title: Terc-/- #9

status: Public on Nov 30 2014

type: RNA

city: Taipei

first: Li-Ying

last: Sung

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description: Terc-/- replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Expression arrays were analyzed by R3.0.1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: ntESC

label_protocol: Total 500 ng RNA is converted to double-stranded cDNA, followed by an amplification step（in vitro transcription, IVT） to generate biotin labeled cRNA. (Ambion)

growth_protocol: ntESCs are cultured in serum free KSR/KO-DMEM medium supplemented with LIF on mitomycin-C treated MEF

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit, followed by DNase I treatment  in accordance with the prescribed protocol provided with the kit. RNA integrity number was determined by Agilent 2100 Bioanalyzer

treatment_protocol: ntESCs are trypsinized and MEF are removed for RNA extraction

tag: strain

tag: genotype/variation

value: Terc-/-


title: E14_WGE_homozygote_rep5

city: Freiburg im Breisgau

first: Julian

last: Jaeger

address: Breisacher Straße 64

country: Germany

institute: Medical Center Freiburg

hyb_protocol: Fragmented cRNA were hybridized for 16h on GeneChip Rat Gene 1.0 ST Array . Subsequent washing and staining was performed in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray data were analyzed with the Partek Genomics Suite v6.4. The Affymetrix raw data (.cel) files were loaded into Partek. The data were Robust Multi-array Average (RMA)-background corrected with quantile normalization and median polish probe-set summarization.  One-way ANOVA tests were performed on all genes (p < 0.05), and multiple test corrections were conducted with the Benjamini and Hochberg False Discovery Rate (FDR < 0.1).

organism: Rattus norvegicus

source_name: whole ganglionic eminence at E14, homozygous for full-length human huntingtin with 96 CAG repeats

label_protocol: Biotinylated cRNA were prepared according to the Ambion WT Expression Kit protocol from 2 ug total RNA.

extract_protocol: RNA extraction was performed with the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: The day of separation was defined as embryonic (E) day 0 (E0). At E14, pregnant dams were sedated by i.p. injections of 150 mg/kg of ketamine and 15 mg/kg of xylazine. The abdomen was opened, and the uterus was dissected and transferred to precooled phosphate-buffered saline (PBS). The embryonic age of each fetus was confirmed by determining the crown-rump length.  The MGE and LGE were dissected from the surrounding tissue. The meninges were completely removed. Only complete and undamaged WGEs were used for downstream applications. WGEs for RNA extraction were immediately placed as biological replicates per embryo into 400 µL of RNAlater (Life Technologies Corporation, Darmstadt, Germany) and then stored  at 4°C. Fetal tail samples were obtained for genotyping with a disposable scalpel and then transferred into 200 µL of DNA lysis buffer.

tag: tissue

value: whole ganglionic eminence

tag: genotype

value: homozygote

tag: age

value: Embyonic day 14


title: Terc+/- #7

description: Terc+/- replicate 3

value: Terc+/-


title: Terc-/- #11

description: Terc-/- replicate 3


title: Terc+/+ #2

description: Terc+/+ replicate 2

value: Terc+/+


title: Terc+/+ #3

description: Terc+/+ replicate 3


title: E14_WGE_homozygote_rep6


title: E14_WGE_homozygote_rep2


title: E14_WGE_wt_rep5

source_name: whole ganglionic eminence at E14, wt

value: wildtype


title: Terc+/+ #1

description: Terc+/+ replicate 1


title: E14_WGE_homozygote_rep3


title: Terc-/- #10

description: Terc-/- replicate 2


title: E14_WGE_wt_rep3


title: Terc+/- #5

description: Terc+/- replicate 1


title: E14_WGE_wt_rep2


title: Terc+/- #6

description: Terc+/- replicate 2


title: E14_WGE_homozygote_rep1


title: E14_WGE_wt_rep1


title: E14_WGE_wt_rep6


title: E14_WGE_homozygote_rep4


title: 1DayReWatering_Rep3

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description:
Gene expression in leaves 1 day after re-watering
GE015_1_1

hyb_protocol: The Cy3-labelled cRNA (1.65 µg) was fragmented at 60°C for 30 min according to the manufacturer’s instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to the Agilent microarray (GPL＿＿＿) for 17 h at 65°C in a rotating Agilent hybridization oven. After hybridization, the microarrays were washed using the optimized protocol (http:// www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf) recommended by Agilent technologies.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A versionC) using one color scan setting for 4 　X 44 K array slides.

data_processing:
Signal intensities were detected from the obtained digital images using Feature Extraction software (Ver. 10.7.3; Agilent Technologies). Three independent biological replicative experiments were performed for each treatment.
Expression data sets obtained by microarray analysis were exported to GeneSpring GX11 (Agilent Technologies) and per chip normalization to the quantile expression level were performed in all samples. For inter-array normalization, the processed raw signal intensity of all probes were subjected to 75-percentile normalization. The microarray data were filtered to remove control probe sets and those probe sets with an intensity value close to background levels.

organism: Jatropha curcas

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1µg of total RNA using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer’s instructions (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf), followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seedlings were then transferred into individual plastic pots (diameter: 9 cm) and grown in a growth chamber for one month at 30 °C (16 hours light; 8 hours dark). All plants were given equal amounts (about 50 ml per pot) of water every two days.

extract_protocol: Total RNA was extracted from frozen tissues collected from leaves of the Jatropha plants grown under each condition using an RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions. The total RNA extracts were treated with DNase I (QIAGEN) to completely remove genomic DNA. The quality of total RNA was assessed using a Bioanalyzer system (Agilent).

treatment_protocol: For drought stress treatment, watering was withheld for three weeks. For rehydration treatment, 50 ml of water was subsequently added to each pot of drought-treated plants and kept in the growth chamber to recover for one day and five days. The plants that were allowed to recover for five days were re-watered every two days. Control plants were continuously given equal amounts (about 50 ml per pot) of water every two days for three weeks.

value: Leaf

tag: treatment

value: 1 day after re-watering


title: E14_WGE_wt_rep4


title: 5DayReWatering_Rep3

description:
Gene expression in leaves 5 days after re-watering
GE015_1_2

value: 5 days after re-watering


title: NonDrought_Con_Rep3

description:
Gene expression in leaves before drought treatment control
GE016_1_3

value: before drought treatment control


title: 5DayReWatering_Rep2

description:
Gene expression in leaves 5 days after re-watering
GE013_1_1


title: 2WksNoWatering_Rep3

description:
Gene expression in leaves 2 weeks after last watering
GE014_1_3

value: 2 weeks after last watering


title: NonDrought_Con_Rep2

description:
Gene expression in leaves before drought treatment control
GE014_1_2


title: 3WksNoWatering_Rep3

description:
Gene expression in leaves 3 weeks after last watering
GE014_1_4

value: 3 weeks after last watering


title: 3WksNoWatering_Rep2

description:
Gene expression in leaves 3 weeks after last watering
GE012_1_3


title: 1DayReWatering_Rep2

description:
Gene expression in leaves 1 day after re-watering
GE012_1_4


title: 5DayReWatering_Rep1

description:
Gene expression in leaves 5 days after re-watering
GE010_1_4


title: NonDrought_Con_Rep1

description:
Gene expression in leaves before drought treatment control
GE012_1_1


title: 2WksNoWatering_Rep2

description:
Gene expression in leaves 2 weeks after last watering
GE012_1_2


title: 3WksNoWatering_Rep1

description:
Gene expression in leaves 3 weeks after last watering
GE010_1_2


title: 2WksNoWatering_Rep1

description:
Gene expression in leaves 2 weeks after last watering
GE010_1_1


title: 1DayReWatering_Rep1

description:
Gene expression in leaves 1 day after re-watering
GE010_1_3


title: TU_IDC_3

type: genomic

city: Hannover

first: Jessica

last: Rößler

address: Carl-Neuberg Str. 1

department: Pathology

institute: Medical School Hannover

hyb_protocol: Bisulfite converted genomic DNA was amplified, fragmented, and hybridized to Illumina´s Infinium HumanMethylation450 BeadChip according to the manufacturer’s protocol

scan_protocol: Arrays were scanned using BeadArray Reader according to the manufacturer´s instructions

data_processing: GenomeStudio® Methylation module software (version 1.9, Illumina Inc.) was used to calculate beta-values and corresponding p-values, by normalizing over internal controls

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: PrimaryTumorTissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted by Proteinase K treatment with subsequent phenol-chloroform extraction

tag: tissue type

value: Tumor

tag: tissue subtype

value: Invasive ductal breast carcinoma

tag: sample type

value: fresh-frozen


title: TU_IDC_8


title: TU_IDC_4


title: TU_IDC_2


title: CellLine_IPH-926

source_name: BreastCancerCellLine

tag: cell line

value: Cell line

value: Breast cancer cell line of ILBC origin

value: fresh


title: TU_ILBC_7

value: Invasive Lobular breast carcinoma


title: TU_IDC_1


title: TU_ILBC_9


title: TU_IDC_10


title: CellLine_MDA-MB-134

value: Breast cancer cell line of putative ILBC origin


title: TU_IDC_9


title: TU_BRCA1_6

value: BRCA1-mutated tumor


title: TU_BRCA1_8


title: TU_BRCA1_7


title: TU_BRCA1_4


title: TU_ILBC_5


title: TU_IDC_7


title: NT_3

source_name: NormalBreastTissue

value: Normal Tissue

value: Normal breast tissue


title: CellLine_PMC42

value: Breast cancer cell line classified as normal-like


title: TU_ILBC_8


title: TU_ILBC_3


title: TU_IDC_5


title: TU_ILBC_2


title: NT_1


title: CellLine_HCC1937

value: Breast cancer cell line harboring BRCA1-mutation


title: TU_ILBC_1


title: TU_BRCA1_5


title: TU_ILBC_6


title: TU_IDC_6


title: TU_ILBC_10


title: VestibularSchwannoma_Sporadic_23

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

country: Spain

institute: Hospital Universitari Germans Trias i Pujol

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip, using standard Illumina protocols.

scan_protocol: Arrays were scanned using BeadArray Reader by standard recommended Illumina scanner settings

data_processing:
M-value was obtained with lumi R package after background correction, color bias adjustment by quantiles and SSN normalization
ProcessedMatrix.txt: Avg_Beta correspond to M-value after processing with lumi package: Barckground correction, color bias adjustment and normalization by ssn. p_value were obtained with GenomeStudio. This table is prepared for using in IMA package.
Rawdata.txt: Value outputed by lumi package after direct import from iDAT files. Was done using importMethyIDAT function, which give this non-processed value.

label: Cy5 and Cy3

source_name: Vestibular Schwannoma (Sporadic)

extract_protocol: DNA was isolated using the Wizard Genomic DNA purification kit (Promega), according to the manufacturer’s instructions. Bisulfite-treated using the EZ DNA methylation Kit (Zymo Research, Orange, CA, USA), according to the manufacturer’s instructions.

tag: cell type

value: Vestibular Schwannoma

tag: subtype

value: Sporadical


title: HealthyNerve_5

description: Non-tumoral patient

source_name: Healthy Nerve

value: Healthy Nerve

value: Control

value: Auricular nerve 4


title: TU_ILBC_4

value: Tumor


title: VestibularSchwannoma_Sporadic_22


title: NT_2

value: fresh-frozen


title: VestibularSchwannoma_Sporadic_25


title: TU_BRCA1_2


title: NT_4


title: HealthyNerve_2

description: Non-tumoral patient

value: Auricular nerve 1


title: HealthyNerve_3

description: Non-tumoral patient

value: Auricular nerve 2


title: VestibularSchwannoma_Sporadic_20


title: VestibularSchwannoma_Sporadic_18


title: VestibularSchwannoma_Sporadic_30


title: VestibularSchwannoma_Sporadic_19


title: VestibularSchwannoma_Sporadic_21


title: VestibularSchwannoma_Sporadic_16


title: TU_BRCA1_1


title: HealthyNerve_1

description: Non-tumoral patient

value: Cervical nerve


title: VestibularSchwannoma_Sporadic_24


title: VestibularSchwannoma_Sporadic_26


title: Non-Vestibular_Schwannoma_4

source_name: Non-Vestibular Schwannoma

value: Non-Vestibular Schwannoma

value: non-vestibular


title: HealthyNerve_4

description: Non-tumoral patient

value: Auricular nerve 3


title: VestibularSchwannoma_NF2_5

description: Neurofibromatosis 2 patient

source_name: Vestibular Schwannoma (NF2)

value: NF2 associated


title: TU_BRCA1_3

value: BRCA1-mutated tumor


title: VestibularSchwannoma_NF2_4

description: Neurofibromatosis 2 patient


title: VestibularSchwannoma_Sporadic_28


title: VestibularSchwannoma_Sporadic_29


title: VestibularSchwannoma_Sporadic_27


title: VestibularSchwannoma_Sporadic_17


title: VestibularSchwannoma_NF2_6

description: Neurofibromatosis 2 patient


title: VestibularSchwannoma_Sporadic_14


title: VestibularSchwannoma_Sporadic_12


title: VestibularSchwannoma_Sporadic_15


title: VestibularSchwannoma_Sporadic_11


title: VestibularSchwannoma_Sporadic_10


title: Non-Vestibular_Schwannoma_3


title: Non-Vestibular_Schwannoma_2


title: VestibularSchwannoma_Sporadic_9


title: VestibularSchwannoma_Sporadic_4


title: VestibularSchwannoma_Sporadic_3


title: VestibularSchwannoma_Sporadic_1


title: VestibularSchwannoma_Sporadic_5


title: VestibularSchwannoma_NF2_3

description: Neurofibromatosis 2 patient


title: VestibularSchwannoma_Sporadic_8


title: 831PancreasN4

city: Baltimore

first: Winston

last: Timp

state: MD

address: 3400 N. Charles St. Clark 102A

department: Biomedical Engineering

country: USA

institute: Johns Hopkins University

description:
6929671120_R03C01
831PancreasN4

hyb_protocol: Standard Illumina Protocol

scan_protocol: iScan Protocol

data_processing: minfi package (bioconductor)

source_name: pancreas

extract_protocol: DNeasy or Masterpure DNA extraction kit

value: pancreas

tag: state

value: normal

tag: phenotype

tag: notes

tag: Sex


title: VestibularSchwannoma_Sporadic_6

value: Vestibular Schwannoma


title: 762PancreasN2

description:
6929671158_R05C02
762PancreasN2


title: ColonN_2 (6929671061_R06C01)

description:
6929671061_R06C01
ColonN_2

source_name: colon

value: colon

value: f


title: 365PancreasNET2

description:
6929671158_R03C01
365PancreasNET2

value: cancer

value: NET


title: 838PancreasNET5

description:
6929671145_R06C02
838PancreasNET5


title: VestibularSchwannoma_NF2_2

description: Neurofibromatosis 2 patient

value: Tumor


title: VestibularSchwannoma_NF2_1

description: Neurofibromatosis 2 patient


title: VestibularSchwannoma_Sporadic_2

value: Sporadical


title: VestibularSchwannoma_Sporadic_7


title: ColonN_2 (6929671158_R02C01)

description:
6929671158_R02C01
ColonN_2


title: 673PancreasNET1

description:
6929671101_R04C02
673PancreasNET1


title: VestibularSchwannoma_Sporadic_13


title: 101PancreasNET4

description:
6929671101_R01C02
101PancreasNET4


title: 405PancreasN3

description:
6929671146_R05C01
405PancreasN3


title: 820PancreasN1

description:
6929671120_R06C01
820PancreasN1


title: Colon_Normal_6

description:
5730504045_R06C02
Colon_Normal_6


title: Thyroid_PTC_5

description:
5730504036_R06C02
Thyroid_PTC_5

source_name: thyroid

value: thyroid

value: m


title: Thyroid_HA_5

description:
5730504036_R04C02
Thyroid_HA_5

value: adenoma


title: Thyroid_HC_5

description:
5730504036_R05C02
Thyroid_HC_5


title: Breast_Cancer_6

description:
5730504045_R05C01
Breast_Cancer_6

source_name: breast

value: breast


title: Thyroid_Normal_5

description:
5730504036_R06C01
Thyroid_Normal_5


title: Thyroid_ADN_5

description:
5730504036_R05C01
Thyroid_ADN_5

value: hyperplastic

value: adenomatoid


title: Thyroid_FVPTC_5

description:
5730504036_R03C02
Thyroid_FVPTC_5


title: Breast_DCIS_5

description:
5730504045_R01C01
Breast_DCIS_5


title: 12PancreasNET3

description:
6929671145_R03C02
12PancreasNET3


title: Colon_Met_Lung_5

description:
5730504035_R05C02
Colon_Met_Lung_5

value: metastasis


title: Thyroid_FA_5

description:
5730504036_R01C02
Thyroid_FA_5


title: Pancreas_IPMN_5

description:
5730504035_R06C02
Pancreas_IPMN_5


title: Lung_Cancer_5

description:
5730504035_R05C01
Lung_Cancer_5

source_name: lung

value: lung


title: Colon_Cancer_5

description:
5730504035_R04C01
Colon_Cancer_5


title: Colon_Adenoma_5

description:
5730504036_R02C01
Colon_Adenoma_5


title: Non-Vestibular_Schwannoma_1

value: Non-Vestibular Schwannoma

value: non-vestibular


title: Pancreas_Cancer_5

description:
5730504035_R01C02
Pancreas_Cancer_5

value: pancreas

value: adenocarcinoma


title: Colon_Met_Liver_5

description:
5730504035_R03C02
Colon_Met_Liver_5

value: colon


title: Lung_Normal_5

description:
5730504035_R06C01
Lung_Normal_5

value: normal


title: Pancreas_Normal_5

description:
5730504035_R02C02
Pancreas_Normal_5


title: Breast_Normal_5

description:
5730504027_R02C02
Breast_Normal_5


title: Thyroid_PTC_4

description:
5730504027_R02C01
Thyroid_PTC_4

value: cancer

value: f


title: Breast_Cancer_5

description:
5730504027_R01C02
Breast_Cancer_5


title: Thyroid_HC_4

description:
5730504027_R01C01
Thyroid_HC_4


title: Colon_Normal_5

description:
5730504035_R03C01
Colon_Normal_5


title: Thyroid_HA_4

description:
5730504026_R06C02
Thyroid_HA_4


title: Colon_Adenoma_4

description:
5730504026_R03C01
Colon_Adenoma_4


title: Thyroid_ADN_4

description:
5730504026_R01C02
Thyroid_ADN_4


title: Thyroid_FA_4

description:
5730504026_R03C02
Thyroid_FA_4


title: Lung_Normal_4

description:
5730504024_R05C01
Lung_Normal_4


title: Thyroid_Normal_4

description:
5730504026_R02C02
Thyroid_Normal_4


title: Breast_Cancer_4

description:
5730504018_R01C02
Breast_Cancer_4


title: Pancreas_Normal_4

description:
5730504024_R04C02
Pancreas_Normal_4


title: Pancreas_Cancer_4

description:
5730504024_R01C02
Pancreas_Cancer_4


title: Colon_Normal_4

description:
5730504024_R01C01
Colon_Normal_4


title: Colon_Cancer_4

description:
5730504024_R02C01
Colon_Cancer_4


title: Pancreas_IPMN_4

description:
5730504026_R02C01
Pancreas_IPMN_4


title: Breast_Normal_6

description:
5730504045_R01C02
Breast_Normal_6


title: Thyroid_FC_5

description:
5730504036_R02C02
Thyroid_FC_5


title: Colon_Met_Liver_4

description:
5730504024_R06C02
Colon_Met_Liver_4


title: Colon_Met_Lung_4

description:
5730504026_R01C01
Colon_Met_Lung_4


title: Breast_Normal_4

description:
5730504018_R06C01
Breast_Normal_4


title: Breast_DCIS_3

description:
5730504018_R01C01
Breast_DCIS_3


title: Thyroid_HA_3

description:
5730504017_R04C02
Thyroid_HA_3


title: Thyroid_HC_3

description:
5730504017_R05C02
Thyroid_HC_3


title: Thyroid_FVPTC_3

description:
5730504017_R03C02
Thyroid_FVPTC_3


title: Thyroid_FC_4

description:
5730504026_R04C02
Thyroid_FC_4


title: Thyroid_FA_3

description:
5730504017_R01C02
Thyroid_FA_3


title: Thyroid_PTC_3

description:
5730504017_R06C02
Thyroid_PTC_3


title: Lung_Cancer_4

description:
5730504024_R04C01
Lung_Cancer_4


title: Thyroid_FC_3

description:
5730504017_R02C02
Thyroid_FC_3


title: Colon_Met_Liver_3

description:
5730504050_R05C02
Colon_Met_Liver_3


title: Pancreas_IPMN_3

description:
5730504017_R01C01
Pancreas_IPMN_3


title: ColonN_2 (5730504018_R02C01)

description:
5730504018_R02C01
ColonN_2


title: Breast_Normal_3

description:
5730504042_R05C01
Breast_Normal_3


title: Lung_Cancer_3

description:
5730504050_R05C01
Lung_Cancer_3


title: Thyroid_FVPTC_4

description:
5730504026_R05C02
Thyroid_FVPTC_4


title: Pancreas_Cancer_3

description:
5730504050_R06C01
Pancreas_Cancer_3


title: Pancreas_Normal_3

description:
5730504050_R03C02
Pancreas_Normal_3


title: Lung_Normal_3

description:
5730504050_R04C01
Lung_Normal_3


title: Colon_Normal_3

description:
5730504050_R01C01
Colon_Normal_3


title: Colon_Cancer_3

description:
5730504050_R02C01
Colon_Cancer_3


title: Thyroid_FC_2

description:
5730504041_R01C02
Thyroid_FC_2


title: Pancreas_IPMN_2

description:
5730504039_R05C02
Pancreas_IPMN_2


title: Breast_Cancer_3

description:
5730504042_R06C01
Breast_Cancer_3


title: Thyroid_PTC_2

description:
5730504041_R05C02
Thyroid_PTC_2


title: Thyroid_FVPTC_2

description:
5730504041_R02C02
Thyroid_FVPTC_2


title: Thyroid_HA_2

description:
5730504041_R03C02
Thyroid_HA_2


title: Colon_Adenoma_2

description:
5730504039_R06C02
Colon_Adenoma_2


title: Breast_DCIS_2

description:
5730504041_R06C02
Breast_DCIS_2


title: Thyroid_Normal_2

description:
5730504041_R05C01
Thyroid_Normal_2


title: Colon_Met_Lung_3

description:
5730504050_R06C02
Colon_Met_Lung_3


title: Thyroid_FA_2

description:
5730504041_R06C01
Thyroid_FA_2


title: Colon_Met_Liver_2

description:
5730504039_R03C02
Colon_Met_Liver_2


title: Thyroid_HC_2

description:
5730504041_R04C02
Thyroid_HC_2


title: Thyroid_Normal_3

description:
5730504017_R06C01
Thyroid_Normal_3


title: Colon_Met_Lung_2

description:
5730504039_R04C02
Colon_Met_Lung_2


title: Colon_Adenoma_3

description:
5730504017_R02C01
Colon_Adenoma_3


title: Pancreas_Cancer_2

description:
5730504039_R04C01
Pancreas_Cancer_2


title: Lung_Normal_2

description:
5730504039_R03C01
Lung_Normal_2


title: Lung_Cancer_2

description:
5730504039_R02C01
Lung_Cancer_2


title: Thyroid_ADN_2

description:
5730504041_R04C01
Thyroid_ADN_2


title: Breast_Cancer_2

description:
5730504038_R03C01
Breast_Cancer_2


title: ?Met_Lung_

description:
5730504042_R01C01
?Met_Lung_


title: siNS_0h_rep1

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

description: rep 1

hyb_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.

data_processing: Bead level data was processed using beadarray (2.8.1) and bead summarized data was normalized using neqc with limma (3.14.4) with poor quality probes removed using illuminaHumanv4.db in R (2.15.3)

growth_protocol: A549 human lung carcinoma cells were purchased from the American Type Culture Collection and grown in DMEM with 10% fetal bovine serum (FBS) at 37°C in a humidified incubator with 5% CO2

extract_protocol: RNA was extracted using the RNeasy mini column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: siRNA was transfected into A549 cells by using Oligofectamine according to the manufacturer’s protocol. Two days after transfection, the media was changed to hormone-free medium (phenol-red free DMEM) supplemented with 5% charcoal-stripped FBS. The next day, cells were subjected to hormone treatment with 100 nM dexamethasone (dex) or ethanol as control for 6 hrs

value: lung carcinoma

tag: hormone

tag: sirna

value: siNS


title: Human Lung Cancer_C433 [gene-extended analysis]

city: Gainesville

first: Xin

last: Qi

state: FL

address: 1600 SW Archer Rd

department: Medicinal Chemistry

institute: University of Florida

description: RMA expression value derived from Expression Console software; extended-gene analysis

hyb_protocol: Hybridization cocktails containing fragmented, end-labeled cDNA were prepared and applied to GeneChip Human Exon 1.0 ST arrays. Hybridization was performed at 60 rpm for 16 hr at 45°C using the FS450_0001 fluidics protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Command Console Software (AGCC) to produce .CEL intensity files.

data_processing: Raw data were processed with Expression Console and Transcriptome Analysis Console softwares. Both core-gene expression analysis and extended-gene expression analysis were performed.

source_name: Lung cancer

label_protocol: 200 ng of each RNA sample was processed using Affymetrix GeneChip Whole Transcript (WT) PLUS Reagent Kit. 15 µg of cRNA were input into the second cycle cDNA reaction. 5.5 µg of ss-cDNA were input for fragmentation. Each DNA fragment is end labeled with biotin using terminal deoxynucleotidyl transferase before being hybridized to the arrays.

extract_protocol: RNA was isolated from 10 mg of each frozen tissue sample with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quality was determined by the A260/A280 ratio (close to 2), A260/A230 (close to 2), and the presence of two distinct ribosomal bands on gel electrophoresis. Qualified RNAs were further tested using Agilent 2100 Bioanalyzer (Agilent), and samples with 28S/18S RNA ratio > 1 were selected for gene expression profiling.

tag: pathology status

value: Primary cancer

tag: age (yrs)

tag: histologic type

value: Large cell carcinoma, NOS


title: Human Lung Cancer_C699 [gene-core analysis]

description: RMA expression value derived from Expression Console software; core-gene analysis

value: Metastatic cancer

value: Synovial sarcoma, NOS


title: Human Lung Cancer_C699 [gene-extended analysis]


title: Human Lung Cancer_C688 [gene-extended analysis]

value: Adenocarcinoma


title: Colon_Normal_2

description:
5730504038_R05C02
Colon_Normal_2

tag: tissue

tag: age


title: Human Lung Normal_N687 [gene-extended analysis]

source_name: Normal control

value: Normal


title: Human Lung Cancer_C696 [gene-extended analysis]

value: Stromal sarcoma, NOS


title: Thyroid_ADN_3

description:
5730504017_R05C01
Thyroid_ADN_3

value: thyroid

value: hyperplastic

value: adenomatoid

value: m


title: Colon_Cancer_2

description:
5730504038_R06C02
Colon_Cancer_2

value: colon


title: Human Lung Cancer_C308 [gene-extended analysis]

value: Adenocarcinoma, NOS


title: Human Lung Cancer_C688 [gene-core analysis]


title: Breast_DCIS_1

description:
5730504037_R03C02
Breast_DCIS_1

value: breast

value: cancer

value: adenoma


title: Human Lung Cancer_C433 [gene-core analysis]


title: Breast_Normal_2

description:
5730504038_R02C01
Breast_Normal_2

value: normal

value: f


title: Thyroid_FA_1

description:
5730504037_R03C01
Thyroid_FA_1


title: Thyroid_PTC_1

description:
5730504037_R02C02
Thyroid_PTC_1


title: siNS_6h_rep4

description: rep 4

scan_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.

value: lung carcinoma

value: siNS


title: Thyroid_FC_1

description:
5730504037_R04C01
Thyroid_FC_1


title: siNS_6h_rep1

description: rep 1

label_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.


title: Mystery_Met_Lung_1

description:
5730504037_R04C02
Mystery_Met_Lung_1

value: metastasis


title: Thyroid_HA_1

description:
5730504037_R06C01
Thyroid_HA_1


title: siCoCoA_0h_rep4

description: rep 4

value: siCoCoA


title: Thyroid_FVPTC_1

description:
5730504037_R05C01
Thyroid_FVPTC_1


title: Human Lung Cancer_C308 [gene-core analysis]

value: Primary cancer


title: Colon_Adenoma_1

description:
5730504025_R04C02
Colon_Adenoma_1


title: siCCAR2_6h_rep3

description: rep 3


title: Thyroid_HC_1

description:
5730504037_R01C02
Thyroid_HC_1


title: Human Lung Cancer_C696 [gene-core analysis]

value: Metastatic cancer

value: Stromal sarcoma, NOS


title: Human Lung Normal_N687 [gene-core analysis]

value: Normal


title: Pancreas_IPMN_1

description:
5730504025_R03C02
Pancreas_IPMN_1

value: pancreas


title: Thyroid_Normal_1

description:
5730504037_R02C01
Thyroid_Normal_1

value: thyroid

value: m


title: siCCAR2_0h_rep2

description: rep 2


title: maternal parent_rep2

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

institute: Kihara Institute for Biological Research

description: Gene expression of maternal parent

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: After washing, signal intensities were immediately detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).

data_processing: Signal intensities were detected from the obtained digital images with Feature Extraction software 9.5 (Agilent Technologies). Fluorescence intensities were analysed with GeneSpring GX v12.6 (Agilent Technologies). Raw data set (raw signal intensity > 1.0 threshold) was transformed to log scale at base 2. Normalization was performed with GeneSpring.

organism: Triticum turgidum subsp. dicoccum

source_name: KU124, replicate 2

label_protocol: Extracted RNAs (500ng) were labelled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) with cyamine 3-cytidine 5C-triphosphate (CTP).

growth_protocol: All plants were grown in growth chamber controlled by at 22℃, relative humidity 40%, in 16 h length with 6000 lux (64,560 fc) and 8 h dark day cycles.

extract_protocol: Total RNA of each line was extracted using Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s method.

treatment_protocol: Ttriploid embryos were rescued 2 weeks later after pollination. Embryos were placed petridishes with half strength of Murashige & Skoog culture medium (Inagaki et al. 1998) in growth chamber which is maintained at 20℃, 12-h light/12-h dark (5000 lux). Chromosome-doubled hexaploid plants obtained by self-pollination of colchicine treated (0.2% in a 2% DMSO solution) of triploid plants.

value: leaf

value: two leaves seedling


title: maternal parent_rep3

description: Gene expression of maternal parent

source_name: KU124, replicate 3


title: Thyroid_ADN_1

description:
5730504037_R01C01
Thyroid_ADN_1

value: cancer

value: hyperplastic

value: adenomatoid


title: siCoCoA_6h_rep1

description: rep 1


title: paternal parent_rep1

description: Gene expression of paternal parent

organism: Aegilops tauschii subsp. strangulata

source_name: KU2074, replicate 1


title: paternal parent_rep3

description: Gene expression of paternal parent

source_name: KU2074, replicate 3


title: siCCAR1_0h_rep4

description: rep 4


title: maternal parent_rep1

description: Gene expression of maternal parent

source_name: KU124, replicate 1


title: siCoCoA_0h_rep1

description: rep 1


title: siNS_0h_rep4

description: rep 4


title: siCoCoA_6h_rep4

description: rep 4


title: paternal parent_rep2

description: Gene expression of paternal parent

source_name: KU2074, replicate 2


title: siCCAR2_0h_rep1

description: rep 1


title: siCoCoA_0h_rep3

description: rep 3


title: ZFP282 #1_6h_rep2

description: rep 2


title: Colon_Met_Lung_1

description:
5730504025_R01C02
Colon_Met_Lung_1

value: colon


title: TU_IDC_8 [aCGH]

hyb_protocol: Standard Agilent Protocol

scan_protocol: Arrays were scanned using Agilent microarray scanner according to the manufacturer´s instructions

data_processing:
For image analysis, default CGH settings of the Feature Extraction software (Agilent) were applied. Output files of the Feature Extraction were further investigated by Agilent´s CHG data analysis software, Genomic-Workbench.
algorithm ADM2

source_name: human DNA reference pool

label_protocol: Standard Agilent Genomic DNA labeling kit Plus Protocol without enzymatic restriction

value: self-made DNA pool, from blood samples of ten healthy female donors

value: Tumor

value: fresh-frozen

value: Invasive ductal breast carcinoma


title: TU_IDC_9 [aCGH]


title: TU_IDC_7 [aCGH]


title: Colon_Met_Liver_1

description:
5730504025_R02C02
Colon_Met_Liver_1

value: metastasis


title: Lung_Cancer_1

description:
5730504025_R06C01
Lung_Cancer_1

value: lung


title: Lung_Normal_1

description:
5730504019_R01C02
Lung_Normal_1

value: normal


title: TU_IDC_10 [aCGH]


title: TU_IDC_1 [aCGH]


title: Pancreas_Cancer_1

description:
5730504019_R02C02
Pancreas_Cancer_1

value: adenocarcinoma


title: siCCAR2_6h_rep4

description: rep 4

value: lung carcinoma


title: Colon_Normal_1

description:
5730504025_R04C01
Colon_Normal_1


title: NT_3 [aCGH]

value: Normal Tissue

value: Normal breast tissue


title: TU_IDC_3 [aCGH]


title: ZFP282 #1_0h_rep2

description: rep 2


title: TU_IDC_2 [aCGH]


title: siNS_6h_rep6

description: rep 6

value: siNS


title: NT_1 [aCGH]


title: ZFP282 #1_0h_rep3

description: rep 3


title: TU_IDC_6 [aCGH]


title: Colon_Cancer_1

description:
5730504025_R03C01
Colon_Cancer_1


title: Breast_Normal_1

description:
5730504019_R01C01
Breast_Normal_1

value: breast

value: f


title: NT_2 [aCGH]


title: Pancreas_LCC1

description:
5730504043_R05C02
Pancreas_LCC1

value: pancreas

value: cancer


title: TU_BRCA1_8 [aCGH]

value: BRCA1-mutated tumor


title: siCCAR1_6h_rep1

description: rep 1


title: Pancreas_LCC2

description:
5730504021_R05C01
Pancreas_LCC2


title: ColonN_2 (5730504019_R04C01)

description:
5730504019_R04C01
ColonN_2

value: colon


title: Breast_Cancer_1

description:
5730504019_R02C01
Breast_Cancer_1


title: TU_BRCA1_5 [aCGH]

value: self-made DNA pool, from blood samples of ten healthy female donors

value: Tumor


title: Pancreas_Cancer_15

description:
5730504043_R02C02
Pancreas_Cancer_15


title: Pancreas_Cancer_16

description:
5730504043_R03C02
Pancreas_Cancer_16


title: siCoCoA_6h_rep2

description: rep 2

value: siCoCoA


title: siNS_0h_rep6

description: rep 6


title: TU_BRCA1_1 [aCGH]

value: fresh-frozen


title: Pancreas_Cancer_14

description:
5730504043_R01C02
Pancreas_Cancer_14


title: TU_BRCA1_4 [aCGH]


title: siCCAR2_6h_rep1

description: rep 1


title: TU_ILBC_10 [aCGH]

value: Invasive Lobular breast carcinoma


title: TU_BRCA1_7 [aCGH]


title: TU_ILBC_9 [aCGH]


title: HVC, biological rep6_testosterone

city: Seewiesen-Starnberg

first: Carolina

last: Frankl-Vilches

state: Bavaria

address: Eberhard-Gwinner-Str. 6a

department: Behavioural Neurobiology

institute: Max Planck Institute for Ornithology

description: HVC was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing: The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version:  E28R1306 Genomatix GmbH (http://www.genomatix.de)

organism: Serinus canaria

source_name: HVC

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult canaries housed in short light cycles in aviaries

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with micro-scalpels (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into Qiazol (Qiagen) and stored at -80 C till RNA preparation.

treatment_protocol: Testosterone

value: brain

tag: gender

value: female

tag: brain region

value: HVC

tag: developmental stage

value: adult

tag: light cycle

value: short day

tag: treatment

value: testosterone


title: TU_BRCA1_3 [aCGH]

tag: sample type

tag: subtype


title: TU_ILBC_8 [aCGH]


title: TU_ILBC_7 [aCGH]


title: siCCAR2_6h_rep2

description: rep 2

tag: cell line

tag: cell type

value: lung carcinoma


title: HVC, biological rep5_testosterone

description: HVC was dissected from cryosections


title: ZFP282 #1_6h_rep3

description: rep 3


title: TU_ILBC_6 [aCGH]


title: TU_IDC_5 [aCGH]

value: Invasive ductal breast carcinoma


title: siNS_6h_rep5

description: rep 5

value: siNS


title: siCCAR1_6h_rep3

description: rep 3


title: TU_ILBC_3 [aCGH]


title: TU_ILBC_2 [aCGH]


title: Thyroid_Normal_13

description:
5730504003_R04C02
Thyroid_Normal_13

value: thyroid

tag: state

value: normal

tag: phenotype

tag: notes

tag: Sex

value: m


title: HVC, biological rep3_testosterone

description: HVC was dissected from cryosections


title: TU_ILBC_4 [aCGH]

value: self-made DNA pool, from blood samples of ten healthy female donors


title: TU_ILBC_5 [aCGH]

value: Tumor


title: siCCAR1_0h_rep1

description: rep 1

tag: hormone

tag: sirna


title: TU_ILBC_1 [aCGH]

tag: tissue


title: HVC, biological rep4_testosterone

description: HVC was dissected from cryosections


title: Pancreas_Cancer_12

description:
5730504003_R03C02
Pancreas_Cancer_12

value: pancreas

value: cancer

value: adenocarcinoma

tag: age


title: HVC, biological rep2_testosterone

description: HVC was dissected from cryosections

value: brain

tag: gender


title: siCCAR2_0h_rep3

description: rep 3


title: HVC, biological rep1_testosterone

description: HVC was dissected from cryosections

value: female

tag: brain region


title: Colon_Normal_12

description:
5730504003_R01C02
Colon_Normal_12

value: colon


title: HVC, biological rep6_no_treatment

description: HVC was dissected from cryosections

value: HVC

tag: developmental stage

value: adult

value: No treatment


title: HVC, biological rep5_no_treatment

description: HVC was dissected from cryosections

tag: light cycle

value: short day


title: siNS_6h_rep2

description: rep 2

value: lung carcinoma


title: siCCAR1_6h_rep4

description: rep 4


title: Pancreas_Cancer_11

description:
5730504043_R06C01
Pancreas_Cancer_11


title: siCoCoA_6h_rep3

description: rep 3

value: siCoCoA


title: Thyroid_Normal_12

description:
5730504003_R02C02
Thyroid_Normal_12

value: thyroid

value: f


title: S_354

description:
Previously analysed Vestibular Schwannoma 29
re-analysis of GSM973658

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

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Vestibular Schwannoma

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

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

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

value: Vestibular Schwannoma

tag: tissue type

tag: batch


title: Pancreas_Cancer_13

description:
5730504003_R05C02
Pancreas_Cancer_13


title: HVC, biological rep4_no_treatment

description: HVC was dissected from cryosections

tag: treatment


title: siNS_0h_rep2

description: rep 2

tag: cell line

value: siNS


title: S_350

description:
Previously analysed Vestibular Schwannoma 31
re-analysis of GSM973660

tag: cell type

value: Tumor


title: siNS_0h_rep5

description: rep 5


title: HVC, biological rep3_no_treatment

description: HVC was dissected from cryosections


title: Thyroid_FA_11

description:
5730504043_R04C01
Thyroid_FA_11

tag: state

value: adenoma


title: HVC, biological rep2_no_treatment

description: HVC was dissected from cryosections


title: S_371

description:
Previously analysed Vestibular Schwannoma 27
re-analysis of GSM973656


title: siCCAR1_0h_rep2

description: rep 2


title: HVC, biological rep1_no_treatment

description: HVC was dissected from cryosections


title: siNS_6h_rep3

description: rep 3


title: S_373

description:
Previously analysed Vestibular Schwannoma 26
re-analysis of GSM973655


title: S_374

description:
Previously analysed Vestibular Schwannoma 25
re-analysis of GSM973654


title: Lung_Normal_11

description:
5730504043_R02C01
Lung_Normal_11

value: lung

value: normal

tag: phenotype


title: GLI1-MCF-7 vs con

city: shanghai

first: juan

last: xu

address: 21F, 415 fengyang road

country: China

institute: endocrinology

description: compare gene expression profiles of control cells

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were incubated at 37℃ and 5% CO2 humidiﬁed atmosphere in RPMI-1640 medium (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (PAA, Pasching, Austria), 100 U/ml penicillin and 100 μg/ml streptomycin (Huashun Technology, Inc., Shanghai, China).

extract_protocol: Stably transfected cells and control cells were harvest, and total RNA was extracted with Trizol Reagent following manufacturer's instructions.

treatment_protocol: Cells were  transiently transfected with 8.0 µg pcDNA3.1-Gli1 or pcDNA3.1 plasmids using LipofectamineTM 2000 Transfection Reagent (Invitrogen) per manufacturer’s instructions. After 48h, cells were plated at low density in medium containing 500 μg/ml geneticin (G418). Once colonies were formed, individual colonies were isolated and expanded. Cells were continuously maintained in medium containing 250μg/ml G418 for MCF-7 or 300μg/ml G418 for T47D as growth protocol.

tag: transfection

value: pcDNA3.1 plasmids


title: S_352

description:
Previously analysed Vestibular Schwannoma 30
re-analysis of GSM973659


title: S_369

description:
Previously analysed Vestibular Schwannoma 28
re-analysis of GSM973657


title: siCoCoA_0h_rep2

description: rep 2


title: Thyroid_ADN_11

description:
5730504043_R03C01
Thyroid_ADN_11

value: cancer

tag: notes

value: adenomatoid

tag: Sex


title: siCCAR2_0h_rep4

description: rep 4

tag: hormone

tag: sirna


title: S_417

description:
Previously analysed Vestibular Schwannoma 22
re-analysis of GSM973651


title: Colon_Normal_11

description:
5730504043_R01C01
Colon_Normal_11

tag: tissue

value: colon

tag: age


title: Thyroid_Normal_11

description:
5730504043_R05C01
Thyroid_Normal_11


title: S_399

description:
Previously analysed Vestibular Schwannoma 24
re-analysis of GSM973653


title: Thyroid_PTC_10

description:
5730504003_R04C01
Thyroid_PTC_10


title: Pancreas_Cancer_10

description:
5730504003_R05C01
Pancreas_Cancer_10

value: pancreas

value: adenocarcinoma


title: siNS_0h_rep3

description: rep 3


title: Thyroid_HA_10

description:
5730504003_R03C01
Thyroid_HA_10

value: m


title: S_407

description:
Previously analysed Vestibular Schwannoma 23
re-analysis of GSM973652


title: S_437

description:
Previously analysed Vestibular Schwannoma 20
re-analysis of GSM973649


title: SiHa cell line treated with ethanol for 48h, biological rep2

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Gene expression data from SiHa cell lines treated with ehtanol for 48hr.

hyb_protocol: total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

scan_protocol: Washed and stain processes were performed in the GeneChip Fluidics Station 450. The probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Computational analysis of the microarray data Cel files was processed with the Affy library in R Bioconductor. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. Differentially expression patterns between calcitriol treatment and controls were determined using the Limma package to perform an adjusted Student’s t-test using a Bayesian estimation of the variance.

growth_protocol: 3×105  SiHa cells were cultures in medium supplemented with charcoal-treated serum.

extract_protocol: Total RNA including the small fraction was isolated using TRIzol reagent

treatment_protocol: SiHa cells were treated with  calcitriol  or ethanol as vehicle for 24h or 48h.

value: SiHa

value: Cervial cancer cell


title: siCCAR1_0h_rep3

description: rep 3

value: lung carcinoma


title: SiHa cell line treated with calcitriol for 48h, biological rep1

description: Gene expression data from SiHa cell lines treated with calcitriol for 48hr.

label_protocol: total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip


title: SiHa cell line treated with calcitriol for 48h, biological rep2


title: Thyroid_FVPTC_10

description:
5730504003_R01C01
Thyroid_FVPTC_10

value: thyroid


title: Thyroid_ADN_10

description:
5730504040_R03C02
Thyroid_ADN_10

value: hyperplastic

value: f


title: S_444

description:
Previously analysed Vestibular Schwannoma 19
re-analysis of GSM973648

value: Vestibular Schwannoma

value: Tumor


title: SiHa cell line treated with ethanol for 48h, biological rep1


title: S_449

description:
Previously analysed Vestibular Schwannoma 17
re-analysis of GSM973646


title: S_422

description:
Previously analysed Vestibular Schwannoma 21
re-analysis of GSM973650


title: Thyroid_FA_10

description:
5730504040_R04C02
Thyroid_FA_10

value: adenoma


title: S_447

description:
Previously analysed Vestibular Schwannoma 18
re-analysis of GSM973647


title: siCCAR1_6h_rep2

description: rep 2


title: SiHa cell line treated with ethanol for 24h, biological rep1

description: Gene expression data from SiHa cell lines treated with ehtanol for 24hr.


title: Thyroid_FC_10

description:
5730504040_R06C02
Thyroid_FC_10


title: Colon_Adenoma_10

description:
5730504001_R05C02
Colon_Adenoma_10


title: Thyroid_Normal_10

description:
5730504040_R05C02
Thyroid_Normal_10

value: normal


title: SiHa cell line treated with calcitriol for 24h, biological rep1

description: Gene expression data from SiHa cell lines treated with calcitriol for 24hr.


title: Breast_Normal_10

description:
5730504001_R04C02
Breast_Normal_10

value: breast


title: S_458

description:
Previously analysed Vestibular Schwannoma 15
re-analysis of GSM973644


title: Lung_Normal_10

description:
5730504040_R02C02
Lung_Normal_10

value: lung


title: S_450

description:
Previously analysed Vestibular Schwannoma 16
re-analysis of GSM973645


title: S_471

description:
Previously analysed Vestibular Schwannoma 13
re-analysis of GSM973642


title: SiHa cell line treated with ethanol for 24h, biological rep2


title: S_467

description:
Previously analysed Vestibular Schwannoma 14
re-analysis of GSM973643


title: SiHa cell line treated with calcitriol for 24h, biological rep2


title: Lung_Cancer_10

description:
5730504001_R01C02
Lung_Cancer_10

value: cancer


title: Colon_Normal_10

description:
5730504040_R06C01
Colon_Normal_10

value: colon


title: S_473

description:
Previously analysed Vestibular Schwannoma 12
re-analysis of GSM973641


title: Pancreas_Normal_10

description:
5730504001_R02C02
Pancreas_Normal_10

value: pancreas


title: S_486

description:
Previously analysed Vestibular Schwannoma 9
re-analysis of GSM973638


title: S_482

description:
Previously analysed Vestibular Schwannoma 10
re-analysis of GSM973639


title: S_491

description:
Previously analysed Vestibular Schwannoma 6
re-analysis of GSM973635


title: S_488

description:
Previously analysed Vestibular Schwannoma 8
re-analysis of GSM973637


title: ColonN_2 (5730504040_R04C01)

description:
5730504040_R04C01
ColonN_2


title: S_490

description:
Previously analysed Vestibular Schwannoma 7
re-analysis of GSM973636


title: Thyroid_HA_9

description:
5730504001_R03C01
Thyroid_HA_9


title: Breast_Cancer_10

description:
5730504040_R01C01
Breast_Cancer_10


title: Pancreas_Cancer_9

description:
5730504001_R06C01
Pancreas_Cancer_9

value: adenocarcinoma


title: MCF-7:PF_v_MCF-7:5C

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

country: New Zealand

institute: University of Otago, Dunedin School of Medicine

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 16.42
ng Cy3 probe hybridized:  1650
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 11.17
ng Cy5 probe hybridized:  825

hyb_protocol: Cy3-labeled probes were co-hybridized with Cy5-labeled reference probes to Agilent 4x44K (V1) expression microarrays following Agilent protocols.

scan_protocol: Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1). Build hg18.

data_processing: Array control features and control targets were removed. Data Log2 transformed and inverted to depict Cy3/Cy5.

source_name: MCF-7:PF breast cancer cells, exponential growth phase

label_protocol: total RNA from all individual sample preparations was used to generate Cy3-labeled (test) or Cy-5-labeled (reference) cRNA probes using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA, Catalog# 5190-2306) following manufacturer's instructions.  Cy dye incorporation efficiency was calculated with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE) following Agilent-recommended protocols. Details for Cy3 and Cy5 incorporation efficiency (pmoL cy dye/μg cRNA) for all probes are provided with this submission.

growth_protocol: All cell lines were grown at 37oC with 5% CO2 at constant humidity in replete media formulated as follows: MCF-7 and MCF-7:WS8 cells, RPMI-1640 medium supplemented with 10% fetal bovine serum; MCF-7:5C and MCF-7:2A cells, phenol-red free RPMI-1640 medium supplemented with 10% dextran-coated charcoal-stripped fetal bovine serum; MCF-7:5:PF cells, phenol-red free RPMI-1640 medium supplemented with 10% dextran-coated charcoal-stripped fetal bovine serum, 1nM 17beta estradiol and 5μM PP2 (c-Src inhibitor).

extract_protocol: Cultured cell line monolayers were rinsed in phosphate buffered saline, then harvested in Trizol reagent (Invitrogen; Carlsbad, CA).  Total RNA was purified from 200 μl TRIzol lysate using the RNeasy micro kit (Qiagen; Valencia, CA) following manufacturer's instructions including the optional DNAse treatment step. RNA concentration and purity was measured using a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA). All samples had an RNA integrity # (RIN#) between 9.4 and 10.0

treatment_protocol: All cell lines were cultured until exponential phase of growth in their respective growth media.

tag: series replicate

tag: estrogen-dependent growth

value: Yes

tag: biomaterial provider

value: Drs. Eric Ariazi, Joan Lewis-Wambi and Ping Fan, Laboratory of Dr. V. Craig Jordan

source_name: MCF-7:5C breast cancer cells, exponential growth phase

value: 1 of 1

value: No


title: S_505

description:
Previously analysed Vestibular Schwannoma 5
re-analysis of GSM973634

tag: tissue type


title: Thyroid_FC_9

description:
5730504001_R01C01
Thyroid_FC_9

value: thyroid


title: MCF-7:PF_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 16.42
ng Cy3 probe hybridized:  1650
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 15.16
ng Cy5 probe hybridized:  825

value: Dr. Ping Fan, Laboratory of Dr. V. Craig Jordan

source_name: MCF-7 breast cancer cells, exponential growth phase

value: American Type Cuture Collection


title: MCF-7:WS8_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 10.69
ng Cy3 probe hybridized:  1650
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 15.16
ng Cy5 probe hybridized:  825

source_name: MCF-7:WS8 breast cancer cells, exponential growth phase

value: Drs. Eric Ariazi, and Joan Lewis-Wambi, Laboratory of Dr. V. Craig Jordan


title: Thyroid_PTC_9

description:
5730504001_R04C01
Thyroid_PTC_9

source_name: thyroid

value: f


title: S_507

description:
Previously analysed Vestibular Schwannoma 3
re-analysis of GSM973632

value: Vestibular Schwannoma

value: Tumor

tag: batch


title: Thyroid_Normal_9

description:
5730504055_R05C02
Thyroid_Normal_9

value: normal


title: S_506

description:
Previously analysed Vestibular Schwannoma 4
re-analysis of GSM973633


title: S_510

description:
Previously analysed Vestibular Schwannoma 1
re-analysis of GSM973630


title: N_432

description:
Previously analysed Nerve 8
re-analysis of GSM973628

source_name: Vestibular Nerve

value: Vestibular Nerve

value: Control


title: MCF-7:2A_rep3_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 7.2
ng Cy3 probe hybridized:  2475
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 19.41
ng Cy5 probe hybridized:  825

source_name: MCF-7:2A breast cancer cells (passage 592), exponential growth phase

value: 3 of 3


title: Colon_Adenoma_9

description:
5730504022_R06C02
Colon_Adenoma_9

source_name: colon

value: colon

value: cancer

value: adenoma


title: N_434

description:
Previously analysed Nerve 7
re-analysis of GSM973627

source_name: Facial Nerve

value: Facial Nerve


title: N_483

description:
Previously analysed Nerve 6
re-analysis of GSM973626

source_name: VIII craneal nerve

value: VIII craneal nerve


title: N_HSC

description:
Previously analysed Nerve 9
re-analysis of GSM973629

source_name: Human Schwann Cells

value: Human Schwann Cells


title: Breast_Normal_9

description:
5730504022_R05C02
Breast_Normal_9

source_name: breast

value: breast


title: MCF-7:2A_rep2_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 7.99
ng Cy3 probe hybridized:  2475
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 19.41
ng Cy5 probe hybridized:  825

source_name: MCF-7:2A breast cancer cells (passage 591), exponential growth phase

value: No

value: Dr. Ping Fan, Laboratory of Dr. V. Craig Jordan

value: 2 of 3

value: Yes


title: S_474

description:
Previously analysed Vestibular Schwannoma 11
re-analysis of GSM973640

value: Vestibular Schwannoma


title: Thyroid_FVPTC_9

description:
5730504001_R02C01
Thyroid_FVPTC_9

value: thyroid

value: f


title: MCF-7:2A_rep1_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 8.27
ng Cy3 probe hybridized:  1650
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 15.16
ng Cy5 probe hybridized:  825

source_name: MCF-7:2A breast cancer cells (passage 590), exponential growth phase

value: 1 of 3

value: American Type Cuture Collection


title: Lung_Normal_9

description:
5730504022_R03C02
Lung_Normal_9

source_name: lung

value: lung

value: normal


title: Thyroid_FA_9

description:
5730504055_R04C02
Thyroid_FA_9

value: cancer


title: S_509

description:
Previously analysed Vestibular Schwannoma 2
re-analysis of GSM973631

value: Tumor


title: Lung_Cancer_9

description:
5730504022_R02C02
Lung_Cancer_9


title: Pancreas_Normal_9

description:
5730504022_R04C02
Pancreas_Normal_9

source_name: pancreas

value: pancreas


title: Breast_Cancer_9

description:
5730504055_R01C01
Breast_Cancer_9


title: Thyroid_ADN_9

description:
5730504055_R03C02
Thyroid_ADN_9

value: hyperplastic

value: adenomatoid


title: N_504

description:
Previously analysed Nerve 4
re-analysis of GSM973624

source_name: Cervical Nerve

value: Cervical Nerve

value: Control


title: N_502

description:
Previously analysed Nerve 5
re-analysis of GSM973625


title: Pancreas_Cancer_8

description:
5730504022_R05C01
Pancreas_Cancer_8

value: adenocarcinoma


title: Thyroid_HC_8

description:
5730504022_R02C01
Thyroid_HC_8


title: Colon_Normal_9

description:
5730504055_R06C01
Colon_Normal_9

value: colon

value: m


title: Thyroid_FVPTC_8

description:
5730504046_R06C02
Thyroid_FVPTC_8


title: Thyroid_HA_8

description:
5730504022_R01C01
Thyroid_HA_8

value: adenoma


title: N_504HIP

description:
Previously analysed Nerve 3
re-analysis of GSM973623

source_name: Hipoglosal Nerve

value: Hipoglosal Nerve


title: MCF-7:5C_rep3_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 16.49
ng Cy3 probe hybridized:  2475
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 19.41
ng Cy5 probe hybridized:  825

source_name: MCF-7:5C breast cancer cells (passage 220), exponential growth phase

value: No

value: Dr. Ping Fan, Laboratory of Dr. V. Craig Jordan

value: 3 of 3

value: Yes


title: MCF-7:5C_rep2_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 7.44
ng Cy3 probe hybridized:  2475
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 19.41
ng Cy5 probe hybridized:  825

source_name: MCF-7:5C breast cancer cells (passage 219), exponential growth phase

source_name: MCF-7 breast cancer cells, exponential growth phase

value: 2 of 3

value: American Type Cuture Collection


title: Colon_Cancer_9

description:
5730504022_R01C02
Colon_Cancer_9

value: cancer


title: N_511

description:
Previously analysed Nerve 2
re-analysis of GSM973622

source_name: Auricular Nerve

value: Auricular Nerve


title: Thyroid_FC_8

description:
5730504046_R05C02
Thyroid_FC_8

source_name: thyroid

value: thyroid


title: Thyroid_Normal_8

description:
5730504046_R04C02
Thyroid_Normal_8

value: normal


title: Thyroid_PTC_8

description:
5730504022_R03C01
Thyroid_PTC_8

value: f


title: MCF-7:5C_rep1_v_MCF-7

description:
Cy3 probe labeling efficiency (pmoL cy3/μg cRNA): 28.65
ng Cy3 probe hybridized:  1650
Cy5 probe labeling efficiency (pmoL cy3/μg cRNA): 15.16
ng Cy5 probe hybridized:  825

source_name: MCF-7:5C breast cancer cells (passage 218), exponential growth phase

value: 1 of 3


title: Thyroid_FA_8

description:
5730504046_R03C02
Thyroid_FA_8


title: N_518

description:
Previously analysed Nerve 1
re-analysis of GSM973621

value: Control


title: NonV4

description: Non-vestibular schwannoma 4

source_name: non-vestibular Schwannoma

value: non-vestibular Schwannoma

value: Tumor


title: Rb and p53 overexpression replicate 3

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: Rb and p53 overexpression replicate 3

hyb_protocol: Cy3- and Cy5-labeled cRNAs were combined and hybridized for 17 hours at 65ºC in an Agilent hybridization oven.

scan_protocol: Microarrays were washed after hydridization and scanned using Agilent DNA Microarray Scanner.

data_processing: Lowess-normalized data were extracted using FeatureExtraction. Values for which both channels were not well above background were removed; features for which more than 50% of values were removed were excluded from analysis.

source_name: Stratagene universal reference RNA

label_protocol: Total RNAs were labeled with either cyanine (Cy)-3-CTP and Cy5-CTP (Perkin Elmer, Waltham, MA) using Agilent QuickAmp cRNA labeling kits.

growth_protocol: WI38 cells were grown in Hyclone MEM/EBSS supplemented with 10% fetal bovine serum and 1% Penicillin Streptomycin. Cells were cultured at 37C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was isolated from WI38 pellets using Life Technology TRIzol reagent according to the manufacturer's prototol.

treatment_protocol: Adenoviral vectors were amplified and titered. For each type of virus, a concentration of 50 MOI (multiplicity of infection) was added to confluent WI38 cells in MEM supplemented with 2% heat-inactivated FBS.  Cell culture media was replaced with 10% FBS and 1% Penicillin/Streptomycin supplemented media 16 hours after virus addition. Cells were collected and pelleted at 48 hours.

tag: sample type

value: Stratagene universal reference RNA

source_name: WI38 normal lung fibroblast cells

value: overexpressed

tag: treatment

value: Rb1 overexpressed, p53 overexpressed


title: Rb and p53 overexpression replicate 4

description: Rb and p53 overexpression replicate 4

tag: cell line


title: NonV3

description: Non-vestibular schwannoma 3

tag: cell type


title: Thyroid_ADN_8

description:
5730504046_R02C02
Thyroid_ADN_8

tag: state

tag: phenotype

value: hyperplastic

value: adenomatoid


title: p53 overexpression replicate 3

description: p53 overexpression replicate 3

value: control

value: Rb1 control, p53 overexpressed


title: Colon_Met_Lung_8

description:
5730504016_R02C02
Colon_Met_Lung_8

source_name: colon

value: colon

value: metastasis

tag: notes


title: Colon_Adenoma_8

description:
5730504016_R05C02
Colon_Adenoma_8

value: cancer

value: adenoma

tag: Sex


title: Lung_Normal_8

description:
5730504016_R01C02
Lung_Normal_8

value: lung

value: normal


title: p53 overexpression replicate 2

description: p53 overexpression replicate 2


title: PG12 3

city: Oslo

first: Arvind

last: Sundaram

state: Oslo

address: Kirkeveien

country: Norway

institute: University of Oslo

description: MicroRNA expression in peptidoglycan stimulated larvae after 12 hour

hyb_protocol: As per manufacturer’s protocol (Agilent, USA). Oven (speed/temperature/time) 10 rpm/55 °C/22 hours

scan_protocol: Hybridised microarrays were scanned using Agilent scanner G2505B-C (Agilent, USA) and the data acquired with the Feature Extraction (Agilent, USA) software v 10.7.3.1

data_processing: Data analysis was performed in R using two biocondutor packages: AgiMicroRna and limma. Normalisation was performed using ‘quantile’ method implemented in robust multiarray average algorithm without background correction

organism: Danio rerio

source_name: Peptidoglycan, 12hr, replicate 3

label_protocol: 100 ng of total RNA was hybridised to the microarray as per manufacturer’s protocol using the Agilent’s labelling protocol (miRNA v2.2) (Agilent, USA)

growth_protocol: Adult zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were maintained at 28.5 °C in E3 medium for 72 hours until the immunostimulation experiment

extract_protocol: Samples were homogenised with a MagNA Lyser (Roche, Germany) using the appropriate silica beads and total RNA was extracted using the mirVana kit (Ambion, USA), following the manufacturer’s protocol

treatment_protocol: Immunostimulation experiments of 72 hours post-fertilisation zebrafish larvae were carried out in triplicate. 200 µg/ml of lipopolysaccharide from Salmonella enterica typhimurium or peptidoglycan from Staphylococcus aureus was added to the larvae in E3 medium, incubated for one hour and then replaced with fresh E3 medium. Samples were taken at 1, 2, and 12 hours post-exposure. Twelve larvae were sampled at each time point, frozen in liquid nitrogen and stored at -80 °C for subsequent RNA extraction

value: larvae

value: peptidoglycan

tag: time


title: Rb and p53 overexpression replicate 1

description: Rb and p53 overexpression replicate 1


title: PG2 2

description: MicroRNA expression in peptidoglycan stimulated larvae after 2 hour

source_name: Peptidoglycan, 2hr, replicate 2


title: PG12 1

source_name: Peptidoglycan, 12hr, replicate 1


title: PG12 2

source_name: Peptidoglycan, 12hr, replicate 2


title: Rb and p53 overexpression replicate 2

description: Rb and p53 overexpression replicate 2


title: p53 overexpression replicate 4

description: p53 overexpression replicate 4


title: NonV1

description: Non-vestibular schwannoma 1

value: non-vestibular Schwannoma


title: NonV2

description: Non-vestibular schwannoma 2

value: Tumor


title: PG2 3

source_name: Peptidoglycan, 2hr, replicate 3


title: p53 overexpression replicate 1

description: p53 overexpression replicate 1

value: Stratagene universal reference RNA


title: Rb overexpression replicate 4

description: Rb overexpression replicate 4

value: overexpressed

value: Rb1 overexpressed, p53 control


title: Pancreas_Normal_8

description:
5730504016_R03C02
Pancreas_Normal_8

source_name: pancreas

value: pancreas

value: m


title: Colon_Cancer_8

description:
5730504046_R05C01
Colon_Cancer_8


title: Breast_Normal_8

description:
5730504016_R04C02
Breast_Normal_8

source_name: breast

value: breast


title: Lung_Cancer_8

description:
5730504046_R06C01
Lung_Cancer_8

source_name: lung


title: PG1 3

description: MicroRNA expression in peptidoglycan stimulated larvae after 1 hour

source_name: Peptidoglycan, 1hr, replicate 3


title: Colon_Normal_8

description:
5730504046_R04C01
Colon_Normal_8


title: Rb overexpression replicate 2

description: Rb overexpression replicate 2

value: control


title: Rb overexpression replicate 1

description: Rb overexpression replicate 1


title: PG1 2

source_name: Peptidoglycan, 1hr, replicate 2


title: Breast_Cancer_8

description:
5730504016_R05C01
Breast_Cancer_8

value: f


title: LPS12 3

description: MicroRNA expression in lipopolysaccharide stimulated larvae after 12 hour

source_name: Lipopolysaccharide, 12hr, replicate 3

value: lipopolysaccharide


title: LPS12 2

source_name: Lipopolysaccharide, 12hr, replicate 2


title: Pancreas_Cancer_7

description:
5730504016_R03C01
Pancreas_Cancer_7

value: cancer

value: adenocarcinoma


title: tumor cell line HepG2 with knockdown of HIF-2α rep1

city: Frankfurt

first: Nathalie

last: Dehne

address: Theodor-Stern-Kai 7

department: Faculty of Medicine, Institute of Biochemestry I

institute: Goethe-University Frankfurt

description: Sp sh2alpha Nr#1

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: HepG2_HIF-2α knockdown

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: HepG2 spheroids were grown from 1x106 cells in coated (Sigmacote) 250-mL spinner flasks (Integra Biosciences, Fernwald, Germany) with 250 mL complete medium (MEM with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 0.1 mM non-essential amino acids) in a Cell Spin stirrer system (22.5 rotations/min, Integra Biosciences). 125 mL cell culture medium was replaced every second day.

extract_protocol: total RNA was isolated using Quiagen RNeasy Kit, RNA was amplified using the One-direct-Kit from NUGEN applied for 250 microdissected cells

treatment_protocol: 10 days old tumor spheroids were processed for RNA isolation using the Quiagen RNeasy Micro Kit.

value: Human hepatocellular liver carcinoma cells

tag: genotype/variation

value: HIF-2α knockdown

tag: cell subtype

value: 10 days old tumor spheroids


title: Control replicate 1

description: Control replicate 1

value: Rb1 control, p53 control


title: tumor cell line HepG2 with knockdown of HIF-1α rep4

description: Sp sh1alpha Nr#4

source_name: HepG2_HIF-1α knockdown

value: HIF-1α knockdown


title: PG2 1

source_name: Peptidoglycan, 2hr, replicate 1

tag: tissue

value: larvae

value: peptidoglycan


title: Rb overexpression replicate 3

description: Rb overexpression replicate 3

source_name: Stratagene universal reference RNA

value: Stratagene universal reference RNA

source_name: WI38 normal lung fibroblast cells

value: overexpressed


title: Purkinje fiber 4

city: New York

first: Eugene

middle: E

last: Kim

state: NY

address: 522 First Ave. Smilow 807

department: Medicine

institute: New York University School of Medicine

hyb_protocol: standard Affymetrix hybridization

scan_protocol: Gene chips were scanned using GeneChip® Scanner 3000.

data_processing: Microarray Suite v5.0.  Global scaling normalization.

source_name: isolated Purkinje cell

label_protocol: standard Affymetrix label

extract_protocol: Cell isolation via Langendorff perfusion and enzymatic digestion. FACS sort of Purkinje cells and ventricular myoyctes. RNA isolation using  Arcturus PicoPure. cDNA generation using Nugen Ovation Pico WTA System v2

tag: genotype

value: Cntn2-EGFP/ a-MHC-Cre/ floxed-tdTomato

tag: strain

value: mixture of CD1, C57/B6, and 129S1 strains

value: Purkinje fiber

tag: developmental stage

value: adult

tag: gender

value: male


title: PG1 1

source_name: Peptidoglycan, 1hr, replicate 1


title: LPS12 1

source_name: Lipopolysaccharide, 12hr, replicate 1

value: lipopolysaccharide


title: LPS2 3

description: MicroRNA expression in lipopolysaccharide stimulated larvae after 2 hour

source_name: Lipopolysaccharide, 2hr, replicate 3


title: tumor cell line HepG2 with knockdown of HIF-2α rep3

description: Sp sh2alpha Nr#3


title: LPS2 2

source_name: Lipopolysaccharide, 2hr, replicate 2


title: tumor cell line HepG2 with knockdown of HIF-1α rep3

description: Sp sh1alpha Nr#3


title: Purkinje fiber 2


title: Control replicate 4

description: Control replicate 4

value: control


title: Purkinje fiber 3


title: LPS2 1

source_name: Lipopolysaccharide, 2hr, replicate 1


title: tumor cell line HepG2 with knockdown of HIF-2α rep2

description: Sp sh2alpha Nr#2


title: Control replicate 2

description: Control replicate 2


title: Control replicate 3

description: Control replicate 3


title: tumor cell line HepG2 with knockdown of HIF-1α rep2

description: Sp sh1alpha Nr#2


title: tumor cell line HepG2 with knockdown of HIF-2α rep4

description: Sp sh2alpha Nr#4


title: LPS1 3

description: MicroRNA expression in lipopolysaccharide stimulated larvae after 1 hour

source_name: Lipopolysaccharide, 1hr, replicate 3


title: Thyroid_FVPTC_7

description:
5730504033_R04C02
Thyroid_FVPTC_7

source_name: thyroid

value: thyroid

value: cancer

tag: age

value: f


title: Thyroid_PTC_7

description:
5730504016_R01C01
Thyroid_PTC_7


title: Purkinje fiber 1


title: Thyroid_HA_7

description:
5730504033_R05C02
Thyroid_HA_7

value: adenoma


title: tumor cell line HepG2 with knockdown of HIF-1α rep1

description: Sp sh1alpha Nr#1

value: Human hepatocellular liver carcinoma cells

value: 10 days old tumor spheroids


title: LPS1 2

source_name: Lipopolysaccharide, 1hr, replicate 2

value: larvae


title: tumor cell line HepG2 rep4

description: Sp wt Nr#4

source_name: HepG2_wild type

value: wild type


title: ventricular myocyte 4

source_name: isolated ventricular myocyte

value: ventricular myocyte


title: tumor cell line HepG2 rep3

description: Sp wt N#3


title: LPS1 1

source_name: Lipopolysaccharide, 1hr, replicate 1


title: tumor cell line HepG2 rep2

description: Sp wt N#2


title: Control2 3

description: MicroRNA expression in control larvae after 2 hour

source_name: Control, 2hr, replicate 3


title: Control12 3

description: MicroRNA expression in control larvae after 12 hour

source_name: Control, 12hr, replicate 3


title: ventricular myocyte 3


title: PGA22-OE-transcriptomics_rep3

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description: Biological replicate 3 of 3

hyb_protocol: Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the A-MEXP-2142 platform (See  arrayexpress database at:http://www.ebi.ac.uk/arrayexpress/arrays/A-MEXP-2142/).

scan_protocol: Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were subsequently analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities

organism: Candida albicans

source_name: Untreated control, grown in YPD medium during 16h

label_protocol: First-strand cDNA synthesis and Cy5 (doxycycline-treated samples)/Cy3 (untreated samples) labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using the hot phenol method as decribed in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.

source_name: Dox-treated at a concentration of 50 µg/mL in YPD medium for 16h


title: Control12 2

source_name: Control, 12hr, replicate 2


title: ventricular myocyte 2


title: tumor cell line HepG2 rep1

description: Sp wt N#1


title: Thyroid_HC_7

description:
5730504033_R06C02
Thyroid_HC_7


title: PGA22-OE-transcriptomics_rep1

description: Biological replicate 1 of 3


title: Control2 1

source_name: Control, 2hr, replicate 1


title: ColonN_2 (5730504033_R03C02)

description:
5730504033_R03C02
ColonN_2

source_name: colon

value: colon

value: normal


title: Thyroid_FC_7

description:
5730504033_R02C02
Thyroid_FC_7

value: m


title: Control2 2

source_name: Control, 2hr, replicate 2


title: ventricular myocyte 1

value: Cntn2-EGFP/ a-MHC-Cre/ floxed-tdTomato

value: mixture of CD1, C57/B6, and 129S1 strains


title: PGA22-OE-transcriptomics_rep2

description: Biological replicate 2 of 3


title: Control1 3

description: MicroRNA expression in control larvae after 1 hour

source_name: Control, 1hr, replicate 3


title: Mouse lung with SARS-CoV (TOR-2) on Day 28, biological rep3

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: Gene expression data from mouse lung on Day 28 after infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using ArrayAssist (Stratagene) default analysis settings.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was isolated from lung tissue using TRIzol reagent by standard protocol (Invitrogen/Life Technologies).  RNA quality was assessed using a UV spectrophotometer and by formaldehyde gel electrophoresis.  RNA was linearly amplified using MessageAMP aRNA kits (Ambion, Austin, Texas) as per the manufacturer’s instructions.  RNA was prepared for oligonucleotide microarray analysis using Affymetrix two-cycle cDNA synthesis and IVT kits according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA).

treatment_protocol: Three-week old female mice, (strain 129/S6/SvEv), (Charles River Lab, Wilmington, MA), weighing between 12-14 g, were multi-housed (6-10) in micro-isolators with absorbent heat treated hardwood bedding in animal biosafety level -3 (ABSL-3) facility. Anesthetized animals were infected intranasally with 0.015 ml of 10^ 6  TCID50/ml (equivalent to 10^ 4.5 TCID50) with SARS-CoV in each nare. Control animals were mock-infected with phosphate buffered saline (PBS). Clinical signs of ruffled fur, abnormal breathing, nasal discharge, ocular discharge, weight loss, inappetence, dyspnea, and level of activity were assessed daily. Three mice were sacrificed at 0 (mocks), 1, 2, 3, 5, 14, and 28 days post infection Lungs were collected, processed and, examined for virus load. In addition, gross pathology, clinical chemistry, and virus titers in blood were assessed. All work with infectious virus and infected animals was performed in ABSL-3 facility within biosafety cabinets by personnel wearing powered air-purifying respirators (HEPA AirMate; 3M, St. Paul, MN).

tag: time point

value: Day 28

tag: biological replicate

value: lung

value: female

tag: infection

value: SARS-CoV (TOR-2)


title: Thyroid_Normal_7

description:
5730504033_R01C02
Thyroid_Normal_7

value: thyroid


title: Thyroid_ADN_7

description:
5730504012_R05C02
Thyroid_ADN_7

value: cancer

value: hyperplastic

value: adenomatoid

value: f


title: Mouse lung with SARS-CoV (TOR-2) on Day 28, biological rep1


title: Mouse lung with SARS-CoV (TOR-2) on Day 28, biological rep2


title: Mouse lung with SARS-CoV (TOR-2) on Day 14, biological rep3

description: Gene expression data from mouse lung on Day 14 after infection

value: Day 14


title: Control1 1

source_name: Control, 1hr, replicate 1

value: larvae

tag: treatment

value: control


title: Pancreas_Normal_7

description:
5730504033_R06C01
Pancreas_Normal_7

source_name: pancreas

value: pancreas

tag: state


title: Colon_Adenoma_7

description:
5730504012_R01C02
Colon_Adenoma_7

value: colon

tag: phenotype

value: adenoma


title: H37Rv_4hr_150uM ATD-3169 3

city: Bangalore

first: Amit

last: Singh

state: Karnatka

address: CIDR,Near CAF,

department: MCBL

country: India

institute: Indian Institute of Sciences (IISc)

description: Gene expression of Mtb early log phase cultures 4h after treatment with 150uM ATD-3169 in 7H9-ADS medium

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040).  The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into thehybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) 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: Mtb H37Rv was seeded at 0.05 OD600 in 7H9-ADS medium and grown till early log phase of ~0.3.

extract_protocol: Gene expression from Treated cultures were fixed using Guanidine thiocyanate, pelleted and total RNA was isolated using FastRNA PRO blue kit (according to manufacturer's instructions). RNA was purified using Qiagen RNeasy plus kit according to manufacturer's instructions. DNAse treatment was done using Ambion TURBO DNA-free kit according to manufacturer's instructions. RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase culture cells were taken. MtbH37Rv was treated with 3uM, 30uM, 150uM final concentration of compound ATD-3169 for 4h. Control Mtb cultures were treated with 7H9-ADS medium.

value: Wild type strain of Mtb H37Rv

tag: growth

value: early log phase


title: Colon_Met_Lung_7

description:
5730504033_R05C01
Colon_Met_Lung_7

hyb_protocol: Standard Illumina Protocol

scan_protocol: iScan Protocol

data_processing: minfi package (bioconductor)

label_protocol: Standard Illumina Protocol

value: metastasis

tag: notes

tag: Sex


title: Mouse lung with SARS-CoV (TOR-2) on Day 5, biological rep3

description: Gene expression data from mouse lung on Day 5 after infection

value: Day 5

value: lung


title: Mouse lung with SARS-CoV (TOR-2) on Day 3, biological rep2

description: Gene expression data from mouse lung on Day 3 after infection

value: Day 3

value: female

value: SARS-CoV (TOR-2)


title: Mouse lung with SARS-CoV (TOR-2) on Day 5, biological rep1


title: Mouse lung with SARS-CoV (TOR-2) on Day 3, biological rep3


title: Mouse lung with SARS-CoV (TOR-2) on Day 14, biological rep2


title: Mouse lung with SARS-CoV (TOR-2) on Day 5, biological rep2


title: H37Rv_4hr_150uM ATD-3169 1


title: Colon_Cancer_7

description:
5730504033_R01C01
Colon_Cancer_7

value: cancer


title: H37Rv_4hr_150uM ATD-3169 2


title: H37Rv_4hr_30uM ATD-3169 3

description: Gene expression of Mtb early log phase cultures 4h after treatment with 30uM ATD-3169 in 7H9-ADS medium


title: H37Rv_4hr_30uM ATD-3169 2


title: Mouse lung with SARS-CoV (TOR-2) on Day 2, biological rep3

description: Gene expression data from mouse lung on Day 2 after infection

value: Day 2


title: Mouse lung with SARS-CoV (TOR-2) on Day 3, biological rep1


title: Lung_Normal_7

description:
5730504033_R03C01
Lung_Normal_7

source_name: lung

value: normal


title: H37Rv_4hr_3uM ATD-3169 3

description: Gene expression of Mtb early log phase cultures 4h after treatment with 3uM ATD-3169 in 7H9-ADS medium


title: H37Rv_4hr_30uM ATD-3169 1


title: Mouse lung with SARS-CoV (TOR-2) on Day 2, biological rep1


title: Breast_Normal_7

description:
5730504032_R06C02
Breast_Normal_7

source_name: breast

value: breast


title: H37Rv_4hr_3uM ATD-3169 1


title: Colon_Normal_7

description:
5730504012_R06C01
Colon_Normal_7


title: H37Rv_4hr_3uM ATD-3169 2


title: Mouse lung with SARS-CoV (TOR-2) on Day 2, biological rep2


title: Mouse lung with SARS-CoV (TOR-2) on Day 14, biological rep1

value: Day 14


title: Mouse lung with SARS-CoV (TOR-2) on Day 1, biological rep1

description: Gene expression data from mouse lung on Day 1 after infection

value: Day 1


title: Mouse lung with SARS-CoV (TOR-2) on Day 1, biological rep2


title: Mouse lung, uninfected, on Day 0, biological rep3

description: Gene expression data from mouse lung before infection

value: Day 0

value: Uninfected


title: Thyroid_PTC_6

description:
5730504032_R02C02
Thyroid_PTC_6

source_name: thyroid

value: thyroid

value: f


title: Mouse lung, uninfected, on Day 0, biological rep2


title: Thyroid_FC_6

description:
5730504002_R04C02
Thyroid_FC_6


title: Thyroid_FVPTC_6

description:
5730504002_R05C02
Thyroid_FVPTC_6


title: H37Rv_4hr 1

description: Gene expression of Mtb early log phase cultures in 7H9-ADS medium

source_name: H37Rv, 4hr

value: Wild type strain of Mtb H37Rv

value: early log phase

value: control


title: Thyroid_HC_6

description:
5730504032_R01C02
Thyroid_HC_6


title: T_PM_MEZI29

status: Public on Nov 29 2014

city: Vancouver

first: Carolyn

middle: J

last: Brown

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using HiScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B.

source_name: sex chromosome aneuploidy, not in analysis from PBMC

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA mini kit according to manufacturer's instructions.

value: F

tag: ethnicity

value: Nzime

value: healthy

value: T

value: PM

value: PBMC

tag: sample in final analysis


title: T_PM_TWA049

value: Batwa

value: sex chromosome aneuploidy, not in analysis


title: Thyroid_HA_6

description:
5730504002_R06C02
Thyroid_HA_6

extract_protocol: DNeasy or Masterpure DNA extraction kit

tag: tissue

value: cancer

value: adenoma


title: T_PM_TWA045


title: T_PM_TWA083


title: Thyroid_ADN_6

description:
5730504002_R01C02
Thyroid_ADN_6

value: hyperplastic

value: adenomatoid


title: H37Rv_4hr 2


title: Mouse lung, uninfected, on Day 0, biological rep1

value: Day 0

value: lung

value: female

value: Uninfected


title: T_PM_MEZI27


title: H37Rv_4hr 3

value: Wild type strain of Mtb H37Rv

value: early log phase

value: control


title: Colon_Met_Lung_6

description:
5730504032_R02C01
Colon_Met_Lung_6

value: colon

value: metastasis


title: T_PM_MEZI19

value: F

value: Nzime

value: healthy

value: T

value: PM


title: Breast_Cancer_7

description:
5730504032_R05C02
Breast_Cancer_7

value: breast

value: cancer

value: f


title: Thyroid_FA_6

description:
5730504002_R03C02
Thyroid_FA_6

value: thyroid

value: adenoma


title: T_PM_KIGA024

value: Bakiga

value: PBMC

value: sex chromosome aneuploidy, not in analysis


title: Thyroid_FA_7

description:
5730504012_R06C02
Thyroid_FA_7


title: Pancreas_Normal_6

description:
5730504002_R06C01
Pancreas_Normal_6

value: pancreas

value: normal


title: Lung_Normal_6

description:
5730504002_R05C01
Lung_Normal_6

value: lung


title: Pancreas_Cancer_6

description:
5730504002_R04C01
Pancreas_Cancer_6

value: adenocarcinoma


title: K_PM_KIGA028

value: M

value: K


title: Pancreas_IPMN_6

description:
5730504032_R03C01
Pancreas_IPMN_6


title: K_PM_TWA042

value: Batwa

value: healthy


title: K_PM_BAKA0914

value: Baka

value: PM


title: M_BS_X279_BS

source_name: final male sample from blood_spot

extract_protocol: Genomic DNA from WhatmanTM 903 Protein Saver Cards was isolated using GenSolve DNA Recovery Kit (GVR100, IntegenX), cleaned with the QiAmp DNA Micro Kit (Qiagen). and concentrated using Microcon DNA Fast Flow Devices, MRCF0R100 (Millipore).

value: BS

value: final male sample


title: T_PM_BOBAK256

value: F

value: T


title: M_BS_X7_BS


title: M_BS_X71_BS


title: M_BS_X51_BS


title: K_PM_BAKA0913


title: M_BS_X275_BS


title: M_BS_X60_BS


title: T_PM_BOBAK149


title: K_PM_BAKA0919


title: M_BS_X318_BS


title: M_BS_X295_BS


title: M_BS_X259_BS


title: Mouse lung with SARS-CoV (TOR-2) on Day 1, biological rep3

value: Day 1

value: female

value: SARS-CoV (TOR-2)


title: K_PM_KIGA016

value: Bakiga

value: PBMC

value: sex chromosome aneuploidy, not in analysis


title: M_BS_X228_BS


title: M_BS_X42_BS


title: M_BS_X225_BS


title: M_BS_X220_BS


title: Colon_Adenoma_6

description:
5730504032_R04C01
Colon_Adenoma_6

value: colon

value: cancer

value: adenoma


title: Colon_Met_Liver_6

description:
5730504032_R01C01
Colon_Met_Liver_6

value: metastasis


title: Lung_Cancer_6

description:
5730504002_R03C01
Lung_Cancer_6

value: lung

value: m


title: Colon_Cancer_6

description:
5730504002_R01C01
Colon_Cancer_6


title: M_BS_X207_BS

value: healthy

value: M


title: M_BS_X202_BS

value: BS

value: final male sample


title: M_BS_X205_BS


title: M_BU_X183i

source_name: final male sample from buccal

extract_protocol: Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects) and purified and concentrated using DNA Clean & Concentrator (Zymo Research) according to manufacturer's instruction.

value: BU

value: buccal


title: M_BU_X185i


title: M_BU_X191i


title: M_BU_X188i


title: M_BU_X181i


title: M_BU_X150i


title: M_BU_X192i


title: M_BU_X141i


title: M_BU_X140i


title: M_BS_X139_BS


title: M_BU_X146i


title: M_BS_X172_BS


title: M_BU_X127i


title: M_BS_X126_BS


title: M_BS_X129_BS


title: M_BU_X129i


title: M_BS_X141_BS_1


title: M_BU_X125i


title: M_BU_X132i


title: M_BU_X164i


title: M_BU_X168i


title: M_BU_X170i


title: M_BS_X141_BS_2


title: M_BU_X124i


title: M_BU_X118i


title: M_BU_X116i


title: M_BS_X109_BS


title: M_BU_X113i


title: M_BU_X111i


title: M_BS_X1069_BS


title: M_BS_X1084_BS


title: M_BU_X105i


title: M_BU_X108i


title: M_BS_X1072_BS


title: M_BS_X1060_BS


title: M_BU_X100i


title: M_BS_X1006_BS


title: M_BU_X098i


title: M_BS_X1016_BS


title: M_BU_X104i


title: M_BU_X094i


title: M_BS_X1017_BS


title: M_BS_X1058_BS


title: M_BU_X101i


title: M_BU_X088i


title: M_BU_X089i


title: M_BU_X093i


title: M_BS_X104_BS


title: M_BU_X090i


title: M_BU_X096i


title: M_BU_X091i


title: M_BU_X083i


title: M_BU_X081i


title: M_BU_X080i


title: M_BU_X075i


title: M_BU_X077i


title: M_BU_X079i


title: M_BU_X058i


title: M_BU_X085i


title: M_BU_X055i


title: M_BU_X073i


title: M_BU_X022i


title: M_BU_X067i


title: M_BU_X054i


title: M_BU_X021i


title: M_BU_X048i


title: M_BU_X037i


title: M_BU_X056i


title: M_BU_X069i


title: M_BU_X030i


title: M_BU_X062i


title: M_BU_X020_R


title: M_BU_X019i


title: M_BU_X038i


title: M_BU_X059i


title: M_BU_X064i


title: M_BU_X025i


title: M_BU_X039i


title: M_BU_X027i


title: M_BU_X017i


title: M_BU_X057i


title: M_BU_X020i


title: M_BU_X066i


title: M_BU_X036i


title: M_BU_X020r


title: M_BU_X061i


title: M_BU_X041i


title: M_BU_X015i


title: M_BU_X016i


title: M_BU_X013i


title: M_BU_X012i


title: M_BU_X008i


title: M_BU_X007i


title: M_BU_X002i


title: M_PM_TWA122

source_name: final male sample from PBMC

value: Batwa

value: PM


title: M_BU_X004i


title: M_PM_TWA105r

value: redone sample


title: M_PM_TWA111

value: PBMC


title: M_PM_TWA041


title: M_PM_TWA033


title: M_PM_TWA072


title: M_PM_TWA040


title: M_PM_TWA018


title: M_PM_TWA106


title: M_PM_TWA047


title: M_PM_TWA070


title: M_BU_X006i


title: M_PM_TWA010


title: M_PM_TWA043


title: M_PM_SABAK049

value: Baka


title: M_PM_TWA101


title: M_PM_TWA038


title: M_PM_TWA031


title: M_PM_SABAK043r


title: M_PM_PBMC245


title: M_PM_PBMC234


title: M_PM_PBMC169_rep

value: replicated sample


title: M_PM_SABAK041r


title: M_PM_SABAK004


title: M_PM_PBMC250_rep


title: M_PM_PBMC135


title: M_PM_PBMC169

value: sample replicated as .rep


title: M_PM_PBMC250


title: M_PM_PBMC101


title: M_PM_PBMC216


title: M_PM_PBMC64


title: M_PM_NZE7038

value: Nzebi


title: M_PM_NZE7040r


title: M_PM_NZE7034


title: M_PM_NZE7037


title: M_PM_SABAK003


title: M_PM_PBMC94


title: M_PM_NZE7032


title: M_PM_PBMC163


title: M_PM_NZE7030


title: M_PM_PBMC133


title: M_PM_PBMC104


title: M_PM_NZE7019


title: M_PM_NZE7039


title: M_PM_NZE7020


title: M_PM_NZE7041


title: M_PM_NZE7033


title: M_PM_NZE7005


title: M_PM_NZE0716


title: M_PM_NZE0710


title: M_PM_NZE7003


title: M_PM_NZE0715


title: M_PM_NZE0708


title: M_PM_MEBAK104


title: M_PM_NZE0703


title: M_PM_MEZI10

value: Nzime


title: M_PM_NZE0709r


title: M_PM_NZE0701


title: M_PM_MEBAK102


title: M_PM_NZE0713


title: M_PM_MEZI30


title: M_PM_NZE0712


title: M_PM_NZE0707r


title: M_PM_NZE0711


title: M_PM_NZE0702


title: M_PM_MEDIV10


title: M_PM_NZE0714


title: M_PM_MEBAK087


title: M_PM_KIGA053

value: Bakiga


title: M_PM_KIGA042


title: M_PM_MEBAK031


title: M_PM_KIGA032r


title: M_PM_KIGA013


title: M_PM_KIGA040


title: M_PM_KIGA031r


title: M_PM_MEBAK066


title: M_PM_MEBAK032


title: M_PM_NZE0705


title: M_BU_EMVC099F


title: M_PM_KIGA005


title: M_PM_KIGA010


title: M_PM_KIGA011


title: M_PM_KIGA007


title: M_BU_EMVC093D


title: M_BU_EMVC084F


title: M_BU_EMVC076H


title: M_PM_KIGA002


title: M_PM_KIGA004


title: M_BU_EMVC075D


title: M_BU_EMVC071L_2


title: M_BU_EMVC078F


title: M_BU_EMVC066L


title: M_BU_EMVC064F


title: M_BU_EMVC073H


title: M_BU_EMVC057H


title: M_BU_EMVC053D


title: M_BU_EMVC052D


title: M_BU_EMVC047D


title: M_BU_EMVC045D_JAN10


title: M_BU_EMVC079H


title: M_BU_EMVC039F


title: M_BU_EMVC042F


title: M_BU_EMVC041D


title: M_BU_EMVC043D


title: M_BU_EMVC037H


title: M_BU_EMVC035D


title: M_BU_EMVC030IF


title: M_BU_EMVC033L


title: M_BU_EMVC027D


title: M_BU_EMVC028D


title: M_BU_EMVC029L


title: M_BU_EMVC017D


title: M_BU_EMVB220D


title: M_BU_EMVC005H


title: M_BU_EMVC004F


title: M_BU_EMVB211H


title: M_BU_EMVB219D


title: M_BU_EMVC020


title: M_BU_EMVB207D


title: M_BU_EMVB218D


title: M_BU_EMVB206D


title: M_BU_EMVB199D


title: M_BU_EMVB203D


title: M_BU_EMVB205D


title: M_BU_EMVC024H


title: M_BU_EMVB200D


title: M_BU_EMVB198D


title: M_BU_EMVB195D


title: M_BU_EMVB204D


title: M_BU_EMVB196D


title: M_BU_EMVB187D


title: M_BU_EMVB188D


title: M_BU_EMVB192F


title: M_BU_EMVB175D


title: M_BU_EMVB179F


title: M_BU_EMVB217D


title: M_BU_EMVB194D


title: M_BU_EMVB185F


title: M_BU_EMVB170D


title: M_BU_EMVB168L


title: M_BU_EMVB140D


title: M_BU_EMVB157F


title: M_BU_EMVB163L


title: M_BU_EMVB161F


title: M_BU_EMVB147F


title: M_BU_EMVB145F


title: M_BU_EMVB146F


title: M_BU_EMVB133D


title: M_BU_EMVB134H


title: M_BU_EMVB159F


title: M_BU_EMVB172F


title: M_BU_EMVB169D


title: M_BU_EMVB128F


title: M_BU_EMVB120L


title: M_BU_EMVB123F_1


title: M_BU_EMVB127F


title: M_BU_EMVB126D


title: M_BU_EMVB105F


title: M_BU_EMVB125F


title: M_BU_EMVB103F


title: M_BU_EMVB108F


title: M_BU_EMVB102F


title: M_BU_EMVB099D


title: M_BU_EMVB113F


title: M_BU_EMVB100D


title: M_BU_EMVB123F_2


title: M_BU_EMVB092D


title: M_BU_EMVB093D


title: M_BU_EMVB080F


title: M_BU_EMVB084L


title: M_BU_EMVB076D


title: M_BU_EMVB081D


title: M_BU_EMVB072D


title: M_BU_EMVB073L


title: M_BU_EMVB071L


title: M_BU_EMVB066F


title: M_BU_EMVB062L_2


title: M_BU_EMVB064L


title: M_BU_EMVB060D


title: M_BU_EMVB061D


title: M_BU_EMVB055L


title: M_BU_EMVB070D


title: M_BU_EMVB063L


title: M_BU_EMVB049H


title: M_BU_EMVB075D


title: M_BU_EMVB082D


title: M_BU_EMVB043L


title: M_BU_EMVB038D


title: M_BU_EMVB044F


title: M_BU_EMVB039D


title: M_BU_EMVB059D


title: M_BU_EMVB048D


title: M_BU_EMVB056D


title: M_BU_EMVB029D


title: M_BU_EMVB032F


title: M_BU_EMVB042D


title: M_BU_EMVB058D


title: M_BU_EMVB026D


title: M_BU_EMVB041L


title: M_BU_EMVB016D


title: M_BU_EMVB006L


title: M_BU_EMVB031F


title: M_BU_EMVB012D


title: M_BU_EMVB016L


title: M_BU_EMVB004D


title: M_BU_CARE100M


title: M_BU_CARE082M


title: M_BU_EMVB017L


title: M_BU_CARE085M


title: M_BU_EMVB003L


title: M_BU_CARE083M


title: M_BU_EMVB087D


title: M_BU_CARE075M


title: M_BU_EMVB0101F


title: M_BU_CARE101M


title: M_BU_CARE098M


title: M_BU_CARE087M


title: M_BU_CARE094M


title: M_BU_CARE069M


title: M_BU_CARE089M


title: M_BU_CARE080M


title: M_BU_CARE095M


title: M_BU_CARE073M


title: M_BU_CARE068M


title: M_BU_CARE093M


title: M_BU_CARE077M


title: M_BU_CARE061M


title: M_BU_CARE066M


title: M_BU_CARE060M


title: M_BU_CARE057M


title: M_BU_CARE052M


title: M_BU_CARE053M


title: M_BU_CARE054M


title: M_BU_CARE044M


title: M_BU_CARE056M


title: M_BU_CARE033M


title: M_BU_CARE046M


title: M_BU_CARE042M


title: M_BU_CARE037M


title: M_BU_CARE045M


title: M_BU_CARE030M


title: M_BU_CARE036M


title: M_BU_CARE050M


title: M_BU_CARE048M


title: M_BU_CARE026M


title: M_BU_CARE031M


title: M_BU_CARE047M


title: M_BU_CARE027M


title: M_BU_CARE034M


title: M_BU_EMVB010D


title: M_BU_CARE021M


title: M_BU_CARE023M


title: M_BU_CARE015M


title: M_BU_CARE019M


title: M_BU_CARE022M


title: M_BU_CARE014M


title: M_BU_CARE020M


title: M_BU_CARE018M


title: M_BU_CARE011M


title: M_BU_CARE013M


title: M_BU_CARE012M


title: M_BU_CARE009M


title: M_BU_CARE007M


title: M_BU_CARE008M


title: M_BU_CARE005M


title: M_PM_C084F


title: M_BU_CARE003M


title: M_BU_CARE002M


title: M_PM_C024H


title: M_PM_C060D


title: M_PM_C060F


title: M_PM_C081H


title: M_PM_C001F


title: M_PM_C072L


title: M_PM_C082H


title: M_BU_EMVB019D


title: M_BU_EMVB098D


title: M_PM_BAKA0932r


title: M_PM_BAKA0938


title: M_PM_BAKA0937


title: M_PM_C058D


title: M_PM_BOBAK011


title: M_PM_C017D


title: M_PM_BAKA0926


title: M_PM_BOBAK195


title: M_PM_BOBAK056