title: Tspan8 pos3

city: Heidelberg

first: Kristin

last: Rattay

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description:
biological replicate to sample 33 and 34
Sample 35

scan_protocol: Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated.

data_processing: The data were normalised using quantile normalisation in R

source_name: Mouse mTECs

label_protocol: Biotin-labeled cRNA for hybridization was prepared according to Illumina`s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992). In brief, 200 ng total RNA was used for cDNA synthesis, followed by an in vitro transcription step for amplification and labeling to synthesize biotin-labelled cRNA using the MessageAmp II RNA amplification kit (Ambion) and biotin-16-UTP (Roche).

extract_protocol: Total RNA of primary sorted mTECs was isolated and purified using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturers` protocol. Quality control was performed using Agilent Bioanalyser.

tag: tra specificity

value: Tspan8 positive mTECs

value: FACS isolated medullary thymic epithelial cells


title: BALB/c 24h post pneumococcal strain D39 infection, replicate 3

status: Public on Oct 28 2015

type: RNA

city: Leicester

first: Peter

middle: W

last: Andrew

address: University Rd

department: Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Leicester

description:
raplicate 3
B39-24-7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGenomeStudio, batch correction was done using dCHIP and differences in expression were analysed in ArrayTrack

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse lung

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

extract_protocol: Lung were extracted, cut and immediatelly immersed in RNA-later. RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: BALB/cOlaHsd

tag: age

value: 9 weeks

tag: gender

value: female

tag: tissue

value: lung

tag: pneumococcal strain

value: D39, serotype 2, ST595


title: BALB/c 12h post pneumococcal strain D39 infection, replicate 4

description:
raplicate 4
B39-12-4


title: SAMPLE 66_PAE-iPS-4_p31

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human iPS cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to  Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.

organism: Homo sapiens

source_name: PAE-iPS-4_passage 31

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human iPSCs and ESCs were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 3 or 5% CO2.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: provenance somatic cell

value: human placental artery-derived endothelial (hPAE) cell

tag: cell line

tag: cell type

value: human iPS cell

tag: passage number


title: SAMPLE 70_MRC-iPS-16 (Fetch)_p13

description: Gene expression in human iPS cell

source_name: MRC-iPS-16 (Fetch)_passage 13

value: MRC-iPS-16 (Fetch)


title: SAMPLE 67_PAE-iPS-4_p31

description: Gene expression in human iPS cell


title: SAMPLE 69_UtE-iPS-7_p26

description: Gene expression in human iPS cell

source_name: UtE-iPS-7_passage 26

value: human uterine endometrium (hUtE) cell


title: BALB/c 24h post pneumococcal strain D39 infection, replicate 2

description:
raplicate 2
B39-24-11


title: CBA/Ca PBS-treated, 6h Tp, replicate-3

description:
raplicate 3
Cpbs-1

value: CBA/CaOlaHsd


title: Tspan8 neg2

country: Germany

description:
biological replicate to sample 30 and 32
Sample 31

value: Tspan8 negative mTECs


title: CBA/Ca PBS-treated, 6h Tp, replicate-6

description:
raplicate 6
Cpbs-5


title: SAMPLE 64_PAE-iPS-1_p31

description: Gene expression in human iPS cell

source_name: PAE-iPS-1_passage 31


title: Ins2 pos3

description:
biological replicate to sample 27 and 28
Sample 29

value: Ins2 positive mTECs


title: BALB/c 24h post pneumococcal strain D39 infection, replicate 5

description:
raplicate 5
B39-24-9


title: BALB/c 12h post pneumococcal strain D39 infection, replicate 5

description:
raplicate 5
B39-12-2


title: BALB/c 12h post pneumococcal strain D39 infection, replicate 1

description:
raplicate 1
B39-12-5


title: Ins2 pos2

description:
biological replicate to sample 27 and 29
Sample 28


title: BALB/c 12h post pneumococcal strain D39 infection, replicate 3

description:
raplicate 3
B39-12-6


title: Tspan8 neg1

description:
biological replicate to sample 31 and 32
Sample 30


title: Tspan8 pos2

description:
biological replicate to sample 33 and 35
Sample 34


title: CBA/Ca PBS-treated, 6h Tp, replicate-4

description:
raplicate 4
Cpbs-3


title: SAMPLE 68_PAE-iPS-4_p31

description: Gene expression in human iPS cell


title: BALB/c 12h post pneumococcal strain D39 infection, replicate 2

description:
raplicate 2
B39-12-3


title: BALB/c 24h post pneumococcal strain D39 infection, replicate 1

description:
raplicate 1
B39-24-10


title: CBA/Ca PBS-treated, 6h Tp, replicate-2

description:
raplicate 2
Cpbs-4


title: Tspan8 pos1

description:
biological replicate to sample 34 and 35
Sample 33


title: CBA/Ca PBS-treated, 6h Tp, replicate-1

description:
raplicate 1
Cpbs-6


title: SAMPLE 63_PAE-iPS-1_p31

description: Gene expression in human iPS cell


title: SAMPLE 65_PAE-iPS-1_p31

description: Gene expression in human iPS cell


title: CBA/Ca PBS-treated, 6h Tp, replicate-5

description:
raplicate 5
Cpbs-2


title: CBA/Ca 6h post pneumococcal strain BS71 infection, replicate 4

description:
raplicate 4
C71-4

value: BS71, serotype 3, ST180


title: Tspan8 neg3

description:
biological replicate to sample 30 and 31
Sample 32


title: Ins2 pos1

description:
biological replicate to sample 28 and 29
Sample 27


title: CBA/Ca 6h post pneumococcal strain BS71 infection, replicate 3

description:
raplicate 3
C71-6


title: SAMPLE 61_UtE-iPS-7_p31

description: Gene expression in human iPS cell

source_name: UtE-iPS-7_passage 31


title: CBA/Ca 6h post pneumococcal strain BS71 infection, replicate 1

description:
raplicate 1
C71-2


title: Ins2 neg2

description:
biological replicate to sample 24 and 26
Sample 25

value: Ins2 negative mTECs


title: CBA/Ca 6h post pneumococcal strain D39 infection, replicate 5

description:
raplicate 5
C39-5


title: CBA/Ca 6h post pneumococcal strain LgtSt215 infection, replicate 1

description:
raplicate 1
C250-2

value: LgtSt215, serotype 19F, ST179


title: CBA/Ca 6h post pneumococcal strain BS71 infection, replicate 2

description:
raplicate 2
C71-3


title: CBA/Ca 6h post pneumococcal strain LgtSt215 infection, replicate 3

description:
raplicate 3
C250-3


title: CBA/Ca 6h post pneumococcal strain D39 infection, replicate 4

description:
raplicate 4
C39-6


title: CBA/Ca 6h post pneumococcal strain LgtSt215 infection, replicate 2

description:
raplicate 2
C250-1


title: Cea1 pos3

description:
biological replicate to sample 21 and 22
Sample 23

value: Cea1 positive mTECs


title: CBA/Ca 6h post pneumococcal strain D39 infection, replicate 3

description:
raplicate 3
C39-3


title: SAMPLE 58_UtE-iPS-6_p30

description: Gene expression in human iPS cell

source_name: UtE-iPS-6_passage 30


title: Cea1 pos1

description:
biological replicate to sample 22 and 23
Sample 21

value: FACS isolated medullary thymic epithelial cells


title: CBA/Ca 6h post pneumococcal strain BHN191 infection, replicate 5

description:
raplicate 5
C248-6

value: BHN191, serotype 6B, ST138


title: SAMPLE 62_UtE-iPS-7_p31

description: Gene expression in human iPS cell


title: CBA/Ca 6h post pneumococcal strain BHN191 infection, replicate 3

description:
raplicate 3
C248-2

value: 9 weeks


title: SAMPLE 59_UtE-iPS-6_p30

description: Gene expression in human iPS cell


title: SAMPLE 60_UtE-iPS-7_p31

description: Gene expression in human iPS cell


title: SAMPLE 56_MRC-iPS-40 (Skipper)_p14

description: Gene expression in human iPS cell

source_name: MRC-iPS-40 (Skipper)_passage 14

value: MRC-iPS-40 (Skipper)


title: Ins2 neg1

description:
biological replicate to sample 25 and 26
Sample 24


title: Cea1 pos2

description:
biological replicate to sample 21 and 23
Sample 22


title: CBA/Ca 6h post pneumococcal strain D39 infection, replicate 2

description:
raplicate 2
C39-4

value: female

value: lung


title: Cea1 neg3

description:
biological replicate to sample 18 and 19
Sample 20

value: Cea1 negative mTECs


title: SAMPLE 57_UtE-iPS-6_p30

description: Gene expression in human iPS cell

value: human iPS cell


title: CBA/Ca 6h post pneumococcal strain LgtSt215 infection, replicate 4

description:
raplicate 4
C250-5


title: CBA/Ca 6h post pneumococcal strain BHN191 infection, replicate 4

description:
raplicate 4
C248-1


title: Ins2 neg3

description:
biological replicate to sample 24 and 25
Sample 26


title: CBA/Ca 6h post pneumococcal strain D39 infection, replicate 1

description:
raplicate 1
C39-2

value: D39, serotype 2, ST595


title: SAMPLE 55_MRC-iPS-40 (Skipper)_p14

description: Gene expression in human iPS cell


title: CBA/Ca 6h post pneumococcal strain BHN191 infection, replicate 1

description:
raplicate 1
C248-4


title: BALB/c PBS-treated, 6h Tp, replicate-4

description:
replicate 4
Bpbs-5

value: BALB/cOlaHsd


title: BALB/c PBS-treated, 6h Tp, replicate-2

description:
replicate 2
Bpbs-4


title: BALB/c PBS-treated, 6h Tp, replicate-6

description:
raplicate 6
Bpbs-6


title: BALB/c PBS-treated, 6h Tp, replicate-1

description:
replicate 1
Bpbs-2


title: BALB/c 6h post pneumococcal strain BHN35 infection, replicate 3

description:
replicate 3
35-4

value: BHN35, serotype 3, ST180


title: SAMPLE 53_MRC-iPS-25 (Tic)_p17

description: Gene expression in human iPS cell

source_name: MRC-iPS-25 (Tic)_passage 17

value: MRC-iPS-25 (Tic)


title: BALB/c 6h post pneumococcal strain BHN35 infection, replicate 1

description:
replicate 1
35-5


title: Gad1 pos2

description:
biological replicate to sample 15 and 17
Sample 16

value: Gad1 positive mTECs


title: SAMPLE 49_AM-iPS-13 (Basil)_p19

description: Gene expression in human iPS cell

source_name: AM-iPS-13 (Basil)_passage 19

value: human amniotic ectoderm and mesoderm layer (hAM) cell

value: AM-iPS-13 (Basil)


title: BALB/c PBS-treated, 6h Tp, replicate-5

description:
replicate 5
Bpbs-1


title: BALB/c 6h post pneumococcal strain BHN35 infection, replicate 2

description:
replicate 2
35-2


title: BALB/c 6h post pneumococcal strain BHN35 infection, replicate 4

description:
replicate 4
35-6


title: SAMPLE 54_MRC-iPS-40 (Skipper)_p14

description: Gene expression in human iPS cell


title: CBA/Ca 6h post pneumococcal strain BHN191 infection, replicate 2

description:
raplicate 2
C248-3

value: CBA/CaOlaHsd


title: Cea1 neg1

description:
biological replicate to sample 19 and 20
Sample 18


title: SAMPLE 48_AM-iPS-13 (Basil)_p17

description: Gene expression in human iPS cell

source_name: AM-iPS-13 (Basil)_passage 17


title: Gad1 pos1

description:
biological replicate to sample 16 and 17
Sample 15


title: Cea1 neg2

description:
biological replicate to sample 18 and 20
Sample 19


title: BALB/c 6h post pneumococcal strain BS71 infection, replicate 4

description:
replicate 4
B71-3

value: BS71, serotype 3, ST180


title: Gad1 neg3

description:
biological replicate to sample 12 and 13
Sample 14

value: Gad1 negative mTECs

value: FACS isolated medullary thymic epithelial cells


title: Gad1 pos3

description:
biological replicate to sample 15 and 16
Sample 17


title: BALB/c 6h post pneumococcal strain BS71 infection, replicate 2

description:
replicate 2
B71-4

value: 9 weeks


title: SAMPLE 51_PAE-iPS-11_p28

description: Gene expression in human iPS cell

source_name: PAE-iPS-11_passage 28

value: human placental artery-derived endothelial (hPAE) cell


title: Gad1 neg1

description:
biological replicate to sample 13 and 14
Sample 12


title: BALB/c 6h post pneumococcal strain D39 infection, replicate 4

description:
replicate 4
B39-4

value: female


title: double KO-nudx6/7 cotyledons, biological rep2

city: Kasugai

first: Kazuya

last: Yoshimura

state: Aichi

address: 1200 Matsumoto-cho

department: Department of Food and Nutritional Science, College of Bioscience and Biotechnology,

institute: Chubu University

description: Gene expression data from 2-week-old double KO-nudx6/7 cotyledons

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix ATH1 GeneChip arrays for 16 h at 45°C according to Affymetrix protocols.

scan_protocol: Arrays were washed on an Affymetrix Fluidics Station 450 and measured for fluorescence intensity with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were processed using Affymetrix Gene Chip Operating Software (GCOS; Version 1.4.0.036).

organism: Arabidopsis thaliana

source_name: Two-week-old double KO-nudx6/7 cotyledons

label_protocol: Total RNA samples were reverse-transcribed, yielding double-strand cDNA, which was transcribed in vitro in the presence of biotin-labeled nucleotides with an IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA), and purified.

growth_protocol: Arabidopsis wild-type, KO-nudx6, KO-nudx7, and double KO-nudx6/7 plants were grown on MS medium in a growth chamber kept at 23°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness.

extract_protocol: Total RNA was semi-automatically purified from various organs of Arabidopsis plants using a QuickGene RNA cultured cell Kit and QuickGene-Mini80 (FUJIFILM corporation, Tokyo, Japan). The quality and purity of the RNA were confirmed for microarray analysis with an Ultrospec 2100 pro (GE Healthcare UK Ltd, Amersham Place, England).

treatment_protocol: At 2 weeks of age, cotyledons were collected as samples.

tag: ecotype

value: cotyledons

value: two weeks

tag: genotype/variation


title: BALB/c 6h post pneumococcal strain D39 infection, replicate 2

description:
replicate 2
B39-5

value: lung


title: Gp2 pos1

description:
biological replicate to sample 11
Sample 10

value: Gp2 positive mTECs


title: BALB/c 6h post pneumococcal strain BS71 infection, replicate 3

description:
replicate 3
B71-1

value: BALB/cOlaHsd


title: SAMPLE 46_PAE-iPS-4_p26

description: Gene expression in human iPS cell

source_name: PAE-iPS-4_passage 26

value: human iPS cell


title: SAMPLE 45_PAE-iPS-4_p26

description: Gene expression in human iPS cell


title: SAMPLE 50_PAE-iPS-5_p25

description: Gene expression in human iPS cell

source_name: PAE-iPS-5_passage 25


title: BALB/c 6h post pneumococcal strain D39 infection, replicate 3

description:
replicate 3
B39-2

value: D39, serotype 2, ST595


title: BALB/c 6h post pneumococcal strain BS71 infection, replicate 1

description:
replicate 1
B71-5


title: BALB/c 6h post pneumococcal strain D39 infection, replicate 5

description:
replicate 5
B39-6


title: double KO-nudx6/7 cotyledons, biological rep1


title: SAMPLE 47_UtE-iPS-7_p26

description: Gene expression in human iPS cell

value: human uterine endometrium (hUtE) cell


title: Gp2 neg3

description:
biological replicate to sample 7 and 8
Sample 9

value: Gp2 negative mTECs


title: Gp2 pos2

description:
biological replicate to sample 10
Sample 11


title: SAMPLE 43_PAE-iPS-1_p26

description: Gene expression in human iPS cell

source_name: PAE-iPS-1_passage 26


title: Gp2 neg2

description:
biological replicate to sample 7 and 9
Sample 8

source_name: Mouse mTECs


title: SAMPLE 42_PAE-iPS-1_p26

description: Gene expression in human iPS cell


title: KO-nudx7 cotyledons, biological rep2

description: Gene expression data from 2-week-old KO-nudx7 cotyledons

source_name: Two-week-old KO-nudx7 cotyledons


title: Gad1 neg2

description:
biological replicate to sample 12 and 14
Sample 13


title: BALB/c 6h post pneumococcal strain LgtSt215 infection, replicate 4

description:
replicate 4
B250-6

source_name: mouse lung

value: LgtSt215, serotype 19F, ST179


title: SAMPLE 44_KhES-2_p31

description: Gene expression in human embryonic stem cell

source_name: KhES-2_passage 31

value: human embryonic stem cell


title: BALB/c 6h post pneumococcal strain D39 infection, replicate 1

description:
replicate 1
B39-3


title: BALB/c 6h post pneumococcal strain LgtSt215 infection, replicate 3

description:
replicate 3
B250-3


title: KO-nudx7 cotyledons, biological rep1


title: KO-nudx6 cotyledons, biological rep2

description: Gene expression data from 2-week-old KO-nudx6 cotyledons

source_name: Two-week-old KO-nudx6 cotyledons


title: BALB/c 6h post pneumococcal strain LgtSt215 infection, replicate 2

description:
replicate 2
B250-1


title: KO-nudx6 cotyledons, biological rep1


title: Pdpn pos3

description:
biological replicate to sample 4 and 5
Sample 6

value: Pdpn positive mTECs


title: Gp2 neg1

description:
biological replicate to sample 8 and 9
Sample 7


title: SAMPLE 40_UtE-iPS-6_p25

description: Gene expression in human iPS cell

source_name: UtE-iPS-6_passage 25


title: Pdpn pos1

description:
biological replicate to sample 5 and 6
Sample 4


title: wild-type cotyledons, biological rep2

description: Gene expression data from 2-week-old wild-type cotyledons

source_name: Two-week-old wild-type cotyledons

value: wild type


title: BALB/c 6h post pneumococcal strain LgtSt215 infection, replicate 1

description:
replicate 1
B250-2


title: BALB/c 6h post pneumococcal strain BHN191 infection, replicate 5

description:
replicate 5
B248-5

value: BHN191, serotype 6B, ST138


title: SAMPLE 36_PAE-iPS-11_p28

description: Gene expression in human iPS cell


title: BALB/c 6h post pneumococcal strain BHN191 infection, replicate 4

description:
replicate 4
B248-3

value: 9 weeks


title: Pdpn neg2

description:
biological replicate to sample 1 and 3
Sample 2

value: Pdpn negative mTECs

value: FACS isolated medullary thymic epithelial cells


title: wild-type cotyledons, biological rep1

value: cotyledons


title: BALB/c 6h post pneumococcal strain BHN191 infection, replicate 2

description:
replicate 2
B248-4

value: female


title: BALB/c 6h post pneumococcal strain BHN191 infection, replicate 3

description:
replicate 3
B248-2

value: lung


title: SAMPLE 41_PAE-iPS-1_p26

description: Gene expression in human iPS cell

value: human placental artery-derived endothelial (hPAE) cell


title: Pdpn neg3

description:
biological replicate to sample 1 and 2
Sample 3


title: Pdpn pos2

description:
biological replicate to sample 4 and 6
Sample 5


title: cotton leaves_normal growth_mock control 6 DAI_rep2

city: Beijing

first: Wei

last: Liu

address: State Key Laboratory for Biology of Plant Diseases and Insect Pests,  Institute of Plant Protection, Chinese Academy of Agricultural Sciences,  100193, Beijing, People’s Republic of China

country: China

description: Gene expression data  from the process of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence

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

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

data_processing: The data were used RMA algorithm as normalization method.

organism: Gossypium hirsutum

source_name: The third-to-fourth cotton leaves, normal growth, mock control 6 DAI

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

growth_protocol: Plants were grown in growth chamber with a 14/10 hours photoperiod, 28℃/22℃.

extract_protocol: The total RNA was extracted from collected leaf samples using a modified CTAB method.

treatment_protocol: Three-to-four leaves stage cotton plants were pre-treated by chilling stress with the low temperatures of 16/12℃ day/night for a fixed time length of 3 days. While, the normal growth plants were sustained growing at optimal temperature of 28/20℃ day/night. And then, both chilling stress pre-treated and normal growth cotton plants were inoculated with Alternaria. alternata isolate A1. The mock inoculations were performed with sterilized water.

value: The third-to-fourth leaves

tag: variety

tag: developmental stage

value: Three-to-four leaves stage


title: Pdpn neg1

description:
biological replicate to sample 2 and 3
Sample 1


title: cotton leaves_normal growth_mock control 6 DAI_rep1

institute: Institute of Plant Protection, Chinese Academy of Agricultural Sciences


title: cotton leaves_normal growth_mock control 6 DAI_rep3


title: SAMPLE 38_UtE-iPS-6_p25

description: Gene expression in human iPS cell

value: human iPS cell


title: SAMPLE 39_UtE-iPS-6_p25

description: Gene expression in human iPS cell

value: human uterine endometrium (hUtE) cell


title: SAMPLE 52_MRC-iPS-16 (Fetch)_p13

description: Gene expression in human iPS cell

source_name: MRC-iPS-16 (Fetch)_passage 13

value: MRC-iPS-16 (Fetch)


title: SAMPLE 35_PAE-iPS-11_p28

description: Gene expression in human iPS cell


title: BALB/c 6h post pneumococcal strain BHN191 infection, replicate 1

description:
replicate 1
B248-1

value: BALB/cOlaHsd


title: BALB/c PBS-treated, 6h Tp, replicate-3

description:
replicate 3
Bpbs-3


title: SAMPLE 37_UtE-iPS-7_p26

description: Gene expression in human iPS cell

source_name: UtE-iPS-7_passage 26


title: SAMPLE 33_PAE-iPS-5_p25

description: Gene expression in human iPS cell


title: SAMPLE 31_AM-iPS-2 (Clary)_p27

description: Gene expression in human iPS cell

source_name: AM-iPS-2 (Clary)_passage 27

value: human amniotic ectoderm and mesoderm layer (hAM) cell

value: AM-iPS-2 (Clary)


title: cotton leaves_normal growth_6 DAI_rep2

source_name: The third-to-fourth cotton leaves, normal growth, 6 DAI


title: cotton leaves_normal growth_mock control 3 DAI_rep3

source_name: The third-to-fourth cotton leaves, normal growth, mock control 3 DAI


title: SAMPLE 26_KhES-2_p31

value: human embryonic stem cell


title: cotton leaves_normal growth_6 DAI_rep3


title: cotton leaves_normal growth_3 DAI_rep3

source_name: The third-to-fourth cotton leaves, normal growth, 3 DAI


title: SAMPLE 28_KhES-2_p32

source_name: KhES-2_passage 32


title: SAMPLE 32_AM-iPS-13 (Basil)_p19

description: Gene expression in human iPS cell

source_name: AM-iPS-13 (Basil)_passage 19

value: AM-iPS-13 (Basil)


title: cotton leaves_chilling stress pre-treated_ mock control 6 DAI_rep3

source_name: The third-to-fourth cotton leaves, chilling stress pre-treated, mock control 6 DAI


title: cotton leaves_chilling stress pre-treated_6 DAI_rep3

source_name: The third-to-fourth cotton leaves, chilling stress pre-treated, 6 DAI


title: cotton leaves_normal growth_6 DAI_rep1


title: SAMPLE 29_AM-iPS-2 (Clary)_p25

description: Gene expression in human iPS cell

source_name: AM-iPS-2 (Clary)_passage 25


title: cotton leaves_chilling stress pre-treated_6 DAI_rep1


title: cotton leaves_normal growth_3 DAI_rep2


title: SAMPLE 25_KhES-2_p31


title: SAMPLE 23_PAE-iPS-11_p23

description: Gene expression in human iPS cell

source_name: PAE-iPS-11_passage 23


title: SAMPLE 34_PAE-iPS-5_p25

description: Gene expression in human iPS cell

source_name: PAE-iPS-5_passage 25


title: SAMPLE 24_PAE-iPS-4_p26

description: Gene expression in human iPS cell

source_name: PAE-iPS-4_passage 26


title: cotton leaves_normal growth_mock control 3 DAI_rep2


title: SAMPLE 30_AM-iPS-2 (Clary)_p26

description: Gene expression in human iPS cell

source_name: AM-iPS-2 (Clary)_passage 26


title: SAMPLE 21_PAE-iPS-11_p23

description: Gene expression in human iPS cell


title: SAMPLE 20_PAE-iPS-5_p20

description: Gene expression in human iPS cell

source_name: PAE-iPS-5_passage 20


title: SAMPLE 22_PAE-iPS-11_p23

description: Gene expression in human iPS cell


title: cotton leaves_chilling stress pre-treated_ mock control 6 DAI_rep2


title: cotton leaves_chilling stress pre-treated_6 DAI_rep2


title: cotton leaves_chilling stress pre-treated_ mock control 3 DAI_rep3

source_name: The third-to-fourth cotton leaves, chilling stress pre-treated, mock control 3 DAI


title: cotton leaves_chilling stress pre-treated_ mock control 3 DAI_rep2


title: cotton leaves_chilling stress pre-treated_3 DAI_rep1

source_name: The third-to-fourth cotton leaves, chilling stress pre-treated, 3 DAI


title: UtE-iPS-11_p23_3

description: Gene expression in human iPS cell

source_name: UtE-iPS-11, passage 23

tag: cell-line name


title: SAMPLE 12_AM-iPS-8 (Thyme)_p21

description: Gene expression in human iPS cell

source_name: AM-iPS-8 (Thyme)_passage 21

value: AM-iPS-8 (Thyme)


title: UtE-iPS-11_p23_1

description: Gene expression in human iPS cell


title: SAMPLE 18_PAE-iPS-5_p20

description: Gene expression in human iPS cell


title: SAMPLE 19_PAE-iPS-5_p20

description: Gene expression in human iPS cell


title: UtE-iPS-11_p23_2

description: Gene expression in human iPS cell


title: cotton leaves_chilling stress pre-treated_3 DAI_rep2


title: SAMPLE 14_AM-iPS-8 (Thyme)_p22

description: Gene expression in human iPS cell

source_name: AM-iPS-8 (Thyme)_passage 22


title: SAMPLE 8_AM-iPS-3 (Sage)_p13

description: Gene expression in human iPS cell

source_name: AM-iPS-3 (Sage)_passage 13

value: AM-iPS-3 (Sage)


title: SAMPLE 5_KhES-1_p26

source_name: KhES-1_passage 26


title: SAMPLE 9_AM-iPS-6 (Hyssop)_p7

description: Gene expression in human iPS cell

source_name: AM-iPS-6 (Hyssop)_passage 7

value: AM-iPS-6 (Hyssop)


title: SAMPLE 6_AM-iPS-3 (Sage)_p11

description: Gene expression in human iPS cell

source_name: AM-iPS-3 (Sage)_passage 11


title: SAMPLE 7_AM-iPS-3 (Sage)_p12

description: Gene expression in human iPS cell

source_name: AM-iPS-3 (Sage)_passage 12


title: SAMPLE 11_AM-iPS-6 (Hyssop)_p10

description: Gene expression in human iPS cell

source_name: AM-iPS-6 (Hyssop)_passage 10


title: cotton leaves_chilling stress pre-treated_3 DAI_rep3


title: cotton leaves_chilling stress pre-treated_ mock control 3 DAI_rep1


title: SAMPLE 13_AM-iPS-8 (Thyme)_p22

description: Gene expression in human iPS cell


title: Exp024-2_H3K36me3_HSPC

status: Public on Oct 27 2015

type: SRA

city: Boston

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

country: USA

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description:
Mint-ChIP
This sample is missing raw data because the patient that did not consent for raw sequence deposition in a public database.

library_source: genomic

data_processing:
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: K562 cells and mouse YAC-1 cells were cultured in RPMI with 10% FCS, penicillin-streptomycin and L-glutamine. Pfeiffer, SKM-1 and Toledo were cultured in RPMI with 20% FCS, penicillin-streptomycin, L-glutamine and β-mercaptoethanol (3.5 µl in 1000 ml).

extract_protocol:
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Mint-ChIP: In vitro transcription, reverse transcription, PCR (see manuscript).

treatment_protocol: K562 cells were treated for 48 hours with C646 (25 µM), 48 hours with GSK126 (2 µM), or 96 hours with KDM5-C70 (5 µM). Pfeiffer, SKM-1 and Toledo were treated for 72 hours with GSK126 (1 µM).

tag: experiment

tag: histone modification

tag: mnase units

tag: treatment


title: Exp024-2_H3K27ac_HSPC


title: Exp024-2_H3K27me3_HSPC


title: SAMPLE 2_KhES-1_p26


title: SAMPLE 3_KhES-1_p26


title: SAMPLE 10_AM-iPS-6 (Hyssop)_p9

description: Gene expression in human iPS cell

source_name: AM-iPS-6 (Hyssop)_passage 9


title: SAMPLE 1_KhES-1_p26


title: SAMPLE 4_KhES-1_p26


title: ectopic endometrium from patient 22371

city: Nanjing City

first: Cheng

last: Zhou

address: Hanzhong Road no.140

institute: Nanjing Medical University

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_3
Biological replicate 3 of 3.Ectopic endometrium,isolated away from areas of obvious uterine adenomyoma of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.

hyb_protocol: Labeled cRNAs and hybridization buffer (2X GEx Hyb Buffer and Formamide) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Agilent Feature Extraction software version 10.7 (Arraystar, USA) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Arraystar).

source_name: ectopic endometrium

label_protocol: Each sample was amplified and transcribed into fluorescent (Cy5 and  Cy3-dCTP) labeled cRNA along the entire length of the transcripts without 3′  bias using a reaction with random primers.

growth_protocol: Endometrial samples were collected from women of childbearing years undergoing hysterectomies for adenomyosis. Specimens of ectopic endometria were isolated away from areas of obvious uterine adenomyoma. Eutopic endometria were full-thickness, 1-cm biopsies of the uterine wall.

extract_protocol: Briefly, total RNA was extracted   using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the  manufacturer’s instructions and purified to remove rRNA using the  NucleoSpin® RNA Clean-up kit (Macherey-Nagel, Cat # 740.948.250).

tag: disease stage

value: adenomyosis

tag: position

value: ectopic

tag: patient

source_name: eutopic endometrium

value: eutopic


title: eutopic endometrium from patient 22371

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_3
Biological replicate 3 of 3. Control eutopic endometrium, harvested from the uterine wall of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.


title: UNTREATED 5

city: Gainesville

first: cuong

last: nguyen

address: 2015 SW 16th Ave

institute: University of Florida

description:
6071811043_K
replicate 5

hyb_protocol: Labeled cRNA was hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina).

scan_protocol: Standard Illumina scanning protocol using Illumina BeadArray Reader

data_processing: Microarray data were normalized via the lumi package in R, using the variance stabilizing transformation of the package and robust spline normalization.

source_name: Human submandibular gland (HSG) cells

label_protocol: Total RNA was isolated and labeled with biotin using Target Amp cDNA synthesis kit (Epicenter).

growth_protocol: Human salivary glands cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum

treatment_protocol: Human salivary gland cells were cultured in complete media and treated with recombinant IL-22 at 100 ng/mL for 45 minutes

value: cultured salivary gland cells

tag: agent

value: control


title: UNTREATED 3

description:
6071811043_I
replicate 3

extract_protocol: Total RNA was isolated and labeled with biotin using Target Amp cDNA synthesis kit (Epicenter).


title: TREATED 6

description:
6071811043_L
replicate 6


title: UNTREATED 6

description:
6071811043_D
replicate 6


title: ectopic endometrium from patient 22506

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_1
Biological replicate 1 of 3. Ectopic endometrium, isolated away from areas of obvious uterine adenomyoma of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.


title: cotton leaves_normal growth_mock control 3 DAI_rep1

source_name: The third-to-fourth cotton leaves, normal growth, mock control 3 DAI

tag: tissue

value: The third-to-fourth leaves

value: Three-to-four leaves stage


title: TREATED 2

description:
6071811043_J
replicate 2


title: TREATED 4

description:
6071811043_G
replicate 4


title: UNTREATED 1

description:
6071811043_A
replicate 1


title: TREATED 1

description:
6071811043_F
replicate 1


title: ectopic endometrium from patient 24594

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_2
Biological replicate 2 of 3.Ectopic endometrium,isolated away from areas of obvious uterine adenomyoma of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.


title: UNTREATED 4

description:
6071811043_B
replicate 4


title: TREATED 5

description:
6071811043_H
replicate 5


title: eutopic endometrium from patient 24594

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_2
Biological replicate 2 of 3. Control eutopic endometrium, harvested from the uterine wall of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.


title: UNTREATED 2

description:
6071811043_E
replicate 2


title: TREATED 3

description:
6071811043_C
replicate 3


title: OCI-Ly3 siFOXP1_308 vs siCtrl replicate 3

city: Kubang Kerian

first: Kah Keng

last: Wong

state: Kelantan

address: School of Medical Sciences, Health Campus

department: Department of Immunology

country: Malaysia

institute: Universiti Sains Malaysia

description: Biological replicate 3 of 3. OCI-Ly3 cells treated with siFOXP1_308, harvested after 48 hours

hyb_protocol: The labeled cRNAs were hybridized to the Agilent-014850 Whole Human Genome Microarray 4x44K G4112F according to manusfacturer's instructions (Agilent Technologies).

scan_protocol: Scanned on Agilent Technologies Scanner G2505C.

data_processing: Feature Extraction (Agilent, version 10.5.1.1), which applied intra-array linear and loess normalizations. Processed slide image data was then imported to GeneSpring GX (Agilent, version 11.5) in which data were quality control-checked and normalized.

source_name: OCI-Ly3 cells silenced with siFOXP1_308 replicate 3

label_protocol: Total RNA (500 ng) was used to generate Cy-3-(siFOXP1 cells) or Cy-5-labeled (siCtrl-treated cells) cRNAs  according to manusfacturer's instructions (Agilent Technologies).

growth_protocol: DLBCL cell lines were maintained in RPMI 1640 media supplemented with 10% foetal calf serum, 2 mM glutamine and antibiotics (streptomycin [50 μg/ml] and penicillin [50 U/ml]) at 37oC and 5% CO2.

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Transient silencing of FOXP1 expression was carried out using Nucleofection in an Amaxa Nuclefector II Device. 2 x 106 cells were resuspended in Cell Line Nucleofector Kit L with 1 µM FOXP1-targeting siRNA (HSS178308 or HSS178309 Stealth siRNA, Invitrogen) or negative control (Stealth Low GC Negative Control Duplex, Invitrogen). Cells were electroporated using programme X-001, and harvested after 48 hours.

tag: cell line

tag: subtype

value: ABC-DLBCL

source_name: OCI-Ly3 cells silenced with control siRNA 308 replicate 3


title: eutopic endometrium from patient 22506

description:
US10313827_253831410122_S01_GE2_107_Sep09_1_1
Biological replicate 1 of 3. Control eutopic endometrium, harvested from the uterine wall of adenomyosis.
The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for sample 22506N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_1 file corresponds to raw data for 22506J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_2 file corresponds to raw data for 24594J; The gProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371N. The rProcessedSignal column of US10313827_253831410122_S01_GE2_107_Sep09_1_3 file corresponds to raw data for 22371J.


title: OCI-Ly3 siFOXP1_309 vs siCtrl replicate 3

description: Biological replicate 3 of 3. OCI-Ly3 cells treated with siFOXP1_309, harvested after 48 hours

source_name: OCI-Ly3 cells silenced with siFOXP1_309 replicate 3

source_name: OCI-Ly3 cells silenced with control siRNA 309 replicate 3


title: OCI-Ly3 siFOXP1_308 vs siCtrl replicate 1

description: Biological replicate 1 of 3. OCI-Ly3 cells treated with siFOXP1_308, harvested after 48 hours

source_name: OCI-Ly3 cells silenced with siFOXP1_308 replicate 1

source_name: OCI-Ly3 cells silenced with control siRNA 308 replicate 1


title: OCI-Ly3 siFOXP1_309 vs siCtrl replicate 1

description: Biological replicate 1 of 3. OCI-Ly3 cells treated with siFOXP1_309, harvested after 48 hours

source_name: OCI-Ly3 cells silenced with siFOXP1_309 replicate 1

source_name: OCI-Ly3 cells silenced with control siRNA 309 replicate 1


title: OCI-Ly3 siFOXP1_308 vs siCtrl replicate 2

description: Biological replicate 2 of 3. OCI-Ly3 cells treated with siFOXP1_308, harvested after 48 hours

source_name: OCI-Ly3 cells silenced with siFOXP1_308 replicate 2

source_name: OCI-Ly3 cells silenced with control siRNA 308 replicate 2


title: HBL-1 siFOXP1_309 vs siCtrl replicate 3

description: Biological replicate 3 of 3. HBL-1 cells treated with siFOXP1_309, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_309 replicate 3

source_name: HBL-1 cells silenced with control siRNA 309 replicate 3


title: HBL-1 siFOXP1_309 vs siCtrl replicate 1

description: Biological replicate 1 of 3. HBL-1 cells treated with siFOXP1_309, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_309 replicate 1

source_name: HBL-1 cells silenced with control siRNA 309 replicate 1


title: HBL-1 siFOXP1_309 vs siCtrl replicate 2

description: Biological replicate 2 of 3. HBL-1 cells treated with siFOXP1_309, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_309 replicate 2

source_name: HBL-1 cells silenced with control siRNA 309 replicate 2


title: HBL-1 siFOXP1_308 vs siCtrl replicate 3

description: Biological replicate 3 of 3. HBL-1 cells treated with siFOXP1_308, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_308 replicate 3

source_name: HBL-1 cells silenced with control siRNA 308 replicate 3


title: HBL-1 siFOXP1_308 vs siCtrl replicate 1

description: Biological replicate 1 of 3. HBL-1 cells treated with siFOXP1_308, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_308 replicate 1

source_name: HBL-1 cells silenced with control siRNA 308 replicate 1


title: K422 siFOXP1_309 vs siCtrl replicate 1

description: Biological replicate 1 of 3. K422 cells treated with siFOXP1_309, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_309 replicate 1

value: GCB-DLBCL

source_name: K422 cells silenced with control siRNA 309 replicate 1


title: OCI-Ly3 siFOXP1_309 vs siCtrl replicate 2

description: Biological replicate 2 of 3. OCI-Ly3 cells treated with siFOXP1_309, harvested after 48 hours

source_name: OCI-Ly3 cells silenced with siFOXP1_309 replicate 2

source_name: OCI-Ly3 cells silenced with control siRNA 309 replicate 2


title: K422 siFOXP1_309 vs siCtrl replicate 2

description: Biological replicate 2 of 3. K422 cells treated with siFOXP1_309, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_309 replicate 2

source_name: K422 cells silenced with control siRNA 309 replicate 2


title: K422 siFOXP1_308 vs siCtrl replicate 3

description: Biological replicate 3 of 3. K422 cells treated with siFOXP1_308, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_308 replicate 3

source_name: K422 cells silenced with control siRNA 308 replicate 3


title: HBL-1 siFOXP1_308 vs siCtrl replicate 2

description: Biological replicate 2 of 3. HBL-1 cells treated with siFOXP1_308, harvested after 48 hours

source_name: HBL-1 cells silenced with siFOXP1_308 replicate 2

source_name: HBL-1 cells silenced with control siRNA 308 replicate 2


title: DB siFOXP1_309 vs siCtrl replicate 3

description: Biological replicate 3 of 3. DB cells treated with siFOXP1_309, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_309 replicate 3

value: DB

source_name: DB cells silenced with control siRNA 309 replicate 3


title: cotton leaves_chilling stress pre-treated_ mock control 6 DAI_rep1

description: Gene expression data  from the process of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence

source_name: The third-to-fourth cotton leaves, chilling stress pre-treated, mock control 6 DAI


title: DB siFOXP1_308 vs siCtrl replicate 3

description: Biological replicate 3 of 3. DB cells treated with siFOXP1_308, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_308 replicate 3

source_name: DB cells silenced with control siRNA replicate 3


title: K422 siFOXP1_308 vs siCtrl replicate 1

description: Biological replicate 1 of 3. K422 cells treated with siFOXP1_308, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_308 replicate 1

source_name: K422 cells silenced with control siRNA 308 replicate 1


title: K422 siFOXP1_309 vs siCtrl replicate 3

description: Biological replicate 3 of 3. K422 cells treated with siFOXP1_309, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_309 replicate 3

source_name: K422 cells silenced with control siRNA 309 replicate 3


title: DB siFOXP1_309 vs siCtrl replicate 1

description: Biological replicate 1 of 3. DB cells treated with siFOXP1_309, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_309 replicate 1

source_name: DB cells silenced with control siRNA 309 replicate 1


title: K422 siFOXP1_308 vs siCtrl replicate 2

description: Biological replicate 2 of 3. K422 cells treated with siFOXP1_308, harvested after 48 hours

source_name: K422 cells silenced with siFOXP1_308 replicate 2

source_name: K422 cells silenced with control siRNA 308 replicate 2


title: DB siFOXP1_308 vs siCtrl replicate 2

description: Biological replicate 2 of 3. DB cells treated with siFOXP1_308, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_308 replicate 2

source_name: DB cells silenced with control siRNA replicate 2


title: 197RDB0242

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. All analyses were performed using R software.

source_name: CRC_FFPE_healthy control

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: Representative sections of fresh tissue specimens were flash frozen in liquid nitrogen and stored at −80°C until RNA isolation. RNA was purified from tissue sections containing >80% epithelial tumor tissue using RNeasy (QIAGEN, Valencia, CA) according to manufacturer’s instructions.

tag: sample type

value: FFPE colon cancer tissue

tag: Stage

value: NA; healthy control


title: DB siFOXP1_309 vs siCtrl replicate 2

description: Biological replicate 2 of 3. DB cells treated with siFOXP1_309, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_309 replicate 2

source_name: DB cells silenced with control siRNA 309 replicate 2


title: DB siFOXP1_308 vs siCtrl replicate 1

description: Biological replicate 1 of 3. DB cells treated with siFOXP1_308, harvested after 48 hours

source_name: DB cells silenced with siFOXP1_308 replicate 1

source_name: DB cells silenced with control siRNA replicate 1


title: BAL Cells biological rep30_SA

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

institute: University of Pittsburgh

description: Bronchial alveolar lavage cells

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4X44K array slides

data_processing:
The data was extracted using the Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies)
The data set was normalized by cyclic-LOESS with use of Bioconductor package as described previously (Wu W et. al. 2005). Probes which did not map to an Entrez ID were excluded

source_name: SA

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.  Labeled RNA   was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays.

extract_protocol:
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011).
Total RNA was extracted from BALF cells the suspended in Trizol solution using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.

tag: cell type

value: Bronchial alveolar lavage cells

tag: group

value: SA


title: cotton leaves_normal growth_3 DAI_rep1

source_name: The third-to-fourth cotton leaves, normal growth, 3 DAI

tag: variety

tag: developmental stage


title: BAL Cells biological rep27_SA

description: Bronchial alveolar lavage cells

hyb_protocol: RNA  was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays


title: SAMPLE 27_KhES-2_p32

description: Gene expression in human embryonic stem cell

source_name: KhES-2_passage 32

value: human embryonic stem cell

tag: passage number


title: BAL Cells biological rep23_SA

description: Bronchial alveolar lavage cells


title: 197RDB0336


title: BAL Cells biological rep26_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep24_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep20_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep25_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep28_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep22_SA

description: Bronchial alveolar lavage cells


title: 197RDB0414

source_name: CRC_FFPE_stage I


title: BAL Cells biological rep19_SA

description: Bronchial alveolar lavage cells


title: 197RDB0254


title: 197RDB0365

source_name: CRC_FFPE_stage II


title: BAL Cells biological rep21_SA

description: Bronchial alveolar lavage cells


title: 197RDB0081


title: BAL Cells biological rep16_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep17_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep14_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep18_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep12_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep15_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep13_SA

description: Bronchial alveolar lavage cells


title: 197RDB0183

source_name: CRC_FFPE_stage III


title: 197RDB0363


title: BAL Cells biological rep11_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep10_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep8_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep9_SA

description: Bronchial alveolar lavage cells


title: 197RDB0299


title: 197RDB0271


title: 197RDB0419


title: 197RDB0169


title: 197RDB0070


title: BAL Cells biological rep7_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep2_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep6_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep1_SA

description: Bronchial alveolar lavage cells

source_name: nonSA


title: BAL Cells biological rep4_SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep3_SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep53_not SA

description: Bronchial alveolar lavage cells

value: not SA


title: 197RDB0002

source_name: CRC_FFPE_stage IV


title: 197RDB0333


title: 197RDB0211


title: BAL Cells control biological rep51_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0073


title: BAL Cells control biological rep48_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep50_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells biological rep5_SA

description: Bronchial alveolar lavage cells


title: 197RDB0264


title: BAL Cells control biological rep52_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep47_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep45_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0432


title: BAL Cells control biological rep44_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep43_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0170


title: BAL Cells control biological rep42_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep41_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0280


title: 197RDB0318


title: BAL Cells control biological rep33_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep32_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0158


title: 197RDB0194


title: BAL Cells control biological rep37_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep39_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep38_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep35_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0247


title: BAL Cells control biological rep20_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0184


title: BAL Cells control biological rep36_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep21_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep40_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep19_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep34_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep17_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep14_not SA

description: Bronchial alveolar lavage cells


title: 197RDBCJ0058


title: 197RDB0249


title: 197RDB0208


title: BAL Cells biological rep29_SA

description: Bronchial alveolar lavage cells


title: 197RDB0163


title: BAL Cells control biological rep11_not SA

description: Bronchial alveolar lavage cells


title: 197RDBCJ0061


title: BAL Cells control biological rep12_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep16_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep13_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep8_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep10_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep9_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0009


title: 197RDB0011


title: BAL Cells control biological rep5_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep3_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep7_not SA

description: Bronchial alveolar lavage cells


title: 197RDB0077


title: 197RDB0289


title: BAL Cells control biological rep4_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep6_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep2_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep31_NC

description: Bronchial alveolar lavage cells

source_name: Control

value: NC


title: 197RDBCJ0065


title: BAL Cells control biological rep49_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep29_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep30_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep1_not SA

description: Bronchial alveolar lavage cells


title: 197RDBCJ0053


title: BAL Cells control biological rep28_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep26_NC

description: Bronchial alveolar lavage cells


title: 197RDB0010


title: BAL Cells control biological rep27_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep24_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep25_NC

description: Bronchial alveolar lavage cells


title: 197RDB0119


title: BAL Cells control biological rep18_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep21_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep46_not SA

description: Bronchial alveolar lavage cells


title: 197RDBCJ0057


title: 197RDB0253


title: BAL Cells control biological rep19_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep16_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep15_NC

description: Bronchial alveolar lavage cells


title: 197RDBCJ0056


title: BAL Cells control biological rep22_NC

description: Bronchial alveolar lavage cells


title: 197RDB0004


title: 197RDB0207


title: 197RDB0281


title: BAL Cells control biological rep13_NC

description: Bronchial alveolar lavage cells


title: 197RDB0005


title: BAL Cells control biological rep10_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep23_NC

description: Bronchial alveolar lavage cells


title: 197RDB0107


title: 197RDB0212


title: BAL Cells control biological rep17_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep12_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep20_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep9_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep14_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep7_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep11_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep8_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep6_NC

description: Bronchial alveolar lavage cells


title: 197RDB0160


title: 197RDB0293


title: BAL Cells control biological rep18_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep15_not SA

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep4_NC

description: Bronchial alveolar lavage cells


title: Lung_HBW_Rep16

city: Edmonton

first: James

middle: Michael

last: Wilkinson

state: Alberta

address: Ag/For Building

department: Agriculture, Food, and Nutritional Science

country: Canada

institute: University of Alberta

hyb_protocol: 825 ng of each dye-labeled aRNA was hybridized for 17 h to Porcine V2 Gene Expression 4x44 Microarrays (Agilent Technologies). Microarray slides were washed using a Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's reccommended protocols.

scan_protocol: Hybridization signal intensities were quantified using GenePixPro v7.0 software (Molecular Devices) using the Autoscan function.

data_processing: Background subtraction was performed on the raw median expression data from each array feature using a ‘norm exp’ method. Next, the background-subtracted expression data were normalized both within array (using a global loess method) and between arrays (using a scale normalization method). The ‘limma simple’ algorithm was then used to assess differential gene expression between the HBW and LBW groups. A fold change threshold of ≥1.75 and a P value of ≤0.05 were set for genes to be classified as differentially expressed. The differential expression of specific genes of interest was validated using an RT-qPCR approach.

organism: Sus scrofa

source_name: Lung from HBW pig

label_protocol: RNA from the cranial lobe of individual animals was hybridized to separate arrays together with a common reference that included RNA from 3 swine tissues (lung, lymph node, and thymus); a total of 32 hybridizations. A 1 μg amount of total RNA was reverse transcribed into cDNA, which was then used to synthesize antisense RNA (aRNA) by in vitro transcription. Two micrograms of aRNA were then labeled in an ozone-free environment with either Cy3 or Cy5 using the Universal Linkage System (ULS). All these processes used the RNAampULSe kit (Kreatech Diagnostics; Amsterdam, The Netherlands). Labeled aRNAs were purified using the PicoPure RNA Isolation kit (Life Technologies; Carlsbad, USA)

growth_protocol: Litters for the study were selected at birth from a farm in Saskatchewan, Canada. Litter eligibility was based on the average weight of all live and stillborn piglets in the litter. High birth weight (HBW) and low birth weight (LBW) litters from parity 1-2 dams were selected based on being ± 0.7 standard deviations from the farm’s historical mean litter birth weight for a given litter size and parity. Two male piglets with birth weights close to the mean for their litter of origin were then selected from each HBW and LBW litter. At 4 weeks of age, the piglets were transported from the farm to a biosafety-level 2 animal care facility at the University of Saskatchewan. All piglets were confirmed negative for antibodies to swine influenza A virus prior to transportation. A further RT-PCR assay for influenza was performed on nasal swabs taken after arrival at the facility, and again, all piglets were confirmed negative for the virus. Pigs were acclimated at the facility for 5 days prior to influenza challenge.

extract_protocol: Total RNA was extracted from lung tissue from the cranial lobe using the All Prep DNA/RNA mini kit (Qiagen; Hilden, Germany) according to the manufacturer’s recommended protocol. Nucleic acids were quantified by spectrophotometry using a Nanodrop ND 2000 (Thermo Fisher Scientific; Waltham, USA). RNA quality was assessed using an Agilent Bioanalyzer (Agilent Technologies; Santa Clara, USA). The mean RNA Integrity Number (RIN) sample value was 8.2 ± 0.09. One pig from each sow was randomly selected for microarray analysis, resulting in a total of 32 animals (16 HBW and 16 LBW).

treatment_protocol: Pigs were inoculated intratracheally with 1x10^7 PFU of SIV strain A/swine/Texas/4199-2/98 H3N2 (TX98) while anaesthetized, and kept in sternal recumbency for 10 minutes. Twice daily during the challenge period, rectal temperatures were taken and the animals were scored for clinical signs of the respiratory disease caused by influenza. Pigs were euthanized 48 hours post-inoculation by pentobarbital injection. Lungs and the attached trachea were removed from the animal and the percentage of lung area affected by consolidation was evaluated and used to select a subset of 'resistant' (RES) and 'susceptible' (SUS) pigs for a separate analysis. Tissue samples from each lobe were then snap-frozen in liquid nitrogen and stored at -80°C for gene expression studies.

tag: animal id

tag: birth weight category

value: HBW

tag: resistance category

tag: gilt id

tag: age

value: 4 weeks old

source_name: Pool of Lung, tonsil, and lymph node tissue from 8 HBW and 8 LBW pigs


title: BAL Cells control biological rep1_NC

description: Bronchial alveolar lavage cells


title: IMR-32 GFP d7

city: Cologne

first: Fakhera

last: Ikram

state: NRW

address: Kerpener str. 62

department: Pediatric Oncology and Hematology

institute: University Children´s Hospital

description: Gene expression after 7 days in GFP-induced IMR-32

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: After washing and scanning, resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.

data_processing: Data normalization using the quantile algorithm, Reference: G. K. Smyth. Limma: linear models for microarray data. In: R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, 2005. pp. 397-420.

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: Cells were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA). Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

tag: transgene

value: GFP

tag: time point (day)


title: 197RDBCJ0052


title: 197RDB0003


title: BAL Cells control biological rep2_NC

description: Bronchial alveolar lavage cells


title: IMR-32 GFP d2

description: Gene expression after 2 days in GFP-induced IMR-32


title: BAL Cells control biological rep3_NC

description: Bronchial alveolar lavage cells


title: BAL Cells control biological rep5_NC

description: Bronchial alveolar lavage cells


title: IMR-32 TFAP2B d2

description: Gene expression after 2 days in TFAP2B-induced IMR-32


title: 197RDB0190


title: 197RDB0291


title: 197RDB0157


title: 197RDB0269


title: IMR-32 TFAP2B d7

description: Gene expression after 7 days in TFAP2B-induced IMR-32


title: Lung_HBW_Rep14


title: Lung_HBW_Rep13


title: Lung_HBW_Rep11

value: Susceptible


title: preterm_rep5

city: Guangzhou

first: Liang

last: Zhang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

hyb_protocol: cRNAs were fragmented and hybridized on SurePrint G3 Human GE 8x60K v2 Microarray Chips using Agilent Gene Expression Hybridization Kit.

scan_protocol: The fluorescence intensities at 635 (Cy5) and 532 (Cy3) nm were scanned by an Agilent microarray scanner (Agilent,USA ). Microarray scan data was extracted by using Agilent Feature Extraction Software.

data_processing: Signals were normalized by using loess normalization.

source_name: pooled controls who delivered at term

label_protocol: Sample total RNAs were reverse transcribed to synthesize cDNAs, then transcripted into antisense cRNAs, which were labeled with Cy3-CTP.  Pooled controls were labled with cy5-CTP.

growth_protocol: Placental Tissue samples were obtained immediately after delivery. Pieces of villous tissue (0.5×0.5×0.5 cm), approximately 2 cm beside the umbilical cord insertion, from the middle layer of placenta midway between maternal and fetal surfaces from different lobes were excised, excluding sites of haemorrhage , infarction, and fibrin deposition. To avoid RNA degradation, tissues were immediately stored in 1.0ml RNAstore Reagent (CWbiotech Company, China), and then stored at -80℃ until use.

extract_protocol: We used RNAiso Plus (Takara, China) to isolate RNA from placental samples in accordance with the manufacturer’s instructions.

value: pooled-sample reference

tag: subject status

value: controls who delivered at term (>36 weeks)

tag: tissue

value: placental tissue

source_name: delivery at preterm_placental tissue

value: controls who delivered preterm (<34 weeks)


title: Lung_HBW_Rep15


title: preterm_rep1


title: Lung_HBW_Rep10


title: 197RDB0221


title: 197RDB0067


title: 197RDBCJ0047


title: Lung_HBW_Rep12


title: Lung_HBW_Rep9


title: Lung_HBW_Rep7


title: Lung_HBW_Rep8


title: Lung_HBW_Rep3


title: 197RDB0268


title: Lung_HBW_Rep6

value: Resistant


title: 197RDB0195


title: 197RDB0192


title: 197RDB0219


title: 197RDB0263


title: at_term_rep2

source_name: delivery at term_placental tissue


title: at_term_rep1


title: preterm_rep3


title: at_term_rep3


title: preterm_rep2


title: Lung_HBW_Rep4


title: preterm_rep4


title: at_term_rep5


title: 197RDB0012


title: 197RDB0006


title: 197RDB0069


title: Lung_HBW_Rep1


title: LOPE_rep6

source_name: LOPE_placental tissue

value: patients with late-onset (>36 weeks) preeclampsia (LOPE)


title: 197RDB0162

value: FFPE colon cancer tissue


title: Lung_HBW_Rep2


title: Lung_HBW_Rep5


title: Lung_LBW_Rep12

source_name: Lung from LBW pig

value: LBW


title: LOPE_rep5


title: at_term_rep4


title: YAP shRNA 1 - 3

city: Basel

first: Yann

last: Abraham

address: Postfach

department: NIBR/DMP

country: Switzerland

institute: Novartis Pharma AG

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed using a custom Bioconductor script based on the affycoretools package

source_name: HuCCT1 cholangiocarcinoma cell line

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 - Affymetrix Hybridization control kit (including B2)

growth_protocol: HuCCT1 cells were maintained in RPMI-1640 supplemented with 10% (v/v) Tetracycline-free fetal bovine serum, 2mM L-Glutamine, 1mM sodium pyruvate and 0.1mM MEM non-essential amino acids

extract_protocol: Total RNA was isolated from cells using the RNeasy Plus mini kit according to the manufacturer’s instructions (Qiagen). RNA quality was assessed with the RNA 6000 Nano Kit (Agilent). 500 µg RNA of each sample were reverse-transcribed using the high capacity cDNA reverse transcription kit (Applied Biosystems)

treatment_protocol: To induce expression of shRNA cells were treated with 100ng/ml DOX (Sigma) 3 days before seeding for an experiment

tag: vector

value: YAP shRNA 1

tag: treatment

value: Doxicycline


title: Lung_LBW_Rep14


title: Lung_LBW_Rep16


title: LOPE_rep8

tag: sample type


title: LOPE_rep7


title: control shRNA - 4

value: control shRNA


title: LOPE_rep2


title: YAP shRNA 1 - 1


title: YAP shRNA 1 - 2


title: YAP shRNA 1 - 4


title: Lung_LBW_Rep15


title: LOPE_rep4


title: Lung_LBW_Rep13


title: EOPE_rep6

source_name: EOPE_placental tissue

value: patients with early-onset (<34 weeks) preeclampsia (EOPE)


title: LOPE_rep3


title: Lung_LBW_Rep10


title: control shRNA - 2


title: control shRNA - 3


title: control shRNA - 1


title: LOPE_rep1


title: Lung_LBW_Rep11


title: EOPE_rep7


title: EOPE_rep5


title: EOPE_rep1


title: EOPE_rep2


title: EOPE_rep4


title: Lung_LBW_Rep9


title: YAPS127A - 3

growth_protocol: HuCCT1 cells were maintained in RPMI-1640 supplemented with 10% (v/v) fetal bovine serum, 2mM L-Glutamine, 1mM sodium pyruvate and 0.1mM MEM non-essential amino acids


title: Lung_LBW_Rep7


title: YAPS127A - 4


title: Lung_LBW_Rep2


title: YAPS127A - 1


title: YAPS127A - 5


title: Lung_LBW_Rep8


title: Lung_LBW_Rep3


title: empty vector - 2

value: empty vector


title: REK 3D, BET+UVB A

status: Public on Oct 26 2015

city: Kuopio

first: Leena

last: Rauhala

address: Yliopistonranta 1 E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: 2-week-old REK 3D cultures with a well-formed epidermal layer; no feeder cells (keratinocytes only)

hyb_protocol: 750 ng of each cRNA sample was hybridized into Illumina’s Sentrix RatRef-12 v1.0 Expression BeadChips at 58°C overnight according to manufacturer’s instructions (Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide).

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor = 1, PMT = 520, Filter = 100%) using 1μg/ml Cyanine3-streptavidine for detection. The numerical data were extracted with GenomeStudio version 2009.2 (Gene Expression Module version 1.5.4) without normalization or background subtraction.

data_processing: Analysis of the microarray data was performed using the R statistical software version 2.11 with associated libraries from Bioconductor project version 2.6. The data was normalized using VST transformation and RSN normalization used as a standard approach for Illumina arrays. Probe sets that were not linked to any known or predicted human gene were also filtered out. Linear Models for Microarray Data (limma) package using linear model fitting for statistical testing with empirical Bayes variance smoothing procedure was applied to the detection of differentially expressed genes. Obtained p-values were corrected for multiple testing using the Benjamini & Hochberg false discovery rate procedure.

label: Biotinylated cRNA hybridization detected by Cy3-streptavidin

organism: Rattus norvegicus

source_name: Rat epidermal keratinocyte, betaine 10 mM + UVB 30 mJ/cm2

label_protocol: Global gene expression was analyzed at the Finnish DNA Microarray centre (Turku, Finland), using RatRef-12 v1.0 Expression BeadChip (Illumina). Briefly: 400 ng of total RNA was amplified with Illumina TotalPrep RNA Amplification kit (Ambion/Life Technologies). In vitro transcription and cRNA biotinylation was performed overnight after which concentration measurements and quality control were conducted using Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and BioRad’s Experion electrophoresis station (BioRad), respectively.

growth_protocol: Cell line originally isolated by Baden & Kubilus (J. Invest. Dermatol. 80:124-30, 1983).

extract_protocol: Samples were collected 24 h after the UVB irradiation. Each culture insert was washed twice with ice-cold PBS prior to extracting the epidermis. Briefly: the insert was cut with a scalpel from its holder and the epidermal layer was separated from the insert membrane and the collagen using fine tweezers. The epidermis was immediately snap-frozen in liquid nitrogen and stored at -70°C until total RNA extraction. The frozen samples were homogenized in Lysing Matrix D tubes (MP Biomedicals) with a FastPrep homogenizer, (Savant, Thermo Fisher Scientific Inc.) and total RNA was extracted using High Pure RNA Tissue Kit (Roche) according to the manufacturer’s protocol. The purity and integrity of the RNA were determined using RNA Nano Chip on a 2100 Bioanalyzer (Agilent Technologies) prior to sending the samples for analysis.

treatment_protocol: The 3D cultures were divided in four treatment groups with three replicates in each: control, betaine (10 mM), UVB (30 mJ/cm2) and betaine + UVB. Betaine was added to the cultures for 11 days, starting from day 4 until sample collection. UVB exposure was performed 24 h prior to sample collection for 2-week-old 3D cultures with a well-formed epidermal layer. The UVB exposure protocol has been described in detail by Rauhala et al. (J. Biol. Chem. 288:17999-18012).

tag: cell type

value: epidermal keratinocyte

value: betaine 10 mM + UVB 30 mJ/cm2


title: Lung_LBW_Rep4

value: 4 weeks old


title: REK 3D, UVB C

source_name: Rat epidermal keratinocyte, UVB 30 mJ/cm2 (no betaine)

value: UVB 30 mJ/cm2 (no betaine)


title: empty vector - 4


title: Lung_LBW_Rep1


title: EOPE_rep3

value: pooled-sample reference


title: empty vector - 1


title: Lung_LBW_Rep5


title: YAPS127A - 2


title: Lung_LBW_Rep6


title: REK 3D, BET+UVB C


title: REK 3D, BET+UVB B


title: REK 3D, UVB B


title: empty vector - 3


title: REK 3D, BET B

source_name: Rat epidermal keratinocyte, betaine 10 mM (mock UVB)

value: betaine 10 mM (mock UVB)


title: REK 3D, UVB A


title: REK 3D, BET C


title: REK 3D, CTRL A

source_name: Rat epidermal keratinocyte, CTRL (mock UVB, no betaine)

value: CTRL (mock UVB, no betaine)


title: REK 3D, CTRL C


title: CON_PLUS_DOX_24h_B

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

institute: The Institute of Cancer Research

hyb_protocol: Cy 3 labelled cRNA was co-hybridized with Cy5 labelled Universal Mouse Reference RNA

scan_protocol: The arrays were scanned using an Agilent Technologies Scanner G2505C US94400327, using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.7.3.1 and extraction protocol GE2_107_Sep09 and grid file 028005_D_F_20110722 or 028005_D_F_20110406.

data_processing: Background subtracted data for sample and reference were entered Arraytools analysis software. Lowess normalization was applied to the samples.

label_protocol: Quick Amp Labeling protocol

growth_protocol:
cultured intestinal organoids established from mice expressing a Doxycycline-inducible mutant beta-catenin (Tet-O-”1-89-beta-Catenin)
[Generation of tet-O-β-catenin mutant mice and organoid cultures] The pBS31 flp-in vector was engineered to contain the following four cassettes. The pgk promoter followed by an ATG and an FRT site. A splice acceptor double polyA cassette derived from the ROSA26 target vector. The CMV minimal promoter containing tetracycline response operator sequences from pTETOP and an SV40 polyA signal. This aid rapid cloning of longer cDNAs, pBS31pgkATGFRTTet-O was converted into a gateway destination vector at the EcoR1 site. Human N-terminal myc-tagged ΔN89β-catenin cDNA was introduced into the vector by gateway cloning. Constructs were introduced into KH2 embryonic stem cells containing M2-rtTA under control of the endogenous ROSA26 promoter as described previously.13 Mice were generated by diploid blastocyst injection into 3.5dpc blastocysts from C57/Bl6-J females. Approximately 30 injected blastocysts were transferred into pseudopregnant CD1 recipient females (Transgenic Facility, Wales Gene Park, Cardiff, UK). Chimeras were crossed with C57/   BL6-J mice. Organoid culture was conducted as previously described. Crypts were released from small intestine tissue fragments by incubation for 30 min at 4 °C in 2 mM EDTA-phosphate-buffered solution. Isolated crypts were mixed with 50 μl of Matrigel (BD Biosciences, Oxford, UK), seeded in 24-well plates and 500 μl of crypt culture medium (Dulbecco's modified Eagle medium/F12 containing 50 ng/ml epidermal growth factor (Sigma-Aldrich, Dorset, UK), 100 ng/ml Noggin (Peprotech, London, UK) and 600 ng/ml R-spondin 1 (R&D, Abingdon, Oxon, UK)) was added. Organoids were maintained in a 37 °C humidified atmosphere under 5% CO2.

extract_protocol: RNA was extracted using the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer’s instructions

treatment_protocol: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline, cultures were subsequently either left in the presence of doxycycline with either compound treatment or vehicle treatment for 24h, or doxycline was removed for 24h

tag: protocol

value: doxycycline

value: Vehicle

source_name: Universal Mouse Reference RNA

value: Reference


title: CON_PLUS_DOX_24h_E

source_name: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline


title: CON_DOX_REMOVED_24h_E

source_name: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline and were cultured in the absence of doxycycline for 24h

value: added doxycycline, then removed doxycycline

tag: time

value: 24 hr


title: REK 3D, CTRL B


title: CON_PLUS_DOX_24H_F


title: CON_PLUS_DOX_24H_G


title: REK 3D, BET A


title: LS-174-T_CPD_6_4_h_1_4

hyb_protocol: Cy 3 labelled cRNA was co-hybridized with Cy5 labelled Universal Human Reference RNA

scan_protocol: The arrays were scanned using an Agilent Technologies Scanner G2505C US84300231, using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.7.3.1 and extraction protocol GE2_107_Sep09 and grid file 028004_D_F_20110708

data_processing: Background subtracted data for sample and reference were entered in the Genespring analysis software (Agilent). Lowess normalization was applied to the samples.

source_name: LS-174-T colon cancer cells were treated with CPD 6 for 4 h

growth_protocol: All cell lines were purchased from the American Type Culture Collection and grown in their recommended culture medium, which was supplemented with 10% fetal bovine serum (FBS) at 37°C in an atmosphere of 5% CO2 and passaged for less than six months

treatment_protocol: The LS-174-T colon cancer cell line was treated for 0, 2 or 24h  hours with Compound 6

tag: cell line

value: Compound 6

value: 4 hr

source_name: Stratagene Universal Human Reference RNA


title: CON_PLUS_DOX_24H_D


title: LS-174-T_CPD_6_0_h_1_4

source_name: LS-174-T colon cancer cells were treated with CPD 6 for 0 h

value: 0 hr


title: CON_PLUS_DOX_24H_C


title: Growing/proliferating LuCaP 93 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
LuCaP93_G_48
Ten growing/proliferating (G) cells plucked from LuCaP 93 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

hyb_protocol: Hybridization probes were prepared by combining 4 ug of Alexa Fluor® 3 labeled sample and 400 ng Alexa Fluor® 5 labeled reference, denatured at 95°C and hybridized at 63°C on Agilent-016162 Human 4x44K microarrays and processed following the manufacturer’s specifications.

scan_protocol: Fluorescence array images were collected for Alexa Fluor® 3 and Alexa Fluor® 5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the GE2_105_Jan09 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of null to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers. Data was further normalized using between-array quantile normalization. All normalizations were performed using the Limma package in R.

label: Alexa Fluor® 5

label_protocol: Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen) (reference cDNA was labeled with Alexa Fluor® 5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA). Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNase using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer's specifications. The second round amplified amino-allyl RNA was then converted to first-strand cDNA and labeled with Alexa Fluor® 5 using the BioPrime® Total Genomic labeling kit (Invitrogen).

value: reference

value: pool of LNCaP, DU145, PC3, and CWR22

value: prostate cancer cell lines

tag: gender

value: male

label: Alexa Fluor® 3

growth_protocol: Bone marrow stromal cells (BMSC) that were isolated from a patient with PCa bone metastases (BM2508) were seeded at 50,000 cells/cm2 overnight. The following day, BM2508 cells were treated with 10 µg/mL mitomycin C (Sigma, St. Louis, MO) for 1 hour. LuCaP PDXs that were routinely passaged in vivo as described previously were excised and dissociated using the Miltenyi human tumor dissociation kit (Miltenyi Biotec Inc., San Diego, CA; #130-95-929) and enriched by positive selection using magnetic microbeads against human epithelial antigen EpCAM/CD326 (Miltenyi Biotec Inc.; #130-061-101) according to the manufacturer’s instructions. LuCaP PDX cells were then seeded on top of the BM2508 cells at either 50,000 cells/cm2 (G; growing/proliferating) or 50 cells/cm2 (NG; not growing/dormant). At day 8, the LuCaP PDX cells were differentially trypsinized and enriched by positive and negative selection with magnetic beads, fluorescently labeled for EpCAM/CD326 and individually plucked with a micromanipulator as described previously.

extract_protocol: Total RNA was amplified from each sample using the WT-OvationTM One-Direct System (NuGEN) according to the manufacturer's directions. Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen).

value: LuCaP 93

value: prostate cancer (PCa) patient-derived xenograft (PDX) cell line

tag: co-culture

tag: dormancy state

value: proliferating


title: LS-174-T_CPD_6_24_h_1_1

source_name: LS-174-T colon cancer cells were treated with CPD 6 for 24 h


title: LS-174-T_CPD_6_4_h_1_1


title: LS-174-T_CPD_6_0_h_2_2


title: LS-174-T_CPD_6_24_h_1_2


title: CON_DOX_REMOVED_24H_F


title: CON_DOX_REMOVED_24H_D


title: CMPD9_2UM_24H_B

source_name: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline and treated with Compound 9 for 24h

value: 2 uM Compound 9


title: CMPD9_2UM_24h_C


title: LS-174-T_CPD_6_24_h_2_1


title: CON_PLUS_DOX_24h_A


title: Growing/proliferating LuCaP 92 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

description:
LuCaP92_G_42
Ten growing/proliferating (G) cells plucked from LuCaP 92 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

value: LuCaP 92


title: CMPD9_2UM_24H_A

value: doxycycline


title: CON_DOX_REMOVED_24H_G

value: Vehicle


title: LS-174-T_CPD_6_0_h_1_3

value: Reference


title: LS-174-T_CPD_6_4_h_1_3


title: CMPD6_2UM_24H_G

source_name: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline and treated with Compound 6 for 24h

value: 2 uM Compound 6


title: CMPD2_2UM_24H_B

source_name: mouse intestinal organoids with a Doxycycline-inducible mutant beta-catenin where stimulated to grow in culture by adding doxycycline and treated with Compound 2 for 24h

value: 2 uM Compound 2

value: 24 hr


title: CMPD2_2UM_24H_C


title: CMPD6_2UM_24H_F


title: 80 micrograms/ml KP1019 Biological Sample 2 Dye reversal A

city: Memphis

first: Mary

middle: Elizabeth

last: Miller

address: 2000 North Parkway

department: Biology

institute: Rhodes College

description:
Dye reversal partner with MA209rawdata.txt
early log phase 0 vs 80 micrograms/mL KP1019 exposure for 3 hours

hyb_protocol: Microarrays were obtained from the Genome Consortium for Active Teaching (http://www.bio.davidson.edu/GCAT/). Hybridization and washes were carried out using the 3DNA Array 900 hybridization steps (Genisphere, catalog number W500180) using SDA hybridization buffer (vial 7).

scan_protocol: Arrays were scanned through the Genome Consortium for Active Teaching at Davidson College (Davidson, NC).

data_processing:
Images were analyzed using MagicTool 2.1 (http://www.bio.davidson.edu/projects/MAGIC/magic.html) using total signal of adaptive circie with default paramters (min radius = 3 pixels; max radius = 8 pizels; threshold 50).
Raw file data: RedFGtot - Cy5 "red" foreground total signal (addition of all values in all pixels designated as signal) RedBGtot - Cy5 "red" background total signal (addition of all values in all pixels designated as signal) GrnFGtot - Cy3 "green" foreground total signal (addition of all values in all pixels designated as signal) GrnBGtot - Cy3 "green" background total signal (addition of all values in all pixels designated as signal) RedFGavg - Cy5 "red" foreground average signal (average of pixels designated as signal) RedBGavg - Cy5 "red" background average signal (average of pixels designated as signal) GrnFGavg - Cy3 "green" foreground average signal (average of pixels designated as signal) GrnBGavg- Cy3 "green" background average signal (average of pixels designated as signal)

organism: Saccharomyces cerevisiae BY4741

source_name: treated cell

label_protocol: RNA was converted to cDNA using the 3DNA Array900 labeling kit (Genisphere, catalog number W500180) using poly T primers and reverse transcriptase enzyme using the manufacturers instructions.

growth_protocol: Yeast strain BY4741 was grown to early log phase (OD600 between 0.2 and 0.3 and then treated with drug for 3 hours.  Growth media was synthetic complete media  with Glucose as carbon source.  Cultures were incubated in shaking water bath at 30C.

extract_protocol: Cells were harvested by centrifugation, resuspended in RNAlater (Qiagen) and frozen at -80C until RNA extraction.  Total RNA was isolated using RNAeasy Mini Kit (Qiagen catalog # 74104) using the enzymatic lysis method as described by the manufacturer.

treatment_protocol: Early log phase cells were split; one half was left untreated and allowed to grow for 3 hours  and the other half was incubated with KP1019 for three hours to a final concentration of 40 microgams/ml or 80 micrograms/mL depending on the sample.

tag: agen

value: 80 micrograms/mL KP1019

source_name: untreated cell

tag: agent

value: no drug


title: CMPD6_2UM_24H_D


title: Not-growing/dormant LuCaP 92 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

description:
LuCaP92_NG_44
Ten not-growing/dormant (NG) cells plucked from LuCaP 92 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

value: reference

value: dormant


title: 80 micrograms/ml KP1019 Biological Sample 1 Dye reversal A

description:
Dye reversal partner with MA207rawdata.txt
early log phase 0 vs 80 micrograms/mL KP1019 exposure for 3 hours


title: 40 micrograms/ml KP1019 Biological Sample 1 Dye reversal B

description:
Dye reversal partner with gp1bcrawdata.txt
early log phase 0 vs 40 micrograms/mL KP1019 exposure for 3 hours

value: 40 micrograms/mL KP1019


title: 80 micrograms/ml KP1019 Biological Sample 1 Dye reversal B

description:
Dye reversal partner with MA206rawdata.txt
early log phase 0 vs 80 micrograms/mL KP1019 exposure for 3 hours


title: 40 micrograms/ml KP1019 Biological Sample 2 Dye reversal B

description:
Dye reversal partner with gp3acrawdata.txt
early log phase 0 vs 40 micrograms/mL KP1019 exposure for 3 hours


title: Not-growing/dormant LuCaP 86.2 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

description:
LuCaP86.2_NG_35
Ten not-growing/dormant (NG) cells plucked from LuCaP 86.2 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

value: pool of LNCaP, DU145, PC3, and CWR22

value: prostate cancer cell lines

value: male

value: LuCaP 86.2


title: COLO205_DMSO_2H_B

scan_protocol: The arrays were scanned using an Agilent Technologies Scanner G2505C US94400327, using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.7.3.1 and extraction protocol GE2_107_Sep09 and grid file 039494_D_F_20120628

source_name: Colo205 colon cancer cells were treated with DMSO for 2H

treatment_protocol: The Colo205 colon cancer cell line was treated for 2 or  6 hours with vehicle control (DMSO) or treated with Compound 1

value: DMSO

value: 2 hr


title: COLO205_DMSO_6H_D

source_name: Colo205 colon cancer cells were treated with DMSO for 6H

value: 6 hr


title: CMPD6_2UM_24H_E

value: doxycycline


title: Not-growing/dormant LuCaP 93 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

description:
LuCaP93_NG_12
Ten not-growing/dormant (NG) cells plucked from LuCaP 93 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

value: LuCaP 93

value: prostate cancer (PCa) patient-derived xenograft (PDX) cell line


title: 80 micrograms/ml KP1019 Biological Sample 2 Dye reversal B

description:
Dye reversal partner with MA208rawdata.txt
early log phase 0 vs 80 micrograms/mL KP1019 exposure for 3 hours


title: Growing/proliferating LuCaP 86.2 cells co-cultured with bone marrow stromal cells from patient with PCa bone metastases

description:
LuCaP86.2_G_3
Ten growing/proliferating (G) cells plucked from LuCaP 86.2 grown in co-culture with bone marrow stromal cells isolated from a patient with PCa bone metastases.

value: proliferating


title: 40 micrograms/ml KP1019 Biological Sample 1 Dye reversal A

description:
Dye reversal partner with gp2acrawdata.txt
early log phase 0 vs 40 micrograms/mL KP1019 exposure for 3 hours


title: 40 micrograms/ml KP1019 Biological Sample 2 Dye reversal A

description:
Dye reversal partner with gp4bcrawdata.txt
early log phase 0 vs 40 micrograms/mL KP1019 exposure for 3 hours


title: COLO205_DMSO_6H_A

value: Reference


title: COLO205_CPD_1_6H_D

source_name: Colo205 colon cancer cells were treated with CPD 1 for 6H

value: Compound 1


title: COLO205_CPD_1_6H_A


title: CMPD2_2UM_24H_A

value: 2 uM Compound 2

value: 24 hr


title: COLO205_CPD_1_6H_C


title: COLO205_CPD_1_6H_B


title: COLO205_DMSO_2H_C


title: COLO205_DMSO_6H_C


title: COLO205_DMSO_2H_D


title: COLO205_DMSO_2H_A


title: COLO205_DMSO_6H_B


title: COLO205_CPD_1_2H_D

source_name: Colo205 colon cancer cells were treated with CPD 1 for 2H