title: genomic DNA from peripheral blood 60

description: normal peripheral blood sample

source_name: peripheral blood 60


title: NSC_iPS_p3_1 Expression

status: Public on Mar 01 2016

type: RNA

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw array data was processed using limma (Ritchie et al., 2015). We perform “normexp” background correction with an offset of 16. We normalize between arrays using quantile normalization. To identify differently expressed genes we create a contrast matrix in which all pairwise comparisons are made. For each probe an empirical Bayes moderated t-statistic test is performed. An FDR correction is applied to the nominal p-values.

molecule: total RNA

organism: Mus musculus

source_name: NSC iPS p3

label_protocol: 500ng of total RNA per sample were labeled using Agilent's QuickAmp labeling kit and hybridized to Agilent 8X60K expression arrays.

growth_protocol: ESCs and iPSCs were cultured on Mitomycin-C treated MEFs in KO-DMEM (Invitrogen) supplemented with 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Invitrogen), 1,000 U/ml LIF (Millipore) and 15% fetal bovine serum (FBS, Invitrogen) (ESC medium). Naïve ESCs were cultured in serum-free N2B27 medium on gelatin-coated dishes. N2B27 medium (500ml) was generated by inclusion of the following: 240ml DMEM/F12 (Invitrogen), 240ml Neurobasal (Invitrogen), 5ml N2 supplement (Invitrogen), 10ml B27 supplement (Invitrogen), 1,000 U/ml LIF (Millipore), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Invitrogen), and the small molecules PD0325901 (Stemgent, 1μM) and CHIR (Stemgent, 3μM). CD19+ pre-B cells and Mac1+ macrophages were isolated from bone marrow with monoclonal antibodies to CD19 and Mac-1 (BD Pharmingen) respectively, using MACS sorting (Miltenyi Biotech). B cells were grown in RPMI medium with 10% FBS and 10ng/ml IL-7 (Peprotech); macrophages in DMEM with 10% FBS and 10ng/ml each of CSF1 and IL-3 (Peprotech). MEFs were established from day 13.5 mouse embryos and cultured in DMEM containing 10% FBS. NSC were isolated and cultured as previously described (Di Stefano et al., 2009). All media were supplemented with L-glutamine and penicillin/streptomycin (GIBCO).

extract_protocol: RNA was isolated with the miRNeasy mini kit (Qiagen), eluted with RNase-free water and quantified by Nanodrop. cDNA was produced with the High Capacity RNA-to-cDNA kit (Applied Biosystem). RNA samples with a RIN greater than 9 were analyzed by expression arrays.

treatment_protocol: Reprogramming experiments with B cells were performed as previously described (Di Stefano et al., 2014); with MEFs, macrophages and NSCs were conducted by plating 100.000 cells/well on gelatinized plates seeded with irradiated MEFs, using ESC medium supplemented with 2 µg/ml of doxycycline. For the isolation of iPSC lines, doxycycline was washed out after 15 days of reprogramming and colonies with ESC-like morphology were picked at 20 days before further passaging.  iPSC lines were expanded for an additional 9 days (3 passages) to obtain P3 iPS cell lines or for 20 passages to obtain P20 iPS cell lines.

tag: cell type

value: NSC iPS p3


title: preB_iPS_p20_1 Expression

source_name: preB iPS p20

value: preB iPS p20


title: genomic DNA from peripheral blood 59

type: genomic

city: Tokushima

first: Makoto

last: Kinoshita

state: Tokushima

address: 3-18-15, Kuramoto

department: Psychiatry

country: Japan

institute: Tokushima University Graduate School

description: normal peripheral blood sample

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software v2011.1; The unmethylated (Signal_A) and methylated (Signal_B) signal intensities are found in the files Methylated_and_unmethylated_signal_samples1-93.txt and Methylated_and_unmethylated_signal_samples101-124.txt located on the series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood 59

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was prepared from peripheral blood samples.

tag: gender

value: Male

tag: tissue

value: peripheral blood

tag: disease state

value: normal


title: stool_LNS237

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

country: USA

institute: Washington University School of Medicine

description: Gene expression data of stool RNAs from study subject

data_processing:
Quantasoft software for the QX100 system reports absolute quantity of each target (copies/ul in reaction).  These data are then uploaded into MS Access where all data are analyzed for average target, average GAPDH, and then the ratio of these values.  Final  output is target/GAPDH ratio (average target/ average GAPDH).
Matrix normalized worksheet reports normalized target/GAPDH ratios.  Matrix non-normalized worksheet reports the copies/ul in the ddPCR reaction.  Fold change data were not calculated or reported in the manuscript, and are therefore not included.

label: duplex VIC/FAM

source_name: stool total RNA

label_protocol: Quantitative PCR (qPCR) was performed using commercially available duplexed Taqman  assays in a droplet digital PCR (ddPCR) system (QX100 - Bio-Rad Laboratories Inc., Hercules, CA). Reactions of 20 µL were prepared using 7.76 µL RNA, 10 µL ddPCR Supermix for Probes (BioRad), 0.08 µL SuperScript III Reverse Transcriptase (200 U/µL, Invitrogen Corporation, Carlsbad, CA), 0.16 µL RNase OUT (40 U/µL, Invitrogen), and 1 µL each of two 20× TaqMan Gene Expression Assay (Applied Biosystems, Carlsbad, CA), one VIC-labeled and one FAM-labeled. Droplets were generated according to manufacturer guidelines with the QX100 Droplet generator (BioRad) before cycling in a C1000 Touch thermal cycler (BioRad) at 50°C (30:00), 95°C (10:00), 40 cycles of 94°C (0:30) followed by 60°C (1:00), 98°C (10:00). Each assay was performed in replicate with GAPDH assays on the same plate.  Plates were held at 4°C between amplification and droplet reading. Data from the QX100 Droplet Reader were analyzed with QuantaSoft software (Kosice, Slovakia).

extract_protocol: Total nucleic acids were extracted using “Specific A” protocol on the NucliSENS EasyMAG system (bioMérieux, Durham, NC) )

treatment_protocol: Fresh stools were collected prior to the dual sugar absorption testing using a small, clean non-absorbant, plastic diaper. The stools were immediately transferred to cryovials and flash frozen in liquid nitrogen. Samples were transferred to a -80°C freezer and transported to Washington University (St. Louis, MO), where they were then processed for nucleic acid extraction.

value: M

tag: age (month)

tag: percent lactulose in urine

value: environmental enteric dysfunction


title: preB_iPS_p3_2 Expression

source_name: preB iPS p3

value: preB iPS p3


title: preB_iPS_p3_1 Expression


title: stool_LNS203


title: genomic DNA from peripheral blood 61

description: normal peripheral blood sample

source_name: peripheral blood 61


title: genomic DNA from peripheral blood 58

description: normal peripheral blood sample

source_name: peripheral blood 58


title: macrophages_2 Expression

source_name: macrophages

value: macrophages


title: stool_LNS135

value: F


title: macrophages_1 Expression


title: stool_LNS134


title: stool_LNS183


title: stool_LNS155


title: genomic DNA from peripheral blood 53

description: normal peripheral blood sample

source_name: peripheral blood 53


title: genomic DNA from peripheral blood 55

description: normal peripheral blood sample

source_name: peripheral blood 55


title: MEF_2 Expression

source_name: MEF

value: MEF


title: genomic DNA from peripheral blood 57

description: normal peripheral blood sample

source_name: peripheral blood 57


title: genomic DNA from peripheral blood 54

description: normal peripheral blood sample

source_name: peripheral blood 54


title: stool_LNS124


title: stool_LNS108


title: stool_LNS130


title: stool_044B


title: MEF_1 Expression


title: stool_LNS138


title: genomic DNA from peripheral blood 52

description: normal peripheral blood sample

source_name: peripheral blood 52


title: stool_LNS25


title: stool_099B


title: NSC_2 Expression

source_name: NSC

value: NSC


title: stool_150A


title: preB_2 Expression

source_name: preB

value: preB


title: stool_LNS119


title: NSC_1 Expression


title: genomic DNA from peripheral blood 50

description: normal peripheral blood sample

source_name: peripheral blood 50


title: preB_1 Expression


title: stool_050B


title: genomic DNA from peripheral blood 49

description: normal peripheral blood sample

source_name: peripheral blood 49


title: stool_LNS247


title: stool_149A


title: genomic DNA from peripheral blood 48

description: normal peripheral blood sample

source_name: peripheral blood 48


title: stool_LNS198


title: stool_LNS50


title: genomic DNA from peripheral blood 56

description: normal peripheral blood sample

source_name: peripheral blood 56


title: stool_LNS192

source_name: stool total RNA


title: stool_LNS228


title: genomic DNA from peripheral blood 51

description: normal peripheral blood sample

source_name: peripheral blood 51


title: genomic DNA from peripheral blood 45

description: normal peripheral blood sample

source_name: peripheral blood 45


title: stool_LNS149


title: stool_LNS137


title: genomic DNA from peripheral blood 43

description: normal peripheral blood sample

source_name: peripheral blood 43


title: stool_LNS148


title: genomic DNA from peripheral blood 38

description: normal peripheral blood sample

source_name: peripheral blood 38

value: Female


title: genomic DNA from peripheral blood 42

description: normal peripheral blood sample

source_name: peripheral blood 42


title: genomic DNA from peripheral blood 44

description: normal peripheral blood sample

source_name: peripheral blood 44


title: genomic DNA from peripheral blood 40

description: normal peripheral blood sample

source_name: peripheral blood 40


title: genomic DNA from peripheral blood 47

description: normal peripheral blood sample

source_name: peripheral blood 47


title: stool_LNS19


title: stool_LNS87


title: stool_LNS73


title: stool_291B


title: genomic DNA from peripheral blood 39

description: normal peripheral blood sample

source_name: peripheral blood 39


title: stool_LNS53


title: genomic DNA from peripheral blood 37

description: normal peripheral blood sample

source_name: peripheral blood 37


title: genomic DNA from peripheral blood 36

description: normal peripheral blood sample

source_name: peripheral blood 36


title: stool_LNS56


title: genomic DNA from peripheral blood 35

description: normal peripheral blood sample

source_name: peripheral blood 35


title: genomic DNA from peripheral blood 33

description: normal peripheral blood sample

source_name: peripheral blood 33


title: genomic DNA from peripheral blood 41

description: normal peripheral blood sample

source_name: peripheral blood 41


title: genomic DNA from peripheral blood 32

description: normal peripheral blood sample

source_name: peripheral blood 32


title: stool_141A


title: genomic DNA from peripheral blood 46

description: normal peripheral blood sample

source_name: peripheral blood 46


title: stool_276A

source_name: stool total RNA


title: stool_270A


title: genomic DNA from peripheral blood 28

description: normal peripheral blood sample

source_name: peripheral blood 28


title: genomic DNA from peripheral blood 29

description: normal peripheral blood sample

source_name: peripheral blood 29


title: macrophages_iPS_p20_1 Expression

source_name: macrophages iPS p20

value: macrophages iPS p20


title: stool_LNS142


title: genomic DNA from peripheral blood 30

description: normal peripheral blood sample

source_name: peripheral blood 30


title: stool_LNS226


title: stool_LNS98


title: stool_LNS232


title: stool_LNS39


title: stool_321A


title: stool_LNS161


title: stool_LNS8


title: stool_089B


title: stool_144B


title: genomic DNA from peripheral blood 27

description: normal peripheral blood sample

source_name: peripheral blood 27


title: stool_LNS114


title: genomic DNA from peripheral blood 26

description: normal peripheral blood sample

source_name: peripheral blood 26


title: stool_LNS48


title: genomic DNA from peripheral blood 25

description: normal peripheral blood sample

source_name: peripheral blood 25


title: genomic DNA from peripheral blood 34

description: normal peripheral blood sample

source_name: peripheral blood 34


title: stool_165


title: genomic DNA from peripheral blood 21

description: normal peripheral blood sample

source_name: peripheral blood 21


title: genomic DNA from peripheral blood 24

description: normal peripheral blood sample

source_name: peripheral blood 24


title: stool_LNS20


title: stool_172


title: genomic DNA from peripheral blood 20

description: normal peripheral blood sample

source_name: peripheral blood 20


title: stool_170


title: genomic DNA from peripheral blood 31

description: normal peripheral blood sample

source_name: peripheral blood 31


title: stool_98


title: genomic DNA from peripheral blood 23

description: normal peripheral blood sample

source_name: peripheral blood 23


title: genomic DNA from peripheral blood 19

description: normal peripheral blood sample

source_name: peripheral blood 19


title: stool_199


title: genomic DNA from peripheral blood 17

description: normal peripheral blood sample

source_name: peripheral blood 17


title: stool_80


title: genomic DNA from peripheral blood 14

description: normal peripheral blood sample

source_name: peripheral blood 14


title: stool_81

source_name: stool total RNA


title: stool_127


title: genomic DNA from peripheral blood 12

description: normal peripheral blood sample

source_name: peripheral blood 12


title: stool_164


title: genomic DNA from peripheral blood 13

description: normal peripheral blood sample

source_name: peripheral blood 13


title: stool_5


title: genomic DNA from peripheral blood 15

description: normal peripheral blood sample

source_name: peripheral blood 15


title: genomic DNA from peripheral blood 4

description: normal peripheral blood sample

source_name: peripheral blood 4


title: genomic DNA from peripheral blood 10

description: normal peripheral blood sample

source_name: peripheral blood 10


title: genomic DNA from peripheral blood 11

description: normal peripheral blood sample

source_name: peripheral blood 11


title: genomic DNA from peripheral blood 9

description: normal peripheral blood sample

source_name: peripheral blood 9


title: genomic DNA from peripheral blood 16

description: normal peripheral blood sample

source_name: peripheral blood 16


title: genomic DNA from peripheral blood 18

description: normal peripheral blood sample

source_name: peripheral blood 18


title: stool_14


title: stool_96


title: genomic DNA from peripheral blood 6

description: normal peripheral blood sample

source_name: peripheral blood 6


title: genomic DNA from peripheral blood 8

description: normal peripheral blood sample

source_name: peripheral blood 8


title: genomic DNA from peripheral blood 2

description: normal peripheral blood sample

source_name: peripheral blood 2


title: stool_50


title: stool_209


title: genomic DNA from peripheral blood 3

description: normal peripheral blood sample

source_name: peripheral blood 3


title: stool_133


title: genomic DNA from peripheral blood 1

description: normal peripheral blood sample

source_name: peripheral blood 1


title: stool_37


title: genomic DNA from peripheral blood 123

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

data_processing: GenomeStudio Software v2011.1; The unmethylated (Signal_A) and methylated (Signal_B) signal intensities are found in the file Methylated_and_unmethylated_signal.txt located on the series record.

source_name: peripheral blood 23


title: stool_59


title: stool_4


title: stool_51


title: genomic DNA from peripheral blood 124

source_name: peripheral blood 24


title: stool_208

source_name: stool total RNA


title: stool_1


title: genomic DNA from peripheral blood 121

source_name: peripheral blood 21


title: genomic DNA from peripheral blood 7

description: normal peripheral blood sample

source_name: peripheral blood 7


title: stool_27


title: genomic DNA from peripheral blood 118


title: stool_238


title: genomic DNA from peripheral blood 120

source_name: peripheral blood 20


title: genomic DNA from peripheral blood 119

source_name: peripheral blood 19


title: stool_94


title: stool_16


title: genomic DNA from peripheral blood 114

source_name: peripheral blood 14


title: stool_131


title: stool_156


title: stool_168


title: stool_134


title: genomic DNA from peripheral blood 5

description: normal peripheral blood sample

source_name: peripheral blood 5


title: genomic DNA from peripheral blood 115

source_name: peripheral blood 15


title: stool_192


title: B8-rep3

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

description: Gene expression under non-stress condition after growth in minimal media until OD600 of 1.

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Ethanol-tolerant Saccharomyces cerevisiae clone B8, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Fresh precultures of yeast cells were diluted to an OD600 of 0.1 in fresh minimal medium. They were cultivated at 30°C and 150 rpm untill they reach the OD600 value of about 1.00. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Yeast cells were not treated with any special agent.

tag: strain

value: CEN.PK 113.7D

tag: mating type

value: MATa


title: B8-rep2

source_name: Ethanol-tolerant Saccharomyces cerevisiae clone B8, replicate 2


title: stool_115


title: genomic DNA from peripheral blood 117

source_name: peripheral blood 17


title: B8-rep1

source_name: Ethanol-tolerant Saccharomyces cerevisiae clone B8, replicate 1


title: genomic DNA from peripheral blood 116

source_name: peripheral blood 16


title: genomic DNA from peripheral blood 113

source_name: peripheral blood 13


title: stool_97


title: genomic DNA from peripheral blood 110

source_name: peripheral blood 10


title: B2-rep2

source_name: Ethanol-tolerant Saccharomyces cerevisiae clone B2, replicate 2


title: stool_198


title: genomic DNA from peripheral blood 112

source_name: peripheral blood 12


title: B2-rep1

source_name: Ethanol-tolerant Saccharomyces cerevisiae clone B2, replicate 1


title: genomic DNA from peripheral blood 109

source_name: peripheral blood 9


title: stool_120

source_name: stool total RNA


title: stool_250


title: genomic DNA from peripheral blood 108

source_name: peripheral blood 8


title: genomic DNA from peripheral blood 106

source_name: peripheral blood 6


title: stool_123


title: genomic DNA from peripheral blood 105


title: genomic DNA from peripheral blood 104

source_name: peripheral blood 4


title: stool_188


title: stool_219


title: genomic DNA from peripheral blood 103

source_name: peripheral blood 3


title: stool_201


title: stool_294A


title: chondrocytes Gal-1 rep4

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and treated with 50 µg/ml Galectin-1 for 24h in starvation medium.

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: biotin

source_name: chondrocytes, Gal-1, 50 µg/ml

label_protocol: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: Osteoarthritic chondrocytes were isolated from femoral condyles and tibial plateaus of articular cartilage. Isolated chondrocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) containing 10% fetal calf serum (Biochrom) and 100 µg/ml gentamicin (Gibco) in a humidified atmosphere of 5% CO2/95% air at 37°C. To preserve the chondrocyte phenotype, only freshly isolated and seeded cells without subculturing were used for all assays.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA II Kit (Macherey-Nagel, Düren, Germany). For quality control and quantification of total RNA, each sample was run on the Agilent 2100 Bioanalyzer Nano LabChip (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Upon 90% confluency, chondrocyte cultures were starved overnight using DMEM supplemented with gentamicin and treated with 50 µg/ml recombinant Galectin-1 in starvation medium for 24 h.

tag: biosource

value: Osteoarthritic knee chondrocytes

tag: treatment


title: chondrocytes untreated rep5

description: Isolated osteoarthritic chondrocytes were cultured to 90% confluency, starved overnight and cultured for 24h in starvation medium.

source_name: chondrocytes, untreated

value: untreated


title: chondrocytes Gal-1 rep3

value: 50 µg/ml Galectin-1 for 24h in starvation medium


title: genomic DNA from peripheral blood 101

source_name: peripheral blood 1

value: peripheral blood


title: stool_221B


title: stool_219A


title: genomic DNA from peripheral blood 102

source_name: peripheral blood 2

value: normal


title: chondrocytes untreated rep3


title: stool_278B


title: genomic DNA from peripheral blood 22

description: normal peripheral blood sample

source_name: peripheral blood 22


title: chondrocytes untreated rep4


title: chondrocytes Gal-1 rep2


title: stool_205A


title: chondrocytes untreated rep1


title: chondrocytes untreated rep2


title: genomic DNA from peripheral blood 122

value: Male


title: chondrocytes Gal-1 rep1


title: genomic DNA from peripheral blood 107

source_name: peripheral blood 7


title: stool_149B

value: environmental enteric dysfunction


title: stool_160B

value: M


title: stool_127A


title: stool_118B


title: stool_098A


title: stool_060A


title: stool_079B


title: stool_054A


title: stool_232


title: stool_010A


title: stool_071B


title: stool_025B


title: stool_004A


title: stool_008A


title: genomic DNA from peripheral blood 111

source_name: peripheral blood 11


title: stool_022A


title: stool_316B


title: stool_109A


title: stool_168A


title: stool_134B


title: stool_007A


title: Comceptus, male, rep3

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

description: Gene expression of male conceptus

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip® BovineGene 1.0 ST Array (Affymetrix)

scan_protocol: GeneChip 3000 7G Scanner with Affymetrix GeneChip Command Console Software (AGCC).

data_processing: Raw data from conceptus and endometrium were processed separately. The RMA data was generated using the rma function of the affy package (version affy_1.36.1) in R (version 2.15.2).

organism: Bos taurus

source_name: Conceptus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual, Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocols

treatment_protocol: The estrous cycles of crossbred beef heifers were synchronized using an 8-day controlled internal drug release (CIDR) device (1.38 g P4; Pfizer Animal Health, Sandwich, Kent, UK) placed intra-vaginally. One day prior to CIDR removal, a 2 ml intramuscular injection of a prostaglandin F2α analogue (Estrumate, Intervert, Dublin, Ireland; equivalent to 0.5 mg cloprostenol) was administered. All heifers were then observed at 4 h intervals and only those observed in standing estrus (=Day 0, n=30) were inseminated with semen from a proven sire.

value: trophectoderm tissue


title: tumor - pancreatic 12

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

description: MYCN-driven neuroendocrine tumor

hyb_protocol: Biotin labelling was performed according the manufacturers recommendations (Affymetrix)

scan_protocol: Hybridisation to human arrays was performed according to the manufacturers recommendations (Affymetrix)

data_processing:
Scanning of chips was performed using a GeneArray scanner (Agilent)
Signal intensities were determined using Partek Genomics Suite (Partek Inc.)

source_name: LSL-MYCN;hGFAP-Cre

label_protocol: QIAGEN RNeasy mini kit

growth_protocol: LSL-MYCN; hGFAP-Cre mice spontaneously develop pancreatic tumors, brain tumors or both

extract_protocol: Total mRNA was isolated from tumor tissue using QIAGEN RNeasy Mini Kit.

treatment_protocol: Untreated tumors were excised from euthanised mice

value: tumor - pancreatic


title: tumor - brain 8

description: MYCN-driven neuroendocrine tumor

value: tumor - brain


title: tumor - brain 7

description: MYCN-driven neuroendocrine tumor


title: ARPE-19_control_rep1

city: Hangzhou

first: Yuchen

last: Lin

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University School of Medicine

description: gene expression

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: control

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

growth_protocol: ARPE-19 cells were cultured in DMEM/F12 medium (Hyclone, Logan, UT, USA), containing 10% fetal bovine serum and 0.1% antibiotics in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: ARPE-19 cells were sham washed or treated with 1 μM adriamycin for 24 h

tag: cell line


title: tumor - pancreatic 10

description: MYCN-driven neuroendocrine tumor


title: ARPE-19_adriamycin_24h_rep1

description: gene expression

source_name: ADR


title: Comceptus, male, rep4

description: Gene expression of male conceptus


title: UF912_Time_192_Rep_4

city: Gainesville

first: Christopher

last: Dervinis

state: FL

address: 2033 Mowry Road, rm 320

department: SFRC

institute: University of Florida

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_4.txt
UF912_4_192

hyb_protocol: Hybridization was performed according to Agilent Two-Color Low Input Quick Amp Labeling Kit v.6.6 protocol

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Median values of signal intensities were quantile normalized and log2 transformed in R.

organism: Populus trichocarpa x Populus deltoides

source_name: Bottom 1cm stem cutting harvested from genotype UF912 8 hours after cutting

label_protocol: Dnased treated RNA (Qiagen) was clean by column (Rneasy, Qiagen).  RNA was amplified and cRNA synthesized and labeled using Two Dyes Agilent Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: To measure gene expression during adventitious root formation in the three selected genotypes from each QTL category (PtQTL and PdQTL), a 1 centimeter section, measured from the base of each cutting, was collected at 0, 24, 48, 96 and 192 hours after placing them in the hydroponic solution. Samples were flash-frozen in liquid nitrogen for posterior RNA extraction. Four biological replicates were collected from each genotype, at each time point. In addition, five biological replicates of each genotype were maintained in hydroponic growth conditions until day 12 to verify that the root development was consistent with the phenotype observed in the QTL detection experiment.

extract_protocol: Total RNA was extracted as described by Chang, Puryear and Cairney (Plant Mol Biol Report 1993, 11:113–116) from the bottom 1 cm stem section collected from each sample. The sample included xylem, phloem and bark.

tag: pedigree

tag: genotype

tag: allele type

value: PdQTL

tag: time (after cutting)

value: 192 hours

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: tumor - pancreatic 9

description: MYCN-driven neuroendocrine tumor


title: tumor - pancreatic 11

description: MYCN-driven neuroendocrine tumor


title: Comceptus, male, rep2

description: Gene expression of male conceptus


title: chondrocytes Gal-1 rep5


title: Comceptus, male, rep1

description: Gene expression of male conceptus


title: tumor - pancreatic 2

description: MYCN-driven neuroendocrine tumor


title: UF912_Time_96_Rep_4

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_3.txt
UF912_4_96

source_name: Bottom 1cm stem cutting harvested from genotype UF912 192 hours after cutting

value: 96 hours


title: tumor - pancreatic 4

description: MYCN-driven neuroendocrine tumor


title: tumor - brain 6

description: MYCN-driven neuroendocrine tumor


title: UF912_Time_0_Rep_4

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_4.txt
UF912_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF912 0 hours after cutting

value: 0 hours


title: tumor - pancreatic 3

description: MYCN-driven neuroendocrine tumor


title: Conceptus, female rep3

description: Gene expression of female conceptus


title: UF912_Time_48_Rep_4

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_2.txt
UF912_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF912 48 hours after cutting

value: 48 hours


title: tumor - pancreatic 1

description: MYCN-driven neuroendocrine tumor


title: Endometrium, male rep4

description: Gene expression of endometrium with male conceptus

source_name: Endometrium

value: intercaruncular endometrial tissue


title: tumor - pancreatic 5

description: MYCN-driven neuroendocrine tumor


title: UF912_Time_192_Rep_3

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_3.txt
UF912_3_192


title: UF912_Time_96_Rep_3

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_2.txt
UF912_3_96


title: Conceptus, female rep2

description: Gene expression of female conceptus


title: Conceptus, female rep4

description: Gene expression of female conceptus


title: UF912_Time_0_Rep_3

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_4.txt
UF912_3_0


title: Endometrium, male rep1


title: Endometrium, male rep3


title: Endometrium, male rep2


title: UF912_Time_24_Rep_4

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_1.txt
UF912_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF912 24 hours after cutting

value: 24 hours


title: UF912_Time_24_Rep_3

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_4.txt
UF912_3_24


title: UF498_Time_192_Rep_4

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_3.txt
UF498_4_192

source_name: Bottom 1cm stem cutting harvested from genotype UF498 8 hours after cutting

value: PtQTL


title: UF912_Time_48_Rep_3

description:
raw data file: US83800208_252412610018_S01_GE2-v5_10_Apr08_1_1.txt
UF912_3_48


title: Endometrium, female rep5

description: Gene expression of endometrium with female conceptus


title: Endometrium, male rep5


title: Endometrium, female rep3


title: UF498_Time_192_Rep_3

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_2.txt
UF498_3_192


title: Endometrium, female rep2


title: UF498_Time_96_Rep_3

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_1.txt
UF498_3_96

source_name: Bottom 1cm stem cutting harvested from genotype UF498 192 hours after cutting


title: UF498_Time_96_Rep_4

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_2.txt
UF498_4_96


title: UF498_Time_0_Rep_4

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_3.txt
UF498_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF498 0 hours after cutting


title: Endometrium, female rep4


title: UF498_Time_48_Rep_4

description:
raw data file: US83800208_252412610017_S01_GE2-v5_10_Apr08_1_1.txt
UF498_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF498 48 hours after cutting


title: stool_223

description: Gene expression data of stool RNAs from study subject

source_name: stool total RNA


title: Pregnant Ipsilateral Ampulla rep 5

description: Gene expression data from ipsilateral ampulla of pregnant heifers, rep5

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the [BovGene-1_0-st] Bovine Gene 1.0 ST Array [CDF: Brainarray bovgene10st_Bt_ENTREZG, version 16.0.0] (Affymetrix)

data_processing: alternative CDF (brainarray; bovgene10stbtentrezgenecdf, version 16.0.0) and  signal intensities called using rma preprocessed data

source_name: Epithelial cells

value: oviduct

tag: region

value: ipsilateral ampulla

tag: group

value: pregnant


title: UF498_Time_24_Rep_4

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_4.txt
UF498_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF498 24 hours after cutting


title: Endometrium, female rep1


title: Pregnant Ipsilateral Ampulla rep 1

description: Gene expression data from ipsilateral ampulla of pregnant heifers, rep1


title: UF498_Time_24_Rep_3

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_3.txt
UF498_3_24


title: Pregnant Ipsilateral Ampulla rep 4

description: Gene expression data from ipsilateral ampulla of pregnant heifers


title: UF498_Time_0_Rep_3

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_3.txt
UF498_3_0


title: UF209_Time_192_Rep_4

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_2.txt
UF209_4_192

source_name: Bottom 1cm stem cutting harvested from genotype UF209 8 hours after cutting


title: Pregnant Ipsilateral Ampulla rep 3

description: Gene expression data from ipsilateral ampulla of pregnant heifers, rep3


title: stool_21

value: environmental enteric dysfunction


title: Pregnant Ipsilateral Ampulla rep 2

description: Gene expression data from ipsilateral ampulla of pregnant heifers, rep2


title: Cyclic Contralateral Isthmus rep 5

description: Gene expression data from contralateral isthmus of cyclic heifers, rep5

value: contralateral isthmus

value: cyclic


title: Cyclic Contralateral Isthmus rep 3

description: Gene expression data from contralateral isthmus of cyclic heifers, rep3


title: UF498_Time_48_Rep_3

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_4.txt
UF498_3_48


title: UF209_Time_96_Rep_4

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_1.txt
UF209_4_96

source_name: Bottom 1cm stem cutting harvested from genotype UF209 192 hours after cutting


title: UF209_Time_0_Rep_4

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_2.txt
UF209_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF209 0 hours after cutting


title: Cyclic Contralateral Isthmus rep 4

description: Gene expression data from contralateral isthmus of cyclic heifers, rep4


title: Cyclic Contralateral Isthmus rep 2

description: Gene expression data from contralateral isthmus of cyclic heifers, rep2


title: UF209_Time_192_Rep_3

description:
raw data file: US83800208_252412610016_S01_GE2-v5_10_Apr08_1_1.txt
UF209_3_192


title: UF209_Time_0_Rep_3

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_2.txt
UF209_3_0


title: UF209_Time_48_Rep_4

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_4.txt
UF209_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF209 48 hours after cutting


title: Cyclic Contralateral Isthmus rep 1

description: Gene expression data from contralateral isthmus of cyclic heifers, rep1


title: Pregnant Contralateral Isthmus rep 5

description: Gene expression data from contralateral  oviduct of pregnant heifers, rep5


title: UF209_Time_24_Rep_4

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_3.txt
UF209_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF209 24 hours after cutting


title: UF209_Time_48_Rep_3

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_3.txt
UF209_3_48


title: UF209_Time_96_Rep_3

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_4.txt
UF209_3_96


title: Pregnant Contralateral Isthmus rep 4

description: Gene expression data from contralateral  oviduct of pregnant heifers, rep4


title: Pregnant Contralateral Isthmus rep 3

description: Gene expression data from contralateral  oviduct of pregnant heifers, rep3


title: UF209_Time_24_Rep_3

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_2.txt
UF209_3_24


title: Pregnant Contralateral Isthmus rep 1

description: Gene expression data from contralateral  oviduct of pregnant heifers, rep1


title: UF352_Time_0_Rep_4

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_1.txt
UF352_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF352 0 hours after cutting


title: UF352_Time_192_Rep_4

description:
raw data file: US83800208_252412610015_S01_GE2-v5_10_Apr08_1_1.txt
UF352_4_192

source_name: Bottom 1cm stem cutting harvested from genotype UF352 8 hours after cutting


title: Pregnant Contralateral Isthmus rep 2

description: Gene expression data from contralateral  oviduct of pregnant heifers, rep2


title: m_52_g_72R_UV_high_t_0

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

institute: University of Amsterdam

description: Sample name: 254711110138_4

hyb_protocol: Labeled test samples and common reference samples were combined and hybridized to the Agilent custom microarrays (Agilent Technologies).

scan_protocol: After washing, the arrays were scanned with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies) and data was extracted with Feature Extraction software v10.7.3.1 (Agilent Technologies).

data_processing:
The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's) the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.
RMA values summarized on the GeneIDs

label_protocol: All procedures were performed per manufacturer’s instructions. Briefly, for each test sample, 100 ng total RNA was combined with Spike A and subsequently amplified and labeled using the Quick Amp Labeling Kit (Agilent Technologies). For use as common reference, an equimolar pool of all test samples was made and amplified as described above with the exception that Spike B was included and Cy5 was used for labeling. Amplified cyanine-dye labeled antisense RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen) and yield and dye incorporation were evaluated using a NanoDrop ND-1000.

growth_protocol: All mice were supposed males of 7-10 weeks of age and at least 10 times backcrossed in SKH hairless strain. Wild-type (WT; p53+/+), p5372R/72R, and p5372P/72P mice received normal feed and water ad libitum.

extract_protocol: Total RNA was isolated as previously described in [13]. In short, frozen skin punch biopsies were pulverized in liquid nitrogen and immediately transferred to 0.3 ml Qiazol reagent (Qiagen). RNA was extracted per the manufacturer’s instructions with the addition of Phase-Lock Gel Heavy (5 Prime) to obtain a better phase separation. Further clean-up of the RNA fractions was performed using the RNeasy Minelute Cleanup Kit (Qiagen). RNA yield was measured on a Nanodrop ND-1000 (Thermo Fisher Scientific) and RNA integrity was evaluated using High Sensitivity R6K ScreenTapes on a 2200 TapeStation instrument (Agilent Technologies). RINe values were at least 6, with the exception of two samples (RINe 4.4 and 5.8) .

treatment_protocol: Mice were UV-B exposed at 2 different doses (90, 540 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated. At various time points after treatment (0, 7.5, 9, 10.5, 12, 13.5 hr. for the 90 J/m2 dose and 0, 1, 2, 3, 4, 5 hr. for the 540 J/m2 dose) both treated and untreated mice were anaesthetized by isoflurane and 1.5 mm biopsies were sampled from the back by punching a half moon shape on folded skin. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C until further processing.

value: male

tag: mouse

tag: uv

value: high

tag: time (hours)

value: skin biopsy

source_name: Common Reference pool of samples

tag: reference composition

value: an equimolar pool of all test samples


title: UF352_Time_48_Rep_4

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_3.txt
UF352_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF352 48 hours after cutting

tag: tissue

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: stool_168A, replicate B

description: Gene expression data of stool RNAs from sick child

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Transcriptome Array 2.0 (HTA2.0) chips. The chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: HTA2.0 arrays were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with Expression Console 1.4.1 software using Affymetrix default analysis settings. The Robust Mutlti-array Averaging (RMA) background correction, median polish probe summarization, and quantile normalization were applied as standard method.

source_name: fecal total RNA from study subject

label_protocol: Biotinylated cDNA were prepared according to the vendor's standard protocol from a minimal 100 ng of total RNA using Life Technologies (Ambion) WT-plus RNA Amplification system.

extract_protocol: Stools were enriched by centrifugation for human content prior to RNA extraction. Fecal total RNA was extracted from human-enriched pellets and bacterial-enriched supernatants separately using “Specific A” protocol on the NucliSENS EasyMAG system (bioMérieux, Durham, NC).

tag: sample type

value: stool

tag: disease state

tag: percent lactulose in urine

tag: gender

value: M

tag: age (month)


title: UF352_Time_192_Rep_3

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_4.txt
UF352_3_192

value: 192 hours


title: m_53_g_72P_UV_0_t_3

description: Sample name: 254711110138_1

tag: strain

value: at least 10 times backcrossed in SKH hairless strain


title: stool_007A, replicate B

value: F


title: m_55_g_WT_UV_0_t_2

description: Sample name: 254711110138_2

value: WT


title: stool_021B


title: stool_142B


title: m_55_g_WT_UV_0_t_1

description: Sample name: 254711110137_2


title: stool_022A, replicate B


title: UF352_Time_48_Rep_3

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_2.txt
UF352_3_48

tag: pedigree

value: PtQTL

value: 48 hours


title: m_44_g_WT_UV_high_t_4

description: Sample name: 254711110136_4

tag: genotype


title: UF352_Time_96_Rep_4

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_4.txt
UF352_4_96

source_name: Bottom 1cm stem cutting harvested from genotype UF352 192 hours after cutting

tag: allele type

value: 96 hours


title: m_54_g_72P_UV_high_t_4

description: Sample name: 254711110138_3


title: stool_109A, replicate B

value: environmental enteric dysfunction


title: m_44_g_WT_UV_high_t_5

description: Sample name: 254711110137_4


title: UF352_Time_96_Rep_3

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_3.txt
UF352_3_96

tag: time (after cutting)


title: UF352_Time_0_Rep_3

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_1.txt
UF352_3_0

value: 0 hours


title: stool_LNS225


title: stool_080B


title: UF352_Time_24_Rep_4

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_2.txt
UF352_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF352 24 hours after cutting

value: 24 hours


title: stool_LNS68


title: m_54_g_72P_UV_high_t_0

description: Sample name: 254711110137_3

value: male


title: UF352_Time_24_Rep_3

description:
raw data file: US83800208_252412610012_S01_GE2-v5_10_Apr08_1_1.txt
UF352_3_24


title: m_52_g_72R_UV_high_t_3

description: Sample name: 254711110136_3

value: high


title: stool_023A


title: UF717_Time_0_Rep_4

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_4.txt
UF717_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF717 0 hours after cutting

value: PdQTL


title: UF717_Time_192_Rep_4

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_4.txt
UF717_4_192

source_name: Bottom 1cm stem cutting harvested from genotype UF717 8 hours after cutting


title: UF717_Time_96_Rep_4

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_3.txt
UF717_4_96

source_name: Bottom 1cm stem cutting harvested from genotype UF717 192 hours after cutting


title: stool_180B


title: stool_LNS24


title: m_53_g_72P_UV_0_t_2

description: Sample name: 254711110136_1

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_LNS188

value: stool


title: Conceptus, female rep1

description: Gene expression of female conceptus

source_name: Conceptus

value: trophectoderm tissue


title: stool_294B

value: M


title: m_52_g_72R_UV_high_t_2

description: Sample name: 254711110135_4

value: at least 10 times backcrossed in SKH hairless strain


title: m_54_g_72P_UV_high_t_5

description: Sample name: 254711110135_3


title: m_55_g_WT_UV_0_t_4

description: Sample name: 254711110135_2


title: stool_142A


title: UF717_Time_24_Rep_4

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_1.txt
UF717_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF717 24 hours after cutting

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: m_55_g_WT_UV_0_t_0

description: Sample name: 254711110134_2

value: WT


title: m_53_g_72P_UV_0_t_1

description: Sample name: 254711110135_1


title: UF717_Time_192_Rep_3

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_3.txt
UF717_3_192

value: 192 hours


title: m_44_g_WT_UV_high_t_3

description: Sample name: 254711110134_4


title: stool_186A


title: stool_LNS235

value: F


title: UF717_Time_0_Rep_3

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_4.txt
UF717_3_0


title: stool_LNS122


title: UF717_Time_48_Rep_4

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_2.txt
UF717_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF717 48 hours after cutting

value: 48 hours


title: UF717_Time_48_Rep_3

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_1.txt
UF717_3_48


title: UF717_Time_96_Rep_3

description:
raw data file: US83800208_252412610011_S01_GE2-v5_10_Apr08_1_2.txt
UF717_3_96

value: 96 hours


title: m_54_g_72P_UV_high_t_1

description: Sample name: 254711110134_3


title: stool_LNS229

description: Gene expression data of stool RNAs from sick child

value: environmental enteric dysfunction


title: m_44_g_WT_UV_high_t_2

description: Sample name: 254711110133_4


title: UF926_Time_192_Rep_4

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_3.txt
UF926_4_192

source_name: Bottom 1cm stem cutting harvested from genotype UF926 8 hours after cutting

value: PtQTL


title: m_55_g_WT_UV_0_t_3

description: Sample name: 254711110133_2

value: male


title: m_1_g_WT_UV_0_t_10.5

description: Sample name: 254711110132_2


title: m_53_g_72P_UV_0_t_4

description: Sample name: 254711110133_1


title: UF717_Time_24_Rep_3

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_4.txt
UF717_3_24

value: 24 hours


title: UF926_Time_96_Rep_4

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_2.txt
UF926_4_96

source_name: Bottom 1cm stem cutting harvested from genotype UF926 192 hours after cutting


title: stool_309A


title: m_8_g_WT_UV_low_t_7.5

description: Sample name: 254711110132_4

value: low


title: UF926_Time_192_Rep_3

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_2.txt
UF926_3_192


title: m_1_g_WT_UV_0_t_7.5

description: Sample name: 254711110131_2

value: skin biopsy


title: UF926_Time_96_Rep_3

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_1.txt
UF926_3_96


title: m_3_g_72R_UV_0_t_12

description: Sample name: 254711110132_1

value: an equimolar pool of all test samples


title: UF926_Time_48_Rep_4

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_1.txt
UF926_4_48

source_name: Bottom 1cm stem cutting harvested from genotype UF926 48 hours after cutting


title: stool_LNS102

value: stool


title: UF926_Time_0_Rep_4

description:
raw data file: US83800208_252412610010_S01_GE2-v5_10_Apr08_1_3.txt
UF926_4_0

source_name: Bottom 1cm stem cutting harvested from genotype UF926 0 hours after cutting

value: 0 hours


title: stool_LNS133

value: M


title: stool_LNS52


title: m_52_g_72R_UV_high_t_1

description: Sample name: 254711110133_3

value: at least 10 times backcrossed in SKH hairless strain

value: high


title: m_6_g_72P_UV_low_t_10.5

description: Sample name: 254711110131_3


title: stool_LNS40


title: stool_168B


title: stool_LNS35


title: m_8_g_WT_UV_low_t_9

description: Sample name: 254711110131_4

value: WT


title: UF926_Time_0_Rep_3

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_3.txt
UF926_3_0

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: UF926_Time_48_Rep_3

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_4.txt
UF926_3_48


title: UF926_Time_24_Rep_4

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_4.txt
UF926_4_24

source_name: Bottom 1cm stem cutting harvested from genotype UF926 24 hours after cutting


title: UF926_Time_24_Rep_3

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_3.txt
UF926_3_24


title: stool_LNS210

value: F


title: stool_LNS67


title: m_5_g_72P_UV_0_t_0

description: Sample name: 254711110130_1


title: m_5_g_72P_UV_0_t_12

description: Sample name: 254711110131_1


title: stool_LNS196


title: m_8_g_WT_UV_low_t_12

description: Sample name: 254711110130_4


title: UF912_Time_192_Rep_2

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_2.txt
UF912_2_192

source_name: Bottom 1cm stem cutting harvested from genotype UF912 8 hours after cutting

value: PdQTL

value: 192 hours


title: stool_LNS38

value: environmental enteric dysfunction


title: UF209_Time_192_Rep_2

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_4.txt
UF209_2_192

source_name: Bottom 1cm stem cutting harvested from genotype UF209 8 hours after cutting


title: m_5_g_72P_UV_0_t_7.5

description: Sample name: 254711110129_1

source_name: Common Reference pool of samples


title: UF717_Time_192_Rep_2

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_2.txt
UF717_2_192


title: m_6_g_72P_UV_low_t_9

description: Sample name: 254711110129_3


title: UF498_Time_192_Rep_2

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_1.txt
UF498_2_192

source_name: Bottom 1cm stem cutting harvested from genotype UF498 8 hours after cutting

value: PtQTL


title: UF926_Time_192_Rep_2

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_2.txt
UF926_2_192


title: stool_LNS189

description: Gene expression data of stool RNAs from sick child

source_name: fecal total RNA from study subject


title: m_4_g_72R_UV_low_t_10.5

description: Sample name: 254711110130_3

value: male


title: m_4_g_72R_UV_low_t_9

description: Sample name: 254711110128_1


title: m_6_g_72P_UV_low_t_12

description: Sample name: 254711110128_3


title: UF498_Time_192_Rep_1

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_4.txt
UF498_1_192


title: stool_079A


title: stool_258A


title: stool_311A


title: UF352_Time_192_Rep_2

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_3.txt
UF352_2_192

source_name: Bottom 1cm stem cutting harvested from genotype UF352 8 hours after cutting


title: UF352_Time_192_Rep_1

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_2.txt
UF352_1_192


title: UF912_Time_192_Rep_1

description:
raw data file: US83800208_252412610009_S01_GE2-v5_10_Apr08_1_1.txt
UF912_1_192


title: stool_112A


title: stool_314A


title: stool_248A


title: UF209_Time_192_Rep_1

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_3.txt
UF209_1_192


title: stool_273A


title: m_3_g_72R_UV_0_t_0

description: Sample name: 254711110128_2


title: m_8_g_WT_UV_low_t_10.5

description: Sample name: 254711110129_4


title: UF926_Time_192_Rep_1

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_1.txt
UF926_1_192


title: stool_117A


title: stool_243B


title: m_23_g_72P_UV_0_t_7.5

description: Sample name: 254711110107_1


title: UF912_Time_96_Rep_2

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_4.txt
UF912_2_96

source_name: Bottom 1cm stem cutting harvested from genotype UF912 192 hours after cutting

value: 96 hours


title: UF717_Time_192_Rep_1

description:
raw data file: US83800208_252412610008_S01_GE2-v5_10_Apr08_1_1.txt
UF717_1_192

source_name: Bottom 1cm stem cutting harvested from genotype UF717 8 hours after cutting


title: m_24_g_72P_UV_low_t_0

description: Sample name: 254711110106_3

value: low


title: m_24_g_72P_UV_low_t_12

description: Sample name: 254711110107_3

value: skin biopsy


title: UF926_Time_96_Rep_2

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_4.txt
UF926_2_96


title: UF912_Time_96_Rep_1

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_3.txt
UF912_1_96


title: UF498_Time_96_Rep_2

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_3.txt
UF498_2_96

source_name: Bottom 1cm stem cutting harvested from genotype UF498 192 hours after cutting


title: stool_126B


title: m_48_g_72P_UV_high_t_1

description: Sample name: 254711110105_3

value: an equimolar pool of all test samples


title: UF352_Time_96_Rep_2

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_1.txt
UF352_2_96

source_name: Bottom 1cm stem cutting harvested from genotype UF352 192 hours after cutting


title: m_23_g_72P_UV_0_t_12

description: Sample name: 254711110106_1


title: stool_152B

value: stool


title: UF498_Time_96_Rep_1

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_2.txt
UF498_1_96


title: stool_088A


title: m_26_g_WT_UV_low_t_10.5

description: Sample name: 254711110106_4


title: m_27_g_72R_UV_0_t_10.5

description: Sample name: 254711110107_2


title: m_50_g_WT_UV_high_t_2

description: Sample name: 254711110105_4


title: UF209_Time_96_Rep_1

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_1.txt
UF209_1_96

source_name: Bottom 1cm stem cutting harvested from genotype UF209 192 hours after cutting


title: stool_060B


title: UF209_Time_96_Rep_2

description:
raw data file: US83800208_252412610007_S01_GE2-v5_10_Apr08_1_2.txt
UF209_2_96


title: m_43_g_WT_UV_0_t_0

description: Sample name: 254711110105_2


title: m_45_g_72R_UV_0_t_5

description: Sample name: 254711110105_1


title: stool_106B


title: stool_049B


title: stool_238A


title: UF352_Time_96_Rep_1

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_4.txt
UF352_1_96


title: stool_206A

description: Gene expression data of stool RNAs from sick child


title: UF717_Time_96_Rep_2

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_4.txt
UF717_2_96

source_name: Bottom 1cm stem cutting harvested from genotype UF717 192 hours after cutting


title: stool_203B


title: m_46_g_72R_UV_high_t_1

description: Sample name: 254711110104_4


title: UF717_Time_96_Rep_1

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_3.txt
UF717_1_96


title: stool_LNS94


title: m_48_g_72P_UV_high_t_3

description: Sample name: 254711110103_3


title: m_45_g_72R_UV_0_t_3

description: Sample name: 254711110104_2


title: UF498_Time_48_Rep_2

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_1.txt
UF498_2_48

source_name: Bottom 1cm stem cutting harvested from genotype UF498 48 hours after cutting

value: 48 hours


title: stool_078A

value: M


title: m_43_g_WT_UV_0_t_2

description: Sample name: 254711110103_2

value: at least 10 times backcrossed in SKH hairless strain


title: stool_157A


title: m_47_g_72P_UV_0_t_4

description: Sample name: 254711110104_1


title: UF926_Time_48_Rep_2

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_2.txt
UF926_2_48


title: UF912_Time_48_Rep_2

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_2.txt
UF912_2_48

source_name: Bottom 1cm stem cutting harvested from genotype UF912 48 hours after cutting


title: stool_LNS27


title: stool_LNS243


title: m_46_g_72R_UV_high_t_0

description: Sample name: 254711110102_3

value: high


title: UF209_Time_48_Rep_2

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_4.txt
UF209_2_48

source_name: Bottom 1cm stem cutting harvested from genotype UF209 48 hours after cutting


title: m_50_g_WT_UV_high_t_0

description: Sample name: 254711110103_4

value: WT


title: m_50_g_WT_UV_high_t_5

description: Sample name: 254711110102_4


title: stool_059A


title: UF498_Time_48_Rep_1

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_4.txt
UF498_1_48

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: m_48_g_72P_UV_high_t_0

description: Sample name: 254711110104_3


title: m_47_g_72P_UV_0_t_5

description: Sample name: 254711110103_1


title: UF912_Time_48_Rep_1

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_1.txt
UF912_1_48


title: stool_LNS29


title: UF352_Time_48_Rep_2

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_3.txt
UF352_2_48

source_name: Bottom 1cm stem cutting harvested from genotype UF352 48 hours after cutting


title: stool_240B


title: m_46_g_72R_UV_high_t_2

description: Sample name: 254711110101_3


title: m_45_g_72R_UV_0_t_0

description: Sample name: 254711110101_1


title: m_43_g_WT_UV_0_t_3

description: Sample name: 254711110102_2


title: m_45_g_72R_UV_0_t_4

description: Sample name: 254711110102_1


title: stool_114A

value: F


title: m_50_g_WT_UV_high_t_1

description: Sample name: 254711110101_4


title: stool_319A


title: stool_260B


title: UF912_Time_24_Rep_2

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_4.txt
UF912_2_24

source_name: Bottom 1cm stem cutting harvested from genotype UF912 24 hours after cutting

value: PdQTL

value: 24 hours


title: UF209_Time_48_Rep_1

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_3.txt
UF209_1_48


title: stool_282B

value: environmental enteric dysfunction


title: UF926_Time_48_Rep_1

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_1.txt
UF926_1_48

source_name: Bottom 1cm stem cutting harvested from genotype UF926 48 hours after cutting

value: PtQTL


title: m_50_g_WT_UV_high_t_3

description: Sample name: 254711110100_4

value: male


title: UF498_Time_24_Rep_2

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_3.txt
UF498_2_24

source_name: Bottom 1cm stem cutting harvested from genotype UF498 24 hours after cutting


title: stool_LNS165


title: UF926_Time_24_Rep_2

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_4.txt
UF926_2_24

source_name: Bottom 1cm stem cutting harvested from genotype UF926 24 hours after cutting


title: UF717_Time_48_Rep_2

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_2.txt
UF717_2_48

source_name: Bottom 1cm stem cutting harvested from genotype UF717 48 hours after cutting


title: UF717_Time_48_Rep_1

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_1.txt
UF717_1_48


title: stool_202A

description: Gene expression data of stool RNAs from sick child

source_name: fecal total RNA from study subject


title: stool_136A


title: UF352_Time_48_Rep_1

description:
raw data file: US83800208_252412610005_S01_GE2-v5_10_Apr08_1_2.txt
UF352_1_48


title: m_43_g_WT_UV_0_t_1

description: Sample name: 254711110100_2

source_name: Common Reference pool of samples


title: stool_014A


title: stool_097A


title: stool_304A


title: m_47_g_72P_UV_0_t_2

description: Sample name: 254711110100_1


title: m_46_g_72R_UV_high_t_4

description: Sample name: 254711110100_3


title: stool_LNS177


title: m_48_g_72P_UV_high_t_2

description: Sample name: 254711110099_3


title: UF209_Time_24_Rep_2

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_2.txt
UF209_2_24

source_name: Bottom 1cm stem cutting harvested from genotype UF209 24 hours after cutting


title: stool_LNS101


title: UF209_Time_24_Rep_1

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_1.txt
UF209_1_24


title: m_50_g_WT_UV_high_t_4

description: Sample name: 254711110098_4


title: stool_LNS217


title: stool_LNS28


title: stool_LNS71


title: m_46_g_72R_UV_high_t_5

description: Sample name: 254711110099_4


title: UF912_Time_24_Rep_1

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_3.txt
UF912_1_24


title: m_48_g_72P_UV_high_t_5

description: Sample name: 254711110098_3


title: UF352_Time_24_Rep_2

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_1.txt
UF352_2_24

source_name: Bottom 1cm stem cutting harvested from genotype UF352 24 hours after cutting


title: stool_LNS173


title: stool_LNS191


title: stool_LNS160


title: UF352_Time_24_Rep_1

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_4.txt
UF352_1_24


title: m_47_g_72P_UV_0_t_3

description: Sample name: 254711110099_1


title: UF498_Time_24_Rep_1

description:
raw data file: US83800208_252412610004_S01_GE2-v5_10_Apr08_1_2.txt
UF498_1_24


title: m_45_g_72R_UV_0_t_2

description: Sample name: 254711110098_2


title: UF926_Time_24_Rep_1

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_3.txt
UF926_1_24


title: UF717_Time_24_Rep_1

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_3.txt
UF717_1_24

source_name: Bottom 1cm stem cutting harvested from genotype UF717 24 hours after cutting


title: stool_020A


title: UF717_Time_24_Rep_2

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_4.txt
UF717_2_24


title: m_52_g_72R_UV_high_t_4

description: Sample name: 254711110097_4


title: m_45_g_72R_UV_0_t_1

description: Sample name: 254711110099_2


title: m_47_g_72P_UV_0_t_0

description: Sample name: 254711110098_1


title: UF926_Time_96_Rep_1

description:
raw data file: US83800208_252412610006_S01_GE2-v5_10_Apr08_1_3.txt
UF926_1_96

source_name: Bottom 1cm stem cutting harvested from genotype UF926 192 hours after cutting

value: 96 hours


title: stool_288A


title: UF926_Time_0_Rep_2

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_2.txt
UF926_2_0

source_name: Bottom 1cm stem cutting harvested from genotype UF926 0 hours after cutting

value: 0 hours


title: stool_091B


title: m_53_g_72P_UV_0_t_5

description: Sample name: 254711110097_1

value: skin biopsy


title: UF498_Time_0_Rep_2

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_1.txt
UF498_2_0

source_name: Bottom 1cm stem cutting harvested from genotype UF498 0 hours after cutting


title: m_44_g_WT_UV_high_t_1

description: Sample name: 254711110096_4

value: an equimolar pool of all test samples


title: stool_186C

value: stool


title: stool_087B


title: m_44_g_WT_UV_high_t_0

description: Sample name: 254711110095_4


title: UF912_Time_0_Rep_1

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_1.txt
UF912_1_0

source_name: Bottom 1cm stem cutting harvested from genotype UF912 0 hours after cutting


title: m_54_g_72P_UV_high_t_3

description: Sample name: 254711110097_3


title: m_54_g_72P_UV_high_t_2

description: Sample name: 254711110095_3


title: m_55_g_WT_UV_0_t_5

description: Sample name: 254711110095_2


title: stool_256A


title: UF498_Time_0_Rep_1

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_4.txt
UF498_1_0


title: m_53_g_72P_UV_0_t_0

description: Sample name: 254711110096_1


title: UF209_Time_0_Rep_2

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_4.txt
UF209_2_0

source_name: Bottom 1cm stem cutting harvested from genotype UF209 0 hours after cutting


title: stool_241B

description: Gene expression data of stool RNAs from sick child


title: stool_201A


title: m_52_g_72R_UV_high_t_5

description: Sample name: 254711110096_3


title: UF912_Time_0_Rep_2

description:
raw data file: US83800208_252412610002_S01_GE2-v5_10_Apr08_1_2.txt
UF912_2_0


title: UF717_Time_0_Rep_2

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_2.txt
UF717_2_0

source_name: Bottom 1cm stem cutting harvested from genotype UF717 0 hours after cutting


title: UF352_Time_0_Rep_1

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_2.txt
UF352_1_0

source_name: Bottom 1cm stem cutting harvested from genotype UF352 0 hours after cutting


title: stool_019A


title: m_43_g_WT_UV_0_t_4

description: Sample name: 254711110101_2


title: stool_LNS246


title: UF352_Time_0_Rep_2

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_3.txt
UF352_2_0


title: UF209_Time_0_Rep_1

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_3.txt
UF209_1_0


title: m_26_g_WT_UV_low_t_9

description: Sample name: 254711110094_4

value: low


title: stool_085A

value: M


title: stool_LNS141


title: UF926_Time_0_Rep_1

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_1.txt
UF926_1_0


title: stool_LNS12


title: m_28_g_72R_UV_low_t_7.5

description: Sample name: 254711110094_3

value: at least 10 times backcrossed in SKH hairless strain


title: stool_LNS60


title: Foxi3 null E15.5 back skin epithelium, biologial replicate 4

city: Helsinki

first: Vera

last: Shirokova

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: Back skin epithelium of one embryo

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute  • Transfer 200μl of hybridization solution to each array, then tape holes • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Probes were re-annotated using CustomCDF annotations. Data were quantile normalized and summarized by using RMA-Cybert-package as applied in statistical environment R.

source_name: back skin epithelium, Foxi3 null

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

growth_protocol: Back skin epithelia isolated from E15.5 mouse embryos

extract_protocol: Fxoi3 null embryos were identified by jawless phenotype and confirmed by genotyping; wt were identified by genotyping. Back skin epithelia were separated enzymatically by dispase. Epithelium from each individual were collected in RNA later (Quigen). RNA was extracted using the RNeasy mini kit (Qiagen).

treatment_protocol: not applicable

tag: age

value: embryonic back skin epithelium


title: wild-type E15.5 back skin epithelium, biologial replicate 3

description: Back skin epithelium of one embryo

source_name: back skin epithelium, wild-type


title: m_25_g_WT_UV_0_t_10.5

description: Sample name: 254711110092_2

value: WT


title: stool_LNS89


title: stool_295B


title: m_27_g_72R_UV_0_t_0

description: Sample name: 254711110094_1


title: m_25_g_WT_UV_0_t_0

description: Sample name: 254711110093_2


title: stool_LNS156


title: m_24_g_72P_UV_low_t_7.5

description: Sample name: 254711110092_3


title: m_26_g_WT_UV_low_t_7.5

description: Sample name: 254711110093_4


title: m_23_g_72P_UV_0_t_9

description: Sample name: 254711110093_1


title: m_28_g_72R_UV_low_t_9

description: Sample name: 254711110092_4


title: wild-type E15.5 back skin epithelium, biologial replicate 2

description: Back skin epithelium of one embryo


title: UF717_Time_0_Rep_1

description:
raw data file: US83800208_252412610001_S01_GE2-v5_10_Apr08_1_1.txt
UF717_1_0

value: Bottom 1cm stem cutting (included xylem, phloem and bark)


title: Foxi3 null E15.5 back skin epithelium, biologial replicate 3

description: Back skin epithelium of one embryo


title: stool_308A

value: F


title: stool_014B


title: m_27_g_72R_UV_0_t_12

description: Sample name: 254711110092_1


title: wild-type E15.5 back skin epithelium, biologial replicate 1

description: Back skin epithelium of one embryo


title: m_25_g_WT_UV_0_t_9

description: Sample name: 254711110091_2


title: stool_207B


title: stool_LNS49


title: m_26_g_WT_UV_low_t_0

description: Sample name: 254711110091_4


title: wild-type E15.5 back skin epithelium, biologial replicate 4

description: Back skin epithelium of one embryo


title: stool_153A


title: Foxi3 null E15.5 back skin epithelium, biologial replicate 2

description: Back skin epithelium of one embryo


title: Foxi3 null E15.5 back skin epithelium, biologial replicate 1

description: Back skin epithelium of one embryo


title: m_27_g_72R_UV_0_t_7.5

description: Sample name: 254711110091_1


title: m_28_g_72R_UV_low_t_12

description: Sample name: 254711110090_4


title: m_24_g_72P_UV_low_t_10.5

description: Sample name: 254711110090_3


title: stool_LNS231


title: stool_LNS111


title: stool_LNS79


title: Cj_mf_MT_stage05_rep3

city: Hitachi

first: Miyoko

last: Tsubomura

state: Ibaraki

department: Forest Tree Breeding Center

institute: Forestry and Forest Products Research Institute

hyb_protocol: Hybridized at 42 °C during 17 h with three μg of Cy3 labeled ds-cDNA in the NimbleGen hybridization system.

scan_protocol: Slides were scanned at 2 μm/pixel resolution using an NimbleGen MS 200 scanner (NimbleGen).

data_processing: Scanned images (TIFF format) were imported into the NimbleScan software version 2.6 (NimbleGen) for grid alignment.

organism: Cryptomeria japonica

source_name: mutant

label_protocol: Ten micrograms of total RNA were transcribed to double strand (ds) cDNA using a Superscript ds-cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) and  labeled by a NimbleGen One-Color Labeling Kit (NimbleGen, Madison, WI, USA)  in accordance with the NimbleGen gene expression analysis protocol. .

growth_protocol: Japanese cedar  was propagated from a single tree by grafting, and grown for several years.

extract_protocol: Male strobili were collected from branches and the developmental stages were classified by cytological analysis.

treatment_protocol: Some branches of each clones were treated with gibberellin A3 in the beginning of July in 2011 for flowering promotion.

value: sterile mutant

value: strobili

tag: Stage

tag: date of sampling


title: Cj_mf_MT_stage03_rep3


title: stool_169A

value: environmental enteric dysfunction


title: m_23_g_72P_UV_0_t_0

description: Sample name: 254711110090_1

tag: mouse

tag: uv


title: Cj_mf_MT_stage05_rep2


title: m_24_g_72P_UV_low_t_9

description: Sample name: 254711110089_3

tag: time (hours)

tag: reference composition


title: stool_LNS153

tag: sample type


title: m_26_g_WT_UV_low_t_12

description: Sample name: 254711110088_4

tag: tissue


title: Cj_mf_MT_stage06_rep3


title: Cj_mf_MT_stage04_rep2


title: Cj_mf_MT_stage06_rep1


title: Cj_mf_MT_stage05_rep1


title: m_23_g_72P_UV_0_t_10.5

description: Sample name: 254711110089_1


title: Cj_mf_MT_stage03_rep2


title: m_25_g_WT_UV_0_t_7.5

description: Sample name: 254711110090_2


title: stool_LNS219

tag: disease state

tag: percent lactulose in urine


title: m_25_g_WT_UV_0_t_12

description: Sample name: 254711110089_2

tag: gender


title: Cj_mf_MT_stage06_rep2


title: Cj_mf_MT_stage04_rep3


title: stool_137A

tag: age (month)


title: stool_273B


title: stool_279A


title: stool_182B


title: m_28_g_72R_UV_low_t_0

description: Sample name: 254711110089_4

tag: strain


title: Cj_mf_MT_stage04_rep1

tag: genotype


title: m_28_g_72R_UV_low_t_10.5

description: Sample name: 254711110088_3


title: m_35_g_72P_UV_0_t_2

description: Sample name: 254711110087_1


title: m_36_g_72P_UV_high_t_1

description: Sample name: 254711110087_3

value: high


title: stool_LNS214


title: m_8_g_WT_UV_low_t_0

description: Sample name: 254711110086_4

value: male


title: stool_LNS112


title: m_4_g_72R_UV_low_t_7.5

description: Sample name: 254711110086_3


title: m_32_g_WT_UV_high_t_0

description: Sample name: 254711110087_4


title: Cj_mf_MT_stage03_rep1


title: m_27_g_72R_UV_0_t_9

description: Sample name: 254711110088_2


title: Cj_mf_WT_stage03_rep3

source_name: wild-type

value: wild type


title: m_31_g_WT_UV_0_t_5

description: Sample name: 254711110087_2


title: Cj_mf_WT_stage09_rep3


title: stool_LNS51


title: Cj_mf_WT_stage08_rep3


title: stool_LNS200


title: Cj_mf_WT_stage10_rep3


title: m_1_g_WT_UV_0_t_9

description: Sample name: 254711110086_2


title: stool_LNS36


title: Cj_mf_WT_stage04_rep3


title: Cj_mf_WT_stage06_rep3


title: stool_LNS205


title: m_3_g_72R_UV_0_t_10.5

description: Sample name: 254711110086_1


title: Cj_mf_WT_stage02_rep3


title: stool_LNS110


title: stool_138B


title: Cj_mf_WT_stage05_rep3


title: Cj_mf_WT_stage07_rep3


title: stool_209A


title: m_6_g_72P_UV_low_t_0

description: Sample name: 254711110085_3


title: stool_LNS88


title: Cj_mf_WT_stage01_rep3


title: stool_LNS75


title: Cj_mf_WT_stage10_rep2


title: m_3_g_72R_UV_0_t_9

description: Sample name: 254711110084_2


title: m_5_g_72P_UV_0_t_10.5

description: Sample name: 254711110084_1


title: stool_177A


title: m_3_g_72R_UV_0_t_7.5

description: Sample name: 254711110085_1


title: m_4_g_72R_UV_low_t_12

description: Sample name: 254711110083_4


title: stool_LNS213


title: m_1_g_WT_UV_0_t_12

description: Sample name: 254711110085_2


title: m_1_g_WT_UV_0_t_0

description: Sample name: 254711110083_2


title: Cj_mf_WT_stage08_rep2


title: m_4_g_72R_UV_low_t_0

description: Sample name: 254711110084_4


title: stool_LNS208


title: Cj_mf_WT_stage07_rep2


title: Cj_mf_WT_stage05_rep2


title: stool_LNS241


title: stool_LNS105


title: m_6_g_72P_UV_low_t_7.5

description: Sample name: 254711110084_3


title: Cj_mf_WT_stage03_rep2


title: Cj_mf_WT_stage09_rep2


title: Cj_mf_WT_stage06_rep2


title: stool_LNS18


title: stool_LNS179


title: Cj_mf_WT_stage04_rep2


title: stool_LNS242


title: m_5_g_72P_UV_0_t_9

description: Sample name: 254711110083_1


title: m_46_g_72R_UV_high_t_3

description: Sample name: 254711110060_4


title: stool_018A


title: Cj_mf_WT_stage02_rep2


title: stool_196B


title: m_47_g_72P_UV_0_t_1

description: Sample name: 254711110060_1


title: m_43_g_WT_UV_0_t_5

description: Sample name: 254711110060_2


title: m_16_g_72R_UV_low_t_7.5

description: Sample name: 254711110059_3


title: m_48_g_72P_UV_high_t_4

description: Sample name: 254711110060_3


title: stool_LNS46


title: m_17_g_72P_UV_0_t_9

description: Sample name: 254711110059_1


title: m_21_g_72R_UV_0_t_12

description: Sample name: 254711110059_2


title: m_14_g_WT_UV_low_t_12

description: Sample name: 254711110034_4


title: Cj_mf_WT_stage10_rep1


title: stool_253A


title: Cj_mf_WT_stage08_rep1


title: stool_231A


title: m_12_g_72P_UV_low_t_9

description: Sample name: 254711110034_3


title: stool_218B


title: Cj_mf_WT_stage07_rep1


title: Cj_mf_WT_stage02_rep1


title: Cj_mf_WT_stage04_rep1


title: Cj_mf_WT_stage06_rep1


title: m_15_g_72R_UV_0_t_10.5

description: Sample name: 254711110034_1


title: stool_103A


title: stool_LNS7


title: stool_146B


title: stool_180A


title: stool_289A


title: Cj_mf_WT_stage05_rep1


title: Cj_mf_WT_stage01_rep2


title: stool_182A


title: Cj_mf_WT_stage03_rep1


title: m_14_g_WT_UV_low_t_0

description: Sample name: 254711110033_4


title: m_10_g_72R_UV_low_t_9

description: Sample name: 254711110033_3


title: m_13_g_WT_UV_0_t_7.5

description: Sample name: 254711110034_2


title: stool_LNS15


title: control, replicate 2

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

description: normalized by SuperNORM data service

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 h at 45C on ATH1 microarrays (Affymetrix) in the Affymetrix GeneChip hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model.

organism: Arabidopsis thaliana

source_name: control seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 nanograms of total RNA using GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: Seeds were germinated and the seedlings were grown aseptically on solid 1/2MS media plus 1% sucrose at 22C under long-day (16 h light / 8 h darkness) photoperiodic conditions.

extract_protocol: Guanidinium thiocyanate extraction of total RNA followed by spin column purification was performed using NucleoSpin RNA II (Macherey-Nagel).

treatment_protocol: Aerial parts of the seedlings were harvested 2 weeks after germination.

tag: developmental stage

value: 2 weeks after germination

value: Aerial part of seedlings

tag: genotype/variation

value: wildtype

tag: genetic background


title: stool_LNS212

source_name: fecal total RNA from study subject

value: stool


title: m_32_g_WT_UV_high_t_2

description: Sample name: 254711110032_4

value: skin biopsy

source_name: Common Reference pool of samples

value: an equimolar pool of all test samples


title: stool_200A

value: M


title: aln-1 mutant, replicate 1

description: normalized by SuperNORM data service

source_name: mutant seedlings

value: aln-1 mutant


title: m_15_g_72R_UV_0_t_7.5

description: Sample name: 254711110033_2

value: at least 10 times backcrossed in SKH hairless strain


title: control, replicate 1

description: normalized by SuperNORM data service


title: m_31_g_WT_UV_0_t_1

description: Sample name: 254711110032_2

value: WT


title: m_32_g_WT_UV_high_t_4

description: Sample name: 254711110031_4


title: m_11_g_72P_UV_0_t_12

description: Sample name: 254711110033_1


title: Cj_mf_WT_stage01_rep1

tag: Stage


title: m_35_g_72P_UV_0_t_0

description: Sample name: 254711110032_1


title: stool_148B

value: F


title: stool_LNS174


title: m_36_g_72P_UV_high_t_3

description: Sample name: 254711110032_3


title: aln-1 mutant, replicate 2

description: normalized by SuperNORM data service


title: patient_10

city: Cologne

first: Kerstin

last: Becker

address: Weyertal 115b

institute: Cologne Center for Genomics

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was analysed with the Illumina GenomeStudio Data Analysis Software, normalized (average), the background was subtracted, the Illumina custom error model applied and p-values were adjusted for multiple testing (Benjamini and Hochberg correction).

source_name: connective tissue from the hand

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from 150mg RNAlater stabilized tissue by phenol/chloroform extraction. Quality control was performed with Agilent Bioanalyser.

tag: age at surgery

tag: tissue source

value: Dupuytren disease tissue


title: stool_LNS42


title: stool_LNS183


title: patient_9


title: stool_LNS209


title: patient_12


title: stool_LNS146


title: patient_11


title: stool_LNS99


title: m_34_g_72R_UV_high_t_0

description: Sample name: 254711110031_3

tag: mouse

tag: uv


title: m_31_g_WT_UV_0_t_4

description: Sample name: 254711110030_2

tag: time (hours)

tag: reference composition


title: patient_8


title: patient_6


title: m_33_g_72R_UV_0_t_5

description: Sample name: 254711110031_2

tag: tissue


title: m_36_g_72P_UV_high_t_0

description: Sample name: 254711110030_3


title: stool_LNS130

tag: sample type

tag: disease state


title: m_35_g_72P_UV_0_t_1

description: Sample name: 254711110031_1

tag: gender


title: m_32_g_WT_UV_high_t_5

description: Sample name: 254711110029_4


title: m_33_g_72R_UV_0_t_1

description: Sample name: 254711110030_1


title: patient_5


title: stool_LNS92

tag: percent lactulose in urine

tag: age (month)


title: patient_7


title: patient_3

value: female


title: patient_4


title: m_34_g_72R_UV_high_t_3

description: Sample name: 254711110029_3

tag: strain

tag: genotype


title: stool_LNS201

value: environmental enteric dysfunction


title: stool_LNS135


title: patient_1


title: stool_LNS21


title: stool_LNS134


title: m_34_g_72R_UV_high_t_2

description: Sample name: 254711110030_4

value: high


title: m_31_g_WT_UV_0_t_0

description: Sample name: 254711110029_2

value: male


title: stool_LNS203


title: patient_2


title: Cj_mf_WT_stage09_rep1

value: wild type

value: strobili

tag: date of sampling


title: stool_LNS237


title: control_11

value: carpal tunnel release


title: stool_LNS155


title: control_12


title: stool_LNS124


title: m_34_g_72R_UV_high_t_1

description: Sample name: 254711110028_4


title: m_33_g_72R_UV_0_t_2

description: Sample name: 254711110029_1


title: m_36_g_72P_UV_high_t_5

description: Sample name: 254711110028_3


title: stool_044B


title: control_7

value: trigger finger release


title: stool_LNS25

value: stool


title: m_35_g_72P_UV_0_t_3

description: Sample name: 254711110027_1

value: skin biopsy


title: stool_LNS108


title: stool_LNS138


title: control_9


title: m_34_g_72R_UV_high_t_4

description: Sample name: 254711110027_3

value: an equimolar pool of all test samples


title: m_32_g_WT_UV_high_t_1

description: Sample name: 254711110027_4


title: m_33_g_72R_UV_0_t_0

description: Sample name: 254711110027_2


title: m_35_g_72P_UV_0_t_4

description: Sample name: 254711110028_1


title: control_3


title: control_2


title: stool_LNS247


title: stool_050B


title: control_8


title: m_33_g_72R_UV_0_t_3

description: Sample name: 254711110028_2


title: control_1


title: control_5


title: control_4


title: control_6


title: control_10


title: stool_099B

value: M


title: stool_LNS119


title: m_36_g_72P_UV_high_t_2

description: Sample name: 254711110026_3


title: stool_150A


title: stool_291B


title: T11DRG_PACS_14Day_rep5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_5

hyb_protocol: Biotinylated aRNA was fragmented and hybridized to Rat 230 2.0 microarrays (Affymetrix) according to manufacturer’s instructions.

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

data_processing: All data analysis was performed in R using bioconductor packages. CEL files were preprocessed and normalized using robust multichip averaging (RMA). Differential expression was performed using Limma.

organism: Rattus norvegicus

source_name: T11 dorsal root ganglion, PACS, 14 day

label_protocol: 100 ng total RNA per DRG was amplified to produce sufficient biotin labeled antisense RNA for GeneChip analysis. Two round linear amplification was performed using MessageAmp®Ⅱ (Ambion) according to manufacturer’s instructions. Total RNA was converted into first-strand cDNA by using a T7-Oligo (dT) Primer. After the first round in vitro transcription, 2 μg aRNA was used as input for the second round of amplification using biotin labelled nucleotides during in vitro transcription (ENZO BioArray® HighYield® RNA Transcript Labeling Kit (T7), Enzo Life Sciences, Farmingdale, NY, USA). The purity and molecular weight range of aRNA products were confirmed by using agarose gel electrophoresis. Amplified RNA was shipped to the Salk Institute (Gage lab) and confirmed to be intact (not degraded) by formamide-gel electrophoresis.

extract_protocol: Total RNA was extracted from single T11 DRGs using RNeasy Kit (Qiagen Inc., Valencia, CA). RNA concentration was determined by using spectrophotometry (Nanodrop, Ambion) and quality was assessed by capillary gel electrophoresis (Bioanalyzer, Agilent). RNA yields were in excess of 200 ng and A260/A280 ratio in nuclease-free water ranged between 2.0 and 2.1.

treatment_protocol: All surgical procedures were performed in accordance with US. Institutional Animal Care and Use Committee’s (IACUC) approval was secured. Adult female Sprague-Dawley rats (260-310 g) were anesthetized with pentobarbital (65 mg/kg, i.p.). Sprouting of T11 DRG neurons was induced with surgical isolation of cutaneous sensory fields by unilateral transection of T9, T10, T12, and T13 of dorsal and lateral cutaneous nerves. Denervation of dermatomes, and subsequent confirmation of PACS, was confirmed by mapping the innervated/denervated skin border using the cutaneous trunci muscle (CTM) reflex in response to pinch. Noxious stimulation of dorsal skin reflexively activates the CTM reflex which is a localized contraction of the skin of the back (Petruska-JC et al., 2014 J Comp Neurol). When a cutaneous nerve field expanded by collateral sprouting, so did the area of skin from which a CTM reflex could be evoked by pinch. Animals were killed after anesthesia overdose with pentobarbital. Six rats were used for Naïve group and seven rats were used for 7 and 14 days group.

value: Sprague-Dawley

tag: developmental stage

value: adult

tag: rat

value: AIW

tag: surgery

value: T9, T10, T12, and T13 dermatomes were denervated, but T11 dermatome remained intact

tag: post-surgery

value: PACS was induced by the surgery

tag: time

value: day 14 post-surgery

value: T11 dorsal root ganglion


title: m_33_g_72R_UV_0_t_4

description: Sample name: 254711110026_1

value: at least 10 times backcrossed in SKH hairless strain

tag: mouse

tag: uv


title: m_31_g_WT_UV_0_t_3

description: Sample name: 254711110026_2

value: male

value: WT

tag: time (hours)

tag: reference composition


title: human neural progenitor cell line_DISC1_siRNA_replicate3

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

country: United Kingdom

institute: Cardiff University

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed.

label: Biotin

source_name: CTXOE03 cell line

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol extraction, RNA dissolved in water.

treatment_protocol: Transfection of Stealth siRNA (Invitrogen), either control siRNA or a siRNA targeting DISC1 using the N-Ter transfection system(Sigma). Cells were harvested using acutase 6 days after transfection.

tag: cell line

value: Male

tag: cell type

value: Neural progenitor

tag: transfection

value: siRNA targeting DISC1

tag: brain region of origin

value: Fetal cortical neuroepithelium


title: T11DRG_PACS_14Day_rep6

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_6

tag: gender

value: female

value: AIX

tag: tissue


title: T11DRG_PACS_14Day_rep4

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_4

tag: strain

value: AJN


title: T11DRG_PACS_14Day_rep7

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_7

value: Sprague-Dawley

value: AIV


title: stool_LNS50

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: F

tag: age (month)


title: T11DRG_PACS_14Day_rep3

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_3

tag: developmental stage

value: adult

tag: rat

value: AJD

tag: surgery

value: T9, T10, T12, and T13 dermatomes were denervated, but T11 dermatome remained intact

tag: post-surgery

value: PACS was induced by the surgery

value: day 14 post-surgery


title: human neural progenitor cell line_DISC1_siRNA_replicate2

value: Male


title: m_36_g_72P_UV_high_t_4

description: Sample name: 254711110025_3

value: at least 10 times backcrossed in SKH hairless strain

value: male

tag: mouse

tag: genotype

tag: uv

value: high

tag: time (hours)

value: skin biopsy

value: an equimolar pool of all test samples


title: human neural progenitor cell line_Control_siRNA_replicate3

tag: cell line

tag: cell type

value: Neural progenitor

tag: transfection

value: control siRNA

value: Fetal cortical neuroepithelium


title: m_32_g_WT_UV_high_t_3

description: Sample name: 254711110025_4

tag: gender

value: WT

tag: tissue

tag: reference composition


title: m_31_g_WT_UV_0_t_2

description: Sample name: 254711110025_2

tag: strain


title: stool_LNS228

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

tag: percent lactulose in urine

value: M


title: human neural progenitor cell line_Control_siRNA_replicate1

tag: brain region of origin


title: T11DRG_PACS_7Day_rep7

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_7

source_name: T11 dorsal root ganglion, PACS, 7 day

value: Sprague-Dawley

tag: developmental stage

value: adult

value: female

tag: rat

value: AJY

tag: surgery

tag: time

value: day 7 post-surgery

value: T11 dorsal root ganglion


title: human neural progenitor cell line_DISC1_siRNA_replicate1

value: Male

value: siRNA targeting DISC1


title: m_35_g_72P_UV_0_t_5

description: Sample name: 254711110025_1

value: at least 10 times backcrossed in SKH hairless strain

value: male

tag: mouse

tag: genotype

tag: uv

value: skin biopsy


title: m_20_g_WT_UV_low_t_7.5

description: Sample name: 254711110024_4

value: low

tag: time (hours)

value: an equimolar pool of all test samples


title: human neural progenitor cell line_Control_siRNA_replicate2

tag: cell line

tag: cell type

value: Neural progenitor

tag: transfection

value: control siRNA

value: Fetal cortical neuroepithelium


title: T11DRG_PACS_14Day_rep2

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_2

tag: gender

value: AIY

value: T9, T10, T12, and T13 dermatomes were denervated, but T11 dermatome remained intact

tag: post-surgery

value: PACS was induced by the surgery

value: day 14 post-surgery

tag: tissue


title: stool_LNS198

tag: sample type

value: stool

tag: disease state

value: environmental enteric dysfunction

value: M

tag: age (month)


title: stool_LNS192

tag: percent lactulose in urine


title: stool_LNS148

value: F


title: stool_LNS149


title: stool_LNS137


title: m_18_g_72P_UV_low_t_10.5

description: Sample name: 254711110024_3

tag: strain

tag: reference composition


title: T11DRG_PACS_14Day_rep1

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_14D_1

value: Sprague-Dawley

tag: developmental stage

value: adult

value: female

tag: rat

value: AIZ

tag: surgery

tag: time

value: T11 dorsal root ganglion


title: T11DRG_PACS_7Day_rep5

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_5

value: AJR

value: day 7 post-surgery


title: m_17_g_72P_UV_0_t_0

description: Sample name: 254711110024_1

value: at least 10 times backcrossed in SKH hairless strain

value: male

tag: mouse

tag: genotype

tag: uv

tag: time (hours)

value: skin biopsy

value: an equimolar pool of all test samples


title: stool_LNS19

description: Gene expression data of stool RNAs from sick child

tag: gender


title: T11DRG_PACS_7Day_rep6

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_6

value: AKA

value: T9, T10, T12, and T13 dermatomes were denervated, but T11 dermatome remained intact

tag: post-surgery

value: PACS was induced by the surgery


title: stool_149A

value: stool

value: environmental enteric dysfunction


title: T11DRG_PACS_7Day_rep3

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_3

value: AJT

tag: tissue


title: T11DRG_PACS_7Day_rep4

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_4

value: Sprague-Dawley

value: AJV


title: m_20_g_WT_UV_low_t_9

description: Sample name: 254711110023_4

value: WT

value: low


title: m_19_g_WT_UV_0_t_7.5

description: Sample name: 254711110023_2


title: m_21_g_72R_UV_0_t_0

description: Sample name: 254711110023_1


title: stool_LNS56

tag: sample type

value: M


title: stool_LNS53

tag: disease state

value: F


title: T11DRG_PACS_7Day_rep2

description:
Gene expression data of T11 PACS dorsal root ganglion (DRG).
PACS_7D_2

value: adult

value: female

value: AKB

value: day 7 post-surgery

value: T11 dorsal root ganglion


title: m_16_g_72R_UV_low_t_12

description: Sample name: 254711110023_3

value: at least 10 times backcrossed in SKH hairless strain

value: male

value: skin biopsy

value: an equimolar pool of all test samples