title: Young tumor-bearing mouse, biological rep2

city: Umeå

last: Sjödin

address: KBC

department: Chemistry

country: Sweden

institute: Umeå University

description: Gene expression data from Sca1+cKit- BMCs isolated by FACS sorting from young tumor-bearing host

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-18 hr at 45C in an Affymetrix Hybridization Oven. Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarrays were analyzed using the statistical software R. The oligo package was used for background adjustment, summarization normalisation. Normalization was made using the Robust Multichip Average (RMA) algorithm. R software (version 3.2.0) with package oligo (version 1.32.0)

label_protocol: Biotinylated cRNA were prepared according to the Nugen Ovation Pico WTA system (cat # 3302). 500pg of total RNA was used to generate biotinylated cRNA

extract_protocol: Extraction of total RNA was performed according to Qiagen Rneasy Plus Micro Kit's instructions.

tag: strain

value: NCR-NU

tag: Sex

value: female

value: bone marrow cells

value: Young


title: Young cancer-free mouse, biological rep2

status: Public on Jul 21 2016

type: RNA

first: Andreas

description: Gene expression data from Sca1+cKit- BMCs isolated by FACS sorting from young cancer-free host

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age


title: AU565--30min-Ins--rep2

type: protein

city: Pittsburgh

first: Alison

middle: M

last: Nagle

state: PENNSYLVANIA

address: 204 Craft Ave

department: Pharmacology and Chemical Biology

country: USA

institute: University of Pittsburgh

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-20

hyb_protocol: The diluted lysates were arrayed on nitrocellulose-coated FAST slides. Each slide was probed with a primary antibody and a biotin-conjugated secondary antibody.

scan_protocol: Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction. Slides were scanned on a flatbed scanner to produce 16-bit tiff image. Spots from tiff images were identified and the density was quantified by MicroVigene.

data_processing:
Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody).
Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as log2 values) are defined as Supercurve Log 2 value  (format reported in the Metadata). All the data points were normalized for protein loading and transformed to linear value designated as Normalized Linear.

molecule: protein

organism: Homo sapiens

source_name: breast cancer

growth_protocol: The cell lines were cultured in DMEM, DMEM/F-12, RPMI, L15 or McCoys 5A media supplemented with 10% FBS or horse serum according to the conditions provided by Neve et al. (2006).

extract_protocol: Cell lysates were harvested by washing in ice-cold PBS twice, and lysing immediately in RPPA lysis buffer with protease inhibitor (1% Triton X-100, 50mM Hepes, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM NaPPi, 10% Glycerol, 1mM Na3VO4, 1mM PMSF, 10g/ml Aprotinin). Lysates were sonicated and centrifuged at 14,000 rpm at 4oC for 10 min. Protein concentrations were determined by BCA. Then, lysates were mixed with 4X SDS/2-ME sample buffer to have final concentration of 1μg/ml. The lysates were boiled for 5 min and diluted two-fold five times.

treatment_protocol: Cells were plated in triplicate 6cm dishes per treatment time point and then switched to serum-free medium (SFM). Cells were serum starved for 24 hours, then treated with 10nM IGF1 or Ins for 5m, 10m, 30m, 6h, 24h, and 48h.

tag: cell line


title: Old tumor-bearing mouse, biological rep1

description: Gene expression data from Sca1+cKit- BMCs isolated by FACS sorting from old tumor-bearing host

value: Old


title: AU565--30min-Ins--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-19


title: Young cancer-free mouse, biological rep3

source_name: Sca1+cKit- BMCs isolated by FACS sorting from young cancer-free host


title: Old tumor-bearing mouse, biological rep3

source_name: Sca1+cKit- BMCs isolated by FACS sorting from old tumor-bearing host


title: Young tumor-bearing mouse, biological rep3

source_name: Sca1+cKit- BMCs isolated by FACS sorting from young tumor-bearing host


title: AU565--30min-IGF--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-18


title: Old cancer-free mouse, biological rep5

description: Gene expression data from Sca1+cKit- BMCs isolated by FACS sorting from old cancer-free host


title: Young tumor-bearing mouse, biological rep1


title: Young cancer-free mouse, biological rep1


title: AU565--10min-Ins--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-15


title: AU565--30min-IGF--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-16


title: AU565--30min-IGF--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-17


title: Old cancer-free mouse, biological rep3

source_name: Sca1+cKit- BMCs isolated by FACS sorting from old cancer-free host


title: Old cancer-free mouse, biological rep2


title: AU565--10min-IGF--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-11


title: AU565--10min-IGF--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-12


title: AU565--10min-IGF--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-10


title: Old cancer-free mouse, biological rep4


title: AU565--10min-Ins--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-14


title: Old tumor-bearing mouse, biological rep2


title: SKM 11:30pm

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

hyb_protocol: GeneChip Hybridization Controls Kit, P/N 900454, GeneChip hybridization, Wash and Stain Kit, Hybridization module according to the manufacturer instructions

data_processing:
Native .CEL files imported into GeneSpring (v13,1,1, Agilent) after quality controls using the Affymetrix Expression Console. The RMA16 algorithm was used for summarization and data was normalized to the median of all samples.
ExonExprChip.HuGene-2_0-st_na34_hg19_2014-04-07

source_name: young healthy male research volunteer

label_protocol: GeneChip WT Terminal Labeling Kit, P/N 900671

extract_protocol: RNAs were extracted from SKM biopsies.  RNA integrity was assessed using a Bioanalyzer 2100 (Agilent) and RIN were above 9.0

tag: gender

value: male

value: m. vastus lateralis


title: SKM 6:30pm


title: SKM 1:30pm


title: AU565--10min-Ins--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-13


title: SKM 8:30am


title: 0591NIDDK_ogt_pol2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

organism: Drosophila melanogaster

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

growth_protocol: 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.

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

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: antibody


title: SKM 4:30am


title: Old cancer-free mouse, biological rep1


title: AU565--5min-Ins--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-7


title: 0591NIDDK_oga_pol2


title: 0591NIDDK_oga_glcnac


title: AU565--5min-Ins--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-8


title: AU565--5min-IGF--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-5


title: AU565--5min-IGF--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-6


title: 0591NIDDK_gfp_psc


title: AU565--5min-Ins--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-9


title: AU565--5min-IGF--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-4


title: AU565--5min-SFM--rep3

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-3


title: Tie2monocytes-ischemia-6

city: London

first: Francesca

last: Ludwinski

address: First Floor, North Wing, St Thomas' Hospital

department: Academic Department of Vascular Surgery

country: United Kingdom

institute: King's College London

hyb_protocol: The Cy3-labelled cDNAs were hybridised overnight for 17 hours at 65 degrees celcius.

scan_protocol: Fluorescent signals of the hybridised microarrays were detected using Agilent's Microarray scanner system.

data_processing: Agilent Feature Extraction software was used to read out and process the microarray image files. Rosetta Resolver was used to determine differential gene expression. Signal intensities are normalised by dividing the intensity values by their median.

source_name: Limb ischemia patient Tie2 monocytes

label_protocol: 250ng of each cDNA was used as a template for Cy3 labelling which was performed by Miltenyi Biotec according to in house protocols.

extract_protocol: SuperAmp RNA amplification was performed by Miltenyi Biotec according to in house procedures. mRNA was isolated via magnetic bead technology.

tag: diagnosis

value: critical limb ischemia (CLI)

value: Tie2-expressing monocytes from whole blood


title: Tie2monocytes-control-6

source_name: Control Tie2 monocytes

value: healthy control


title: Tie2monocytes-control-5


title: Tie2monocytes-ischemia-3


title: Tie2monocytes-ischemia-4


title: AU565--5min-SFM--rep2

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-2


title: 0591NIDDK_gfp_pc


title: 0591NIDDK_gfp_pho


title: 0591NIDDK_gfp_input


title: 0591NIDDK_gfp_pol2


title: 0591NIDDK_gfp_cg3065


title: 03-117 2

status: Public on Jul 20 2016

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

hyb_protocol: Incubation with the appropriate biotinylated detection antibody cocktail was performed as outlined in the protocol, followed by incubation with streptavidin-PE. Following the final wash step, beads were re-suspended in the designated buffer.

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA).

data_processing: Serum concentrations were interpolated from standard curves for each respective analyte in Bio-Plex Manager 5.0 software. Values out of range below the standard curve were set to zero, while any value out of range above the standard curve was set to 4x the highest observed standard concentration.  For descriptive analyses of the multiplex biomarker data, data were analyzed using the log of the “ratio to cohort average”. This value was computed for each analyte by first setting any value less than 1 pg/mL to 1 pg/mL and then calculating the log base 2 of [(observed value)/(average value in the cohort)].

label: PE

source_name: serum

label_protocol: Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. All assays were performed using 96-well flat-bottom plates and a Bio-Plex Pro II magnetic wash station. Standards, quality controls and experimental sera were diluted in provided diluents and then incubated with the respective multiplex bead mix according to manufacturer protocol.

extract_protocol: Serum was isolated from coagulated blood using standard protocols.  All sera were frozen and aliquoted within four hours of sampling.

tag: subject id

tag: visit number (1 = baseline)

value: M

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

value: N

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: 03-117 3


title: PV-4 wild type 1

city: Norman

first: Ming

last: Xie

state: Oklahoma

address: 101 L DAVID BOREN BLVD

department: Microbiology and plant biology

institute: Institute for Environmental Genomics

hyb_protocol: Hybridization was done in Maui hybridization system at 42 degree C for 16 hours, followed by washing with wash buffer I, II, and III, breifly spinned before scanning

scan_protocol: Scanning was done using the Nimblegen MS200 microarray scanner

data_processing:
Data was extracted from scanned image using the NimbleScan software, the raw data is processed using the pure culture microarray data analysis pipeline developed in our lab
The scanned images were gridded using the void gridding files. The local background signal for each probe was calculated as the mean signal intensity of the four neighbouring void spots. When all of the four neighbouring void spots were not valid, the set of eight void spots surrounding its closest neighbours was used.

organism: Shewanella loihica PV-4

source_name: Shewanella loihica PV-4 wild type

label_protocol: DNA labeling is done with Cy-3 using random primers and Klenow fragment of DNA polymerase I.  RNA is labeled with Cy5 using random primers and Reverse transcriptase II.

growth_protocol: both strains were revived from frozen stock and subsequently transferred into 50ml of LB medium, 200 rpm, 30 degree celsius.

extract_protocol: genomic DNA is extracted using the GenElute bacterial gDNA extraction kit from Sigma; RNA is extracted using trizol reagent, followed by column collection and washing using the Nucleospin RNA kit from Macherey-Nagel.

treatment_protocol: No treatment, we compare the wild type cell (non ppix accumulating) versus the PPIX accumulating deltahemH1 strain

tag: genotype

value: Wild-type

tag: phenotype

value: normal


title: 03-117 1

tag: Sex


title: PV-4 wild type 2


title: 03-117 4


title: AU565--5min-SFM--rep1

description:
Lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slide in 11x11 format. Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.
AU565-1


title: 03-117 5


title: PV-4 wild type 3


title: 03-089 3


title: PV-4 deltahemH1 2

source_name: Shewanella loihica PV-4 deltahemH1

value: delta hemH1

value: PPIX accumulating


title: 03-089 2


title: PV-4 deltahemH1 1


title: PV-4 deltahemH1 3


title: Tie2monocytes-control-4

tag: tissue


title: Tie2monocytes-ischemia-2


title: 03-089 1


title: 03-085 6


title: 03-085 4


title: Tie2monocytes-ischemia-5


title: Tie2monocytes-ischemia-1


title: 03-089 4


title: 03-089 6


title: 03-089 5


title: Tie2monocytes-control-1


title: 03-085 1


title: Tie2monocytes-control-2


title: Tie2monocytes-control-3


title: 03-079 4


title: 03-079 6


title: 03-079 5


title: 01-025 7

value: F


title: 03-065 2


title: 03-085 3


title: 03-085 2


title: 03-079 3


title: 03-065 4


title: 03-065 3


title: 03-065 5


title: 03-065 1


title: 01-009 7


title: 01-094 6


title: 03-079 2


title: 01-045 7


title: 03-079 1


title: 01-050 7


title: 01-023 7


title: 03-065 6


title: 01-025 6


title: 01-075 5


title: 01-050 5


title: 01-009 6


title: 01-023 6


title: 01-094 5


title: 01-045 5


title: 01-023 5


title: 01-009 5


title: 01-075 6


title: 01-003 5


title: 01-045 4


title: 01-094 4


title: 01-050 4


title: 01-045 6


title: 01-075 4


title: 01-025 4


title: 01-050 3


title: 01-045 3


title: 01-075 3


title: 01-094 3


title: 01-003 4


title: 01-009 4


title: 01-003 3


title: 01-025 3


title: 01-009 3


title: 01-023 3


title: 01-094 2


title: 01-023 4


title: 01-025 5


title: 01-050 2


title: 01-075 2


title: 01-045 2


title: 01-023 2


title: 01-009 2


title: 01-025 2


title: 01-094 1


title: 01-025 1

value: Y


title: 01-023 1


title: 01-050 1


title: 01-045 1


title: 01-075 1


title: 01-003 1


title: 01-009 1


title: 01-016 7


title: 01-027 7


title: 01-001 7


title: 01-027 6


title: 01-003 2


title: 01-016 6


title: 01-016 5


title: 01-027 5


title: 01-001 5


title: 01-016 3


title: 01-016 4


title: 01-027 4


title: 01-001 4


title: 01-027 3


title: 01-001 3


title: 01-027 2


title: 01-016 2


title: 01-001 2


title: 01-016 1


title: 01-027 1


title: 01-054 7


title: 01-049 7


title: 01-053 7


title: 01-052 7


title: 01-001 6


title: 01-042 7


title: 01-039 7


title: 01-040 7


title: 01-037 7


title: 01-044 7


title: 01-047 7


title: 01-028 7


title: 01-014 7


title: 01-001 1


title: 01-036 7


title: 01-034 7


title: 01-033 7


title: 01-024 7


title: 01-029 7


title: 01-020 7


title: 01-017 7


title: 01-013 7


title: 01-012 7


title: 01-030 7


title: 01-011 7


title: 01-031 7


title: 01-026 7


title: 01-005 7


title: 01-004 7


title: 01-006 7


title: 01-002 7


title: 01-010 7


title: 01-088 6


title: 01-101 6


title: 01-095 6


title: 01-090 6


title: 01-092 6


title: 01-007 7


title: 01-100 6


title: 01-081 6


title: 01-082 6


title: 01-086 6


title: 01-087 6


title: 01-074 6


title: 01-077 6


title: 01-093 6


title: 01-078 6


title: 01-068 6


title: 01-076 6


title: 01-052 6


title: 01-070 6


title: 01-073 6


title: 01-072 6


title: 01-071 6


title: 01-069 6


title: 01-080 6


title: 01-066 6


title: 01-063 6


title: 01-064 6


title: 01-047 6


title: 01-048 6


title: 01-053 6


title: 01-046 6


title: 01-054 6


title: 01-040 6


title: 01-044 6


title: 01-034 6


title: 01-037 6


title: 01-033 6


title: 01-042 6


title: 01-029 6


title: 01-049 6


title: 01-039 6


title: 01-036 6


title: 01-013 6


title: 01-032 6


title: 01-031 6


title: 01-017 6


title: 01-030 6


title: 01-006 6


title: 01-004 6


title: 01-007 6


title: 01-118 5


title: 01-026 6


title: 01-024 6


title: 01-028 6


title: 01-014 6


title: 01-112 5


title: 01-002 6


title: 01-020 6


title: 01-119 5


title: 01-011 6


title: 01-010 6


title: 01-095 5


title: 01-100 5


title: 01-005 6


title: 01-116 5


title: 01-092 5


title: 01-012 6


title: 01-101 5


title: 01-081 5


title: 01-080 5


title: 01-093 5


title: 01-074 5


title: 01-087 5


title: 01-086 5


title: 01-090 5


title: 01-114 5


title: 01-082 5


title: 01-088 5


title: 01-073 5


title: 01-113 5


title: 01-053 5


title: 01-064 5


title: 01-077 5


title: 01-069 5


title: 01-047 5


title: 01-068 5


title: 01-066 5


title: 01-052 5


title: 01-078 5


title: 01-048 5


title: 01-054 5


title: 01-039 5


title: 01-042 5


title: 01-072 5


title: 01-063 5


title: 01-040 5


title: 01-071 5


title: 01-030 5


title: 01-044 5


title: 01-046 5


title: 01-034 5


title: 01-033 5


title: 01-049 5


title: 01-029 5


title: 01-031 5


title: 01-036 5


title: 01-024 5


title: 01-032 5


title: 01-013 5


title: 01-012 5


title: 01-010 5


title: 01-014 5


title: 01-026 5


title: 01-004 5


title: 01-028 5


title: 01-037 5


title: 01-017 5


title: 01-011 5


title: 01-118 4


title: 01-119 4


title: 01-006 5


title: 01-007 5


title: 01-116 4


title: 01-101 4


title: 01-113 4


title: 01-095 4


title: 01-100 4


title: 01-114 4


title: 01-092 4


title: 01-002 5


title: 01-005 5


title: 01-088 4


title: 01-020 5


title: 01-112 4


title: 01-086 4


title: 01-082 4


title: 01-081 4


title: 01-087 4


title: 01-093 4


title: 01-078 4


title: 01-080 4


title: 01-090 4


title: 01-072 4


title: 01-071 4


title: 01-074 4


title: 01-073 4


title: 01-077 4


title: 01-076 4


title: 01-070 4


title: 01-066 4


title: 01-068 4


title: 01-048 4


title: 01-047 4


title: 01-046 4


title: 01-054 4


title: 01-053 4


title: 01-052 4


title: 01-063 4


title: 01-040 4


title: 01-034 4


title: 01-032 4


title: 01-033 4


title: 01-064 4


title: 01-044 4


title: 01-070 5


title: 01-042 4


title: 01-036 4


title: 01-039 4


title: 01-037 4


title: 01-069 4


title: 01-020 4


title: 01-024 4


title: 01-030 4


title: 01-031 4


title: 01-029 4


title: 01-076 5


title: 01-049 4


title: 01-014 4


title: 01-006 4


title: 01-004 4


title: 01-007 4


title: 01-026 4


title: 01-002 4


title: 01-005 4


title: 01-012 4


title: 01-119 3


title: 01-114 3


title: 01-010 4


title: 01-017 4


title: 01-013 4


title: 01-101 3


title: 01-093 3


title: 01-118 3


title: 01-116 3


title: 01-112 3


title: 01-095 3


title: 01-090 3


title: 01-100 3


title: 01-087 3


title: 01-092 3


title: 01-082 3


title: 01-081 3


title: 01-071 3


title: 01-077 3


title: 01-073 3


title: 01-011 4


title: 01-086 3


title: 01-068 3


title: 01-063 3


title: 01-072 3


title: 01-078 3


title: 01-080 3


title: 01-113 3


title: 01-074 3


title: 01-049 3


title: 01-069 3


title: 01-066 3


title: 01-040 3


title: 01-039 3


title: 01-037 3


title: 01-053 3


title: 01-088 3


title: 01-047 3


title: 01-054 3


title: 01-042 3


title: 01-031 3


title: 01-044 3


title: 01-026 3


title: 01-034 3


title: 01-014 3


title: 01-032 3


title: 01-033 3


title: 01-036 3


title: 01-012 3


title: 01-005 3


title: 01-006 3


title: 01-020 3


title: 01-030 3


title: 01-046 3


title: 01-029 3


title: 01-002 3


title: 01-116 2


title: 01-112 2


title: 01-013 3


title: 01-114 2


title: 01-010 3


title: 01-007 3


title: 01-011 3


title: 01-095 2


title: 01-118 2


title: 01-004 3


title: 01-119 2


title: 01-101 2


title: 01-113 2


title: 01-087 2


title: 01-086 2


title: 01-092 2


title: 01-090 2


title: 01-100 2


title: 01-093 2


title: 01-078 2


title: 01-080 2


title: 01-088 2


title: 01-073 2


title: 01-070 2


title: 01-072 2


title: 01-081 2


title: 01-017 3


title: 01-063 2


title: 01-077 2


title: 01-049 2


title: 01-074 2


title: 01-053 2


title: 01-064 2


title: 01-076 2


title: 01-054 2


title: 01-071 2


title: 01-068 2


title: 01-069 2


title: 01-066 2


title: 01-044 2


title: 01-046 2


title: 01-042 2


title: 01-037 2


title: 01-033 2


title: 01-082 2


title: 01-030 2


title: 01-052 2


title: 01-048 2


title: 01-039 2


title: 01-040 2


title: 01-024 2


title: 01-014 2


title: 01-017 2


title: 01-031 2


title: 01-036 2


title: 01-026 2


title: 01-034 2


title: 01-013 2


title: 01-028 2


title: 01-029 2


title: 01-020 2


title: 01-119 1


title: 01-047 2


title: 01-012 2


title: 01-011 2


title: 01-005 2


title: 01-007 2


title: 01-010 2


title: 01-002 2


title: 01-113 1


title: 01-118 1


title: 01-100 1


title: 01-116 1


title: Visceral adipose tissue subject 7

city: Mexico City

first: Esau

middle: Floriano

last: Sanchez

address: Cerrada de Palomas SN

department: Military School of Graduate of Health

country: Mexico

institute: SEDENA

description:
VAT-7
Biological replicate 7 of 8. Visceral adipose tissue.

hyb_protocol: The fragmented, labeled cRNAs were hybridized to Agilent-039494 SurePrint Human GE 8x60K Microarrays for 17.5 h at 6ºC. The quality control parameters used for cRNA labeling and hybridization were specified the manufacturers.

scan_protocol: The arrays were scanned using a NimbleGen microarray scanner (Roche), and the signal intensities in TIFF images were calculated using Feature Extraction software (FE, version 12.0; Agilent Technologies, Palo Alto, CA). All of the arrays were scanned and quantified using Feature Extraction software.

data_processing: The relative expression of 16 slides were imported in GeneSpring GX software version 13.0 (Agilent Inc., California), a global gene comparison of tissues was using the gene annotations available in June 2016. The signal intensity was normalized using Lowess method, taking the relative abundances of all slides. A two-tailed student’s t-test was used to determine significance of the differences observed between the SAT and VAT samples. Benjamini Hochberg algorithm was used to compute the false discovery rate. The final lists of genes differentially expressed were chosen based on p-value threshold of ≤ 0.05 and by at least two-fold change for each tissue.

source_name: visceral adipose tissue, obese

label_protocol: The synthesis of cDNA and subsequent fluorescent labeling of cRNA were performed using eight replicates for both the control (n=8) and obese (n=8) groups, according to the manufacturer’s protocol (Two-Color Microarray-Based Gene Expression Analysis/Low Input Quick Amp Labeling; Agilent Technologies, Palo Alto, CA). Briefly, 25 ng of total RNA was converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNAs.

extract_protocol: SAT and VAT samples were obtained from each patient. SAT was obtained at a location approximately 2 cm deep in the abdominal skin. VAT was obtained during inguinal hernia repair and laparoscopic cholecystectomy. The biopsy samples were immediately frozen on ice and maintained at -80ºC until analysis. Isolation of total RNA from the frozen adipose tissues was performed using an RNeasy Lipid Tissue Mini Kit (Qiagen, Germany). RNA quality and integrity were assessed using QIAxcel and QIAxpert equipment (Qiagen, Germany).

value: visceral adipose tissue

tag: disease status

value: obese

tag: population

value: Mexican

tag: subject identifier

source_name: visceral adipose tissue, control

tag: sample type

value: control


title: Visceral adipose tissue subject 3

description:
VAT-3
Biological replicate 3 of 8. Visceral adipose tissue.


title: 01-114 1

tag: subject id


title: Visceral adipose tissue subject 6

description:
VAT-6
Biological replicate 6 of 8. Visceral adipose tissue.


title: Visceral adipose tissue subject 8

description:
VAT-8
Biological replicate 8 of 8. Visceral adipose tissue.


title: Visceral adipose tissue subject 5

description:
VAT-5
Biological replicate 5 of 8. Visceral adipose tissue.


title: 01-101 1

tag: visit number (1 = baseline)


title: Visceral adipose tissue subject 4

description:
VAT-4
Biological replicate 4 of 8. Visceral adipose tissue.


title: 01-090 1

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: Visceral adipose tissue subject 2

description:
VAT-2
Biological replicate 2 of 8. Visceral adipose tissue.


title: 01-095 1

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: 01-088 1

tag: illness duration (days of illness prior to treatment beginning)


title: 01-093 1

tag: # of symptoms


title: 01-006 2

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 01-092 1

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 01-112 1

tag: mcgill pain total score (range 0-45)


title: 01-004 2


title: 01-087 1


title: 01-080 1


title: 01-081 1


title: Subcutaneous adipose tissue subject 8

description:
SAT-8
Biological replicate 8 of 8. Subcutaneous adipose tissue.

source_name: subcutaneous adipose tissue, obese

value: subcutaneous adipose tissue

source_name: subcutaneous adipose tissue, control


title: Visceral adipose tissue subject 1

description:
VAT-1
Biological replicate 1 of 8. Visceral adipose tissue.


title: Subcutaneous adipose tissue subject 7

description:
SAT-7
Biological replicate 7 of 8. Subcutaneous adipose tissue.


title: 01-071 1


title: Subcutaneous adipose tissue subject 6

description:
SAT-6
Biological replicate 6 of 8. Subcutaneous adipose tissue.


title: Subcutaneous adipose tissue subject 5

description:
SAT-5
Biological replicate 5 of 8. Subcutaneous adipose tissue.


title: 01-073 1


title: Subcutaneous adipose tissue subject 3

description:
SAT-3
Biological replicate 3 of 8. Subcutaneous adipose tissue.


title: Subcutaneous adipose tissue subject 2

description:
SAT-2
Biological replicate 2 of 8. Subcutaneous adipose tissue.


title: Subcutaneous adipose tissue subject 1

description:
SAT-1
Biological replicate 1 of 8. Subcutaneous adipose tissue.


title: Subcutaneous adipose tissue subject 4

description:
SAT-4
Biological replicate 4 of 8. Subcutaneous adipose tissue.


title: 01-082 1


title: 01-076 1


title: 01-074 1


title: 01-072 1


title: 01-054 1


title: 01-063 1


title: 01-070 1


title: 01-077 1


title: 01-078 1


title: 01-052 1


title: 01-086 1


title: 01-068 1


title: 01-064 1


title: 01-069 1


title: 01-066 1


title: 01-053 1


title: 01-044 1


title: 01-048 1


title: 01-047 1


title: 01-046 1


title: 01-049 1


title: 01-036 1


title: 01-037 1


title: 01-034 1


title: 01-042 1


title: Act.T4.IL12.8h#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: spleen

tag: cytokine

tag: treatment time

tag: age

value: 6 Weeks Old

tag: genetic background

value: Male

tag: cell family

value: CD4+ T cell

tag: phenotype markers

tag: source prep description

value: EasySep Neg Sel. & IL12 in vitro

tag: separation method

value: Dissection / Trimming

tag: amplification technique

value: Ambion WT Expression Kit


title: 01-040 1

tag: subject id

tag: visit number (1 = baseline)

tag: Sex


title: 01-033 1

value: M

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

value: N

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)


title: 01-039 1

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: Act.T4.IL12.8h#2

tag: tissue

tag: cytokine

tag: treatment time


title: Act.T4.Baseline#5

value: Untreated

value: Baseline

tag: age

tag: genetic background

tag: cell family

value: EasySep Neg Sel. & untreated  in vitro


title: Act.T4.IL12.2h#3

tag: phenotype markers

tag: source prep description

tag: separation method


title: Act.T4.Unt.2h#7

tag: amplification technique


title: Act.T4.IL12.2h#2

tag: Sex


title: Act.T4.Unt.2h#8


title: Act.T4.IL12.8h#6


title: Act.T4.IL12.2h#5


title: Act.T4.IL12.2h#4


title: 01-030 1

tag: subject id

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

value: Y

tag: mcgill pain total score (range 0-45)


title: Act.T4.IL12.8h#5


title: Act.T4.IFN.8h#1

value: IFNa

value: EasySep Neg Sel. & IFNa+/-JAK inhibitors in vitro


title: Act.T4.IL12.2h#6


title: Act.T4.IFN.2h#1


title: Act.T4.Baseline#2

value: untreated

value: baseline

value: EasySep Neg Sel. & untreated in vitro


title: 01-032 1

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 01-020 1

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 01-031 1

value: F


title: Act.T4.IFN.2485.2h#1

tag: tissue

value: spleen

tag: jak inhibitor

tag: treatment time

tag: age

value: 6 Weeks Old

value: Male

value: CD4 T cell


title: Act.T4.Baseline#1

tag: cytokine

tag: genetic background

tag: cell family

value: CD4+ T cell

tag: phenotype markers

tag: source prep description

value: Dissection / Trimming

value: Ambion WT Expression Kit


title: 01-028 1

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

value: M

value: N


title: 01-024 1

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: mcgill pain total score (range 0-45)


title: 01-026 1

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: Act.T4.IFN.3404.2h#1

tag: tissue

tag: jak inhibitor

tag: separation method

tag: amplification technique


title: 01-013 1

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: Act.T4.IFN.2485.8h#1

tag: treatment time

tag: age

tag: genetic background

tag: cell family


title: 01-017 1

tag: subject id

tag: visit number (1 = baseline)


title: 01-029 1

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: 01-012 1

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: mcgill pain total score (range 0-45)


title: Act.T4.IFN.3404.8h#1

tag: phenotype markers

tag: source prep description


title: 01-006 1

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 01-007 1


title: 01-014 1


title: 01-005 1


title: Act.T4.IFN.6221.2h#1

tag: tissue

tag: jak inhibitor

tag: separation method

tag: amplification technique


title: Act.T4.IFN.3885.2h#1

tag: treatment time

tag: age

tag: genetic background


title: 01-010 1

tag: subject id

tag: visit number (1 = baseline)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: Act.T4.IFN.6222.8h#1

value: PAN

tag: Sex

tag: cell family


title: 01-011 1

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

value: Y

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: mcgill pain total score (range 0-45)


title: Act.T4.IFN.6221.8h#1

tag: phenotype markers

tag: source prep description


title: Act.T4.IFN.6226.8h#1

tag: tissue


title: Act.T4.IFN.6226.2h#1

tag: jak inhibitor


title: 01-004 1

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: Act.T4.IFN.3885.8h#1

tag: treatment time

tag: age

tag: separation method

tag: amplification technique


title: 01-002 1

tag: subject id

tag: visit number (1 = baseline)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 02-083 4

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: 02-059 4

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: mcgill pain total score (range 0-45)


title: NK.IL2.250u#1_reanalyzed

tag: cytokine

tag: genetic background

tag: cell family

value: NK cell

tag: phenotype markers

tag: source prep description

value: EasySep Neg Sel. & IL2 in vitro


title: NK.IL2.250u#2_reanalyzed

tag: tissue


title: 02-084 4

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: Act.T4.IFN.6228.8h#1

tag: jak inhibitor

tag: treatment time

tag: age

value: EasySep Neg Sel. & IFNa+/-JAK inhibitors in vitro

tag: separation method

tag: amplification technique


title: NK.IL2.250U.8h#4_reanalyzed

tag: Sex


title: Act.T4.IFN.6222.2h#1


title: 02-056 4

tag: subject id

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 02-057 4

tag: mcgill pain total score (range 0-45)


title: 02-058 4


title: 02-102 4


title: 02-055 4


title: NK.Unt.8h#3_reanalyzed

tag: cytokine

value: untreated

tag: genetic background

tag: cell family

tag: phenotype markers

tag: source prep description


title: 02-022 4

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 02-021 4


title: Act.T4.IFN.6228.2h#1

tag: tissue

tag: jak inhibitor

tag: treatment time

tag: age

tag: separation method


title: 02-041 4

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: 02-019 4

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: NK.Unt#2_reanalyzed

tag: cytokine

tag: genetic background

tag: cell family

tag: phenotype markers

value: EasySep Neg Sel. & untreated in vitro

tag: amplification technique


title: 02-018 4

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: NK.IL2.250U.3404.0.25uM#2

tag: tissue

tag: jak inhinitor

tag: concentration

tag: age

tag: source prep description

value: EasySep Neg Sel. & IL2+/-JAK inhibitors in vitro


title: NK.IL2.250U.8h#3_reanalyzed

value: spleen

tag: treatment time

tag: Sex

tag: separation method


title: NK.IL2.250U.6226.0.25uM#2

value: 6 Weeks Old


title: NK.IL2.250U.3404.0.0625uM#1

value: Male


title: NK.Unt.8h#4_reanalyzed


title: NK.IL2.250U.3404.4uM#2


title: NK.IL2.250U.3404.1uM#2


title: 02-098 3

tag: subject id

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: 02-102 3

tag: illness duration (days of illness prior to treatment beginning)


title: NK.IL2.250u.6226.4um#1

tag: genetic background

tag: cell family

tag: phenotype markers

tag: amplification technique


title: 02-096 3

value: F

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 02-097 3


title: NK.IL2.250U.6226.1uM#2

tag: tissue

tag: jak inhinitor

tag: concentration

tag: age

tag: source prep description


title: 02-060 3

tag: subject id

tag: visit number (1 = baseline)

tag: Sex


title: 02-058 3

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 02-083 3

tag: illness duration (days of illness prior to treatment beginning)

tag: mcgill pain total score (range 0-45)


title: NK.IL2.250U.6226.4uM#2

tag: genetic background

tag: cell family

tag: phenotype markers

tag: separation method


title: 02-061 3

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: NK.IL2.250U.8h#3

tag: tissue

tag: jak inhinitor

value: IL2 only

tag: concentration

tag: amplification technique


title: NK.IL2.250U.8h#4

tag: age

tag: source prep description

value: Dissection / Trimming


title: 02-059 3

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: 02-041 3

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: NK.Unt.8h#3

tag: genetic background

tag: cell family

tag: phenotype markers

tag: separation method

value: Ambion WT Expression Kit


title: 02-084 3

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: NK.IL2.250u#1

tag: tissue

tag: jak inhinitor

tag: concentration

tag: amplification technique


title: NK.IL2.250u.3404.1um#1

tag: age

tag: source prep description


title: 02-055 3

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

value: M

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: NK.IL2.250u#2


title: NK.IL2.250u.3404.0.25um#1


title: NK.IL2.250u.6226.0.25um#1


title: 02-056 3

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: NK.IL2.250u.6226.1um#1

tag: genetic background

tag: cell family

tag: phenotype markers

tag: separation method


title: 02-021 3

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: NK.Unt.8h#4

tag: tissue

tag: jak inhinitor

tag: concentration

tag: amplification technique


title: Act.B.DMSO.CCM.2h#3

tag: cytokine

tag: treatment time

tag: age

value: B cell

tag: source prep description


title: 02-057 3

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)


title: Act.B.DMSO.CCM.2h#2

tag: genetic background

tag: cell family

tag: phenotype markers

tag: separation method


title: NK.Unt#2

tag: tissue

tag: jak inhinitor


title: Act.B.IFN.2h#2

value: IFNa

tag: amplification technique


title: 02-019 3

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: Act.B.IFN.2h#3

tag: cytokine

tag: treatment time

tag: age

tag: source prep description


title: 02-018 3

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: 02-022 3

tag: illness duration (days of illness prior to treatment beginning)


title: 02-111 2


title: Act.B.IFN.8h#3

tag: tissue

tag: genetic background

tag: cell family

tag: phenotype markers

tag: separation method


title: Act.B.IFN.8h#2

tag: amplification technique


title: 02-110 2

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: Act.B.IFN.6228.8h#1

tag: jak inhibitor

tag: treatment time

tag: age

tag: source prep description


title: 02-108 2

tag: subject id

tag: visit number (1 = baseline)

tag: Sex

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: Act.B.IFN.6228.2h#1

tag: tissue

tag: genetic background


title: 02-109 2

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)


title: 02-106 2


title: 02-104 2


title: 02-105 2


title: 02-102 2


title: 02-103 2


title: Act.B.IFN.6222.2h#1

value: PAN

tag: cell family

tag: phenotype markers

tag: separation method

tag: amplification technique


title: Act.B.IFN.6222.8h#1


title: 02-098 2

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: Act.B.IFN.6226.8h#1

tag: jak inhibitor

tag: treatment time

tag: age

tag: source prep description


title: Act.B.IFN.6226.2h#1

tag: Sex


title: Act.B.IFN.3885.8h#1

tag: tissue


title: Act.B.IFN.3885.2h#1

tag: genetic background


title: 02-097 2

tag: subject id

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: Act.B.IFN.6221.2h#1

tag: cell family

tag: phenotype markers

tag: separation method


title: 02-096 2

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]


title: 02-084 2

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: Act.B.IFN.3404.2h#1

tag: jak inhibitor

tag: treatment time

tag: age

tag: amplification technique


title: 02-060 2

tag: Sex


title: 02-083 2

tag: subject id


title: 02-061 2

tag: visit number (1 = baseline)


title: 02-058 2

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]


title: 02-059 2

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: Act.B.IFN.3404.8h#1

tag: tissue

tag: genetic background

tag: cell family

tag: source prep description


title: Act.B.IFN.2845.8h#1

tag: phenotype markers

tag: separation method


title: Act.B.IFN.2845.2h#1


title: Act.B.IFN.6221.8h#1


title: 02-057 2

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: Act.B.Baseline#1

tag: jak inhibitor

value: Untreated

tag: treatment time

value: baseline

tag: age

value: EasySep Neg Sel. & untreated  in vitro


title: Act.B.IFN.6228.8h#2

tag: Sex

value: EasySep Neg Sel. & IFNa+/-JAK inhibitors in vitro

tag: amplification technique


title: 02-056 2

tag: subject id

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: mcgill pain total score (range 0-45)


title: Act.B.Baseline#2

tag: tissue

tag: genetic background

tag: cell family


title: 02-022 2

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: 02-055 2

tag: illness duration (days of illness prior to treatment beginning)


title: 02-021 2

tag: # of symptoms


title: Act.B.IFN.6228.2h#2

tag: phenotype markers

tag: source prep description

tag: separation method


title: Act.B.IFN.6226.2h#3

tag: jak inhibitor

tag: treatment time


title: 02-018 2

tag: Sex

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: 02-111 1

tag: subject id

tag: visit number (1 = baseline)

value: N


title: 02-110 1

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: mcgill pain total score (range 0-45)


title: 02-041 2


title: 02-108 1


title: 02-109 1


title: 02-106 1


title: Act.B.IFN.6226.8h#2

tag: tissue

tag: age

tag: genetic background

tag: amplification technique


title: 02-105 1

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms


title: 02-019 2


title: Act.B.IFN.6221.2h#2

tag: cell family

tag: phenotype markers

tag: source prep description

tag: separation method


title: Act.B.IFN.6222.2h#2

tag: jak inhibitor

tag: treatment time

tag: Sex


title: Act.B.IFN.6226.2h#2


title: Act.B.IFN.6221.8h#2


title: Act.B.IFN.6226.8h#3


title: 02-103 1

tag: subject id

tag: visit number (1 = baseline)

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]


title: Act.B.IFN.3885.8h#3

tag: tissue

tag: age


title: 02-104 1

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: mcgill pain total score (range 0-45)


title: Act.B.IFN.3404.8h#2

tag: genetic background

tag: amplification technique


title: Act.B.IFN.3404.2h#2

tag: cell family


title: Act.B.IFN.6222.8h#2

tag: phenotype markers


title: Act.B.IFN.3885.2h#2

tag: source prep description


title: Act.B.IFN.2845.8h#2

tag: separation method


title: eWAT, Rev-erb alpha KO replicate 3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Standard Affymetrix protocol

scan_protocol: The array was read by GCS3000 laser scanner (Affymetrix).

data_processing: Raw data were preprocessed and normalized using affy package in Bioconductor.

source_name: Epididymal white adipose tissue

label_protocol: Each RNA sample was processed with the Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix).

extract_protocol: Total RNA was isolated from tissues using TRIzol (Invitrogen) followed by purification with the RNEasy mini kit (Qiagen).  1μg of purified RNA was used to generate cDNA (Applied Biosystems).

treatment_protocol: Mice were maintained on a standard diet under 12h-light/12h-dark (LD) cycles. The experiments were performed on 12-15 weeks-old males. The tissues were harvested at Zeitgeber Time (ZT) 10 (5PM) when Rev-erb alpha protein level peaks in wild type (WT) mice.

value: Epididymal white adipose tissue

tag: genotype

value: Rev-erb alpha KO

value: 12-15 weeks-old

tag: gender

value: male

tag: strain


title: eWAT, Rev-erb alpha KO replicate 2


title: 02-102 1

tag: subject id

tag: Sex

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms


title: eWAT, Rev-erb alpha KO replicate 4

tag: tissue

tag: age


title: eWAT, Rev-erb alpha KO replicate 1


title: 02-097 1

tag: visit number (1 = baseline)

value: F

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: 02-098 1


title: eWAT, Wildtype replicate 4

value: WT


title: 02-096 1


title: eWAT, Wildtype replicate 3


title: Act.B.IFN.2845.2h#2

value: spleen

tag: jak inhibitor

tag: treatment time

value: 6 Weeks Old

tag: genetic background

value: Male

tag: cell family

tag: phenotype markers

tag: source prep description

value: Dissection / Trimming

tag: amplification technique


title: 02-084 1

tag: subject id

tag: Sex

tag: multiple em (y = multiple erythema migrans lesions, n = single erythema migrans lesion)


title: 02-083 1

tag: illness duration (days of illness prior to treatment beginning)

tag: # of symptoms


title: eWAT, Wildtype replicate 2

tag: tissue

tag: genotype

tag: age

tag: gender

tag: strain


title: 02-061 1

tag: visit number (1 = baseline)

tag: elevated liver enzyme [ast, alk, or alk-phos at pre-treatment visit (v1). 0 = no, 1 = yes]

tag: fatigue severity [range from 9-63]  scores ≥36 are considered "high"]

tag: ptlds status [ptlds status  0 = returned to health, 1 = symptoms only, 2 = ptlds]

tag: mcgill pain total score (range 0-45)


title: 02-059 1

value: M


title: 02-060 1

value: Y


title: 02-055 1


title: eWAT, Wildtype replicate 1


title: 02-041 1


title: 02-021 1


title: 02-057 1


title: 02-056 1


title: 02-022 1


title: 02-019 1


title: 02-018 1


title: 02-058 1


title: 6Day_Seedling_tt8-3_Rep2

city: Singapore

first: Sanjay

last: Swarup

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description:
Gene expression in tt8-3
tt8-3_1_2 [10165]

hyb_protocol: 1.65µg of labeled cRNA was hybridized onto Agilent SurePrint G2 Agilent Arabidopsis V4 (4x44K) for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37 C. Hybridization: Gene Expression Hybridization Kit (Agilent: 5188-5242), Wash buffer: Gene Expression Wash Buffer Kit (Agilent: 5188-5327)

scan_protocol: Scanning was performed using on Agilent High Resolution Microarray Scanner (C-model)

data_processing:
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1)
Normalization method: All probes were normalized using percentile shift to 75% and were baseline corrected to the median.
Software: Agilent GeneSpring

organism: Arabidopsis thaliana

source_name: Whole seedling, 6 day old, tt8-3, replicate 2

label_protocol: 100 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) following manufacturer instruction (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, version 6.5). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.

growth_protocol:
Arabidopsis seeds were surface sterilized using 30% Clorox with seven minutes incubation. This was followed by 6 times washing with autoclaved water.
Seeds were then placed on full strength MS media with 5% sucrose and 5% Phytoagar® for 4 days before placing them in growth chamber at 22°C for 16 hr light/8 hr dark cycle with relative humidity of 60-70   and illumination 70wm-2. Seedlings were harvested 6 days.

extract_protocol: Total RNA was extracted using Omega® plant RNA extraction kit (Omega BIO-TEK) following manufacturer's guidelines. RNA was purified using an RNeasy purification kit (Qiagen).

value: Whole seedling

tag: genotype/variation

value: tt8-3 mutant


title: 6Day_Seedling_tt8-3_Rep3

description:
Gene expression in tt8-3
tt8-3_2_3 [11074]

source_name: Whole seedling, 6 day old, tt8-3, replicate 3


title: 6Day_Seedling_tt8-3_Rep4

description:
Gene expression in tt8-3
tt8-3_2_4 [11074]

source_name: Whole seedling, 6 day old, tt8-3, replicate 4


title: 6Day_Seedling_WildType_Rep1

description:
Gene expression in control
Ws_1_1 [10165]

source_name: Whole seedling, 6 day old, Ws, replicate 1

value: Control


title: 6Day_Seedling_tt8-3_Rep1

description:
Gene expression in tt8-3
tt8-3_1_1 [10165]

source_name: Whole seedling, 6 day old, tt8-3, replicate 1


title: 6Day_Seedling_WildType_Rep4

description:
Gene expression in control
Ws_2_4 [11074]

source_name: Whole seedling, 6 day old, Ws, replicate 4


title: 6Day_Seedling_WildType_Rep2

description:
Gene expression in control
Ws_1_2 [10165]

source_name: Whole seedling, 6 day old, Ws, replicate 2


title: 6Day_Seedling_WildType_Rep3

description:
Gene expression in control
Ws_2_3 [11074]

source_name: Whole seedling, 6 day old, Ws, replicate 3


title: Rep_Drought_rep2

city: Fayetteville

first: Chirag

last: Gupta

state: AR

address: 115 Plant Sciences Building

department: Crop Soil and Environmental Sciences

institute: University of Arkansas

description: Gene expression data from reproductive stage

hyb_protocol: 4 µg RNA samples were hybridized to the Affymetrix Rice Genome Array. Hybridization was done using the GeneChip Hybridization, Wash, and Stain kit.

scan_protocol: Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).

data_processing: Raw data were background corrected, normalized and summarized according to the custom CDF (GPL11322) using RMA (Irizarry et al., 2003). The custom CDF was built by uniquely mapping 442,810 probe sequences to 35,161 rice gene-based probe sets.

organism: Oryza sativa Japonica Group

source_name: Plant tissue from Reproductive stage drought lines

label_protocol: Following second-strand synthesis, in vitro transcription was performed using the GeneChip® IVT Labeling Kit.

growth_protocol: seeds were germinated in hydroponic half-strength Hoagland solution and seedlings were grown about a week in a environmentally controlled growth chambers maintained at 280c ± 1 temperature, 65% relative humidity with a daily photoperiodic cycle of 14hrs light and 10hrs dark, and then plants allowed to reach the reproductive stages were grown in soil under green house conditions. Samples of well-watered and drought stressed were collected at various developmental stages which include seven-day old seedlings, vegetative (V4) and reproductive (R4) stages based on discrete morphological criteria as described by Counce et al ( 2000).

extract_protocol: Total RNA was isolated from the rice seedlings, vegetative (V4) and reproductive (R4) tissues of both control and stress treated plants using the RNeasy plant kit (Qiagen, USA) according to  manufactures protocol. For each stage/treatment, three independent biological replicates were used for RNA isolation.

treatment_protocol: plants were gradually subjected to field drought stress in order to reach 50% field capacity (FC) by regulating the water supply, where as control plants were maintained 100% FC. During the stress period the pots were weighed daily and the difference in weight on subsequent days was corrected by adding water to maintain the required field capacity. The physiological condition of plants at 50% FC was monitored by chlorophyll fluorescence, quantum yield (Fv/Fm) and the relative water content (RWC).

tag: cultivar

value: Nipponbare

tag: developmental stage

value: reproductive (R4)


title: Rep_Drought_rep1


title: Veg_Ctrl_rep1

description: Gene expression data from vegetative stage

source_name: Plant tissue from Vegetative stage control lines

value: vegetative (V4)


title: Veg_Ctrl_rep3


title: Seedling_Ctrl_rep2

description: Gene expression data from seedling stage

source_name: Plant tissue from Seedling stage control lines

value: seedling


title: Seedling_Ctrl_rep1


title: Rep_Ctrl_rep2

source_name: Plant tissue from Reproductive stage control lines


title: ABYSF3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: raw data file: ABYSF34_252828211748_1.txt

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

organism: Rattus norvegicus

source_name: prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30; controls received vehicle (normal saline) instead. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four females. The rats prenatally exposed (G15) to betamethasone had repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with either ATCH, PMX53 (a potent C5ar1 antagonist) or saline to act as a control, on days 13, 14 and 15 prior to NMDA administration to determine what effects each treatment had on transcriptome recovery.

value: Sprague-Dawley

tag: Sex

value: female

tag: prenatal exposure to

value: betamethasone at 0.4 mg/kg

tag: infantile spasms

value: yes

tag: postnatally treated with

value: saline

value: hypothalamic arcuate nucleus


title: Rep_Ctrl_rep1


title: ABYAF2

description: raw data file: ABYAF12_252828211750_2.txt

source_name: prenatally exposed to betamethasone_with infantile spasms_postnatally treated with ACTH P15

value: ACTH

tag: tissue


title: Veg_Drought_rep2

source_name: Plant tissue from Vegetative stage drought lines


title: ABYSF2

description: raw data file: ABYSF12_252828211748_2.txt


title: ABYAF4

description: raw data file: ASNSM2-ABYAF4_252828211750_1.txt


title: ABYAF3

description: raw data file: ASNSM1-ABYAF3_252828211742_2.txt


title: ABYPF3

description: raw data file: ABYPF34_252828211741_1.txt

source_name: prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15


title: ABYAF1


title: Seedling_Drought_rep1

source_name: Plant tissue from Seedling stage drought lines


title: Veg_Drought_rep1


title: Veg_Drought_rep3


title: ABYPF2

description: raw data file: ABYPF12_252828211741_2.txt


title: ABYPF1


title: Seedling_Drought_rep2


title: ABYPF4


title: Veg_Ctrl_rep2


title: ABNSF4

description: raw data file: ABNSF34_252828211749_1.txt

source_name: prenatally exposed to betamethasone_no infantile spasms_postnatally treated with saline P15

value: no


title: ABYSF1


title: Patient Female M368 Post-vaccine

city: Edinburgh

first: Paul

last: Dickinson

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

institute: University of Edinburgh

description: Sample name: M368B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor.  Array probe features that had a present count in one or more samples were retained.

source_name: peripheral blood

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

extract_protocol: RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: peripheral blood

value: Female

value: 10 months

tag: vaccine group

value: Measles vaccine + DTP vaccine

tag: vaccine challenge

value: Post-vaccine


title: ABYSF4


title: Patient Male M366 Post-vaccine

description: Sample name: M366B

value: Male

tag: age

value: DTP vaccine


title: Patient Female M365 Post-vaccine

description: Sample name: M365B


title: ABNSF3

tag: strain


title: Patient Female M365 Pre-vaccine

description: Sample name: M365A

value: 9 months

value: Pre-vaccine


title: Patient Female M368 Pre-vaccine

description: Sample name: M368A


title: Patient Male M363 Post-vaccine

description: Sample name: M363B

value: Measles vaccine


title: Patient Male M366 Pre-vaccine

description: Sample name: M366A


title: PMA_24H_rep3

city: Québec

first: Patricia

middle: G

last: Tremblay

state: Québec

address: 2440 Hochelaga Blvd

department: Sciences animales

country: Canada

institute: Laval University

hyb_protocol: Samples were hybridized on the human gene expression 4 × 44K v2 microarray (Agilent) using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

label_protocol: The labelling aRNA was done using the ULS Fluorescent Labelling Kit for Agilent arrays (Cy3-Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: KGN cells were cultured in supplemented with 10% FBS (Corning) DMEM/F12 (Life technologies), 100X Penicillin-Streptomycin (10,000 U/mL) (Life technologies) in an atmosphere of 5% CO2/95% O2 at 37 °C.

extract_protocol: Total RNA extraction using TRIzol Reagent (Life technologies) according to the manufacturer’s instruction. Total RNA integrity and concentration were evaluated on a 2100-Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA NanoLab Chip (Agilent Technologies). To generate enough material for hybridization, the samples were linearly amplified. Anti-sense RNA (aRNA) was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems). After two amplification rounds of 6 hrs each, the aRNA output was quantified using the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: KGN cells were thawed on day 1, placed in a 75 cm cell culture flask (Sigma-Aldrich) and subcultured on day 3. The confluence was never over 80%. On day 6, KGN cells were plated in a 6-well dish containing 3 × 105 viable cells in 3 ml of medium. KGN cells were grown for the next 24 hours before treatments. For all experimental conditions, medium was replaced by a supplemented 10% Fetal Bovine Serum, charcoal stripped (SVFA) DMEM/F12 (Life technologies), 100X Penicillin-Streptomycin (10,000 U/mL) (Life technologies) and 4-androstene-3,17-dione (A4) 100nM. KGN cells were treated for 24 hours with either ETOH 95% (less than 0.05% of final volume) for control or two other treatments such as forskolin at final concentration of 10M and PMA at final concentration of 0,1M. The experiment was repeated 4 times (4 different weeks).

value: KGN cell line (human granulosa-like cell like)

value: Dominant follicle


title: PMA_24H_rep4


title: PMA_24H_rep2


title: PMA_24H_rep1


title: Patient Male M363 Pre-vaccine

description: Sample name: M363A


title: ABNSF2

description: raw data file: ABNSF12_252828211749_2.txt

value: Sprague-Dawley

value: female

value: betamethasone at 0.4 mg/kg


title: FSK_24H_rep4


title: ASNSF4

description: raw data file: ASNSF34_252828211744_1.txt

source_name: prenatally exposed to saline_no infantile spasms_postnatally treated with saline P15

value: saline

value: hypothalamic arcuate nucleus


title: Patient Female M347 Post-vaccine

description: Sample name: M347B

value: peripheral blood


title: ASNSF1

description: raw data file: ASNSF12_252828211744_2.txt

value: no


title: ABNSF1


title: Patient Male M352 Pre-vaccine

description: Sample name: M352A


title: Patient Male M352 Post-vaccine

description: Sample name: M352B

value: 10 months


title: Human LEC sample 3

city: Baltimore

first: Jonathan

middle: S

last: Bromberg

address: 800 West Baltimore Street

department: Center for Vascular and inflammatory Diseases

institute: University of Maryland School of Medicine

description: This is one of the triplicates of human LEC.

hyb_protocol: GeneChip® Mouse Gene 2.0 ST Array and GeneChip® Human Gene 2.0 ST Array

data_processing: Transcriptome Analysis Console v3.0 (Affymetrix). Processed with RMA.

source_name: primary LEC

growth_protocol:
SVEC4-10 were cultured in Dulbecco's modified Eagle's medium with 4 mM Lglutamine adjusted to contain 1.5 g/L sodium bicarbonate and 4.5 g/L glucose, 90%; heatinactivated fetal bovine serum, 10%.
Mouse LEC were cultured in mouse endothelial Cell Medium supplemented with 5% FBS, 2 mM L-glutamine, 100 IU/ml penicillin, VEGF, ECGS, Heparin, EGF, hydrocortisone; human endothelial cell medium with 10% FBS, 2% endothelial cell supplement, 2 mM L-glutamine, 100 IU/ml penicillin, VEGF, Heparin, EGF, FGF, hydrocortisone
human LEC were cultured in human endothelial cells medium supplemented with 5% FBS, 2 mM L-glutamine, 100 IU/ml penicillin, VEGF, ECGS, Heparin, EGF, hydrocortisone; human endothelial cell medium with 10% FBS, 2% endothelial cell supplement, 2 mM L-glutamine, 100 IU/ml penicillin, VEGF, Heparin, EGF, FGF, hydrocortisone

extract_protocol: Qiagen Rneasy Mini Kit (Cat No. 74104)

tag: cell type

value: primary lymphatic endothelial cells


title: ASNSF2


title: FSK_24H_rep3


title: Patient Female M343 Pre-vaccine

description: Sample name: M343A

value: Female

value: Measles vaccine + DTP vaccine


title: ASNSF3


title: Patient Male M354 Post-vaccine

description: Sample name: M354B

value: Male

value: Post-vaccine


title: Patient Male M361 Pre-vaccine

description: Sample name: M361A

value: 9 months

value: DTP vaccine

value: Pre-vaccine


title: Patient Male M361 Post-vaccine

description: Sample name: M361B


title: Patient Female M350 Pre-vaccine

description: Sample name: M350A


title: Patient Female M343 Post-vaccine

description: Sample name: M343B


title: FSK_24H_rep2

value: KGN cell line (human granulosa-like cell like)

value: Dominant follicle


title: Patient Female M347 Pre-vaccine

description: Sample name: M347A


title: FSK_24H_rep1


title: Patient Female M339 Post-vaccine

description: Sample name: M339B

value: Measles vaccine


title: Patient Female M342 Post-vaccine

description: Sample name: M342B


title: Human LEC sample 2

scan_protocol: GeneChip® Mouse Gene 2.0 ST Array and GeneChip® Human Gene 2.0 ST Array


title: Mouse LEC sample 3

description: This is one of the triplicates of mouse LEC.

label_protocol: GeneChip® Mouse Gene 2.0 ST Array and GeneChip® Human Gene 2.0 ST Array

value: skin dermal primary lymphatic endothelial cells


title: Patient Male M338 Post-vaccine

description: Sample name: M338B


title: Human LEC sample 1


title: BX_M3_P6641

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: 3month kidney biopsy post transplant

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console and Batch effects from different labeling protocols were adjusted using the ComBat R package (Johnson WE)

source_name: 3 month kidney biopsy post transplant

label_protocol:
pico
ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation PICO amplification kit (NuGen, San Carlos, CA) was applied.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from percutaneous allograft biopsy samples obtained at 3 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: not applicable

tag: tissue type

value: percutaneous allograft biopsy

tag: m3 cadi

tag: m12 cadi


title: Patient Male M335 Post-vaccine

description: Sample name: M335B


title: BX_M3_P36051

description: 3month kidney biopsy post transplant


title: Patient Female M339 Pre-vaccine

description: Sample name: M339A


title: Patient Female M334 Pre-vaccine

description: Sample name: M334A


title: SVEC4-10 sample 3

description: This is one of the triplicates of SVEC4-10.

source_name: SVEC4-10 lymphatic cell line

tag: cell line


title: SVEC4-10 sample 2


title: Patient Female M334 Post-vaccine

description: Sample name: M334B


title: BX_M3_P36244

description: 3month kidney biopsy post transplant

label_protocol:
encor
ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip. For samples with a low RNA concentration, the Nugen Ovation PICO amplification kit (NuGen, San Carlos, CA) was applied.


title: BX_M3_P27107

description: 3month kidney biopsy post transplant


title: Patient Male M335 Pre-vaccine

description: Sample name: M335A


title: Patient Female M341 Pre-vaccine

description: Sample name: M341A


title: Mouse LEC sample 2


title: BX_M3_P35925

description: 3month kidney biopsy post transplant


title: Patient Female M326 Post-vaccine

description: Sample name: M326B


title: Mouse LEC sample 1


title: Patient Male M329 Pre-vaccine

description: Sample name: M329A


title: Patient Male M329 Post-vaccine

description: Sample name: M329B


title: Patient Female M337 Pre-vaccine

description: Sample name: M337A


title: Patient Male M328 Post-vaccine

description: Sample name: M328B


title: Patient Male M338 Pre-vaccine

description: Sample name: M338A


title: Patient Female M326 Pre-vaccine

description: Sample name: M326A


title: Patient Male M328 Pre-vaccine

description: Sample name: M328A


title: SVEC4-10 sample 1


title: Patient Male M311 Post-vaccine

description: Sample name: M311B


title: BX_M3_P13799

description: 3month kidney biopsy post transplant


title: BX_M3_P34400

description: 3month kidney biopsy post transplant


title: BX_M3_P33263

description: 3month kidney biopsy post transplant


title: Patient Male M310 Post-vaccine

description: Sample name: M310B


title: Patient Male M310 Pre-vaccine

description: Sample name: M310A


title: BX_M3_P14027

description: 3month kidney biopsy post transplant


title: BX_M3_P36682

description: 3month kidney biopsy post transplant


title: Patient Male M311 Pre-vaccine

description: Sample name: M311A


title: Patient Female M308 Pre-vaccine

description: Sample name: M308A


title: Patient Female M313 Pre-vaccine

description: Sample name: M313A


title: BX_M3_P35241

description: 3month kidney biopsy post transplant


title: BX_M3_P30944

description: 3month kidney biopsy post transplant


title: Patient Male M312 Pre-vaccine

description: Sample name: M312A


title: Patient Female M308 Post-vaccine

description: Sample name: M308B


title: Patient Male M305 Post-vaccine

description: Sample name: M305B


title: Patient Female M313 Post-vaccine

description: Sample name: M313B


title: BX_M3_P35866

description: 3month kidney biopsy post transplant


title: BX_M3_P15517

description: 3month kidney biopsy post transplant


title: Patient Male M321 Pre-vaccine

description: Sample name: M321A


title: Patient Male M307 Pre-vaccine

description: Sample name: M307A


title: Patient Male M312 Post-vaccine

description: Sample name: M312B


title: Patient Male M321 Post-vaccine

description: Sample name: M321B


title: Patient Male M307 Post-vaccine

description: Sample name: M307B


title: Patient Female M324 Pre-vaccine

description: Sample name: M324A


title: BX_M3_P29561

description: 3month kidney biopsy post transplant


title: BX_M3_P28901

description: 3month kidney biopsy post transplant


title: BX_M3_P24797

description: 3month kidney biopsy post transplant


title: BX_M3_P29934

description: 3month kidney biopsy post transplant


title: Patient Male M305 Pre-vaccine

description: Sample name: M305A


title: Patient Female M301 Post-vaccine

description: Sample name: M301B


title: BX_M3_P26670

description: 3month kidney biopsy post transplant


title: Patient Male M302 Post-vaccine

description: Sample name: M302B


title: Patient Male M300 Pre-vaccine

description: Sample name: M300A


title: Patient Female M304 Post-vaccine

description: Sample name: M304B


title: Patient Female M299 Post-vaccine

description: Sample name: M299B


title: BX_M3_P15811

description: 3month kidney biopsy post transplant


title: BX_M3_P29719

description: 3month kidney biopsy post transplant


title: Patient Male M300 Post-vaccine

description: Sample name: M300B


title: Patient Female M325 Post-vaccine

description: Sample name: M325B


title: Patient Female M291 Post-vaccine

description: Sample name: M291B


title: BX_M3_P22987

description: 3month kidney biopsy post transplant


title: BX_M3_P27071

description: 3month kidney biopsy post transplant


title: Patient Male M302 Pre-vaccine

description: Sample name: M302A


title: Patient Female M295 Pre-vaccine

description: Sample name: M295A


title: Patient Female M325 Pre-vaccine

description: Sample name: M325A


title: Patient Female M304 Pre-vaccine

description: Sample name: M304A


title: Patient Female M292 Post-vaccine

description: Sample name: M292B


title: Patient Male M296 Post-vaccine

description: Sample name: M296B


title: Patient Female M301 Pre-vaccine

description: Sample name: M301A


title: Patient Female M291 Pre-vaccine

description: Sample name: M291A


title: Patient Female M295 Post-vaccine

description: Sample name: M295B


title: Patient Female M292 Pre-vaccine

description: Sample name: M292A


title: BX_M3_P22830

description: 3month kidney biopsy post transplant


title: Patient Male M296 Pre-vaccine

description: Sample name: M296A


title: Patient Female M324 Post-vaccine

description: Sample name: M324B


title: BX_M3_P22526

description: 3month kidney biopsy post transplant


title: BX_M3_P21008

description: 3month kidney biopsy post transplant


title: Patient Female M288 Post-vaccine

description: Sample name: M288B


title: BX_M3_P21279

description: 3month kidney biopsy post transplant


title: BX_M3_P21093

description: 3month kidney biopsy post transplant


title: BX_M3_P20787

description: 3month kidney biopsy post transplant


title: Patient Female M281 Pre-vaccine

description: Sample name: M281A


title: BX_M3_P20891

description: 3month kidney biopsy post transplant


title: Patient Female M279 Pre-vaccine

description: Sample name: M279A


title: Patient Male M285 Pre-vaccine

description: Sample name: M285A


title: Patient Male M277 Post-vaccine

description: Sample name: M277B


title: Patient Male M287 Post-vaccine

description: Sample name: M287B


title: Patient Female M278 Pre-vaccine

description: Sample name: M278A


title: Patient Male M285 Post-vaccine

description: Sample name: M285B


title: BX_M3_P19884

description: 3month kidney biopsy post transplant


title: BX_M3_P19996

description: 3month kidney biopsy post transplant


title: Patient Female M271 Pre-vaccine

description: Sample name: M271A


title: Patient Female M273 Pre-vaccine

description: Sample name: M273A


title: Patient Female M278 Post-vaccine

description: Sample name: M278B


title: Patient Female M273 Post-vaccine

description: Sample name: M273B


title: Patient Female M279 Post-vaccine

description: Sample name: M279B


title: Patient Female M276 Post-vaccine

description: Sample name: M276B


title: Patient Female M281 Post-vaccine

description: Sample name: M281B


title: Patient Female M288 Pre-vaccine

description: Sample name: M288A


title: Patient Male M287 Pre-vaccine

description: Sample name: M287A


title: BX_M3_P19792

description: 3month kidney biopsy post transplant


title: BX_M3_P20741

description: 3month kidney biopsy post transplant


title: Patient Female M276 Pre-vaccine

description: Sample name: M276A


title: BX_M3_P18805

description: 3month kidney biopsy post transplant


title: BX_M3_P17064

description: 3month kidney biopsy post transplant


title: BX_M3_P17145

description: 3month kidney biopsy post transplant


title: Patient Male M268 Pre-vaccine

description: Sample name: M268A


title: BX_M3_P18557

description: 3month kidney biopsy post transplant


title: BX_M3_P18496

description: 3month kidney biopsy post transplant


title: Patient Male M270 Pre-vaccine

description: Sample name: M270A


title: Patient Male M268 Post-vaccine

description: Sample name: M268B


title: Patient Male M277 Pre-vaccine

description: Sample name: M277A


title: Patient Female M267 Pre-vaccine

description: Sample name: M267A


title: Patient Male M270 Post-vaccine

description: Sample name: M270B


title: Patient Female M265 Pre-vaccine

description: Sample name: M265A


title: Patient Female M267 Post-vaccine

description: Sample name: M267B


title: Patient Female M261 Pre-vaccine

description: Sample name: M261A


title: Patient Male M266 Post-vaccine

description: Sample name: M266B


title: Patient Female M259 Post-vaccine

description: Sample name: M259B


title: Patient Female M265 Post-vaccine

description: Sample name: M265B


title: BX_M3_P16637

description: 3month kidney biopsy post transplant


title: BX_M3_P15762

description: 3month kidney biopsy post transplant


title: BX_M3_P15313

description: 3month kidney biopsy post transplant


title: BX_M3_P17063

description: 3month kidney biopsy post transplant


title: Patient Male M266 Pre-vaccine

description: Sample name: M266A


title: Patient Female M261 Post-vaccine

description: Sample name: M261B


title: BX_M3_P14768

description: 3month kidney biopsy post transplant


title: Patient Female M255 Pre-vaccine

description: Sample name: M255A


title: BX_M3_P14608

description: 3month kidney biopsy post transplant


title: Patient Female M257 Pre-vaccine

description: Sample name: M257A


title: Patient Female M259 Pre-vaccine

description: Sample name: M259A


title: Patient Female M255 Post-vaccine

description: Sample name: M255B


title: Patient Female M257 Post-vaccine

description: Sample name: M257B


title: BX_M3_P14690

description: 3month kidney biopsy post transplant


title: BX_M3_P12683

description: 3month kidney biopsy post transplant


title: Patient Female M254 Pre-vaccine

description: Sample name: M254A


title: Patient Female M254 Post-vaccine

description: Sample name: M254B


title: Patient Male M246 Pre-vaccine

description: Sample name: M246A


title: Patient Female M251 Pre-vaccine

description: Sample name: M251A


title: BX_M3_P12839

description: 3month kidney biopsy post transplant


title: Patient Female M250 Pre-vaccine

description: Sample name: M250A


title: Patient Female M244 Post-vaccine

description: Sample name: M244B


title: Patient Male M246 Post-vaccine

description: Sample name: M246B


title: Patient Male M247 Post-vaccine

description: Sample name: M247B


title: Patient Female M250 Post-vaccine

description: Sample name: M250B


title: Patient Female M251 Post-vaccine

description: Sample name: M251B


title: Patient Male M247 Pre-vaccine

description: Sample name: M247A


title: Patient Female M244 Pre-vaccine

description: Sample name: M244A


title: BX_M3_P8751

description: 3month kidney biopsy post transplant


title: BX_M3_P12673

description: 3month kidney biopsy post transplant


title: BX_M3_P12616

description: 3month kidney biopsy post transplant


title: BX_M3_P7145

description: 3month kidney biopsy post transplant


title: BX_M3_P8403

description: 3month kidney biopsy post transplant


title: Patient Male M231 Post-vaccine

description: Sample name: M231B


title: Patient Male M239 Post-vaccine

description: Sample name: M239B


title: Patient Female M237 Post-vaccine

description: Sample name: M237B


title: BX_M3_P6610

description: 3month kidney biopsy post transplant


title: Patient Female M242 Post-vaccine

description: Sample name: M242B


title: Patient Female M230 Pre-vaccine

description: Sample name: M230A


title: Patient Female M242 Pre-vaccine

description: Sample name: M242A


title: BX_M3_P6607

description: 3month kidney biopsy post transplant


title: BX_M3_P6491

description: 3month kidney biopsy post transplant


title: Patient Male M231 Pre-vaccine

description: Sample name: M231A


title: BX_M3_P6485

description: 3month kidney biopsy post transplant


title: Patient Female M243 Post-vaccine

description: Sample name: M243B


title: Patient Male M239 Pre-vaccine

description: Sample name: M239A


title: Patient Female M243 Pre-vaccine

description: Sample name: M243A


title: Patient Male M228 Post-vaccine

description: Sample name: M228B


title: Patient Female M229 Post-vaccine

description: Sample name: M229B


title: Patient Female M229 Pre-vaccine

description: Sample name: M229A


title: Patient Male M227 Post-vaccine

description: Sample name: M227B


title: Patient Female M237 Pre-vaccine

description: Sample name: M237A


title: Patient Female M230 Post-vaccine

description: Sample name: M230B


title: Patient Female M271 Post-vaccine

description: Sample name: M271B


title: Patient Female M226 Post-vaccine

description: Sample name: M226B


title: Patient Male M227 Pre-vaccine

description: Sample name: M227A


title: BX_M3_P36313

description: 3month kidney biopsy post transplant


title: BX_M3_P5889

description: 3month kidney biopsy post transplant


title: Patient Male M228 Pre-vaccine

description: Sample name: M228A


title: BX_M3_P36312

description: 3month kidney biopsy post transplant


title: Patient Female M225 Post-vaccine

description: Sample name: M225B


title: Patient Female M220 Post-vaccine

description: Sample name: M220B


title: BX_M3_P35132

description: 3month kidney biopsy post transplant


title: BX_M3_P35536

description: 3month kidney biopsy post transplant


title: BX_M3_P32937

description: 3month kidney biopsy post transplant


title: BX_M3_P35131

description: 3month kidney biopsy post transplant


title: Patient Female M213 Pre-vaccine

description: Sample name: M213A


title: Patient Female M213 Post-vaccine

description: Sample name: M213B


title: Patient Female M226 Pre-vaccine

description: Sample name: M226A


title: Patient Male M218 Post-vaccine

description: Sample name: M218B


title: BX_M3_P32851

description: 3month kidney biopsy post transplant


title: Patient Male M218 Pre-vaccine

description: Sample name: M218A


title: Patient Male M210 Pre-vaccine

description: Sample name: M210A


title: Patient Male M219 Post-vaccine

description: Sample name: M219B


title: Patient Male M219 Pre-vaccine

description: Sample name: M219A


title: Patient Male M217 Pre-vaccine

description: Sample name: M217A


title: Patient Female M220 Pre-vaccine

description: Sample name: M220A


title: Patient Male M214 Pre-vaccine

description: Sample name: M214A


title: Patient Male M214 Post-vaccine

description: Sample name: M214B


title: Patient Female M225 Pre-vaccine

description: Sample name: M225A


title: Patient Male M210 Post-vaccine

description: Sample name: M210B


title: Patient Male M217 Post-vaccine

description: Sample name: M217B


title: BX_M3_P34943

description: 3month kidney biopsy post transplant


title: BX_M3_P34886

description: 3month kidney biopsy post transplant


title: Patient Male M206 Post-vaccine

description: Sample name: M206B


title: Patient Male M206 Pre-vaccine

description: Sample name: M206A


title: BX_M3_P30765

description: 3month kidney biopsy post transplant


title: BX_M3_P30009

description: 3month kidney biopsy post transplant


title: Patient Male M202 Pre-vaccine

description: Sample name: M202A


title: Patient Female M205 Pre-vaccine

description: Sample name: M205A


title: Patient Male M202 Post-vaccine

description: Sample name: M202B


title: Patient Male M201 Pre-vaccine

description: Sample name: M201A


title: BX_M3_P29221

description: 3month kidney biopsy post transplant


title: BX_M3_P29757

description: 3month kidney biopsy post transplant


title: Patient Female M205 Post-vaccine

description: Sample name: M205B


title: Patient Female M200 Pre-vaccine

description: Sample name: M200A


title: Patient Male M201 Post-vaccine

description: Sample name: M201B


title: BX_M3_P30106

description: 3month kidney biopsy post transplant


title: Patient Male M204 Pre-vaccine

description: Sample name: M204A


title: BX_M3_P30609

description: 3month kidney biopsy post transplant


title: Patient Female M199 Pre-vaccine

description: Sample name: M199A


title: BX_M3_P29077

description: 3month kidney biopsy post transplant


title: BX_M3_P28992

description: 3month kidney biopsy post transplant


title: BX_M3_P28942

description: 3month kidney biopsy post transplant


title: BX_M3_P29987

description: 3month kidney biopsy post transplant


title: Patient Female M199 Post-vaccine

description: Sample name: M199B


title: Patient Male M198 Post-vaccine

description: Sample name: M198B


title: Patient Male M198 Pre-vaccine

description: Sample name: M198A


title: Patient Female M200 Post-vaccine

description: Sample name: M200B


title: Patient Male M197 Pre-vaccine

description: Sample name: M197A


title: Patient Male M192 Post-vaccine

description: Sample name: M192B


title: Patient Female M193 Pre-vaccine

description: Sample name: M193A


title: BX_M3_P28900

description: 3month kidney biopsy post transplant


title: Patient Female M196 Pre-vaccine

description: Sample name: M196A


title: Patient Male M192 Pre-vaccine

description: Sample name: M192A


title: Patient Male M197 Post-vaccine

description: Sample name: M197B


title: Patient Female M193 Post-vaccine

description: Sample name: M193B


title: BX_M3_P28214

description: 3month kidney biopsy post transplant


title: BX_M3_P28655

description: 3month kidney biopsy post transplant


title: BX_M3_P28317

description: 3month kidney biopsy post transplant


title: Patient Male M191 Pre-vaccine

description: Sample name: M191A


title: Patient Female M189 Post-vaccine

description: Sample name: M189B


title: Patient Male M188 Post-vaccine

description: Sample name: M188B


title: BX_M3_P28211

description: 3month kidney biopsy post transplant


title: Patient Female M187 Pre-vaccine

description: Sample name: M187A


title: BX_M3_P28899

description: 3month kidney biopsy post transplant


title: Patient Female M186 Post-vaccine

description: Sample name: M186B


title: Patient Female M187 Post-vaccine

description: Sample name: M187B


title: Patient Female M186 Pre-vaccine

description: Sample name: M186A


title: Patient Male M183 Post-vaccine

description: Sample name: M183B


title: BX_M3_P27222

description: 3month kidney biopsy post transplant


title: BX_M3_P28104

description: 3month kidney biopsy post transplant


title: Patient Female M182 Post-vaccine

description: Sample name: M182B


title: Patient Male M191 Post-vaccine

description: Sample name: M191B


title: Patient Male M188 Pre-vaccine

description: Sample name: M188A


title: Patient Female M178 Post-vaccine

description: Sample name: M178B


title: Patient Female M178 Pre-vaccine

description: Sample name: M178A


title: Patient Male M180 Pre-vaccine

description: Sample name: M180A


title: Patient Male M181 Post-vaccine

description: Sample name: M181B