title: Amyotrophic Lateral Sclerosis ALS-s15

status: Public on Jul 04 2018

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

data_processing:
Mapping fastq on hg38 using STAR 2.5.1 aligner  using default settings implemented in docker4seq package, https://github.com/kendomaniac/docker4seq
gene counting with RSEM 1.3.0 implemented in docker4seq package, https://github.com/kendomaniac/docker4seq
Genome_build: Human ENSEMBL GRCh38.p7
Supplementary_files_format_and_content: counts table, tab delimited

source_name: Amyotrophic Lateral Sclerosis_blood

extract_protocol:
Trizol® reagent
Illumina TruSeq Stranded RNA Library Prep, version 2, Protocol D

tag: subject status

value: Amyotrophic Lateral Sclerosis

value: blood

value: PBMC


title: healthy donor CTRL5

type: SRA

country: Italy

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: healthy donor_blood

value: healthy donor

tag: tissue

tag: cell type


title: healthy donor CTRL7


title: healthy donor CTRL6


title: NoAb_500000cells

status: Public on Jul 20 2018

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

country: USA

institute: University of Pittsburgh

library_source: genomic

data_processing:
library strategy: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Mus musculus

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol:
The CUT&RUN protocol was modified from Skene and Henikoff (eLife 2017), who made their modified protocol available online (http://blocks.fhcrc.org/steveh/papers/CUT&RUN_protocol.htm). Mouse ES cells were counted using a TC-10 cell counter (Biorad) and diluted manually to respective cell amounts. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were washed with 1mL cold PBS. Cells were pelleted at 600g for 3 minutes at 4°C, the supernatant was discard and cells were resuspended in 1mL cold nuclear extraction (NE) buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% TritonX-100, 20% glycerol, freshly added protease inhibitors). Cells were pelleted at 600g for 3min at 4°C, the supernatant was discard and cells were resuspended in 600uL NE buffer. During the cell washes, Concanavalin A beads (Polysciences) were prepared. For 500,000 cells 200uL bead slurry were used, for 50,000 cells 150uL bead slurry were used, for 5,000 cells, 100uL bead slurry were used, for 500 cells and 50 cells 50uL bead slurry were used, and for 10 cells 20uL bead slurry were used. Beads were withdrawn and transferred to a microfuge tube containing 3X volume cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Beads were washed twice in 1mL cold Binding buffer and resuspended in 300uL binding buffer. Extracted nuclei were added to beads with gentle vortexing and incubated for 10 minutes at room temperature. After nuclei binding, cytosolic fraction was discarded and beads were blocked with 1mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) which was added with repeated gentle pipetting and incubated for 5 minutes at room temperature. Supernatant was discarded and nuclei/beads were washed in 1mL cold Wash Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250uL cold Wash Buffer. Primary antibody was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:100. Samples were incubated with rotation at 4°C for 2 hours. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 250uL cold Wash Buffer. ProteinA-MNase (kindly provided by Steven Henikoff) was added with gentle vortexing of the nuclei in 250uL cold Wash Buffer to a final concentration of 1:400. Samples were incubated with rotation at 4°C for 1 hour. Supernatant was discarded and samples were washed twice in 1mL cold Wash Buffer. Supernatant was discarded and samples were resuspended in 150uL cold Wash Buffer. Samples were equilibrated to 0°C on ice water for 5-10 minutes. 3uL 100mM CalC2 was added during gentle vortexing, samples were flicked quickly to mix and returned to 0C on ice water. After 5 minutes of digestion, reactions were stopped with addition of 150uL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen, 10pg/mL yeast spike-in DNA). Samples were incubated at 37°C for 20 minutes to activate RNase and release fragments. Samples were centrifuged at 16,000g for 5minutes and supernatants were transferred to a new microfuge tube while pellets and beads were discarded. Following addition of 3uL 10% SDS and 2.5uL 20m/gmL ProteinaseK, samples were mixed by inversion and incubated at 70°C for 10 minutes. DNA was cleaned using PCI followed by chloroform extraction, and precipitated with glycogen and ethanol. DNA was pelleted with a high speed spin at 4C, washed, air dried for ~5 minutes and resuspended in 36.5uL 0.1XTE.
Libraries were prepared using a modification of the Henikoff available protocol. DNA end-repair, phosphorylation, and A-tailing was performed in a single reaction, as follows. T4 DNA Polymerase (NEB) was diluted 1:20. 5uL 10X T4 DNA ligase buffer (NEB), 2.5uL 10mM dNTPs, 1.25uL 10mM ATP, 3.13uL 40% PEG4000, 0.63uL T4 PNK (NEB), 0.5uL diluted T4 DNA Polymerase, and 0.5uL Taq polymerase (homemade) was added to 36.5uL of CUT&RUN enriched DNA. Samples were incubated at 12°C for 15 minutes, 37°C for 15 minutes, followed by 72°C for 20 minutes in a thermocycler. Samples were put on ice immediately and the following adapter ligation reaction was performed. PE inline Illumina adapters were used for these experiments. 55uL of 1X Quick ligase buffer (NEB), 5uL Quick ligase (NEB), and 5uL of 1.5uM adapter mix was added to 50uL of A-tailed DNA and samples were incubated at 20°C for 15 minutes in a thermocycler. Immediately following adapter ligation, samples were cleaned using Ampure XP beads (Beckman Coulter). Beads were warmed to room temperature during adapter ligation and 38uL well-mixed beads were added to libraries. Samples were mixed thoroughly and incubated for 15 minutes at room temperature. Following solution clearing on a magnetic rack, supernatants were discarded and beads were washed two times with 200uL 80% EtOH. Samples were briefly spun, residual liquid was discarded, and beads were allowed to air dry for ~5 minutes. DNA was eluted from beads by resuspending beads in 30uL 10mM Tris-HCL pH 8.0 and incubation at room temperature for 2 minutes. Following solution clearing on a magnetic rack, 27.5uL DNA was transferred to a 0.2mL PCR tube and library enrichment was performed. Libraries were enriched for 14-19 cycles of PCR, with the following conditions. 10uL 5X KAPA buffer, 1.5uL 10mM dNTPs, 5uL 20uM PE PCR 1.0, 20uM PE PCR 2.0, 1uL KAPA hotstart HiFi polymerase (KAPA) was added to 27.5uL of library DNA. The following PCR program was used to enrich the samples: 98°C 45 seconds, 98°C 15 seconds, 60°C 10 seconds, steps two and three were repeated specified number of times, 72°C 1 minute. Following library enrichment, samples were loaded on an agarose gel and DNA corresponding to 150-700 bases was extracted using the Qiagen extraction buffer and Econospin columns. Size distribution of libraries was determined using a Fragment analyzer, and libraries were sequenced on an Illumina NextSeq 500.

treatment_protocol: Unfixed nuclei were bound to Concanavalin A beads (Polysciences, Inc), washed, followed by successive addition of primary antibody followed by proteinA-MNase. Cleavage of MNase was initiated by calcium chloride addition and chelated by EDTA. Fragments were released and deep sequencing libraries were prepared.

value: E14 mouse embryonic stem cells (ESCs)

tag: secondary antibody

value: proteinA-MNase kindly provided by Steven Henikoff, used at 1:400


title: ERX2452521

status: Public on Jul 18 2018

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
We created a pre-alignment pipeline to identify technical metadata and generate sample quality metrics. We downloaded FASTQs from SRA using fastq-dump (sra-tools v2.8.2) --split-files -M 0, and counted the number of reads and estimated average read lengths. A sample was considered paired end if two files were generated by fastq-dump and each file had an equal number of reads, ≥ 10,000 reads, and an average read length ≥ 10 bp. We filtered individual reads that were ≤ 25 bp using atropos (v1.1.18) with --minimum-length 25. We simultaneously verified samples were indeed Drosophila and estimated contamination with FastQ Screen (v0.11.3) and bowtie 2 (v2.3.3.1); by mapping 100,000 reads to 8 references (dm6, rRNA, wolbachia, human, yeast, e. coli, PhiX, ERCC-SRM2374). Next we aligned all reads with Hisat2 (v2.1.0) with --max_intronlen 300000 and --known-splicesite-file to the Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4). This was followed with samtools (v1.7) and bamtools (v2.4.1) with default settings to generate summary statistics. We estimated various metrics with Picard CollectRNASeqMetrics (v2.15.0) using three separate parameters STRAND=NONE, STRAND=FIRST_READ_TRANSCRIPTION_STRAND, and STRAND=SECOND_READ_TRANSCRIPTION_STRAND. These metrics allowed us estimate library strandedness. Finally we identified duplicates using Picard MarkDuplicates (v2.15.0).
To generate counts tables and coverage tracks we used parameters discovered in the pre-alignment pipeline in our alignment pipeline. The alignment pipeline uses FASTQ file(s) downloaded by the pre-alignment pipeline, but trimms adapter sequence and low quality bases using atropos (v1.1.18) with -q 20 --minimum-length 25. The remaining reads were mapped using Hisat2 (v2.1.0) with --dta --max-intronlen 300000 --known-splicesite-infile and the --rna-strandedness using ‘F’, ‘R’, ‘FR’, or ‘RF’ depending on the strandedness. We merged alignments from individual SRA runs (SRRs) to the library level (SRX) and generated gene level, junction level, and intergenic coverage counts using FeatureCounts from the subread package (v1.5.3). Finally we created browser tracks using bamCoverage from the deeptools package (v2.5.4) using --binSize 1 --normalizeTo1x 129000000 --ignoreForNormalization chrX.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: Processed data files include:
*.bw are BigWig files generated using deeptools bamCoverage
*.counts are gene level coverage counts
*.jcounts are gene level junction counts
*.intergenic.counts are intergenic coverage counts
*.intergenic.jcounts are intergenic junction counts
Series level supplementary files:
dmel_r6-11.intergenic.gtf intergenic GTF generated by the pipeline for estimating intergenic coverage counts.
supplemental_metadata.tsv supplemental metadata file containing additional metadata for each sample including QC values and various flags generated by each pipeline
gene_counts.tsv supplemental file containing all gene counts as a single matrix
intergenic_counts.tsv supplemental file containing all intergenic counts as a single matrix

organism: Drosophila melanogaster

source_name: Sample 37

extract_protocol: see original sample

tag: Sex

value: female

tag: developmental stage

value: adult

value: ovary

tag: attributes

value: wolbachia|dahomey|ovary|genotype|sample


title: Amyotrophic Lateral Sclerosis VCP-m1


title: SRX032509


title: ERX2452534

source_name: Sample 52

value: arthropod|wolbachia|dahomey|fat


title: Human_hESC_RNA-Seq_re2

status: Public on May 03 2018

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.37
RNA-Seq reads were aligned to the hg19 genome assembly using tophat 2.1.1, transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: hg19

molecule: polyA RNA

source_name: human embryo

growth_protocol: hESCs were maintained on Matrigel (BD Biosciences)-coated plates (Corning) in E8 medium (STEMCELL Technologies)

extract_protocol:
ES is incubated in lysis buffe for further ATAC-seq experiment
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

value: hESC


title: CK-1

status: Public on Jun 30 2018

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0)
Genome_build: ASM676v1 (NC_002516.2)
Supplementary_files_format_and_content: .txt file containing rawcounts and comparisons between RpoN mutant and wild-type

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture in LB (Luria-Bertani)  medium

growth_protocol: LB

extract_protocol:
To examine the effect of RpoN on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0). GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase in LB

tag: genotype

value: WT


title: Amyotrophic Lateral Sclerosis ALS-s12


title: Human_ICM_3PN_ATAC-Seq_re2

data_processing:
Basecalls performed using CASAVA version 1.11
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: hg19
Supplementary_files_format_and_content: *peaks.bed: Bed files include ATAC-seq peaks.

growth_protocol: All the 3PN zygotes were cultured to 2-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

treatment_protocol: Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 3PN zygote were and cultured to 2Cell stag,and zona-pelucida was removed using laser. 2Cell stages embryos were frozen for ATAC-seq.

tag: development stage

value: ICM


title: ERX278734

value: third instar larval stage


title: Amyotrophic Lateral Sclerosis ALS-s13


title: Human_zygote_3PN_ATAC-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: hg19

growth_protocol: G1-plus medium

extract_protocol: ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

treatment_protocol: Human embryos are incubated in lysis buffe for further ATAC-seq experiment

value: human embryo

value: zygote


title: NoAb_50cells


title: Human_hESC_RNA-Seq_re1

data_processing:
Basecalls performed using CASAVA version 1.36
RNA-Seq reads were aligned to the hg19 genome assembly using tophat 2.1.1, transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: hg19


title: CK-2


title: DNase-seq from glomerular visceral epithelial cell (ENCLB351UZL)

status: Public on Jun 21 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR432SZT/
***************
biological replicate number: 1
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR432SZT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-01-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB351UZL
instrument models: Illumina NextSeq 500,Illumina HiSeq 4000,Illumina HiSeq 2000

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens child (3 years) glomerular visceral epithelial primary cell

extract_protocol: not provided

value: glomerular visceral epithelial cell

value: primary cell

tag: description

tag: biosample encode accession

value: not collected

tag: dev stage

value: child

tag: age

value: 3 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS826RSQ at ENCODE; https://www.encodeproject.org/ENCBS826RSQ/

value: Derived from ENCODE donor ENCDO879VOF; https://www.encodeproject.org/ENCDO879VOF/


title: DNase-seq from kidney glomerular epithelial cell (ENCLB351APN)

description:
https://www.encodeproject.org/experiments/ENCSR136KEL/
***************
biological replicate number: 1
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR136KEL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB351APN
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens male adult (43 years) kidney glomerular epithelial primary cell

value: kidney glomerular epithelial cell

value: male

value: adult

value: 43 year

value: ENCBS572CPY at ENCODE; https://www.encodeproject.org/ENCBS572CPY/

value: Derived from ENCODE donor ENCDO484OWJ; https://www.encodeproject.org/ENCDO484OWJ/


title: DNase-seq from glomerular visceral epithelial cell (ENCLB731CZE)

description:
https://www.encodeproject.org/experiments/ENCSR432SZT/
***************
biological replicate number: 2
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR432SZT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-01-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB731CZE
instrument models: Illumina HiSeq 4000,Illumina HiSeq 2000,Illumina NextSeq 500

value: ENCBS094MGI at ENCODE; https://www.encodeproject.org/ENCBS094MGI/


title: Human_8-cell_3PN_ATAC-seq_amanitin_re2

source_name: Preimplantation embryo

treatment_protocol: α-amanitin treated human embryos are incubated in lysis buffe for further ATAC-seq experiment

value: human embryo

tag: treated with

value: α-amanitin


title: Human_ICM_3PN_ATAC-Seq_re1

data_processing:
Basecalls performed using CASAVA version 1.10
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: hg19
Supplementary_files_format_and_content: *peaks.bed: Bed files include ATAC-seq peaks.

value: ICM


title: DNase-seq from kidney glomerular epithelial cell (ENCLB400KJC)

description:
https://www.encodeproject.org/experiments/ENCSR136KEL/
***************
biological replicate number: 2
technical replicate number: 1
description: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures
experiment encode accession: ENCSR136KEL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB400KJC

source_name: Homo sapiens male adult (62 years) kidney glomerular epithelial primary cell

value: primary cell

value: 62 year

value: ENCBS360AGM at ENCODE; https://www.encodeproject.org/ENCBS360AGM/

value: Derived from ENCODE donor ENCDO730EZR; https://www.encodeproject.org/ENCDO730EZR/


title: Human_8-cell_3PN_ATAC-seq_amanitin_re3


title: Amyotrophic Lateral Sclerosis FUS-m3

value: Amyotrophic Lateral Sclerosis

value: blood

value: PBMC


title: healthy donor CTRL4

value: healthy donor


title: Amyotrophic Lateral Sclerosis ALS-s16


title: Amyotrophic Lateral Sclerosis SOD1-m3


title: Human_8-cell_3PN_ATAC-seq_amanitin_re1


title: Human_8-cell_3PN_ATAC-seq_Ctrl_re1

treatment_protocol: DMSO treated human embryos are incubated in lysis buffe for further ATAC-seq experiment

value: DMSO (control)


title: alb-SREBP-1a∆P_7

status: Public on Mar 30 2018

type: RNA

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses for gene default and exon default .CHP files.  These samples include gene-level RMA values.

label: biotin

source_name: alb-SREBP-1a∆P liver [Kotzka  et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609]

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).   All synthesis steps were monitored with an RNA 6000 nano kit (Agilent, Taufkirchen, Germany) for quality control.

growth_protocol: Mice were bred and maintained in a regular 12h light/dark cycle under constant temperature and humidity (22°C ± 1°C, 50% ± 5% humidity) with unrestricted access to water and standart chow.

extract_protocol: Total RNA was extracted from 50-100 mg liver tissue with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).

treatment_protocol: At 24 weeks of age male mice were sacrifced by CO2 asphyxation, liver was isolated and 100 mg aliquots were snap frozen in liquid nitrogen. Samples were stored at -80°C until processing.

tag: background strain

value: liver

value: male

value: 24 weeks


title: alb-SREBP-1a_7

source_name: alb-SREBP-1a liver [Kotzka  et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609]


title: alb-SREBP-1a∆P_2


title: alb-SREBP-1a∆P_3


title: cl231_shRNA-1_1

status: Public on May 01 2018

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
batch1
Replicate_1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw idat files were processed with beadarray Bioconductor package.

source_name: shRNA-1 replicate 1

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

growth_protocol: Cells were grown in DMEM with 10% FBS and 10% pen-strep media

extract_protocol: RNA was extracted with the Axyprep™ multisource total RNA miniPrep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Breast cancer

tag: cell line

tag: condition

value: SETDB1 knock-down


title: alb-SREBP-1a_2

tag: tissue


title: cl231_shRNA-1_2

description:
batch1
Replicate_2

source_name: shRNA-1 replicate 2

tag: cell type


title: cl453_shCtrl

description:
batch1
Replicate_1

source_name: control replicate 1

value: SETDB1 control


title: alb-SREBP-1a_6

tag: Sex


title: alb-SREBP-1a∆P_1


title: Human_8-cell_3PN_ATAC-seq_Ctrl_re2

value: human embryo

tag: developmental stage


title: alb-SREBP-1a∆P_4


title: cl231_shCtrl_2

description:
batch1
Replicate_2

source_name: control replicate 2


title: alb-SREBP-1a∆P_8


title: alb-SREBP-1a∆P_6


title: alb-SREBP-1a_4


title: alb-SREBP-1a_5


title: C57Bl6_4

source_name: C57/Bl6 liver

value: wildtype


title: C57Bl6_5


title: Soil_46_rep1

type: genomic

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

hyb_protocol: A total of 42 µL of buffer, including 1× HI-RPM hybridization buffer,1× aCGH blocking agent, 0.05 µg·µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations), was added to each sample. After mixing completely, the solution was spun down and incubated at 95°C for 3 min, then incubated at 37°C for 30 min. The prepared samples were hybridized with GeoChip 5.0 arrays (60 K) at 67°C for 24 h with a rotation at 20 rpm in a hybridization oven.

scan_protocol: scanned on a NimbleGen MS200 array system (Roche) and the spot intensity data recorded

data_processing: The raw GeoChip data was processed using GeoChip Microarray Data Manager pipeline (http://ieg.ou.edu/microarray/) with the following steps: (i) remove the spots with a signal-to-noise ratio (SNR) less than 2.0; (ii) log-transformed the data and then, on each microarray, divide them by the mean intensity of all the genes; Finally we acquired GeoChip data for further analysis.

organism: uncultured soil bacterium

source_name: Soil_46, gDNA extraction

label_protocol: DNA for all samples was labelled with Cy-3 (using random primers) and the Klenow fragment

extract_protocol: DNA was extracted using the PowerSoil DNA extraction kit (MoBio Inc, USA) following the manufacturer's protocols

tag: grazing system

value: dairy

tag: land use

tag: soil type

value: Pumice


title: alb-SREBP-1a_1

tag: genotype


title: Soil_50_rep1

source_name: Soil_50, gDNA extraction

value: sheep and beef

value: other

value: Pallic


title: C57Bl6_2


title: Soil_45_rep1

source_name: Soil_45, gDNA extraction

value: Allophanic


title: C57Bl6_8


title: C57Bl6_3


title: Soil_48_rep1

source_name: Soil_48, gDNA extraction

value: Brown


title: Soil_39_rep1

source_name: Soil_39, gDNA extraction

value: sheep


title: Soil_41_rep1

source_name: Soil_41, gDNA extraction


title: cl453_shRNA-3

description:
batch1
Replicate_1

source_name: shRNA-3 replicate 1


title: Soil_42_rep1

source_name: Soil_42, gDNA extraction


title: Soil_43_rep1

source_name: Soil_43, gDNA extraction

value: beef

value: Ultic


title: Soil_40_rep1

source_name: Soil_40, gDNA extraction

value: sheep, beef & dairy grazing


title: Soil_44_rep1

source_name: Soil_44, gDNA extraction

value: Granular


title: alb-SREBP-1a_3

source_name: alb-SREBP-1a liver [Kotzka  et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609]

value: liver

value: male

value: 24 weeks


title: C57Bl6_7


title: alb-SREBP-1a∆P_5

source_name: alb-SREBP-1a∆P liver [Kotzka  et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609]


title: alb-SREBP-1a_8


title: C57Bl6_6


title: Soil_47_rep1

source_name: Soil_47, gDNA extraction

value: Recent


title: Soil_49_rep1

source_name: Soil_49, gDNA extraction


title: cl231_shCtrl_1

description:
batch1
Replicate_1

source_name: control replicate 1

value: Breast cancer

value: SETDB1 control


title: C57Bl6_1

source_name: C57/Bl6 liver

value: wildtype


title: Soil_31_rep1

source_name: Soil_31, gDNA extraction

value: dairy grazing


title: Soil_26_rep1

source_name: Soil_26, gDNA extraction

value: sheep and beef

value: other


title: Soil_33_rep1

source_name: Soil_33, gDNA extraction


title: Soil_24_rep1

source_name: Soil_24, gDNA extraction


title: Soil_37_rep1

source_name: Soil_37, gDNA extraction

value: dairy


title: Soil_35_rep1

source_name: Soil_35, gDNA extraction

value: Semiarid


title: Soil_25_rep1

source_name: Soil_25, gDNA extraction

value: sheep


title: Soil_13_rep1

source_name: Soil_13, gDNA extraction


title: Soil_27_rep1

source_name: Soil_27, gDNA extraction

value: Brown


title: Soil_38_rep1

source_name: Soil_38, gDNA extraction


title: Soil_19_rep1

source_name: Soil_19, gDNA extraction


title: Soil_32_rep1

source_name: Soil_32, gDNA extraction

value: beef

value: Pallic


title: Soil_29_rep1

source_name: Soil_29, gDNA extraction


title: Soil_36_rep1

source_name: Soil_36, gDNA extraction


title: Soil_20_rep1

source_name: Soil_20, gDNA extraction


title: Soil_22_rep1

source_name: Soil_22, gDNA extraction


title: Soil_18_rep1

source_name: Soil_18, gDNA extraction

value: Podzol


title: Soil_15_rep1

source_name: Soil_15, gDNA extraction


title: Soil_21_rep1

source_name: Soil_21, gDNA extraction


title: Soil_30_rep1

source_name: Soil_30, gDNA extraction


title: Soil_10_rep1

source_name: Soil_10, gDNA extraction


title: Soil_16_rep1

source_name: Soil_16, gDNA extraction


title: Soil_34_rep1

source_name: Soil_34, gDNA extraction


title: Soil_14_rep1

source_name: Soil_14, gDNA extraction


title: Soil_28_rep1

source_name: Soil_28, gDNA extraction

value: dairy run-off


title: Soil_23_rep1

source_name: Soil_23, gDNA extraction


title: Soil_12_rep1

source_name: Soil_12, gDNA extraction


title: Soil_17_rep1

source_name: Soil_17, gDNA extraction


title: Soil_11_rep1

source_name: Soil_11, gDNA extraction


title: TroyGFPallSEZb

status: Public on Jan 12 2018

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Troy-GFPiresCreER mouse strain GFP+ cells), library 2

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. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: *.coutt.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: mouse brain, the subependymal zone

extract_protocol:
RNA extraction was performed in 384-wells where cells were sorted using FACS. In brief, cells were sorted in a mixture of primers and dNTPs, heated to 60C for 5', followed by incubation 1' on ice (repeated twice) for lysis.
RNA was processed using the previously described SORT-seq technique, which is a combination of FACS and CEL-seq technique in a 384-well format. In brief, reverse transcription, second strand synthesis and in vitro transcription for RNA amplification were performed in 384-well format. Libraries were generate using Truseq small RNA primer (rpi) library primers, Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain

value: 8 - 10 weeks


title: TroyGFPallSEZa

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Troy-GFPiresCreER mouse strain GFP+ cells), library 1


title: Prom1CD24d

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-PROM1 (CD133) antibody and anti-CD24, library 4


title: Soil_9_rep1

source_name: Soil_9, gDNA extraction

value: Gley


title: Prom1CD24c

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-PROM1 (CD133) antibody and anti-CD24, library 3


title: Ki67_TOM_d2_3

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 2 days after 1x5mg Tmx administration (tdTomato+ cells), library 3


title: Ki67_TOM_d2_4

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 2 days after 1x5mg Tmx administration (tdTomato+ cells), library 4


title: Ki67TOM2mtSEZmixOBd

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone or the olfactory bulb of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), as well as O4+ oligodendrocytes, library 4

source_name: mouse brain, the subependymal zone and the olfactory bulb

value: 8 - 19 weeks


title: TroyGFPallSEZd

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Troy-GFPiresCreER mouse strain GFP+ cells), library 4


title: Ki67_TOM_d2_2

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 2 days after 1x5mg Tmx administration (tdTomato+ cells), library 2


title: Ki67TOM2mtSEZmixOBb

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone or the olfactory bulb of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), as well as O4+ oligodendrocytes, library 2


title: Ki67TOM2mtSEZd

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), library 4

value: 16 - 19 weeks


title: Ki67TOM2mtSEZc

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), library 3


title: Ki67TOM2mtSEZmixOBc

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone or the olfactory bulb of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), as well as O4+ oligodendrocytes, library 3


title: Soil_4_rep1

source_name: Soil_4, gDNA extraction

value: Melanic


title: Ki67TOM2mtSEZmixOBa

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone or the olfactory bulb of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), as well as O4+ oligodendrocytes, library 1


title: Soil_8_rep1

source_name: Soil_8, gDNA extraction


title: Ki67TOM2mtSEZb

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), library 2


title: Soil_6_rep1

source_name: Soil_6, gDNA extraction


title: Soil_5_rep1

source_name: Soil_5, gDNA extraction


title: Soil_3_rep1

source_name: Soil_3, gDNA extraction


title: Ki67rfpSEZd

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67tagRFP mouse strain (RFP+ cells), library 4


title: Soil_7_rep1

source_name: Soil_7, gDNA extraction


title: Ki67TOM2mtSEZa

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 60 days after 1x5mg Tmx administration (tdTomato+ cells), library 1


title: Ki67_TOM_d2_1

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67iresCreER;Rosa-tdTomato mouse strain, 2 days after 1x5mg Tmx administration (tdTomato+ cells), library 1


title: Soil_2_rep1

source_name: Soil_2, gDNA extraction


title: TroyGFPallSEZc

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Troy-GFPiresCreER mouse strain GFP+ cells), library 3


title: Prom1CD24b

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-PROM1 (CD133) antibody and anti-CD24, library 2


title: Prom1CD24a

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-PROM1 (CD133) antibody and anti-CD24, library 1


title: Ki67rfpSEZc

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67tagRFP mouse strain (RFP+ cells), library 3


title: GLASTEGFmixSEZd

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-GLAST (SLC1A3) antibody and/or Alexa647-conjugated EGF ligand, library 4


title: GLASTEGFmixSEZb

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-GLAST (SLC1A3) antibody and/or Alexa647-conjugated EGF ligand, library 2


title: GLASTEGFmixSEZa

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-GLAST (SLC1A3) antibody and/or Alexa647-conjugated EGF ligand, library 1


title: GLASTEGFmixSEZc

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone using anti-GLAST (SLC1A3) antibody and/or Alexa647-conjugated EGF ligand, library 3


title: Soil_1_rep1

source_name: Soil_1, gDNA extraction


title: Ki67rfpSEZa

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67tagRFP mouse strain (RFP+ cells), library 1


title: Ki67rfpSEZb

description: Extracted RNA from single cells isolated by FACS from the adult mouse subependymal zone of Ki67tagRFP mouse strain (RFP+ cells), library 2


title: liver-rc_day28-2_tech_rep

status: Public on Dec 26 2017

city: Houston

first: Doris

last: Taylor

state: Texas

address: 6770 Bertner Ave MC2-255

department: Regenerative Medicine Research Laboratories

institute: Texas Heart Institute

description: Hepatocytes grown on decellularized matrix for 28 days, replicate 2, technical duplicate

hyb_protocol: Hybridization was performed by the University of Minnesota's Biomedical Genomics Center.

scan_protocol: The University of Minnesota's Biomedical Genomics Center performed the scan.

data_processing: Using limma, we processed the raw data for background correction, quantile normalization,  and log2 transformation.

organism: Rattus norvegicus

source_name: liver

label_protocol: Samples were biotin labeled and processed by the University of Minnesota’s BioMedical Genomics Center.

growth_protocol: Livers recellularized with rat cells were perfused with Williams’ Medium E (Sigma) containing 2 mM GlutaMax-1 (Life Technologies), 0.1 mM MEM non-essential amino acids solution (Sigma), 10% fetal bovine serum (Hyclone), 10 ug/mL insulin (Sigma), 1X penicillin/streptomycin (Life Technologies), and 1 M dexamethasone (Sigma).

extract_protocol: Samples were stored in RNAlater (Qiagen) until processing. RNA was isolated by using the Qiagen RNeasy Mini Kit per the manufacturer’s guidelines.

treatment_protocol: No treatments were performed.

value: liver

value: rat hepatocytes

tag: days hepatocytes were grown on matrix


title: KB9_WT2_C

status: Public on Dec 01 2017

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequence reads were aligned to the mm10 genome assembly using the STAR aligner version 2.3.1z4
BAM files were sorted using Samtools and filtered to retain only primary alignments
Reads were quantified as gene level integer counts using featureCounts
Gene level integer counts were normalized for library size using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts were obtained using featureCounts and normalized counts were obtained using DESeq2

source_name: BW5147  T-cell line

growth_protocol: BW5147 T-cells were maintained at a density of 0.5-1 x 10^6 cells in a T75 flask in high glucose DMEM medium (Sigma-Aldrich) supplemented with 20 % (v/v) fetal bovine serum (FBS) (Sigma-Aldrich), 100 U/ml penicillin, 100 U/ml streptomycin (Life technologies), 2 mM glutamine (Life technologies).

extract_protocol:
RNA was extracted from the T-cells using the RNeasy kit (QIAGEN) following the manufacturer instructions and total RNA was quantified using the Qubit RNA Assay Kit (Life Tech) and RNAquality was determined on the Bioanalyzer using the RNA Pico Kit (Agilent).
The NuGen Ovation Human RNA-Seq Multiplex system (NuGen, part 0341) Prep Kit, was used to target deletion of unwanted high abundance transcripts and ribosomal RNA. More than 100ng of total RNA was converted into each DNA library following the manufacturer’s protocol without modification. Following library construction, DNA libraries were quantified using the Qubit High Sensitivity DNA Kit (Life Tech) and library size was determined using the Bioanalyzer High Sensitivity Chip Kit (Agilent). Finally, qPCR was carried-out on the libraries using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) and run on the 7900HT Fast qPCR machine (ABI). Libraries passing quality control were diluted to 2nM in sterile water and then sequenced on the NextSeq500 (Illumina) at a final concentration of 12pM, following all manufacturer protocols.

tag: strain background

value: AKR/J

value: Lymphoma T-cell line

tag: passages

tag: genotype/variation

value: wild type


title: KB8_WT2_B


title: liver-rc_day28-2

description: Hepatocytes grown on decellularized matrix for 28 days, replicate 2


title: liver-rc_day15-2

description: Hepatocytes grown on decellularized matrix for 15 days, replicate 2


title: liver-rc_day28-1

description: Hepatocytes grown on decellularized matrix for 28 days, replicate 1


title: liver-rc_day15-3

description: Hepatocytes grown on decellularized matrix for 15 days, replicate 3


title: liver-rc_day2-1_tech_rep

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 1, technical duplicate


title: liver-cadaveric-4

description: Cadaveric liver, RNA isolated after harvest, replicate 4


title: liver-cadaveric-2

description: Cadaveric liver, RNA isolated after harvest, replicate 2


title: liver-rc_day15-1

description: Hepatocytes grown on decellularized matrix for 15 days, replicate 1


title: liver-rc_day15-4

description: Hepatocytes grown on decellularized matrix for 15 days, replicate 4


title: liver-hep-4

description: Freshly isolated hepatocytes, RNA isolated immediately, replicate 4


title: liver-rc_day2-1

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 1


title: liver-rc_day2-3_tech_rep

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 3, technical duplicate


title: liver-rc_day15-2_tech_rep

description: Hepatocytes grown on decellularized matrix for 15 days, replicate 2, technical dupicate


title: liver-rc_day2-2

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 2


title: liver-rc_day2-4

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 4


title: liver-rc_day28-1_tech_rep

description: Hepatocytes grown on decellularized matrix for 28 days, replicate 1, technical duplicate


title: liver-hep-3

description: Freshly isolated hepatocytes, RNA isolated immediately, replicate 3


title: liver-rc_day28-3

description: Hepatocytes grown on decellularized matrix for 28 days, replicate 3


title: liver-rc_day2-3

description: Hepatocytes grown on decellularized matrix for 2 days, replicate 3


title: liver-hep-2

description: Freshly isolated hepatocytes, RNA isolated immediately, replicate 2


title: liver-cadaveric-3

description: Cadaveric liver, RNA isolated after harvest, replicate 3


title: KB7_WT2_A


title: liver-hep-1

description: Freshly isolated hepatocytes, RNA isolated immediately, replicate 1


title: KB6_K256L_C

source_name: BW5147  T-cell line with TCRα K256L mutation

value: TCRalpha K256L mutation


title: KB4_K256L_A


title: KB3_R251L_C

source_name: BW5147  T-cell line with TCRα R251L mutation

value: TCRalpha R251L mutation


title: KB5_K256L_B


title: KB1_R251L_A


title: KB2_R251L_B


title: liver-cadaveric-1

description: Cadaveric liver, RNA isolated after harvest, replicate 1


title: Cont-Ter-AGA, rep26

status: Public on May 10 2016

city: Toronto

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

country: Canada

institute: University of Toronto

description:
SAMPLE_9681
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

hyb_protocol: Hybridization was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

scan_protocol: Scanning was performed by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

data_processing:
Data was processed, normalized, and converted into log2 values in R 3.0.1 using the Affy library from Bioconductor.
The file complete_dataset.csv contains the expression information for 14,651 genes found in common across the different array platforms analyzed. Row names contain gene symbols.

source_name: Human placenta from Cont-Ter-AGA pregnancy

label_protocol: Biotinylated cDNA was prepared by the Princess Margaret Genomics Centre (Toronto, Canada) as per Affymetrics protocols.

extract_protocol: To control for batch affect, samples were randomized into groups of 20 for processing. A 100 mg aliquot was used to prepare an mRNA extract using Trizol followed by RNAeasy spin columns. RNA purity and integrity were determined using 28S to 18S rRNA ratio (Agilent Bioanalyzer).

treatment_protocol: Four tissue biopsies (one sample/quadrant, excluding the chorionic plate) are collected per placenta, rinsed in PBS to remove contaminating maternal blood, pooled, crushed into a powder, and snap-frozen in liquid nitrogen.

tag: diagnosis

value: non-PE

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: B

tag: previous nulliparity

value: Yes

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

value: C-Section

tag: ga (week)

tag: ga (day)

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-Term-SGA, rep13

description:
SAMPLE_9524
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-Term-SGA pregnancy

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

value: Vaginal

value: M


title: Cont-Ter-AGA, rep27

description:
SAMPLE_9910
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: A

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: Cont-Ter-AGA, rep19

description:
SAMPLE_8580
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Ter-AGA, rep20

description:
SAMPLE_8997
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: ga (day)


title: Cont-Ter-AGA, rep18

description:
SAMPLE_8344
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: im_S_XCR1+_LT_SetD_2

status: Public on Aug 22 2016

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: immature (total) spleen XCR1+ DC

label_protocol: 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol.

treatment_protocol: Mice were untreated or infected for 1.5 days i.p. with 2.5x10E4 pfu of salivary-gland extracted MCMV Smith strain.

value: spleen

tag: phenotype

tag: cell type

value: immature (total) spleen XCR1+ DC

tag: treatment

value: Untreated


title: Cont-Ter-AGA, rep21

description:
SAMPLE_9267
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: O

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-PreT-CH, rep10

description:
SAMPLE_9572
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-PreT-CH pregnancy

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: ga (day)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: Cont-Ter-AGA, rep23

description:
SAMPLE_9365
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: Placenta

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer


title: Cont-PreT-CH, rep8

description:
SAMPLE_8230
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Black

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Ter-AGA, rep15

description:
SAMPLE_8172
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: AB

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PE-PreT-SGA, rep17

description:
SAMPLE_8282
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-PreT-SGA pregnancy

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer


title: Cont-Ter-AGA, rep22

description:
SAMPLE_9342
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: Caucasian

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

value: C-Section

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Ter-AGA, rep16

description:
SAMPLE_8207
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: infant gender

value: F

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: PE-PreT-SGA, rep18

description:
SAMPLE_9058
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: PE

value: Asian

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer


title: Cont-Ter-AGA, rep14

description:
SAMPLE_8083
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: ga (day)

value: M

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-PreT-CH, rep9

description:
SAMPLE_8730
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)


title: Cont-Term-CH, rep14

description:
SAMPLE_8563
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from Cont-Term-CH pregnancy

tag: diagnosis

tag: tissue

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: previous nulliparity

tag: previous miscarriage

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: nicu transfer


title: Cont-Ter-AGA, rep17

description:
SAMPLE_8218
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: im_S_XCR1+_LT_SetD_1

tag: tissue

value: spleen

tag: phenotype

tag: cell type

value: immature (total) spleen XCR1+ DC

tag: treatment


title: Cont-Ter-AGA, rep12

description:
SAMPLE_7962
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Ter-AGA, rep11

description:
SAMPLE_7788
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

value: O

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep16

description:
SAMPLE_8008
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: attempted vaginal delivery

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: PE-Term-SGA, rep12

description:
SAMPLE_7855
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: iugr diagnosis

value: Vaginal

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-PreT-SGA, rep15

description:
SAMPLE_7543
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

value: Placenta

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: attempted vaginal delivery

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Ter-AGA, rep25

description:
SAMPLE_9414
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

value: non-PE

tag: tissue

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: Cont-Ter-AGA, rep24

description:
SAMPLE_9397
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-SGA, rep11

description:
SAMPLE_7513
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-Term-CH, rep13

description:
SAMPLE_7298
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: Cont-PreT-CH, rep7

description:
SAMPLE_7277
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-SGA, rep10

description:
SAMPLE_5851
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-PreT-CH, rep4

description:
SAMPLE_6802
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: Cont-Ter-AGA, rep9

description:
SAMPLE_15241
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-Term-CH, rep1

description:
SAMPLE_15811
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

source_name: Human placenta from PE-Term-CH pregnancy

tag: tissue

value: Black

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep11

description:
SAMPLE_15257
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: PE-Term-SGA, rep7

description:
SAMPLE_15015
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

value: AB

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: PE-PreT-SGA, rep8

description:
SAMPLE_14801
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

tag: previous nulliparity

value: Yes

tag: previous miscarriage

tag: iugr diagnosis

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: PE-PreT-SGA, rep14

description:
SAMPLE_6791
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

value: Caucasian

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

tag: newborn weight z-score


title: PE-PreT-SGA, rep9

description:
SAMPLE_14985
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: previous nulliparity

tag: previous miscarriage

value: No

tag: iugr diagnosis

tag: attempted vaginal delivery

tag: apgar score (1 min)

tag: apgar score (5 min)

tag: nicu transfer


title: Cont-Term-CH, rep12

description:
SAMPLE_7012
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: tissue

value: East Indian

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: maximum systolic bp

tag: maximum diastolic bp

tag: mode proteinuria

tag: hellp diagnosis

value: C-Section

tag: ga (day)

tag: placental weight z-score

tag: umbilical cord diameter

tag: chorioamnionitis diagnosis


title: Cont-PreT-CH, rep6

description:
SAMPLE_7147
Placenta sample purchased from the Research Centre for Women’s and Infants’ Health (RCWIH) BioBank (Toronto, Canada), which utilizes a systematic sampling procedure in which four tissue biopsies (one sample/quadrant) are collected and pooled per placenta. At the time of sample collection and purchase, PE was defined as the onset of systolic pressure ≥ 140 mmHg and/or diastolic pressure ≥ 90 mmHg after the 20th week of gestation, accompanied by proteinuria (greater than 300 mg protein/day, or greater ≥ 2+ by dipstick). CH: chronic maternal hypertension; systolic pressure ≥ 140 mmHg and/or sustained diastolic ≥ 90 mmHg before the 20th week of gestation. Preterm: delivery prior to 34 weeks gestation. SGA: small-for-gestational-age infant; neonatal birth weight < 10th percentile for gestational age and sex. AGA: average-for-gestational age infant.

tag: diagnosis

tag: maternal age

tag: maternal bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: previous nulliparity

tag: previous miscarriage

tag: iugr diagnosis

tag: mode of delivery

tag: ga (week)

tag: infant gender

value: F

tag: newborn weight z-score