arthritis HF-21453


title: Rheumatoid Arthritis HF-27038


title: Rheumatoid Arthritis HF-27955


title: Rheumatoid Arthritis HF-27101

value: finger


title: Rheumatoid Arthritis HF-21501


title: Rheumatoid Arthritis HF-21422


title: Rheumatoid Arthritis HF-27330


title: Rheumatoid Arthritis HF-20646


title: Rheumatoid Arthritis HF-27046


title: Rheumatoid Arthritis HF-27069

value: Synovial Fluid Only


title: Rheumatoid Arthritis HF-21507


title: Rheumatoid Arthritis HF-27035


title: Rheumatoid Arthritis HF-21388


title: Rheumatoid Arthritis HF-21361


title: Rheumatoid Arthritis HF-21498

value: TKA


title: Rheumatoid Arthritis HF-20639

value: Rheumatoid Arthritis patient


title: Rheumatoid Arthritis HF-20660

value: Synovial tissue


title: Rheumatoid Arthritis HF-21500


title: Rheumatoid Arthritis HF-21437


title: Rheumatoid Arthritis HF-21371

value: elbow


title: Rheumatoid Arthritis HF-306172

value: unknown


title: HK-2 cells_0hr_treated by oxalate monohydrate crystals_rep1

city: Wuhan

first: BH

last: Wang

address: jiefang road 1095

country: China

institute: Tongji hospital

description: miRNAs expression after 0h oxalate monohydrate crystals

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456,Agilent technologies,Santb Clara,CA,US)in hybridization Oven(Cat#G2545A, Agilent technologies,Santa Clara,CA,US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section.After hybridization,slides were washed in staining dishes (Cat#121, Thermo Shandon,Waltham, MA, US)with Gene Expression Wash Buffer Kit(Cat#5188-5327,Agilent technologies,Santa Clara,CA,US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies,Santa Clara,CA,US)and Featuren Extraction software 10.7 (Agilent technologies,Santa Clara,CA,US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: HK-2 cells, 0h, replicate 1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer's instructions,labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: HK-2 cells were treated with oxalate monohydrate crystals for 0h and 24h.


title: HK-2 cells_24hr_treated by oxalate monohydrate crystals_rep1

description: miRNAs expression after 24h oxalate monohydrate crystals

source_name: HK-2 cells, 24h, replicate 1


title: Rheumatoid Arthritis HF-27123


title: Rheumatoid Arthritis HF-21469

value: female


title: Lung Met, biological rep2

city: Barcelona

first: Xabier

last: Garcia-Albeniz

address: Baldiri Reixac 10

institute: IRB Barcelona

hyb_protocol: Hybridization of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

scan_protocol: Gene chips were scanned using GeneChip Scanner 3000 from affymetrix

data_processing: Data analysis was performed using R (Bioconductor). Quantile normalization and RMA summarization were used to obtain probeset level expression estimates as implemented in the “oligo” package of Bioconductor. In order to prevent non-specific or miss-targeted probesets to bias the gene level expression estimates, for each gene we selected the 50% of the probesets with highest inter-quartile range across all samples and obtained a gene level expression estimate via median polish, in a fashion analogous to RMA

source_name: Lung metastasis derivative

label_protocol: Labeling of the samples to HG1.0ST gene expression chip (Affymetrix) were performed by Functional Genomics Core Facility of IRB, Barcelona using standard methodology

growth_protocol: cells were maintained in 5% CO2 at 37oC in DMEM medium (Gibco) supplemented with 5% fetal bovine serum (FBS) (Biological Industries), Glutamine 0.29 mg/ml (Biological Industries), Penicillin 100 U/ml (Biological Industries) and Streptomycin 0.1 mg/ml (Biological Industries)

extract_protocol: RNA was extracted from cells using RNeasy mini kit (Qiagen)

tag: strain

value: balb/c

tag: sample type

value: lung metastasis


title: Lung Met, biological rep3


title: 60 days old SOD1G93A transgenic mice replicate 4

city: Sao Paulo

first: Jessica

middle: Ruivo

last: Maximino

state: SP

address: Av. Dr. Arnaldo, 455

department: Neurology

institute: University of Sao Paulo (FMUSP)

description: SG11440004_252800512672_S001_GE2_1105_Oct12_2_4

hyb_protocol: Hybridation following manufacturer's instructions (Agilent)

scan_protocol: Scanned on an Agilent scanner

data_processing: Agilent Feature Extraction Software (version 11.0.1.1) was used for extract data and limma Bioconductor packages were used for background correction and normalization in R.

source_name: SOD1G93A_sciatic nerve

label_protocol: RNA amplification and labeling following manufacturer's instructions (Agilent)

extract_protocol: Total RNA extracted using Miniprep kit (Zymo, USA) following manufacturer's instructions

value: SOD1G93A transgenic

value: 60 days

tag: tissue

value: Sciatic nerve

source_name: Pool of neonatal organs

value: wild type and SOD1G93A (pooled)

value: Pool of neonatal organs (heart, liver, kidney)


title: Uninfected fibroblasts vs. uninfected neuron cells

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

description:
F_N_chip7
Uninfected fibroblasts vs. uninfected neurons. We generated 95%-pure populations of neurons from hESC.
Biological replicate 2 of 2, technical replicate 2 of 2.

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer's protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1 (Agilent) and then Gene Expression Wash Buffer 2 (Agilent). This was followed by an acetonitrile wash and finally the slides were placed in Stabilization & Drying Solution (Agilent). The washed slides were scanned on an Agilent G2565BA scanner. Feature extraction was performed using the Feature Extraction software from Agilent.

scan_protocol: Scanned on an Agilent G2565BA microarray scanner.

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

source_name: Uninfected neonatal fibroblasts

label_protocol: 200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer's protocol.

growth_protocol: The fibroblasts are primary cells obtained from a single biopsy. Fibroblasts were grown according to standard protocol. hESC-derived (line H9) neurons were generated by PA6 induction as described in Grigoryan S et al. J. Neurovirol. 2012.

extract_protocol: Total RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit (sigma) according to the manual protocol.

treatment_protocol: GFP fluorescence was used to determine infection. Cells were harvested for RNA extraction when 80% of the neurons and over 90% of the fibroblasts expressed GFP.

value: neonatal foreskin fibroblasts

source_name: Uninfected neurons

value: H9 hESC-derived neurons


title: VZV-GFP23- neuron cells vs. VZV-GFP23- fibroblasts

description:
N23_F23_chip8
Infected neurons vs. infected fibroblasts. We generated 95%-pure populations of neurons from hESC.
Biological replicate 2 of 2, technical replicate 2 of 2.

source_name: Infected neurons, 21 days post infection

value: infection with recombinant varicella zoster virus (VZV)

tag: recombinant virus type

value: pOka derivative with GFP as a fusion to the ORF23 capsid protein

tag: infection day

value: 21 days after infection

source_name: Infected neonatal fibroblasts, 14 days post infection

value: 14 days after infection


title: 60 days old SOD1G93A transgenic mice replicate 2

description: SG11440004_252800512672_S001_GE2_1105_Oct12_2_2

value: male


title: Lung Met, biological rep1

tag: cell line


title: 60 days old SOD1G93A transgenic mice replicate 1

description: SG11440004_252800512672_S001_GE2_1105_Oct12_2_1


title: 60 days old wild-type mice replicate 2

description: SG11440004_252800512672_S001_GE2_1105_Oct12_1_2

source_name: WT_sciatic nerve

value: wild-type


title: Rheumatoid Arthritis HF-21526

value: Rheumatoid Arthritis patient

value: Synovial tissue

value: knee

value: Inf


title: VZV-GFP23- neuron cells vs. uninfected neuron cells

description:
N_N23_chip2
Infected neurons vs. uninfected neurons. We generated 95%-pure populations of neurons from hESC.
Biological replicate 1 of 2, technical replicate 1 of 2.

tag: cell type


title: Uninfected neuron cells vs. VZV-GFP23- neuron cells

description:
N23_N_chip6
Uninfected neurons vs. infected neurons. We generated 95%-pure populations of neurons from hESC.
Biological replicate 2 of 2, technical replicate 1 of 2.


title: 252800514428-8

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: OneChannelGui analysis, interslide quantile normalization. Normalization has been performed using the Limma package available from Bioconductor (http://www.bioconductor.org).

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol:
Total RNA from mouse thyroids was extracted using Nucleospin RNAII (Machereyl-Nagel, France) and RNA quality was checked using the bioanalyzer 2100 (Agilent Technologies).
amp protocol: cRNA Agilent

value: thyroid

tag: amount in (µg)


title: 60 days old SOD1G93A transgenic mice replicate 3

description: SG11440004_252800512672_S001_GE2_1105_Oct12_2_3

value: SOD1G93A transgenic

tag: gender

value: 60 days


title: VZV-GFP23- fibroblasts vs. VZV-GFP23- neuron cells

description:
F23_N23_chip4
Infected fibroblasts vs. infected neurons. We generated 95%-pure populations of neurons from hESC.
Biological replicate 1 of 2, technical replicate 2 of 2.

tag: treatment


title: 60 days old wild-type mice replicate 4

description: SG11440004_252800512672_S001_GE2_1105_Oct12_1_4

tag: genotype/variation

value: Sciatic nerve

value: wild type and SOD1G93A (pooled)


title: Uninfected fibroblasts vs. VZV-GFP23- fibroblasts

description:
F_F23_chip5
Uninfected fibroblasts vs. infected fibroblasts.
Biological replicate 2 of 2, technical replicate 1 of 2.

value: neonatal foreskin fibroblasts


title: Uninfected neuron cells vs. uninfected fibroblasts

description:
N_F_chip3
Uninfected neurons vs. uninfected fibroblasts. We generated 95%-pure populations of neurons from hESC.
Biological replicate 1 of 2, technical replicate 2 of 2.

value: H9 hESC-derived neurons


title: 252800514428-1

description: Tc (S539)


title: 60 days old wild-type mice replicate 3

description: SG11440004_252800512672_S001_GE2_1105_Oct12_1_3

tag: age

value: Pool of neonatal organs (heart, liver, kidney)


title: MEFs_SKOM+Ga_rep1

city: Guangzhou

first: Keshi

address: 190 Kai Yuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

description: miRNAs expression of MEFs infected with SKOM+Ga

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: MEF, SKOM+Ga, Day8, Rep1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

treatment_protocol: MEFs were infected with certain virus and then cultured in DMEM/High Glucose plus +15%FBS+NEAA+Gluta Max+Sodium Pyruvate+lif for 6 days.

value: embryonic fibroblast


title: 60 days old wild-type mice replicate 1

description: SG11440004_252800512672_S001_GE2_1105_Oct12_1_1


title: 252800514428-7


title: MEFs_SKOM+Flag_rep1

description: miRNAs expression of MEFs infected with SKOM+Flag

source_name: MEF, SKOM+Flag, Day8, Rep1


title: MEFs_SKO+Ga_rep1

description: miRNAs expression of MEFs infected with SKO+Ga

source_name: MEF. SKO+Ga, Day8, Rep1


title: SerpinB1a_Lu.gdTcell#2

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: Lung gd T cells FACS-sorted from naïve, SerpinB1a-/- mice

hyb_protocol: The labeled fragmented DNA was hybridized to MoGene1.0ST Gene Arrays for 16-18 hours in GeneChip Hybridization oven 640 at 45 °C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Standard Affymetrix protocol on an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental *.mps file)

source_name: Lung gd T cells from SerpinB1a-/- naïve T cells

label_protocol: biotin

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.

tag: background strain

value: Serpinb1a homozygous null

tag: tissue-type

value: gd+ T cells

value: lung


title: MEFs_SKO+Flag_rep1

description: miRNAs expression of MEFs infected with SKO+Flag

source_name: MEF, SKO+Flag, Day8, Rep1


title: 252800514428-3

description: Tc (S589)


title: VZV-GFP23- fibroblasts vs. uninfected fibroblasts

description:
F23_F_chip1
Infected fibroblasts vs. uninfected fibroblasts.
Biological replicate 1 of 2, technical replicate 1 of 2.

value: infection with recombinant varicella zoster virus (VZV)

value: pOka derivative with GFP as a fusion to the ORF23 capsid protein

value: 14 days after infection


title: SerpinB1a_Lu.Treg#2

description: Lung Treg cells FACS-sorted from naïve, SerpinB1a-/- mice

source_name: Lung Treg cells from SerpinB1a-/- naïve T cells

value: CD4+ CD25hiCD127low regulatory T cells


title: SerpinB1a_Lu.Tmem.R6+#1

description: Lung CD4+ CCR6+ cells FACS-sorted from naïve, SerpinB1a-/- mice

source_name: Lung CD4+ CCR6+ cells from SerpinB1a-/- naïve T cells

value: CD4+ CCR6+ effector/ memory T cells


title: SerpinB1a_Lu.Tmem.R6+#2


title: SerpinB1a_Lu.gdTcell#1


title: 252800514428-4

description: Tc (S590)

value: thyroid


title: SerpinB1a_Lu.Treg#1


title: 252800514428-5


title: 252800514428-2

description: Tc (S588)


title: 252800514428-6


title: WT_Lu.gdTcell#1

description: Lung gd T cells FACS-sorted from naïve, wild-type mice

source_name: Lung gd T cells from wild-type naïve T cells

value: wild-type


title: rtt103-del-1-b

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
genes, no bg corr, dye corr
limma

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.17

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: genetic background

tag: genetic modification

source_name: refpool

value: refpool


title: Diabetic lung 6

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: Lung

hyb_protocol: standard Affymetric protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

organism: Rattus norvegicus

source_name: Lung

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

treatment_protocol: animals made diabetic using streptozotocin given at age 8 weeks (thus 4 weeks of diabetes)

value: Wistar

tag: organ

value: Lung

value: 12 weeks


title: WT_Lu.Tmem.R6+#1

city: Cambridge

description: Lung CD4+ CCR6+ cells FACS-sorted from naïve, wild-type mice

source_name: Lung CD4+ CCR6+ cells from wild-type naïve T cells


title: WT_Lu.Tmem.R6+#2


title: sen1-mut-ts-1-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.18

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: rrp6-del-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.15


title: rtt103-del-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.16


title: WT_Lu.gdTcell#2


title: sen1-mut-ts-1-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.19


title: MEFs_SKO+G39A_Rep2

description: Gene expression of MEFs infected with SKO+G39A

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: MEF, SKO+G39A, Day8, Rep2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).


title: Diabetic lung 5

description: Lung

tag: strain


title: Diabetic lung 4

description: Lung


title: Diabetic lung 7

description: Lung


title: MEFs_SKO+Ga_rep2

description: Gene expression of MEFs infected with SKO+Ga

source_name: MEF, SKO+Ga, Day8, Rep2


title: rrp6-del-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.14


title: MEFs_SKO+Flag_rep2

description: Gene expression of MEFs infected with SKO+Flag

source_name: MEF, SKO+Flag, Day8, Rep2


title: rpb1-mut-S2A-matA-ypd-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.12


title: Diabetic lung 3

description: Lung


title: WT_Lu.Treg#2

description: Lung Treg cells FACS-sorted from naïve, wild-type mice

source_name: Lung Treg cells from wild-type naïve T cells


title: WT_Lu.Treg#1


title: MEFs_SKO+Ga_rep1

source_name: MEF, SKO+Ga, Day8, Rep1


title: Diabetic lung 1

description: Lung


title: MEFs_SKO+G39A_Rep1

source_name: MEF, SKO+G39A, Day8, Rep1


title: pcf11-mut-ts-ts2-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.9


title: rpb1-mut-S2A-matA-ypd-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.13


title: pcf11-mut-ts-2-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.8


title: Diabetic lung 2

description: Lung


title: Normal lung 5

description: Lung

treatment_protocol: At age 8 weeks rats had IP buffer


title: MEFs_SKO+Flag_rep1


title: Hs294T_EphA2_rep2

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: cRNA were hybridized onto Human AffymetrixHuGene St 1.0 GeneChip array according to the standard Affymetrix protocol

scan_protocol: Scanning was performed according to the standard Affymetrix protocol

data_processing: The data were analyzed with R/Bioconductor and RMA algorithm in affypackage was used as normalization method

source_name: Hs294T human melanoma cells

extract_protocol: Total RNA was isolated from Hs294T cells using RNeasy Plus Mini kit (Qiagen)

treatment_protocol: Hs294T were serum starved for 48h and in the presence of 50 µmol/L Ilomastat or serum starved for 48 h and treated with the Rho activator Calpeptin 1 U/ml for the last 2 h of incubation. EphA2-overexpressing Hs294Tcells were serum starved for 48 h

tag: replicate


title: young.naive

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: Healthy brain tissue from young naive rats.

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to microarrays. Washing and staining were performed with the Affymetrix Fluidics Station 450 using script FS450_002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v2.14.0 environment with Bioconductor package affy; background correction, normalization and probeset summary were performed with the rma command using default parameter settings.

source_name: healthy brain tissue from young naive rats

label_protocol: 200ng of total RNA were amplified with the WT Expression Kit (Ambion), followed by ssDNA labeling with the WT Terminal Labeling Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: Male Sprague-Dawley rats were kept in standard cages in a temperature- (22 °C), humidity- (40-60%), and light period- (07:00-19:00 h) controlled environment and had free access to food and water.

extract_protocol: After the tissue was homogenized, total RNA was extracted from microdissected tissue using TRIzol reagent (Invitrogen Life Technologies, Karlsruhe, Germany). Genomic DNA was removed using the RNeasy Plus kit (Qiagen).

treatment_protocol: Cerebral infarction was induced by transcranial interruption of blood flow by transiently lifting the middle cerebral artery with a tungsten hook as previously described [PMID: 10197512].

tag: strain/background

value: Sprague-Dawley

value: male

value: 3 to 5 months

tag: body weight

tag: stroke

value: no

tag: post-stroke time

value: 0 days

tag: tissue

value: healthy brain

tag: pool size


title: lrp1-del-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.7


title: aged.naive

description: Healthy brain tissue from aged naive rats.

source_name: healthy brain tissue from aged naive rats

tag: gender

value: 18 to 20 months


title: Normal lung 4

description: Lung


title: Hs294T_Ctrl_rep2

tag: cell line

tag: treatment

value: CTRL


title: ctk1-del-ypd-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.2


title: Normal lung 3

description: Lung

tag: age


title: Normal lung 2

description: Lung


title: lrp1-del-1-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.6


title: Hs294T_EphA2_rep1

description: EphA2-overexpressing Hs294Tcells were serum starved for 48 h


title: young.PN.14d

description: Perilesional brain tissue from young infarcted rats 14d post-stroke.

source_name: perilesional brain tissue from young infarcted rats 14d post-stroke

value: 3 to 4 months

value: yes

value: 14 days

value: periinfarcted brain area


title: Hs294T_Ctrl_rep1


title: Hs294T_Ilomastat_rep1

description: Hs294T were serum starved for 48h and in the presence of 50 µmol/L Ilomastat

value: Ilomastat


title: Hs294T_Ilomastat_rep2


title: ctk1-del-4-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.1

value: refpool


title: Hs294T_AttRho_rep2

description: Hs294T were serum starved for 48 h and treated with the Rho activator Calpeptin 1 U/ml for the last 2 h of incubation

value: AttRho


title: aged.PN.3d

description: Perilesional brain tissue from aged infarcted rats 3d post-stroke.

source_name: perilesional brain tissue from aged infarcted rats 3d post-stroke

value: 19 to 20 months

value: 3 days


title: ctk1-del-4-a

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0


title: Normal lung 1

description: Normal lung

value: Wistar

value: Lung

value: 12 weeks


title: ctk1-del-ypd-1-b

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.3


title: aged.PN.14d

description: Perilesional brain tissue from aged infarcted rats 14d post-stroke.

source_name: perilesional brain tissue from aged infarcted rats 14d post-stroke

value: Sprague-Dawley

value: male


title: 13949 TST+

status: Public on Apr 21 2014

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: miRNA expression in whole blood

hyb_protocol: Labeled samples were mixed and hybridized using 1x Hi hybridization buffer together with blocking buffer according to the supplier`s recommendations (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1) according supplier's recommendations (Agilent Technologies). Data analysis was carried out on the Rosetta Resolver gene expression data management and analysis system (Build 7.2.2.0.SP1.31) on reporter level.

source_name: Peripheral Blood, subject 13949

label_protocol: Labelling was perfomed using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies) according supplier's recommendations.

extract_protocol: Total RNA extraction of human blood samples were performed using Trizol LS (Invitrogen), according to manufacturer’s instructions.

value: whole blood

tag: disease status

value: TST+


title: KO_WT replicate 1

city: Albany

first: Dorina

last: Avram

state: NY

address: 43 New Scotland Avenue

department: Center for Immunology and Microbial Disease

institute: Albany Medical Center

description: biological replicate 1 of 2

hyb_protocol: Agilent GeneExpression protocol

scan_protocol: Scanned on an Agilent C scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear LOWESS normalization.

source_name: Bcl11bF/F/dLck-iCre naïve CD44low CD25low CD8+ T cells

label_protocol: Amplified RNA was generated using Agilent linear amplication kit then labeled using Kreatech ULS kit

growth_protocol: CD44low CD25low CD8+ T cells sorted at a purity of more than 90% from naïve Bcl11bF/F/dLck-iCre and wild type mice

extract_protocol: Trizol and columns

tag: cell type

value: naïve CD44low CD25low CD8+ T cells

tag: background strain

source_name: wild type naïve CD44low CD25low CD8+ T cells


title: Hs294T_AttRho_rep1


title: 13827 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13827


title: 14170 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 14170


title: KO_WT replicate 2

description: biological replicate 2 of 2


title: 13812 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13812


title: young.PN.3d

description: Perilesional brain tissue from young infarcted rats 3d post-stroke.

source_name: perilesional brain tissue from young infarcted rats 3d post-stroke

value: 3 to 4 months


title: 13697 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13697


title: 13732 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13732


title: 13876 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13876


title: 13824 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13824

value: TB


title: 13667 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13667


title: 14167 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 14167


title: 13862 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13862


title: 13660 TST+

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13660


title: 13803 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13803


title: 13944 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13944


title: 13720 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13720


title: 13652 TB

description: miRNA expression in whole blood

source_name: Peripheral Blood, subject 13652


title: Ara-C treatment for 0 day, biological rep3

city: shanghai

first: dengli

last: hong

address: Chongqing South Road 280

institute: Shanghai Jiao-Tong University School of Medicine

hyb_protocol: Biotinylated cRNA was hybridized using HGU133Plus 2.0 GeneChip arrays (Affymetrix).

scan_protocol: The chips were subsequently scanned using a GeneChip scanner 3000 (Affymetrix).

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
DAVID 6.7 was used to create a functional annotation and classification of these genes.

source_name: NALM-6 cell line (human, peripheral blood, leukemia, pre-B cell)

label_protocol: cRNAs were Labeled with biotin according to Affymetrix “One-Cycle Target Labeling Assays” protocols.

extract_protocol: Total RNA was isolated using RNeasy micro kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Engrafted NALM-6-GFP+ cells from model (A0D) mice and residual cells from Ara-C treatment for 2 days (A2D) mice were flow sorted.

tag: tumor

value: acute lymphoblastic leukemia

tag: host

value: A0D mice

value: no Ara-C treatment

value: engrafted NALM-6-GFP+ cells


title: BLT2KO

city: Tokyo

first: Takehiko

last: Yokomizo

address: Hongo 2-1-1, Bunkyo-ku

institute: Juntendo University School of Medicine

description: SAMPLE 2; replicate 1(3 mice)

hyb_protocol: Standard Illumina hybridization protocol (Illumina MouseWG-6 Expression BeadChip arrays)

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation with IlluminaGUI in R

label: Biotin

label_protocol: Probe cDNA was amplified and labeled with an Illumina total prep RNA amplification kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol

extract_protocol: Total RNA was prepared from punch biopsies (5 mm in diameter) by using the Qiagen RNeasy Fibrous Tissue Kit (Qiagen, Valencia, CA, USA).

tag: strain background

tag: genotype/variation

value: BLT2KO; deficient in BLT2 receptor

value: Skin


title: WT

description: SAMPLE 1; replicate 1(3 mice)

value: WT; control


title: Ara-C treatment for 0 day, biological rep2


title: shKAT2B, Glucagon B

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: shKAT2B, 100nM Glucagon, 90min.

hyb_protocol: 17 hours at 45 degrees

scan_protocol: Chips were scanned using an Affymetrix genechip scanner 3000 7G

data_processing: Data was processed using the Affymetrix Expression Console software v1.1.1.

source_name: Primary hepatocytes, transduced for 72 hours with KAT2B-specific shRNA. Ttreated with 100nM glucagon for 90 minutes.

label_protocol: Standard Affymetrix protocol

growth_protocol: Primary hepatocytes were grown in Medium 199 from Mediatech supplemented with 100mg/ml Penicillin/Streptomycin. Medium was changed daily.

extract_protocol: Total RNA was extracted using Trizol followed by the Qiagen RNAeasy kit according to manufacturer's instructions. Each sample contains RNA from three separate culture dishes.

treatment_protocol: Primary hepatocytes were transduced with non-specific shRNA, shKAT2B or shWDR5 (2-4 pfu/cell) and cultured for 72 hours. Cells treated with 100nM glucagon or PBS for 90 min.

tag: strain

value: Male

value: 10 weeks

value: Primary hepatocytes


title: Ara-C treatment for 2 days, biological rep1

value: A2D mice

value: Ara-C treatment for 2 days

value: residual cells


title: Ara-C treatment for 2 days, biological rep3


title: ifm67_67_VELCADE MM_5294_3_Prog_2

city: Boston

first: Nikhil

middle: C

last: Munshi

address: 450 Brookline Ave, DB106

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: UUID-2afcd42a-7e12-11e3-9145-5fcc1e060548

hyb_protocol: Samples were analyzed using the Affymetrix GeneChip Human Exon 1.0 ST Array (Affymetirx, Santa Clara, CA) according to the manufacturer's instructions.

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

data_processing:
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.full.mps
Pre-processing and normalization of dataset was carried out using dChip (http://www.hsph.harvard.edu/cli/complab/dchip/exon.htm#expressio) and R package - aroma.affymetrx (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalsis)
Final processed data represent dChip U133Plus2 transformed and invariant set normalized expression values.
See mapping files (1) u133_to_exon_mapping.txt [at http://www.hsph.harvard.edu/cli/complab/dchip/u133_to_exon_mapping.rar] and (2) map.hg-u133-2.0-plus-cons.txt [at http://www.hsph.harvard.edu/cli/complab/dchip/map.hg-u133-2.0-plus-cons.zip], linked as supplementary files on the Series record.

source_name: CD-138 purified plasma cells from a newly diagnosed patient with multiple myeloma - IFM-2005 trial

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix), and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA extraction by trizol method

treatment_protocol: pre-treatment samples

tag: post-induction (bortezomib) treatment response

value: Prog (Progressive disease, no treatment response)


title: Ara-C treatment for 2 days, biological rep2


title: shKAT2B, Control A

description: shKAT2B, PBS control, 90min.

source_name: Primary hepatocytes, transduced for 72 hours with KAT2B-specific shRNA. Control treated with PBS for 90 minutes.


title: shWDR5, Control A

description: shWDR5, PBS control, 90min.

source_name: Primary hepatocytes, transduced for 72 hours with WDR5-specific shRNA. Control treated with PBS for 90 minutes.


title: Ara-C treatment for 0 day, biological rep1


title: WT_punched

description: SAMPLE 3; replicate 1(3 mice)


title: shWDR5, Glucagon B

description: shWDR5, 100nM Glucagon, 90min.

source_name: Primary hepatocytes, transduced for 72 hours with WDR5-specific shRNA. Ttreated with 100nM glucagon for 90 minutes.


title: shKAT2B, Glucagon A

description: shKAT2B, 100nM Glucagon, 90min.


title: shNS, Glucagon A

description: shNS, 100nM Glucagon, 90min.

source_name: Primary hepatocytes, transduced for 72 hours with non-specific shRNA. Ttreated with 100nM glucagon for 90 minutes.


title: shWDR5, Glucagon A

description: shWDR5, 100nM Glucagon, 90min.


title: ifm67_66_VELCADE MM_5999_3_TBRP_2

value: TBRP (VGPR or very good partial treatment response)


title: shNS, Control B

description: shNS, PBS control, 90min.

source_name: Primary hepatocytes, transduced for 72 hours with non-specific shRNA. Control treated with PBS for 90 minutes.


title: shNS, Control A

description: shNS, PBS control, 90min.


title: ifm67_65_VELCADE MM_6381_3_TBRP_2


title: GNX_tumor_3

city: Turku

first: Matias

last: Knuuttila

address: Kiinamyllynkatu 10

department: Department of Physiology

country: Finland

institute: University of Turku

description: GNX tumor 3

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with R

source_name: xenograft tumor

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extracted with Tri Reagent solution and RNeasy mini kit (Qiagen), followed by DNase treatment using DNAse I amplification kit (Invitrogen). Proceedings were done in accordance with the prescribed protocols provided with the kits.

value: xenograft tumor

value: Athymic Nude Foxn 1nu

tag: host gonadal status

value: castrated


title: ifm67_62_VELCADE MM_6548_3_Stable_2

value: stable (stable disease, no treatment response)


title: ifm67_63_VELCADE MM_6452_3_CR un_2

value: CR un (Complete treatment, other than RCIF or RCEP)


title: shNS, Glucagon B

description: shNS, 100nM Glucagon, 90min.


title: ifm67_60_VELCADE MM_6572_3_TBRP_2


title: GNX_tumor_4

description: GNX tumor 4


title: ifm67_61_VELCADE MM_6560_3_TBRP_2


title: CRPC2_tumor_4

description: CRPC 2 tumor 4


title: GNX_tumor_1

description: GNX tumor 1


title: CRPC2_tumor_1

description: CRPC 2 tumor 1


title: ifm67_59_VELCADE MM_6602_3_Stable_2


title: ifm67_58_VELCADE MM_6673_3_TBRP_2


title: CRPC2_tumor_3

description: CRPC 2 tumor 3


title: CRPC2_tumor_2

description: CRPC 2 tumor 2


title: ifm67_64_VELCADE MM_6415_3_Prog_2


title: GNX_tumor_2

description: GNX tumor 2


title: CRPC1_tumor_2

description: CRPC 1 tumor 2


title: ifm67_55_VELCADE MM_6700_3_Prog_2


title: CRPC1_tumor_4

description: CRPC 1 tumor 4


title: Intact2_tumor_3

description: Intact 2 tumor 3

value: intact


title: CRPC1_tumor_1

description: CRPC 1 tumor 1


title: CRPC1_tumor_3

description: CRPC 1 tumor 3


title: Intact2_tumor_4

description: Intact 2 tumor 4


title: Intact2_tumor_2

description: Intact 2 tumor 2


title: ifm67_56_VELCADE MM_6686_3_TBRP_2


title: ifm67_54_VELCADE MM_6717_3_TBRP_2


title: ifm67_52_VELCADE MM_6844_3_CR un_2


title: ifm67_49_VELCADE MM_6878_3_CR un_2


title: Intact2_tumor_1

description: Intact 2 tumor 1


title: ifm67_48_VELCADE MM_6908_3_Stable_2


title: Olfactory epithelium NO side 1 rep3

city: Lexington

first: Timothy

middle: Scott

last: McClintock

state: KY

address: 138 Leader Avenue

department: Physiology

institute: University of Kentucky College of Medicine

description:
RMA expression value derived from Expression Console software; core-gene analysis
Unilateal naris occlusion was used to decrease odor stimulation ipsilataral to naris occlusion and increase odor stimulation contralateral to naris occlusion.

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Kentucky Microarray Core Facility.

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

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data from the 10% of genes with the lowest average signal intensities were discarded. Significant differecenes were judged as mRNA had p < 0.05 one T test, and greater than a 25% difference in abundance.

source_name: Olfactory epithelium ipsilateral to NO

extract_protocol: RNA was isolated from epithelial tissue homogenized in 700 µL TriReagent  according to the manufacturer’s instructions. RNA purity was checked using an Agilent Bioanalyzer

value: unilateral naris occlusion

value: Olfactory epithelium


title: BRAF-V600E melanoma_451Lu_subline_drug resistant

city: Philadelphia

first: Katherine

last: Nathanson

state: PA

address: 421 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: Hybridization was performed following Agilent's Array-based CGH for Genomic DNA Analysis - Enzymatic Labeling protocol, using reagents supplied in the Agilent Oligo aCGH Hybridization Kit.

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and linear normalization.

source_name: 451Lu_drug resistant

label_protocol: Experimental and Control DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH following standard labeling and purification protocol.

growth_protocol: Melanoma cells are grown in DMEM + 5% FBS  as previously described (Villanueva, et al. Cancer Cell. 2010 Dec 14;18(6):683-95 - PMID: 21156289)

extract_protocol: Cells were scrapped, pelleted, and genomic DNA extracted using Qiagen genomic DNA purification kit.

treatment_protocol: Drug resistant sublines were generated by chronic exposure to escaliting doses of trametinib

value: BRAF-V600E melanoma 451Lu cell line

value: isogenic drug resistant-derived subline

tag: tissue origin

value: lung metastasis

value: 24 hrs

source_name: reference sample

tag: sample type

value: Female Control DNA from Promega


title: Intact1_tumor_4

description: Intact 1 tumor 4

tag: tissue


title: BRAF-V600E melanoma_Mel1617_parental_drug senstive

source_name: Mel1617_drug sensitive

value: BRAF-V600E melanoma Mel1617 cell line

value: parental (drug sensitive)


title: BRAF-V600E melanoma_451Lu_parental_drug senstive

source_name: 451Lu_drug sensitive


title: ifm67_50_VELCADE MM_6871_3_Stable_2


title: Olfactory epithelium control side 1 rep2

source_name: Olfactory epithelium contralateral NO

value: control


title: ifm67_43_VELCADE MM_7047_3_Prog_2

value: Prog (Progressive disease, no treatment response)


title: ifm67_46_VELCADE MM_6963_3_Prog_2


title: ifm67_41_VELCADE MM_7083_3_CR un_2


title: ifm67_51_VELCADE MM_6859_3_TBRP_2

value: TBRP (VGPR or very good partial treatment response)


title: ifm67_47_VELCADE MM_6944_3_TBRP_2


title: Olfactory epithelium NO side 1 rep2


title: ifm67_44_VELCADE MM_7041_3_TBRP_2


title: Olfactory epithelium control side 1 rep3

source_name: Olfactory epithelium contralateral to NO


title: Intact1_tumor_3

description: Intact 1 tumor 3

value: xenograft tumor

value: Athymic Nude Foxn 1nu


title: ifm67_42_VELCADE MM_7059_3_Stable_2

value: stable (stable disease, no treatment response)


title: BRAF-V600E melanoma_Mel1617_subline_drug resistant

source_name: Mel1617_drug resistant


title: Intact1_tumor_2

description: Intact 1 tumor 2


title: Olfactory epithelium NO side 1 rep1


title: ifm67_45_VELCADE MM_6991_3_CR un_2

value: CR un (Complete treatment, other than RCIF or RCEP)


title: Intact1_tumor_1

description: Intact 1 tumor 1

value: intact


title: ifm67_39_VELCADE MM_7188_3_TBRP_2


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-deficient diet rep3

city: Stanford

first: Angela

middle: M

last: Marcobal

state: California

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The raw data were RMA-MS normalized using R-2.9.1. and log2 transformed, excluding other species present on chip.

organism: Bacteroides thetaiotaomicron

source_name: BT_Fut2_KO mouse cecum_polysaccharide-deficient diet

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen Rneasy mini column extraction, Ambion DNA free treatment

tag: host/mouse strain

tag: host/mouse genotype

tag: host fed with

value: polysaccharide-deficient diet

tag: bacteria harvested from

value: BT-colonized mice cecum


title: ifm67_38_VELCADE MM_7195_3_CR un_2


title: ifm67_37_VELCADE MM_7227_3_TBRP_2


title: BLT2KO_punched

description: SAMPLE 4; replicate 1(3 mice)

value: BLT2KO; deficient in BLT2 receptor

value: Skin


title: Olfactory epithelium control side 1 rep1

tag: treatment

value: Olfactory epithelium


title: ifm67_36_VELCADE MM_7254_3_TBRP_2


title: ifm67_53_VELCADE MM_6837_3_TBRP_2


title: ifm67_35_VELCADE MM_7415_3_TBRP_2


title: ifm67_34_VELCADE MM_4675_3_RMin_1

value: RMin (Minimal treatment response)


title: ifm67_32_VELCADE MM_4921_3_RCEP_1

value: RCEP (nCR or near Complete Response)


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-deficient diet rep2


title: ifm67_28_VELCADE MM_5041_3_RCIF_1

value: RCIF (Complete treatment response)


title: ifm67_31_VELCADE MM_4958_3_RCIF_1


title: ifm67_33_VELCADE MM_4901_3_Stable_1


title: ifm67_30_VELCADE MM_4979_3_RCEP_1


title: ifm67_27_VELCADE MM_5088_3_RCIF_1


title: ifm67_40_VELCADE MM_7143_3_Prog_2


title: ifm67_24_VELCADE MM_5261_3_RMin_1


title: ifm67_22_VELCADE MM_5322_3_RCEP_1


title: ifm67_23_VELCADE MM_5263_3_RCIF_1


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-deficient diet rep2

source_name: BT_WT mouse cecum_polysaccharide-deficient diet

value: wild type


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-deficient diet rep1


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-deficient diet rep4


title: ifm67_21_VELCADE MM_5422_3_Prog_1

source_name: CD-138 purified plasma cells from a newly diagnosed patient with multiple myeloma - IFM-2005 trial


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-deficient diet rep1


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-deficient diet rep4


title: ifm67_25_VELCADE MM_5156_3_RMin_1


title: Bacteroides thetaiotaomicron response in cecum of Fut2(+/-)_KO mouse fed with polysaccharide-rich diet rep1

source_name: BT_Fut2(+/-)_KO mouse cecum_polysaccharide-rich diet

value: polysaccharide-rich diet


title: ifm67_20_VELCADE MM_5452_3_RCIF_1


title: Bacteroides thetaiotaomicron response in cecum of Fut2(+/-)_KO mouse fed with polysaccharide-rich diet rep3


title: ifm67_19_VELCADE MM_5505_3_RCEP_1


title: ifm67_29_VELCADE MM_5030_3_Prog_1

value: Prog (Progressive disease, no treatment response)


title: Bacteroides thetaiotaomicron response in cecum of Fut2(+/-)_KO mouse fed with polysaccharide-rich diet rep2


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-deficient diet rep3


title: ifm67_17_VELCADE MM_5552_3_RMin_1


title: ifm67_18_VELCADE MM_5549_3_RCIF_1


title: ifm67_16_VELCADE MM_5572_3_RCEP_1


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-rich diet rep4

source_name: BT_Fut2_KO mouse cecum_polysaccharide-rich diet


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-rich diet rep3


title: ifm67_26_VELCADE MM_5107_3_RMin_1


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-rich diet rep2


title: ifm67_14_VELCADE MM_5614_3_Prog_1


title: ifm67_13_VELCADE MM_5664_3_RCEP_1


title: ifm67_11_VELCADE MM_5694_3_RCIF_1


title: ifm67_12_VELCADE MM_5682_3_Stable_1


title: ifm67_09_VELCADE MM_5745_3_RCIF_1


title: ifm67_08_VELCADE MM_5809_3_Prog_1


title: ifm67_10_VELCADE MM_5735_3_Prog_1


title: ifm67_15_VELCADE MM_5609_3_RCIF_1


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-rich diet rep1


title: Bacteroides thetaiotaomicron response in cecum of Fut2_KO mouse fed with polysaccharide-rich diet rep5


title: ifm67_07_VELCADE MM_5843_3_RCIF_1


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-rich diet rep2

source_name: BT_WT mouse cecum_polysaccharide-rich diet


title: Bacteroides thetaiotaomicron response in cecum of mouse fed with polysaccharide-rich diet rep1


title: ifm67_05_VELCADE MM_6041_3_RMin_1


title: ifm67_57_VELCADE MM_6680_3_Stable_2


title: ifm67_04_VELCADE MM_6073_3_Prog_1


title: ifm67_03_VELCADE MM_6145_3_RCEP_1


title: Col-0, WT, at HL 3h, biological rep1

city: Potsdam

first: Ning

last: Shao

address: Wissenschaftpark Golm

institute: Max-Planck Institute for Molecular Plant Physiology

description: seedlings grown on agar plates, HL stress (1000 µE m−2 s−1)

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ 3’ GeneChip Expression  Analysis Technical Manual . The final concentration of cDNA is 17 ng/μl. • Hybridization was performed for 18+/-2 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.

data_processing: The data was analyzed with rma function in R/Bioconductor package affy using default settings.

organism: Arabidopsis thaliana

source_name: Col-0, WT, whole seedlings without root, at HL 3h

label_protocol: NuGEN’s Encore Biotin Module (Cat. No. 4200-12) was used to fragment 3.95 µg cDNA followed by Biotin-labeling according to the manufacturers’ instructions.

extract_protocol: Total cellular RNA was extracted using the NucleoSpin RNA Plant kit (Macherey-Nagel) according to the manufacturer’s instructions, without DNase digestion. The remaining DNA was digested using Ambion® DNA-free™ DNase Treatment and Removal Reagents (Invitrogen).

treatment_protocol: 12 day-old Arabidopsis seedlings grown on ½ MS agar plates with 1% sucrose and adapted to 10 µE m−2 s−1 continuous light for 7 d were exposed to HL stress (1000 µE m−2 s−1) following a 3h dark period

value: whole seedlings without root

tag: genotype

value: Col-0, WT

value: HL stress (1000 µE m−2 s−1)


title: Col-0, WT, at HL 3h, biological rep3

growth_protocol: 12 day-old Arabidopsis seedlings grown on ½ MS agar plates with 1% sucrose and adapted to 10 µE m−2 s−1 continuous light for 7 d


title: ifm67_02_VELCADE MM_6159_3_Stable_1

value: stable (stable disease, no treatment response)


title: ifm67_06_VELCADE MM_5994_3_RCEP_1


title: Col-0, WT, at HL 0h, biological rep3

description: seedlings grown on agar plates, without high light treatment

source_name: Col-0, WT, whole seedlings without root, at HL 0h

value: without high light treatment


title: Col-0, WT, at HL 3h, biological rep2


title: Col-0, WT, at HL 0h, biological rep1


title: Col-0, WT, at HL 0h, biological rep2


title: Col-0, RNAi-MBS2/mbs1-1, at HL 3h, biological rep3

source_name: Col-0, RNAi-MBS2/mbs1-1, whole seedlings without root, at HL 3h

value: Col-0, RNAi-MBS2/mbs1-1


title: ifm67_01_VELCADE MM_6199_3_Stable_1


title: Col-0, RNAi-MBS2/mbs1-1, at HL 0h, biological rep3

source_name: Col-0, RNAi-MBS2/mbs1-1, whole seedlings without root, at HL 0h


title: Col-0, RNAi-MBS2/mbs1-1, at HL 3h, biological rep1


title: Col-0, RNAi-MBS2/mbs1-1, at HL 3h, biological rep2


title: Col-0, mbs1-1, at HL 3h, biological rep3

source_name: Col-0, mbs1-1, whole seedlings without root, at HL 3h

value: Col-0, mbs1-1


title: Col-0, RNAi-MBS2/mbs1-1, at HL 0h, biological rep2


title: Col-0, RNAi-MBS2/mbs1-1, at HL 0h, biological rep1


title: Col-0, mbs1-1, at HL 3h, biological rep1


title: Col-0, mbs1-1, at HL 0h, biological rep2

source_name: Col-0, mbs1-1, whole seedlings without root, at HL 0h


title: Col-0, mbs1-1, at HL 0h, biological rep3


title: DksA_wt_untreated_rep2

city: San Francisco

first: Yan

last: Zhang

address: 600 16th Street

institute: UC San Francisco

description: DksA ChIP-chip wt cells

hyb_protocol: The labeled IP DNA and input DNA samples were hybridized to a NimbleGen high-density 2.1M promoter tiling array using a Maui hybridization apparatus (BioMicro Systems) by following the protocol from NimbleGen.

scan_protocol: The arrays were scanned by using the Axon 4000B scanner.

data_processing: The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

organism: Escherichia coli

source_name: DksA ChIP DNA from wt cells

label_protocol: The IP DNA samples and input DNA samples (recovered after similar treatment but without immunoprecipitation) were amplified by linker-mediated PCR as described in the protocol from NimbleGen. The amplified DNA was then labeled with Cy3 (input DNA) or Cy5 (IP DNA) dye by following the protocol from NimbleGen.

growth_protocol: Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase (OD600~0.4) at 37°C with vigorous shaking.

extract_protocol: Cells were fixed with 1% formaldehyde for 5min before quenching with ice-cold glycine (100mM). Cells were harvested, washed with ice-cold PBS and flash-frozen in liquid nitrogen. Cell pellets were resuspended in 500 ml of IP buffer (100 mM Tris pH 8, 300mM NaCl, 2% TritonX-100) and sonicated using a Misonix sonicator (S-4000) with a cup horn (431C) set at 60% output, 10 sec ON and 10 sec OFF, for a total sonication time of 16 min. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml; USB, Inc.) and the samples were centrifuged at 20,000 x g for 10 min at 4 °C to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads (Upstate; now Millipore) and protein G beads (GE Healthcare) in IP buffer for 3 hours at 4 °C. The beads were removed by centrifugation (1000 x g for 2 min at 4 °C) and antibodies were added to the pre-cleared lysate for an overnight incubation. For ChIP, we used anti-RNAP b subunit NT63 monoclonal antibodies (Neoclone W0002), anti-RNAP s70 subunit monoclonal antibodies (Neoclone W0004), or anti-DksA rabbit polyclonal antisera (a kind gift from Diana Downs). The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in 250 μl IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% Triton X-100), twice with 1 ml 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% SDS), twice with 1 ml 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% SDS), and twice with 1 ml TE (10 mM Tris pH 8, 1 mM EDTA). Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation (1000 x g for 2 min at 25 °C) to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted in a final volume of 65 μl with 10 mM Tris pH 8.

tag: antibody

value: anti-DksA rabbit polyclonal antisera

source_name: Input DNA from wt cells

growth_protocol: Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase at 37°C with vigorous shaking.

value: None, input DNA


title: DksA_DdksA_untreated

description: DksA ChIP-chip DdksA cells

source_name: DksA ChIP DNA from DdksA cells

growth_protocol: DdksA cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase (OD600~0.4) at 37°C with vigorous shaking.

value: MG1655 DdksA

source_name: Input DNA from DdksA cells

growth_protocol: DdksA cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase at 37°C with vigorous shaking.


title: Col-0, mbs1-1, at HL 0h, biological rep1


title: miR223KO d21 lung exp1 vs B6 d21 lung exp2

description: miRNA expression in lung tissue

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1) according supplier's recommendations (Agilent Technologies). Data analysis was carried out on the Rosetta Resolver gene expression data management and analysis system (Build 7.2.2.0.SP1.31) on sequence level.

source_name: miR223KO d21 M.tuberculosis infection

extract_protocol: Total RNA extraction of murine lungs were performed using Trizol (Invitrogen), according to manufacturer’s instructions.

treatment_protocol: A Glas-Col inhalation exposure system was employed for M.tuberculosis infection.

value: lung

tag: infection status

value: d21 M.tuberculosis infection

source_name: C57Bl/6 wt d21  M.tuberculosis infection


title: DksA_wt_untreated_rep1

description: DksA ChIP-chip wt cells


title: s70_DdksA_SHX_rep2

description: s70 ChIP-chip starved DdksA cells

source_name: s70 ChIP DNA from starved DdksA cells

growth_protocol: DdksA cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase and treated with 0.5mg/ml serine hydroxamate (SHX) for 20min at 37°C with vigorous shaking.

treatment_protocol: 0.5mg/ml SHX for 20min

value: 0.5mg/ml serine hydroxamate for 20min

value: anti-s70 monoclonal antibodies

source_name: Input DNA from starved DdksA cells


title: B6 d21 lung exp1 vs miR223KO d21 lung exp2

description: miRNA expression in lung tissue

source_name: C57Bl/6 wt d21 M.tuberculosis infection

value: wild type

source_name: miR223KO d21  M.tuberculosis infection


title: Col-0, mbs1-1, at HL 3h, biological rep2


title: s70_DdksA_SHX_rep1

description: s70 ChIP-chip starved DdksA cells


title: miR223KO d14 lung exp1 vs B6 d14 lung exp2

description: miRNA expression in lung tissue

source_name: miR223KO d14 M.tuberculosis infection

value: d14 M.tuberculosis infection

source_name: C57Bl/6 wt d14  M.tuberculosis infection


title: Col-0, flu, at HL 3h, biological rep3

source_name: Col-0, flu, whole seedlings without root, at HL 3h

value: Col-0, flu


title: hESCs originated from 8-cell stage embryo 4 [UCSFB9]

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

data_processing: Standard Illumina protocol (GenomeStudio). All the cnvi probes were removed from the analysis

label: biotin and dinitrophenyl

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled

growth_protocol: Lis Cell Lines: Intact ICM clumps were placed on a feeder cell layer of mitomycin C-inactivated treated mouse embryo fibroblasts (MEFs), and cultured in hESC media; Following 5-7 passages,  cell lines were propagated by collagenase type IV. UCSFB Cell Lines: Quinn’s Cleavage medium for 24 h; transferred onto irradiated human foreskin fibroblasts (HFF) Quinn’s Blastocyst medium and cultured for 4 days; transferred to hESC medium at day 5

extract_protocol: genomic DNA was extracted using Quiagen DNeasy Blood & Tissue Kit

tag: hesc line

tag: gender

value: female


title: Col-0, flu, at HL 3h, biological rep2

value: whole seedlings without root


title: B6 d14 lung exp1 vs miR223KO d14 lung exp2

description: miRNA expression in lung tissue

source_name: C57Bl/6 wt d14 M.tuberculosis infection

tag: genotype/variation

source_name: miR223KO d14  M.tuberculosis infection


title: s70_DdksA_untreated_rep2

description: s70 ChIP-chip DdksA cells

source_name: s70 ChIP DNA from DdksA cells


title: Col-0, flu, at HL 3h, biological rep1

value: HL stress (1000 µE m−2 s−1)


title: s70_DdksA_untreated_rep1

description: s70 ChIP-chip DdksA cells


title: Col-0, flu, at HL 0h, biological rep3

source_name: Col-0, flu, whole seedlings without root, at HL 0h


title: hESCs originated from 8-cell stage embryo 1 [UCSFB4]


title: miR223KO naive lung vs B6 naive lung

description: miRNA expression in lung tissue

source_name: miR223KO naive

tag: strain

value: naive

source_name: C57Bl/6 wt naive


title: hESCs originated from 8-cell stage embryo 2 [UCSFB5]


title: hESCs originated from blastocyst [Lis12_DM1_Late]

source_name: hESCs originated from blastocyst


title: hESCs originated from 8-cell stage embryo 1 [UCSFB1]


title: hESCs originated from 8-cell stage embryo 1 [UCSFB3]


title: B6 naive lung vs miR223KO naive lung

description: miRNA expression in lung tissue


title: Col-0, flu, at HL 0h, biological rep2

value: without high light treatment


title: hESCs originated from 8-cell stage embryo 2 [UCSFB7]


title: hESCs originated from 8-cell stage embryo 3 [UCSFB8]

value: male


title: hESCs originated from 8-cell stage embryo 2 [UCSFB6]


title: hESCs originated from 8-cell stage embryo 1 [UCSFB2]


title: s70_wt_SHX_rep2

description: s70 ChIP-chip starved wt cells

source_name: s70 ChIP DNA from starved wt cells

growth_protocol: Wild-types cells were grown in MOPS medium with 0.2% glucose, leucine, isoleucine, valine, glycine, phenylalanine, threonine (40 mg/ml) and uracil (50 mg/ml) until mid-log phase and treated with 0.5mg/ml serine hydroxamate (SHX) for 20min at 37°C with vigorous shaking.

source_name: Input DNA from starved wt cells


title: Col-0, flu, at HL 0h, biological rep1


title: Father of Lis_25_FAP [Paternal from Lis25_FAP]

source_name: Father of Lis_25_FAP

value: Paternal from Lis25_FAP


title: Huh7; 12 hours after Y27632 treatment

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: Huh7; 12 hours after Y27632 treatment

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Huh7 cell maintained in Dulbecco’s modified Eagle medium,supplemented with 10% fetal bovine serum

extract_protocol: Total RNA extraction of  cell lines was performed according to the manufacturer’s instructions by ISOGEN

treatment_protocol: Huh7 cell was treated with 10μM Y27632 for 12 hours

tag: cell line


title: Col-0, 35S:MBS1, at HL 3h, biological rep3

source_name: Col-0, 35S:MBS1, whole seedlings without root, at HL 3h

value: Col-0, 35S:MBS1


title: 293T;control;three hours

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: 293T ctr

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: 293T cell maintained in Dulbecco’s modified Eagle medium,supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extraction of cell lines was performed according to the manufacturer’s instructions by ISOGEN.

treatment_protocol: 293T cell was treated with 10μM Y27632 for three and six hours

tag: time point

tag: agent

value: three hours after treatment


title: 293T;control;six hours

value: six hours after treatment


title: Mother of Lis_25_FAP [Maternal from Lis25_FAP]

source_name: Mother of Lis_25_FAP

value: Maternal from Lis25_FAP


title: Col-0, 35S:MBS1, at HL 0h, biological rep3

source_name: Col-0, 35S:MBS1, whole seedlings without root, at HL 0h


title: hESCs originated from blastocyst [Lis12_DM1_Early]


title: Col-0, 35S:MBS1, at HL 3h, biological rep1


title: s70_wt_SHX_rep1

description: s70 ChIP-chip starved wt cells

value: None, input DNA


title: Col-0, 35S:MBS1, at HL 0h, biological rep2


title: Father of Lis_12_DM1 [Paternal from Lis12_DM1]

source_name: Father of Lis_12_DM1

value: Paternal from Lis12_DM1


title: hESCs originated from blastocyst [Lis25_FAP_Late]


title: RNAP_DdksA_SHX_rep2

description: RNAP ChIP-chip starved DdksA cells

source_name: RNAP ChIP DNA from starved DdksA cells

value: MG1655 DdksA

value: 0.5mg/ml serine hydroxamate for 20min

value: anti-RNAP b subunit NT63 monoclonal antibodies

source_name: Input DNA from starved DdksA cells


title: s70_wt_untreated_rep2

description: s70 ChIP-chip wt cells

source_name: s70 ChIP DNA from wt cells

value: anti-s70 monoclonal antibodies

source_name: Input DNA from wt cells


title: Col-0, 35S:MBS1, at HL 3h, biological rep2


title: Col-0, 35S:MBS1, at HL 0h, biological rep1


title: Mother of Lis_12_DM1 [Maternal from Lis12_DM1]

source_name: Mother of Lis_12_DM1

value: Maternal from Lis12_DM1

value: female


title: Mother of Lis_04_Twist [Maternal from Lis04_Twist]

source_name: Mother of Lis_04_Twist

value: Maternal from Lis04_Twist


title: hESCs originated from blastocyst [Lis04_Twist1_Early]


title: HMGN1 overexpression 4

status: Public on Apr 20 2014

first: David

last: Weinstock

address: 450 Brookline Ave

institute: DFCI

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) per the standard Affymetrix protocol in the Dana-Farber microarray core (http://chip.dfci.harvard.edu/).

scan_protocol: After staining, the genechip arrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Gene Pattern (http://www.broadinstitute.org/cancer/software/genepattern) package was used for RMA normalization using the ExpressionFileCreator module.

label: biotin allonamide triphosphat

source_name: proB cell colonies

label_protocol: following the Affymetrix standard protocol

growth_protocol: bone marrow harvested and placed in B cell methylcellulose medium to generate proB cell colonies

extract_protocol: For total RNA, 10e6 cells were harvested in Trizol according to the manufacturers instructions.

treatment_protocol: proB cell colonies were harvested at 1 week

tag: b cell stage

value: proB

value: HMGN1 over-expressing


title: wild-type 4

value: wild-type


title: HMGN1 overexpression 3


title: HMGN1 overexpression 1


title: Huh7; control

source_name: Huh7; control


title: HMGN1 overexpression 2


title: hESCs originated from blastocyst [Lis25_FAP_Early]

source_name: hESCs originated from blastocyst


title: RNAP_wt_untreated_rep2

description: RNAP ChIP-chip wt cells

source_name: RNAP ChIP DNA from wt cells


title: hESCs originated from blastocyst [Lis04_Twist1_Late]