title: G186AR Y/C

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Samples were labeled with Cy5 or with Cy3 and competitively hybridized to custom glass slide 70-mer oligomer microarrays in a closed-circuit experimental design (e.g. direct, pairwise comparisons of yeast and mycelial samples, mycelial and conidial samples, and yeast and conidial samples). Dye-swap hybridizations were performed for these pairwise comparisons.

scan_protocol: The microarrays were scanned using Gene PixPro 6.0 software on an Axon 4000B scanner (Molecular Devices).

data_processing:
The microarrays were gridded with Gene Pix 6.0 (Molecular Devices) and uploaded to the NOMAD database (http://ucsf-nomad.sourceforge.net/) for quality control, normalization and data storage. To eliminate the analysis of microarray features with low signal intensities, we excluded features from the analysis for which the sum of the medians for the 635-nm and 532-nm channels was <=500 intensity units from this analysis; normalized expression ratios are reported in the VALUE column for the remaining spots.
The results of downstream BAGEL analysis for the G186AR strain are available as supplemental data set S4 of the accompanying publication.

organism: Histoplasma capsulatum

source_name: Yeast Y7

label_protocol: 1 ug of total RNA per conidia, mycelia or yeast sample was amplified according to the manufacturer's instructions using the MessageAmp II kit (Ambion). Average yields were 75 ug aRNA (amplified complementary RNA).  Four to five ug aRNA were fragmented with RNA fragmentation reagent (Ambion) prior to hybridizing the samples to microarrays.  Fluorescent labeling was performed as previously described (Mol. Biol. Cell 16:4792).

extract_protocol: Frozen conidial pellets were homogenized by bead beating in 2 mL tubes with 0.5 mM Zirconia/Silica beads (Biospec Products, OK) and Trizol (Invitrogen) in 2mL screw-cap tubes. RNA was isolated according to the manufacturer's instructions. On average, 3 ug conidial RNA was obtained from each 15 cm plate. Yeast and mycelial RNA was prepared as previously described (Mol. Biol. Cell 14:2314) with the following modification: pellets were homogenized by bead beating with 0.5 mM Zirconia/Silica beads in guanadinium lysis buffer. RNA quality was measured with an Agilent Bioanalyzer using RNA Nano LabChips.

value: Histoplasma capsulatum G186AR

source_name: Conidia C21


title: Growth at 220 min

status: Public on Apr 10 2013

type: RNA

city: Atlanta

first: CHun-Kai

last: Yang

state: GA

address: 166 Jesse Hill Jr. Dr.

department: Biology

country: USA

institute: Georgia state University

description: Bacillus subtilis 168 in exponential phase

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Bacillus subtilis subsp. subtilis str. 168

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

growth_protocol: Bacillus subtilis 168 cells were grown in Luria-Bertani medium supplemented with glucose 0.2 % at 37°C with  vigorous shaking in flasks. Overnight cultures were diluted 100-fold in fresh pre-warmed medium and samples were collected at indicated time points

extract_protocol: Total RNA was extracted by method provided by Qiagen and Qiagen Rneasy kit was used for total RNA extraction

treatment_protocol: Cells were centrifuged at 1,3000rpm and pellets were kept at -80OC for further extraction

tag: growth time

value: 220 min

tag: growth stage

value: exponential phase

tag: optical density


title: G186AR M/Y

state: CA

source_name: Mycelia M12

tag: strain


title: G186AR C/M


title: normal prostate from cancer patient array 1

status: Public on Apr 11 2013

city: Reykjavik

first: Sigrun

middle: Helga

last: Lund

address: Dunhagi 3

country: Iceland

institute: University of Iceland

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: This experiment was used to estimate general properties of signal intensities for tiled microarrays and therefore are processed data files irrelevant.

organism: Homo sapiens

source_name: Subject 1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Performed according to NimbleGen protocols

tag: disease state

value: prostate cancer

tag: tissue

value: normal prostate


title: Growth at 240 min

source_name: Bacillus subtilis 168 in exponential phase

value: 240 min


title: G186AR Y/M


title: G186AR C/Y 2


title: Growth at 200 min

value: 200 min


title: G186AR C/Y 1


title: glioma-98, rep1

city: Shanghai

first: juxiang

last: chen

address: 415#,Fengyang Road

country: China

institute: Changzheng Hospital

description:
0286-98
Gene expression data from astrocytoma, WHO II.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by the MAS 5.0 algorithm, GeneSpring Software (Agilent Technologies, Santa Clara, CA, US).

source_name: grade II glioma

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions to obtain biotin-labeled cRNA.

growth_protocol: Glioma tissue samples were obtained in surgical operations and maintained in liquid nitrogen at -80°C within 15 minutes since resection.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: The sample preparation were performed based on the manufacturer's standard protocols.

value: glioma

tag: glioma type

value: astrocytoma

tag: grade

value: II


title: glioma-88, rep1

description:
0286-88
Gene expression data from astrocytoma, WHO III.

source_name: grade III glioma

value: III


title: glioma-90, rep1

description:
0286-90
Gene expression data from astrocytoma, WHO IV.

source_name: grade IV glioma

value: IV


title: glioma-52, rep1

description:
0286-52
Gene expression data from ependymoma, WHO II.

value: ependymoma


title: glioma-94, rep1

description:
0286-94
Gene expression data from astrocytoma, WHO III.


title: glioma-58, rep1

description:
0286-58
Gene expression data from ependymoma, WHO II.


title: glioma-100, rep1

description:
0286-100
Gene expression data from astrocytoma, WHO I.

source_name: grade I glioma

value: I


title: glioma-95, rep1

description:
0286-95
Gene expression data from astrocytoma, WHO I.


title: G186AR M/C


title: glioma-29, rep1

description:
0286-29
Gene expression data from astrocytoma, WHO II.


title: glioma-92, rep1

description:
0286-92
Gene expression data from astrocytoma, WHO IV.


title: glioma-27, rep1

description:
0286-27
Gene expression data from astrocytoma, WHO III.


title: glioma-71, rep1

description:
0286-71
Gene expression data from astrocytoma, WHO II.


title: glioma-53, rep1

description:
0286-53
Gene expression data from oligodendroglioma, WHO II.

value: oligodendroglioma


title: glioma-04, rep1

description:
0286-04
Gene expression data from oligodendroglioma, WHO II.


title: glioma-83, rep1

description:
0286-83
Gene expression data from astrocytoma, WHO IV.


title: fibroblast_Slow_D72_Media_8

city: Gaithersburg

first: Sriram

last: Sridhar

state: MD

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

hyb_protocol: Array washing, staining and scanning was performed according to standard Affymetrix protocols .

data_processing: Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.

source_name: Slow progressing fibrosis

label_protocol: Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.

growth_protocol: Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study.  The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer.  The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n = 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).

extract_protocol: Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits

treatment_protocol: No additional treatments were applied to the cultured cell lines

tag: status

value: Slow

tag: age

tag: gender

value: female

value: cultured human fibroblasts


title: fibroblast_Slow_D98_Media_11

scan_protocol: Array washing, staining and scanning was performed according to standard Affymetrix protocols .

value: male


title: fibroblast_Slow_D69_Media_7


title: glioma-76, rep1

description:
0286-76
Gene expression data from ependymoma, WHO II.


title: fibroblast_Slow_D76_Media_9


title: glioma-89, rep1

description:
0286-89
Gene expression data from astrocytoma, WHO IV.


title: glioma-69, rep1

description:
0286-69
Gene expression data from oligodendroglioma, WHO II.


title: glioma-86, rep1

description:
0286-86
Gene expression data from astrocytoma, WHO II.


title: glioma-78, rep1

description:
0286-78
Gene expression data from oligodendroglioma, WHO II.


title: glioma-12, rep1

description:
0286-12
Gene expression data from oligodendroglioma, WHO II.


title: glioma-72, rep1

description:
0286-72
Gene expression data from ependymoma, WHO II.


title: fibroblast_Rapid_D26_Media_15

source_name: Rapid progressing fibrosis

value: Rapid


title: fibroblast_Slow_D223_Media_12


title: fibroblast_Slow_D123_Media_10


title: fibroblast_Normal_D160_Media_5

source_name: Normal - no fibrosis

value: Normal


title: fibroblast_Rapid_D200_Media_14


title: fibroblast_Rapid_D10_Media_13


title: fibroblast_Normal_D139_Media_4


title: fibroblast_Normal_D133_Media_3


title: BAEC TGFB-REP3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Primary bovine aortic endothelial cells. Treated with TGFB. Rep3

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

label: Biotin

organism: Bos taurus

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bovine primary aortic endothelial cells were isolated from bovine aorta by collagenase treatment. Cells were grown on RPMI culture medium under standard culture conditions.

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

treatment_protocol: Primary aortic endothelial cells seeded on 10 mm diameter plates were incubated with TGF-beta 1 (5 ng/ml) for 24 hours or left under basal conditions.

tag: cell type

value: primary aortic endothelial


title: Lung cancer tissue sample 265T

city: Taipei

first: Yih-Jyh

last: Shann

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: Nation Yang-Ming University

description: Gene expression data from lung cancer patient tissue 265T

hyb_protocol: Fragmentated cRNA were hybridized for 16 hr on HG-U133 Plus2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Data were imported into GeneSpring version 7.31 software (RMA probe summarization), Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) are used as normalization method.

source_name: Lung cancer tissue sample 265T

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

extract_protocol: Total RNA was extracted according to the instruction of QIAGEN RNeasy mini kit.

tag: egfr mutation

value: No

tag: Stage

value: Ib


title: fibroblast_Normal_D207_Media_6


title: BAEC Basal-REP2

description: Primary bovine aortic endothelial cells. No treatment. Rep2


title: BAEC TGFB-REP2

description: Primary bovine aortic endothelial cells. Treated with TGFB. Rep2


title: Lung cancer tissue sample 265N

description: Gene expression data from lung cancer patient tissue 265N

source_name: Lung cancer tissue sample 265N


title: Lung cancer tissue sample 259T

description: Gene expression data from lung cancer patient tissue 259T

source_name: Lung cancer tissue sample 259T

value: Yes


title: Lung cancer tissue sample 257T

description: Gene expression data from lung cancer patient tissue 257T

source_name: Lung cancer tissue sample 257T

value: Ia


title: Lung cancer tissue sample 226T

description: Gene expression data from lung cancer patient tissue 226T

source_name: Lung cancer tissue sample 226T


title: BAEC Basal-REP3

description: Primary bovine aortic endothelial cells. No treatment. Rep3


title: BAEC TGFB-REP1

description: Primary bovine aortic endothelial cells. Treated with TGFB. Rep1


title: Lung cancer tissue sample 259N

description: Gene expression data from lung cancer patient tissue 259N

source_name: Lung cancer tissue sample 259N


title: BAEC Basal-REP1

description: Primary bovine aortic endothelial cells. No treatment. Rep1


title: Lung cancer tissue sample 257N

description: Gene expression data from lung cancer patient tissue 257N

source_name: Lung cancer tissue sample 257N


title: Lung cancer tissue sample 234T

description: Gene expression data from lung cancer patient tissue 234T

source_name: Lung cancer tissue sample 234T


title: B3

city: Kunming

first: Hua-Tang

last: Zhang

state: Yunnan

address: No.32 Jiaochang Donglu

department: key laboratory of animal models and human diseases mechanisms

institute: Kunming Institute of Zoology, Chinese Academy of Science

description: Gene expression of CD4+T cells costimulated by CD3/CD28 coated beads for 6 day

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: CD4+T cells costimulated by CD3/CD28 coated beads for 6 days

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

growth_protocol: Cells were cultured in 6-well plates at 37℃, 5% CO2 in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 20mM HEPES

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

treatment_protocol: Fresh normal donors peripheral blood mononuclear cells isolated by Ficool-Hypaque (TBD sciences) centrifugation were enriched for CD4+ T cells (>97% purity by FACS) by magnetic negatively selection (CD4+T cell Isolation Kit II, Miltenyi Biotec). For PHA/IL-2 stimulation, cells were cultured at a density of 2×106/well with human recombinant IL-2 (100 units/ml, Pepro Tech) and PHA (5µg/ml, Sigma). For CD3/CD28 costimulation, cells were cultured at a density of 0.5×106/well with polystyrene beads coated of CD3 and CD28 antibodies (Dynabeads CD3/CD28 T Cell Expander, Dynal). The ratio of beads to cells was 3:1.

value: human CD4+T cells


title: P3

description: Gene expression of CD4+T cells stimulated by PHA/IL-2 for 6 days


title: Lung cancer tissue sample 226N

description: Gene expression data from lung cancer patient tissue 226N

source_name: Lung cancer tissue sample 226N


title: Lung cancer tissue sample 234N

description: Gene expression data from lung cancer patient tissue 234N

source_name: Lung cancer tissue sample 234N


title: B2


title: B1


title: R3

description: Gene expression of resting CD4+T cells

source_name: Resting CD4+T cells


title: Lung cancer tissue sample 212N

description: Gene expression data from lung cancer patient tissue 212N

source_name: Lung cancer tissue sample 212N


title: P1

source_name: CD4+T cells stimulated by PHA/IL-2 for 6 days


title: R2

description: Gene expression of resting CD4+T cells


title: Lung cancer tissue sample 212T

description: Gene expression data from lung cancer patient tissue 212T

source_name: Lung cancer tissue sample 212T


title: P2


title: R1

description: Gene expression of resting CD4+T cells


title: normal prostate from cancer patient array 7

source_name: Subject 7

value: prostate cancer

value: normal prostate


title: Lung cancer tissue sample 208N

description: Gene expression data from lung cancer patient tissue 208N

source_name: Lung cancer tissue sample 208N


title: Lung cancer tissue sample 181N

description: Gene expression data from lung cancer patient tissue 181N

source_name: Lung cancer tissue sample 181N


title: Lung cancer tissue sample 181T

description: Gene expression data from lung cancer patient tissue 181T

source_name: Lung cancer tissue sample 181T


title: Lung cancer tissue sample 196N

description: Gene expression data from lung cancer patient tissue 196N

source_name: Lung cancer tissue sample 196N


title: Lung cancer tissue sample 210N

description: Gene expression data from lung cancer patient tissue 210N

source_name: Lung cancer tissue sample 210N


title: Lung cancer tissue sample 184N

description: Gene expression data from lung cancer patient tissue 184N

source_name: Lung cancer tissue sample 184N


title: Lung cancer tissue sample 209T

description: Gene expression data from lung cancer patient tissue 209T

source_name: Lung cancer tissue sample 209T


title: Lung cancer tissue sample 209N

description: Gene expression data from lung cancer patient tissue 209N

source_name: Lung cancer tissue sample 209N


title: Lung cancer tissue sample 196T

description: Gene expression data from lung cancer patient tissue 196T

source_name: Lung cancer tissue sample 196T


title: Lung cancer tissue sample 208T

description: Gene expression data from lung cancer patient tissue 208T

source_name: Lung cancer tissue sample 208T


title: Lung cancer tissue sample 210T

description: Gene expression data from lung cancer patient tissue 210T

source_name: Lung cancer tissue sample 210T


title: Lung cancer tissue sample 164T

description: Gene expression data from lung cancer patient tissue 164T

source_name: Lung cancer tissue sample 164T


title: Lung cancer tissue sample 184T

description: Gene expression data from lung cancer patient tissue 184T

source_name: Lung cancer tissue sample 184T


title: Lung cancer tissue sample 164N

description: Gene expression data from lung cancer patient tissue 164N

source_name: Lung cancer tissue sample 164N


title: Lung cancer tissue sample 156N

description: Gene expression data from lung cancer patient tissue 156N

source_name: Lung cancer tissue sample 156N


title: Lung cancer tissue sample 134T

description: Gene expression data from lung cancer patient tissue 134T

source_name: Lung cancer tissue sample 134T


title: Lung cancer tissue sample 159N

description: Gene expression data from lung cancer patient tissue 159N

source_name: Lung cancer tissue sample 159N


title: Lung cancer tissue sample 134N

description: Gene expression data from lung cancer patient tissue 134N

source_name: Lung cancer tissue sample 134N


title: Lung cancer tissue sample 122T

description: Gene expression data from lung cancer patient tissue 122T

source_name: Lung cancer tissue sample 122T


title: Lung cancer tissue sample 127N

description: Gene expression data from lung cancer patient tissue 127N

source_name: Lung cancer tissue sample 127N


title: Lung cancer tissue sample 159T

description: Gene expression data from lung cancer patient tissue 159T

source_name: Lung cancer tissue sample 159T


title: Lung cancer tissue sample 127T

description: Gene expression data from lung cancer patient tissue 127T

source_name: Lung cancer tissue sample 127T


title: Lung cancer tissue sample 122N

description: Gene expression data from lung cancer patient tissue 122N

source_name: Lung cancer tissue sample 122N


title: Lung cancer tissue sample 104T

description: Gene expression data from lung cancer patient tissue 104T

source_name: Lung cancer tissue sample 104T


title: Lung cancer tissue sample 156T

description: Gene expression data from lung cancer patient tissue 156T

source_name: Lung cancer tissue sample 156T


title: Lung cancer tissue sample 107N

description: Gene expression data from lung cancer patient tissue 107N

source_name: Lung cancer tissue sample 107N


title: Lung cancer tissue sample 107T

description: Gene expression data from lung cancer patient tissue 107T

source_name: Lung cancer tissue sample 107T


title: Lung cancer tissue sample 097T

description: Gene expression data from lung cancer patient tissue 097T

source_name: Lung cancer tissue sample 097T


title: Lung cancer tissue sample 104N

description: Gene expression data from lung cancer patient tissue 104N

source_name: Lung cancer tissue sample 104N


title: Lung cancer tissue sample 070T

description: Gene expression data from lung cancer patient tissue 070T

source_name: Lung cancer tissue sample 070T


title: Lung cancer tissue sample 095T

description: Gene expression data from lung cancer patient tissue 095T

source_name: Lung cancer tissue sample 095T


title: Sarcoma cell line  - Dicer Null -rep3

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.0, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.0, Biobase_2.8.0

organism: Mus musculus

source_name: Sarcoma cell line Null for Dicer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: Cells were cultured in DMEM supplemented with penicillin/streptomycin, L-glutamine, and 10% FBS.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was DNAseI treated and further purified using the QIAgen Rneasy mini columns

treatment_protocol: Dicer-heterozygous and Dicer KO cells were grown to confluence in T25s and harvested for extraction of total RNA.

value: Sarcoma cell line

tag: genotype/variation

value: Dicer Null


title: Lung cancer tissue sample 064T

description: Gene expression data from lung cancer patient tissue 064T

source_name: Lung cancer tissue sample 064T


title: Sarcoma cell line  - Dicer Heterozygote -rep3

source_name: Sarcoma cell line heterozygous for Dicer

value: Dicer Heterozygote


title: Lung cancer tissue sample 064N

description: Gene expression data from lung cancer patient tissue 064N

source_name: Lung cancer tissue sample 064N


title: Sarcoma cell line  - Dicer Null -rep2


title: Sarcoma cell line  - Dicer Heterozygote -rep2


title: Sarcoma cell line - Dicer Null -rep1


title: Lung cancer tissue sample 095N

description: Gene expression data from lung cancer patient tissue 095N

source_name: Lung cancer tissue sample 095N


title: Lung cancer tissue sample 070N

description: Gene expression data from lung cancer patient tissue 070N

source_name: Lung cancer tissue sample 070N


title: 109_O-113

city: Tokushima city

first: toshihito

last: tanahashi

address: Kuramoto-cho 3-18-15

country: Japan

institute: Tokushima University

hyb_protocol: Hybridization were performed in accordance with the manufacturer’s procedure.

scan_protocol: The array was scanned with a laser scanner (G2565BA; Agilent).

data_processing: Feature Extraction 9.5 software (Agilent) was used to obtain the microarray raw data.

source_name: HCC

label_protocol: One-color microRNA labeling with Cy3 fluorescence were performed in accordance with the manufacturer’s procedure.

extract_protocol: Extraction protocol The miRNeasy mini kit (Qiagen, Valencia, CA) was used to extract total RNA including microRNA.

tag: histology

value: moderate


title: 110_O-115


title: Lung cancer tissue sample 056T

description: Gene expression data from lung cancer patient tissue 056T

source_name: Lung cancer tissue sample 056T


title: 107_O-111


title: 108_O112


title: Sarcoma cell line  - Dicer Heterozygote -rep1


title: Lung cancer tissue sample 097N

description: Gene expression data from lung cancer patient tissue 097N

source_name: Lung cancer tissue sample 097N


title: lung_vehicle_d35_M8

hyb_protocol: RNA from samples was hybridized to Affymetrix Mouse 430 2.0 arrays. Array washing and staining were performed according to standard Affymetrix protocols.

scan_protocol: Array scanning was performed according to standard Affymetrix protocols.

data_processing: Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded. The probe curation and normalization were performed in an internal pipeline using R and SAS.

source_name: Lung, saline, d35

label_protocol: Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA).

extract_protocol: Total RNA was isolated from the mouse lung tissue of bleomycin- and saline-treated mice across 7 time points (1, 2, 7, 14, 21, 28, and 35 days, n=8 per group) and homogenized in QIAzol reagent.

treatment_protocol: Mice were intratracheally treated with bleomycin or saline once. Lung tissue was harvested from sacrificed mice at 7 timepoints following treatment.

tag: strain/background

value: lung homogenate

tag: treatment

value: saline

tag: time point

value: day 35


title: lung_bleomycin_d35_N8

source_name: Lung, bleomycin, d35

value: male

value: bleomycin


title: lung_bleomycin_d35_N4


title: lung_bleomycin_d35_N5


title: Lung cancer tissue sample 056N

description: Gene expression data from lung cancer patient tissue 056N

source_name: Lung cancer tissue sample 056N


title: lung_bleomycin_d35_N1


title: lung_bleomycin_d35_N6


title: lung_bleomycin_d35_N2


title: 105_O-109

value: female

value: well


title: 104_O-108


title: lung_bleomycin_d35_N7


title: lung_bleomycin_d35_N3


title: 103_O-105


title: 106_O-110


title: 102_O-104


title: 101_O-103


title: 100_O-100


title: 99_O-098


title: lung_vehicle_d35_M7


title: 98_O-093


title: 97_O-092


title: lung_vehicle_d35_M4


title: lung_bleomycin_d28_L8

source_name: Lung, bleomycin, d28

value: day 28


title: 88_O-002


title: 96_O-090


title: fibroblast_Rapid_D56_Media_16

source_name: Rapid progressing fibrosis

value: Rapid

value: cultured human fibroblasts


title: 92_O-006


title: lung_vehicle_d35_M3


title: lung_vehicle_d35_M2


title: 91_O-005


title: 90_O-004


title: 95_O-089


title: lung_bleomycin_d28_L7


title: lung_bleomycin_d28_L3


title: lung_bleomycin_d28_L6


title: lung_vehicle_d35_M1


title: lung_bleomycin_d28_L1


title: 89_O-003


title: lung_vehicle_d28_K6

source_name: Lung, saline, d28


title: lung_vehicle_d28_K8


title: 93_O-086


title: lung_bleomycin_d28_L4


title: lung_vehicle_d35_M5


title: 94_O-088


title: lung_bleomycin_d28_L5


title: lung_vehicle_d28_K5


title: 87_O-001


title: 86_K-209

value: not available


title: 84_K-183


title: 85_K-204

value: poor


title: lung_vehicle_d28_K3


title: 76_CU-85


title: 79_CU-91


title: 80_K-023


title: 81_K-122


title: lung_vehicle_d28_K2


title: lung_vehicle_d28_K7


title: lung_bleomycin_d21_J7

source_name: Lung, bleomycin, d21

value: day 21


title: lung_vehicle_d28_K1


title: synthetic nasal medium (SNM), biological rep3

city: Tuebingen

first: Bernhard

last: Krismer

address: Elfriede-Aulhorn-Str. 6

department: IMIT

country: Germany

institute: University of Tuebingen

description: Gene expression data of aerobic S. aureus cultures in exponential phase of growth

hyb_protocol: Hybridization of cDNA and following washing and staining of GeneChips were carried out according to standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Chapter 6 Prokaryotic; 702232, Rev.3).

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 (Affymetrix; P/N 00-00212)

data_processing: The data were analyzed with GCOS version 1.1 using Affymetrix default analysis settings.

organism: Staphylococcus aureus

source_name: synthetic nasal medium (SNM) at OD578nm 0.02

label_protocol: cDNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (GeneChip Expression Analysis Technical Manual, Chapter 4 Prokaryotic; 702232, Rev.3). cDNA were labeled with GeneChip® DNA Labeling Reagent (Affymetrix P/N 900542).

growth_protocol: Basic medium (BM composed of 1% tryptone, 0.5% yeast extract, 0.5% NaCl, 0.1% K2HPO4 x H2O, and 0.1% glucose) or a chemically defined synthetic medium (SNM) were inoculated with bacterial over-night cultures in SNM at an OD578 of 0.005 and cultivated aerobically with vigorous shaking at 37°C (baffled Erlenmeyer flasks on shaker).

extract_protocol: cells were lysed in 100 µl TE buffer containing 10 µl lysostaphin (2 mg/ml) and incubated for 3 min at room temperature. After the addition of 350 µl RLT buffer (RNeasy Kit, QIAGEN GmbH, Germany) cells were lysed with 0.2 ml zirconia-silica beads in a homogenizer and RNA was purified with the RNeasy Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were harvested by centrifugation at an OD578 of 0.02 after RNA was stabilised in the culture with 1/9 volume of ice cold phenol:ethanol mixture (1:9). Cell pellets were washed with ice cold ethanol:acetone (1:1), and a final washing and stabilistaion step was made with RNAprotect bacteria reagent (QIAGEN). Finally cells were immediately frozen at -80°C.


title: complex medium (BM), biological rep2

source_name: complex medium (BM) at OD578nm 0.02


title: complex medium (BM), biological rep3


title: synthetic nasal medium (SNM), biological rep2


title: complex medium (BM), biological rep1


title: lung_bleomycin_d21_J3


title: synthetic nasal medium (SNM), biological rep1


title: lung_bleomycin_d21_J8


title: lung_bleomycin_d21_J4


title: lung_bleomycin_d21_J6


title: lung_bleomycin_d21_J2


title: lung_bleomycin_d21_J1


title: lung_bleomycin_d21_J5


title: mPC 4 hours 2

city: Aachen

first: Ralf

last: Weiskirchen

state: NRW

address: Pauwelsstr. 30

department: Institute of Clinical Chemistry and Pathobiochemistry

institute: RWTH University Hospital Aachen

hyb_protocol: Standard Affyemtrix protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: mPC 4 hours 2

label_protocol: biotin

growth_protocol: Primary murine hepatocytes were isolated from male C57BL/6 mice according to the collagenase method described by Seglen (Meth Cell Biol 1976;13:29-83). Cells were plated in collagen coated 6-well dishes at a density of 1.2 x 106 cells/plate using HepatoZYME-SFM (Gibco Life Technologies, Darmstadt, Germany). Four hours after seeding the medium was renewed and cells were grown for a further 24 hrs period. One hour before stimulation, the medium was exchanged. Cells were then stimulated with 1 ng/ml recombinant human TGF-β1 (R&D Systems, Wiesbaden, Germany). The cells were harvested after indicated time points and total RNA prepared using a pre-formatted RNA isolation kit (Qiagen, Hilden, Germany).

extract_protocol: RNeasy kit (Quiagen)

value: primary murine hepatocytes

tag: agent

tag: time

value: 4 hours


title: lung_vehicle_d35_M6


title: mPC 4 hours 1

source_name: mPC 4 hours 1

tag: strain


title: mPC 2 hours 2

source_name: mPC 2 hours 2

value: 2 hours


title: 75_CU-83

value: moderate


title: 74_CU-70


title: 77_CU-87


title: mPC 4 hours 3

source_name: mPC 4 hours 3


title: lung_vehicle_d21_I8

source_name: Lung, saline, d21

tag: tissue

value: lung homogenate


title: mPC 2 hours 1

source_name: mPC 2 hours 1


title: 83_K-177

source_name: HCC


title: 73_347


title: 82_K-160


title: mPC 2 hours 3

source_name: mPC 2 hours 3


title: 72_346


title: 71_345


title: lung_vehicle_d28_K4

value: saline


title: 70_340


title: mPC 20 min 3

source_name: mPC 20 min 3

value: 20 min


title: lung_vehicle_d21_I6

value: male


title: 69_336


title: mPC 20 min 1

source_name: mPC 20 min 1


title: mPC 20 min 2

source_name: mPC 20 min 2


title: lung_vehicle_d21_I7


title: 68_335


title: mPC control 2

source_name: mPC control 2

value: untreated

value: control


title: lung_vehicle_d21_I5


title: mPC control 1

source_name: mPC control 1


title: C3_IKAm_10_4

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Based on Affymetrix protocols.

scan_protocol: Based on Affymetrix protocols.

data_processing: Data was processed/normalized by the RMA algorithm using Affymetrix Expression Console version 1.1.

source_name: Type II alveolar epithelial cells, control

label_protocol: Based on Affymetrix protocols.

extract_protocol: Alveolar type II cells were isolated from 8-week-old sex- and age-matched littermate control and Gpr116 knockout mice using collagenase and differential plating. Type II cells from 3 mice were pooled to obtain one pellet. Two hours after isolation, type II cells were homogenized with TRIzol reagent (Invitrogen, Carlsbad, CA). RNA concentration was measured by spectrophotometer and normalized for cDNA synthesis.

value: lung

value: type II alveolar epithelial cells

value: 8 weeks

tag: developmental stage

value: adult


title: lung_vehicle_d21_I2


title: C2_IKAm_8_9


title: mPC control 3

source_name: mPC control 3


title: lung_vehicle_d21_I1


title: 66_330

value: female


title: KO2_IKAm_9_7

source_name: Type II alveolar epithelial cells, Gpr116 KO


title: KO1_IKAm_9_4


title: lung_vehicle_d21_I4


title: 65_329


title: 67_333


title: KO3_IKAm_11_11


title: C1_IKAm_8_1


title: 64_328

value: poor


title: PBS_d28_5

city: Cologne

first: Manuel

last: Montesinos-Rongen

address: Kerpenerstr. 62

department: Institute for Neuropathology

institute: University Hospital Cologne

hyb_protocol: affymetrix standard protocol

scan_protocol: affymetrix standard protocol

data_processing: affymetrix software (Expression Console; RMA; quantile normalization)

source_name: whole brain of PBS injected control mice at day 28 post opertation

label_protocol: affymetrix standard protocol

extract_protocol: frozen tissue section; trizol

value: BALB/c

value: whole brain


title: PBS_d28_4


title: lung_vehicle_d21_I3

value: day 21


title: PBS_d28_3


title: lung_bleomycin_d14_H7

source_name: Lung, bleomycin, d14

value: bleomycin

value: day 14


title: BAL17_d28_5

source_name: whole brain of BAL17-induced lymphoma at day 28 post implantation


title: 63_327


title: BAL17_d28_4


title: lung_bleomycin_d14_H8

value: lung homogenate


title: PBS_d28_1


title: lung_bleomycin_d14_H6


title: PBS_d28_2


title: 62_325


title: 61_324


title: BAL17_d28_2


title: BAL17VII_d21_5

source_name: whole brain of BAL17VII-induced lymphoma at day 21 post implantation


title: 59_321

value: moderate


title: lung_bleomycin_d14_H3


title: BAL17VII_d21_1


title: BAL17_d28_1


title: lung_bleomycin_d14_H5


title: lung_bleomycin_d14_H4


title: BAL17VII_d21_3


title: 60_322


title: lung_bleomycin_d14_H1


title: BAL17VII_d21_2


title: BAL17_d28_3


title: BAL17_d21_5

source_name: whole brain of BAL17-induced lymphoma at day 21 post implantation


title: lung_bleomycin_d14_H2


title: 57_318


title: 58_319


title: BAL17VII_d21_4


title: BAL17_d21_4


title: lung_bleomycin_d28_L2

source_name: Lung, bleomycin, d28

value: day 28


title: BAL17_d21_1


title: BAL17_d21_3


title: BAL17_5

source_name: BAL17 cell line

value: BAL17 cell line


title: lung_vehicle_d14_G6

source_name: Lung, saline, d14

value: male

value: saline


title: BAL17_d21_2


title: lung_vehicle_d14_G7


title: lung_vehicle_d14_G5


title: 55_314

source_name: HCC


title: 56_315


title: BAL17_6


title: 53_299


title: 54_310


title: BAL17_2


title: 52_297


title: lung_vehicle_d14_G4


title: BAL17_3


title: 51_295


title: 50_282


title: lung_vehicle_d14_G3


title: BAL17VII_5

source_name: BAL17-derived cell line

value: BAL17-derived cell line


title: BAL17VII_4


title: lung_vehicle_d14_G2


title: BAL17VII_6


title: BAL17VII_3


title: BAL17VII_2


title: 78_CU-89


title: BAL17_1


title: BAL17VII_1


title: 49_281


title: HepG2 24 hours 3

source_name: HepG2 24 hours 3

growth_protocol: HepG2 cells originally originate from a 15 years adolescent male Caucasian with primary hepatoblastoma (Aden et al., Nature 1979;282:615-616). Cells were obtained from the DSMZ (DSM ACC180) and cultured in RPMI (PAA, Pasching, Austria) containing 10% fetal calf serum (PAA), 1 x Penicillin/Streptomycin (Lonza, Cologne, Germany). Medium was renewed every second day. For the experiment, the cells were passaged and plated at a density of 4 x 105 cells in 6-well dishes using accutase (PAA). One day before the experiment, cells were washed with PBS, medium changed to HepatoZYME-SFM (Gibco Life Technologies, Darmstadt, Germany) and cultured for a further 24 hrs period. Cells were then stimulated with 1 ng/ml recombinant human TGF-β1 (R&D Systems, Wiesbaden, Germany) for indicated time points (20 min, 1 hour, 2 hours, 4 hours, and 24 hours), harvested, and total RNA prepared using a pre-formatted RNA preparation kit (Qiagen, Hilden, Germany).

tag: cell line

value: hepatocellular carcinoma cell line (HepG2)

tag: tissue origin

value: human liver carcinoma

value: 24 hours


title: HepG2 24 hours 1

source_name: HepG2 24 hours 1


title: HepG2 4 hours 3

source_name: HepG2 4 hours 3

value: 4 hours


title: HepG2 24 hours 2

source_name: HepG2 24 hours 2


title: lung_bleomycin_d7_F6

source_name: Lung, bleomycin, d7

value: day 7


title: HepG2 4 hours 2

source_name: HepG2 4 hours 2


title: lung_bleomycin_d7_F8


title: HepG2 4 hours 1

source_name: HepG2 4 hours 1


title: 47_277

tag: age


title: 48_278

tag: gender

value: poor


title: lung_vehicle_d14_G1


title: lung_bleomycin_d7_F7


title: lung_bleomycin_d7_F4


title: 46_275

value: well


title: HepG2 2 hours 1

source_name: HepG2 2 hours 1

value: 2 hours


title: HepG2 2 hours 3

source_name: HepG2 2 hours 3


title: 45_274


title: HepG2 1 hours 1

source_name: HepG2 1 hours 1

value: 1 hour


title: HepG2 1 hours 2

source_name: HepG2 1 hours 2


title: HepG2 2 hours 2

source_name: HepG2 2 hours 2


title: lung_bleomycin_d7_F3

value: bleomycin


title: HepG2 20 min 2

source_name: HepG2 20 min 2

value: 20 min


title: 44_272

value: female

value: moderate


title: HepG2 20 min 1

source_name: HepG2 20 min 1


title: HepG2 control 3

source_name: HepG2 control 3

value: untreated

value: control


title: lung_bleomycin_d7_F2

value: male

value: lung homogenate


title: lung_bleomycin_d7_F1


title: HepG2 control 2

source_name: HepG2 control 2

value: hepatocellular carcinoma cell line (HepG2)


title: lung_vehicle_d7_E8

source_name: Lung, saline, d7

value: saline


title: lung_bleomycin_d7_F5


title: 43_271

source_name: HCC


title: HepG2 1 hours 3

source_name: HepG2 1 hours 3

value: human liver carcinoma


title: HepG2 20 min 3

source_name: HepG2 20 min 3


title: 42_269


title: 41_268


title: 39_260


title: 40_261


title: 38_258


title: lung_vehicle_d7_E7


title: 37_253


title: 36_251


title: Control Capan cells

first: Dusten

middle: John

last: Unruh

address: 3125 Edan Ave

department: Hematology/Oncology

institute: University of Cincinnati

hyb_protocol: The labeled samples were hybridized onto Affymetrix Human Gene 1.0 ST chips.

scan_protocol: Affymetrix scanner 2500.

data_processing: CEL files were processed by RMA 16.

source_name: Capan-1, control

label_protocol: Total RNA was reverse transcribed, amplified, fragmented, and labeled for microarray analysis using the Nugen WTA Ovation FFPE kit and Encore biotin module (Nugen, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated using RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Pt45P1 and Capan-1 cells were treated with recombinant human asTF preparations generated and characterized as previously described (7) for 4 hrs at a final concentration of 50 nM; equal volumes of 50% glycerol in PBS served as the vehicle control.

value: vehicle


title: lung_vehicle_d7_E5

value: day 7


title: HepG2 control 1

source_name: HepG2 control 1


title: Alt spliced Tissue Factor pt45 cells

source_name: Pt45P1, asTF

value: 50nM alternatively spliced tissue factor (asTF)


title: Control nasal epithelium_biological rep5

city: Lisboa

first: Luka

last: Clarke

address: Campo Grande

department: BioFIG

country: Portugal

institute: University of Lisboa

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. A final volume of 200µl was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (EukGE-WS2v5) were used on an Affymetrix GeneChip Fluidics Station 400.

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

data_processing: The data were normalized and summarized with RMA Express using default settings (Background Adjust: Yes, Normalization: Quantile).

source_name: Nasal epithelial cells obtained by bilateral nasal brushing from control patient not suffering from CF ands assumed to be expressing wild type CFTR gene.

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip HsAirwaya520108F Arrays according to the manufacturer’s Two-Cycle Target Labelling Assay. Briefly, 90 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) were used in a reverse transcription reaction (Two-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (MEGAscript T7 kit; Ambion, Austin, TX). 600 ng of the cRNA obtained was used for a second round of cDNA and cRNA synthesis, resulting in biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, were assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: The study was conducted at the Faculty of Sciences of the University of Lisboa with samples collected at the CF Clinic of the Department of Pediatrics of the Santa Maria Hospital of Lisboa, and was approved by the Santa Maria Hospital Ethical Review Board. Informed consent was obtained from each participant, or parent/tutor where the participant was a minor. To be eligible for the study, individuals with CF had been previously confirmed to be homozygous for the F508del mutation. Individuals with recent viral infection, or active CF exacerbation were excluded. Non-CF control subjects were recruited from healthy volunteers attending the paediatric clinic for unrelated reasons. If participants demonstrated obvious turbinate inflammation or haemorrhage on initial brushing, the sample was excluded. Bilateral nasal mucosal brushing to collect respiratory epithelium was performed on each subject. An aliquot was set aside for cytological evaluation, and the remainder used for RNA extraction. A cytospin centrifuge (Shandon, Thermo Scientific, USA) was used to prepare formaldehyde-fixed respiratory epithelial samples for standard May-Grünwald-Giemsa (MGG) staining. Identity of samples was obscured with randomly numbered labels for blind counting. Slides were then evaluated twice using light microscopy and digital photography of 5 high power fields of view per sample, and cells were categorized as epithelial or inflammatory.  Samples with more than 10% inflammatory cells were excluded from the study.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Concentration and purity was determined by spectrophotometry (Nanodrop) and integrity (RIN>7.0: mean RIN, CF - 8.2; Control - 8.4) was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Following washing and centrifugation in PBS, the aliquot of cells destined for RNA extraction was suspended in RLT extraction buffer from the Qiagen RNeasy kit on ice, and RNA extracted immediately upon return to the laboratory, as described below.

tag: disease

value: F


title: lung_vehicle_d7_E3


title: Control pt45 cells

source_name: Pt45P1, control


title: Control nasal epithelium_biological rep4

value: M


title: CF nasal epithelium_biological rep5

source_name: Nasal epithelial cells obtained by bilateral nasal brushing from CF patient with confirmed F508del homozygosity for the CFTR gene.

value: cystic fibrosis


title: lung_vehicle_d7_E1


title: BAL17_4

source_name: BAL17 cell line

value: BALB/c

tag: cell type

value: BAL17 cell line


title: lung_vehicle_d7_E4


title: lung_vehicle_d7_E2


title: lung_vehicle_d7_E6


title: Alt spliced Tissue Factor Capan cells

source_name: Capan-1, asTF


title: CF nasal epithelium_biological rep1


title: lung_bleomycin_d2_D8

source_name: Lung, bleomycin, d2

value: bleomycin

value: day 2


title: 34_248

value: moderate


title: 33_246


title: 32_241

value: female


title: 35_249


title: 31_238

value: male


title: 30_235

value: poor


title: CF nasal epithelium_biological rep4


title: CF nasal epithelium_biological rep2


title: lung_bleomycin_d2_D6

value: lung homogenate


title: lung_bleomycin_d2_D7


title: Control nasal epithelium_biological rep2


title: 29_229


title: 26_223


title: 28_228


title: 27_224


title: Control nasal epithelium_biological rep1


title: Control nasal epithelium_biological rep3


title: CF nasal epithelium_biological rep3


title: lung_bleomycin_d2_D3


title: lung_vehicle_d2_C8

source_name: Lung, saline, d2

value: saline


title: lung_vehicle_d2_C7


title: lung_vehicle_d2_C6


title: 25_222


title: lung_bleomycin_d2_D1


title: 24_221


title: lung_bleomycin_d2_D2


title: lung_bleomycin_d2_D4


title: lung_vehicle_d2_C5


title: 23_219


title: 22_216

value: well


title: High-editing monocyte-enriched PBMCs, sample 3

city: Buffalo

first: Biao

last: Liu

state: NY

address: Elm and Carlton streets

department: Center for Personalized Medicine

institute: Roswell Park Cancer Institute

description: 2901 agg 9-20

hyb_protocol: 750ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the HT-12 v4 BeadChips.

scan_protocol: Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: The background corrected gene expression levels were extracted from BeadChip using Illumina's Genome Studio (v2011.1) gene expression module (v1.9.0). The log2 transformed expression levels were quantile normalized using Lumi module in the R-based Bioconductor package.

source_name: PBMCs, high-editing

label_protocol: 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer's instructions.

growth_protocol: PBMCs were subjected to cold-aggregation for monocyte-enrichment and cultured in standard culture conditions with RPMI with 10% FBS.

extract_protocol: Total RNA is extracted by RNAzol.

value: monocyte-enriched peripheral blood mononuclear cells

value: adult

tag: Stage

value: high-editing

tag: donor


title: 20_208

tag: histology


title: High-editing monocyte-enriched PBMCs, sample 5

description: 3279 agg 10-24


title: lung_vehicle_d2_C2

tag: strain/background


title: lung_vehicle_d2_C4

tag: treatment


title: Uncultured monocyte-enriched PBMCs, sample 4

description: 2937 9-17

source_name: PBMCs, uncultured

value: uncultured


title: lung_vehicle_d2_C3

tag: time point


title: Low-editing monocyte-enriched PBMCs, sample 3

description: 2901 agg 9-17

source_name: PBMCs, low-editing

value: low-editing


title: High-editing monocyte-enriched PBMCs, sample 2

description: 2897 agg 9-22


title: Uncultured monocyte-enriched PBMCs, sample 1

description: 2523 agg 8-17


title: Uncultured monocyte-enriched PBMCs, sample 3

description: 2901 agg 9-14


title: Low-editing monocyte-enriched PBMCs, sample 2

description: 2897 agg 9-17


title: lung_vehicle_d2_C1


title: Uncultured monocyte-enriched PBMCs, sample 2

description: 2897 agg 9-14


title: Low-editing monocyte-enriched PBMCs, sample 5

description: 3279 agg 10-22


title: 19_202


title: Low-editing monocyte-enriched PBMCs, sample 1

description: 2523 agg 8-20


title: 17_198


title: 21_211


title: lung_bleomycin_d2_D5


title: lung_bleomycin_d1_B8

source_name: Lung, bleomycin, d1

value: day 1


title: 18_200

source_name: HCC


title: lung_bleomycin_d1_B7


title: lung_bleomycin_d1_B6


title: NOD.B10 Islet - sample 4

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 4

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Data were processed using Genespring 11.5.

source_name: pancreatic islet

label_protocol: Aminoallyl-cRNA samples were labelled with Cy3 and Cy5 dyes.  Dyes were reconstituted in DMSO. 3 ug of aminoallyl-cRNA (10 ul) was combined with 10 ul of 0.1M NaHCO3 (pH 8.7), 15 ul DMSO and 5 ul of Cy3 or Cy5.  After 90 minutes of incuabation at room temperature, 15 ul of 4M hydroxylamine was added.  Samples were incubated for 15 mins.  The Cy5 and Cy3 labeled cRNA were then purified using the ArrayGrade cRNA clean up kit (SABiosciences).

extract_protocol: Total RNA was extracted from islets isolated by laser microdissection using the RNeasy micro kit (Qiagen).  Total RNA samples, and the mouse universal RNA control were preamplified using the TrueLabeling-PicoAMP kit (SA Biosciences) to generate aminoallyl-cRNA.

value: 12 weeks old

tag: Sex

source_name: Mouse universal RNA control

tag: supplier

value: Universal mouse total RNA purchased from SABiosciences


title: High-editing monocyte-enriched PBMCs, sample 1

description: 2523 agg 8-23


title: NOD.B10 Islet - sample 6

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 6

tag: strain


title: lung_bleomycin_d1_B5

tag: tissue

value: bleomycin


title: 16_190


title: 15_188


title: 10_149


title: 13_178


title: 14_183


title: 12_151


title: lung_bleomycin_d1_B4


title: lung_bleomycin_d1_B2


title: lung_bleomycin_d1_B3


title: lung_vehicle_d1_A8

source_name: Lung, saline, d1


title: NOD.B10 Islet - sample 5

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 5


title: NOD.B10 Islet - sample 3

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 3


title: lung_vehicle_d1_A7


title: lung_bleomycin_d1_B1


title: NOD Islet - sample 6

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 6

value: NOD


title: NOD.B10 Islet - sample 2

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 2


title: 11_150


title: 07_108

extract_protocol:
Extraction protocol The miRNeasy mini kit (Qiagen, Valencia, CA) was
used to extract total RNA including microRNA.


title: 08_143


title: 06_070


title: 09_144


title: NOD Islet - sample 5

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 5


title: NOD Islet - sample 3

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 3


title: NOD.B10 Islet - sample 1

description: Gene expression in pancreatic islet of 12 wk old NOD.B10 mouse compared to a mouse universal control - Sample 1


title: lung_vehicle_d1_A6


title: lung_vehicle_d1_A5


title: NOD Islet - sample 4

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 4


title: NOD Islet - sample 1

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 1


title: lung_vehicle_d1_A4


title: NOD Islet - sample 2

description: Gene expression in pancreatic islet of 12 wk old NOD mouse compared to a mouse universal control - Sample 2


title: lung_vehicle_d1_A3


title: 04_022


title: 05_064


title: 03_011


title: KO_12.4_U

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.

data_processing:
Data processing was done using Partek Genomics Suite 6.5 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
probe set file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.ps
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps

source_name: Mesencymal stem cell line

label_protocol: Affymetrix GeneChip® WT Sense Target Labeling

growth_protocol: Primary mesenchymal stem cells were isolated from the hindlimb bone marrow of a one-year old Dicerflox/flox mouse, transduced with retrovirus encoding SV40 Large T Antigen for immortalization, and then plated at low density for monoclonal isolation.  Cells were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.  The MIT Institutional Animal Care and Use Committee approved all animal studies and procedures.

extract_protocol: RNA was extracted using Qiazol (Qiagen).

treatment_protocol: To determine gene expression alterations induced Dicer loss, the cells were infected with Adeno-Cre-GFP, sorted for GFP to enrich for infected cells, and plated at low density for monoclonal isolation.  Homozygous deletion within clones was confirmed by genotyping PCR.  For isolation of total RNA, cells were passaged under normal culture conditions.

value: Mesencymal stem cell line clone 12.4

tag: genotype

value: Dicer-/-

tag: differentiation status

value: undifferentiated


title: 01_001

extract_protocol: The miRNeasy mini kit (Qiagen, Valencia, CA) was used to extract total RNA including microRNA.

value: male


title: 02_004


title: KO_12.2_U

value: Mesencymal stem cell line clone 12.2


title: lung_vehicle_d1_A2

value: lung homogenate

value: saline


title: lung_vehicle_d1_A1


title: WT_6_U

value: Mesencymal stem cell line clone 6

value: Dicer+/+


title: KO_6.8_U

value: Mesencymal stem cell line clone 6.8


title: G217B M/C

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

institute: University of California

hyb_protocol: Samples were labeled with Cy5 or with Cy3 and competitively hybridized to custom glass slide 70-mer oligomer microarrays in a closed-circuit experimental design (e.g. direct, pairwise comparisons of yeast and mycelial samples, mycelial and conidial samples, and yeast and conidial samples). Dye-swap hybridizations were performed for these pairwise comparisons.

scan_protocol: The microarrays were scanned using Gene PixPro 6.0 software on an Axon 4000B scanner (Molecular Devices).

data_processing:
The microarrays were gridded with Gene Pix 6.0 (Molecular Devices) and uploaded to the NOMAD database (http://ucsf-nomad.sourceforge.net/) for quality control, normalization and data storage. To eliminate the analysis of microarray features with low signal intensities, we excluded features from the analysis for which the sum of the medians for the 635-nm and 532-nm channels was <=500 intensity units from this analysis; normalized expression ratios are reported in the VALUE column for the remaining spots.
The results of downstream BAGEL analysis for the G217B strain are available as supplemental data set S3 of the accompanying publication.

source_name: Mycelia M8

label_protocol: 1 ug of total RNA per conidia, mycelia or yeast sample was amplified according to the manufacturer's instructions using the MessageAmp II kit (Ambion). Average yields were 75 ug aRNA (amplified complementary RNA).  Four to five ug aRNA were fragmented with RNA fragmentation reagent (Ambion) prior to hybridizing the samples to microarrays.  Fluorescent labeling was performed as previously described (Mol. Biol. Cell 16:4792).

extract_protocol: Frozen conidial pellets were homogenized by bead beating in 2 mL tubes with 0.5 mM Zirconia/Silica beads (Biospec Products, OK) and Trizol (Invitrogen) in 2mL screw-cap tubes. RNA was isolated according to the manufacturer's instructions. On average, 3 ug conidial RNA was obtained from each 15 cm plate. Yeast and mycelial RNA was prepared as previously described (Mol. Biol. Cell 14:2314) with the following modification: pellets were homogenized by bead beating with 0.5 mM Zirconia/Silica beads in guanadinium lysis buffer. RNA quality was measured with an Agilent Bioanalyzer using RNA Nano LabChips.

value: Histoplasma capsulatum G217B

source_name: Conidia C29


title: T_g2 [KN2]

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing: Data processing was done using Partek Genomics Suite 6.4 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files (provided on the Series record). The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.

source_name: Mouse Lung Tumor

growth_protocol: Tumors were initiated in KrasFSF-G12D/+;Nkx2-1F/F;RosaCreERT2 mice by intratracheal delivery of adenovirus expressing Flp recombinase. 6-7 months later,  mice were treated with Tamoxifen dissolved in corn oil by intraperitoneal injection 112 micrograms per gram total body weight to delete Nkx2-1. Tumors were initiated in KrasLSL-G12D/+; Nkx2-1F/F mice by intratracheal delivery of adenovirus expressing Cre recombinase.

extract_protocol: RNA was extracted using Trizol (Invitrogen) and analyzed for RNA integrity

treatment_protocol: Mouse lung tumor samples were collected and immediately snap frozen in liquid nitrogen.

value: KrasLSL-G12D/+; Nkx2-1F/F

tag: tumor type

value: Simultaneous KrasG12D activation and Nkx2-1 deletion.


title: G217B Y/M

source_name: Yeast Y6


title: T_g2 [KN1]


title: G217B M/Y


title: G217B C/M 2


title: T_g2 [KN3]


title: WT_12_U

value: Mesencymal stem cell line clone 12


title: KO_6.9_U


title: G217B C/Y 1

source_name: Conidia C30


title: T_g3b [T3]

value: Nkx2-1 deletion in established tumor


title: G217B C/Y 2


title: T_g3b [T2]


title: T47D_RHBDD2siRNA_rep1

city: La Plata

first: Martin

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

description: human oligo chip　25k ver.2.1

hyb_protocol: Ten micrograms of labeled RNA were probed (during 16hrs, 37°C, 250 rpm) using the whole genome Toray 3D-GeneTM Human Oligo Chip 25k V2.1.

scan_protocol: The arrays were scanned with a Toray 3D-GeneTM Scanner.

data_processing: TIFF images of all arrays were quantified using ExtractionTM Software (Toray).  For genes of which the signal was more than Background mean + 2SD, the raw signal was subtracted with the Background mean. Data were normalized to the level in which the median value was 25.

label_protocol: Aminoallyl-amplified RNA were synthesized from one microgram of total RNA with the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion) and subsequently labeled with Cy5 Mono-ReactiveDyePack (GE Health Care Bioscience).

growth_protocol: Estrogen dependent breast cancer cell lines MCF7 and T47D were cultured in RPMI medium (GIBCO, Gaithersburg, MD) and DMEM (GIBCO, Gaithersburg, MD) respectively, supplemented with 10% FBS (Bioser, Argentina), 10 U/ml penicillin G and 10 μg/ml streptomycin.

extract_protocol: Total RNAs were isolated and purified using the TRIreagent and Nucleo Spin RNA Clean-up Kit (Macherey-Nagel) from two breast cancer cell lines (MCF7 and T47D) derived from the negative control-siRNA and the RHBDD2-siRNA treatments in duplicate experiments. RNA concentration and integrity were measured on Agilent Bioanalyzer RNA 6000 Nanochip (Agilent Technologies).

treatment_protocol: MCF7 and T47D cell lines were cultured on a 12 well plate at 40% of confluence in Opti-MEM I Reduced Serum Medium, and were transiently transfected with 40 pmoles/ul of siRNA mixed with Lipofectamine according to the manufacturer's protocol (Invitrogen, USA).

tag: cell line

value: breast adenocarcinoma


title: T_g3b [T4]


title: T_g1 [V3]

value: Nkx2-1-positive control


title: T_g1 [V2]


title: T_g1 [V5]


title: T47D_Scramble_rep2

description: human oligo chip　25k ver.2.1


title: G217B C/M 1


title: T_g1 [V1]


title: T_g3b [T1]


title: T_g1 [V4]


title: G217B Y/C


title: T47D_RHBDD2siRNA_rep2

description: human oligo chip　25k ver.2.1


title: H3f3b WT MEF 2

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

description: Replicate D

hyb_protocol: Standard Illumina hybridization protocol-Direct Hybridization

scan_protocol: Standard Illumina scanning protocol-Illumina iScan System

data_processing: The data were normalized using average normalization using genome studio software

source_name: E12.5 H3f3b WT/WT MEFs

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

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Prep kit. Quality control was performed with Agilent Bioanalyser.
RNA amplification: Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

value: H3f3b WT/WT

tag: age

value: Mouse Embryonic Fibroblasts


title: H3f3b KO MEF 2

description: Replicate C


title: T47D_Scramble_rep1

description: human oligo chip　25k ver.2.1


title: MCF7_Scramble_rep1

description: human oligo chip　25k ver.2.1


title: MCF7_Scramble_rep2

description: human oligo chip　25k ver.2.1


title: H3f3b WT MEF 1

description: Replicate B


title: MCF7_RHBDD2siRNA_rep2

description: human oligo chip　25k ver.2.1


title: MCF7_RHBDD2siRNA_rep1

description: human oligo chip　25k ver.2.1


title: H3f3b KO MEF 1

description: Replicate A


title: hsfa2 KO HS-2

status: Public on Apr 09 2013

city: Shulin City, Taipei County

first: Hsiang-chin

address: 9F., No.332, Xuefu Rd.

institute: Academia sinica

description:
a2h2
Gene expression at heat shock condition (37°C for 1 hr).

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

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

data_processing: The data were RMA normalized using GeneSpring 11.5.1.

organism: Arabidopsis thaliana

source_name: whole seedling of 7-day-old plants at 37°C for 1 hr, hsfa2 KO mutant

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

growth_protocol: The seeds were sowed in 0.5X MS medium, then treated in 4°C for 3 days to synchronize the germination and grown in 22°C for 7 days with 16 h of light (120 mmol m-2 s-1).

extract_protocol: Total RNA of plant tissues was isolated according to the method of Oñate-Sánchez and Vicente-Carbajosa (2008, BMC Research Notes, 1, 93 (PMID 18937828)).

treatment_protocol: The samples were incubated for 1 h at 37°C in a water bath.

value: hsfa2 KO mutant

value: whole seedling

value: 7 days

tag: condition

value: heat shock (37°C)


title: hsfa2 KO control-1

description:
a2c1
Gene expression at control condition (22°C).

source_name: whole seedling of 7-day-old plants at control condition, hsfa2 KO mutant

value: control (22°C)


title: hsfa2 KO HS-1

description:
a2h1
Gene expression at heat shock condition (37°C for 1 hr).


title: Bone Marrow - GTEx Control Sample - SM-2D454

first: Kristin

last: Ardlie

address: 7 Cambridge Center

institute: The Broad Institute of MIT and Harvard

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
Probe level data were summarized using custom probeset definitions provided by the BrainArrray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp). RMA normalization was using Ensembl gene definitions.
probe group file: HuGene11stv1_Hs_ENSG.cdf

source_name: Cells - Leukemia cell line (CML) - GTEx Control Sample

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: gender

value: Female

value: 50-59 years

tag: rin

value: Bone Marrow

value: Cells - Leukemia cell line (CML)

value: Not Available


title: Blood Vessel - Low post-mortem interval - SM-2XV4X

source_name: Artery - Tibial - Low post-mortem interval

value: Male

value: 20-29 years

value: Blood Vessel

value: Artery - Tibial

value: 4-7 hours


title: Bone Marrow - GTEx Control Sample - SM-2TO4S


title: Bone Marrow - GTEx Control Sample - SM-2XV5K


title: Bone Marrow - GTEx Control Sample - SM-2QU31


title: Bone Marrow - GTEx Control Sample - SM-2D439


title: Heart - Low post-mortem interval - SM-2XV6G

source_name: Heart - Left Ventricle - Low post-mortem interval

value: Heart

value: Heart - Left Ventricle

value: 0-3 hours


title: Bone Marrow - GTEx Control Sample - SM-2IZHW


title: Bone Marrow - GTEx Control Sample - SM-2AXVE


title: Bone Marrow - GTEx Control Sample - SM-2XU9E


title: Thyroid - Low post-mortem interval - SM-2XV6M

source_name: Thyroid - Low post-mortem interval

value: 60-69 years

value: Thyroid

value: 16-19 hours


title: Skin - Low post-mortem interval - SM-2XV54

source_name: Skin - Sun Exposed (Lower leg) - Low post-mortem interval

value: Skin

value: Skin - Sun Exposed (Lower leg)


title: Bone Marrow - GTEx Control Sample - SM-2TWBO

value: Female

value: 50-59 years


title: Control BY 398

type: genomic

city: shenyang

first: lu

last: yongping

address: huanggu strict puhe street

institute: key lab of liaoning province family planning research institution

description:
Control BY_398
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

hyb_protocol: To prepare Cy3 labeled single strand products, 10μL allele-specific extension products were added 10μL mix containing 1.33×SSC, 0.067% SSC, 0.033mg/ml salmon sperm DNA, and 50nM Cy3-labeled com-tag. The mix was denatured at 94°C for 10 min and cooled 5 min on ice. Hybridization was then performed using this hybridization solution in a hybridization chamber at 60°C for 2 hours. Hybridization was followed by two washes in 2×SSC/0.1%SDS (preheated to 50°C) for 5min, proceeded by washing in 0.2×SSC/0.1%SDS for 1 min, then rinsed in dH2O and dried by centrifugation 3 min at 500 r.p.m.

scan_protocol: Microarrays were scanned at 100-μm resolution, using GenePix 4000B scanner (Axon instruments, USA), the TIFF images were imported into GenePix 6.0 software (Axon Instruments, USA).

data_processing:
The sample data table contains the mean single value of the spot subtracted the mean single of background as the spot's single (F532 Mean - B532), used for AF (allele B/allele A + allele B) calculation.
For example, for mother kq_001,  The single of allele T= (27709+27469)/2=27589, The single of allele C= (22835+32770)/2=27802.5, thus, the AF of rs3771494=27589/27859+27802.5=0.498, which is between 0.4 and 0.6, so the genotype was heterozygote.For mother kq_002, the single of allele T=(27709+32380)/2=30044.5, the single of allele C=(305+545)/2=425. The AF of rs3771494=30044.5/30044.5+425=0.985, which was >0.6, so the genotype was T homozygote.

molecule: genomic DNA

label_protocol: Multiplex PCR was amplified with the Multiplex PCR Assay Kit (Takara) in 20μL [Multiplex PCR mix2 10μL, Multiplex PCR mix1 0.2μL, 0.2μM primers, 50ng DNA]. Thermocycling was performed with an initial 60 second denaturation at 94°C followed by 35 cycles of: 30 seconds at 94°C, 90 seconds at 57°C and 90 seconds at 72°C, and final extension at 72°C for 10 minutes. The PCR product was used as a template for Multiplex allele-specific primer extension. In order to remove excess dNTPs and primers, a mix was added into 10μL PCR product, containing 2 units of shrimp alkaline phosphatase (Takara) and 4 units EXO I(Takara) with incubation at 37°C for 30 min followed by 96°C for 10 min. 10μL of treated PCR products was added to 5μL ASPE mix containing 1×Thermopol reaction buffer, 80μM of each dATP, dGTP, dTTP (Takara), 40μM Cy3-dCTP (GE), 0.2 unit of a vent exo- DNA polymerase(New England Biolabs), 25nM allele-specific primers. The extension conditions were as follows: an initial 3min at 94°C, 35 cycles of 94°C for 30 second, 60°C for 30 second 72°C for 1 min, and final extension at 72°C for 5minutes.

extract_protocol: DNA was obtained from the blood samples using TIANamp Blood DNA kit (TianGen).

tag: sample group

value: control individuals

tag: clinical type

value: non cleft

value: blood


title: Blood - Pre-mortem blood draw - SM-2XV4M

source_name: Whole Blood - Pre-mortem blood draw

value: Male

value: 20-29 years

value: Blood

value: Whole Blood


title: Control BY 399

description:
Control BY_399
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 400

description:
Control BY_400
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 397

description:
Control BY_397
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Bone Marrow - GTEx Control Sample - SM-2D45Y

value: Bone Marrow

value: Cells - Leukemia cell line (CML)

value: Not Available


title: Bone Marrow - GTEx Control Sample - SM-2AXTU


title: Bone Marrow - GTEx Control Sample - SM-2M47Q


title: Bone Marrow - GTEx Control Sample - SM-2AXWK


title: Muscle - Low post-mortem interval - SM-2XV57

source_name: Muscle - Skeletal - Low post-mortem interval

value: 60-69 years

value: Muscle

value: Muscle - Skeletal


title: Muscle - Low post-mortem interval - SM-2XV6L

value: 4-7 hours


title: hsfa2 KO control-2

description:
a2c2
Gene expression at control condition (22°C).

tag: strain/background

value: hsfa2 KO mutant

value: whole seedling

value: 7 days

value: control (22°C)


title: Nerve - Low post-mortem interval - SM-2XV4O

source_name: Nerve - Tibial - Low post-mortem interval

value: Nerve

value: Nerve - Tibial

value: 16-19 hours


title: Blood Vessel - Low post-mortem interval - SM-2XV53

value: Male

value: Blood Vessel

value: Artery - Tibial


title: Control BY 395

description:
Control BY_395
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: control individuals

value: non cleft

value: blood


title: Control BY 396

description:
Control BY_396
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Skin - Low post-mortem interval - SM-2XV4I

value: 60-69 years

value: Skin

value: Skin - Sun Exposed (Lower leg)


title: Control BY 394

description:
Control BY_394
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 393

description:
Control BY_393
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 392

description:
Control BY_392
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 391

description:
Control BY_391
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Blood - Low post-mortem interval - SM-2XV6A

source_name: Whole Blood - Low post-mortem interval

value: Blood

value: Whole Blood

value: 12-15 hours


title: Control BY 390

description:
Control BY_390
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 388

description:
Control BY_388
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 389

description:
Control BY_389
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 387

description:
Control BY_387
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 385

description:
Control BY_385
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 386

description:
Control BY_386
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Heart - Low post-mortem interval - SM-2XV65

value: 50-59 years

value: Heart

value: Heart - Left Ventricle

value: 20-23 hours


title: Lung - Low post-mortem interval - SM-2XV6Q

source_name: Lung - Low post-mortem interval

value: Lung


title: Thyroid - Low post-mortem interval - SM-2XV5R

value: Male

value: Thyroid


title: Muscle - Low post-mortem interval - SM-2XV5O

value: Muscle

value: Muscle - Skeletal


title: Thyroid - Low post-mortem interval - SM-2XV72

value: 0-3 hours


title: Blood - Low post-mortem interval - SM-2XV6N

value: 16-19 hours


title: Heart - Low post-mortem interval - SM-2XV6U


title: Lung - Low post-mortem interval - SM-2XV5V


title: Skin - Low post-mortem interval - SM-2XV58


title: Muscle - Low post-mortem interval - SM-2XV6Z


title: Nerve - Low post-mortem interval - SM-2XV4V

value: Nerve

value: Nerve - Tibial


title: Adipose Tissue - Low post-mortem interval - SM-2XV4Q

source_name: Adipose - Subcutaneous - Low post-mortem interval

value: Adipose Tissue

value: Adipose - Subcutaneous


title: Lung - Low post-mortem interval - SM-2XV6Y

value: Female

value: 40-49 years


title: Control BY 384

description:
Control BY_384
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: control individuals

value: non cleft

value: blood


title: Blood Vessel - Low post-mortem interval - SM-2XV5P

value: 60-69 years

value: Blood Vessel

value: Artery - Tibial

value: 4-7 hours


title: Control BY 381

description:
Control BY_381
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 383

description:
Control BY_383
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 379

description:
Control BY_379
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 380

description:
Control BY_380
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 378

description:
Control BY_378
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Nerve - Low post-mortem interval - SM-2XV56

value: Male


title: Blood Vessel - Low post-mortem interval - SM-2XU93

value: 20-29 years


title: Muscle - Low post-mortem interval - SM-2XV5A

value: Muscle

value: Muscle - Skeletal


title: Control BY 377

description:
Control BY_377
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 382

description:
Control BY_382
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 376

description:
Control BY_376
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 373

description:
Control BY_373
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 375

description:
Control BY_375
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 374

description:
Control BY_374
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 372

description:
Control BY_372
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 371

description:
Control BY_371
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Muscle - Low post-mortem interval - SM-2XU9J


title: Lung - Low post-mortem interval - SM-2XUAV

value: Lung


title: Heart - Low post-mortem interval - SM-2XUAI

value: Heart

value: Heart - Left Ventricle


title: Blood - Pre-mortem blood draw - SM-2XV5N

value: Blood

value: Whole Blood


title: Thyroid - Low post-mortem interval - SM-2XUAJ

value: Female

value: Thyroid


title: Control BY 370

description:
Control BY_370
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: control individuals

value: non cleft


title: Brain - Low post-mortem interval - SM-2XV6R

source_name: Brain - Cerebellum - Low post-mortem interval

value: 50-59 years

value: Brain

value: Brain - Cerebellum

value: 16-19 hours


title: Control BY 369

description:
Control BY_369
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: blood


title: Control BY 368

description:
Control BY_368
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Blood - Pre-mortem blood draw - SM-2XUAD

value: 20-29 years


title: Control BY 367

description:
Control BY_367
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 365

description:
Control BY_365
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 366

description:
Control BY_366
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 364

description:
Control BY_364
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Lung - Low post-mortem interval - SM-2XV63

value: Male


title: Control BY 363

description:
Control BY_363
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Skin - Low post-mortem interval - SM-2XV4K

value: Skin

value: Skin - Sun Exposed (Lower leg)

value: 0-3 hours


title: Thyroid - Low post-mortem interval - SM-2XV5T


title: Skin - Low post-mortem interval - SM-2XU9K

value: 4-7 hours


title: Control BY 361

description:
Control BY_361
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Control BY 362

description:
Control BY_362
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Brain - Low post-mortem interval - SM-2XV6X

source_name: Brain - Hypothalamus - Low post-mortem interval

value: Brain - Hypothalamus

value: Not Available


title: Skin - Low post-mortem interval - SM-2XV4Z

value: 12-15 hours


title: Brain - Low post-mortem interval - SM-2XV6D

source_name: Brain - Putamen (basal ganglia) - Low post-mortem interval

value: Brain - Putamen (basal ganglia)


title: Blood Vessel - Low post-mortem interval - SM-2XV4N

value: Blood Vessel

value: Artery - Tibial


title: Blood - Pre-mortem blood draw - SM-2XV74

source_name: Cells - EBV-transformed lymphocytes - Pre-mortem blood draw

value: Female

value: Blood

value: Cells - EBV-transformed lymphocytes


title: Brain - Low post-mortem interval - SM-2XV62

source_name: Brain - Nucleus accumbens (basal ganglia) - Low post-mortem interval

value: 50-59 years

value: Brain


title: Brain - Low post-mortem interval - SM-2XV6H

source_name: Brain - Amygdala - Low post-mortem interval

value: Brain - Amygdala


title: Control BY 359

description:
Control BY_359
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: control individuals

value: non cleft

value: blood


title: Control BY 357

description:
Control BY_357
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Brain - Low post-mortem interval - SM-2XV6C

source_name: Brain - Caudate (basal ganglia) - Low post-mortem interval

value: Male

value: Brain - Caudate (basal ganglia)