title: Subject_1_LABOR_Subcutaneous [gene-level]

value: Subject 1

value: labor

value: Subcutaneous


title: Subject_30_NOLABOR_Visceral [gene-level]

status: Public on Dec 31 2015

type: RNA

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

country: USA

institute: Wayne State University

hyb_protocol: Standard Affymetrix Exon Array hyb protocol.

scan_protocol: Standard Affymetrix Exon Array scan protocol.

data_processing:
Probe intensities were summarized and processed with RMA implemented in arroma.affymetrix package in R-3.2.2. For transcript level summaries ExonRmaPlm function from arroma.affymetrix was used (option mergeGroups=TRUE), while for probeset (exon) level summaries the option mergeGroups=FALSE was used.
probe group file: HuEx-1_0-st-v2.na30.hg19.probeset.csv
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv
Log2 transformed probeset (exon) and transcript (group) level expression summaries for core transcripts based on NetAffx Nov. 12, 2007 (R3) (HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) .

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: no labor_Visceral

label_protocol: Standard Affymetrix Exon Array labeling protocol.

growth_protocol: Paired visceral and subcutaneous adipose tissue samples were obtained after an eight-hour fast. Subcutaneous adipose tissue samples were collected at the site of a transverse lower abdominal incision, in the middle of the Pfannenstiel incision, from the deeper strata of subcutaneous fat. Visceral samples were obtained from the most distal portion of the greater omentum.(Visceral and subcutaneous adipose tissues were collected using Metzenbaum scissors and measured approximately 1.0 cm3. Tissues were snap-frozen in liquid nitrogen, and were kept at –80°C until use.

extract_protocol: Total RNA was isolated from snap-frozen adipose tissue samples using TRI Reagent® (Ambion®, Life Technologies Corporation, Austin, TX, USA) combined with the Qiagen RNeasy Lipid Tissue Kit protocol (Qiagen, Valencia, CA, USA), according to the manufacturers’ recommendations. The RNA concentrations and the A260 nm/A280 nm ratios were assessed using a NanoDrop® 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA integrity numbers were determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: No treatments were involved.

tag: subject id

value: Subject 30

tag: subject status

value: no labor

tag: tissue

value: adipose

tag: region

value: Visceral


title: Subject_33_NONPREGNANT_Visceral [gene-level]

source_name: non pregnant_Visceral

value: Subject 33

value: non pregnant


title: Subject_47_LABOR_Visceral [gene-level]

value: Subject 47


title: Subject_29_NOLABOR_Visceral [gene-level]

value: Subject 29


title: Subject_37_NONPREGNANT_Subcutaneous [gene-level]

source_name: non pregnant_Subcutaneous

value: Subject 37


title: Subject_48_NOLABOR_Subcutaneous [gene-level]

source_name: no labor_Subcutaneous

value: Subject 48


title: Subject_51_LABOR_Visceral [gene-level]

value: Subject 51


title: Subject_46_LABOR_Visceral [gene-level]

value: Subject 46


title: Subject_10_NOLABOR_Subcutaneous [gene-level]

value: Subject 10


title: Subject_34_NOLABOR_Visceral [gene-level]

value: Subject 34


title: Subject_16_NOLABOR_Subcutaneous [gene-level]

value: Subject 16


title: Subject_8_LABOR_Subcutaneous [gene-level]

value: Subject 8

value: labor


title: Subject_32_NOLABOR_Visceral [gene-level]

value: Subject 32


title: Subject_10_NOLABOR_Visceral [gene-level]

value: no labor


title: Subject_47_LABOR_Subcutaneous [gene-level]

value: adipose

value: Subcutaneous


title: Subject_39_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 39


title: Subject_23_NOLABOR_Subcutaneous [gene-level]

value: Subject 23


title: Subject_28_NOLABOR_Visceral [gene-level]

value: Subject 28

value: Visceral


title: Subject_26_LABOR_Visceral [gene-level]

value: Subject 26


title: Subject_40_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 40

value: non pregnant


title: Subject_15_NOLABOR_Visceral [gene-level]

value: Subject 15


title: Subject_20_NOLABOR_Visceral [gene-level]

value: Subject 20


title: Subject_6_LABOR_Visceral [gene-level]

value: Subject 6


title: Subject_29_NOLABOR_Subcutaneous [gene-level]

value: Subject 29


title: Subject_24_NOLABOR_Subcutaneous [gene-level]

value: Subject 24


title: Subject_45_NONPREGNANT_Visceral [gene-level]

value: Subject 45


title: Subject_5_NOLABOR_Visceral [gene-level]

value: Subject 5


title: Subject_43_LABOR_Visceral [gene-level]

value: Subject 43

value: labor


title: Subject_8_LABOR_Visceral [gene-level]

value: Subject 8

value: adipose


title: Subject_17_NOLABOR_Subcutaneous [gene-level]

value: Subject 17

value: no labor

value: Subcutaneous


title: Subject_14_NOLABOR_Subcutaneous [gene-level]

value: Subject 14


title: Subject_43_LABOR_Subcutaneous [gene-level]


title: Subject_49_LABOR_Visceral [gene-level]

value: Subject 49

value: Visceral


title: Subject_36_NONPREGNANT_Visceral [gene-level]

value: Subject 36

value: non pregnant


title: Subject_4_LABOR_Visceral [gene-level]

value: Subject 4


title: Subject_14_NOLABOR_Visceral [gene-level]


title: Subject_12_NOLABOR_Subcutaneous [gene-level]

value: Subject 12


title: Subject_11_NOLABOR_Visceral [gene-level]

value: Subject 11


title: Subject_9_NOLABOR_Visceral [gene-level]

value: Subject 9


title: Subject_42_LABOR_Subcutaneous [gene-level]

value: Subject 42


title: Subject_27_LABOR_Visceral [gene-level]

value: Subject 27


title: Subject_23_NOLABOR_Visceral [gene-level]

value: Subject 23


title: Subject_7_NOLABOR_Visceral [gene-level]

value: Subject 7


title: Subject_31_NONPREGNANT_Visceral [gene-level]

value: Subject 31

value: adipose


title: Subject_33_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 33


title: Subject_27_LABOR_Subcutaneous [gene-level]

value: labor

value: Subcutaneous


title: Subject_41_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 41


title: Subject_45_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 45


title: Subject_25_LABOR_Subcutaneous [gene-level]

value: Subject 25


title: Subject_37_NONPREGNANT_Visceral [gene-level]

value: Subject 37

value: non pregnant

value: Visceral


title: Subject_46_LABOR_Subcutaneous [gene-level]

value: Subject 46


title: Subject_20_NOLABOR_Subcutaneous [gene-level]

value: Subject 20

value: no labor


title: Subject_38_NONPREGNANT_Subcutaneous [gene-level]

value: Subject 38


title: Subject_19_NONPREGNANT_Visceral [gene-level]

value: Subject 19


title: Subject_50_NOLABOR_Visceral [gene-level]

value: Subject 50


title: Subject_3_LABOR_Visceral [gene-level]

value: Subject 3


title: Subject_15_NOLABOR_Subcutaneous [gene-level]

value: Subject 15

value: adipose


title: Subject_11_NOLABOR_Subcutaneous [gene-level]

value: Subject 11


title: Subject_31_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 31

value: Subcutaneous


title: Subject_2_LABOR_Visceral [exon-level]

value: Subject 2

value: labor


title: Subject_36_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 36


title: Subject_5_NOLABOR_Subcutaneous [exon-level]

value: Subject 5


title: Subject_30_NOLABOR_Subcutaneous [exon-level]

value: Subject 30


title: Subject_35_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 35

value: non pregnant


title: Subject_21_NOLABOR_Visceral [exon-level]

value: Subject 21

value: no labor

value: Visceral


title: Subject_1_LABOR_Visceral [exon-level]

value: Subject 1


title: Subject_17_NOLABOR_Visceral [exon-level]

value: Subject 17


title: Subject_18_NOLABOR_Visceral [exon-level]

value: Subject 18


title: Subject_9_NOLABOR_Subcutaneous [exon-level]

value: Subject 9

value: adipose


title: Subject_26_LABOR_Subcutaneous [exon-level]

value: Subject 26


title: Subject_38_NONPREGNANT_Visceral [exon-level]

value: Subject 38


title: Subject_48_NOLABOR_Visceral [exon-level]

value: Subject 48


title: Subject_28_NOLABOR_Subcutaneous [exon-level]

value: Subject 28

value: Subcutaneous


title: Subject_51_LABOR_Subcutaneous [exon-level]

value: Subject 51

value: labor


title: Subject_42_LABOR_Visceral [exon-level]

value: Subject 42


title: Subject_16_NOLABOR_Visceral [exon-level]

value: Subject 16


title: Subject_4_LABOR_Subcutaneous [exon-level]

value: Subject 4


title: Subject_22_NOLABOR_Visceral [exon-level]

value: Subject 22

value: no labor


title: Subject_2_LABOR_Subcutaneous [exon-level]

value: Subject 2


title: Subject_21_NOLABOR_Subcutaneous [exon-level]

value: Subject 21


title: Subject_25_LABOR_Visceral [exon-level]

value: Subject 25

value: Visceral


title: Subject_18_NOLABOR_Subcutaneous [exon-level]

value: Subject 18

value: adipose


title: Subject_50_NOLABOR_Subcutaneous [exon-level]

value: Subject 50


title: Subject_32_NOLABOR_Subcutaneous [exon-level]

value: Subject 32


title: Subject_13_NOLABOR_Visceral [exon-level]

value: Subject 13


title: Subject_44_NOLABOR_Subcutaneous [exon-level]

value: Subject 44

value: Subcutaneous


title: Subject_3_LABOR_Subcutaneous [exon-level]

value: Subject 3

value: labor


title: Subject_13_NOLABOR_Subcutaneous [exon-level]


title: Subject_19_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 19

value: non pregnant


title: Subject_35_NONPREGNANT_Visceral [exon-level]

value: Subject 35


title: Subject_22_NOLABOR_Subcutaneous [exon-level]

value: Subject 22

value: no labor


title: Subject_46_LABOR_Visceral [exon-level]

value: Subject 46


title: Subject_48_NOLABOR_Subcutaneous [exon-level]

value: Subject 48


title: Subject_8_LABOR_Subcutaneous [exon-level]

value: Subject 8


title: Subject_47_LABOR_Subcutaneous [exon-level]

value: Subject 47


title: Subject_51_LABOR_Visceral [exon-level]

value: Subject 51

value: adipose

value: Visceral


title: Subject_12_NOLABOR_Visceral [exon-level]

value: Subject 12


title: Subject_7_NOLABOR_Subcutaneous [exon-level]

value: Subject 7


title: Subject_1_LABOR_Subcutaneous [exon-level]

value: Subject 1

value: Subcutaneous


title: Subject_49_LABOR_Subcutaneous [exon-level]

value: Subject 49

value: labor


title: Subject_34_NOLABOR_Subcutaneous [exon-level]

value: Subject 34


title: Subject_16_NOLABOR_Subcutaneous [exon-level]

value: Subject 16


title: Subject_24_NOLABOR_Visceral [exon-level]

value: Subject 24


title: Subject_24_NOLABOR_Subcutaneous [exon-level]

value: no labor


title: Subject_29_NOLABOR_Visceral [exon-level]

value: Subject 29


title: Subject_44_NOLABOR_Visceral [exon-level]

value: Subject 44


title: Subject_10_NOLABOR_Visceral [exon-level]

value: Subject 10


title: Subject_39_NONPREGNANT_Visceral [exon-level]

value: Subject 39

value: non pregnant


title: Subject_34_NOLABOR_Visceral [exon-level]

value: adipose


title: Subject_40_NONPREGNANT_Visceral [exon-level]

value: Subject 40

value: Visceral


title: Subject_6_LABOR_Subcutaneous [exon-level]

value: Subject 6


title: Subject_32_NOLABOR_Visceral [exon-level]

value: Subject 32


title: Subject_33_NONPREGNANT_Visceral [exon-level]

value: Subject 33


title: Subject_40_NONPREGNANT_Subcutaneous [exon-level]

value: Subcutaneous


title: Subject_30_NOLABOR_Visceral [exon-level]

value: Subject 30


title: Subject_37_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 37


title: Subject_10_NOLABOR_Subcutaneous [exon-level]


title: Subject_41_NONPREGNANT_Visceral [exon-level]

value: Subject 41


title: Subject_39_NONPREGNANT_Subcutaneous [exon-level]


title: Subject_28_NOLABOR_Visceral [exon-level]

value: Subject 28


title: Subject_47_LABOR_Visceral [exon-level]

value: Subject 47

value: labor


title: Subject_23_NOLABOR_Subcutaneous [exon-level]

value: Subject 23

value: no labor


title: Subject_26_LABOR_Visceral [exon-level]

value: Subject 26


title: Subject_14_NOLABOR_Subcutaneous [exon-level]

value: Subject 14


title: Subject_15_NOLABOR_Visceral [exon-level]

value: Subject 15

value: adipose


title: Subject_38_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 38

value: non pregnant


title: Subject_5_NOLABOR_Visceral [exon-level]

value: Subject 5

value: Visceral


title: Subject_43_LABOR_Visceral [exon-level]

value: Subject 43


title: Subject_17_NOLABOR_Subcutaneous [exon-level]

value: Subject 17

value: Subcutaneous


title: Subject_9_NOLABOR_Visceral [exon-level]

value: Subject 9


title: Subject_12_NOLABOR_Subcutaneous [exon-level]

value: Subject 12


title: Subject_37_NONPREGNANT_Visceral [exon-level]

value: Subject 37


title: Subject_8_LABOR_Visceral [exon-level]

value: Subject 8

value: labor


title: Subject_45_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 45


title: Subject_49_LABOR_Visceral [exon-level]

value: Subject 49


title: Subject_36_NONPREGNANT_Visceral [exon-level]

value: Subject 36


title: Subject_20_NOLABOR_Visceral [exon-level]

value: Subject 20

value: no labor


title: Subject_43_LABOR_Subcutaneous [exon-level]

value: adipose


title: Subject_7_NOLABOR_Visceral [exon-level]

value: Subject 7


title: Subject_14_NOLABOR_Visceral [exon-level]

value: Subject 14


title: Subject_29_NOLABOR_Subcutaneous [exon-level]

value: Subject 29


title: Subject_6_LABOR_Visceral [exon-level]

value: Subject 6

value: Visceral


title: Subject_11_NOLABOR_Visceral [exon-level]

value: Subject 11


title: Subject_27_LABOR_Visceral [exon-level]

value: Subject 27


title: Subject_42_LABOR_Subcutaneous [exon-level]

value: Subject 42

value: Subcutaneous


title: Subject_19_NONPREGNANT_Visceral [exon-level]

value: Subject 19

value: non pregnant


title: Subject_4_LABOR_Visceral [exon-level]

value: Subject 4

value: labor


title: Subject_23_NOLABOR_Visceral [exon-level]

value: Subject 23


title: Subject_25_LABOR_Subcutaneous [exon-level]

value: Subject 25


title: Subject_20_NOLABOR_Subcutaneous [exon-level]

value: Subject 20

value: no labor


title: Subject_46_LABOR_Subcutaneous [exon-level]

value: Subject 46

value: adipose


title: Subject_31_NONPREGNANT_Visceral [exon-level]

value: Subject 31


title: Subject_15_NOLABOR_Subcutaneous [exon-level]

value: Subject 15


title: Subject_45_NONPREGNANT_Visceral [exon-level]

value: Subject 45

value: Visceral


title: Subject_27_LABOR_Subcutaneous [exon-level]

value: Subject 27


title: Subject_11_NOLABOR_Subcutaneous [exon-level]

value: Subject 11


title: Subject_41_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 41

value: Subcutaneous


title: 7327M

status: Public on Jan 21 2015

description:
CONTROL
9345725029_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probes without an entry in the keys of the package illuminaHumanv4.db (Bioconductor) were removed. All values were offset by adding 1 and then log2 transformed. Quantile normalization was performed using normalize.quantiles function form the preprocessCore package.

source_name: fetal membranes

label_protocol: Total RNA (500 ng) was amplified and biotin-labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: Total RNA was isolated from snap-frozen tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ recommendations.

value: fetal membranes

tag: neurocognitive impairment

value: CONTROL

tag: pair


title: 3764M

description:
CONTROL
9345725008_K


title: Subject_50_NOLABOR_Visceral [exon-level]

value: Subject 50


title: 7113M

description:
CASE
9345725029_A

value: CASE


title: Subject_3_LABOR_Visceral [exon-level]

value: Subject 3

value: labor


title: 4033M

description:
CONTROL
9345725029_B


title: 13582M

description:
CONTROL
9345725008_D


title: 13041M

description:
CASE
9345725008_G


title: 10285M

description:
CONTROL
9345725008_F


title: 9212M

description:
CONTROL
9345725029_H


title: Subject_33_NONPREGNANT_Subcutaneous [exon-level]

value: Subject 33

value: non pregnant


title: 8710M

description:
CASE
9345725004_L


title: 11302M

description:
CASE
9345725008_C


title: 8178M

description:
CASE
9345725004_G


title: 7853M

description:
CONTROL
9345725004_I


title: 3236M

description:
CASE
9250939003_K


title: 8708M

description:
CASE
9250939003_L


title: 10375M

description:
CASE
9345725004_H


title: 11164M

description:
CONTROL
9250939003_C


title: 13855M

description:
CONTROL
9234985013_L


title: 9308M

description:
CONTROL
9234985013_G


title: 12695M

description:
CONTROL
9234985013_E


title: 10544M

description:
CASE
9234985013_K


title: 9926M

description:
CASE
9250939003_H


title: 12865M

description:
CASE
9250939003_A


title: 13431M

description:
CONTROL
9345725004_A


title: 3968M

description:
CASE
9345725029_K


title: 4147M

description:
CASE
9250939003_B


title: 4698M

description:
CONTROL
9234985013_A


title: 4643M

description:
CONTROL
9250939003_J


title: 7755M

description:
CASE
9234985013_C


title: 52798_Maternal Blood

status: Public on Apr 01 2012

description: SAMPLE 39

hyb_protocol: Standard Illumina hybridization protocol for DASL assays;  see WGDASL_HT_Experienced_User_Card_15018211_B.pdf from Illumnia Inc.

scan_protocol: Standard Illumina scaning protocol for DASL assays;  see WGDASL_HT_Experienced_User_Card_15018211_B.pdf from Illumnia Inc.

data_processing: Data was extracted using BeadStudio, no background correction was applied. A constant value of 1 was added to the raw data then log2 transformed and quantile normalized using preprocessCore package in R. The data was further analyzed using limma package.

label_protocol: Standard Illumina labeling protocol for DASL assays;  see WGDASL_HT_Experienced_User_Card_15018211_B.pdf from Illumnia Inc.

extract_protocol: See the technical manual PAXgene_Blood_RNA_Kit_Handbook_(Version_2)2009.pdf from http://www.preanalytix.com/ , pages  34-39.

tag: case identifier

tag: group

value: Normal

tag: fetus gender

value: male

tag: preterm-delivery

value: Maternal Blood


title: 15963_Maternal Blood

description: SAMPLE 45


title: 57167_Maternal Blood

description: SAMPLE 48

value: female


title: 12379_Maternal Blood

description: SAMPLE 33


title: 12877_Maternal Blood

description: SAMPLE 42


title: 14297_Maternal Blood

description: SAMPLE 44


title: 14941_Maternal Blood

description: SAMPLE 41


title: 58947_Maternal Blood

description: SAMPLE 46


title: 12831_Maternal Blood

description: SAMPLE 40


title: 57446_Maternal Blood

description: SAMPLE 47


title: 57437_Maternal Blood

description: SAMPLE 34


title: 59131_Maternal Blood

description: SAMPLE 43


title: 57670_Maternal Blood

description: SAMPLE 35


title: 15057_Maternal Blood

description: SAMPLE 37


title: 57560_Maternal Blood

description: SAMPLE 36


title: 10164_Maternal Blood

description: SAMPLE 31


title: 58947_Cord Blood

description: SAMPLE 22

value: Cord Blood


title: 58753_Maternal Blood

description: SAMPLE 28


title: 13667_Maternal Blood

description: SAMPLE 26


title: 57470_Cord Blood

description: SAMPLE 19


title: 14297_Cord Blood

description: SAMPLE 21


title: 12267_Maternal Blood

description: SAMPLE 25


title: 12831_Cord Blood

description: SAMPLE 14


title: 58753_Cord Blood

description: SAMPLE 24


title: 57470_Maternal Blood

description: SAMPLE 30


title: 12073_Maternal Blood

description: SAMPLE 29


title: 12889_Maternal Blood

description: SAMPLE 32


title: 12889_Cord Blood

description: SAMPLE 13


title: 57560_Cord Blood

description: SAMPLE 11


title: 57446_Cord Blood

description: SAMPLE 18


title: 13667_Cord Blood

description: SAMPLE 15


title: 12379_Cord Blood

description: SAMPLE 8


title: 57670_Cord Blood

description: SAMPLE 9


title: 15057_Cord Blood

description: SAMPLE 12


title: 57087_Maternal Blood

description: SAMPLE 27


title: 57040_Cord Blood

description: SAMPLE 10


title: 59131_Cord Blood

description: SAMPLE 23


title: 57167_Cord Blood

description: SAMPLE 16


title: 52798_Cord Blood

description: SAMPLE 6


title: 13382_Maternal Blood

description: SAMPLE 38


title: 14941_Cord Blood

description: SAMPLE 7


title: 57437_Cord Blood

description: SAMPLE 17


title: 12877_Cord Blood

description: SAMPLE 4


title: 13382_Cord Blood

description: SAMPLE 1


title: Short Day, 28 days (080212MJA_rat230-2.0_LRe20)

status: Public on Feb 21 2012

city: Aberdeen

first: Alexander

middle: William

last: Ross

state: Aberdeenshire

address: Ashgrove Road West

country: United Kingdom

institute: University of Aberdeen

hyb_protocol: The labeled and fragmented cRNA (10ug) was used for the hybridization to the Affymetrix Rat 230 2.0 Genome Genechips for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.

scan_protocol: Affymetrix arrays were scanned using the Affymetrix 3000G scanner. Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.

data_processing: CEL files were transferred to MadMax website (https://madmax.bioinformatics.nl), and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor. We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v10.0.0).

organism: Rattus norvegicus

source_name: Short Day, 28 days

label_protocol: 2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.

extract_protocol: Total RNA was extracted from the arcuate nucleus tissue using an RNeasy Mini Kit (Qiagen, UK) following the manufacturer's instructions. The RNA, whilst on the RNeasy columns, was treated with DNase1 (Qiagen, UK) and washed following the manufacturer's instructions.

tag: strain

value: hypothalamic arcuate nucleus

tag: protocol

value: Short Day

tag: time

value: 28 days


title: Long Day, 28 days (080212MJA_rat230-2.0_LRe21)

source_name: Long Day, 28 days

value: Long Day


title: Long Day, 14 days (080212MJA_rat230-2.0_LRe15)

source_name: Long Day, 14 days

value: 14 days


title: Short Day, 14 days (080212MJA_rat230-2.0_LRe16)

source_name: Short Day, 14 days


title: 12267_Cord Blood

description: SAMPLE 3


title: Short Day, 14 days (080212MJA_rat230-2.0_LRe14)


title: 57087_Cord Blood

description: SAMPLE 5


title: Long Day, 28 days (080212MJA_rat230-2.0_LRe17)


title: Short Day, 14 days (080212MJA_rat230-2.0_LRe10)


title: Short Day, 28 days (080212MJA_rat230-2.0_LRe22)


title: Long Day, 3 days (080212MJA_rat230-2.0_LRe07)

source_name: Long Day, 3 days

value: 3 days


title: Long Day, 28 days (080212MJA_rat230-2.0_LRe19)


title: Long Day, 14 days (080212MJA_rat230-2.0_LRe09)


title: 12073_Cord Blood

description: SAMPLE 2


title: Long Day, 3 days (080212MJA_rat230-2.0_LRe03)


title: Short Day, 3 days (080212MJA_rat230-2.0_LRe04)

source_name: Short Day, 3 days


title: Long Day, 3 days (080212MJA_rat230-2.0_LRe05)


title: Short Day, 28 days (080212MJA_rat230-2.0_LRe18)


title: Short Day, 3 days (080212MJA_rat230-2.0_LRe06)


title: Long Day, 14 days (080212MJA_rat230-2.0_LRe13)


title: Short Day, 28 days (080212MJA_rat230-2.0_LRe24)


title: Short Day, 3 days (080212MJA_rat230-2.0_LRe08)


title: Short Day, 3 days (080212MJA_rat230-2.0_LRe02)


title: Short Day, 14 days (080212MJA_rat230-2.0_LRe12)


title: Long Day, 28 days (080212MJA_rat230-2.0_LRe23)


title: Long Day, 14 days (080212MJA_rat230-2.0_LRe11)


title: 10164_Cord Blood

description: SAMPLE 20


title: Long Day, 3 days (080212MJA_rat230-2.0_LRe01)


title: sw71102-5_CoCl2_400nM

status: Public on Nov 15 2011

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The normalized data provided represents the value obtained after quantile normalization, exponentiated back to an intensity scale. We used preprocessCore package implemented in the software R to do the quantile normalization.

label: Biotin

source_name: Swan 71 trophoblasts

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp Premier RNA Amplification kit.

growth_protocol: Human first trimester trophoblast cell line, Swan 71 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Mediatech Inc., Herndon, VA) supplemented with 10% FBS (Invitrogen, Carlsbad, CA) and 1% Penicillin/Streptomycin (Sigma). The cells were split into 6 well plates (3 x 105 cells per well) and kept overnight.

extract_protocol: Total cellular RNA was isolated using RNeasy Mini Kit (Qiagen).

treatment_protocol: Swan 71 cells were treated with TNFα (1, 10 and 100 ng/ml), IL-1β (1, 10 and 100 ng/ml), and CoCl2 (200, 400 and 600 ng/ml; Sigma) for 24 hours.

tag: cell line

value: Swan 71

tag: ligand

tag: dose

tag: unit

value: nM


title: sw71102-3_CoCl2_400nM


title: sw71102-4_CoCl2_200nM


title: sw71102-1_CoCl2_400nM


title: sw71101-2_CoCl2_600nM


title: sw71100-4_TNFa_1ng/ml

value: TNFα

value: ng/ml


title: sw71101-5_PBS_0nM

value: PBS


title: sw71101-4_CoCl2_600nM


title: sw7199-6_TNFa_100ng/ml


title: sw71101-1_PBS_0nM


title: sw71100-6_TNFa_1ng/ml


title: sw71101-3_PBS_0nM


title: sw71102-6_CoCl2_200nM


title: sw71102-2_CoCl2_200nM


title: sw7198-5_IL1B_10ng/ml


title: sw71100-2_TNFa_1ng/ml


title: sw71100-3_TNFa_10ng/ml


title: sw7199-5_PBS_0ng/ml


title: sw7199-1_PBS_0ng/ml


title: sw7199-4_TNFa_100ng/ml


title: sw71101-6_CoCl2_600nM


title: sw7198-2_IL1B_1ng/ml


title: sw71100-5_TNFa_10ng/ml


title: sw7198-6_IL1B_1ng/ml


title: sw7198-4_IL1B_1ng/ml


title: sw7198-3_IL1B_10ng/ml


title: sw7199-2_TNFa_100ng/ml


title: sw71100-1_TNFa_10ng/ml


title: sw7199-3_PBS_0ng/ml


title: sw7197-6_IL1B_100ng/ml


title: sw7198-1_IL1B_10ng/ml


title: sw7197-4_IL1B_100ng/ml


title: sw7197-5_PBS_0ng/ml


title: sw7195-5_PBS_0ng/ml


title: MB_23

type: genomic

hyb_protocol: DNA sapmles were hybridized with the Illumina Human Methylation27 BeadChip according to the manufacturer’s instructions.

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

data_processing: Average Beta values were normalized using the quantile.normalize function from the preprocessCore package of Bioconductor.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Maternal Blood

label_protocol: DNA (500 ng) samples were bisulfite modified using EZ DNA Methylation Kit (Zymo Research Corporation, Orange, CA, USA).

extract_protocol: Genomic DNA was isolated using a QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA). DNA (500 ng) samples were bisulfite modified using an EZ DNA Methylation Kit (Zymo Research Corporation, Irvine, CA, USA), and were hybridized with the Illumina Human Methylation27 BeadChip (Illumina, Inc., San Diego, CA, USA).

tag: patient id

tag: cell type

value: maternal blood monocytes


title: Villi_20

source_name: Placenta

value: villous macrophages


title: Villi_22


title: CB_24

source_name: Cord Blood

value: cord blood monocytes


title: Deci_17

value: decidual macrophages


title: MB_18


title: sw7195-3_PBS_0ng/ml


title: sw7197-3_PBS_0ng/ml


title: Deci_16


title: sw7197-1_PBS_0ng/ml


title: Deci_14


title: CB_21


title: MB_5


title: Villi_12


title: Deci_6


title: sw7195-1_PBS_0ng/ml


title: sw7197-2_IL1B_100ng/ml


title: Villi_4


title: Deci_9


title: MB_10


title: CB_3


title: MB_8


title: MB_19


title: CB_11


title: Villi_7


title: Villi_15


title: Deci_1


title: CB_13


title: CB_2


title: 6567PA

status: Public on Sep 01 2011

description: Placental amnion and reflected amnion were obtained from singleton placentas of patients at term with no labor (TNL; n=5) and in labor (TIL; n=5). Approximately a quadrant of placental amnion was sampled in each placenta by blunt dissection. Reflected amnion samples were taken from regions at least 2 cm apart from the rupture sites and the placental margin, also by blunt dissection.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 0 – Ritchie et al., 2007, Bioinformatics (2007), Vol. 23 no. 20) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. These steps were performed using the limma package of Bioconductor using the R language (2.12.1). Normalized Log2 Hy3/Hy5 values were averaged over all spots corresponding to a unique miRNA. Only miRNAs with 2 or more spots having a foreground signal greater than background were considered present in a given sample. miRNAs not present in at least 4 samples were not considered for differential expression analysis.

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 0.3 µg total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Amnion tissues were liquid nitrogen-pulverized using a mortar and pestle, and total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA), and treated with DNase. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE).

tag: tissue

value: Placental Amnion

tag: labor status

value: term in labor TIL

source_name: common reference

value: pooled reflected and placental amnions (pool of all samples in this study)


title: 3851PA


title: 5675PA


title: 8951PA


title: 3851RA

value: Reflected Amnion


title: 8545PA

value: term no labor TNL


title: 8950RA


title: 7875PA


title: 9884RA


title: 5521RA


title: 8106PA


title: 8106RA


title: 5521PA


title: 8951RA


title: 6567RA


title: 7875RA


title: 8950PA


title: 9884PA


title: 5675RA


title: 8545RA