title: Adjacent non-tumor tissue, 83

description: Sample name: ANTT83


title: Adjacent non-tumor tissue, 58

status: Public on May 26 2017

type: RNA

city: Singapore

first: Surya Pavan

last: Yenamandra

address: 30, Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute

description: Sample name: ANTT58

hyb_protocol: Illumina HumanHT-12 v4 Expression BeadChip arrays using Illumina standard protocol.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Reader and the BeadScan Software (Illumina).

data_processing: Raw data was obtained via the GenomeStudio; data have been normalized using the RSN method from R-package lumi.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: adjacent non-tumor tissue

label_protocol: 500 ng of RNA from each sample were reverse transcribed into cDNA and thereby labeled with biotin-UTP following manufacturer protocols.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: diagnosis

value: hepatocellular carcinoma (HCC)

tag: patient id

tag: tissue

value: adjacent non-tumor liver tissue


title: Adjacent non-tumor tissue, 25

description: Sample name: ANTT25


title: Adjacent non-tumor tissue, 53

description: Sample name: ANTT53


title: Adjacent non-tumor tissue, 101

description: Sample name: ANTT101


title: Adjacent non-tumor tissue, 73

description: Sample name: ANTT73


title: Adjacent non-tumor tissue, 54

description: Sample name: ANTT54


title: Adjacent non-tumor tissue, 41

description: Sample name: ANTT41


title: Adjacent non-tumor tissue, 85

description: Sample name: ANTT85


title: Adjacent non-tumor tissue, 61

description: Sample name: ANTT61


title: Adjacent non-tumor tissue, 24

description: Sample name: ANTT24


title: Adjacent non-tumor tissue, 66

description: Sample name: ANTT66


title: Adjacent non-tumor tissue, 8

description: Sample name: ANTT8


title: Adjacent non-tumor tissue, 17

description: Sample name: ANTT17


title: Adjacent non-tumor tissue, 60

description: Sample name: ANTT60


title: Adjacent non-tumor tissue, 46

description: Sample name: ANTT46


title: Adjacent non-tumor tissue, 21

description: Sample name: ANTT21


title: Primary HCC tumor tissue, 77

description: Sample name: PT77

source_name: hepatocellular carcinoma tumor tissue

value: primary hepatocellular carcinoma tumor

tag: age (years)

tag: gender (1=m, 2=f)

value: A

value: I


title: Adjacent non-tumor tissue, 62

description: Sample name: ANTT62


title: Primary HCC tumor tissue, 75

description: Sample name: PT75

value: B

value: II


title: Primary HCC tumor tissue, 74

description: Sample name: PT74


title: Primary HCC tumor tissue, 68

description: Sample name: PT68


title: Adjacent non-tumor tissue, 63

description: Sample name: ANTT63


title: Primary HCC tumor tissue, 69

description: Sample name: PT69


title: Primary HCC tumor tissue, 71

description: Sample name: PT71


title: Primary HCC tumor tissue, 52

description: Sample name: PT52

value: IIIA


title: Adjacent non-tumor tissue, 19

description: Sample name: ANTT19


title: Primary HCC tumor tissue, 45

description: Sample name: PT45


title: Primary HCC tumor tissue, 39

description: Sample name: PT39


title: Primary HCC tumor tissue, 55

description: Sample name: PT55


title: Primary HCC tumor tissue, 38

description: Sample name: PT38


title: Primary HCC tumor tissue, 49

description: Sample name: PT49


title: Primary HCC tumor tissue, 64

description: Sample name: PT64


title: Primary HCC tumor tissue, 67

description: Sample name: PT67

value: IVA


title: Primary HCC tumor tissue, 65

description: Sample name: PT65


title: Primary HCC tumor tissue, 27

description: Sample name: PT27


title: Primary HCC tumor tissue, 28

description: Sample name: PT28


title: Primary HCC tumor tissue, 56

description: Sample name: PT56


title: Primary HCC tumor tissue, 50

description: Sample name: PT50


title: Primary HCC tumor tissue, 42

description: Sample name: PT42


title: Primary HCC tumor tissue, 59

description: Sample name: PT59


title: Primary HCC tumor tissue, 91

description: Sample name: PT91


title: Primary HCC tumor tissue, 20

description: Sample name: PT20


title: Primary HCC tumor tissue, 13

description: Sample name: PT13


title: Primary HCC tumor tissue, 10

description: Sample name: PT10


title: Primary HCC tumor tissue, 108

description: Sample name: PT108


title: Primary HCC tumor tissue, 9

description: Sample name: PT9


title: Primary HCC tumor tissue, 106

description: Sample name: PT106


title: Primary HCC tumor tissue, 15

description: Sample name: PT15


title: Primary HCC tumor tissue, 12

description: Sample name: PT12


title: Primary HCC tumor tissue, 111

description: Sample name: PT111

value: C

value: IVB


title: Primary HCC tumor tissue, 113

description: Sample name: PT113


title: Primary HCC tumor tissue, 89

description: Sample name: PT89


title: Primary HCC tumor tissue, 90

description: Sample name: PT90


title: Primary HCC tumor tissue, 87

description: Sample name: PT87


title: Primary HCC tumor tissue, 105

description: Sample name: PT105


title: Primary HCC tumor tissue, 80

description: Sample name: PT80


title: Primary HCC tumor tissue, 2

description: Sample name: PT2


title: Primary HCC tumor tissue, 86

description: Sample name: PT86


title: Primary HCC tumor tissue, 81

description: Sample name: PT81


title: Primary HCC tumor tissue, 1

description: Sample name: PT1


title: Primary HCC tumor tissue, 35

description: Sample name: PT35


title: Primary HCC tumor tissue, 114

description: Sample name: PT114


title: Primary HCC tumor tissue, 44

description: Sample name: PT44


title: Primary HCC tumor tissue, 43

description: Sample name: PT43


title: Primary HCC tumor tissue, 95

description: Sample name: PT95

value: IIIB


title: Primary HCC tumor tissue, 94

description: Sample name: PT94


title: Primary HCC tumor tissue, 48

description: Sample name: PT48


title: Primary HCC tumor tissue, 79

description: Sample name: PT79


title: Primary HCC tumor tissue, 93

description: Sample name: PT93


title: Primary HCC tumor tissue, 96

description: Sample name: PT96


title: Primary HCC tumor tissue, 30

description: Sample name: PT30


title: Primary HCC tumor tissue, 109

description: Sample name: PT109


title: Primary HCC tumor tissue, 110

description: Sample name: PT110


title: Primary HCC tumor tissue, 115

description: Sample name: PT115


title: Primary HCC tumor tissue, 33

description: Sample name: PT33


title: Primary HCC tumor tissue, 112

description: Sample name: PT112


title: Primary HCC tumor tissue, 29

description: Sample name: PT29


title: Primary HCC tumor tissue, 92

description: Sample name: PT92


title: Primary HCC tumor tissue, 51

description: Sample name: PT51


title: Primary HCC tumor tissue, 100

description: Sample name: PT100


title: Primary HCC tumor tissue, 82

description: Sample name: PT82


title: Primary HCC tumor tissue, 104

description: Sample name: PT104


title: Primary HCC tumor tissue, 37

description: Sample name: PT37


title: Primary HCC tumor tissue, 14

description: Sample name: PT14


title: Primary HCC tumor tissue, 70

description: Sample name: PT70


title: Primary HCC tumor tissue, 84

description: Sample name: PT84


title: Primary HCC tumor tissue, 47

description: Sample name: PT47


title: Primary HCC tumor tissue, 23

description: Sample name: PT23


title: Primary HCC tumor tissue, 4

description: Sample name: PT4


title: Primary HCC tumor tissue, 107

description: Sample name: PT107


title: Primary HCC tumor tissue, 36

description: Sample name: PT36


title: Primary HCC tumor tissue, 32

description: Sample name: PT32


title: Primary HCC tumor tissue, 103

description: Sample name: PT103


title: Primary HCC tumor tissue, 102

description: Sample name: PT102


title: Primary HCC tumor tissue, 11

description: Sample name: PT11


title: Primary HCC tumor tissue, 72

description: Sample name: PT72


title: Primary HCC tumor tissue, 7

description: Sample name: PT7


title: Primary HCC tumor tissue, 31

description: Sample name: PT31


title: Primary HCC tumor tissue, 5

description: Sample name: PT5


title: Primary HCC tumor tissue, 22

description: Sample name: PT22


title: Primary HCC tumor tissue, 34

description: Sample name: PT34


title: Primary HCC tumor tissue, 6

description: Sample name: PT6


title: Primary HCC tumor tissue, 26

description: Sample name: PT26


title: Primary HCC tumor tissue, 101

description: Sample name: PT101


title: Primary HCC tumor tissue, 99

description: Sample name: PT99


title: Primary HCC tumor tissue, 76

description: Sample name: PT76


title: Primary HCC tumor tissue, 98

description: Sample name: PT98


title: Primary HCC tumor tissue, 57

description: Sample name: PT57


title: Primary HCC tumor tissue, 41

description: Sample name: PT41


title: Primary HCC tumor tissue, 78

description: Sample name: PT78


title: Primary HCC tumor tissue, 16

description: Sample name: PT16


title: Primary HCC tumor tissue, 40

description: Sample name: PT40


title: Primary HCC tumor tissue, 97

description: Sample name: PT97


title: Primary HCC tumor tissue, 3

description: Sample name: PT3


title: Primary HCC tumor tissue, 53

description: Sample name: PT53


title: Primary HCC tumor tissue, 18

description: Sample name: PT18


title: Primary HCC tumor tissue, 88

description: Sample name: PT88


title: Primary HCC tumor tissue, 73

description: Sample name: PT73


title: Primary HCC tumor tissue, 60

description: Sample name: PT60


title: Primary HCC tumor tissue, 85

description: Sample name: PT85


title: Primary HCC tumor tissue, 46

description: Sample name: PT46


title: Primary HCC tumor tissue, 8

description: Sample name: PT8


title: Primary HCC tumor tissue, 21

description: Sample name: PT21


title: Primary HCC tumor tissue, 24

description: Sample name: PT24


title: Primary HCC tumor tissue, 25

description: Sample name: PT25


title: Primary HCC tumor tissue, 58

description: Sample name: PT58


title: Primary HCC tumor tissue, 63

description: Sample name: PT63


title: Primary HCC tumor tissue, 66

description: Sample name: PT66


title: Primary HCC tumor tissue, 83

description: Sample name: PT83


title: Primary HCC tumor tissue, 54

description: Sample name: PT54


title: Primary HCC tumor tissue, 17

description: Sample name: PT17


title: Primary HCC tumor tissue, 61

description: Sample name: PT61


title: CD4+_IL7_TCA_rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System

data_processing: Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 11.0.1.1; Agilent Technologies). Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies).

source_name: CD4+ T cells, IL7, 6h + TCA, 16h

label_protocol: Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp  Labeling Kit

growth_protocol: Flow cytometry analysis for cell markers, size, and granularity

extract_protocol: TriZOL RNA extraction method

treatment_protocol: Human recombinant IL-7 (10ng/ml), untreated control, 6h; CD3/CD28 stimulation, additional 16h

tag: cell type

value: CD4+ T cells

tag: treatment

value: IL7 + TCA

tag: time


title: 100%URR/0%Brain rep 4

status: Public on May 25 2017

type: SRA

city: Carlsbad

first: Joanne

last: Yeakley

state: CA

address: 1945 Camino Vida Roble Ste i

country: USA

institute: BioSpyder Technologies, Inc.

description: processed data file: Fold Difference Limit Read Counts.xlsx

library_source: transcriptomic

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: Multiple pseudo transcriptomes and hg38 (for GSM2422725 to GSM2422736). Processed data files include the sequences used for alignment in column "Probe_Sequence".
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

source_name: pooled cell lines

extract_protocol: TempO-Seq targeted expression assay. Addition of adapters by amplification.

tag: cell lines

value: pooled cell lines

tag: sample preparation

value: purified total RNA

tag: input

tag: source material manufacturer

value: Agilent


title: 100%URR/0%Brain rep 3


title: 100%URR/0%Brain rep 2


title: 100%URR/0%Brain rep 6


title: 100%URR/0%Brain rep 5


title: 60%URR/40%Brain rep 5

source_name: pooled cell lines and donors

value: pooled cell lines and donors

value: Agilent and Thermo Fisher


title: CD4+_IL7_rep1

source_name: CD4+ T cells, IL7, 6h


title: CD4+_IL7_TCA_rep1


title: 60%URR/40%Brain rep 6


title: Primary HCC tumor tissue, 62

description: Sample name: PT62

value: hepatocellular carcinoma (HCC)

value: primary hepatocellular carcinoma tumor


title: CD4+_IL7_rep2


title: CD4+_untreated_TCA_rep1

source_name: CD4+ T cells, untreated, 6h + TCA, 16h

value: untreated + TCA


title: CD4+_IL7_rep3


title: CD4+_untreated_TCA_rep2


title: CD4+_untreated_rep3

source_name: CD4+ T cells, untreated, 6h

value: untreated


title: CD4+_untreated_rep2


title: CD4+_untreated_TCA_rep3


title: 60%URR/40%Brain rep 4


title: CD4+_untreated_rep1


title: 100%URR/0%Brain rep 1


title: 60%URR/40%Brain rep 3


title: 60%URR/40%Brain rep 2


title: 50%URR/50%Brain rep 4


title: CD4+_IL7_TCA_rep3


title: 40%URR/60%Brain rep 4


title: Primary HCC tumor tissue, 19

description: Sample name: PT19

value: B

value: I


title: 50%URR/50%Brain rep 5


title: 0%URR/100% Brain rep 5

source_name: pooled donors

value: pooled donors


title: 50%URR/50%Brain rep 3


title: 40%URR/60%Brain rep 3


title: 0%URR/100% Brain rep 2

value: Thermo Fisher


title: 60%URR/40%Brain rep 1


title: 50%URR/50%Brain rep 6


title: 40%URR/60%Brain rep 6


title: 50%URR/50%Brain rep 2


title: 0%URR/100% Brain rep 3


title: 0%URR/100% Brain rep 6


title: 40%URR/60%Brain rep 2


title: 40%URR/60%Brain rep 1


title: 40%URR/60%Brain rep 5


title: Liver_gestationalday110_runt_rep3

city: Beltsville

first: Jakub

last: Kwintkiewicz

state: MD

address: 10300 Baltimore Ave. BARC-East

institute: USDA

description: gestational day 110

hyb_protocol: The cRNA was fragmented before hybrdizatttion with probes on a 4 X 44K porcine e-array (Agilent Technologies) platform using Agilent reagents according to the manufacturer’s guidelines. For each probe, 1.65 µg of Cy3 labeled cRNA was fragmented in a reaction mix containing the Blocking Agent and  Fragmentation buffer by incubating 30 min at 60oC.  Following the addition of Hi-RPM Hybridization Buffer to a 1X concentration, one sample was added per array and hybridized at 65oC for 17 h with a rotation of 10 X g in a SurHyb chamber (Agilent Technologies).

scan_protocol: Data was obtained using the Agilent Microarray scanner (Agilent Technologies) Gene Expression v.5.0 using a scan resolution of 5 µm.

data_processing: Raw Agilent gProcessedSignal values were log2 transformed and quantile normalized in Partek GS v6.6

organism: Sus scrofa

source_name: Liver, gestational day 110, runt, replicate 3

label_protocol: For microarray analysis, PND37, PND50, PND70 and PND110 liver samples from four GW and IUGR littermate pairs of from distinct gilts were used to generate cRNA targets labeled  with Cyanine (Cy) 3 using the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer’s instructions. Briefly, reverse transcription was carried out for each sample in a 10 µl reaction volume containing 200 ng total RNA. Samples were incubated at 40oC for 2 h, then 70oC for 15 min to inactivate enyzmes. Synthesis of cRNA from cDNA, Cy3 labeling and cRNA amplification were performed using the kit reagents. The resultant Cy3-labeled cRNA was purified according to protocol and quantified on the Nanodrop 2000 Spectrophotometer

growth_protocol: Unilatterally hysterectomized:ovariectomized gilts were artificially inseminated. Fetuses at gestetional day 37, 50, 70 and 110 were collected and liver samples were isolated for RNA isolation.

extract_protocol: For microarray analysis, PND 37, 50, 70 and 110 liver samples were obtained each from four distinct gilts. Total RNA from the individual liver tissue specimen was isolated using the RNeasy mini Kit (Qiagen, Valencia, CA). An on-column DNase I digest of each sample was performed according to the manufacturer’s instructions to remove genomic DNA contaminants. Total RNA integrity and quantification were determined with the Agilent RNA 6000 Nano LabChip Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the quality was very good and consistent between samples.

treatment_protocol: Surgically induced uterine overcrowding constituted the bases for development of IUGR offspring

tag: group

value: runt

tag: gestational age days


title: Liver_gestationalday110_control_rep1

description: gestational day 110

source_name: Liver, gestational day 110, control, replicate 1

value: control


title: Liver_gestationalday110_runt_rep1

description: gestational day 110

source_name: Liver, gestational day 110, runt, replicate 1


title: Liver_gestationalday110_runt_rep2

description: gestational day 110

source_name: Liver, gestational day 110, runt, replicate 2


title: 0%URR/100% Brain rep 4


title: Liver_gestationalday110_control_rep4

description: gestational day 110

source_name: Liver, gestational day 110, control, replicate 4


title: 0%URR/100% Brain rep 1


title: Liver_gestationalday70_runt_rep4

description: gestational day 70

source_name: Liver, gestational day 70, runt, replicate 4


title: Liver_gestationalday110_control_rep2

description: gestational day 110

source_name: Liver, gestational day 110, control, replicate 2


title: Liver_gestationalday70_runt_rep3

description: gestational day 70

source_name: Liver, gestational day 70, runt, replicate 3


title: Liver_gestationalday110_control_rep3

description: gestational day 110

source_name: Liver, gestational day 110, control, replicate 3


title: Liver_gestationalday50_runt_rep4

description: gestational day 50

source_name: Liver, gestational day 50, runt, replicate 4


title: Liver_gestationalday70_runt_rep2

description: gestational day 70

source_name: Liver, gestational day 70, runt, replicate 2


title: Liver_gestationalday50_control_rep4

description: gestational day 50

source_name: Liver, gestational day 50, control, replicate 4


title: Liver_gestationalday70_control_rep4

description: gestational day 70

source_name: Liver, gestational day 70, control, replicate 4


title: Liver_gestationalday70_runt_rep1

description: gestational day 70

source_name: Liver, gestational day 70, runt, replicate 1


title: Liver_gestationalday50_control_rep3

description: gestational day 50

source_name: Liver, gestational day 50, control, replicate 3


title: Liver_gestationalday70_control_rep1

description: gestational day 70

source_name: Liver, gestational day 70, control, replicate 1


title: Liver_gestationalday70_control_rep2

description: gestational day 70

source_name: Liver, gestational day 70, control, replicate 2


title: Liver_gestationalday50_runt_rep3

description: gestational day 50

source_name: Liver, gestational day 50, runt, replicate 3


title: Liver_gestationalday50_runt_rep2

description: gestational day 50

source_name: Liver, gestational day 50, runt, replicate 2


title: Liver_gestationalday50_runt_rep1

description: gestational day 50

source_name: Liver, gestational day 50, runt, replicate 1


title: Liver_gestationalday110_runt_rep4

description: gestational day 110

source_name: Liver, gestational day 110, runt, replicate 4


title: Liver_gestationalday50_control_rep2

description: gestational day 50

source_name: Liver, gestational day 50, control, replicate 2


title: Liver_gestationalday37_runt_rep1

description: gestational day 37

source_name: Liver, gestational day 37, runt, replicate 1


title: Liver_gestationalday37_control_rep1

description: gestational day 37

source_name: Liver, gestational day 37, control, replicate 1


title: Liver_gestationalday37_runt_rep4

description: gestational day 37

source_name: Liver, gestational day 37, runt, replicate 4


title: Liver_gestationalday50_control_rep1

description: gestational day 50

source_name: Liver, gestational day 50, control, replicate 1


title: Liver_gestationalday37_control_rep2

description: gestational day 37

source_name: Liver, gestational day 37, control, replicate 2


title: Liver_gestationalday37_runt_rep2

description: gestational day 37

source_name: Liver, gestational day 37, runt, replicate 2


title: Liver_gestationalday37_control_rep3

description: gestational day 37

source_name: Liver, gestational day 37, control, replicate 3


title: Liver_gestationalday37_runt_rep3

description: gestational day 37

source_name: Liver, gestational day 37, runt, replicate 3


title: CFBE41o- vs. HEK replicate 3

status: Public on May 24 2017

city: Glasgow

first: Sebastian

last: Kirchner

address: 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

description: Biological replicate 3 of 3.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and storred in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenPix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on median fluorescence signal (background fluorescence subtraction).
3. Cy3/Atto635 ratios were normalized to Cy3/Atto635 values of tRNA standars (e.g. median Cy3/Atto635 ratios of the three tRNA standards E. coli tRNALys2, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3/Atto635 or Cy3/Cy5 ratios for individual blocks were averaged, representing final Cy3/Atto635 or Cy3/Cy5 ratios.

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (16 nM each; E. coli tRNALys2, E. coli tRNATyr2, Yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. Total RNA containing tRNA standards was treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation.
3. Cy3, Cy5 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
Cells were cultivated at 37°C and 5% CO2 in MEM (Biochrome) (HEK, CFBE41o-) or DMEM (PAN Biotech) (HeLa) medium supplemented with 10% FCS (PAN Biotech) and 2 mM L-glutamine (Gibco) until 70 to 80% confluency.
Primary HBE cells were cultivated as air liquide interface (ALI) cultures on transwell filters in ALI medium until confluency at 37°C and 5% CO2.
Cell were grown independently for each biological experiment and checked frequently for mycoplasma contamination.

extract_protocol: Total RNA was extracted using TriReagent (Sigma-Aldrich) according to manufacturer's protocol.

tag: cell line

tag: patient identifier

value: HEK-293 (ATCC no. CRL-1573)


title: control HEK vs. HEK replicate 3

description: Biological replicate 3 of 4.

extract_protocol: Total RNA was extracted using TriReagent (Sigma-Aldrich) according to manufacturer's protocol and for total HeLa tRNA estimates was purified on polyacrylamide gels.


title: primary HBE vs. HEK (Patient 1)

description: 1 indepent biological experiment was performed. HBE cells were isolated from explanted cystic fibrosis lungs and further cultivated.

value: CF patients derived bronchial epithelial cells


title: control HEK vs. HEK replicate 2

description: Biological replicate 2 of 4.


title: Liver_gestationalday70_control_rep3

description: gestational day 70

source_name: Liver, gestational day 70, control, replicate 3


title: Liver_gestationalday37_control_rep4

description: gestational day 37

source_name: Liver, gestational day 37, control, replicate 4


title: control HEK vs. HEK replicate 4

description: Biological replicate 4 of 4.


title: control HEK vs. HEK replicate 1

description: Biological replicate 1 of 4.


title: 50%URR/50%Brain rep 1

source_name: pooled cell lines and donors


title: Hela vs. HeLa_1-1

description:
tRNA
Biological replicate 1 of 2, Technical replicate 1 of 3

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

source_name: cultivated cells_tRNA

value: HeLa (ATCC no. CCL-2)


title: primary HBE vs. HEK (Patient 4)


title: primary HBE vs. HEK (Patient 2)


title: primary HBE vs. HEK (Patient 3)


title: HeLa vs. HEK replicate 4

description: Biological replicate 4 of 4.


title: CFBE41o- vs. HEK replicate 1

description: Biological replicate 1 of 3.


title: CFBE41o- vs. HEK replicate 2

description: Biological replicate 2 of 3.


title: Hela vs. HeLa_2-3

description:
tRNA
Biological replicate 2 of 2, Technical replicate 3 of 3


title: HeLa vs. HEK replicate 1

description: Biological replicate 1 of 4.


title: HeLa vs. HEK replicate 3

description: Biological replicate 3 of 4.


title: HeLa vs. HEK replicate 2

description: Biological replicate 2 of 4.


title: Hela vs. HeLa_2-1

description:
tRNA
Biological replicate 2 of 2, Technical replicate 1 of 3


title: Hela vs. HeLa_1-2

description:
tRNA
Biological replicate 1 of 2, Technical replicate 2 of 3


title: Hela vs. HeLa_2-2

description:
tRNA
Biological replicate 2 of 2, Technical replicate 2 of 3


title: CDH1deficient-3

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Cdh1 deficient N-myc induced B cell leukemia cells, replicate 3

hyb_protocol: Hybridization and signal detection of Mouse Genome 430 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data was normalized by robust multichip analysis (RMA) using justRMA function in R/Bioconductor.

label: biotin

organism: Mus musculus

source_name: bone marrow mononuclear cells

label_protocol: Biotin-labeled aRNA probes were synthesized from the total RNA following the manufacturer's instruction.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) and an RNeasy Minikit (Qiagen, Tokyo, Japan) from GFP positive cells out of bone marrow mononuclear cells (BM-MNCs) harvested from each moribund mouse, sorted by Moflo flow-cytometer.

treatment_protocol: Cdh1-intact and Cdh1-deficient myc-induced B-ALL bone marrow cells (n = 3 in each group) were used.

tag: genotype

value: CDH1 deficient


title: CDH1deficient-1

description: Cdh1 deficient N-myc induced B cell leukemia cells, replicate 1


title: FXR S154D transfected COS-1 cells_CDCA_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 24 hr in CDCA-treated COS-1 cells expressing FXR S154D

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

organism: Chlorocebus sabaeus

source_name: COS-1 cells, FXR S154D, CDCA, replicate 2

label_protocol: Gene expression analysis was conducted using Agilent Whole Human Genome 4x44 multiplex format oligo arrays (014850) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: COS-1 cells are grown and maintained in DMEM supplemented with 10% FBS, 100U/mL penicillin and 100 mg/mL streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Life Technologies) following the manufacturer's instruction. The extracted RNA was subsequently purified using RNeasy mini kit (Quaigen)

treatment_protocol: After 24 hr transient expression of FXR S154A or FXR S154D, 0.1% DMSO or 50 mM chenodeoxycholic acid (CDCA) was added to the media for 24 hr.

tag: mutant strain

value: FXR S154D


title: CDH1intact-2

description: Cdh1 intact N-myc induced B cell leukemia cells, replicate 2

value: CDH1 intact


title: FXR S154D transfected COS-1 cells_DMSO_rep3

description: Gene expression after 24 hr in DMSO-treated COS-1 cells expressing FXR S154D

source_name: COS-1 cells, FXR S154D, DMSO, replicate 3


title: CDH1intact-1

description: Cdh1 intact N-myc induced B cell leukemia cells, replicate 1


title: FXR S154D transfected COS-1 cells_DMSO_rep2

source_name: COS-1 cells, FXR S154D, DMSO, replicate 2


title: FXR S154A transfected COS-1 cells_CDCA_rep3

description: Gene expression after 24 hr in CDCA-treated COS-1 cells expressing FXR S154A

source_name: COS-1 cells, FXR S154A, CDCA, replicate 3

value: FXR S154A


title: Hela vs. HeLa_1-3

description:
tRNA
Biological replicate 1 of 2, Technical replicate 3 of 3


title: FXR S154D transfected COS-1 cells_DMSO_rep1

source_name: COS-1 cells, FXR S154D, DMSO, replicate 1


title: CDH1deficient-2

description: Cdh1 deficient N-myc induced B cell leukemia cells, replicate 2


title: FXR S154A transfected COS-1 cells_CDCA_rep1

source_name: COS-1 cells, FXR S154A, CDCA, replicate 1


title: FXR S154A transfected COS-1 cells_CDCA_rep2

source_name: COS-1 cells, FXR S154A, CDCA, replicate 2


title: FXR S154A transfected COS-1 cells_DMSO_rep3

description: Gene expression after 24 hr in DMSO-treated COS-1 cells expressing FXR S154A

source_name: COS-1 cells, FXR S154A, DMSO, replicate 3


title: CDH1intact-3

description: Cdh1 intact N-myc induced B cell leukemia cells, replicate 3


title: FXR S154D transfected COS-1 cells_CDCA_rep1

source_name: COS-1 cells, FXR S154D, CDCA, replicate 1


title: FXR S154A transfected COS-1 cells_DMSO_rep2

source_name: COS-1 cells, FXR S154A, DMSO, replicate 2


title: invitroCells_48hr_10 μmol/L_rep1

city: Beijing

first: dongping

last: xu

address: #100 Xisihuan Middle Road, Beijing

country: China

institute: Research Center for Clinical and Translational Medicine, Beijing 302 Hospital, Beijing

description: Gene expression after 48hr in 10 μmol/L-entecavir treated HepG2.2.15

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）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 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HepG2.2.15 cells were seeded at 5X10^5 cells/well in 12-well plates and cultured in DMEM medium supplemented with 10% FBS at 37℃ for 18 h for cell adherence. Afterwards, medium was replaced with fresh DMEM containing different concentrations of drug (0 and 10.0 μmol/L of entecavir). After 48 h incubation, total RNA was extracted from these cells.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: Entecavir-regulated genes in HepG2.2.15 cells was measured at 48 hours after exposure to doses of 0 μmol/L, 10 μmol/L.

value: 48hr in 10 μmol/L-entecavir


title: FXR S154A transfected COS-1 cells_DMSO_rep1

source_name: COS-1 cells, FXR S154A, DMSO, replicate 1


title: 11: invitroCells_48hr_0.001 μg/ml_rep1

description: Gene expression after 48hr in 0.001 μg/ml-Suduxing treated HepG2.2.15

growth_protocol: HepG2.2.15 cells were seeded at 5X10^5 cells/well in 12-well plates in triplicates and cultured in DMEM medium supplemented with 10% FBS at 37℃ for 18 h for cell adherence. Afterwards, medium was replaced with fresh DMEM containing different concentrations of drug (0μg/mL、0.001 μg/mL and 0.01 μg/mL of Suduxing). After 48 h incubation, total RNA was extracted from these cells .

treatment_protocol: Suduxing-regulated genes in HepG2.2.15 cells was measured at 48 hours after exposure to doses of 0 μg/ml, 0.001 μg/ml,and 0.01 μg/ml.Three independent experiments were performed at each time (48 hours) using different doses for each experiment.

value: 48hr in 0.001μg/ml-Suduxing


title: Spleen Teff TAC+IL-2 rep3

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

institute: King's College London

description: Spleen Teff TAC+IL-2

hyb_protocol: Complex probes were hybridized to each Mouse Gene 2.1 ST Array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v3.2) 'affy' in R.3.3.1

source_name: FOXP3-YFP mice, Spleen sorted T cells

label_protocol: Biotin

extract_protocol: RNA was extracted using TRIZOL according to the manufacturer's recommendations (Thermo Fisher Scientific)

treatment_protocol: T cells isolated from spleens from FOXP3-YFP mouse treated for 7 days with PBS (CN), tacrolimus (TAC), IL-2 at days 2,3 and 4 (IL-2) or combination of tacrolimus and IL-2 at days 2,3 and 4 (TAC+IL-2)

value: Teff

value: TAC + IL-2


title: Spleen Treg TAC rep3

description: Spleen Treg TAC

value: Treg

value: TAC


title: FXR S154D transfected COS-1 cells_CDCA_rep3

source_name: COS-1 cells, FXR S154D, CDCA, replicate 3


title: Spleen Treg TAC+IL-2 rep3

description: Spleen Treg TAC+IL-2


title: invitroCells_48hr_0 μmol/L_rep1

description: Gene expression after 48hr in 0 μmol/L-entecavir treated HepG2.2.15

source_name: HepG2.2.15_48hr_0 μmol/L_rep1

value: 48hr in 0 μmol/L-entecavir


title: 11: invitroCells_48hr_0.01 μg/ml_rep1

description: Gene expression after 48hr in 0.01 μg/ml-Suduxing treated HepG2.2.15

value: 48hr in 0.01μg/ml-Suduxing


title: Spleen Teff TAC rep4

description: Spleen Teff TAC


title: 9: invitroCells_48hr_0.01 μg/ml_rep1


title: Spleen Teff IL-2 rep3

description: Spleen Teff IL-2


title: Spleen Teff IL-2 rep4

description: Spleen Teff IL-2


title: 9: invitroCells_48hr_0.001 μg/ml_rep1


title: 11: invitroCells_48hr_0.00 μg/ml_rep1

description: Gene expression after 48hr in 0.00 μg/ml-Suduxing treated HepG2.2.15

value: 48hr in 0.00 μg/ml-Suduxing


title: Spleen Teff CN rep4

description: Spleen Teff CN

value: CN


title: Spleen Teff CN rep5

description: Spleen Teff CN rep5


title: 9: invitroCells_48hr_0.00 μg/ml_rep1


title: Spleen Treg IL-2 rep4

description: Spleen Treg IL-2


title: 8: invitroCells_48hr_0.01 μg/ml_rep1

description: Gene expression after 48hr in 0.01μg/ml-Suduxing treated HepG2.2.15


title: Ma-Mel-54a

type: genomic

city: Essen

first: Klaus

middle: Georg

last: Griewank

address: Hufelandstr. 55

department: Dermatology

institute: University of Duisburg-Essen

description: CytoScanHD-Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: According to manufacturers instructions.

data_processing:
The array image was acquired using Affymetrix® Chromosome Analysis Suite (ChAS) Software
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

source_name: melanoma cell line from LN metastasis

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines and peripheral blood cells using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and PicoGreen

tag: patient id

value: melanoma cell line from LN metastasis


title: Spleen Treg CN rep4

description: Spleen Treg CN


title: 8: invitroCells_48hr_0.001 μg/ml_rep1

description: Gene expression after 48hr in 0.001μg/ml-Suduxing treated HepG2.2.15


title: Ma-Mel-54-EDTA

description: CytoScanHD-Array

source_name: germline DNA of Ma-Mel-54 Cell lines

tag: tissue

value: peripheral blood


title: 8: invitroCells_48hr_0.00 μg/ml_rep1


title: Spleen Teff TAC+IL-2 rep2

description: Spleen Teff TAC+IL-2


title: Spleen Treg IL-2 rep3

description: Spleen Treg IL-2


title: Spleen Treg TAC+IL-2 rep1

description: Spleen Treg TAC+IL-2


title: Spleen Treg CN rep3

description: Spleen Treg CN


title: Spleen Teff TAC rep3

description: Spleen Teff TAC


title: Spleen Treg TAC+IL-2 rep2

description: Spleen Treg TAC+IL-2


title: Spleen Teff TAC+IL-2 rep1

description: Spleen Teff TAC+IL-2


title: Ma-Mel-61e

description: CytoScanHD-Array


title: Ma-Mel-36-EBV

description: CytoScanHD-Array

source_name: germline DNA of Ma-Mel-36 Cell lines


title: Spleen Teff TAC rep1

description: Spleen Teff TAC


title: Ma-Mel-36-Bulk

description: CytoScanHD-Array


title: Ma-Mel-61g

description: CytoScanHD-Array


title: Spleen Treg TAC rep2

description: Spleen Treg TAC


title: C.elegans L4_pOPC7

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

description:
Raised on NGM supplemented with 2 µg/mL pOPC7 for 48 hours (L1 to L4 stage)
pOPC7 exposed

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing: To summarize the probe level data in the Affymetrix GeneChip® arrays, CEL files of C.elegans pOPC7 control condition was imported into the Affymetrix Expression ConsoleTM software for the quality control, data normalization and fold change algorithm. RMA normalization was carried out in R console (version 3.1.1). Exported excel file with all genes and their exposure/control fold changes are listed.

organism: Caenorhabditis elegans

source_name: C.elegans L4_pOPC7

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach preparation and grew to L4 stage.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

tag: developmental stage

tag: gender

value: hermaphrodite


title: Ma-Mel-36-HLA-DR+ (HLA-DR_sens)

description: CytoScanHD-Array


title: C.elegans L4_control

description:
Raised on NGM for 48 hours (L1 to L4 stage)
Control (unexposed)

source_name: C.elegans L4_control

value: control


title: Ma-Mel-54b

description: CytoScanHD-Array


title: Spleen Teff IL-2 rep2

description: Spleen Teff IL-2

tag: cell type


title: Spleen Treg TAC rep1

description: Spleen Treg TAC

tag: treatment


title: Ma-Mel-61c

description: CytoScanHD-Array


title: Spleen Treg IL-2 rep1

description: Spleen Treg IL-2


title: Spleen Teff CN rep2

description: Spleen Teff CN


title: Spleen Treg IL-2 rep2

description: Spleen Treg IL-2


title: Spleen Treg CN rep2

description: Spleen Treg CN


title: Spleen Teff IL-2 rep1

description: Spleen Teff IL-2


title: Spleen Teff CN rep1

description: Spleen Teff CN


title: Spleen Teff CN rep3

description: Spleen Teff CN


title: Spleen Treg CN rep1

description: Spleen Treg CN


title: Ma-Mel-61h

description: CytoScanHD-Array


title: Ma-Mel-61b

description: CytoScanHD-Array


title: Ma-Mel-36-HLA-DR- (HLA-DR_res)

description: CytoScanHD-Array


title: Colon polyp with villous component from patient 4

status: Public on May 23 2017

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: polyp

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

source_name: polyp with villous component

label_protocol: Standard Affymetrix protocol

growth_protocol: Polyps and adjacent normal mucosa were obtained from patients by biopsy forceps, polypectomy or endoscopic mucosal resection. Once specimens were obtained, a  small piece of tissues were sent for RNA analysis.

extract_protocol: Total RNA was extracted with TRIsure (bioline) by following manufacturer's instructions.

treatment_protocol: Tissues obtained from human normal colon mucosa and polyps were putted into TRIzol and sent to RNA extraction immediately.

value: Colon polyp


title: Ma-Mel-61a

description: CytoScanHD-Array


title: Colon polyp with villous component from patient 3

description: polyp


title: Colon polyp with villous component from patient 1

description: polyp


title: Colon polyp with villous component from patient 5

description: polyp


title: Normal colon mucosa tiisue from patient 3

description: Normal mucosa

source_name: normal colon mucosa cells

value: colon normal mucosa


title: Normal colon mucosa tiisue from patient 2

description: Normal mucosa


title: Normal colon mucosa tiisue from patient 5

description: Normal mucosa


title: Normal colon mucosa tiisue from patient 4

description: Normal mucosa


title: Ma-Mel-61_germline

description: CytoScanHD-Array

source_name: germline DNA of Ma-Mel-61 Cell lines


title: Colon polyp with villous component from patient 2

description: polyp


title: 200kPa PAG_rep1

city: Minneapolis

first: David

middle: J.

last: Odde

state: MN

address: 312 Church St. SE

department: Biomedical Engineering

institute: University of Minnesota

description:
SAMPLE 7
200kPa replicate #1

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Assay Guide was used

scan_protocol: Illumina iScan machine was used with the standard iScan image acquisition protocol controlled by iScan Control Software

data_processing: Illumina Inc. GenomeStudio version 1.9.0, Normalization = none

source_name: 200kPa PAG

label_protocol: Illumina® TotalPrep™-96 RNA Amplification Kit was used for generating biotinylated amplified RNA.

growth_protocol: U251 cells were cultured on large polyacrylamide gels covering the surface of a one well chamber glass slide (Lab-Tek 154453). Cells were cultured on U251 cells were cultured in a 37oC 5% CO2 incubator in media comprised of 45.5% F12+GlutaMAX 371 supplement (Gibco 31765-035), 45.5% high glucose Dulbecco’s Modified Eagle Medium 372 (DMEM, Gibco 10566-024), 8% heat-inactivated fetal bovine serum (FBS, Gibco 10438-026), 373 and 1% penicillin/streptomycin solution (Cellgro 30-001-CI). After one day of culture on the gels, mRNA was purified from the cells using an RNeasy Mini Kit (Qiagen 74104).

extract_protocol: RNeasy Mini Kit (Qiagen 74104) protocol was used

treatment_protocol: U251 cells were cultured on different stiffnesses of polyacrylamide hydrogels

tag: origin

value: Glioblastoma

value: Male

tag: culture condition

value: 200kPa PAG


title: 200kPa PAG_rep2

description:
SAMPLE 8
200kPa replicate #2


title: 4.6kPa PAG_rep1

description:
SAMPLE 1
4.6kPa replicate #1

source_name: 4.6kPa PAG

value: 4.6kPa PAG


title: 20kPa PAG_rep1

description:
SAMPLE 4
20kPa replicate #1

source_name: 20kPa PAG

value: 20kPa PAG


title: TCP_rep2

description:
SAMPLE 11
Tissue culture plastic replicate #2

source_name: TCP

value: Tissue culture plastic


title: 200kPa PAG_rep3

description:
SAMPLE 9
200kPa replicate #3


title: 4.6kPa PAG_rep3

description:
SAMPLE 3
4.6kPa replicate #3


title: TCP_rep3

description:
SAMPLE 12
Tissue culture plastic replicate #3


title: 20kPa PAG_rep2

description:
SAMPLE 5
20kPa replicate #2


title: TCP_rep1

description:
SAMPLE 10
Tissue culture plastic replicate #1


title: 4.6kPa PAG_rep2

description:
SAMPLE 2
4.6kPa replicate #2


title: 20kPa PAG_rep3

description:
SAMPLE 6
20kPa replicate #3


title: Non-tumor lung_patient 12_6cm

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Laval University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by log2-transformation and quantile normalized using the lumi package in R (Du et al 2008)

source_name: patient 12 non-tumor lung at 6 cm

label_protocol: IlluminaTotalPrep™-96 RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted from 30 mg of frozen lung specimens using RNeasy Plus Universal Mini kit (Qiagen)

tag: age

value: male


title: Non-tumor lung_patient 11_4cm

source_name: patient 11 non-tumor lung at 4 cm


title: Lung adenocarcinoma_patient 12

source_name: patient 12 tumor


title: Spleen Teff TAC rep2

description: Spleen Teff TAC

source_name: FOXP3-YFP mice, Spleen sorted T cells

value: Teff

value: TAC


title: Non-tumor lung_patient 11_0cm

source_name: patient 11 non-tumor lung at 0 cm


title: Non-tumor lung_patient 12_2cm

source_name: patient 12 non-tumor lung at 2 cm


title: Non-tumor lung_patient 12_0cm

source_name: patient 12 non-tumor lung at 0 cm


title: Non-tumor lung_patient 10_4cm

source_name: patient 10 non-tumor lung at 4 cm

value: female


title: Non-tumor lung_patient 12_4cm

source_name: patient 12 non-tumor lung at 4 cm


title: Non-tumor lung_patient 10_6cm

source_name: patient 10 non-tumor lung at 6 cm


title: Non-tumor lung_patient 11_6cm

source_name: patient 11 non-tumor lung at 6 cm


title: Lung adenocarcinoma_patient 11

source_name: patient 11 tumor


title: Non-tumor lung_patient 10_2cm

source_name: patient 10 non-tumor lung at 2 cm


title: Lung adenocarcinoma_patient 10

source_name: patient 10 tumor


title: Non-tumor lung_patient 10_0cm

source_name: patient 10 non-tumor lung at 0 cm


title: Non-tumor lung_patient 9_6cm

source_name: patient 9 non-tumor lung at 6 cm


title: Lung adenocarcinoma_patient 9

source_name: patient 9 tumor


title: Non-tumor lung_patient 9_2cm

source_name: patient 9 non-tumor lung at 2 cm


title: Non-tumor lung_patient 9_0cm

source_name: patient 9 non-tumor lung at 0 cm


title: Non-tumor lung_patient 8_4cm

source_name: patient 8 non-tumor lung at 4 cm


title: Non-tumor lung_patient 8_6cm

source_name: patient 8 non-tumor lung at 6 cm


title: Non-tumor lung_patient 8_0cm

source_name: patient 8 non-tumor lung at 0 cm


title: Lung adenocarcinoma_patient 8

source_name: patient 8 tumor


title: Non-tumor lung_patient 7_4cm

source_name: patient 7 non-tumor lung at 4 cm


title: Non-tumor lung_patient 8_2cm

source_name: patient 8 non-tumor lung at 2 cm


title: Non-tumor lung_patient 9_4cm

source_name: patient 9 non-tumor lung at 4 cm


title: Non-tumor lung_patient 7_6cm

source_name: patient 7 non-tumor lung at 6 cm


title: Non-tumor lung_patient 7_2cm

source_name: patient 7 non-tumor lung at 2 cm


title: Lung adenocarcinoma_patient 7

source_name: patient 7 tumor


title: Non-tumor lung_patient 6_2cm

source_name: patient 6 non-tumor lung at 2 cm


title: Non-tumor lung_patient 5_4cm

source_name: patient 5 non-tumor lung at 4 cm


title: Non-tumor lung_patient 3_6cm

source_name: patient 3 non-tumor lung at 6 cm


title: Non-tumor lung_patient 4_4cm

source_name: patient 4 non-tumor lung at 4 cm


title: Non-tumor lung_patient 3_4cm

source_name: patient 3 non-tumor lung at 4 cm


title: Non-tumor lung_patient 5_6cm

source_name: patient 5 non-tumor lung at 6 cm


title: Non-tumor lung_patient 6_4cm

source_name: patient 6 non-tumor lung at 4 cm


title: Lung adenocarcinoma_patient 5

source_name: patient 5 tumor


title: Lung adenocarcinoma_patient 6

source_name: patient 6 tumor


title: Non-tumor lung_patient 6_0cm

source_name: patient 6 non-tumor lung at 0 cm


title: Non-tumor lung_patient 6_6cm

source_name: patient 6 non-tumor lung at 6 cm


title: Non-tumor lung_patient 4_0cm

source_name: patient 4 non-tumor lung at 0 cm


title: Non-tumor lung_patient 4_6cm

source_name: patient 4 non-tumor lung at 6 cm


title: Non-tumor lung_patient 5_2cm

source_name: patient 5 non-tumor lung at 2 cm


title: Non-tumor lung_patient 4_2cm

source_name: patient 4 non-tumor lung at 2 cm


title: Non-tumor lung_patient 3_0cm

source_name: patient 3 non-tumor lung at 0 cm


title: Lung adenocarcinoma_patient 3

source_name: patient 3 tumor


title: Non-tumor lung_patient 2_2cm

source_name: patient 2 non-tumor lung at 2 cm


title: Non-tumor lung_patient 2_6cm

source_name: patient 2 non-tumor lung at 6 cm


title: Non-tumor lung_patient 1_6cm

source_name: patient 1 non-tumor lung at 6 cm


title: Lung adenocarcinoma_patient 2

source_name: patient 2 tumor


title: Non-tumor lung_patient 1_2cm

source_name: patient 1 non-tumor lung at 2 cm


title: Non-tumor lung_patient 1_0cm

source_name: patient 1 non-tumor lung at 0 cm


title: Lung adenocarcinoma_patient 1

source_name: patient 1 tumor


title: Non-tumor lung_patient 5_0cm

source_name: patient 5 non-tumor lung at 0 cm


title: Non-tumor lung_patient 2_4cm

source_name: patient 2 non-tumor lung at 4 cm


title: Non-tumor lung_patient 3_2cm

source_name: patient 3 non-tumor lung at 2 cm


title: Bone marrow MSC 3387 LSS

city: Houston

first: Pamela

middle: L

last: Wenzel

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharmacology

institute: University of Texas Health Science Center at Houston

description: 3387 LSS

data_processing:
Raw signals of all the build-in controls were checked as quality control for the performance of the arrays. Sample-independent controls were used to check: a. Hybridization (control molecules at low, medium and high concentrations); b. Signal generation (background, noise, biotin labeling and hybridization at high and low stringency). Housekeeping genes were used as sample-dependent controls.
All data processing, including quantile normalization and background correction, were performed using GenomeStudio software (Illumina, Inc.).

source_name: Bone marrow MSC 3387 LSS

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

growth_protocol: Bone marrow MSCs were derived from whole bone marrow from independent human donors (AllCells). Briefly, mononuclear cells were enriched in the buffy layer of whole bone marrow by phase separation in Ficoll-Paque. Cells were either cryopreserved or resuspended for immediate expansion in complete culture medium consisting of MEM-α (Thermo Scientific), 20% fetal bovine serum (Atlanta Biologicals), 100 units/ml penicillin (Gibco), 100 μg/ml streptomycin (Gibco), and 2 mM L-glutamine (Gibco). Nonadherent cells were removed after 2 days. Adherent colonies were expanded further and frozen as Passage 1. Thawed MSCs were plated at 1x10^5 cells/ml, and medium was changed every three days. At 80% confluence, cells were passaged into IBIDI channels (μ-Slide VI 0.4) at a density of 3x10^6 cells/ml for culture under static or LSS conditions.

extract_protocol: Cells were directly lysed on microfluidic slides with RLT lysis buffer. Total RNA was immediately extracted with the QIAGEN RNeasy kit.

treatment_protocol: Microfluidics consisted of IBIDI VI^0.4 channel slides in line with a recirculating medium system driven by a peristaltic pump (REGLO analog MS4/12, Ismatec) to produce laminar shear stress (LSS) of 15 dyne/cm2. After 18 hours of attachment to the 100 ng/ml fibronectin-coated culture surface, non-adherent cells were washed away and cells were cultured for 6 hours in static conditions (0 dyne/cm^2) or in the presence of LSS (15 dyne/cm^2).

tag: donor id

tag: age of donor (years)

tag: weight of donor (pounds)

tag: height of donor (feet, inches)

tag: smoker

value: No

tag: blood type

value: O+

tag: race

value: Caucasian

value: Bone marrow MSC

tag: duration

value: 6 hours

tag: force

value: 15 dyne/cm^2


title: Bone marrow MSC 3390 LSS

description: 3390 LSS

source_name: Bone marrow MSC 3390 LSS

value: A+


title: Non-tumor lung_patient 1_4cm

source_name: patient 1 non-tumor lung at 4 cm


title: Bone marrow MSC 3387 Static

description: 3387 Static

source_name: Bone marrow MSC 3387 Static

value: 0 dyne/cm^2


title: Bone marrow MSC 3388 Static

description: 3388 Static

source_name: Bone marrow MSC 3388 Static

value: Female

value: Black or African-American


title: Bone marrow MSC 3390 Static

description: 3390 Static

source_name: Bone marrow MSC 3390 Static

value: Male


title: Non-tumor lung_patient 11_2cm

source_name: patient 11 non-tumor lung at 2 cm


title: Bone marrow MSC 3388 LSS

description: 3388 LSS

source_name: Bone marrow MSC 3388 LSS


title: Mouse T cell_1wkTamoxifen_ERCre-LAT f/-_LATWT_rep1

city: San Francisco

first: Jeroen

last: Roose

address: 513 Parnassus Ave, HSW 1330A

department: Anatomy

institute: University of California, San Francisco

hyb_protocol: Equal amounts of labeled material were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 hours and the arrays were scanned using the Agilent microarray scanner in the UCSF Shared Microarray Core Facility.

scan_protocol: Arrays were scanned using an Agilent 2uM scanner

data_processing: Raw signal intensities were extracted with Feature Extraction v10.5 software. The dataset was normalized using the quantile normalization method, and the one-way ANOVA model was used to estimate relevant statistics for the comparisons of interest. The R package (limma in bioconductor) was utilized for these procedures.

source_name: LAT WT_tamoxifen for 1 wk_sorted naïve T cell

label_protocol: The RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits (using manufacturer's protocol).

extract_protocol: Cells were lysed in Trizol and RNA was isolated using the RNeasy Minelute kit (Qiagen). RNA was further cleaned up using the RNA Clean and Concentrator-5 kit (Zymo Research). RNA was quantified on a Nanodrop and quality was monitored using an Agilent 2100 Bioanalyzer.

tag: strain background

tag: Sex

tag: genotype/variation

value: LAT WT

tag: treated with

value: tamoxifen for 1 wk

value: sorted naïve T cell (CD44low CD4+)


title: Mouse T cell_1wkTamoxifen_ERCre-LAT f/-_LATWT_rep2

tag: cell type


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/-_LATKO_rep1

source_name: LAT KO_tamoxifen for 4 wks_sorted naïve T cell

value: male

value: LAT KO

value: tamoxifen for 4 wks


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/-_LATKO_rep1

source_name: LAT KO_tamoxifen for 1 wk_sorted naïve T cell

value: female


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/m_LATY136F_rep1

source_name: LAT Y136F_tamoxifen for 4 wks_sorted naïve T cell

value: LAT Y136F


title: Normal colon mucosa tiisue from patient 1

description: Normal mucosa

source_name: normal colon mucosa cells

tag: tissue

value: colon normal mucosa


title: Mouse T cell_4wkTamoxifen_ERCre-LAT f/-_LATWT_rep3

source_name: LAT WT_tamoxifen for 4 wks_sorted naïve T cell


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/m_LATY136F_rep2

source_name: LAT Y136F_tamoxifen for 1 wk_sorted naïve T cell


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/m_LATY136F_rep2


title: Mouse T cell_4wkTamoxifen_ERCre-LAT f/-_LATWT_rep1


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/m_LATY136F_rep3


title: FC TN2

city: Berlin

first: Dieter

last: Blottner

address: Phillipstrasse 12

institute: Charité Universitaetsmedizin Berlin

description: Gene expression data from tongue of mouse  haused in a standard animal facility (during the Bion  flight) for 30 days

hyb_protocol: 15 μg of each labeled and fragmented cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix GeneChip Mouse 430A 2.0 Array

scan_protocol: Arrays were scanned at 1.56-μm resolution using the Affymetrix GeneChip System confocal scanner 3000

data_processing:
Data analysis was performed importing cel files to the Partek® Genomics Suite® 6.6 software. Robust Multichip Average algorithm (RMA) was used for data normalization.
Annotation (Mouse430A_2.na35.annot.csv ) and cdf Files from: http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430A-20.

label_protocol: The amplification and labeling of 100 ng of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA) using the GeneChip® 3’ IVT Express Protocol.

extract_protocol: Total RNA was isolated from mouse longissimus dorsi (n = 5) and tongue (n = 3) muscles of each experimental group (BF, BG and FC) using a two step isolation protocol: modified Chomczinsky extraction followed by column purification (RNeasy micro Kit, Qiagen, Hilden,Germany)

value: tongue muscle

tag: genotype

value: Male C57/BL6 mice


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/m_LATY136F_rep1


title: Mouse T cell_1wkTamoxifen_ERCre-LAT f/-_LATWT_rep3


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/-_LAT KO_rep2


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/-_LATKO_rep2


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/-_LATKO_rep3


title: Mouse T cell_4wkTamoxifen_ERCre+LAT f/m_LATY136F_rep3


title: Mouse T cell_4wkTamoxifen_ERCre-LAT f/-_LATWT_rep2


title: FC TN1

source_name: mouse  haused in a standard animal facility (during the Bion  flight)


title: Mouse T cell_1wkTamoxifen_ERCre+LAT f/-_LAT KO_rep3


title: BG TN3

description: Gene expression data from tongue of mouse  haused for 30 days in a replicate habitat of  Bion M1 biosatellite

source_name: mouse  haused in a replicate habitat of  Bion M1 biosatellite


title: BF TN2

description: Gene expression data from tongue muscle of mouse flown 30 days aboard on Bion M1

source_name: mouse flown aboard on Bion M1


title: BG TN2


title: BG TN1


title: BF TN1


title: BF TN3


title: FC LD3

description: Gene expression data from longissimus dorsi of mouse  haused in a standard animal facility (during the Bion  flight) for 30 days

value: longissimus dorsi muscle


title: BG LD4

description: Gene expression data from longissimus dorsi of mouse  haused for 30 days in a replicate habitat of  Bion M1 biosatellite


title: FC LD1


title: BG LD2


title: FC LD5


title: BG LD5


title: BG LD3


title: FC LD2


title: FC LD4


title: BG LD1


title: BF LD3

description: Gene expression data from longissimus dorsi muscle of mouse flown 30 days aboard on Bion M1


title: BF LD5


title: BF LD1


title: Polysomal fraction of 5FU-untreated HCT116 cells, biological rep3

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Analyses were obtained using the Affymetrix Power Tools software ; core probesets, and antigenomic probes for background correction. The plier-gcbg-sketch algorithm was used to determine gene-level expression data and the RMA-sketch algorithm for the exon-level expression data.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps (for gene-level analyses) and HuEx-1_0-st-v2.r2.dt1.hg18.core.ps (for exon-level analyses)

source_name: HCT116 cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HCT116 cells were cultured in DMEM medium with 10 % SVF and 1% antibiotict

extract_protocol: Total RNA was isolated using Trizol LS total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: HCT116 cells were treated or not by 10µM 5-FU for 24h

tag: treatment

value: No treatment

tag: fraction

value: polysome


title: Non-Polysomal fraction of 5FU-untreated HCT116 cells, biological rep3

value: non-polysome


title: BF LD2


title: Non-Polysomal fraction of 5FU-treated HCT116 cells, biological rep3


title: Non-Polysomal fraction of 5FU-untreated HCT116 cells, biological rep2


title: Polysomal fraction of 5FU-untreated HCT116 cells, biological rep2


title: BF LD4


title: Polysomal fraction of 5FU-treated HCT116 cells, biological rep3


title: CTRL  K562  untreated vs treated replicate 3

status: Public on May 22 2017

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

country: Italy

institute: IGB - Institute of Genetics and Biophysics - CNR

description: Biological replicate 3 of3. Control K562 , untreated, vs K562  SAHA treated

hyb_protocol: LC SCIENCES service  procedure

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: LC SCIENCES service  procedure using global normalization method.

source_name: K562 (Human erythromyeloblastoid leukemia cell line)_untreated

label_protocol: LC SCIENCES service  procedure

growth_protocol: K562, Human erythromyeloblastoid leukemia cell line was cultured in RPMI 1640, containing 10% decomplemented FBS.

extract_protocol: Total RNA, including miRNA, extracted using Trizol following protocol described in method and material session

treatment_protocol: SAHA treatment at 5 µM concentration for 6 hours

tag: cell line

value: erythromyeloblastoid leukemia

source_name: K562 (Human erythromyeloblastoid leukemia cell line) treated with SAHA at 5µM concentration for 6 hours


title: CTRL U937 untreated vs treated replicate 3

description: Biological replicate 3 of3. Control U937, untreated, vs U937 SAHA treated

data_processing: LC SCIENCES service  procedure using global normalization

source_name: U937 (Human leukemic monocyte lymphoma cell line)_untreated

growth_protocol: U937, Human leukemic monocyte lymphoma cell line was cultured in RPMI 1640, containing 10% decomplemented FBS.

value: leukemic monocyte lymphoma

source_name: U937 (Human leukemic monocyte lymphoma cell line) treated with SAHA at 5ÂµM concentration for 6 hours


title: CTRL  K562  untreated vs treated replicate 2

description: Biological replicate 2 of3. Control K562 , untreated, vs K562  SAHA treated


title: GMP_ BM_ACKR1-KO rep1

city: Munich

first: Johan

last: Duchene

state: State...

address: Pettenkorfer Str 8

institute: LMU

hyb_protocol: Samples were hybridized to the SurePrint G3 Mouse GE 8x60K Microarray (Agilent-028005).

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner (scan resolution: 3µm)

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) with no background substraction. Feature intensities were background-subtracted according to the normal-exponential convolution model and normalised using quantile normalisation.

label_protocol: Sample labeling and hybridization was performed according to the manufacturer’s protocols using the One-Color  Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version)

growth_protocol: ACKR1-deficient (KO) mice were backcrossed for more than 12 generations onto a C57Bl/6J background and maintained as a heterozygous breed. WT and ACKR1-KO littermates were used. Mice were housed in specific pathogen-free facility.

extract_protocol: RNA was extracted from FACS sorted LSK (lineage-neg, Sca1-pos, cKit-pos) and GMP (lineage-neg, Sca1-neg, cKit-pos, CD34-pos, CD16/32-pos)  populations using Trizol.

treatment_protocol: Bone marrow of 12wks old wild-type and ACKR1 deficient mice was flushed and cells were stained with appropriate antibodies for LSK and GMP (Granulocyte-macrophage progenitor).

tag: strain

tag: age

tag: gender

value: Bone marrow

value: FACS-sorted GMP (Granulocyte-macrophage progenitor; lineage-neg, Sca1-neg, cKit-pos, CD34-pos, CD16/32-pos)


title: GMP_ BM_WT rep1

value: wild type


title: CTRL  KASUMI-1  untreated vs treated replicate 3

description: Biological replicate 3 of3. Control KASUMI-1, untreated, vs KASUMI-1 SAHA treated

source_name: KASUMI-1 (acute myeloblastic leukemia cell line)_untreated

growth_protocol: KASUMI-1 (acute myeloblastic leukemia cell line) was cultured in RPMI 1640, containing 20% decomplemented FBS.

value: acute myeloblastic leukemia

source_name: KASUMI-1 (acute myeloblastic leukemia cell line) treated with SAHA at 5µM concentration for 6 hours


title: CTRL  KASUMI-1  untreated vs treated replicate 2

description: Biological replicate 2 of3. Control KASUMI-1, untreated, vs KASUMI-1 SAHA treated


title: CTRL  KASUMI-1  untreated vs treated replicate 1

description: Biological replicate 1 of3. Control KASUMI-1, untreated, vs KASUMI-1 SAHA treated


title: GMP_ BM_WT rep2


title: LSK_ BM_WT rep2

value: FACS-sorted LSK (lineage-neg, Sca1-pos, cKit-pos)


title: GMP_ BM_ACKR1-KO rep2


title: CTRL U937 untreated vs treated replicate 2

description: Biological replicate 2 of3. Control U937, untreated, vs U937 SAHA treated

source_name: U937 (Human leukemic monocyte lymphoma cell line)_untreated


title: CTRL  K562  untreated vs treated replicate 1

description: Biological replicate 1 of3. Control K562 , untreated, vs K562  SAHA treated


title: LSK_ BM_ACKR1-KO rep1


title: LSK_ BM_ACKR1-KO rep2


title: CTRL  U937 untreated vs treated replicate 1

description: Biological replicate 1 of3. Control U937, untreated, vs U937 SAHA treated

source_name: U937 (Human leukemic monocyte lymphoma cell line)_untreated


title: BY4741 with 0 μg/mL HNK, biological rep1

city: Wuhu

first: xiao

middle: long

last: zhu

state: Anhui

address: 2 Zheshan western road

institute: Yijishan Hospital

description: Gene expression data from wild-type S. cerevisiae (BY4741) cells which were treated with 0 μg/mL HNK for 2 h.

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

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

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

organism: Saccharomyces cerevisiae

source_name: BY4741 with 0 μg/mL HNK for 2h

label_protocol: Biotin-labeled cRNA were prepared using MessageAmp™ Premier RNA Amplification Kit (Ambion) and the protocol of the kit manufacturer from 100 ng total RNA.

growth_protocol: Wild-type S. cerevisiae (BY4741) was grown in YPD to an OD600 of ~0.4 in 10 mL of medium.

extract_protocol: Extraction of Total RNA from yeast by phenol method

treatment_protocol: Cells were treated with 12 μg/mL HNK for 2 h (or an equal volume of ethanol for controls)


title: Non-polysomal  fraction of 5FU-treated HCT116 cells, biological rep2


title: BY4741 with 12 μg/mL HNK, biological rep2

description: Gene expression data from wild-type S. cerevisiae (BY4741) cells which were treated with 12 μg/mL HNK for 2 h.

source_name: BY4741 with 12 μg/mL HNK for 2h


title: BY4741 with 0 μg/mL HNK, biological rep2


title: LSK_ BM_WT rep1


title: BY4741 with 12 μg/mL HNK, biological rep1


title: EBC1-PR2

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Cell line with adquired resistance to MET tyrosine kinase inhibitors

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: EBC1 cells

value: lung cancer

tag: phenotype


title: EBC1-PR4

value: adquired resistance to MET tyrosine kinase inhibitors


title: EBC1-C1


title: EBC1-V8


title: ASCL1 siRNA 3, biological rep3

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

description: Control RNA 48 hrs post transfection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip  Scanner 3000

data_processing: GCOS software

source_name: Glioma cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: U87MG glioma cells were grown in DMEM medium containing 10% FBS.

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

treatment_protocol: 100nM scrambled or siRNA against ASCL1

tag: transfection

value: siRNA targeted against ASCL1


title: Scrambled siRNA 1, biological rep2

description: Control RNA 48 hrs post transfection

value: scrambled siRNA


title: EBC1

source_name: Parental cell line

value: sensitive to TKIs against MET


title: ASCL1 siRNA 1, biological rep1

description: Control RNA 48 hrs post transfection


title: colonic organoid, PPARγ KO, vehicle, replicate 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2)

source_name: organoid isolated from colon from intestinal epithelium-specific PPARγ (PparγΔIEC) kockout mouse, treated with vehicle (DMSO, 0.1%) for 24 hrs

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Intestine epithelial-selective PPARγ knockout (PparγΔIEC) mice  were generated by cross-breeding of mice with loxP sites flanking exon 1 and 2 of the Pparγ gene (PPARγloxP; described by He et al., 2003, PMID: 14660788), with mice harboring cre-recombinase under the control of the villin promoter (Villin-Cre mice; described by Madison et al., 2002, PMID: 12065599). Animals were maintained on a C57BL/6J background. Animals were housed in a light- and temperature-controlled facility and received standard laboratory chow (RMH-B, AB diets, Woerden, The Netherlands) and water ad libitum. For organoid isolation only male homozygous knockout mice (PparγΔIEC) and wild-type (WT) littermates were used.

extract_protocol: Total RNA was prepared from the organoid samples using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Colonic organoids were isolated essentially as described before (Sato et al. 2011, PMID: 21889923), with minor modifications. Briefly, colon tissue was isolated from 3 WT and 3 PparγΔIEC mice and washed with ice-cold PBS, where after the epithelial layer was gently scraped. The remaining tissue with intact crypts was washed several times with ice-cold PBS and subsequently incubated for 1hr in 5mM EDTA in PBS to isolate crypt cells. The washed and filtered crypt cells were embedded in Matrigel and seeded in a 24-well plates containing advanced DMEM/F12 supplemented with Penicillin/Streptomycin, 10 mM Hepes, Glutamax, Wnt, n-Acetyl-cysteine, growth factors (Noggin, R-spondin, mEGF), B27, kinase inhibitor, Nicotinamide, A83 and p38. Organoids were treated with Rosiglitazone (1µM). Vehicle only (DMSO, 0.1%) served as control. After 24 hours organoids were harvested and stored at -80C until RNA isolation.

tag: sexe

value: male

tag: mouse donor id

value: PPARγ KO

value: vehicle (0.1% DMSO)

tag: treatment duration (h)


title: colonic organoid, PPARγ KO, Rosiglitazone, replicate 2

source_name: organoid isolated from colon from intestinal epithelium-specific PPARγ (PparγΔIEC) kockout mouse, treated with Rosiglitazone (1 µM) for 24 hrs

value: Rosiglitazone (1 µM)


title: colonic organoid,wild type, vehicle, replicate 1

source_name: organoid isolated from colon fromwild type (C57BL/6J) mouse, treated with vehicle (DMSO, 0.1%) for 24 hrs

value: WT


title: colonic organoid, wild type, Rosiglitazone, replicate 3

source_name: organoid isolated from colon from wild type (C57BL/6J) mouse, treated with Rosiglitazone (1 µM) for 24 hrs


title: EBC1-PR3


title: colonic organoid, wild type, Rosiglitazone, replicate 2


title: Scrambled siRNA 1, biological rep3

description: Control RNA 48 hrs post transfection


title: colonic organoid, PPARγ KO, Rosiglitazone, replicate 3


title: Polysomal fraction of 5FU-treated HCT116 cells, biological rep2

source_name: HCT116 cells

value: polysome


title: Scrambled siRNA 1, biological rep1

description: Control RNA 48 hrs post transfection


title: colonic organoid, wild type, Rosiglitazone, replicate 1


title: colonic organoid, PPARγ KO, Rosiglitazone, replicate 1


title: AH016-10

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: single replicate

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: iPS cell line derived from dermal fibroblasts, control donor AH016, clone 10

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: induced pluripotent stem (iPS) cell line derived from dermal fibroblasts

tag: culture conditions

value: mTeSR-1 + matrigel


title: AH016-6

description: single replicate

source_name: iPS  cell line derived from dermal fibroblasts, control donor AH016, clone 6


title: EBC1-PR1


title: SFC841-03-02

description: single replicate

source_name: iPS cell line derived from dermal fibroblasts, control donor 841, clone 2


title: METs6

first: Tiewei

last: Cheng

state: United States

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

description: mouse #6

data_processing: The data were normalized using quantile normalization in the Linear Models for Microarray Data (LIMMA) package in the R language environment.

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

growth_protocol: Spontaneous tumor tissues including primaries, lymph node metastasis, distant metastasis (lung and bone) and circulating tumor cells (CTCs)  were obtained from orthotopic recycling of UM-UC3 in vivo

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

tag: xenograft tissue

value: distant metastasis


title: CTC6

description: mouse #6

value: circulation tumor cells


title: CTC5

description: mouse #5


title: METs5

description: mouse #5


title: CTC2

description: mouse #2


title: CTC4

description: mouse #4


title: METs4

description: mouse #4


title: METs3

description: mouse #3


title: LN4

description: mouse #4

value: lynph node metastasis


title: LN5

description: mouse #5


title: CTC1

description: mouse #1


title: METs2

description: mouse #2


title: LN3

description: mouse #3


title: LN6

description: mouse #6


title: ASCL1 siRNA 2, biological rep2

description: Control RNA 48 hrs post transfection


title: METs1

description: mouse #1


title: AH016-6 [SNP genotype]

description:
iPS-AH016-6
cluster file: HumanCytoSNP-12v2-1_H
manifest: HumanCytoSNP-12v2-1_H

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file and manifest HumanCytoSNP-12v2-1_H provided by Illumina for GPL13829, and humanomniexpress_24v1-0_a for GPL19699. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: iPS cell line derived from dermal fibroblasts, control donor AH017, clone 6

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest


title: LN1

description: mouse #1


title: PM6

description: mouse #6

value: primaries


title: PM5

description: mouse #5


title: LN2

description: mouse #2


title: PM4

description: mouse #4


title: PM1

description: mouse #1


title: PM3

description: mouse #3


title: PM2

description: mouse #2


title: AH016-10 [SNP genotype]

description:
iPS-AH016-10
cluster file: HumanCytoSNP-12v2-1_H
manifest: HumanCytoSNP-12v2-1_H

source_name: iPS cell line derived from dermal fibroblasts, control donor AH017, clone 10


title: colonic organoid,wild type, vehicle, replicate 2


title: PLX4720_10uM_WM9_96h_42

city: Philadelphia

first: Gao

last: Zhang

state: PA

address: 3601 SPRUCE ST

department: Molecular and Cellular Oncogenesis Program

institute: Wistar Institute

description:
PLX4720_10uM_WM9_96h_42
PLX4720 at 96h replicate 2

data_processing: The data were normalized using quantile normalization with lumi in R

source_name: human melanoma cells

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

growth_protocol: Human melanoma cells WM9 were grown in 10% RPMI-1640 medium before they reached the 70% confluency.

extract_protocol: Cells were washed with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Human melanoma cells were treated with BRAF inhibitor PLX4720 at 10uM.

tag: disease state

value: skin cancer

value: WM9 melanoma cells

tag: agent

value: BRAF inhibitor PLX4720

tag: time


title: PLX4720_10uM_WM9_72h_37

description:
PLX4720_10uM_WM9_72h_37
PLX4720 at 72h replicate 2


title: PLX4720_10uM_WM9_12h_21

description:
PLX4720_10uM_WM9_12h_21
PLX4720 at 12h replicate 1


title: PLX4720_10uM_WM9_72h_38

description:
PLX4720_10uM_WM9_72h_38
PLX4720 at 72h replicate 1


title: PLX4720_10uM_WM9_60h_34

description:
PLX4720_10uM_WM9_60h_34
PLX4720 at 60h replicate 2


title: PLX4720_10uM_WM9_24h_26

description:
PLX4720_10uM_WM9_24h_26
PLX4720 at 24h replicate 1


title: PLX4720_10uM_WM9_24h_25

description:
PLX4720_10uM_WM9_24h_25
PLX4720 at 24h replicate 2


title: PLX4720_10uM_WM9_60h_33

description:
PLX4720_10uM_WM9_60h_33
PLX4720 at 60h replicate 1


title: PLX4720_10uM_WM9_96h_41

description:
PLX4720_10uM_WM9_96h_41
PLX4720 at 96h replicate 1


title: DMSO_WM9_96h_3

description:
DMSO_WM9_96h_3
DMSO at 96h replicate 2

value: control


title: PLX4720_10uM_WM9_48h_30

description:
PLX4720_10uM_WM9_48h_30
PLX4720 at 48h replicate 2


title: chr 18 maternal gain

city: San Juan Capistrano

first: Jared

last: Taylor

address: 33608 Ortega Highway

institute: Quest Diagnostics Inc

description:
60604320
detection of maternal copy number microduplications, confirmed by microarray, which yield false positive results for trisomy in the fetus as previously assessed by non-invasive prenatal screen

data_processing:
according to the Affymetrix user manual `Cytoscan HD assay´
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.1

source_name: whole blood

extract_protocol: Qiagen whole blood extraction kit

tag: individual

value: pregnant female

tag: positive for

value: maternal duplication on chromosome 18

tag: tissue

value: peripheral blood


title: PLX4720_10uM_WM9_12h_22

description:
PLX4720_10uM_WM9_12h_22
PLX4720 at 12h replicate 2

tag: cell line


title: PLX4720_10uM_WM9_48h_29

description:
PLX4720_10uM_WM9_48h_29
PLX4720 at 48h replicate 1


title: colonic organoid, PPARγ KO, vehicle, replicate 1

value: male

tag: genotype

value: PPARγ KO

tag: treatment

value: vehicle (0.1% DMSO)

tag: strain


title: SFC841-03-02 [SNP genotype]

description:
single replicate
cluster file: humanomniexpress_24v1-0_a
manifest: humanomniexpress_24v1-0_a

tag: gender

tag: cell type


title: DMSO_WM9_96h_1

description:
DMSO_WM9_96h_1
DMSO at 96h replicate 1


title: CTC3

description: mouse #3


title: 8Gy_d35_rep3

city: Menlo Park

first: J. Tyson

last: McDonald

address: 333 Ravenswood Avenue

institute: SRI International

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data files were opened with Illlumina's GenomeStudio software. Duplicate run short-term samples (d1,d4,d6) for replicate 1 were combined by averaging (rep1a, rep1b). Quantile normalization and log2 transformation was performed separately for short- (day 1, 4 and 6) and long- (day 35) term samples.  Short-term samples were also processed with ComBat to remove non-biological batch effects due to the use of multiple microarray chips.

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

growth_protocol: The U87-MG glioblastoma cell line was obtained from the American Type Culture Collection (ATTC, Bethesda, MD).  Cells were grown in Minimum Essential Media (Life Technologies, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (Lonza, Hopkinton, MA) and maintained in a humidified 37ºC incubator with 5% CO2.

extract_protocol: Total RNA was extracted after treatment using TRIzol (Life Technologies, Grand Island, NY) according to the manufacturer’s instructions. RNA quality and quantity was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were irradiated acutely with 8 or 16Gy using a Cesium-137 (Cs-137) GammaCell 40 irradiator with a dose-rate of 0.48Gy per minute.  For each experimental replicate, in parallel with irradiation exposures, control samples were sham irradiated.  For short-term time points (d1,d4,d6), cells were plated overnight before irradiation and harvested at days 1, 4 or 6 after irradiation.  For long-term time points, cells were plated overnight to achieve the same cell density as short-term cultures.  Following irradiation, cells were harvested for counting, viability testing and replating every 4 to 5 days with the same cell density.  Trypan-blue negative (viable) cells were measured using a Cellometer Auto T4 Cell Counter (Nexcelom Bioscience, Lawrence, MA).

tag: radiation exposure

tag: collection date


title: chr 21 maternal gain

description:
62262647
detection of maternal copy number microduplications, confirmed by microarray, which yield false positive results for trisomy in the fetus as previously assessed by non-invasive prenatal screen

hyb_protocol: according to the Affymetrix user manual `Cytoscan HD assay´

value: maternal duplication on chromosome 21


title: 16Gy_d35_rep2


title: 0Gy_d35_rep4


title: 8Gy_d35_rep2


title: 16Gy_d6_rep2


title: 0Gy_d35_rep3


title: 0Gy_d35_rep1


title: 16Gy_d35_rep4


title: 16Gy_d35_rep3


title: 8Gy_d35_rep4


title: 16Gy_d35_rep1


title: 8Gy_d35_rep1


title: 16Gy_d4_rep2


title: 8Gy_d6_rep3

source_name: U87-MG, 8Gy, d6, rep3


title: 16Gy_d4_rep1a&1b

description: For normalized data, replicate1 is the average rep1a & rep1b


title: 8Gy_d4_rep3

source_name: U87-MG, 8Gy, d4, rep3


title: 0Gy_d35_rep2


title: 8Gy_d4_rep2

source_name: U87-MG, 8Gy, d4, rep2


title: 0Gy_d6_rep3

source_name: U87-MG, 0Gy, d6, rep3


title: 16Gy_d4_rep3


title: 16Gy_d6_rep1a&1b


title: 0Gy_d6_rep2

source_name: U87-MG, 0Gy, d6, rep2


title: 8Gy_d6_rep2

source_name: U87-MG, 8Gy, d6, rep2


title: 16Gy_d6_rep3


title: 0Gy_d6_rep1a&1b

source_name: U87-MG, 0Gy, d6, rep1a&1b


title: 8Gy_d4_rep1a&1b

source_name: U87-MG, 8Gy, d4, rep1a&1b


title: 8Gy_d6_rep1a&1b

source_name: U87-MG, 8Gy, d6, rep1a&1b


title: 0Gy_d4_rep3

source_name: U87-MG, 0Gy, d4, rep3


title: 0Gy_d4_rep1a&1b

source_name: U87-MG, 0Gy, d4, rep1a&1b


title: hiPS-HEP_DMSO_14d_2

city: Stockholm

first: Magnus

last: Ingelman-Sundberg

address: Nanna Svartz väg 2

country: Sweden

institute: Karolinska Institutet

description: Gene expression after 14 day treatment (6 re-dosings) with 0.4% DMSO

hyb_protocol: Agilent 8x60K Whole Human Genome Oligo Microarray slides (G4851B) were hybridised, washed and then scanned on an Agilent Microarray Scanner

data_processing: Images from the Agilent scanner were processed using Agilent Feature Extraction Software v10.7.3.1.

source_name: hiPS-Hep 2D

label_protocol: Total RNA samples (45ng) were labelled with Cy3 using the Low Input Quick Amp Labeling Kit–One Colour (Agilent# 5190-2305)

growth_protocol: hiPS-Hep cells were obtained by differentiation from the human induced pluripotent cell line ChiPSC18 (DEF-hiPSC™ ChiPSC18, Cellartis, Takara Bio Europe AB) using the Cellartis® DE Differentiation Kit and Cellartis® HEP Differentiation kit (Takara Bio Europe AB) according to manufacturer’s instructions. After initiation of differentiation at day 22, the HLCs were dissociated and reseeded

extract_protocol: RNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and quality was assessed using the Agilent Bioanalyzer

treatment_protocol: Medium supplemented with 0.4% DMSO was changed every 2-3 days. For PHH spheroids cells were also treated with either aflatoxin B1 (0.002uM), amiodarone (4uM) or chlorpromazine (6uM).

value: stem cell-derived hepatocytes (hiPS-Hep)

tag: treatment time

value: DMSO


title: 0Gy_d4_rep2

source_name: U87-MG, 0Gy, d4, rep2


title: 8Gy_d1_rep3

source_name: U87-MG, 8Gy, d1, rep3


title: hiPS-HEP_DMSO_14d_1

scan_protocol: Agilent 8x60K Whole Human Genome Oligo Microarray slides (G4851B) were hybridised, washed and then scanned on an Agilent Microarray Scanner


title: hiPS-HEP_DMSO_7d_3

description: Gene expression after 7 day treatment (3 re-dosings) with 0.4% DMSO


title: hiPS-HEP_DMSO_7d_1


title: 16Gy_d1_rep2


title: 16Gy_d1_rep1a&1b


title: 16Gy_d1_rep3


title: PHH_Chlorpromazine_14d_2

description: Gene expression after 14 day treatment (6 re-dosings) with 2uM chlorpromazine (0.4% DMSO), PHH 3D spheroid

source_name: Primary human hepatocyte 3D spheroid

growth_protocol: Primary human hepatocytes were seeded in ultra-low attachment plates at  1500 cells/well in 100ul Williams E basal medium supplemented with 10% FBS and centrifuged at 100g for 2 minutes. From day 4 onwards daily medium changes with FBS-free medium were performed. Treatments were initiated on day 7.

value: Primary human hepatocyte (PHH)

value: Chlorpromazine


title: ∆moago3_b

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_01294.6, replicate 2

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Magnaporthe oryzae genome assembly 8 from Broad Institute
Supplementary_files_format_and_content: tag count file

organism: Pyricularia oryzae

source_name: Mycelium

extract_protocol:
Mycelial tissues were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol Reagent (Ambion by Life Technologies) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-930-1012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-930-2001).

value: Mycelium grown in complete media for 5 days

tag: genotype/variation


title: hiPS-HEP_DMSO_48h_2

description: Gene expression after 48h treatment with 0.4% DMSO


title: hiPS-HEP_DMSO_7d_2


title: PHH_Chlorpromazine_14d_1


title: 8Gy_d1_rep1a&1b

source_name: U87-MG, 8Gy, d1, rep1a&1b


title: hiPS-HEP_DMSO_48h_3


title: hiPS-HEP_DMSO_14d_3


title: hiPS-HEP_DMSO_48h_1


title: PHH_Aflatoxin_14d_3

description: Gene expression after 14 day treatment (6 re-dosings) with 0.002uM aflatoxin B1 (0.4% DMSO), PHH 3D spheroid

value: Aflatoxin B1


title: HMVEC-L exposed to 0.3 Gy, biological rep 4

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

hyb_protocol: 5 µg of end-labeled, fragmented cDNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 17 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0007; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Analysis was carried out using Partek Genomics Suite 6.4. Here the 8 arrays were normalized and modeled using Robust Multichip Averaging (RMA). Probe sets showing differential expression were determined using 1-way Analysis of Variance (ANOVA) with a p-value cut-off of 0.03.

source_name: HMVEC-L_exposed to 0.3 Gy

label_protocol: RNA was processed for use on Affymetrix GeneChip HuGene 1.0 ST Arrays, according to the manufacturer’s Whole Transcript Sense Target Labeling Assay. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls  was used in a reverse transcription reaction to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA . 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis. 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix).

growth_protocol: Lung Human Microvascular Endothelial Cells (HMEC-L) were purchased from Cambrex and cultured according to manufacturer’s  instructions. Cells were used up to passage 6.

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (QIAGEN) including DNase treatment to remove potential genomic DNA contamination.

treatment_protocol: HMVEC-L cultures were transferred to an acrylic phantom box in order to achieve a certain thicknessa and exposed or not to 0.3 Gy.

value: Lung Human Microvascular endothelial cells (HMVEC-L)

tag: exposed to

value: low-dose (0.3 Gy) ionizing radiation


title: HMVEC-L exposed to 0.3 Gy, biological rep 3


title: HMVEC-L exposed to 0.3 Gy, biological rep 2


title: HMVEC-L not irradiated, biological rep 4

source_name: HMVEC-L_not irradiated

value: none (not-irradiated control)


title: HMVEC-L exposed to 0.3 Gy, biological rep 1


title: 0Gy_d1_rep3

source_name: U87-MG, 0Gy, d1, rep3


title: 0Gy_d1_rep1a&1b

source_name: U87-MG, 0Gy, d1, rep1a&1b


title: 0Gy_d1_rep2

source_name: U87-MG, 0Gy, d1, rep2


title: ∆moago3_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_01294.6, replicate 1


title: 8Gy_d1_rep2

source_name: U87-MG, 8Gy, d1, rep2


title: PHH_Aflatoxin_14d_2


title: PHH_Chlorpromazine_14d_3


title: HMVEC-L not irradiated, biological rep 2


title: PHH_Aflatoxin_14d_1


title: HMVEC-L not irradiated, biological rep 3


title: HMVEC-L not irradiated, biological rep 1


title: PHH_Chlorpromazine_7d_3

description: Gene expression after 7 day treatment (3 re-dosings) with 2uM chlorpromazine (0.4% DMSO), PHH 3D spheroid


title: PHH_Amiodarone_14d_1

description: Gene expression after 14 day treatment (6 re-dosings) with 4uM amiodarone (0.4% DMSO), PHH 3D spheroid

value: Amiodarone


title: PHH_Amiodarone_14d_2


title: cervix after delivery after PTL_105

first: Aurelija

last: Dubicke

address: Karolinska University Hospital Solna

department: Department of Women's and Children's Health

description: human cervical tissues after delivery at PTL, 34 full gestational weeks

hyb_protocol: Hybridization coctail was prepared according to the standard protocol. Samples were hybridizedin arrays for 16 hours, at 45C in Affymetrics Gene Chip Hybridization Oven 640

scan_protocol: GeneChips were scanned using the Affymetrics Gene Chip Scanner 30

data_processing: The data was analyzed in the Plier using ANOVA and  false discovery rate

label_protocol: Biotinylated cRNA were prepared according to the Gene Chip  Whole Transcript (WT)  Sense Target Labeling Assay Manual, 100 ng RNA was used as input

growth_protocol: Cervical biopsies were obtained from women immediately postpartum (within 30 minutes). The biopsies were taken transvaginally with scissors and tweezers at twelve o'clock position.

treatment_protocol: The samples for mRNA analysis were immediately immersed in RNAlater® (Ambion Inc, Austin, TX, USA), kept at 4o C for 24 hours and thereafter frozen and stored at -70o.

tag: maternal age

tag: delivery

value: preterm delivery (PTL)

tag: gestation time

value: 34 full gestational weeks

value: cervix


title: cervix after delivery after TL_219

description: human cervical tissues after delivery at TL, 39 full gestational weeks

value: term delivery (TL)

value: 39 full gestational weeks


title: cervix after delivery after TL_112

source_name: human cervical tissues after delivery at TL, 39 full gestational weeks


title: cervix after delivery after PTL_106

source_name: human cervical tissues after delivery at PTL, 34 full gestational weeks


title: PHH_DMSO_14d_1

description: Gene expression after 14 day treatment (6 re-dosings) with 0.4% DMSO, PHH 3D spheroid


title: PHH_DMSO_14d_2


title: PHH_Chlorpromazine_7d_1


title: PHH_DMSO_14d_3


title: PHH_Aflatoxin_7d_3

description: Gene expression after 7 day treatment (3 re-dosings) with 0.002uM aflatoxin B1 (0.4% DMSO), PHH 3D spheroid