title: HIPPO_Control_Br1304

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-H06


title: ERC_Control_Br1494

status: Public on Jan 31 2019

type: genomic

city: Baltimore

first: Stephen

middle: A

last: Semick

state: MD

address: 655 W Baltimore St S

country: USA

institute: University of Maryland School of Medicine

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-G02

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
idat files were imported with minfi then stratified quantile normalized in minfi.
[matrix_processed.csv]  Stratified quantile normalized beta values for tested probes (see publication).
[matrix_signal_intensities.csv]  Unmethylated and methylated signal intensities

molecule: genomic DNA

organism: Homo sapiens

source_name: ERC

label_protocol: Following manufacturer's protocol

extract_protocol: Following manufacturer's protocol

value: Plate 2

tag: brnum

value: brain

tag: tissue region

value: ERC

tag: disease state (dx)

value: Control

tag: age

tag: Sex

value: F

tag: race

value: AA


title: TriFLU-MF59_BL_8h_3

type: RNA

city: London

first: Deniz

last: Cizmeci

address: Imperial College London

country: United Kingdom

institute: Imperial College London

description:
m.blood.TriFluMF59.08.3
Gene expression in blood 8hrs after injection with Fluad.

hyb_protocol: Quantity and labeling efficiency were verified before hybridization to whole-genome 8×60 k mouse expression arrays (Agilent design ID 028005).

scan_protocol: Scanned at 5 μm using an Agilent scanner.

data_processing:
Image analysis and data extraction were performed with Agilent's Feature Extraction software (version 11.5) to generate the raw expression data.
Microarray data were pre-processed and normalised using R package limma. The raw data were first background corrected using the normexp method. Background corrected signals were quantile normalised between arrays.

label: not provided

molecule: total RNA

organism: Mus musculus

source_name: Peripheral Blood, 8hr, Fluad, replicate 3

label_protocol: Gene expression data were generated from high-quality RNA samples on an Agilent microarray platform (Agilent Technologies). RNA was labeled with a Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol:
Tissue Samples - Small pieces of tissue (3mm x 3mm x 3mm) were harvested and flash frozen in liquid nitrogen. Total RNA isolation including the miRNA species was performed using the miRNeasy mini kit (Qiagen, UK), as described in the standard protocol for purification of microRNA and total RNA from tissues and cells. Briefly, 700 µL QIAzol lysis reagent was added to the tissue sample, and disrupted and homogenized using a tissueruptor probe. Homogenate was incubated at room temperature (15–25°C) for 5 min before addition of 140 µL chloroform and vigorous shaking for 15 s. After incubation at room temperature for 2–3 min the homogenate was centrifuged for 15 min at 12,000 x g at 4°C. The upper aqueous phase was then transferred to a new collection tube (350 µL). 1.5 volumes (525 µL) of 100% ethanol was added and mixed thoroughly by pipetting then all sample was transferred into an RNeasy® Mini column, the sample being pulled through the column by vacuum manifold. The sample on the column was washed using 700 µL Buffer RWT, followed by 2 washes using 500 µL Buffer RPE. The RNeasy Mini column was then placed into a new 2 mL collection tube and centrifuged at full speed for 1 min to completely dry the membrane. The RNeasy Mini column was then transferred to a new 1.5 mL collection tube and 30 µL RNase-free water was directly pipetted onto the column membrane, then centrifuged for 1 min at ≥8000 x g to elute. Purified RNA was stored at -80°C until required for microarray hybridisation.
Blood Samples - 100 µL of peripheral blood harvested from the mouse tail was collected directly into an RNAprotect Animal Blood Tube and the tubes incubated at room temperature (15–25°C) for 2 hours. The blood tubes were then flash frozen in liquid nitrogen for storage. RNA isolation was performed as described in the kit protocol for purification of Total RNA, including miRNA, from RNAprotect stabilized animal blood tubes (100 µL). Briefly, completely thawed tubes were first centrifuged for 3 min at 5000 x g, then the supernatant removed by careful pipetting. The pellet was resuspended in 1 mL of RNase-free water and transferred to a clean RNase-free 2 mL tube. The pellet was completely resuspended in the water, centrifuged for 3 min at 5000 x g and the supernatant carefully removed by pipetting. The pellet was then dissolved in 240 µL Buffer RSB before addition of 200 µL Buffer RBT and 20 µL proteinase K enzyme solution. The tube was vortexed for 5 s then incubated at 55°C for 10 min in a shaking incubator at 1200 rpm. After incubation the sample was added into a Qiashredder spin column and centrifuged for 3 min at 10,000 x g. The supernatant was then transferred to a clean tube and 690 µL 100% ethanol added, mixed thoroughly by pipetting then all sample was transferred into an RNeasy Mini column, the sample being pulled through the column by vacuum manifold. The sample on the column was washed using 350 µL Buffer RWT, followed by addition of 80 µL DNase I solution (in Buffer RDD) and incubation at room temperature for 15 min. After DNase 1 treatment the column was washed with a further 350 µL of RWT followed by 2 washes using 500 µL Buffer RPE and a final wash with 500 µL 80% RNase-free ethanol. The RNeasy Mini column was then placed into a new 2 mL collection tube and centrifuged at full speed for 1 min to completely dry the membrane. The column was then transferred to a new 1.5 mL collection tube and 30 µL RNase-free REB buffer was directly pipetted onto the column membrane, then centrifuged for 1 min at ≥8000 x g to elute. Purified RNA was stored at -80°C until required for microarray hybridisation.

treatment_protocol: 6- to 8-week-old female CB6F1 mice were purchased from Charles River. Animals received a single injection in their right hind leg quadricep muscle and were then culled at specific intervals after the vaccination, either 4, 8, 24, 48, 72 or 168 Hrs. A control group that did not receive a vaccination was culled and tissues harvested. A further control group was employed that received a single saline injection in the right hind leg quadriceps muscle and were culled at the same intervals as the animals that received an active formulation. When each animal was culled the injected muscle site and the iliac lymph nodes that drain the hind leg quadriceps muscles were harvested and flash frozen in liquid nitrogen. Peripheral blood, sampled from the mouse tail vein immediately before humane euthanasia was collected (100 µL) in RNAprotect animal blood tubes (Qiagen, UK). Groups of mice (n = 5 per group per timepoint) received 1/10th of the human dose in 50 µL of one of the following licensed vaccines: Pentavac SD (Diphtheria, Tetanus, Pertussis (Whole Cell), Hepatitis B (rDNA) and Haemophilus Type b Conjugate Vaccine); Agrippal (Trivalent Flu Subunits – H3N2, H1N1 and Influenza B); Fluad (Trivalent Flu Subunits – H3N2, H1N1 and Influenza B + MF59® (oil-in-water emulsion)); Engerix B (Recombinant Hepatitis B) and either Poly I:C (Sigma, UK – P0913: 50 µL of a 1 mg/mL solution), LPS (Invivogen, UK – LPS-EB Ultrapure: 50 µL of a 0.5 mg/mL solution), IFA (Seppic, France – Montanide ISA 51 VG: 50 µL of a 1:1 mixture of IFA and Saline) or Saline alone (Sigma, UK – 50 µL).

tag: strain/background

tag: gender

value: Female

tag: tissue

value: PBMC

tag: treatment

value: Fluad

tag: timepoint

tag: animal replicate


title: ENG_MLN_8h_3

description:
m.MLN.Engerix.08.3
Gene expression in lymph nodes 8hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 8hr, Engerix B, replicate 3

value: draining medial iliac lymph nodes (MLN)

value: Engerix B


title: ERC_Alzheimer_Br5095

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-G01

value: Alzheimer

value: CAUC


title: TriFLU_BL_8h_5

description:
m.blood.TriFlu.08.5
Gene expression in blood 8hrs after injection with Agrippal.

source_name: Peripheral Blood, 8hr, Agrippal, replicate 5

value: Agrippal


title: ERC_Alzheimer_Br5088

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F12


title: ENG_MLN_8h_1

description:
m.MLN.Engerix.08.1
Gene expression in lymph nodes 8hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 8hr, Engerix B, replicate 1


title: TriFLU_BL_8h_3

description:
m.blood.TriFlu.08.3
Gene expression in blood 8hrs after injection with Agrippal.

source_name: Peripheral Blood, 8hr, Agrippal, replicate 3


title: TriFLU-MF59_BL_8h_2

description:
m.blood.TriFluMF59.08.2
Gene expression in blood 8hrs after injection with Fluad.

source_name: Peripheral Blood, 8hr, Fluad, replicate 2


title: TriFLU-MF59_BL_8h_1

description:
m.blood.TriFluMF59.08.1
Gene expression in blood 8hrs after injection with Fluad.

source_name: Peripheral Blood, 8hr, Fluad, replicate 1


title: TriFLU_BL_8h_4

description:
m.blood.TriFlu.08.4
Gene expression in blood 8hrs after injection with Agrippal.

source_name: Peripheral Blood, 8hr, Agrippal, replicate 4


title: TriFLU_BL_8h_2

description:
m.blood.TriFlu.08.2
Gene expression in blood 8hrs after injection with Agrippal.

source_name: Peripheral Blood, 8hr, Agrippal, replicate 2


title: TriFLU-MF59_BL_8h_5

description:
m.blood.TriFluMF59.08.5
Gene expression in blood 8hrs after injection with Fluad.

source_name: Peripheral Blood, 8hr, Fluad, replicate 5


title: TriFLU_BL_8h_1

description:
m.blood.TriFlu.08.1
Gene expression in blood 8hrs after injection with Agrippal.

source_name: Peripheral Blood, 8hr, Agrippal, replicate 1


title: ERC_Control_Br1069

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F11


title: HIPPO_Alzheimer_Br5102

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-G07

source_name: HIPPO

value: HIPPO


title: ERC_Alzheimer_Br5105

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F10

value: M


title: SAL_BL_8h_5

description:
m.blood.saline.08.5
Gene expression in blood 8hrs after injection with saline.

source_name: Peripheral Blood, 8hr, Saline, replicate 5

value: saline


title: ERC_Control_Br1034

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F07

value: Plate 2


title: ERC_Control_Br1305

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F08

value: brain


title: SAL_BL_8h_4

description:
m.blood.saline.08.4
Gene expression in blood 8hrs after injection with saline.

source_name: Peripheral Blood, 8hr, Saline, replicate 4


title: ERC_Control_Br1156

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F04

value: ERC


title: SAL_BL_8h_1

description:
m.blood.saline.08.1
Gene expression in blood 8hrs after injection with saline.

source_name: Peripheral Blood, 8hr, Saline, replicate 1


title: SAL_BL_8h_2

description:
m.blood.saline.08.2
Gene expression in blood 8hrs after injection with saline.

source_name: Peripheral Blood, 8hr, Saline, replicate 2


title: ERC_Control_Br1539

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E12

source_name: ERC

value: Control


title: SAL_BL_8h_3

description:
m.blood.saline.08.3
Gene expression in blood 8hrs after injection with saline.

source_name: Peripheral Blood, 8hr, Saline, replicate 3


title: PolyIC_BL_8h_5

description:
m.blood.PolyIC.08.5
Gene expression in blood 8hrs after injection with Poly I:C.

source_name: Peripheral Blood, 8hr, Poly I:C, replicate 5

value: PolyIC


title: PolyIC_BL_8h_4

description:
m.blood.PolyIC.08.4
Gene expression in blood 8hrs after injection with Poly I:C.

source_name: Peripheral Blood, 8hr, Poly I:C, replicate 4


title: ERC_Control_Br1113

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E08

value: F


title: ERC_Control_Br1522

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E09

value: AA


title: ERC_Control_Br909

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E05


title: ERC_Control_Br1613

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E11


title: ERC_Alzheimer_Br5089

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-F01


title: PolyIC_BL_8h_3

description:
m.blood.PolyIC.08.3
Gene expression in blood 8hrs after injection with Poly I:C.

source_name: Peripheral Blood, 8hr, Poly I:C, replicate 3

value: Female

value: PBMC


title: ERC_Control_Br1109

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E02


title: ENG_MU_8h_3

description:
m.muscle.Engerix.08.3
Gene expression in muscle 8hrs after injection with Engerix B.

source_name: Muscle, 8hr, Engerix B, replicate 3

value: muscle


title: ERC_Alzheimer_Br5098

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E03


title: DLPFC_Control_Br1695

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D12

source_name: DLPFC

value: DLPFC


title: PolyIC_BL_8h_1

description:
m.blood.PolyIC.08.1
Gene expression in blood 8hrs after injection with Poly I:C.

source_name: Peripheral Blood, 8hr, Poly I:C, replicate 1


title: PERT_BL_8h_3

description:
m.blood.Pertussis.08.3
Gene expression in blood 8hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 8hr, Pentavac SD, replicate 3

value: Pentavac SD


title: PERT_BL_8h_5

description:
m.blood.Pertussis.08.5
Gene expression in blood 8hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 8hr, Pentavac SD, replicate 5


title: DLPFC_Control_Br1494

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D11


title: ERC_Control_Br1135

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E06


title: DLPFC_Alzheimer_Br5100

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D10

value: Alzheimer

value: CAUC


title: PERT_BL_8h_1

description:
m.blood.Pertussis.08.1
Gene expression in blood 8hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 8hr, Pentavac SD, replicate 1


title: DLPFC_Control_Br894

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D09


title: LPS_BL_8h_4

description:
m.blood.LPS.08.4
Gene expression in blood 8hrs after injection with LPS.

source_name: Peripheral Blood, 8hr, LPS, replicate 4

value: LPS


title: LPS_BL_8h_2

description:
m.blood.LPS.08.2
Gene expression in blood 8hrs after injection with LPS.

source_name: Peripheral Blood, 8hr, LPS, replicate 2


title: LPS_BL_8h_3

description:
m.blood.LPS.08.3
Gene expression in blood 8hrs after injection with LPS.

source_name: Peripheral Blood, 8hr, LPS, replicate 3


title: DLPFC_Control_Br1960

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D08

value: M


title: ERC_Alzheimer_Br5115

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-E04


title: PERT_BL_8h_2

description:
m.blood.Pertussis.08.2
Gene expression in blood 8hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 8hr, Pentavac SD, replicate 2


title: DLPFC_Alzheimer_Br5095

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D07


title: TriFLU_MLN_8h_4

description:
m.MLN.TriFlu.08.4
Gene expression in lymph nodes 8hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 8hr, Agrippal, replicate 4

value: draining medial iliac lymph nodes (MLN)

value: Agrippal


title: PERT_BL_8h_4

description:
m.blood.Pertussis.08.4
Gene expression in blood 8hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 8hr, Pentavac SD, replicate 4


title: LPS_BL_8h_5

description:
m.blood.LPS.08.5
Gene expression in blood 8hrs after injection with LPS.

source_name: Peripheral Blood, 8hr, LPS, replicate 5


title: DLPFC_Alzheimer_Br5075

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D03

value: Plate 2

value: brain


title: DLPFC_Control_Br1264

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D06

value: Control


title: PolyIC_BL_8h_2

description:
m.blood.PolyIC.08.2
Gene expression in blood 8hrs after injection with Poly I:C.

source_name: Peripheral Blood, 8hr, Poly I:C, replicate 2

value: PolyIC


title: IFA_BL_8h_5

description:
m.blood.IFA.08.5
Gene expression in blood 8hrs after injection with IFA.

source_name: Peripheral Blood, 8hr, IFA, replicate 5

value: IFA


title: DLPFC_Control_Br2003

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-D02

value: AA


title: LPS_BL_8h_1

description:
m.blood.LPS.08.1
Gene expression in blood 8hrs after injection with LPS.

source_name: Peripheral Blood, 8hr, LPS, replicate 1

value: Female


title: DLPFC_Alzheimer_Br5087

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C12

value: F


title: DLPFC_Control_Br2026

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C11


title: IFA_BL_8h_3

description:
m.blood.IFA.08.3
Gene expression in blood 8hrs after injection with IFA.

source_name: Peripheral Blood, 8hr, IFA, replicate 3

value: PBMC


title: ENG_BL_8h_5

description:
m.blood.Engerix.08.5
Gene expression in blood 8hrs after injection with Engerix B.

source_name: Peripheral Blood, 8hr, Engerix B, replicate 5

value: Engerix B


title: DLPFC_Control_Br1537

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C08

source_name: DLPFC

value: DLPFC


title: DLPFC_Alzheimer_Br5089

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C09

value: Alzheimer


title: IFA_BL_8h_2

description:
m.blood.IFA.08.2
Gene expression in blood 8hrs after injection with IFA.

source_name: Peripheral Blood, 8hr, IFA, replicate 2


title: DLPFC_Alzheimer_Br5094

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C05

value: CAUC


title: ENG_BL_8h_4

description:
m.blood.Engerix.08.4
Gene expression in blood 8hrs after injection with Engerix B.

source_name: Peripheral Blood, 8hr, Engerix B, replicate 4


title: ENG_BL_8h_1

description:
m.blood.Engerix.08.1
Gene expression in blood 8hrs after injection with Engerix B.

source_name: Peripheral Blood, 8hr, Engerix B, replicate 1


title: ENG_BL_8h_2

description:
m.blood.Engerix.08.2
Gene expression in blood 8hrs after injection with Engerix B.

source_name: Peripheral Blood, 8hr, Engerix B, replicate 2


title: TriFLU-MF59_MU_4h_3

description:
m.muscle.TriFluMF59.04.3
Gene expression in muscle 4hrs after injection with Fluad.

source_name: Muscle, 4hr, Fluad, replicate 3

value: muscle

value: Fluad


title: IFA_BL_8h_4

description:
m.blood.IFA.08.4
Gene expression in blood 8hrs after injection with IFA.

source_name: Peripheral Blood, 8hr, IFA, replicate 4


title: Pca270

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Samples were hybridized on oligonucleotide glass arrays with sequences representing probes for 2006 human miRs from miRbase v19 (Human miR Microarray Version 19, Agilent Technologies).

scan_protocol: After 20 hours, slides were washed and scanned using an Agilent G2505C dual-laser microarray scanner.

data_processing: Images obtained were analysed using Feature Extraction software version 10.7 and txt files with raw or semi-processed data (by the GeneView tool of Feature Extraction) were given as output.  Raw data were loaded into R and processed using the limma package for microarray analysis.  Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Normalized log2 Intensities of replicated probes were then averaged.

source_name: plasma

label_protocol: Briefly, 4ul of totRNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed

extract_protocol: Extraction was performed using miRNEasy serum/plasma kit from Qiagen. A carrier (bacteriophage MS2 from Roche Diagnostic) was added, together with cel-miR-39-3p mimic.

tag: class

value: Prostate Cancer

tag: psa

tag: gs


title: IFA_BL_8h_1

description:
m.blood.IFA.08.1
Gene expression in blood 8hrs after injection with IFA.

source_name: Peripheral Blood, 8hr, IFA, replicate 1


title: ENG_BL_8h_3

description:
m.blood.Engerix.08.3
Gene expression in blood 8hrs after injection with Engerix B.

source_name: Peripheral Blood, 8hr, Engerix B, replicate 3


title: DLPFC_Control_Br1023

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-C04

value: M


title: TriFLU_MU_4h_5

description:
m.muscle.TriFlu.04.5
Gene expression in muscle 4hrs after injection with Agrippal.

source_name: Muscle, 4hr, Agrippal, replicate 5

value: Agrippal


title: TriFLU-MF59_MU_4h_2

description:
m.muscle.TriFluMF59.04.2
Gene expression in muscle 4hrs after injection with Fluad.

source_name: Muscle, 4hr, Fluad, replicate 2


title: TriFLU-MF59_MU_4h_4

description:
m.muscle.TriFluMF59.04.4
Gene expression in muscle 4hrs after injection with Fluad.

source_name: Muscle, 4hr, Fluad, replicate 4


title: TriFLU_MU_4h_2

description:
m.muscle.TriFlu.04.2
Gene expression in muscle 4hrs after injection with Agrippal.

source_name: Muscle, 4hr, Agrippal, replicate 2


title: TriFLU-MF59_MU_4h_5

description:
m.muscle.TriFluMF59.04.5
Gene expression in muscle 4hrs after injection with Fluad.

source_name: Muscle, 4hr, Fluad, replicate 5


title: TriFLU_MU_4h_1

description:
m.muscle.TriFlu.04.1
Gene expression in muscle 4hrs after injection with Agrippal.

source_name: Muscle, 4hr, Agrippal, replicate 1


title: TriFLU_MU_4h_4

description:
m.muscle.TriFlu.04.4
Gene expression in muscle 4hrs after injection with Agrippal.

source_name: Muscle, 4hr, Agrippal, replicate 4


title: CRB_Alzheimer_Br5115

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B11

source_name: CRB

value: Plate 2

value: brain

value: CRB


title: SAL_MU_4h_5

description:
m.muscle.saline.04.5
Gene expression in muscle 4hrs after injection with saline.

source_name: Muscle, 4hr, Saline, replicate 5

value: saline


title: TriFLU-MF59_MU_4h_1

description:
m.muscle.TriFluMF59.04.1
Gene expression in muscle 4hrs after injection with Fluad.

source_name: Muscle, 4hr, Fluad, replicate 1


title: TriFLU_MU_4h_3

description:
m.muscle.TriFlu.04.3
Gene expression in muscle 4hrs after injection with Agrippal.

source_name: Muscle, 4hr, Agrippal, replicate 3


title: CRB_Control_Br1023

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B10

value: Control


title: SAL_MU_4h_4

description:
m.muscle.saline.04.4
Gene expression in muscle 4hrs after injection with saline.

source_name: Muscle, 4hr, Saline, replicate 4

value: Female


title: Pca141


title: CRB_Alzheimer_Br5087

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B09

value: F

value: AA


title: CRB_Alzheimer_Br5078

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B08


title: Pca212


title: Pca176


title: BPH274

value: Benign Prostatic Hyperplasia


title: SAL_MU_4h_3

description:
m.muscle.saline.04.3
Gene expression in muscle 4hrs after injection with saline.

source_name: Muscle, 4hr, Saline, replicate 3


title: CRB_Control_Br1113

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B06


title: Normal32

value: Healthy Donor


title: SAL_MU_4h_1

description:
m.muscle.saline.04.1
Gene expression in muscle 4hrs after injection with saline.

source_name: Muscle, 4hr, Saline, replicate 1


title: PolyIC_MU_4h_4

description:
m.muscle.PolyIC.04.4
Gene expression in muscle 4hrs after injection with Poly I:C.

source_name: Muscle, 4hr, Poly I:C, replicate 4

value: PolyIC


title: PolyIC_MU_4h_3

description:
m.muscle.PolyIC.04.3
Gene expression in muscle 4hrs after injection with Poly I:C.

source_name: Muscle, 4hr, Poly I:C, replicate 3


title: PolyIC_MU_4h_1

description:
m.muscle.PolyIC.04.1
Gene expression in muscle 4hrs after injection with Poly I:C.

source_name: Muscle, 4hr, Poly I:C, replicate 1


title: PERT_MU_4h_5

description:
m.muscle.Pertussis.04.5
Gene expression in muscle 4hrs after injection with Pentavac SD.

source_name: Muscle, 4hr, Pentavac SD, replicate 5

value: Pentavac SD


title: PERT_MU_4h_4

description:
m.muscle.Pertussis.04.4
Gene expression in muscle 4hrs after injection with Pentavac SD.

source_name: Muscle, 4hr, Pentavac SD, replicate 4

value: muscle


title: PolyIC_MU_4h_5

description:
m.muscle.PolyIC.04.5
Gene expression in muscle 4hrs after injection with Poly I:C.

source_name: Muscle, 4hr, Poly I:C, replicate 5


title: PolyIC_MU_4h_2

description:
m.muscle.PolyIC.04.2
Gene expression in muscle 4hrs after injection with Poly I:C.

source_name: Muscle, 4hr, Poly I:C, replicate 2


title: BPH264

source_name: plasma


title: SAL_MU_4h_2

description:
m.muscle.saline.04.2
Gene expression in muscle 4hrs after injection with saline.

source_name: Muscle, 4hr, Saline, replicate 2


title: BPH240


title: PERT_MU_4h_3

description:
m.muscle.Pertussis.04.3
Gene expression in muscle 4hrs after injection with Pentavac SD.

source_name: Muscle, 4hr, Pentavac SD, replicate 3


title: CRB_Control_Br1249

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A12

source_name: CRB


title: CRB_Control_Br1314

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B01


title: CRB_Alzheimer_Br5108

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A11

value: Alzheimer


title: PERT_MU_4h_1

description:
m.muscle.Pertussis.04.1
Gene expression in muscle 4hrs after injection with Pentavac SD.

source_name: Muscle, 4hr, Pentavac SD, replicate 1


title: Pca230

value: Prostate Cancer


title: PERT_MU_4h_2

description:
m.muscle.Pertussis.04.2
Gene expression in muscle 4hrs after injection with Pentavac SD.

source_name: Muscle, 4hr, Pentavac SD, replicate 2


title: Pca58


title: CRB_Control_Br1160

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A10

value: M


title: LPS_MU_4h_4

description:
m.muscle.LPS.04.4
Gene expression in muscle 4hrs after injection with LPS.

source_name: Muscle, 4hr, LPS, replicate 4

value: LPS


title: Pca360


title: CRB_Control_Br1611

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A09

value: Plate 2


title: LPS_MU_4h_2

description:
m.muscle.LPS.04.2
Gene expression in muscle 4hrs after injection with LPS.

source_name: Muscle, 4hr, LPS, replicate 2


title: LPS_MU_4h_3

description:
m.muscle.LPS.04.3
Gene expression in muscle 4hrs after injection with LPS.

source_name: Muscle, 4hr, LPS, replicate 3


title: CRB_Control_Br1669

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A07

value: brain

value: CAUC


title: Pca276


title: CRB_Control_Br1494

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-B04

value: CRB


title: IFA_MU_4h_4

description:
m.muscle.IFA.04.4
Gene expression in muscle 4hrs after injection with IFA.

source_name: Muscle, 4hr, IFA, replicate 4

value: IFA


title: CRB_Control_Br1305

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A06

value: Control


title: IFA_MU_4h_3

description:
m.muscle.IFA.04.3
Gene expression in muscle 4hrs after injection with IFA.

source_name: Muscle, 4hr, IFA, replicate 3

value: Female


title: CRB_Alzheimer_Br5099

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A05


title: Normal30


title: BPH206


title: IFA_MU_4h_1

description:
m.muscle.IFA.04.1
Gene expression in muscle 4hrs after injection with IFA.

source_name: Muscle, 4hr, IFA, replicate 1


title: BPH229


title: FT-CtrD-D3

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

description:
DD(FT47)
non transformed human primary cells

hyb_protocol: bisulfite converted DNA was further processed according to Illumina MethylationEPIC standard protocol

scan_protocol: arrays were imaged using the Illumina iScan System with recommended scanner settings

data_processing: Subset-quantile Within Array Normalization (SWAN) using the R-Bioconductor/ChAMP package, applied filters are specified in the manuscript

label: Cy3, C5

source_name: 9 month infected human fallopian tube organoid culture,  Donor 3

label_protocol: Standard Illumina labeling protocol

growth_protocol: human primary fallopian tube organoids were cultivated as specified in the manuscript

extract_protocol: genomic DNA was isolated using the Qiagen AllPrep Kit

treatment_protocol: Infection with CtrD was performed as indicated in the manuscript

value: female

value: fallopian tube

tag: condition

value: infected

tag: patient


title: CRB_Alzheimer_Br5077

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
2-A04

tag: brnum

value: F


title: FT-BL-D3

description:
BL(FT47)
non transformed human primary cells

source_name: 3 weeks human fallopian tube organoid culture,  Donor 3

value: baseline


title: HIPPO_Control_Br1156

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H12

source_name: HIPPO

value: Plate 1

tag: tissue region

value: HIPPO

value: AA


title: ENG_MU_4h_5

description:
m.muscle.Engerix.04.5
Gene expression in muscle 4hrs after injection with Engerix B.

source_name: Muscle, 4hr, Engerix B, replicate 5

value: muscle

value: Engerix B


title: ENG_MU_4h_3

description:
m.muscle.Engerix.04.3
Gene expression in muscle 4hrs after injection with Engerix B.

source_name: Muscle, 4hr, Engerix B, replicate 3


title: BPH259

source_name: plasma

value: Benign Prostatic Hyperplasia


title: ENG_MU_4h_1

description:
m.muscle.Engerix.04.1
Gene expression in muscle 4hrs after injection with Engerix B.

source_name: Muscle, 4hr, Engerix B, replicate 1


title: ENG_MU_4h_4

description:
m.muscle.Engerix.04.4
Gene expression in muscle 4hrs after injection with Engerix B.

source_name: Muscle, 4hr, Engerix B, replicate 4


title: Pca359

value: Prostate Cancer


title: TriFLU-MF59_MLN_4h_5

description:
m.MLN.TriFluMF59.04.5
Gene expression in lymph nodes 4hrs after injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Fluad, replicate 5

value: draining medial iliac lymph nodes (MLN)

value: Fluad


title: ENG_MU_4h_2

description:
m.muscle.Engerix.04.2
Gene expression in muscle 4hrs after injection with Engerix B.

source_name: Muscle, 4hr, Engerix B, replicate 2


title: FT-BL-D4

description:
BL(FT43)
non transformed human primary cells

source_name: 3 weeks human fallopian tube organoid culture,  Donor 4


title: IFA_MU_4h_5

description:
m.muscle.IFA.04.5
Gene expression in muscle 4hrs after injection with IFA.

source_name: Muscle, 4hr, IFA, replicate 5

value: IFA


title: TriFLU-MF59_MLN_4h_4

description:
m.MLN.TriFluMF59.04.4
Gene expression in lymph nodes 4hrs after injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Fluad, replicate 4


title: IFA_MU_4h_2

description:
m.muscle.IFA.04.2
Gene expression in muscle 4hrs after injection with IFA.

source_name: Muscle, 4hr, IFA, replicate 2


title: FT-NI-D2

description:
NINI(FT46)
non transformed human primary cells

source_name: 9 month not infected human fallopian tube organoid culture,  Donor 2

value: not infected


title: TriFLU-MF59_MLN_4h_3

description:
m.MLN.TriFluMF59.04.3
Gene expression in lymph nodes 4hrs after injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Fluad, replicate 3

value: Female


title: Pca358


title: TriFLU-MF59_MLN_4h_2

description:
m.MLN.TriFluMF59.04.2
Gene expression in lymph nodes 4hrs after injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Fluad, replicate 2


title: HIPPO_Control_Br1003

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H10

value: brain

tag: disease state (dx)

value: Control


title: HIPPO_Control_Br894

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H08

tag: age


title: HIPPO_Control_Br1113

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H06

tag: Sex

value: CAUC


title: HIPPO_Control_Br1305

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H03

value: M

tag: race


title: HIPPO_Control_Br1109

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H02

value: F


title: FT-CtrD-D2

description:
DD(FT46)
non transformed human primary cells

source_name: 9 month infected human fallopian tube organoid culture,  Donor 2

value: female

value: fallopian tube

value: infected


title: FT-CtrD-D4

description:
DD(FT43)
non transformed human primary cells

source_name: 9 month infected human fallopian tube organoid culture,  Donor 4


title: Pca164


title: Normal28

value: Healthy Donor


title: Normal29


title: HIPPO_Control_Br1249

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G11

source_name: HIPPO

value: Plate 1

value: HIPPO

value: AA


title: BPH191

value: Benign Prostatic Hyperplasia


title: BPH194


title: BPH251


title: TriFLU-MF59_MLN_4h_1

description:
m.MLN.TriFluMF59.04.1
Gene expression in lymph nodes 4hrs after injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Fluad, replicate 1

tag: strain/background

value: draining medial iliac lymph nodes (MLN)

value: Fluad


title: LPS_MU_4h_5

description:
m.muscle.LPS.04.5
Gene expression in muscle 4hrs after injection with LPS.

source_name: Muscle, 4hr, LPS, replicate 5

tag: gender

value: muscle

value: LPS


title: FT-NI-D4

description:
NINI(FT43)
non transformed human primary cells

source_name: 9 month not infected human fallopian tube organoid culture,  Donor 4

tag: tissue

value: not infected


title: LPS_MU_4h_1

description:
m.muscle.LPS.04.1
Gene expression in muscle 4hrs after injection with LPS.

source_name: Muscle, 4hr, LPS, replicate 1

value: Female

tag: treatment


title: SAL_MLN_4h_5

description:
m.MLN.saline.04.5
Gene expression in lymph nodes 4hrs after injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Saline, replicate 5

value: saline

tag: timepoint


title: FT-NI-D3

description:
NINI(FT47)
non transformed human primary cells

source_name: 9 month not infected human fallopian tube organoid culture,  Donor 3


title: SAL_MLN_4h_2

description:
m.MLN.saline.04.2
Gene expression in lymph nodes 4hrs after injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Saline, replicate 2

tag: animal replicate


title: PolyIC_MLN_4h_5

description:
m.MLN.PolyIC.04.5
Gene expression in lymph nodes 4hrs after injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Poly I:C, replicate 5

value: PolyIC


title: Pca242

source_name: plasma

tag: class

value: Prostate Cancer


title: SAL_MLN_4h_1

description:
m.MLN.saline.04.1
Gene expression in lymph nodes 4hrs after injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Saline, replicate 1


title: TriFLU_MLN_4h_3

description:
m.MLN.TriFlu.04.3
Gene expression in lymph nodes 4hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Agrippal, replicate 3

value: Agrippal


title: TriFLU_MLN_4h_1

description:
m.MLN.TriFlu.04.1
Gene expression in lymph nodes 4hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Agrippal, replicate 1


title: TriFLU_MLN_4h_5

description:
m.MLN.TriFlu.04.5
Gene expression in lymph nodes 4hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Agrippal, replicate 5


title: TriFLU_MLN_4h_2

description:
m.MLN.TriFlu.04.2
Gene expression in lymph nodes 4hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Agrippal, replicate 2


title: TriFLU_MLN_4h_4

description:
m.MLN.TriFlu.04.4
Gene expression in lymph nodes 4hrs after injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Agrippal, replicate 4


title: SAL_MLN_4h_4

description:
m.MLN.saline.04.4
Gene expression in lymph nodes 4hrs after injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Saline, replicate 4


title: SAL_MLN_4h_3

description:
m.MLN.saline.04.3
Gene expression in lymph nodes 4hrs after injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Saline, replicate 3


title: HIPPO_Alzheimer_Br5089

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-H01

source_name: HIPPO

value: brain

value: Alzheimer

value: M

value: CAUC


title: HIPPO_Control_Br1214

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G10

value: Plate 1

value: HIPPO

value: Control


title: HIPPO_Alzheimer_Br5100

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G08

value: F


title: HIPPO_Control_Br1099

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G06

value: AA


title: HIPPO_Alzheimer_Br5110

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G04


title: Pca241

tag: psa


title: HIPPO_Control_Br1539

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G03


title: HIPPO_Control_Br1157

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G02


title: HIPPO_Alzheimer_Br5081

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-G01


title: HIPPO_Alzheimer_Br5088

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F12


title: BPH181

value: Benign Prostatic Hyperplasia

tag: gs


title: Edom_KRT7+_2

city: Shinjuku-ku

first: Nanae

last: Tsuchida

state: Tokyo

address: 6-7-1 Nishishinjuku

department: Obstetrics and Gynecology

country: Japan

institute: Tokyo Medical University

description: Gene expression of KRT7+ cells extracted from hiPSCs treated with BMP4 for 10 days.

hyb_protocol: For each hybridization, 2μg of Cy3 labeled cDNA were fragmented, and hybridized at 65 ℃ for 17 hours to an Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID: 072363).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software version 11.5.1.1 (Agilent).

source_name: Menstrual blood, human induced pluripotent stem cells

label_protocol: Amplified cDNA was labeled with Cyanine 3 (Cy3) using SureTag DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA.) following the manufacturer's instructions.

extract_protocol: Total RNA from sorted cells was extracted using RNeasy Micro RNA Kit (Qiagen, Hilden, Germany) based on the manufacturer’s instructions. Total RNA was amplified using Ovation Pico WTA System V2 (NuGEN Technologies, Inc, San Carlos, CA, USA.) following the manufacturer's instructions.

treatment_protocol: hiPSCs were treated with 50ng/ml BMP4 for 10 days. Subsequently, KRT7-positive cells were purified from differentiated cells.

tag: source tissue

value: Menstrual blood

tag: donor gender

value: female

tag: cell type

value: KRT7-positive differentiated cells

value: 10-day treatment of 50ng/ml BMP4


title: BPH208


title: PolyIC_MLN_4h_2

description:
m.MLN.PolyIC.04.2
Gene expression in lymph nodes 4hrs after injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Poly I:C, replicate 2

value: Female

value: draining medial iliac lymph nodes (MLN)

value: PolyIC


title: Edom_KRT7+_1


title: Edom_iPS_2

description: Gene expression of hiPSCs cultured for 10 days without BMP4.

value: human induced pluripotent stem cells


title: Pca234

value: Prostate Cancer


title: PL_KRT7+_2

source_name: Placental artery endothelium, human induced pluripotent stem cells

value: Placental artery endothelium

value: male


title: PERT_MLN_4h_5

description:
m.MLN.Pertussis.04.5
Gene expression in lymph nodes 4hrs after injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Pentavac SD, replicate 5

value: Pentavac SD


title: Normal27

value: Healthy Donor


title: PolyIC_MLN_4h_4

description:
m.MLN.PolyIC.04.4
Gene expression in lymph nodes 4hrs after injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Poly I:C, replicate 4


title: BPH221


title: PL_iPS_1


title: Edom_iPS_1


title: PolyIC_MLN_4h_1

description:
m.MLN.PolyIC.04.1
Gene expression in lymph nodes 4hrs after injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Poly I:C, replicate 1


title: PolyIC_MLN_4h_3

description:
m.MLN.PolyIC.04.3
Gene expression in lymph nodes 4hrs after injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Poly I:C, replicate 3


title: UTE A4_KRT7+_2

source_name: Endometrium, human induced pluripotent stem cells

value: Endometrium


title: PERT_MLN_4h_2

description:
m.MLN.Pertussis.04.2
Gene expression in lymph nodes 4hrs after injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Pentavac SD, replicate 2


title: PERT_MLN_4h_4

description:
m.MLN.Pertussis.04.4
Gene expression in lymph nodes 4hrs after injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Pentavac SD, replicate 4


title: PL_KRT7+_1


title: ERC_Control_Br1023

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F11

source_name: ERC

value: Plate 1

tag: brnum

value: brain

tag: tissue region

value: ERC

value: Control

value: M

value: CAUC


title: UTE A4_KRT7+_1

value: female

value: KRT7-positive differentiated cells

value: 10-day treatment of 50ng/ml BMP4


title: Pca213

source_name: plasma


title: BPH187

value: Benign Prostatic Hyperplasia


title: ERC_Control_Br1654

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F10

tag: disease state (dx)

tag: age


title: ERC_Control_Br1314

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F07

tag: Sex

value: F

tag: race

value: AA


title: PERT_MLN_4h_3

description:
m.MLN.Pertussis.04.3
Gene expression in lymph nodes 4hrs after injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Pentavac SD, replicate 3

tag: strain/background

tag: gender

value: Female

value: draining medial iliac lymph nodes (MLN)


title: PL_iPS_2

value: Placental artery endothelium

value: male

value: human induced pluripotent stem cells

tag: treatment


title: ERC_Control_Br2003

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F06

value: Plate 1


title: ERC_Control_Br1960

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F03

value: brain


title: Pca200

value: Prostate Cancer


title: ERC_Control_Br1304

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E12

value: ERC

value: Control


title: ERC_Alzheimer_Br5099

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-F04

value: Alzheimer

value: M

value: CAUC


title: Normal25

value: Healthy Donor


title: Pca184


title: BPH199

value: Benign Prostatic Hyperplasia


title: BPH207


title: Mouse E16.5 S3

type: SRA

city: Houston

first: Peter

middle: Y

last: Lwigale

state: Texas

address: 6100 Main street

department: BioSciences

institute: Rice University

library_source: transcriptomic

data_processing:
Raw reads produced by Illumina HS2000 are subjected to quality control (QC) to remove reads with adaptors, with more than 10% unknowns, and low quality reads. Resulting clean reads are stored in FASTQ format.
Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. An average mapping ratio of 77.71% to the reference gene and 91.47% to the genome were generated from Genome Reference Consortium Build 38 (GRCm38)
Reads are quantified using RSEM and normalized to FPKM values to determine transcript expression.
Differentially expressed genes (DEGs) were screened for using NOISeq method with parameter of abs(log2) ≥1 and probability ≥0.8.
Data was further annotated for functional classification using GO and pathway enrichment using KEGG.
Supplementary_files_format_and_content: FPKM values for each sample

extract_protocol:
pNC (E10.5) or Cornea (E14.5, E16.5) were dissected from embryonic tissue and immersed in Trizol. RNA extraction performed by BGI.US®. In brief, mRNA is purified by Dnase I and oligodt magnetic beads, followed by the addition of sequencing adaptors and PCR amplification. Quality and Quantity of library fragments are assessed by Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-time PCR system.
Libraries were prepared by BGI.US® with Standard Illumina Protocols.

tag: strain

tag: developmental stage

tag: tissue

value: cornea


title: ERC_Control_Br1160

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E11

value: AA


title: Mouse E16.5 S2


title: UTE A4_iPS_2

value: Endometrium

value: female


title: ERC_Control_Br1185

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E09

value: F


title: PERT_MLN_4h_1

description:
m.MLN.Pertussis.04.1
Gene expression in lymph nodes 4hrs after injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Pentavac SD, replicate 1

value: Female

value: draining medial iliac lymph nodes (MLN)

value: Pentavac SD

tag: timepoint

tag: animal replicate


title: UTE B5_KRT7+_2

description: Gene expression of KRT7+ cells extracted from hiPSCs treated with BMP4 for 10 days.

tag: source tissue

value: KRT7-positive differentiated cells

value: 10-day treatment of 50ng/ml BMP4


title: LPS_MLN_4h_5

description:
m.MLN.LPS.04.5
Gene expression in lymph nodes 4hrs after injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 4hr, LPS, replicate 5

value: LPS


title: LPS_MLN_4h_3

description:
m.MLN.LPS.04.3
Gene expression in lymph nodes 4hrs after injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 4hr, LPS, replicate 3


title: LPS_MLN_4h_4

description:
m.MLN.LPS.04.4
Gene expression in lymph nodes 4hrs after injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 4hr, LPS, replicate 4


title: Pca182

tag: class

value: Prostate Cancer

tag: psa

tag: gs


title: LPS_MLN_4h_2

description:
m.MLN.LPS.04.2
Gene expression in lymph nodes 4hrs after injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 4hr, LPS, replicate 2


title: BPH172


title: LPS_MLN_4h_1

description:
m.MLN.LPS.04.1
Gene expression in lymph nodes 4hrs after injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 4hr, LPS, replicate 1


title: BPH180


title: UTE A4_iPS_1

description: Gene expression of hiPSCs cultured for 10 days without BMP4.

tag: donor gender

tag: cell type

value: human induced pluripotent stem cells


title: Mouse E14.5 S3


title: IFA_MLN_4h_4

description:
m.MLN.IFA.04.4
Gene expression in lymph nodes 4hrs after injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 4hr, IFA, replicate 4

value: IFA


title: UTE B5_iPS_2


title: ERC_Control_Br1264

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E05

value: Plate 1

tag: brnum

value: brain

tag: tissue region

value: ERC

tag: disease state (dx)

value: Control

tag: age

value: CAUC


title: UTE B5_KRT7+_1

value: Endometrium


title: IFA_MLN_4h_5

description:
m.MLN.IFA.04.5
Gene expression in lymph nodes 4hrs after injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 4hr, IFA, replicate 5

tag: strain/background

tag: gender


title: UTE B5_iPS_1

value: female

tag: treatment


title: Pca100


title: ERC_Control_Br1615

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E03

tag: Sex

value: F

tag: race

value: AA


title: BPH145

value: Benign Prostatic Hyperplasia


title: Pca45


title: IFA_MLN_4h_3

description:
m.MLN.IFA.04.3
Gene expression in lymph nodes 4hrs after injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 4hr, IFA, replicate 3

value: Female

tag: tissue

value: draining medial iliac lymph nodes (MLN)

tag: timepoint


title: Mouse E10.5 S3

source_name: E10.5_periocular neural crest

tag: strain

tag: developmental stage

value: periocular neural crest


title: DLPFC_Control_Br1007

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E01

source_name: DLPFC

value: DLPFC

value: M


title: Mouse E14.5 S2

value: cornea


title: Mouse E10.5 S2


title: IFA_MLN_4h_1

description:
m.MLN.IFA.04.1
Gene expression in lymph nodes 4hrs after injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 4hr, IFA, replicate 1

value: IFA

tag: animal replicate


title: ERC_Control_Br1249

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E07

value: Plate 1


title: Mouse E16.5 S1


title: DLPFC_Control_Br909

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D11

value: brain


title: DLPFC_Control_Br1275

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D09


title: Mouse E14.5 S1


title: ENG_MLN_4h_5

description:
m.MLN.Engerix.04.5
Gene expression in lymph nodes 4hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Engerix B, replicate 5

value: Engerix B


title: Mouse E10.5 S1


title: Gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

city: Utrecht

first: Helmuth

last: Gehart

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
sorted cells from small intestinal crypts (M03)
Extracted RNA from gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. CEL-Seq
Genome_build: mm10
Supplementary_files_format_and_content: coutc files contain raw counts (not normalized)

source_name: murine small intestinal crypts

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing (Samples Neurog3ChronoBulk01-06) or on an Illumina Hiseq4000 using 150bp paired end sequencing (Samples Neurog3ChronoBulk09-16)

tag: genotype

value: Neurog3Chrono hom

value: intestine

tag: sequencing

value: HiSeq4000 150 bp paired end

tag: barcode number

tag: barcode sequence

value: ACTGATCG


title: BPH78

tag: class

tag: psa

tag: gs


title: Normal22

value: Healthy Donor


title: ERC_Alzheimer_Br5086

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-E02

source_name: ERC

tag: brnum

tag: tissue region

value: ERC

tag: disease state (dx)

value: Alzheimer

tag: age

value: F

value: CAUC


title: BPH161

source_name: plasma

value: Benign Prostatic Hyperplasia


title: DLPFC_Alzheimer_Br5086

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D08

value: DLPFC

tag: Sex

tag: race


title: Gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 4

description:
sorted cells from small intestinal crypts (M03)
Extracted RNA from gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 4

tag: tissue

value: CAGTCATC


title: BPH150


title: Norm47


title: ENG_MLN_4h_3

description:
m.MLN.Engerix.04.3
Gene expression in lymph nodes 4hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Engerix B, replicate 3

tag: strain/background

tag: gender

value: Female

value: draining medial iliac lymph nodes (MLN)

tag: treatment

tag: timepoint


title: Norm45


title: Gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 4

description:
sorted cells from small intestinal crypts (M03)
Extracted RNA from gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 4

tag: genotype

tag: sequencing

tag: strain

value: TGCATATC


title: ENG_MLN_4h_1

description:
m.MLN.Engerix.04.1
Gene expression in lymph nodes 4hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Engerix B, replicate 1

tag: animal replicate


title: DLPFC_Control_Br1314

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D06

value: Plate 1

value: brain

value: Control

value: AA


title: DLPFC_Alzheimer_Br5112

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D04

value: M


title: ENG_MLN_4h_2

description:
m.MLN.Engerix.04.2
Gene expression in lymph nodes 4hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Engerix B, replicate 2

value: Engerix B


title: ENG_MLN_4h_4

description:
m.MLN.Engerix.04.4
Gene expression in lymph nodes 4hrs after injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 4hr, Engerix B, replicate 4


title: Gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

description:
sorted cells from small intestinal crypts (M03)
Extracted RNA from gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

value: Neurog3Chrono hom

value: intestine

value: HiSeq4000 150 bp paired end

tag: barcode number

tag: barcode sequence

value: ACTGAATC


title: Norm44

tag: class

value: Healthy Donor

tag: psa

tag: gs


title: TriFLU-MF59_BL_4h_5

description:
m.blood.TriFluMF59.04.5
Gene expression in blood 4hrs after injection with Fluad.

source_name: Peripheral Blood, 4hr, Fluad, replicate 5

value: PBMC

value: Fluad


title: TriFLU-MF59_BL_4h_4

description:
m.blood.TriFluMF59.04.4
Gene expression in blood 4hrs after injection with Fluad.

source_name: Peripheral Blood, 4hr, Fluad, replicate 4


title: DLPFC_Control_Br1504

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D03

tag: brnum

tag: tissue region

value: DLPFC

tag: disease state (dx)

tag: age


title: TriFLU-MF59_BL_4h_3

description:
m.blood.TriFluMF59.04.3
Gene expression in blood 4hrs after injection with Fluad.

source_name: Peripheral Blood, 4hr, Fluad, replicate 3

tag: strain/background

value: Female

tag: tissue


title: Gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

description:
sorted cells from small intestinal crypts (M02)
Extracted RNA from gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

value: GTACGCGA


title: DLPFC_Control_Br1249

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-D02

tag: Sex

value: F

tag: race


title: Norm43


title: DLPFC_Alzheimer_Br5098

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C12

value: Plate 1

value: Alzheimer

value: CAUC


title: Gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

description:
sorted cells from small intestinal crypts (M02)
Extracted RNA from gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

tag: genotype

value: TGCATCGA


title: Gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

description:
sorted cells from small intestinal crypts (M02)
Extracted RNA from gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 3

tag: sequencing

value: CAGTCCGA


title: TriFLU-MF59_BL_4h_2

description:
m.blood.TriFluMF59.04.2
Gene expression in blood 4hrs after injection with Fluad.

source_name: Peripheral Blood, 4hr, Fluad, replicate 2

tag: gender

tag: treatment

tag: timepoint


title: PCa196

value: Prostate Cancer


title: DLPFC_Control_Br1654

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C11

value: brain

value: Control

value: M


title: Gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

description:
sorted cells from small intestinal crypts (M02)
Extracted RNA from gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

value: Neurog3Chrono hom

value: intestine

value: HiSeq4000 150 bp paired end

tag: strain

tag: barcode number

tag: barcode sequence

value: ACTGACGA


title: PCa193

tag: class

tag: psa

tag: gs


title: BPH149

value: Benign Prostatic Hyperplasia


title: DLPFC_Alzheimer_Br5105

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C09

tag: brnum

tag: tissue region

value: DLPFC

tag: disease state (dx)


title: C57Bl6_Thiomac_GRO_Veh_SD_16-08-16-SD272

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Library strategy: GRO-seq
Reads from each RNA-Seq sample were aligned to the mm10 genome using STAR.
Aligned read files were analyzed with HOMER (http://homer.ucsd.edu/homer/) to calculate RPKM from the exons of RefSeq genes (using the following command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -rpkm)
BigWig tracks were created using the HOMER makeBigWig.pl command
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files showing transcriptional activity around the binding sites of several transcription factors of interest in this study (number of GRO-seq reads within 500 basepairs of transcription factor binding sites).

source_name: mouse thioglycollate elicited macrophage cells

growth_protocol: TGEMs were grown for 3 days in 10%FBS, 1%Penicillin Streptomycin, DMEM

extract_protocol:
Nascent transcription was captured by global nuclear run-on sequencing (GRO-seq). Nuclei isolation. Nuclei were isolated from TGEMs using hypotonic lysis (10 mM Tris-HCl (pH 7.5), 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL CA-630) and flash frozen in GRO-freezing buffer (50 mM Tris-HCl (pH 7.8), 5 mM MgCl2, 40% Glycerol). Run-on. 3-5 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (Duttke et al., 2015) with 3x NRO buffer (15mM Tris-Cl (pH 8.0), 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/uL of SUPERase In, 1.5% Sarkosyl, 366 uM ATP, GTP (Roche), Br-UTP (Sigma 40 Aldrich) and 1.2 uM CTP (Roche, to limit run-on length to ~40 nt)). Reactions were stopped after five minutes by addition of 500 uL Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer. Fragmentation. RNA pellets were resuspended in 18 ul ddH2O + 0.05% Tween (dH2O+T) and 2 ul fragmentation mix (100 mM ZnCl2, 10 mM Tris-HCl (pH 7.5)), then incubated at 70°C for 15 minutes. Fragmentation was stopped by addition of 2.5 ul 100 mM EDTA. BrdU enrichment. BrdU enrichment was performed using BrdU Antibody (IIB5) AC beads (Santa Cruz, sc-32323 AC, lot #A0215 and #C1716), as described in detail by Hetzel et al (Hetzel et al., 2016). Beads were washed once with GRO binding buffer (0.25×saline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA) + 300 mM NaCl followed by three washes in GRO binding buffer and resuspend as 25% (vol/vol) slurry with 0.1 U/uL SUPERase-in. To fragmented RNA, 500 uL cold GRO binding buffer and 40 uL equilibrated BrdU antibody beads were added and samples slowly rotated at 4°C for 80 minutes. Beads were subsequently spun down at 1000xG for 15 seconds, supernatant removed and the beads transferred to a Millipore Ultrafree MC column (UFC30HVNB; Millipore) in 2x 200 uL GRO binding buffer. The IP reaction was washed twice with 400 uL GRO binding buffer before RNA was eluted by incubation in 200 uL Trizol LS (Thermo Fisher) under gentle agitation for 3 minutes. The elution was repeated a second time, 120 uL of dH2O+T added to increase the supernatant and extracted as described by the manufacturer. End repair and decapping. For end-repair and decapping, RNA pellets were dissolved in 8 ul TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.05 % Tween20) by vigorous vortexing, heated to 70°C for 2 minutes and placed on ice. After a quick spin, 22 ul Repair MM (3 ul 10x PNK buffer, 15.5 ul dH2O+T, 0.5 ul SUPERase-In RNase Inhibitor (10 U), 2 ul PNK (20U), 1 ul RppH (5U)) was added, mixed and incubated at 37°C for 1 hour. 5' Phosphorylation. To phosphorylate the 5'end, 0.5 ul 100 mM ATP was subsequently added and the reactions were incubated for another 45 minutes at 37°C (the high ATP concentration quenches RppH activity). Following end repair, 2.5 ul 50 mM EDTA was added, reactions mixed and then heated to 70°C for 2 minutes before being placed on ice. A second BrdU enrichment was performed as detailed above. Adapter Ligation. RNA pellets were dissolved in 2.75  TET + 0.25  Illumina TruSeq 3'Adapter (10  M), heated to 70°C for 2 minutes and placed on ice. 7  of 3'MM (4.75  50% PEG8000, 1  10x T4 RNA ligase buffer, 0.25  SUPERase-In, 1  T4 RNA Ligase 2 truncated (200U; NEB)) was added, mixed well and reactions incubated at 20°C for 1 hour. Reactions were diluted by addition of 10  TET + 2 ul 50 mM EDTA, heated to 70°C for 2 minutes, placed on ice and a third round of BrdUTP enrichment was performed. RNA pellets were transferred to PCR strips during the 75% ethanol wash and dried. Samples were dissolved in 4  TET (10 mM Tris-HCl (pH 7.5), 0.1 mM EDTA, 0.05% Tween 20) + 1  10  M reverse transcription (RT) primer. To anneal the RTprimer, the mixture was incubated at 75°C for 5 minutes, 37°C for 15 minutes and 25°C for 10 minutes. To ligate the 5' Illumina TruSeq adapter, 10  5'MM (1.5  ddH2O + 0.2% Tween20, 0.25  denaturated 5'TruSeq adapter (10  M), 1.5  10x T4 RNA ligase buffer, 0.25  SUPERase-In, 0.2  10 mM ATP, 5.8  50% PEG8000, 0.5  T4 RNA ligase 1 (5U; NEB)) was added and reactions were incubated at 25°C for 1 hour. Reverse Transcription. Reverse transcription was performed using Protoscript II (NEB) (4  5x NEB FirstStrand buffer (NEB; E7421AA), 0.25  SUPERase-In, 0.75  Protoscript II (150U; NEB)) at 50°C for 1 hour. After addition of 30  PCR MM (25  2X LongAmp Taq 2X Master Mix (NEB), 0.2  100  M forward primer, 2.8  5M Betaine and 2  10  M individual barcoding primer), mixtures were amplified (95°C for 3 minutes, (95°C for 60 seconds, 62°C for 30 seconds, 72°C for 15 seconds) x13, 72°C for 3 minutes). PCR reactions were cleaned up using 1.5 volumes of SpeedBeads™ (GE Healthcare) in 2.5M NaCl/20% PEG8000 Library selection and cleaning. Libraries were size selected on a PAGE/TBE gels to 160-225 base pairs. Gel slices were shredded by spinning through a 0.5 ml perforated PCR tube placed on top of a 1.5 ml tube. 150 ul Gel EB (0.1% LDS, 1M LiCl, 10 mM Tris-HCl (pH 7.8)) was added and the slurry incubate under agitation overnight. To purify the eluted DNA, 700 ul Zymogen ChIP DNA binding buffer was added into the 1.5 ml tube containing the shredded gel slice and the Gel EB, mixed by pipetting and the slurry transferred to a ZymoMiniElute column. Samples were first spun at 1000xG for 3 minutes, then 10,000xG for 30 seconds. Flow through was removed, and samples washed with 200 ul Zymo WashBuffer (with EtOH). Gel remainders were removed by flicking and columns washed by addition of another 200 ul Zymo WashBuffer (with EtOH). Flow through was 42 removed, columns spun dry by centrifugation at 14,000xG for 1 minute and DNA eluted by addition of 20 ul pre-warmed Sequencing TET (10 mM Tris-HCl (pH 8.0), 0.1 mM EDTA, 0.05% Tween 20). Libraries were sequenced.
RNA pellets were resuspended in 18 ul ddH2O + 0.05% Tween (dH2O+T) and 2 ul fragmentation mix [100 mM ZnCl2, 10 mM Tris-HCl (pH 7.5)], then incubated at 70°C for 15 minutes. Fragmentation was stopped by addition of 2.5 ul 100 mM EDTA. BrdU enrichment was performed using BrdU Antibody (IIB5) AC beads (Santa Cruz, sc-32323 AC, lot #A0215 and #C1716), as described in detail by Hetzel et al (Hetzel et al., 2016). Beads were washed once with GRO binding buffer [0.25×saline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA] + 300 mM NaCl followed by three washes in GRO binding buffer and resuspend as 25% (vol/vol) slurry with 0.1 U/uL SUPERase-in. To fragmented RNA, 500 uL cold GRO binding buffer and 40 uL equilibrated BrdU antibody beads were added and samples slowly rotated at 4°C for 80 minutes. Beads were subsequently spun down at 1000xG for 15 seconds, supernatant removed and the beads transferred to a Millipore Ultrafree MC column (UFC30HVNB; Millipore) in about 2x 200 uL GRO binding buffer. The IP reaction waswashed twice with 400 uL GRO binding buffer before RNA was eluted by incubation in 200 uL Trizol LS (Thermo Fisher) under gentle agitation for 3 minutes. The elution was repeated a second time, 120 uL of dH2O+T added to increase the supernatant and extracted as described by the manufacturer. For end-repair and decapping, RNA pellets were dissolved in 8 ul TET [10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.05 % Tween20] by vigorous vortexing, heated to 70°C for 2 minutes and placed on ice. After a quick spin, 22 ul Repair MM [3 ul 10x PNK buffer, 15.5 ul dH2O+T, 0.5 ul SUPERase-In RNase Inhibitor (10 U), 2 ul PNK (20U), 1 ul RppH (5U)] was added, mixed by flicking and incubated at 37°C for 1 hour. To phosphorylate the 5'end, 0.5 ul 100 mM ATP was subsequently added and the reactions were incubated for another 45 minutes at 37°C (the high ATP concentration quenches RppH activity). Following end repair, 2.5 ul 50 mM EDTA was added, reactions mixed and then heated to 70°C for 2 minutes before being placed on ice. A second BrdU enrichment was performed as detailed above. For li

treatment_protocol: Veh (PBS) or KLA were added directly to the media

tag: tissue

value: male

value: Vehicle


title: C57Bl6_Thiomac_GRO_Veh_SD_16-08-16-SD271

value: mouse thioglycollate elicited macrophage cells

tag: Sex


title: PCa177


title: Norm41

value: Healthy Donor


title: Norm40


title: TriFLU_BL_4h_4

description:
m.blood.TriFlu.04.4
Gene expression in blood 4hrs after injection with Agrippal.

source_name: Peripheral Blood, 4hr, Agrippal, replicate 4

tag: strain/background

value: Female

value: PBMC

value: Agrippal

tag: animal replicate


title: C57Bl6_Thiomac_GRO_KLA-1h_SD_16-08-16-SD274

value: KLA 1h

tag: genotype


title: DLPFC_Alzheimer_Br5103

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C05

value: Plate 1

value: brain

value: Alzheimer

tag: age

tag: race

value: CAUC


title: Norm39


title: DLPFC_Control_Br2053

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C06

value: Control

value: M

value: AA


title: C57Bl6_Thiomac_GRO_KLA-1h_SD_16-08-16-SD273

tag: treatment


title: Balbc_Thiomac_ChIP_JunD_Veh

library_source: genomic

data_processing:
Reads from each ChIP-seq sample were aligned to the mm10 build of the mouse genome using bowtie2 (with default parameters).
Sam files were converted to tag directories with HOMER
Peaks were called with HOMER with the findPeaks command using the corresponding input file and the parameters -L 0 -C 0 -fdr 0.9
HOMER peak scores from peak files corresponding to replicate experiments were used as input for IDR; peaks with IDR < 0.05 were retained
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file giving the genomic coordinates of putative binding site for each ChIP target. The "count" column indicates the HOMER peak score

extract_protocol:
Protein A and G Dynabeads 50/50 mix from Invitrogen are sued for ChIP (10001D, 10003D). IP mix consists of 20ul beads/2ug antibody per 2 million cell ChIP. For preparation, beads were washed with 0.5%BSA-PBS (BSA: , then incubate beads-antibody with 0.5%BSA-PBS for at least 1h on rotator (4oC). Wash 2X with 0.5%BSA-PBS, then resuspend in dilution buffer. Double Crosslinking for ChIP. Media was decanted from cells in 10 cm plates, wash once briefly with PBS (RT). Disuccinimidyl glutarate (Pierce Cat # 20593)  (diluted in DMSO at 200mM)/PBS (RT) was used for 10 min. Then Formaldehyde was added to a final concentration of 1% for an additional 10 min. Reaction was quenched with 1:10 Tris pH 7.4 on ice. Cells were collected and washed twice with cold PBS, spinning at 1000 rcf for 5 min. Nuclei Isolation and Sonication. Resuspend cell pellets in 1 ml of Nuclei Isolation Buffer (50 mM Tris-Ph 8.0, 60 mM KCl, 0.5% NP40) + PI and incubate on ice for 10 minutes. Centrifuge 2,000 g for 3 minutes at 4º C. Resuspend nuclei in 200 ul of fresh Lysis Buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (ph8))+ PI. Sonication. Nuclei were then sonicated (10 million cells) for 25 minutes in a Biorupter (settings= 30 seconds=On, 30 seconds=Off, Medium) using thin wall tubes (Diagenode Cat# C30010010). After sonication spin max speed for 10 minute at 4C.  ChIP set up. Sonicated DNA was diluted 5X with 800 Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (ph8), 1X Protease Inhibitors).  An aliquot is removed for input samples (5%).  Samples ON at 4º C while rotating. Washing. ChIP are washed 1X with TSE I (20mM Tris-HCl pH7.4, 150mM NaCl, 0.1%SDS, 1% Triton X-100, 2mM EDTA), 2X with TSE III (10mM Tris-HCl pH7.4, 250mM LiCl, 1%IGEPAL, 1%Deoxycholate, 1mM EDTA), 1X with TE+0.1%TritonX-100, transfer to new tube and then wash another time with TE+0.1%TritonX-100.   Elution. Elute with 200 uL Elution Buffer (1% SDS, 10mM Tris pH7.5) for 20 minutes at RT, shaking on the vortex or a nutator or rotator.  De-crosslinking. Add 10 uL of 5 M NaCl and incubate ON at 65º C (or at least 8 hours).  Clean up samples using Zymo ChIP DNA Clean & Concentrator. Elute in 100uL. Take 40uL and proceed to library prep protocol.
dsDNA End Repair. We mixed 40uL of DNA from ChIP or RNA protocols with 2.9uL of H2O, 0.5uL 1% Tween-20, 5uL 10X T4 ligase buffer (Enzymatics cat# L6030-HC-L), 1uL dNTP mix (10 mM  Affymetrix 77119), 0.3 uL T4 DNA pol (Enzymatics P7080L), 0.3uL T4 PNK (Enzymatics Y9040L), 0.06uL Klenow (Enzymatics P7060L) and incubated for 30min at 20°C. 1uL of Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) in 93 μL 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Bead clean-up. Beads were collected on a magnet and washed 2X with 80% ethanol. Beads were air-dried for 10 min and then eluted in 15uL ddH2O. dA-Tailing. DNA was mixed with 10.8uL ddH2O, 0.3uL 1% Tween-20, 3uL Blue Buffer (Enzymatics cat# B0110L), 0.6uL dATP (10mM Tech 10216-018), 0.3uL Klenow 3’- 5’ Exo (Enzymatics P7010-LC-L) and incubated for 30min at 37°C. 55.8uL 20% PEG8000/2.5 M NaCl (13% final) was added an incubated for 10 min. Then bead clean up was done. Beads were eluted in 14uL. Y-Shape Adapter Ligation. Sample was mixed with 0.5uL of a BIOO barcode adapter (BIOO Scientific cat# 514104), 15uL Rapid Ligation Buffer (Enzymatics cat@ L603-LC-L), 0.33uL 1% Tween-20 and 0.5uL T4 DNA ligase  HC (Enzymatics L6030-HC-L) and incubated for 15 min at RT.  7 μL of 20% PEG8000/2.5 M NaCl was added and incubated for 10min at RT. Bead clean up was performed and beads were eluted in 21uL. 10uL was then used for PCR amplification (14 cycles) with IGA and IGB primers (AATGATACGGCGACCACCGA, CAAGCAGAAGACGGCATACGA).

value: Veh

value: Balb/cJ

tag: antigen target

value: JunD (sc-74)

tag: library prep

value: ChIP


title: Norm38


title: TriFLU_BL_4h_3

description:
m.blood.TriFlu.04.3
Gene expression in blood 4hrs after injection with Agrippal.

source_name: Peripheral Blood, 4hr, Agrippal, replicate 3

tag: gender

tag: timepoint


title: DLPFC_Control_Br1157

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C10

source_name: DLPFC

value: DLPFC


title: DLPFC_Control_Br1764

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C04


title: TriFLU_BL_4h_2

description:
m.blood.TriFlu.04.2
Gene expression in blood 4hrs after injection with Agrippal.

source_name: Peripheral Blood, 4hr, Agrippal, replicate 2


title: TriFLU-MF59_BL_4h_1

description:
m.blood.TriFluMF59.04.1
Gene expression in blood 4hrs after injection with Fluad.

source_name: Peripheral Blood, 4hr, Fluad, replicate 1

value: Fluad


title: TriFLU_BL_4h_5

description:
m.blood.TriFlu.04.5
Gene expression in blood 4hrs after injection with Agrippal.

source_name: Peripheral Blood, 4hr, Agrippal, replicate 5

value: Female


title: TriFLU_BL_4h_1

description:
m.blood.TriFlu.04.1
Gene expression in blood 4hrs after injection with Agrippal.

source_name: Peripheral Blood, 4hr, Agrippal, replicate 1

value: PBMC


title: DLPFC_Alzheimer_Br5107

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C08


title: PCa169

source_name: plasma

tag: class

value: Prostate Cancer

tag: psa


title: SAL_BL_4h_5

description:
m.blood.saline.04.5
Gene expression in blood 4hrs after injection with saline.

source_name: Peripheral Blood, 4hr, Saline, replicate 5

value: saline


title: SAL_BL_4h_4

description:
m.blood.saline.04.4
Gene expression in blood 4hrs after injection with saline.

source_name: Peripheral Blood, 4hr, Saline, replicate 4


title: BPH148

value: Benign Prostatic Hyperplasia

tag: gs


title: DLPFC_Control_Br1987

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C03

value: Plate 1

tag: brnum

value: brain

tag: tissue region


title: Balbc_Thiomac_ChIP_JunB_Veh

tag: tissue

value: mouse thioglycollate elicited macrophage cells

value: male

value: JunB (sc-73)


title: Balbc_Thiomac_ChIP_JunB_KLA-1h

tag: Sex


title: DLPFC_Alzheimer_Br5078

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C02

tag: disease state (dx)

value: Alzheimer

value: M

value: CAUC


title: Balbc_Thiomac_ChIP_JunD_KLA-1h

value: Balb/cJ

value: JunD (sc-74)


title: CRB_Control_Br1069

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B12

source_name: CRB

value: CRB

value: Control

value: F

value: AA


title: CRB_Control_Br1960

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-C01


title: PCa156

value: Prostate Cancer


title: BPH142


title: PCa165


title: CRB_Control_Br1156

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B10


title: Balbc_Thiomac_ChIP_Input_Veh

value: Veh

value: ChIP


title: CRB_Alzheimer_Br5095

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B08

value: Plate 1


title: SAL_BL_4h_3

description:
m.blood.saline.04.3
Gene expression in blood 4hrs after injection with saline.

source_name: Peripheral Blood, 4hr, Saline, replicate 3

tag: strain/background

value: Female

value: PBMC

value: saline

tag: animal replicate


title: SAL_BL_4h_2

description:
m.blood.saline.04.2
Gene expression in blood 4hrs after injection with saline.

source_name: Peripheral Blood, 4hr, Saline, replicate 2


title: Balbc_Thiomac_ChIP_Fos_KLA-1h

value: mouse thioglycollate elicited macrophage cells

value: male

tag: genotype


title: Balbc_Thiomac_ChIP_Input_KLA-1h


title: Balbc_Thiomac_ChIP_cJun_Veh


title: CRB_Control_Br1613

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B07

value: brain

tag: age

value: M

tag: race


title: BPH103

value: Benign Prostatic Hyperplasia


title: SAL_BL_4h_1

description:
m.blood.saline.04.1
Gene expression in blood 4hrs after injection with saline.

source_name: Peripheral Blood, 4hr, Saline, replicate 1

tag: treatment


title: BPH107


title: CRB_Alzheimer_Br5100

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B05

value: Alzheimer

value: CAUC


title: BPH99


title: PCa155


title: Balbc_Thiomac_ChIP_cJun_KLA-1h

value: Balb/cJ

tag: antigen target

tag: library prep


title: CRB_Control_Br1537

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B04

value: CRB

value: Control

value: F


title: PolyIC_BL_4h_4

description:
m.blood.PolyIC.04.4
Gene expression in blood 4hrs after injection with Poly I:C.

source_name: Peripheral Blood, 4hr, Poly I:C, replicate 4

tag: gender

value: PolyIC

tag: timepoint


title: PolyIC_BL_4h_2

description:
m.blood.PolyIC.04.2
Gene expression in blood 4hrs after injection with Poly I:C.

source_name: Peripheral Blood, 4hr, Poly I:C, replicate 2


title: PolyIC_BL_4h_5

description:
m.blood.PolyIC.04.5
Gene expression in blood 4hrs after injection with Poly I:C.

source_name: Peripheral Blood, 4hr, Poly I:C, replicate 5


title: Balbc_Thiomac_ChIP_Fos_Veh

source_name: mouse thioglycollate elicited macrophage cells

value: Veh

value: ChIP


title: PolyIC_BL_4h_1

description:
m.blood.PolyIC.04.1
Gene expression in blood 4hrs after injection with Poly I:C.

source_name: Peripheral Blood, 4hr, Poly I:C, replicate 1

value: Female


title: PCa154

tag: class

value: Prostate Cancer

tag: psa


title: Balbc_Thiomac_ChIP_ATF3_Veh


title: PERT_BL_4h_5

description:
m.blood.Pertussis.04.5
Gene expression in blood 4hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 4hr, Pentavac SD, replicate 5

value: PBMC

value: Pentavac SD


title: PolyIC_BL_4h_3

description:
m.blood.PolyIC.04.3
Gene expression in blood 4hrs after injection with Poly I:C.

source_name: Peripheral Blood, 4hr, Poly I:C, replicate 3


title: Balbc_Thiomac_ChIP_ATF3_KLA-1h

value: mouse thioglycollate elicited macrophage cells

value: male


title: CRB_Control_Br1297

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B01

value: Plate 1

tag: brnum

value: brain

value: M

value: AA


title: CRB_Control_Br1054

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-B03

tag: tissue region


title: C57Bl6_Thiomac_ChIP_PU1_Veh

tag: tissue


title: PCa146

tag: gs


title: PERT_BL_4h_3

description:
m.blood.Pertussis.04.3
Gene expression in blood 4hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 4hr, Pentavac SD, replicate 3


title: CRB_Control_Br1987

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A11

tag: disease state (dx)

tag: Sex

value: CAUC


title: CRB_Control_Br1003

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A09

value: CRB


title: PCa139


title: C57Bl6_Thiomac_ChIP_JunD_Veh

value: JunD (sc-74)


title: CRB_Alzheimer_Br5103

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A08

value: Alzheimer


title: BPH136

value: Benign Prostatic Hyperplasia


title: C57Bl6_Thiomac_ChIP_JunD_KLA-1h


title: BPH132


title: BPH130


title: PERT_BL_4h_2

description:
m.blood.Pertussis.04.2
Gene expression in blood 4hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 4hr, Pentavac SD, replicate 2

tag: strain/background

tag: animal replicate


title: CRB_Alzheimer_Br5112

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A07

tag: age


title: PERT_BL_4h_4

description:
m.blood.Pertussis.04.4
Gene expression in blood 4hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 4hr, Pentavac SD, replicate 4


title: LPS_BL_4h_5

description:
m.blood.LPS.04.5
Gene expression in blood 4hrs after injection with LPS.

source_name: Peripheral Blood, 4hr, LPS, replicate 5

value: LPS


title: PERT_BL_4h_1

description:
m.blood.Pertussis.04.1
Gene expression in blood 4hrs after injection with Pentavac SD.

source_name: Peripheral Blood, 4hr, Pentavac SD, replicate 1


title: LPS_BL_4h_4

description:
m.blood.LPS.04.4
Gene expression in blood 4hrs after injection with LPS.

source_name: Peripheral Blood, 4hr, LPS, replicate 4


title: C57Bl6_Thiomac_ChIP_Input_KLA-1h

tag: genotype

value: ChIP


title: CRB_Alzheimer_Br5075

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A05

source_name: CRB

tag: race


title: PCa34

source_name: plasma


title: CRB_Control_Br1522

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A04

value: Control

value: F


title: BPH129


title: CRB_Alzheimer_Br5098

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A03


title: C57Bl6_Thiomac_ChIP_JunB_Veh

tag: treatment

value: Veh

tag: antigen target

value: JunB (sc-73)


title: CRB_Alzheimer_Br5094

description:
Postmortem human brain tissue samples from four brain regions in an Alzheimers disease case-control series used to generate Human450k DNA methylation data.
1-A06


title: C57Bl6_Thiomac_ChIP_Input_Veh

value: mouse thioglycollate elicited macrophage cells

tag: library prep


title: PCa25

value: Prostate Cancer


title: PCa17


title: LPS_BL_4h_3

description:
m.blood.LPS.04.3
Gene expression in blood 4hrs after injection with LPS.

source_name: Peripheral Blood, 4hr, LPS, replicate 3

tag: gender

value: Female

value: PBMC

tag: timepoint


title: BPH69

tag: class

tag: psa


title: IFA_MLN_4h_2

description:
m.MLN.IFA.04.2
Gene expression in lymph nodes 4hrs after injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 4hr, IFA, replicate 2

value: draining medial iliac lymph nodes (MLN)

value: IFA


title: IFA_BL_4h_5

description:
m.blood.IFA.04.5
Gene expression in blood 4hrs after injection with IFA.

source_name: Peripheral Blood, 4hr, IFA, replicate 5


title: C57Bl6_Thiomac_ChIP_Fra2_KLA-1h

value: male


title: C57Bl6_Thiomac_ChIP_cJun_KLA-1h


title: LPS_BL_4h_1

description:
m.blood.LPS.04.1
Gene expression in blood 4hrs after injection with LPS.

source_name: Peripheral Blood, 4hr, LPS, replicate 1


title: C57Bl6_Thiomac_ChIP_cJun_Veh


title: C57Bl6_Thiomac_ChIP_CEBPa_KLA-1h

value: Cebpa (sc-61)


title: C57Bl6_Thiomac_ChIP_CEBPa_Veh


title: PCa4


title: LPS_BL_4h_2

description:
m.blood.LPS.04.2
Gene expression in blood 4hrs after injection with LPS.

source_name: Peripheral Blood, 4hr, LPS, replicate 2


title: IFA_BL_4h_4

description:
m.blood.IFA.04.4
Gene expression in blood 4hrs after injection with IFA.

source_name: Peripheral Blood, 4hr, IFA, replicate 4


title: BPH137


title: BPH31


title: C57Bl6_Thiomac_ChIP_ATF3_Veh

source_name: mouse thioglycollate elicited macrophage cells


title: C57Bl6_Thiomac_ChIP_ATF3_KLA-1h


title: C57Bl6-PPARgKO_Thiomac_ChIP_JunD_Veh

value: PPARgKO

value: JunD (sc-74)


title: PCa126


title: PCa123


title: C57Bl6-PPARgKO_Thiomac_ChIP_cJun_Veh