title: T4P mNET-seq siLuc R1

value: 61361:RNA Pol II CTD phospho Thr4 antibody (mAb). Active Motif


title: Total mNET-seq siSpt6 R1

status: Public on Nov 21 2018

type: SRA

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

library_source: transcriptomic

data_processing:
Library strategy: mNET-seq
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
Nascent RNAs were purified from Pol II IP products of solublilized chromatin. DNA were purified from chromatin IP products.
Libraries were prepared according to the protocols of NEBNext small RNA library preparation kit (NEB) for mNET-seq; NEBNext Ultra II Directional RNA Library preparation kit (NEB) for Chromatin, Nucleoplasmic, Cytoplasmic and Nuclear poly(A)+ RNA-seq and RDIP-seq; QuantSeq 3' mRNA-Seq library preparation kit REV for Illumina (Lexogen) for 3'RNA-seq; NEBNext Ultra II DNA Library preparation kit (NEB) for mNucD-seq and ChIP-seq

treatment_protocol: siRNAs were transfected for 55-60 hours according to RNAiMAX reagent protocol.

tag: cell line

value: HeLa

tag: antibody

value: MABIO601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation

tag: knockdown


title: T4P mNET-seq siLuc R2

value: siLuc


title: Chromatin RNA-seq siLuc R1

data_processing:
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples


title: Chromatin RNA-seq siLuc R2


title: Chromatin RNA-seq siSpt6 R3


title: DG75_pBABE_OLAP_3

status: Public on Oct 24 2018

city: Philadelphia

first: Italo

last: Tempera

state: PA

address: 3307 N. Broad Street, PAHB, Room 206

department: Fels Institute

country: USA

institute: Temple University

description: Olaparib was dissolved in DMSO and cells were treated with 1 μM olaparib for 72 hrs in the appropriate media.

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the hg19 genome assembly using the Star software suite
ht-seq-count  with default settings to generate counts of each gene
Cuffdiff to generate FPKM
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in tsv text file. The first column is gene name.  The next columns are the FPKMs of the individual samples.

source_name: DG75 B cells

growth_protocol: DG75 cells were cultured in suspension in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from 5 × 106 cells using a Qiagen RNeasy Plus Mini Kit according to the manufacturer’s protocol. Total RNA was depleted of the ribosomal RNA component using RiboZero (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: treatment

value: 1 uM olaprib 72 hr


title: Total mNET-seq siLuc R2


title: Chromatin RNA-seq siSpt6 R4


title: DG75_LMP1_OLAP_3

treatment_protocol: Olaparib was dissolved in DMSO and cells were treated with 1 μM olaparib for 72 hrs in the appropriate media.


title: Chromatin RNA-seq siSpt6 R2


title: Chromatin RNA-seq siSpt6 R1


title: DG75_LMP1_3

description: Control

value: untreated


title: Chromatin RNA-seq siLuc R3


title: SCARNA13 ASO rep 1

status: Public on Sep 19 2018

city: Chengdu

first: Tian

last: Lan

state: Sichuan

address: No. 37 of Guoxue Lane

department: Department of Liver Surgery & Liver Transplantation

country: China

institute: West China Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HCC cells

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCCLM3 cells

tag: transfection

value: SCARNA13 ASO


title: SCARNA13 ASO rep 3


title: ALL-SIL_ATAC

status: Public on Sep 11 2018

city: Ghent

first: Karen

last: Verboom

address: De Pintelaan 185

department: Pediatrics and Genetics

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
fastq files were aligned with STARv2.4.2a to GRCh38 with --alignIntronMax 1 --alignMatesGapMax 1000 to avoid splice awareness.
Peak calling was performed with MACS2 using broad setting
Genome_build: GRCh38
Supplementary_files_format_and_content: xls file with MACS2 output

molecule: genomic DNA

source_name: ALL-SIL cell line

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: ATAC-seq was performed as previously described (Buenrostro et al. 2015) with minor changes. In brief, 50,000 cells were lysed and fragmented using Tn5 transposase (Illumina). Next, the samples were purified using the MinElute kit (Qiagen). The transposased DNA fragments were amplified and purified using the PCR Cleanup kit (Qiagen).

value: ALL-SIL


title: DG75_LMP1_OLAP_1


title: T4P mNET-seq siSpt6 R1


title: DG75_pBABE_OLAP_2


title: Total mNET-seq siLuc R1


title: T4P mNET-seq siSpt6 R2


title: DG75_pBABE_OLAP_1


title: DG75_pBABE_2

description: Control


title: mNucD-seq siLuc H3 R2

data_processing:
Library strategy: mNucD-seq
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

value: MABIO301:Anti-Histone H3 mAb. MBL International Corporation


title: SCARNA13 ASO rep 2


title: DG75_LMP1_OLAP_2


title: Pituitary gland KO Biological Replicate 2

status: Public on Sep 06 2018

type: RNA

city: Edinburgh

first: Clare

last: Pridans

address: 47 Little France Crescent

department: University of Edinburgh

institute: Centre for Inflammation Research

description: Gene expression data from adult striatum

hyb_protocol: GeneTitan

scan_protocol: GeneChip Command Console

data_processing: CEL files were normalised (RMA) in R/Bioconductor.

label: Biotin

organism: Rattus norvegicus

source_name: Pituitary gland

label_protocol: GeneChip Whole Transcript Labeling Kit (Applied Biosystems)

extract_protocol: Trizol extraction of total RNA followed by purification with Rneasy Mini kit

tag: age

value: Adult

tag: genotype

value: Csf1r -/-

tag: Sex

value: Female

tag: strain

value: DA/SD


title: DG75_pBABE_3

description: Control


title: DG75_LMP1_1

description: Control


title: DG75_LMP1_2

description: Control


title: DG75_pBABE_1

description: Control


title: H3K4me3 ChIP-seq

extract_protocol: DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 1*107 cells were cross-linked with 1,1 % formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, M220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 20 μl of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 2 μg of H3K4me1 specific (Abcam, ab8895) or H3K4me3 specific (Abcam, ab8580) antibody. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.


title: Control ASO rep 2

value: Control ASO


title: Control ASO rep 1


title: Control ASO rep 3


title: H3K4me1 ChIP-seq


title: Cold stressed callus, rep 1

status: Public on Aug 31 2018

city: London

first: Stefano

last: Pirro

address: Chartehouse Square

department: Molecular Oncology

institute: Barts Cancer Institute, Queen Mary University of London

description: total miRNAs

data_processing:
The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC
The adapter sequences were removed using Cutadapt with default parameters.
miRDeep2 was used to detect a set of high-confidence and novel miRNAs, whereas Blast alignment respect to all plant-related mature miRNAs annotated in miRBase (Release 21) was performed to detect low-confidence sequences.
DESeq2 was used to normalize the data and perform differential miRNA expression analysis.
Genome_build: The FASTA with miRNA sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Moringa oleifera

source_name: Callus

extract_protocol:
Total RNA was extracted from M. oleifera leaves, callus and cold stress treated callus using the NucleoSpin miRNA kit (Macherey-Nagel GmbH&Co., Germany), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1 month

tag: stress type

value: cultivation at 4 degrees C for 7 days

tag: tissue

value: Callus


title: Olfactory bulbs KO Biological Replicate 2

source_name: Olfactory bulbs


title: Olfactory bulbs HET Biological Replicate 2

value: Csf1r +/-


title: Olfactory bulbs HET Biological Replicate 1


title: Olfactory bulbs WT Biological Replicate 1

value: Csf1r +/+


title: Pituitary gland WT Biological Replicate 2


title: Pituitary gland HET Biological Replicate 2


title: Olfactory bulbs WT Biological Replicate 2


title: Unstressed leaf, rep 3

description: total miRNAs

source_name: Leaf

value: Leaf


title: Cold stressed callus, rep 2

description: total miRNAs


title: RNA-seq: Top2-1-Hmo1-37degree

status: Public on Jul 02 2018

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Log cells from 28 degree moved to 37 degree for 60 mins

data_processing:
FASTX Toolkit (fatsq_quality_filter) is used to filter raw reads based on the quality value -q 20 and -p 30
STAR is used to generate required genome files for alignment using fasta (SacCer2011) and gtf file (Saccharomyces_cerevisiae.R64-1-1.89.gtf) along with the following parameters; (STAR --runThreadN 20 --runMode genomeGenerate --genomeDir $OUTDIR --genomeFastaFiles $FASTA-FILE --sjdbGTFfile $GTF-FILE --genomeSAindexNbases 10)
STAR tool is used to align the filtered fastq files with reference genome. The genome files generated from the previous step and the following parameters are used for alignment (STAR --genomeDir $STAR-DependencyFilePATH --readFilesIn $FASTQ-FILE --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --runThreadN 20 --outFileNamePrefix $OUTPUTPATH)
RSEM (rsem-prepare-reference) is used to prepare reference files for transcript quantification using gtf and reference fasta file (rsem-prepare-reference --gtf $GTF-FILE $FASTA-FILE $NAME)
RSEM (rsem-calculate-expression) is used to calculate FPKM value using the aligned bam file and dependency files generated from the previous step. (rsem-calculate-expression --bam --no-bam-output -p 10 $BAM $RSEM-DependencyfilePath $OUTDIRPATH)
Genome_build: SacCer2011 fasta and Saccharomyces_cerevisiae.R64-1-1.89 GTF file
Supplementary_files_format_and_content: Tab delimited text files (One file per sample) containing FPKM value for each gene

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae strains wildtype, top2-1, hmo1∆, and hmo1∆;top2-1 were grown at 28 C till 1X10e7, then shifted to 37 C for 60 mins and cells were collected for RNA isolation

extract_protocol:
RNA was isolated from 5X10e7 cells by using QIAGEN Rneasy mini kit (50) (Cat no 74104) QIAGEN. Prior to library preparation cytoplasmic and mitochondrial ribosomal RNA was removed by using "Ribo-Zero Gold rRNA Removal Kit (Yeast) cat no. MRZY1324"
Libraries for RNA sequencing  were prepared following the manufacturer protocols for transcriptome sequencing with the Ion Proton sequencer (Thermo Fisher Scientific/Life Technologies). Briefly 1 ug of Total RNA was poly-A selected using the Dynabeads mRNA Direct Micro Purification kit (ThermoFisher, catalog no. 61021) according to manufacturer’s protocol. About 50 ng of poly-A RNA were used to prepare strand-specific barcoded RNA libraries with the Ion Total RNA-Seq kit v2.0 (ThermoFisher Scientific, catalog no. 4475936). Briefly poly-A RNA were fragmented with RNAse III and purify with Nucleic Acid Binding Beads.  After purification the poly-A RNA fragmented were hybridized and ligated with Ion Adaptor and subsequently reverse transcribed for cDNA preparation.  cDNA were amplified with Ion Torrent barcode primer and purified with  Nucleic Acid Binding Beads.Final libraries were quantified on Qubit fluorometer with HS DNA (Thermo Fisher Scientific/Life Technologies) and checked for size on an Agilent Bioanalyzer with HS DNA kit (Agilent, Santa Clara, CA). Four barcoded libraries were pooled together on an equimolar basis according to the final concentration of 11 pM and clonally amplified using the Ion Proton™ Hi Q™Template Kit (Thermo Fisher Scientific/Life Technologies) with IonOneTouch 2 instrument (Thermo Fisher Scientific/Life Technologies) . After emulsion PCR, DNA positive ISPs were recovered and enriched according to standard protocols with the IonOneTouch ES Instrument (Thermo Fisher Scientific/Life Technologies). A sequencing primer was annealed to DNA positive ISPs and the sequencing polymerase bound, prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was conducted according to the Ion Proton™  Hi-Q  Sequencing Kit Protocol on Ion Proton instrument.

tag: temperature

tag: cell cycle

value: Log Cells


title: Pituitary gland WT Biological Replicate 1


title: Pituitary gland HET Biological Replicate 1


title: Unstressed callus, rep 3

description: total miRNAs


title: Cold stressed callus, rep 3

description: total miRNAs


title: RNA-seq: Hmo1-37degree


title: Unstressed leaf, rep 2

description: total miRNAs


title: ebv_LCL_input_olaparib

status: Public on Jun 27 2018

description: DNA input olaparib

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605) using the Star software suite
Bowtie algorithm was used for allignment of reads and all of the redundant tags were removed before downstream analysis. Peak calling was performed using the Homer algorithm with input DNA used as a reference set. All peaks with false discovery rates (FDRs) of 1% for untreated or treated cells were overlapped to create a list of unique binding sites and used for further analysis. Integrative Genomics Viewer was used for data visualization.
Genome_build: NC_007605
Supplementary_files_format_and_content: bigwig,  bedgraph and narrowPeak

organism: human gammaherpesvirus 4

source_name: DNA input olaparib

growth_protocol: LCL cells were cultured in RPMI medium with 15% fetal bovine serum

extract_protocol:
The de-crosslinked DNA was purified with Zymo Spin I columns and eluted twice with 25 μL of 10 mM Tris-HCl (pH. 7.5)
For next generation sequencing, 20 ng of input DNA and 20 ng of FAIRE-DNA, each combined from two biological replicates, were used to prepare sequencing libraries

treatment_protocol: Formaldehyde-assisted isolation of regulatory elements (FAIRE) assay was performed according to an established protocol. Per sample, 1×10^7 LCLs were crosslinked with 1% formaldehyde and the reaction was quenched by adding glycine to a final concentration of 125 mM after 5 min. Cells were washed twice with PBS and cell pellets collected by centrifugation at 300×g for 5 min at 4°C. Fixed cells were then resuspended in cold lysis buffer [1% SDS, 10 mM EDTA, 50 mM Tris (pH 8.0)] and chromatin was sonicated  to generate 300−500-bp fragments. 1/10 of the chromatin was saved and used as input material and the remaining chromatin was diluted with 3 volumes of dilution buffer [0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.0), 167 mM NaCl]. Chromatin was centrifuged at 15,000×g for 5 min at 4°C to pellet cell debris and DNA was isolated from the supernatant by phenol/chloroform extraction and ethanol precipitation. The DNA pellet was resuspended in 100 μL of 10 mM Tris-HCl (pH. 7.5) and incubated with 10 μg of RNAse A (New England Biolabs) at 37°C. After 30 min, 20 μg of Proteinase K (Roche) were added to the samples and incubated at 55°C for 1 hr and then at 65°C to reverse any DNA-DNA cross-links.

value: LCL


title: Pituitary gland KO Biological Replicate 1


title: Olfactory bulbs KO Biological Replicate 1


title: ebv_LCL_FAIRE_olaparib

description: FAIRE

source_name: FAIRE


title: Unstressed callus, rep 1

description: total miRNAs


title: RNA-seq: Top2-1-37degree


title: RNA-seq: WT-37degree

value: Wildtype


title: ebv_LCL_FAIRE_control

description: FAIRE


title: ebv_LCL_Parp1B_control

description: PARP1 immunoprecipitation

source_name: PARP1 immunoprecipitation


title: ebv_LCL_Parp1A_control

description: PARP1 immunoprecipitation


title: RNA-seq: WT-28degree

description: Arrested in G1 and released in S phase 28 degree for 15 mins

value: S Phase


title: ebv_LCL_CTCF_control

description: Immunoprecipitated DNA by CTCF

source_name: Immunoprecipitated DNA by CTCF


title: ebv_LCL_input_control

description: DNA Input

source_name: DNA Input


title: ebv_LCL_CTCF_olaparib

description: Immunoprecipitated DNA by CTCF/ Olpaprib


title: cqs1△_YPG_1h

status: Public on May 15 2018

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S (for non-strand-specific RNA-seq)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to XL280α whole genome using HISAT v0.1.6beta with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Stingtie v1.2.1 with parameters stringtie -p -e -G -o -A-C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD v1.1.2 with parameters gfold count -ann -tag -o
Genome_build: XL280α
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Cryptococcus deneoformans

growth_protocol: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25℃ in dark. ;about 50 OD of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 OD, dropped onto YPD or YPG plates, and incubated for 1, 6, 12, 24,72 hour at 25℃ in dark

extract_protocol:
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.

treatment_protocol: Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.

tag: time point

value: serotype D XL280 MATalpha

tag: protocol

value: YPG solid plate (20g/l galactose, 20g/l peptone, 10g/l yeast extract, 2% agar) at 30C


title: WT_YPG_24h

source_name: wild type

value: wild strain


title: cqs1△_YPG_12h


title: cqs1△_YPG_6h


title: WT_YPG_72h


title: WT_YPG_12h


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate5

status: Public on Jun 06 2018

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

institute: IBSBC CNR

description: Biological replicate 5 of 6.

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

source_name: Human breast cancer MDA-MB-231 cell line

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Respective untreated cell lines, were used as a control. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: Non tumorigenic (MCF10A) and tumorigenic breast (MCF7 and MDA-MB-231) immortalized cell lines; and healthy (HMEC) and BC (BCpc7 and BCpcEMT) primary cultures, were collected after 24 hours post treatments.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: harvest time post treatment

value: 24 hours

tag: original tissue

value: breast

value: MDA-MB-231 breast cancer cell line not exposed to IR treatments


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate1

description: Biological replicate 1 of 6.


title: WT_YPG_6h


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate5

description: Biological replicate 5 of 6

tag: cell line

value: 9 Gy of IR

value: no exposure to IR treatments


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate4

description: Biological replicate 4 of 6.


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate2

description: Biological replicate 2 of 6.


title: cqs1△_YPD_72h

value: YPD solid plate (20g/l glucose, 20g/l peptone, 10g/l yeast extract, 2% agar) at 30C


title: Unstressed callus, rep 2

description: total miRNAs

value: 1 month

value: Callus


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate6

description: Biological replicate 6 of 6


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate2

description: Biological replicate 2 of 6


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate6

description: Biological replicate 6 of 6.


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate4

description: Biological replicate 4 of 6


title: cqs1△_YPG_24h


title: MDA-MB-231 tumorigenic BC cells treated with 23 Gy of IR dose - replicate3

description: Biological replicate 3 of 6.


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate3

description: Biological replicate 3 of 6


title: cqs1△_YPG_72h


title: WT_YPG_1h


title: cqs1△_YPD_1h


title: MDA-MB-231 tumorigenic BC cells treated with 9 Gy of IR dose - replicate1

description: Biological replicate 1 of 6


title: cqs1△_YPD_12h


title: cqs1△_YPD_6h


title: WT_YPD_72h


title: WT_YPD_6h


title: WT_YPD_1h


title: WT_YPD_24h


title: WT_YPD_12h


title: cqs1△_YPD_24h


title: Unstressed leaf, rep 1

description: total miRNAs


title: genomic DNA from PM285 term control placenta

status: Public on May 11 2018

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

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

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

data_processing:
R version 3.2.5
The matrix_signal_Wilson_PEIUGR.csv contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: subject id

tag: pathology group

value: Term

tag: fetal sex

value: FEMALE

tag: gestational age

tag: sample tissue

value: Chorionic Villi

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: genomic DNA from PL104 pre-term control placenta

value: PreT


title: genomic DNA from PM115 LOPE placenta

value: LOPE

value: MALE


title: genomic DNA from PM53 LOPE placenta


title: genomic DNA from PM320 term control placenta


title: genomic DNA from PM44 LOPE placenta


title: genomic DNA from PM98 LOPE placenta


title: genomic DNA from PM119 LOPE placenta


title: genomic DNA from PM275 term control placenta


title: genomic DNA from PM123 IUGR placenta

value: IUGR


title: genomic DNA from PM87 term control placenta


title: genomic DNA from PM306 term control placenta


title: genomic DNA from PM97 EOPE placenta

value: EOPE


title: genomic DNA from PM30 IUGR placenta


title: genomic DNA from PM38 LOPE placenta


title: genomic DNA from PM71 LOPE placenta


title: genomic DNA from PL86 IUGR placenta


title: genomic DNA from PM139r2 IUGR placenta


title: genomic DNA from PM252 term control placenta


title: genomic DNA from PM86 EOPE placenta


title: genomic DNA from PM130 IUGR placenta


title: genomic DNA from PM47 IUGR placenta


title: genomic DNA from PM307 IUGR placenta


title: genomic DNA from PL145 IUGR placenta


title: genomic DNA from PM272 IUGR placenta


title: genomic DNA from PM66 LOPE placenta


title: genomic DNA from PM269 LOPE placenta


title: genomic DNA from PM4 IUGR placenta


title: genomic DNA from PM80 EOPE placenta


title: genomic DNA from PM51 EOPE placenta


title: genomic DNA from PM99 EOPE placenta


title: genomic DNA from PM64 EOPE placenta


title: genomic DNA from PM12 EOPE placenta


title: genomic DNA from PM313 EOPE  placenta


title: genomic DNA from PM138 EOPE  placenta


title: genomic DNA from PM6 EOPE placenta


title: genomic DNA from PM116 EOPE  placenta


title: Cont-Ter-AGA, rep27 (methylation)

status: Public on Mar 07 2018

city: Toronto

first: Brian

last: Cox

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

hyb_protocol: Illumina HumanMethylation450 BeadChip protocol

scan_protocol: Arrays were imaged using an Illumina HiScan on a two-colour channel

data_processing: Data was processed in R 3.1.3. Loading was performed with the ChAMP package, functional normalization with the minfi package, batch correction for slide and array position with the sva package (ComBat)

source_name: Human placenta

extract_protocol: Genomic DNA was purified using the Wizard® Genomic DNA Purification Kit from Promega followed by bisulphite conversion using Zymo's EZ DNA Methylation Kit following manufacturers' protocols

tag: diagnosis

value: non-PE

value: placenta

tag: maternal age

tag: bmi

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

value: A

tag: nulliparous

value: No

tag: previous miscarriage

tag: previous hypertensive pregnancy

value: Yes

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

value: C-Section

tag: ga week

tag: ga day

tag: gender

value: M

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: PE-PreT-AGA, rep18 (methylation)

label_protocol: Illumina HumanMethylation450 BeadChip protocol

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

value: O

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

value: F


title: Cont-Ter-AGA, rep17 (methylation)

value: Asian

value: B

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: Cont-preT-AGA, rep24 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Cont-PreT-CH, rep9 (methylation)

value: Black

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: genomic DNA from PM39 EOPE placenta

tag: subject id

tag: pathology group

tag: fetal sex

value: MALE

tag: gestational age

tag: sample tissue

value: Chorionic Villi

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: Cont-PreT-CH, rep10 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: genomic DNA from PM321 EOPE placenta

tag: subject id

tag: pathology group

value: EOPE

tag: fetal sex

value: FEMALE

tag: gestational age

tag: sample tissue

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: genomic DNA from PM49 EOPE placenta


title: PE-PreT-CH, rep8 (methylation)

tag: diagnosis

tag: tissue

value: placenta

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: PE-PreT-CH, rep9 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: Caucasian

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: genomic DNA from PM129 EOPE  placenta

tag: subject id

tag: pathology group

tag: fetal sex

tag: gestational age

tag: sample tissue

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: PE-PreT-SGA, rep12 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: Cont-Ter-AGA, rep8 (methylation)

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: bmi

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: PE-PreT-SGA, rep8 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr


title: Cont-Ter-AGA, rep23 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: Yes

tag: attempted vaginal delivery

tag: mod

value: Vaginal

tag: ga week

tag: ga day

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: PE-PreT-SGA, rep17 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

value: C-Section

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: PE-PreT-SGA, rep5 (methylation)

tag: diagnosis

value: PE

tag: tissue

tag: maternal age

tag: bmi

value: A

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: PE-PreT-AGA, rep12 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: gender

value: F

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: genomic DNA from PM36 EOPE placenta

tag: subject id

tag: pathology group

tag: fetal sex

tag: gestational age

tag: sample tissue

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: Cont-Ter-AGA, rep14 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day

value: M

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Cont-Ter-AGA, rep16 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: B

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: PE-Term-SGA, rep11 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: Cont-PreT-CH, rep3 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: PE-Term-AGA, rep3 (methylation)

tag: maternal ethnicity

tag: maternal blood type

value: O

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: PE-PreT-AGA, rep3 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: Black

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: attempted vaginal delivery

tag: mod

tag: ga week

tag: ga day


title: Cont-Ter-AGA, rep15 (methylation)

tag: maternal ethnicity

tag: maternal blood type

value: AB

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: placenta weight z-score

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Other-INI182

status: Public on Aug 13 2017

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

label: biotin

source_name: Tumor

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: tissue

value: SMARCB1 deficient tumor


title: PE-Term-SGA, rep10 (methylation)

tag: diagnosis

value: placenta

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: attempted vaginal delivery

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: PE-Term-CH, rep1 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: mod

tag: ga week

tag: ga day

tag: placenta weight z-score


title: PE-PreT-CH, rep11 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: attempted vaginal delivery

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Other-INI185


title: Cont-preT-AGA, rep17 (methylation)

tag: maternal ethnicity

value: Caucasian

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: PE-Term-CH, rep5 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

tag: ga week

tag: ga day

tag: placenta weight z-score


title: Other-INI65


title: Other-INI86


title: PE-PreT-SGA, rep1 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: ES-PT26

source_name: Epithelioid Sarcoma

tag: tissue

value: ES


title: Other-INI61


title: RT-INI26

source_name: Rhabdoid Tumor

value: RT


title: Cont-PreT-CH, rep5 (methylation)

tag: diagnosis

value: non-PE

tag: maternal age

tag: bmi

value: Yes

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

tag: gender

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: ES-PT25


title: PE-PreT-AGA, rep1 (methylation)

value: PE

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

value: C-Section

tag: ga week

tag: ga day

tag: placenta weight z-score


title: Other-INI20

tag: tissue


title: PE-Term-SGA, rep7 (methylation)

tag: diagnosis

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

value: Vaginal

tag: gender

value: F

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: PE-Term-SGA, rep2 (methylation)

tag: maternal ethnicity

tag: maternal blood type

value: A

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: Other-INI44

tag: tissue


title: PE-PreT-CH, rep1 (methylation)

tag: diagnosis

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

tag: ga week

tag: ga day

tag: gender

tag: placenta weight z-score


title: Other-INI174


title: Other-INI38


title: Other-INI21


title: Other-INI152


title: ES-INI66


title: UC-INI144

source_name: Undifferentiated Chordoma

value: UC


title: UC-INI142T


title: Other-INI64


title: PE-Term-SGA, rep6 (methylation)

tag: maternal ethnicity

value: Asian

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Cont-Ter-AGA, rep11 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: O

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

value: M

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: Other-INI135

value: SMARCB1 deficient tumor


title: UC-INI138T


title: PE-PreT-CH, rep4 (methylation)

value: placenta

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: ga week

tag: ga day

tag: gender

tag: placenta weight z-score


title: PE-PreT-SGA, rep2 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: Caucasian

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: attempted vaginal delivery

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Other-INI37


title: ES-INI126

value: ES


title: PE-Term-SGA, rep4 (methylation)

tag: maternal ethnicity

tag: maternal blood type

value: B

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: mod

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: Cont-Ter-AGA, rep3 (methylation)

tag: diagnosis

value: non-PE

tag: tissue

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: ga week

tag: ga day

tag: gender

tag: placenta weight z-score


title: ES-INI124


title: Other-INI175


title: Cont-preT-AGA, rep6 (methylation)

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

value: Yes

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: attempted vaginal delivery

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: Cont-preT-AGA, rep12 (methylation)

tag: diagnosis

tag: tissue

tag: maternal age

tag: bmi

value: No

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: mod

tag: fetal weight z-score

tag: apgar score 1min

tag: apgar score 5min


title: Other-INI176


title: Other-INI136


title: Other-INI133


title: Other-INI106


title: PE-Term-AGA, rep2 (methylation)

value: PE

tag: maternal ethnicity

tag: maternal blood type

tag: nulliparous

tag: previous miscarriage

tag: max diastolic

tag: mode proteinuria

tag: hellp

tag: iugr

tag: ga week

tag: ga day

tag: gender

tag: placenta weight z-score


title: Other-INI132

tag: tissue


title: Other-INI134


title: PE-Term-AGA, rep1 (methylation)

tag: diagnosis

tag: maternal age

tag: bmi

tag: previous hypertensive pregnancy

tag: mean uterine pi

tag: mean umbilical pi

tag: max systolic

tag: attempted vaginal delivery

tag: mod

tag: cord diameter

tag: nicu transfer

tag: chorioamnionitis


title: NKL positive T-ALL cell line JURKAT

status: Public on Jan 19 2017

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HGU133plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalization of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

source_name: NKL positive T-ALL cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

tag: cell line

value: JURKAT

tag: cell line type

value: T-ALL cell line

tag: nkl status

value: positive


title: Other-INI131


title: Other-INI130


title: ES-INI121


title: BLCA_Cx_260

status: Public on Mar 13 2017

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.
The file Processed_Data_Supplement.txt contains ready-to-use median centered gene expression data for 307 tumor samples, with EntrezID and GeneSymbol. Sample order is derived from ConsensusClusterPlus, performed on the top 50% variance genes (n=7031) and matches the Sjodahl 2017 publication. Metadata: CEL Filename, GEO_SampleName, Labeling Batch, Hybridisation Number, TURB Stage, TURB Grade, Lund 2012 Taxonomy By Centroid Correlation, ConsensusClusterPlus Cluster, Sjodahl 2017 mRNA-cluster/Phenotype, Publication Heatmap Order.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: stage and grade

value: pT2   G3

tag: labeling batch


title: NKL positive T-ALL cell line ALL-SIL

value: ALL-SIL


title: ES-INI125

tag: tissue


title: Other-INI129


title: NKL positive T-ALL cell line CCRF-CEM

value: CCRF-CEM


title: Other-INI123


title: Other-INI127


title: Other-INI105


title: Other-INI128


title: Post_intervention_17

status: Public on Jun 29 2016

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 17

hyb_protocol: According to the Affymetrix expression protocol (HWS kit) including minor changes as suggested by the Encore Biotin protocol

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (build 1.4.0.38) including median polish and Sketch-Quantile normalisation

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 17

label_protocol: Ovation Pico WTA System V2 and Encore Biotin Module (Nugen)

extract_protocol: miRNeasy Mini kit (Qiagen) including DNase digestion

treatment_protocol: As described in the paper. Briefly, before and after the training period, all participants underwent lactate diagnostics and maximal bicycle spiroergometry to determine the individual anaerobic threshold (IAT) and maximal oxygen uptake (VO2max). The training program lasted 8 weeks and consisted of three supervised exercise sessions per week. Each training session consisted of 30 min each bicycle ergometer exercise and 30 min treadmill exercise. The training intensity was individually set at 80% of VO2max, based on the performance test and controlled by heart rate.

tag: insulin sensitivity

value: non-responder

value: muscle

tag: Sex

value: female

tag: age


title: Post_intervention_20

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 20

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 20

value: low-responder


title: Other-INI120

value: SMARCB1 deficient tumor


title: ES-INI122

value: ES


title: Other-INI115


title: Other-INI114


title: BLCA_Cx_296


title: Post_intervention_14

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 14

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 14

value: high-responder


title: Post_intervention_11

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 11

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 11

value: male


title: BLCA_Cx_84


title: BLCA_Cx_46

value: pTa   G2


title: Post_intervention_7

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 7

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 7


title: Post_intervention_10

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 10

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 10


title: Post_intervention_4

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 4

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 4


title: NKL positive T-ALL cell line PEER

value: PEER


title: NKL positive T-ALL cell line LOUCY

value: LOUCY


title: Baseline_rep18

description: Gene expression data from muscle biopsy before intervention derived from subject 18

source_name: Muscle biopsy before intervention derived from subject 18


title: Post_intervention_9

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 9

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 9


title: BLCA_Cx_35


title: Post_intervention_19

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 19

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 19


title: BLCA_Cx_125

value: pT1   G3


title: Other-INI117


title: Baseline_rep9

description: Gene expression data from muscle biopsy before intervention derived from subject 9

source_name: Muscle biopsy before intervention derived from subject 9


title: Post_intervention_18

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 18

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 18


title: Baseline_rep12

description: Gene expression data from muscle biopsy before intervention derived from subject 12

source_name: Muscle biopsy before intervention derived from subject 12


title: Baseline_rep6

description: Gene expression data from muscle biopsy before intervention derived from subject 6

source_name: Muscle biopsy before intervention derived from subject 6


title: Baseline_rep20

description: Gene expression data from muscle biopsy before intervention derived from subject 20

source_name: Muscle biopsy before intervention derived from subject 20


title: Post_intervention_13

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 13

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 13


title: Post_intervention_16

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 16

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 16


title: Post_intervention_5

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 5

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 5


title: RTK_INI97

status: Public on Mar 08 2016

source_name: Rhabdoid Tumor of the Kidney

value: RTK


title: RTK_INI93


title: Baseline_rep2

description: Gene expression data from muscle biopsy before intervention derived from subject 2

source_name: Muscle biopsy before intervention derived from subject 2


title: Post_intervention_6

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 6

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 6


title: Post_intervention_3

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 3

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 3


title: Post_intervention_12

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 12

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 12


title: Post_intervention_2

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 2

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 2


title: Post_intervention_8

description: Gene expression data from muscle biopsy after an eight weeks endurance training intervention derived from subject 8

source_name: Muscle biopsy after an eight weeks endurance training intervention derived from subject 8


title: Baseline_rep13

description: Gene expression data from muscle biopsy before intervention derived from subject 13

source_name: Muscle biopsy before intervention derived from subject 13


title: Baseline_rep14

description: Gene expression data from muscle biopsy before intervention derived from subject 14

source_name: Muscle biopsy before intervention derived from subject 14


title: RTK_INI18


title: Baseline_rep19

description: Gene expression data from muscle biopsy before intervention derived from subject 19

source_name: Muscle biopsy before intervention derived from subject 19


title: Hs_CNS_MRT (hIC3._.INI158)

status: Public on Jan 27 2016

source_name: Atypical Teratoid and Rhabdoid Tumor

value: ATRT


title: Hs_CNS_MRT (hNA._.INI108)


title: Hs_CNS_MRT (hIC3._.INI99)


title: Baseline_rep17

description: Gene expression data from muscle biopsy before intervention derived from subject 17

source_name: Muscle biopsy before intervention derived from subject 17


title: Hs_CNS_MRT (hIC2._.INI51)


title: Hs_CNS_MRT (hIC2._.INI164)


title: Hs_CNS_MRT (hIC2._.INI57)


title: Hs_CNS_MRT (hIC2._.INI94)


title: Baseline_rep10

description: Gene expression data from muscle biopsy before intervention derived from subject 10

source_name: Muscle biopsy before intervention derived from subject 10


title: Baseline_rep3

description: Gene expression data from muscle biopsy before intervention derived from subject 3

source_name: Muscle biopsy before intervention derived from subject 3


title: RTK_INI90


title: Baseline_rep8

description: Gene expression data from muscle biopsy before intervention derived from subject 8

source_name: Muscle biopsy before intervention derived from subject 8


title: Baseline_rep11

description: Gene expression data from muscle biopsy before intervention derived from subject 11

source_name: Muscle biopsy before intervention derived from subject 11


title: Baseline_rep7

description: Gene expression data from muscle biopsy before intervention derived from subject 7

source_name: Muscle biopsy before intervention derived from subject 7


title: Hs_CNS_MRT (hIC1._.INI88)


title: Baseline_rep4

description: Gene expression data from muscle biopsy before intervention derived from subject 4

source_name: Muscle biopsy before intervention derived from subject 4


title: Hs_CNS_MRT (hIC1._.INI96)


title: Hs_CNS_MRT (hIC1._.INI84)


title: Hs_CNS_MRT (hIC3._.INI166)


title: Hs_CNS_MRT (hIC1._.INI163)


title: Baseline_rep5

description: Gene expression data from muscle biopsy before intervention derived from subject 5

source_name: Muscle biopsy before intervention derived from subject 5


title: Hs_CNS_MRT (hIC2._.INI157)


title: Hs_CNS_MRT (hIC2._.INI92)


title: Hs_CNS_MRT (hIC3._.INI165)


title: Baseline_rep16

description: Gene expression data from muscle biopsy before intervention derived from subject 16

source_name: Muscle biopsy before intervention derived from subject 16


title: Hs_CNS_MRT (hIC2._.INI160)


title: Hs_CNS_MRT (hIC2._.INI167)


title: Hs_CNS_MRT (hIC3._.INI170)


title: Hs_CNS_MRT (hIC1._.INI87)


title: Hs_CNS_MRT (hNA._.INI27)


title: Hs_CNS_MRT (hIC1._.INI104)


title: Hs_CNS_MRT (hIC2._.INI30)


title: Hs_CNS_MRT (hIC2._.MB115)


title: Hs_CNS_MRT (hIC1._.INI103)


title: Hs_CNS_MRT (hIC1._.INI89)


title: genomic DNA from PM9 abnormal MSS placental chorionic villi

status: Public on Dec 22 2015

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

data_processing: GenomeStudio software v2011.1

tag: status/group

value: Ab. MSS

tag: fetal sex/sex

value: M

tag: sample tissue

value: placental chorionic villi

tag: fetal gestational age (weeks)/trimester

tag: age (years)

tag: 450k plate id

tag: 450k sentrix_id

tag: 450k sentrix_position


title: Hs_CNS_MRT (hIC1._.INI162)


title: RTK_INI39

source_name: Rhabdoid Tumor of the Kidney


title: Hs_CNS_MRT (hIC1._.INI169)


title: Hs_CNS_MRT (hIC1._.INI161)


title: Hs_CNS_MRT (hIC1._.INI159)


title: Hs_CNS_MRT (hIC1._.INI168)


title: genomic DNA from PM92 control placental chorionic villi

value: control


title: genomic DNA from PM46 LOPET placental chorionic villi

value: LOPET

value: F


title: genomic DNA from PM161 control placental chorionic villi


title: genomic DNA from PM84 control placental chorionic villi


title: microglia_WT_1

status: Public on Nov 04 2015

city: Utrecht

first: Elly

middle: M

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

description:
raw data in Cy5 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: Prior to hybridization, equal amounts (825 ng) of Cy3- and Cy5-labelled RNA were hydrolyzed for 30 min at 60C in 1x fragmentation buffer (Agilent Technologies). The fragmented targets were hybridized to a microarray by incubating for 17 h at 60C in 1 x target solution (Agilent Technologies) in a rotating hybridization chamber. Specifically, each hybridization consisted of two individual samples, one labelled with Cy3 and one with Cy5. After hybridization, the arrays were washed at room temperature for 5 min in 6x salinesodium phosphate–EDTA (SSPE)/0.005% N-Lauroylsarcosine (Sigma-Aldrich, St Louis, MO, USA), 1 min in 0.06x SSPE/0.005% N-Lauroylsarcosine and 30 s in acetonitrile (Sigma-Aldrich), then dried in a nitrogen flow.

scan_protocol: The arrays were scanned at a resolution of 5 um at 5% and 100% photomultiplier tube (PMT) with an Agilent Technologies Scanner G2505A. Scan data were extracted using Agilent Feature Extraction software (version 8.5.1, Agilent).

data_processing: Raw data from the extraction software was imported to R statistical processing environment using a LIMMA/Bioconductor package. Nonuniformity outliers and background outliers were removed. Data were normalized using between-array normalization with the “quantile” algorithm (Bolstad et al., 2003). The Cy3 and Cy5 normalized log2 intensities were used as separate channels for further analysis, as previously shown in Bossers et al. (2010).  Inter-sample gene variation because of technical reasons, such as contamination of myelin, were defined using the Weighted Gene Co-expression Network Analysis (WGCNA) (Langfelder and Horvath, 2008) as shown previously (see Orre et al., 2014) and excluded before normalization in this current analysis.

organism: Mus musculus

source_name: cortical microglia (cd11b), WT mouse

label_protocol: RNA was linearly amplified and fluorescently labelled with either Cy3-CTP or Cy5-CTP using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: Sorted cells were incubated in TRIsure (Bioline) for 5 minutes on ice with thorough mixing and/or vortexing. For all samples, RNA was isolated by overnight precipitation in isopropanol to which 20 microgram of glycogen had been added.

treatment_protocol: The mice were anesthetized by pentobarbital and transcardially perfused with HBSS (-Ca/-Mg) (Invitrogen). Thereafter, cortical tissue was macro-dissected and, subsequently, used for mechanical dissociation using a Tissue Chopper, the tissue was subjected to enzymatic dissociation using Papain (Worthington) at a final concentration of 8 U/mL in combination with DNase I at 80 Kunitz units/mL final concentration (Sigma; D4263) in a PIPES based buffer with addition of L-cystein- HCl and EDTA in 37C incubator for 50 minutes on a rocker, followed by the addition of another 25 Kunits/mL DNase I and a further incubation at 37C for 15 minutes. A Percoll gradient and myelin removal were performed on single cells before labeling (Myelin Removal Beads II [MiltenyiBiotec; 130-096e733]) according to the manufacturer’s protocol. Pelleted cells were resuspended in PBS (0.5% BSA) and stained with unconjugated rabbit polyclonal GLT-1 (1:100, custom made, Biomatik, 0.6 mg/mL), mouse anti O4 (1:400, Millipore, MAB345), CD11b-APC (1:200, eBioscience, 17-0112-82), CD45-(1:200, eBioscience, 12-0451-82), Fc-receptor block CD16/32 (1:200, BD Pharmingen, 553142), and polyclonal rabbit IgG isotype control (1:150; Thermo Scientific, NC-100-P1) (at 4 _C for 30 minutes). After washing, secondary anti-rabbit biotin antibody (1:100, Jackson Immunoresearch, 111-065e144) and PE conjugated goat anti-mouse (1:125, eBioscience, 12-4010-82) (for visualization of O4 staining) was added and incubated for 30 minutes at 4C. After washing, streptavidin-APC-Cy7 (1:125, Biolegend, 405208) was allowed to incubate for 15 minutes at 4C in the dark. The cells were washed and resuspended in GKN/PBS and cell viability staining 7AAD (BD bioscience). Using BD FACS Aria I (BD bioscience), GLT1 positive cells were sorted on GLT1+/CD11b- expression and microglia cells were sorted on CD11b+/CD45+ expression after gating away the dead cell population on 7AAD signal. The sorted cells were directly subjected to RNA isolation.

value: brain

tag: genotype

value: WT

value: 15-18 months

tag: strain

tag: cell population selection

value: myelin- / O4- / cd11b+ / cd45+


title: genomic DNA from PM135 control placental chorionic villi


title: genomic DNA from PM155 control placental chorionic villi


title: genomic DNA from PM249 control placental chorionic villi


title: genomic DNA from PM124 control placental chorionic villi


title: microglia_WT_7

description:
raw data in Cy5 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_2.txt


title: genomic DNA from PM153 control placental chorionic villi


title: microglia_AD_6

description:
raw data in Cy5 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_1.txt

source_name: cortical microglia (cd11b), APPswe/PS1dE9 mouse


title: genomic DNA from PM76 control placental chorionic villi


title: genomic DNA from PM77 control placental chorionic villi


title: genomic DNA from PM112 control placental chorionic villi


title: genomic DNA from PM55 LOPET placental chorionic villi


title: microglia_WT_5

description:
raw data in Cy5 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_AD_4

description:
raw data in Cy5 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_3.txt


title: microglia_AD_1

description:
raw data in Cy3 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_3.txt


title: genomic DNA from PM233 control placental chorionic villi


title: genomic DNA from PM136 control placental chorionic villi


title: microglia_AD_2

description:
raw data in Cy5 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_AD_5

description:
raw data in Cy3 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_4.txt


title: microglia_WT_3

description:
raw data in Cy5 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_WT_6

description:
raw data in Cy3 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_1.txt


title: microglia_AD_3

description:
raw data in Cy3 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_2.txt


title: genomic DNA from PM227 abnormal MSS placental chorionic villi


title: genomic DNA from PM74 control placental chorionic villi


title: genomic DNA from PM181 control placental chorionic villi


title: genomic DNA from PM264 control placental chorionic villi


title: genomic DNA from PM120 control placental chorionic villi


title: genomic DNA from PM205 control placental chorionic villi


title: genomic DNA from PM104 control placental chorionic villi


title: genomic DNA from PM17 control placental chorionic villi


title: genomic DNA from PM114 control placental chorionic villi


title: genomic DNA from PM122 control placental chorionic villi


title: genomic DNA from PM142 control placental chorionic villi


title: genomic DNA from PM167 control placental chorionic villi


title: genomic DNA from PM20 control placental chorionic villi


title: genomic DNA from PM58 LOPET placental chorionic villi


title: microglia_WT_4

description:
raw data in Cy3 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_3.txt


title: genomic DNA from PM243 control placental chorionic villi


title: microglia_AD_7

description:
raw data in Cy3 channel of file:
US12302316_252665511015_S01_GE2-v5_95_Feb07_1_2.txt


title: microglia_WT_2

description:
raw data in Cy3 channel of file:
US12302316_252665511011_S01_GE2-v5_95_Feb07_1_1.txt


title: methylation_Placental Tissue_Preeclamptic_Subject_8

status: Public on Sep 24 2015

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

hyb_protocol: Standard Illumina Hyb

scan_protocol: Data were processed at Expression Analysis using standard in house processing

data_processing: Data were processed following the Morris et al 2014 pipeline (PMID 24336642).

source_name: Placental Tissue

label_protocol: Standard Illumina Labeling

extract_protocol: Trizol

tag: diagnosis

value: preeclamptic

value: placenta

tag: maternal age

tag: gestational age

value: Caucasian

tag: race


title: methylation_Placental Tissue_Preeclamptic_Subject_9

tag: tissue

value: African American


title: methylation_Placental Tissue_Preeclamptic_Subject_20


title: methylation_Placental Tissue_Preeclamptic_Subject_12


title: methylation_Placental Tissue_Normotensive_Subject_16

value: normotensive


title: methylation_Placental Tissue_Normotensive_Subject_17


title: methylation_Placental Tissue_Normotensive_Subject_13


title: methylation_Placental Tissue_Normotensive_Subject_19


title: methylation_Placental Tissue_Normotensive_Subject_1


title: methylation_Placental Tissue_Normotensive_Subject_6


title: methylation_Placental Tissue_Preeclamptic_Subject_14


title: methylation_Placental Tissue_Normotensive_Subject_11


title: methylation_Placental Tissue_Preeclamptic_Subject_15


title: methylation_Placental Tissue_Normotensive_Subject_2


title: methylation_Placental Tissue_Preeclamptic_Subject_1


title: methylation_Placental Tissue_Preeclamptic_Subject_7


title: methylation_Placental Tissue_Normotensive_Subject_18


title: methylation_Placental Tissue_Normotensive_Subject_12


title: methylation_Placental Tissue_Normotensive_Subject_9


title: Placenta_GDM_Yes_Sample80

status: Public on Aug 03 2015

city: Los Angeles

first: Alexandra

last: Binder

state: California

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

description: chart-reported case of gestational diabetes

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

data_processing:
Color bias adjustment and quantile normalization was performed on signal intensities, adjustment for probe-type bias was performed on the beta-values using beta-mixture quantile normalization (BMIQ)
Unmethylated and methylated signal intensities in Series supplementary file

source_name: Placenta tissue from the maternal (decidual basalis) side near the umbilical cord

extract_protocol: DNA was isolated from placenta tissue using the QIAmp DNA Mini Kit (Qiagen) according to manufacturer’s instruction

tag: gestational diabetes

value: Yes


title: Placenta_GDM_Yes_Sample82


title: methylation_Placental Tissue_Normotensive_Subject_10


title: methylation_Placental Tissue_Preeclamptic_Subject_6


title: Placenta_GDM_Yes_Sample81


title: Placenta_GDM_No_Sample79

description: pregnancy without maternal complications

value: No


title: methylation_Placental Tissue_Normotensive_Subject_14

value: Asian


title: Placenta_GDM_No_Sample76


title: methylation_Placental Tissue_Preeclamptic_Subject_2


title: methylation_Placental Tissue_Preeclamptic_Subject_10


title: Placenta_GDM_No_Sample77


title: Placenta_GDM_No_Sample78


title: Placenta_GDM_No_Sample72


title: Placenta_GDM_No_Sample67


title: Placenta_GDM_Yes_Sample71


title: Placenta_GDM_No_Sample69


title: Placenta_GDM_No_Sample73


title: Placenta_GDM_Yes_Sample64


title: Placenta_GDM_Yes_Sample70


title: Placenta_GDM_No_Sample66


title: Placenta_GDM_Yes_Sample63


title: Placenta_GDM_Yes_Sample65


title: Placenta_GDM_No_Sample54


title: Placenta_GDM_No_Sample56


title: Placenta_GDM_Yes_Sample74


title: Placenta_GDM_No_Sample59


title: Placenta_GDM_Yes_Sample58


title: Placenta_GDM_No_Sample57


title: Placenta_GDM_Yes_Sample75


title: Placenta_GDM_Yes_Sample60


title: Placenta_GDM_Yes_Sample43


title: Placenta_GDM_Yes_Sample52


title: Placenta_GDM_No_Sample53


title: Placenta_GDM_Yes_Sample61


title: Placenta_GDM_No_Sample55


title: Placenta_GDM_Yes_Sample51


title: Placenta_GDM_Yes_Sample62


title: Placenta_GDM_Yes_Sample45


title: Placenta_GDM_Yes_Sample33


title: Placenta_GDM_Yes_Sample40


title: Placenta_GDM_Yes_Sample48


title: Placenta_GDM_Yes_Sample35


title: Placenta_GDM_Yes_Sample25


title: Placenta_GDM_No_Sample50


title: Placenta_GDM_Yes_Sample47


title: Placenta_GDM_Yes_Sample27


title: Placenta_GDM_No_Sample39


title: Placenta_GDM_No_Sample42


title: Placenta_GDM_Yes_Sample24


title: Placenta_GDM_No_Sample31


title: Placenta_GDM_Yes_Sample28


title: Placenta_GDM_No_Sample23


title: Placenta_GDM_Yes_Sample36


title: Placenta_GDM_Yes_Sample49


title: Placenta_GDM_No_Sample32


title: Placenta_GDM_Yes_Sample21


title: Placenta_GDM_Yes_Sample29


title: Placenta_GDM_No_Sample18


title: Placenta_GDM_Yes_Sample37


title: Placenta_GDM_No_Sample19


title: Placenta_GDM_No_Sample15


title: GSC923-InvasiveArea-rep5

status: Public on Feb 20 2014

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

description: sample was taken from the area of tumor invasion, mixed human/mouse

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Alternative CDF's were generated by masking probes which showed non-specific hybridization towards mouse in the human arrays and vice versa.  Briefly, using raw intensity signals from cel files, individual probes were filtered if they met the following criteria: the net intensity (PM-MM) of each probe pair from the cross-reactive species was less than 10 and greater than 50% of the corresponding signal from human tumor core.  Alternatively, to detect cross-reactive human signal on the mouse microarrays, mouse chips were hybridized with pure human cell line RNA and the corresponding same criteria were applied. The remaining probes were grouped into their original probe sets and those that had at least 4 remaining probes were retained in the new chip definition file (cdf). This resulted in alternative cdf’s containing 26,954 probe sets for the HG-U133 plus2 array and 21,675 probe sets for the Mouse430_2 array. The gene expression data were calculated using the MAS5 algorithm following quantile normalization, and the results subjected to statistical analysis using a two-way Anova.

organism:
Homo sapiens
Mus musculus

source_name: Area of invading GSC

label_protocol: Standard Affymetrix protocol

growth_protocol: Primary GBM glioma stem cells were cultured in NBE medium consisting of Neurobasal A medium with N2 and B27 supplements (Invitrogen, Carlsbad, CA), and human recombinant basic fibroblast growth factor and epidermal growth factor (50 ng/mL each; R&D Systems, Minneapolis, MN).  0923 and 1228A1 (ex vivo culture of 1228 GSCs following one in vivo cycle) GSC lines were used for intracranial mouse glioma models.

extract_protocol: RNA extraction was performed via Rneasy

treatment_protocol: An intracranial orthotopic model in severe combined immunodeficiency (SCID) mice was utilized in order to generate infiltrative glioma xenograft tumors. Brains were handled in RNase free conditions, imbedded in OCT compound, frozen immediately and kept at -80°C. Total cellular RNA isolation was carried out for Affymetrix HG-U133 plus2 or Mouse430_2 GeneChip Arrays, according to the manufacturer instructions (Affymetrix, CA)

value: tumor invaded mouse brain


title: GSC923-DistalBrain-rep4

description: sample was taken from a distal area (uninfiltrated) mouse brain, 100% mouse

source_name: Mouse brain parenchyma

value: distal mouse brain


title: GSC923-InvasiveArea-rep6


title: GSC923-InvasiveArea-rep4


title: GSC923-InvasiveArea-rep2


title: Placenta_GDM_No_Sample8


title: GSC923-DistalBrain-rep2


title: GSC923-DistalBrain-rep6


title: GSC923-DistalBrain-rep5


title: GSC1228-InvasiveArea-rep8


title: Placenta_GDM_No_Sample16


title: Placenta_GDM_Yes_Sample9


title: Placenta_GDM_Yes_Sample6


title: GSC1228-InvasiveArea-rep10


title: Placenta_GDM_No_Sample5


title: Placenta_GDM_No_Sample4


title: GSC1228-DistalBrain-rep3


title: Placenta_GDM_Yes_Sample3


title: Placenta_GDM_No_Sample46


title: Placenta_GDM_No_Sample17


title: GSC1228-InvasiveArea-rep2


title: GSC1228-DistalBrain-rep10


title: GSC1228-InvasiveArea-rep3


title: GSC1228-DistalBrain-rep2


title: Placenta_GDM_No_Sample11


title: Placenta_GDM_Yes_Sample13


title: Placenta_GDM_No_Sample1


title: GSC1228-InvasiveArea-rep8


title: GSC1228-TumorCore-rep3

description: sample was taken from the tumor core, 100% human

source_name: Tumor core

value: human glioma tumor core


title: GSC1228-TumorCore-rep2


title: Placenta_GDM_No_Sample14


title: Placenta_GDM_No_Sample2


title: Placenta_GDM_No_Sample10


title: Placenta_GDM_No_Sample7


title: GSC923-TumorCore-rep4


title: GSC923-InvasiveArea-rep6


title: GSC923-TumorCore-rep6


title: GSC923-TumorCore-rep8


title: GSC923-TumorCore-rep2


title: GSC1228-InvasiveArea-rep2


title: GSC923-InvasiveArea-rep8


title: GSC1228-DistalBrain-rep8


title: GSC1228-TumorCore-rep10


title: GSC923-InvasiveArea-rep4


title: GSC1228-TumorCore-rep8


title: GSC923-InvasiveArea-rep2


title: NK92 cells

status: Public on Jan 21 2014

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

country: Taiwan

institute: National Taiwan University

description: Total RNA were extracted from NK92 cells.

hyb_protocol: Hybridization and washing of the arrays was done according to GeneChip Expression Analysis Technical Manual from Affymetrix

scan_protocol: The arrays were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).

data_processing: The data were extracted with Affymetrix Microarray suite (MAS) software.

label_protocol: The Affymetrix chip, Human Genome U133 plus 2.0, was used. First-strand cDNAs were synthesized from 10 ug total RNAs with a T7-ptomoter-oligo(dT) primer. After second-strand synthesis, biotin-labeled cRNAs were transcribed from the T7 promoter. The quality of cRNAs was checked by gel electrophoresis with an Agilent 6000 Bioanalyzer (Agilent Technologies, Foster City, CA). The cRNAs were fragmented into sizes from 35 to 200 nucleotides, and labeled with streptavidin-PE. The fragmented cRNAs were mixed with control RNAs (bioB, bioC, bioD, and cre) and hybridized with the membrane.

growth_protocol: YT cells were grown in 80% IMDM plus 20% fetal bovine serum (FBS), NK92 cells were grown in 75% α-MEM, 12.5% FBS, 12.5% horse serum, 2 mM L-glutamate, and 10 ng/mL IL-2.

extract_protocol: Total RNA sample was extracted by TRIzol® reagent (Invitrogen )

tag: cell line

value: NK92,  non-Hodgkin's lymphoma cell line


title: GSC1228-InvasiveArea-rep10


title: NK-cell line SNK6

status: Public on Mar 18 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from NK cell lines.
SNK6

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried out using BRB-ArrayTools version (3.7.0).

source_name: NK-cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

tag: cell type

value: NK

tag: age

tag: gender

value: male


title: NK-cell line KHYG1

description:
Gene expression data from NK cell lines.
KHYG1

value: female


title: NK-cell line IMC-1

description:
Gene expression data from NK cell lines.
IMC-1


title: mutant3 [methylation]

status: Public on Jun 08 2013

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

description: SAMPLE 6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using a HiScanSQ using standard recommended Illumina scanner setting

data_processing:
GenomeStudio V2011.1
HY_450k_signal_intensity.txt (linked as supplementary file on Series record) reports: Unmethylated and methylated signal intensities with background correction normalized to Illumina controls.

source_name: HCT116 mutant derived cell line with altered DNA methylation

growth_protocol: Cells were cultured in McCoy's 5A medium supplemented with 10% FBS and antibiotics.

extract_protocol: Genomic DNA was prepared using the DNeasy Tissue kit following manufacturer’s instructions

tag: genotype/variation

value: mutant with altered DNA methylation


title: parental1 [methylation]

description: SAMPLE 1

source_name: HCT116 cell line

value: parental


title: 450k

description:
SAMPLE 1
embryonic stem cell line

data_processing:
GenomeStudio V2011.1
Josh_450k_signal_intensity.txt (linked as supplementary file on Series record) reports: Unmethylated and methylated signal intensities with background correction normalized to Illumina controls

growth_protocol: HES-2 (ES02) human embryonic stem cells were adapted from mitotically inactive MEF feeders to matrigel substrate (BD Biosciences) and mTesR1 medium (STEMCELL Technologiesaccording to manufacturer's protocol.  Adaptation was for 4 passages and the final passage number was p72.  DNA was extracted from Tra 1-60+ cells isolated by flow cytometry. (Sigma).

extract_protocol: DNA was purified using Dneasy Blood and Tissue Kit (Qiagen) and Bisulfite converted using the EpiTect Bisulfite Kit (Qiagen)

value: embryonic stem cell line HES-2


title: mutant1 [methylation]

description: SAMPLE 4


title: mutant2 [methylation]

description: SAMPLE 5


title: parental2 [methylation]

description: SAMPLE 2


title: parental3 [methylation]

description: SAMPLE 3