title: whole blood gene expression profile_ALS04108

description: unique sample


title: whole blood gene expression profile_ALS04033

status: Public on Apr 05 2018

type: RNA

city: Utrecht

first: Jan

middle: Herman

last: Veldink

state: Utrecht

address: Heidelberglaan 100, F.02.230

department: Neurology, Brain Center Rudolf Magnus

country: Netherlands

institute: University Medical Center Utrecht

description: unique sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Before RNA hybridization, samples were randomized to avoid batch effects correlated to the diagnosis. Samples were hybridized to Illumina’s HumanHT-12 version 3 BeadChips according to manufacturer’s protocol (Illumina, Inc., San Diego, CA, U.S.A.).
Final Reports from Illumina’s GenomeStudio were imported in R (http://.cran.r-project.org). After quantile normalization, gender was checked by expression of gender-specific Y chromosomal probes (JARID1D and RPS4Y1). Samples with gender mismatches were excluded. Subsequently expression values were log2 transformed and quantile normalized. Arrays were projected along the first and second principal component and outliers were dismissed. This resulted in the exclusion of 34 patients and 33 control subjects from the training set and exclusion of 13 patients and 7 control subjects from the test-validation set.
High quality probes were selected, including true autosomal probes only. Using the BLAT function in UCSC’s Genome Browser, all probes were aligned to the NCBI reference genome build 36. Probes with multiple BLAT hits with a sequence homology of > 95% were defined as aspecific and excluded from further analysis. We looked for retired probes using the RefSeq and UniGene (build #228) databases. Retired probes were excluded from further analysis. Finally, probes with identical probe IDs that overlapped between the Illumina HumanHT12 v3 and v4 platform were selected.
Surrogate variable analysis: To eliminate expression heterogeneity caused by known and unknown technical and biological background, data from both training and test sets were combined and normalized, applying surrogate variable analysis (SVA). This produces surrogate variables for which expression levels can be corrected by calculating residuals in a linear regression model. In previous studies, this correction has been proven to reduce batch-specific background noise, thereby increasing the ability to detect biologically meaningful signals.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood_CON

label_protocol: The Illumina TotalPrep‐96 RNA Amplification Kit was used to generate Biotin labeled (biotin‐16‐UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: Venous blood was collected in PAXgene tubes stabilizing messengerRNA (mRNA). PAXgene extraction kits (Qiagen) for RNA extraction were used according to the manufacturer’s protocol. Globin reduction treatments were not performed. Quality of isolated RNA was assessed using the Agilent 2100 Bioanalyzer system.

tag: Sex

value: m

tag: diagnosis

value: CON

tag: censored


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source_name: whole blood_ALS

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value: ALS

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description: unique sample


title: whole blood gene expression profile_ALS00619

description: unique sample


title: whole blood gene expression profile_ALS02856

description: unique sample


title: whole blood gene expression profile_ALS00506

description: unique sample


title: whole blood gene expression profile_ALS02992

description: unique sample


title: whole blood gene expression profile_ALS02580

description: unique sample


title: whole blood gene expression profile_ALS02816

description: unique sample


title: whole blood gene expression profile_ALS03034

description: unique sample


title: whole blood gene expression profile_ALS02923

description: unique sample


title: whole blood gene expression profile_ALS01456

description: unique sample


title: whole blood gene expression profile_ALS02806

description: unique sample


title: whole blood gene expression profile_ALS00559

description: unique sample


title: whole blood gene expression profile_ALS02983

description: unique sample


title: whole blood gene expression profile_ALS03725

description: unique sample


title: whole blood gene expression profile_ALS00175

description: unique sample


title: whole blood gene expression profile_ALS03276

description: unique sample


title: whole blood gene expression profile_ALS02885

description: unique sample


title: whole blood gene expression profile_ALS03312

description: unique sample


title: whole blood gene expression profile_ALS02521

description: unique sample


title: whole blood gene expression profile_ALS02684

description: unique sample


title: whole blood gene expression profile_ALS03022

description: unique sample


title: whole blood gene expression profile_ALS02976

description: unique sample


title: whole blood gene expression profile_ALS03160

description: unique sample


title: whole blood gene expression profile_ALS02883

description: unique sample


title: whole blood gene expression profile_ALS02642

description: unique sample


title: whole blood gene expression profile_ALS02963

description: unique sample


title: whole blood gene expression profile_ALS02477

description: unique sample


title: whole blood gene expression profile_ALS02420

description: unique sample


title: whole blood gene expression profile_ALS01632

description: unique sample


title: whole blood gene expression profile_ALS02689

description: unique sample


title: whole blood gene expression profile_ALS00579

description: unique sample


title: whole blood gene expression profile_ALS02584

description: unique sample


title: whole blood gene expression profile_ALS02850

description: unique sample


title: whole blood gene expression profile_ALS02126

description: unique sample


title: whole blood gene expression profile_ALS02551

description: unique sample


title: whole blood gene expression profile_ALS02662

description: unique sample


title: whole blood gene expression profile_ALS02606

description: unique sample


title: whole blood gene expression profile_ALS02651

description: unique sample


title: whole blood gene expression profile_ALS02273

description: unique sample


title: whole blood gene expression profile_ALS01908

description: unique sample


title: whole blood gene expression profile_ALS02261

description: unique sample


title: whole blood gene expression profile_ALS03071

description: unique sample


title: whole blood gene expression profile_ALS02303

description: unique sample


title: whole blood gene expression profile_ALS02136

description: unique sample


title: whole blood gene expression profile_ALS02793

description: unique sample


title: whole blood gene expression profile_ALS02615

description: unique sample


title: whole blood gene expression profile_ALS01951

description: unique sample


title: whole blood gene expression profile_ALS02613

description: unique sample


title: whole blood gene expression profile_ALS03699

description: unique sample


title: whole blood gene expression profile_ALS02241

description: unique sample


title: whole blood gene expression profile_ALS02270

description: unique sample


title: whole blood gene expression profile_ALS02631

description: unique sample


title: whole blood gene expression profile_ALS02024

description: unique sample


title: whole blood gene expression profile_ALS03082

description: unique sample


title: whole blood gene expression profile_ALS02789

description: unique sample


title: whole blood gene expression profile_ALS02227

description: unique sample


title: whole blood gene expression profile_ALS02146

description: unique sample


title: whole blood gene expression profile_ALS02908

description: unique sample


title: whole blood gene expression profile_ALS02456

description: unique sample


title: whole blood gene expression profile_ALS02971

description: unique sample


title: whole blood gene expression profile_ALS02834

description: unique sample


title: whole blood gene expression profile_ALS02786

description: unique sample


title: whole blood gene expression profile_ALS02322

description: unique sample


title: whole blood gene expression profile_ALS02677

description: unique sample


title: whole blood gene expression profile_ALS02842

description: unique sample


title: whole blood gene expression profile_ALS01537

description: unique sample


title: whole blood gene expression profile_ALS02500

description: unique sample


title: whole blood gene expression profile_ALS02302

description: unique sample


title: whole blood gene expression profile_ALS02594

description: unique sample


title: whole blood gene expression profile_ALS02675

description: unique sample


title: whole blood gene expression profile_ALS03093

description: unique sample


title: whole blood gene expression profile_ALS01524

description: unique sample


title: whole blood gene expression profile_ALS02454

description: unique sample


title: whole blood gene expression profile_ALS02647

description: unique sample


title: whole blood gene expression profile_ALS03205

description: unique sample


title: whole blood gene expression profile_ALS02405

description: unique sample


title: whole blood gene expression profile_ALS02612

description: unique sample


title: whole blood gene expression profile_ALS02809

description: unique sample


title: whole blood gene expression profile_ALS04153

description: unique sample


title: whole blood gene expression profile_ALS02828

description: unique sample


title: whole blood gene expression profile_ALS02794

description: unique sample


title: whole blood gene expression profile_ALS03110

description: unique sample


title: whole blood gene expression profile_ALS04150

description: unique sample


title: whole blood gene expression profile_ALS03851

description: unique sample


title: whole blood gene expression profile_ALS02290

description: unique sample


title: whole blood gene expression profile_ALS02777

description: unique sample


title: whole blood gene expression profile_ALS02464

description: unique sample


title: whole blood gene expression profile_ALS01695

description: unique sample


title: whole blood gene expression profile_ALS02925

description: unique sample


title: whole blood gene expression profile_ALS02726

description: unique sample


title: whole blood gene expression profile_ALS02459

description: unique sample


title: whole blood gene expression profile_ALS01344

description: unique sample


title: whole blood gene expression profile_ALS02836

description: unique sample


title: whole blood gene expression profile_ALS02896

description: unique sample


title: whole blood gene expression profile_ALS01377

description: unique sample


title: whole blood gene expression profile_ALS03854

description: unique sample


title: whole blood gene expression profile_ALS03716

description: unique sample


title: whole blood gene expression profile_ALS02517

description: unique sample


title: whole blood gene expression profile_ALS02907

description: unique sample


title: whole blood gene expression profile_ALS03012

description: unique sample


title: whole blood gene expression profile_ALS02785

description: unique sample


title: whole blood gene expression profile_ALS02463

description: unique sample


title: whole blood gene expression profile_ALS03000

description: unique sample


title: whole blood gene expression profile_ALS02661

description: unique sample


title: whole blood gene expression profile_ALS02548

description: unique sample


title: whole blood gene expression profile_ALS02692

description: unique sample


title: whole blood gene expression profile_ALS03825

description: unique sample


title: whole blood gene expression profile_ALS02811

description: unique sample


title: whole blood gene expression profile_ALS02553

description: unique sample


title: whole blood gene expression profile_ALS01888

description: unique sample


title: whole blood gene expression profile_ALS03717

description: unique sample


title: whole blood gene expression profile_ALS02871

description: unique sample


title: whole blood gene expression profile_ALS02339

description: unique sample


title: whole blood gene expression profile_ALS00539

description: unique sample


title: whole blood gene expression profile_ALS01653

description: unique sample


title: whole blood gene expression profile_ALS01317

description: unique sample


title: whole blood gene expression profile_ALS02984

description: unique sample


title: whole blood gene expression profile_ALS01626

description: unique sample


title: whole blood gene expression profile_ALS01373

description: unique sample


title: whole blood gene expression profile_ALS02838

description: unique sample


title: whole blood gene expression profile_ALS02999

description: unique sample


title: whole blood gene expression profile_ALS02590

description: unique sample


title: whole blood gene expression profile_ALS01630

description: unique sample


title: whole blood gene expression profile_ALS02703

description: unique sample


title: whole blood gene expression profile_ALS03721

description: unique sample


title: whole blood gene expression profile_ALS02959

description: unique sample


title: whole blood gene expression profile_ALS02507

description: unique sample


title: whole blood gene expression profile_ALS03206

description: unique sample


title: whole blood gene expression profile_ALS02894

description: unique sample


title: whole blood gene expression profile_ALS02687

description: unique sample


title: whole blood gene expression profile_ALS02727

description: unique sample


title: whole blood gene expression profile_ALS02851

description: unique sample


title: whole blood gene expression profile_ALS03809

description: unique sample


title: whole blood gene expression profile_ALS02528

description: unique sample


title: whole blood gene expression profile_ALS01563

description: unique sample


title: whole blood gene expression profile_ALS02952

description: unique sample


title: whole blood gene expression profile_ALS03020

description: unique sample


title: whole blood gene expression profile_ALS01374

description: unique sample


title: whole blood gene expression profile_ALS02787

description: unique sample


title: whole blood gene expression profile_ALS02802

description: unique sample


title: whole blood gene expression profile_ALS02790

description: unique sample


title: whole blood gene expression profile_ALS03235

description: unique sample


title: whole blood gene expression profile_ALS03030

description: unique sample


title: whole blood gene expression profile_ALS03023

description: unique sample


title: whole blood gene expression profile_ALS01331

description: unique sample


title: whole blood gene expression profile_ALS02574

description: unique sample


title: whole blood gene expression profile_ALS01332

description: unique sample


title: whole blood gene expression profile_ALS03252

description: unique sample


title: whole blood gene expression profile_ALS03106

description: unique sample


title: whole blood gene expression profile_ALS02815

description: unique sample


title: whole blood gene expression profile_ALS02932

description: unique sample


title: whole blood gene expression profile_ALS02537

description: unique sample


title: whole blood gene expression profile_ALS01640

description: unique sample


title: whole blood gene expression profile_ALS02861

description: unique sample


title: whole blood gene expression profile_ALS02407

description: unique sample


title: whole blood gene expression profile_ALS02919

description: unique sample


title: whole blood gene expression profile_ALS01618

description: unique sample


title: whole blood gene expression profile_ALS03167

description: unique sample


title: whole blood gene expression profile_ALS02021

description: unique sample


title: whole blood gene expression profile_ALS02525

description: unique sample


title: whole blood gene expression profile_ALS02810

description: unique sample


title: whole blood gene expression profile_ALS01333

description: unique sample


title: whole blood gene expression profile_ALS01356

description: unique sample


title: whole blood gene expression profile_ALS02627

description: unique sample


title: whole blood gene expression profile_ALS02619

description: unique sample


title: whole blood gene expression profile_ALS02649

description: unique sample


title: whole blood gene expression profile_ALS03029

description: unique sample


title: whole blood gene expression profile_ALS02791

description: unique sample


title: whole blood gene expression profile_ALS02488

description: unique sample


title: whole blood gene expression profile_ALS03014

description: unique sample


title: whole blood gene expression profile_ALS02305

description: unique sample


title: whole blood gene expression profile_ALS03821

description: unique sample


title: whole blood gene expression profile_ALS02911

description: unique sample


title: whole blood gene expression profile_ALS01128

description: unique sample


title: whole blood gene expression profile_ALS01378

description: unique sample


title: whole blood gene expression profile_ALS03831

description: unique sample


title: whole blood gene expression profile_ALS01645

description: unique sample


title: whole blood gene expression profile_ALS02808

description: unique sample


title: whole blood gene expression profile_ALS02277

description: unique sample


title: whole blood gene expression profile_ALS02513

description: unique sample


title: whole blood gene expression profile_ALS03033

description: unique sample


title: whole blood gene expression profile_ALS03240

description: unique sample


title: whole blood gene expression profile_ALS01370

description: unique sample


title: whole blood gene expression profile_ALS01679

description: unique sample


title: whole blood gene expression profile_ALS02897

description: unique sample


title: whole blood gene expression profile_ALS02577

description: unique sample


title: whole blood gene expression profile_ALS01558

description: unique sample


title: IgG ChIP control replicate 2

type: SRA

city: Richmond

first: Joseph

middle: L

last: McClay

state: VA

address: 410 N 12th Street

department: Pharmacotherapy

country: USA

institute: Virginia Commonwealth University

library_source: genomic

data_processing:
alignment to hg19 using BioScope 1.2
Multi-mapping reads dropped and only single alignments retained
Files written to .bam
combine reads for K-12 (sc-48947) ChIP into single bam file
combine reads for N-16 (sc-48949) ChIP into single bam file
combine reads for IgG control ChIP replicate 1 into single bam file
combine reads for IgG control ChIP replicate 2 into single bam file
combine reads for IgG control ChIP replicate 3 into single bam file
PCR duplicates removed ('rmdup', Samtools)
Written to tagAlign.gz
Peaks called using SPP distributed with phantompeakqualtools using default settings and FDR<0.01
Each ChIP used the composite IgG control experiment as background to call peaks
Genome_build: hg19
Supplementary_files_format_and_content: tagAlign.gz files contain read positions, columns are: chrom, chromStart, chromEnd, sequence, score, strand (see https://genome.ucsc.edu/FAQ/FAQformat.html#format15)
regionPeak files contain ChIP-seq peak calls, columns are: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak (see https://genome.ucsc.edu/FAQ/FAQformat.html#format12)

molecule: genomic DNA

source_name: SH-SY5Y cells

growth_protocol: SH-SY5Y cells were grown in Dulbecco’s Modified Eagle’s Medium/Ham’s Nutrient Mixture F12 (Sigma) supplemented with 10% fetal bovine serum at 37oC in 5% CO2.

extract_protocol:
ChIP assay was performed using SOLiD ChIP-Seq Kit (Applied Biosystems) according to manufacturer’s guide. 1.2X10^7 SH-SY5Y cells were  suspended 500ul of PBS and subjected to chromatin cross-linking by 1% of formaldehyde for 10 minutes. The reaction was stopped by incubation with 57 ul of 1.25M glycine for 5 minutes and washing cells three times by PBS. Cells were lysed in 1ml of Lysis Buffer containing protease inhibitor and chromatin shearing was performed by sonication with Covaris S2 (5% duty cycle, for ten cycles, each 1 minutes, at 4oC intensity 2). Cell debris was removed by centrifugation at 20000g for 5 minutes. For immunoprecipitation, 50 ul supernatants were mixed 50 ul Dilution Buffer and incubated overnight at 4oC with 10 ul Dynabeads conjugated with anti-TCF4 antibodies K-12, N-16, 1G4 or control IgG. After washing with IP Buffers, beads were incubated with Proteinase K(370 ul/ml) at 55oC for one hour to reverse crosslinking and to elute DNA.
ChIP-Seq library was prepared by end repairing ChIP DNA, ligating with P1 adaptor and barcode by T4 ligase and nick translating and amplification, each step followed by DNA purification by Agencourt AMPure XP beads.
ChIP-seq, multiplex loading, single end sequencing, target 25 million raw tags per ChIP sample

tag: cell type

value: SH-SY5Y ATCC (validated)

tag: chip antibody

value: anti-goat IgG control antibody (Santa Cruz)


title: IgG ChIP control replicate 1


title: whole blood gene expression profile_ALS01649

description: unique sample


title: TCF4 ChIP-seq Ab K12

value: anti-TCF4 antibody K-12, sc-48947 (Santa Cruz, lot# A2507)


title: whole blood gene expression profile_ALS03164

description: unique sample


title: IgG ChIP control replicate 3


title: TCF4 ChIP-seq Ab N16

value: anti-TCF4 antibody N-16, sc-48949 (Santa Cruz, lot# A2507)


title: whole blood gene expression profile_ALS00720

description: unique sample


title: whole blood gene expression profile_ALS03085

description: unique sample


title: whole blood gene expression profile_ALS01606

description: unique sample


title: whole blood gene expression profile_ALS02805

description: unique sample


title: whole blood gene expression profile_ALS03207

description: unique sample


title: whole blood gene expression profile_ALS03403

description: unique sample


title: whole blood gene expression profile_ALS03201

description: unique sample


title: whole blood gene expression profile_ALS02652

description: unique sample


title: whole blood gene expression profile_ALS01948

description: unique sample


title: whole blood gene expression profile_ALS02536

description: unique sample


title: whole blood gene expression profile_ALS01308

description: unique sample


title: whole blood gene expression profile_ALS02559

description: unique sample


title: whole blood gene expression profile_ALS02611

description: unique sample


title: whole blood gene expression profile_ALS03202

description: unique sample


title: whole blood gene expression profile_ALS02756

description: unique sample


title: whole blood gene expression profile_ALS01500

description: unique sample


title: whole blood gene expression profile_ALS02508

description: unique sample


title: whole blood gene expression profile_ALS02149

description: unique sample


title: whole blood gene expression profile_ALS01950

description: unique sample


title: whole blood gene expression profile_ALS01361

description: unique sample


title: whole blood gene expression profile_ALS02259

description: unique sample


title: whole blood gene expression profile_ALS02123

description: unique sample


title: whole blood gene expression profile_ALS02576

description: unique sample


title: whole blood gene expression profile_ALS02020

description: unique sample


title: whole blood gene expression profile_ALS02970

description: unique sample


title: whole blood gene expression profile_ALS01910

description: unique sample


title: whole blood gene expression profile_ALS02203

description: unique sample


title: whole blood gene expression profile_ALS02575

description: unique sample


title: whole blood gene expression profile_ALS02238

description: unique sample


title: whole blood gene expression profile_ALS03823

description: unique sample


title: whole blood gene expression profile_ALS02578

description: unique sample


title: HPC 3

city: Cambridge

first: Michael

last: Guo

state: MA

address: 415 Main St

institute: Broad Institute

description: miRNA

hyb_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.

data_processing: RCC files were processed through the nSOLVER software to normalize for negative and positive controls and filter for probes with counts >10. These values were then normalized by the average geometric means across all lanes. Filtering was done as suggested by nSOLVER recommendations.

label: NanoString labels

source_name: HPC

growth_protocol: Refer to the STAR methods of the related manuscript.

extract_protocol: RNA was extracted using miRNeasy (Qiagen)

treatment_protocol: HSC, PROG and HPC cells isolated according to specific panels of cell surface markers. Full details on the STAR methods of the related manuscript.

value: IPSC-derived Hematopoietic Progenitor Cells


title: HPC 2

description: miRNA

scan_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.


title: whole blood gene expression profile_ALS02124

description: unique sample


title: HPC 1

description: miRNA

label_protocol: Nanostring miRNA profiling was performed according to manufacturer's specifications.


title: FL PROG 3

description: miRNA

source_name: FL PROG

value: Fetal Liver Hematopoietic Progenitor Cells


title: 12412 98047129-08

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Dr

department: Epidemiology

institute: UNC

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). The data displayed in the Sample data table has been downloaded from the UNC Microarray database (UMD) where a Lowess normalization procedure was performed to adjust the Cy3 and Cy5  channels. The Lowess normalized log2 ratio fo Cy5 to Cy3 intensity values were filtered to select genes that had a signal intensity of at least 10 dpi.  There are blanks because there was no signal for that gene in the Sample.

source_name: Mastectomy

label_protocol: Labelled by following Agilent's Low Input Quick Amp Standard Protocol.

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

tag: weight category

value: Normal

tag: age

tag: race

value: Black

tag: surgery type

value: Mastectomy

tag: tissue

value: normal breast tissue

source_name: Universal Human Reference

tag: content

value: total RNA from 10 human cell lines

tag: vendor

value: Stratagene


title: FL PROG 2

description: miRNA


title: 12458 95136107-04

value: Overweight

value: White


title: 12415 93403558-02


title: 12424 97412332-04

value: Obese


title: 12437 96644687-02

source_name: Reduction

value: Reduction


title: 12428 90139379-02


title: FL PROG 1

description: miRNA


title: 10118 96454897-02


title: 12440 90918558-04


title: 10049 98717911-02


title: 10081 99274342-02


title: 12402 97315493-01


title: 10151 95801551-02


title: 12378 90191529-02


title: 12401 94733060-01


title: 12377 91154260-01


title: 10129 92367044-02


title: 10133 98085434-02


title: 12376 91131474-01


title: FL HSC 3

description: miRNA

source_name: CB PROG

value: Cord Blood Hematopoietic Progenitor Cells


title: monos_H167R-b_2

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr

department: Dept. of Lab Medicine

institute: NIH Clinical Center

description: LPS-stimulated

library_source: transcriptomic

data_processing:
We performed gene-level differential expression analysis of targeted RNASeq data using the Bioconductor DESeq2 package [Love MI, Huber W and Anders S (2014)]. Briefly, for each cell type (naïve CD4+ and monocytes) we merged raw count files, filtered out systematically lowly expressed transcripts, defined groups (control, patient), genotypes (IKZF1 wildtype, IKZF1 mutant), and phenotypes (healthy, haploinsufficient dominant negative). The 'genotype’ and ‘phenotype’ factors were combined to assess the interaction of these two factors. We then constructed a DESeq2 object, estimated size factors, log2-normalized counts, collapsed the technical replicates, contrasted groups, annotated results, transformed the data (variance stabilization), and performed Pearson correlation analyses.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts per sample

source_name: blood

extract_protocol: Each sample was run in duplicate and a cDNA library was first generated from a minimum of 10 ng of total RNA. The cDNA was barcoded and amplified using Ion AmpliSeq technology (Life Technologies)

tag: genotype

value: mutant - heterozygous

tag: phenotype

value: haploinsufficient

value: Monocytes


title: CCR6+ ILC3s, Tnfsf11fl/fl, Rep 3

city: Saint Louis

first: Jennifer

middle: Kaoru

last: Bando

address: 660 South Euclid Ave

institute: WUSM

description:
27213
Gene expression from Tnfsf11fl/fl intestinal CCR6+ ILC3s

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression. Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-1_0-st-v1
program-name = Expression Console
program-version = 1.4.1.46

organism: Mus musculus

source_name: CCR6+ ILC3s from Tnfsf11fl/fl mouse

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

growth_protocol: Cells were not cultured prior to extraction

extract_protocol: RNA was extracted with the RNeasy microkit from Qiagen following manufacturer's instructions.

treatment_protocol: Cells were isolated by digestion with Collagenase IV and cell sorting with an AriaII

tag: strain background

tag: genotype/variation

value: small intestine lamina propria

value: CCR6+ ILC3


title: monos_H167R-b_1

description: LPS-stimulated


title: monos_G1_2

description: LPS-stimulated

value: dominant negative


title: CCR6+ ILC3s, RorccreTnfsf11fl/fl, Rep 3

description:
27212
Gene expression from RorccreTnfsf11fl/fl intestinal CCR6+ ILC3s

source_name: CCR6+ ILC3s from RorccreTnfsf11fl/fl mouse


title: CCR6+ ILC3s, Tnfsf11fl/fl, Rep 1

description:
27208
Gene expression fromTnfsf11fl/fl intestinal CCR6+ ILC3s


title: CCR6+ ILC3s, RorccreTnfsf11fl/fl, Rep 2

description:
27210
Gene expression from RorccreTnfsf11fl/fl intestinal CCR6+ ILC3s


title: 11349 97838650-08

value: Normal


title: 11369 90338823-08

value: Asian


title: monos_G1_1

description: LPS-stimulated


title: CCR6+ ILC3s, Tnfsf11fl/fl, Rep 2

description:
27211
Gene expression from Tnfsf11fl/fl intestinal CCR6+ ILC3s


title: CCR6+ ILC3s, RorccreTnfsf11fl/fl, Rep 1

description:
27209
Gene expression from RorccreTnfsf11fl/fl intestinal CCR6+ ILC3s


title: monos_H167R-a_2

description: LPS-stimulated


title: 11345 90466491-08

value: Mastectomy


title: FL HSC 2

description: miRNA


title: whole blood gene expression profile_ALS05161

description: unique sample

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Before RNA hybridization, samples were randomized to avoid batch effects correlated to the diagnosis. Samples were hybridized to Illumina’s HumanHT-12 version 4 BeadChips according to manufacturer’s protocol (Illumina, Inc., San Diego, CA, U.S.A.).
Final Reports from Illumina’s GenomeStudio were imported in R (http://.cran.r-project.org). After quantile normalization, gender was checked by expression of gender-specific Y chromosomal probes (JARID1D and RPS4Y1). Samples with gender mismatches were excluded. Subsequently expression values were log2 transformed and quantile normalized. Arrays were projected along the first and second principal component and outliers were dismissed. This resulted in the exclusion of 34 patients and 33 control subjects from the training set and exclusion of 13 patients and 7 control subjects from the test-validation set.
High quality probes were selected, including true autosomal probes only. Using the BLAT function in UCSC’s Genome Browser, all probes were aligned to the NCBI reference genome build 36. Probes with multiple BLAT hits with a sequence homology of > 95% were defined as aspecific and excluded from further analysis. We looked for retired probes using the RefSeq and UniGene (build #228) databases. Retired probes were excluded from further analysis. Finally, probes with identical probe IDs that overlapped between the Illumina HumanHT12 v3 and v4 platform were selected.
Surrogate variable analysis: To eliminate expression heterogeneity caused by known and unknown technical and biological background, data from both training and test sets were combined and normalized, applying surrogate variable analysis (SVA). This produces surrogate variables for which expression levels can be corrected by calculating residuals in a linear regression model. In previous studies, this correction has been proven to reduce batch-specific background noise, thereby increasing the ability to detect biologically meaningful signals.

value: v

value: CON


title: whole blood gene expression profile_ALS06998

description: unique sample

value: m

value: ALS

value: s


title: 11326 90247669-08

value: Obese

value: White

value: normal breast tissue

value: total RNA from 10 human cell lines

value: Stratagene


title: whole blood gene expression profile_ALS06059

description: unique sample


title: 11357 90321670-08


title: whole blood gene expression profile_ALS06170

description: unique sample


title: whole blood gene expression profile_ALS06166

description: unique sample


title: whole blood gene expression profile_ALS04910

description: unique sample


title: whole blood gene expression profile_ALS06060

description: unique sample


title: monos_H167R-a_1

description: LPS-stimulated

value: mutant - heterozygous

value: haploinsufficient

value: Monocytes


title: whole blood gene expression profile_ALS06168

description: unique sample


title: whole blood gene expression profile_ALS04688

description: unique sample


title: whole blood gene expression profile_ALS05648

description: unique sample


title: monos_C1_2

description: LPS-stimulated

value: dominant negative


title: whole blood gene expression profile_ALS04978

description: unique sample


title: monos_C1_1

description: LPS-stimulated


title: monos_HC5_2

description: LPS-stimulated

value: wildtype

value: healthy


title: 11325 96008594-02

value: Mastectomy


title: 11317 98522964-08


title: 11320 90019498-08


title: monos_HC5_1

description: LPS-stimulated


title: whole blood gene expression profile_ALS05466

description: unique sample

value: v


title: whole blood gene expression profile_ALS05566

description: unique sample

value: CON


title: whole blood gene expression profile_ALS06811

description: unique sample


title: monos_HC4_2

description: LPS-stimulated


title: whole blood gene expression profile_ALS06152

description: unique sample


title: whole blood gene expression profile_ALS04280

description: unique sample

value: m


title: whole blood gene expression profile_ALS06135

description: unique sample


title: 11321 95535928-08

value: Overweight


title: whole blood gene expression profile_ALS06151

description: unique sample


title: 11311 95181889-04

value: Normal


title: 11316 92676253-02

value: Other


title: monos_HC4_1

description: LPS-stimulated


title: 11310 91471011-02

value: Obese

value: White

value: Reduction


title: whole blood gene expression profile_ALS06536

description: unique sample


title: monos_HC3_2

description: LPS-stimulated


title: whole blood gene expression profile_ALS06034

description: unique sample


title: 11301 93807204-02

value: Black

value: normal breast tissue

value: total RNA from 10 human cell lines

value: Stratagene


title: whole blood gene expression profile_ALS06150

description: unique sample


title: whole blood gene expression profile_ALS05861

description: unique sample

value: ALS

value: b


title: whole blood gene expression profile_ALS05743

description: unique sample


title: monos_HC3_1

description: LPS-stimulated

value: wildtype

value: healthy

value: Monocytes


title: whole blood gene expression profile_ALS06229

description: unique sample

value: v

value: CON


title: 11300 99662678-08

value: Asian

value: Mastectomy


title: whole blood gene expression profile_ALS06110

description: unique sample

value: m


title: monos_HC2_2

description: LPS-stimulated


title: monos_HC2_1

description: LPS-stimulated


title: 11299 93144020-04

value: Obese


title: whole blood gene expression profile_ALS06326

description: unique sample


title: whole blood gene expression profile_ALS06535

description: unique sample


title: monos_HC1_2

description: LPS-stimulated


title: monos_HC1_1

description: LPS-stimulated


title: nCD4s_G1_2

value: mutant - heterozygous

value: dominant negative

value: Naïve CD4+ cells


title: 11287 95807681-01

value: Overweight

value: White

value: normal breast tissue


title: 11276 93023968-02

value: Black

value: total RNA from 10 human cell lines

value: Stratagene


title: whole blood gene expression profile_ALS05747

description: unique sample

value: ALS

value: b


title: whole blood gene expression profile_ALS06125

description: unique sample


title: whole blood gene expression profile_ALS06748

description: unique sample

value: v


title: 11272 91511352-01


title: whole blood gene expression profile_ALS07183

description: unique sample

value: s


title: whole blood gene expression profile_ALS05694

description: unique sample


title: nCD4s_G1_1


title: whole blood gene expression profile_ALS06549

description: unique sample

value: CON


title: 11265 99386831-08

value: Normal

value: Mastectomy


title: nCD4s_H167R-a_2

value: haploinsufficient


title: whole blood gene expression profile_ALS06747

description: unique sample


title: 11285 99094021-08


title: whole blood gene expression profile_ALS06041

description: unique sample

value: m


title: nCD4s_H167R-a_1

value: mutant - heterozygous


title: nCD4s_C1_2

value: dominant negative

value: Naïve CD4+ cells


title: whole blood gene expression profile_ALS03354

description: unique sample

source_name: whole blood_MIM

value: MIM


title: nCD4s_C1_1


title: nCD4s_HC5_2

value: wildtype

value: healthy


title: 11240 93278828-02

value: Overweight

value: White

value: Reduction

value: normal breast tissue

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS07181

description: unique sample

value: v

value: ALS

value: b


title: whole blood gene expression profile_ALS06181

description: unique sample


title: 11251 94435138-08

value: Mastectomy

value: Stratagene


title: 11239 94963998-02

value: Black


title: whole blood gene expression profile_ALS06995

description: unique sample

value: m

value: s


title: whole blood gene expression profile_ALS06213

description: unique sample

value: CON


title: 11237 90375635-02

value: Normal


title: nCD4s_HC5_1

value: wildtype

value: Naïve CD4+ cells


title: whole blood gene expression profile_ALS05084

description: unique sample


title: 11252 90684911-01


title: 11256 90088402-02


title: whole blood gene expression profile_ALS05267

description: unique sample


title: 12399 96361233-04

value: Obese


title: whole blood gene expression profile_ALS05935

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS06925

description: unique sample


title: whole blood gene expression profile_ALS06048

description: unique sample


title: whole blood gene expression profile_ALS06463

description: unique sample


title: whole blood gene expression profile_ALS06580

description: unique sample


title: whole blood gene expression profile_ALS06694

description: unique sample


title: whole blood gene expression profile_ALS06924

description: unique sample


title: whole blood gene expression profile_ALS06068

description: unique sample


title: 11229 95524989-08


title: nCD4s_HC4_2

value: healthy


title: whole blood gene expression profile_ALS02473

description: unique sample


title: nCD4s_HC4_1


title: nCD4s_HC3_2


title: nCD4s_HC3_1


title: whole blood gene expression profile_ALS06103

description: unique sample


title: 11220 98256464-08

value: Overweight

value: normal breast tissue


title: nCD4s_HC2_1


title: nCD4s_HC2_2


title: whole blood gene expression profile_ALS06546

description: unique sample


title: 11210 98807324-02

value: White

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS06541

description: unique sample

value: v

value: ALS


title: whole blood gene expression profile_ALS06791

description: unique sample


title: 11206 92614429-02

value: Reduction

value: Stratagene


title: whole blood gene expression profile_ALS06225

description: unique sample

value: m


title: 11207 90415522-08

value: Mastectomy


title: whole blood gene expression profile_ALS06782

description: unique sample

value: CON


title: 11209 97705206-08


title: whole blood gene expression profile_ALS06790

description: unique sample


title: 11218 92357102-08

value: Normal


title: whole blood gene expression profile_ALS04732

description: unique sample

value: b


title: nCD4s_HC1_1

value: wildtype

value: Naïve CD4+ cells


title: whole blood gene expression profile_ALS04519

description: unique sample

value: s


title: whole blood gene expression profile_ALS06186

description: unique sample


title: 11200 92642727-08

value: Obese

value: Black


title: whole blood gene expression profile_ALS06094

description: unique sample


title: 11201 92921469-02

value: normal breast tissue


title: whole blood gene expression profile_ALS05523

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS06198

description: unique sample


title: whole blood gene expression profile_ALS03066

description: unique sample


title: whole blood gene expression profile_ALS04765

description: unique sample


title: nCD4s_HC1_2

value: healthy


title: whole blood gene expression profile_ALS06789

description: unique sample


title: 11198 95714861-08

value: White

value: total RNA from 10 human cell lines


title: 11193 99777039-09

value: Overweight


title: X1_1M

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description: Lexogen Quantseq 8’mRNA-Seq kit

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.2_b with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --sjdbScore 1
counts were generated by featureCounts v1.5.1 with parameters -p -t exon -g gene_id -B -T8 -M -O --fraction
normalized log2-transformed count table was generated by the voom function from the R/Bioconductor limma package
mouse data was processed according to lexogen proprietary software
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited matrices including raw counts and log2-normalized counts for all samples.

source_name: brain

extract_protocol:
Total RNA was extracted from flow cytometry-sorted microglia cells using an RNeasy and AllPrep Micro Kit (Qiagen) and from whole brain tissue using RNeasy Lipid Tissue Mini kit (Qiagen), according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit was used with 60 ng of total RNA for the construction of sequencing libraries of 23 samples. Clontech SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara Bio, Japan) cDNA libraries were prepared for 16 samples starting with 500 pg of total RNA.
Human RNA libraries were prepared for sequencing using standard Illumina and Clontech protocols. Mouse  RNA samples were prepared with a Quantseq 3’mRNA-Seq kit. (Lexogen, USA)

tag: strain

value: brain

value: 10 weeks

tag: gender

value: M


title: X2_1F

description: Lexogen Quantseq 7’mRNA-Seq kit

value: F


title: 10181 94349438-08

value: Mastectomy

value: Stratagene


title: X3_2M

description: Lexogen Quantseq 6’mRNA-Seq kit


title: whole blood gene expression profile_ALS06935

description: unique sample

tag: Sex

value: v

tag: diagnosis

value: CON


title: X4_2F

description: Lexogen Quantseq 5’mRNA-Seq kit


title: whole blood gene expression profile_ALS06965

description: unique sample

value: m

tag: censored


title: 10180 98048572-08

value: Normal


title: whole blood gene expression profile_ALS06081

description: unique sample

value: ALS

value: s


title: 10176 93168235-08

value: Obese

value: normal breast tissue


title: whole blood gene expression profile_ALS04475

description: unique sample

value: MIM


title: 11197 97695712-02

value: Black

value: Reduction

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS05512

description: unique sample


title: whole blood gene expression profile_ALS05941

description: unique sample


title: whole blood gene expression profile_ALS04149

description: unique sample


title: 10175 90633538-01

value: Overweight

value: White


title: whole blood gene expression profile_ALS06981

description: unique sample


title: whole blood gene expression profile_ALS04264

description: unique sample


title: whole blood gene expression profile_ALS05323

description: unique sample


title: whole blood gene expression profile_ALS04989

description: unique sample


title: whole blood gene expression profile_ALS04143

description: unique sample


title: whole blood gene expression profile_ALS05934

description: unique sample

value: b


title: 11191 99541583-08

value: Mastectomy


title: whole blood gene expression profile_ALS06016

description: unique sample


title: whole blood gene expression profile_ALS06011

description: unique sample


title: whole blood gene expression profile_ALS05862

description: unique sample


title: X5_3M

description: Lexogen Quantseq 4’mRNA-Seq kit

value: brain

value: 10 weeks

value: M


title: X6_3F

description: Lexogen Quantseq 3’mRNA-Seq kit

value: F


title: whole blood gene expression profile_ALS06210

description: unique sample

value: m

value: CON


title: microRNA-150, replicate 5

first: Jonathan

last: Lin

state: MO

address: 660 S. Euclid Ave, Campus Box 8096

institute: Washington University School of Medicine

data_processing:
We mapped the sequencing reads to the genome with STAR.
We performed a standard EdgeR and Sailfish analysis of gene-level features on the unique count of aligned, unambiguous reads per feature as determined by Subread:featureCounts using a negative binomial test or generalize-linear negative-binomial model, respectively.
Genome_build: Mus_musculus reference build Ensembl_R76
Supplementary_files_format_and_content: text file with data and statistical analysis

source_name: peritoneal macrophages

extract_protocol:
We extracted total RNA with TRIzol (Invitrogen) followed by column purification with the RNeasy Plus Mini Kit (Qiagen).
We prepared sequencing libraries with standard protocols.

tag: cell type

value: peritoneal macrophages

value: female

tag: treatment

value: microRNA-150 mimic

tag: index

value: TGATTAC


title: microRNA-150, replicate 4

value: GCCGTTT


title: 10170 96136254-08

tag: weight category

value: Obese

tag: age

tag: race

value: normal breast tissue

value: Stratagene


title: 10167 95275913-02

value: Black

tag: surgery type

tag: tissue

tag: content

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS05863

description: unique sample

value: ALS

value: s


title: 10174 97842975-08

value: White

value: Mastectomy

tag: vendor


title: whole blood gene expression profile_ALS06087

description: unique sample

value: v


title: whole blood gene expression profile_ALS06074

description: unique sample


title: microRNA-150, replicate 3

value: GTACGGC


title: microRNA-150, replicate 2

value: TACATGG


title: microRNA-150, replicate 6

value: peritoneal macrophages

value: CCTAATC


title: whole blood gene expression profile_ALS06540

description: unique sample

value: m

value: CON


title: whole blood gene expression profile_ALS06109

description: unique sample


title: whole blood gene expression profile_ALS06203

description: unique sample


title: 10165 94543204-02

value: Overweight

value: Other

value: Reduction


title: 10164 97383111-02

value: Obese

value: normal breast tissue

value: Stratagene


title: 10169 92556307-02

value: Normal

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS06035

description: unique sample


title: whole blood gene expression profile_ALS08509

description: unique sample

value: ALS

value: s


title: whole blood gene expression profile_ALS05605

description: unique sample


title: 10161 96935374-02

value: White


title: whole blood gene expression profile_ALS06328

description: unique sample


title: whole blood gene expression profile_ALS03352

description: unique sample

value: v

value: MIM


title: 10159 91081125-02

value: Mastectomy


title: microRNA-150, replicate 1

value: peritoneal macrophages

value: female

value: microRNA-150 mimic

value: CGGTGGC


title: negative control, replicate 6

value: negative control

value: ATGACAG


title: whole blood gene expression profile_ALS06192

description: unique sample

value: m

value: CON


title: negative control, replicate 4

value: TCCCAGC


title: negative control, replicate 3

value: GCAACGC


title: negative control, replicate 2

value: CTCCCGA


title: 10155 96533807-02

value: Normal

value: normal breast tissue

value: total RNA from 10 human cell lines

value: Stratagene


title: negative control, replicate 1

value: CCGGACC


title: 10158 94865557-02

value: Obese

value: White

value: Mastectomy


title: 10149 95130985-02

value: Overweight


title: whole blood gene expression profile_ALS06706

description: unique sample


title: whole blood gene expression profile_ALS05693

description: unique sample

value: ALS

value: b


title: 10148 97208243-08

value: Black


title: whole blood gene expression profile_ALS06002

description: unique sample

value: m


title: whole blood gene expression profile_ALS01962

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS06960

description: unique sample

value: s


title: whole blood gene expression profile_ALS05409

description: unique sample


title: whole blood gene expression profile_ALS06143

description: unique sample


title: 10143 92877471-08


title: Pali_dKO_ES_H3K27me3

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates. ChIP samples have a 1.67% spike in of Drosophila S2 chromatin that were cultured according to established protocols.

data_processing:
Reads were aligned to the mouse reference genome (mm10) using Bowtie2. Only unique alignments were retained.
BigWig files were generated at a resolution of 10bp using bamCoverage from the deepTools suite. Tracks were normalised using spike-in derived normalisation factors.
Genome_build: mm10

source_name: Embryonic Stem Cell

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS.

extract_protocol:
Embryonic stem cells were washed once with PBS before crosslinking for 10 minutes with PBS containing 1% formaldehyde (Sigma). Crosslinking was quenched with 0.125M Glycine for 5 minutes before two PBS washes. The crosslinked cells were lysed in 6mL of SDS-Lysis buffer (100mM NaCl, 50mM Tris pH8.1, 5mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF). Chromatin was pelleted by centrifugation at 1200RPM for 5 minutes at room temperature. The supernatant was then discarded and the chromatin was resuspended in 3mL of ChIP buffer (2:1 dilution of SDS-Lysis buffer: Triton dilution buffer [100mM Tris pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 0.02% NaN3, 5% Triton X-100, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF]). Chromatin was sheared to approximately 100bp-1000bp fragments by successive 30 second rounds of sonication at 5-8% amplitude. Sonicated chromatin was pre-cleared for 30 minutes using equilibrated protein A beads (Sigma) that had been blocked in TE (10mM Tris pH8.1, 1mM EDTA pH 8.0) containing 0.5mg/mL BSA and 0.2mg/mL Herring Sperm DNA. 10-100µg (DNA) of chromatin was incubated overnight with antibody while rotating at 4°C. For ChIP-RX 250 µg of chromatin (protein) was used per ChIP with a 1.67% spike in of Drosophila S2 chromatin and 5µg of antibody was used per ChIP.  Following clarification of insoluble precipitates the chromatin was incubated for 3 hours with 50µL of blocked protein A beads. After incubation the beads were washed three times in Mixed Micelle Buffer (150mM NaCl, 20mM Tris pH 8.1, 5mM EDTA pH 8.0, 5.2% Sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with Buffer 500 (0.1% Sodium Deoxycholate, 1mM EDTA pH 8.0, 50mM HEPES pH7.5, 1% Triton X-100, 0.02% NaN3), twice with LiC detergent wash (0.5% Sodium Deoxycholate, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris pH 8.0, 0.02% NaN3) and finally one wash with TE. Immunoprecipitated material was eluted from the beads with Elution buffer (0.1M NaHCO3, 1% SDS) while shaking for 1 hour at 65°C. The supernatant of the elution was retained and incubated overnight at 65°C while shaking to reverse the crosslinks. The eluted complexes were then subject to RNase (Thermo Fisher) and Proteinase K (Sigma) treatment prior to DNA clean up through Phenol Chloroform clean up and Ethanol precipitation. ChIP enrichment was analysed by qPCR using the SYBR Green I detection chemistry (Applied Biosystems) on the ABI Prism 7500 Fast Real–Time PCR System.
For library prep, we used the NEBNext Ultra DNA library preparation kit (NEB) for library prep and the Kapa library quantification for Illumina (Roche #KK4835). Sequencing was performed with Illumina HiSeq v4 chemistry on a HiSeq 2500.

value: Embryonic Stem Cell

tag: genotype

tag: antibody

tag: spike-in reference cell line

value: Drosophila melanogaster S2


title: whole blood gene expression profile_ALS06149

description: unique sample


title: whole blood gene expression profile_ALS04349

description: unique sample


title: 10146 96186002-08

value: Normal


title: whole blood gene expression profile_ALS06783

description: unique sample

value: CON


title: whole blood gene expression profile_ALS05270

description: unique sample


title: Pali1_sKO_ES_H3K27me3


title: whole blood gene expression profile_ALS05045

description: unique sample


title: whole blood gene expression profile_ALS06030

description: unique sample


title: whole blood gene expression profile_ALS06572

description: unique sample

value: v


title: Pali_WT_ES_H3K27me3

value: Wild type


title: whole blood gene expression profile_ALS06171

description: unique sample


title: Aebp2_Gt_ES_H3K27me3


title: 10125 99220113-08

value: normal breast tissue

value: total RNA from 10 human cell lines

value: Stratagene


title: whole blood gene expression profile_ALS05877

description: unique sample


title: 10141 99988438-08

value: Obese

value: Mastectomy


title: whole blood gene expression profile_ALS06187

description: unique sample

value: ALS


title: Aebp2_WT_ES_H3K27me3


title: 10116 99556326-01


title: 10115 91497685-02


title: 10109 92171917-01

value: White


title: 10126 96503198-08


title: whole blood gene expression profile_ALS06391

description: unique sample

value: b


title: whole blood gene expression profile_ALS05702

description: unique sample


title: whole blood gene expression profile_ALS06128

description: unique sample

value: m


title: whole blood gene expression profile_ALS04877

description: unique sample


title: whole blood gene expression profile_ALS04764

description: unique sample


title: whole blood gene expression profile_ALS04408

description: unique sample


title: whole blood gene expression profile_ALS04874

description: unique sample


title: whole blood gene expression profile_ALS06788

description: unique sample


title: 10097 97519847-02

value: Reduction


title: whole blood gene expression profile_ALS06781

description: unique sample


title: 10098 94152899-02


title: whole blood gene expression profile_ALS06199

description: unique sample


title: 10104 90158635-02


title: whole blood gene expression profile_ALS05279

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS05371

description: unique sample


title: whole blood gene expression profile_ALS05737

description: unique sample


title: whole blood gene expression profile_ALS04607

description: unique sample


title: whole blood gene expression profile_ALS04565

description: unique sample


title: 10095 94183647-02

value: Black


title: whole blood gene expression profile_ALS05672

description: unique sample


title: whole blood gene expression profile_ALS06996

description: unique sample


title: whole blood gene expression profile_ALS04350

description: unique sample

value: s


title: whole blood gene expression profile_ALS06205

description: unique sample


title: 10093 90915042-01

value: Overweight


title: 10083 91543579-03

value: Normal


title: whole blood gene expression profile_ALS04472

description: unique sample

value: v


title: whole blood gene expression profile_ALS04436

description: unique sample


title: 10096 90900150-02


title: 10082 91224048-02


title: 10074 92042407-01


title: 10080 95475745-06


title: whole blood gene expression profile_ALS06012

description: unique sample


title: whole blood gene expression profile_ALS04154

description: unique sample


title: whole blood gene expression profile_ALS04263

description: unique sample


title: whole blood gene expression profile_ALS05909

description: unique sample


title: whole blood gene expression profile_ALS04147

description: unique sample


title: whole blood gene expression profile_ALS06204

description: unique sample

value: CON


title: whole blood gene expression profile_ALS05852

description: unique sample


title: whole blood gene expression profile_ALS02568

description: unique sample


title: 10086 91551937-02

value: normal breast tissue


title: 10062 96209762-02

value: total RNA from 10 human cell lines


title: whole blood gene expression profile_ALS04524

description: unique sample


title: whole blood gene expression profile_ALS06551

description: unique sample


title: whole blood gene expression profile_ALS04148

description: unique sample


title: whole blood gene expression profile_ALS06175

description: unique sample


title: 10058 91068346-02

value: Stratagene


title: WT12 Rep 3

city: Stanford

first: Jessica

middle: Kay

last: Chang

state: CA

address: 300 Pasteur Drive, Alway Building M311

department: Genetics

institute: Stanford University

data_processing:
Reads were aligned to TAIR10 genome assembly with Tophat with default parameters
Multi-mapped or unmapped reads were filtered using Samtools
Gene counts were calculated with HTSeq
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files provide summaries of total gene counts organized by genomic position (normalized by size factor via DESeq2).

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: WT and homozygous transgenic lines were sterilized and cold treated for two days.  Seeds were germinated in liquid MS culture medium supplemented with 1% sucrose and grown on a rotating platform (90 rpm) for 7 days.

extract_protocol:
Total RNA was extracted with the Rneasy Micro Kit (Qiagen).
Barcoded mRNA libraries were constructed with the Illumina Poly-A Purification TruSeq library kit. Replicates 1 and 2 of each line/condition were multiplexed together on one lane, Replicates 3 and 4 were multiplexed on a second lane.

treatment_protocol: At 7 dpg, seedlings were treated with 100 μM dexamethasone solution to induce the translocation of GR-SCPH1-4A to the nucleus. Four replicates were collected at 0 (un-treated) and 12 hours post treatment for each line.

tag: replicated series

value: Wild Type

value: 7 dpg

tag: treatment time point

value: 12hr post dex treatment


title: WT12 Rep 2


title: 10053 95184032-09

value: Mastectomy


title: WT12 Rep 4


title: 10055 93071371-02

value: White


title: whole blood gene expression profile_ALS05639

description: unique sample

source_name: whole blood_CON

tag: Sex

tag: diagnosis


title: whole blood gene expression profile_ALS05853

description: unique sample

source_name: whole blood_ALS

value: m

value: ALS

tag: censored


title: whole blood gene expression profile_ALS06209

description: unique sample


title: WT12 Rep 1


title: whole blood gene expression profile_ALS08161

description: unique sample

value: b


title: whole blood gene expression profile_ALS06705

description: unique sample


title: 09010 98627409-02

value: Obese

value: Black


title: whole blood gene expression profile_ALS05624

description: unique sample


title: whole blood gene expression profile_ALS07003

description: unique sample


title: whole blood gene expression profile_ALS06193

description: unique sample


title: 10037 95786794-02


title: whole blood gene expression profile_ALS05723

description: unique sample

value: s


title: whole blood gene expression profile_ALS05724

description: unique sample


title: whole blood gene expression profile_ALS08164

description: unique sample


title: whole blood gene expression profile_ALS07050

description: unique sample

value: MIM


title: whole blood gene expression profile_ALS05100

description: unique sample


title: whole blood gene expression profile_ALS04144

description: unique sample


title: whole blood gene expression profile_ALS06153

description: unique sample


title: whole blood gene expression profile_ALS06678

description: unique sample

value: v


title: whole blood gene expression profile_ALS06158

description: unique sample

value: CON


title: whole blood gene expression profile_ALS07046

description: unique sample


title: whole blood gene expression profile_ALS06538

description: unique sample


title: WT0 Rep 4

value: time 0 (no dex treatment)


title: WT0 Rep 2


title: whole blood gene expression profile_ALS06136

description: unique sample


title: WT0 Rep 1


title: WT0 Rep 3


title: ID12 Rep 4


title: ID0 Rep 4


title: ID12 Rep 2


title: ID12 Rep 1


title: ID12 Rep 3


title: ID0 Rep 3


title: whole blood gene expression profile_ALS06987

description: unique sample


title: whole blood gene expression profile_ALS05277

description: unique sample


title: ID0 Rep 2


title: whole blood gene expression profile_ALS04573

description: unique sample


title: whole blood gene expression profile_ALS05328

description: unique sample


title: whole blood gene expression profile_ALS06298

description: unique sample


title: whole blood gene expression profile_ALS06625

description: unique sample


title: whole blood gene expression profile_ALS05377

description: unique sample


title: whole blood gene expression profile_ALS05994

description: unique sample


title: whole blood gene expression profile_ALS06013

description: unique sample


title: whole blood gene expression profile_ALS05086

description: unique sample


title: whole blood gene expression profile_ALS05869

description: unique sample


title: whole blood gene expression profile_ALS04998

description: unique sample


title: ID0 Rep 1


title: whole blood gene expression profile_ALS05085

description: unique sample


title: whole blood gene expression profile_ALS04977

description: unique sample


title: whole blood gene expression profile_ALS06142

description: unique sample


title: whole blood gene expression profile_ALS05087

description: unique sample


title: whole blood gene expression profile_ALS06990

description: unique sample


title: whole blood gene expression profile_ALS06132

description: unique sample


title: S147

description: Illumina TruSeq RNA Sample Prep Kit

source_name: brain biopsy

value: brain

tag: gender

value: F


title: whole blood gene expression profile_ALS06707

description: unique sample


title: whole blood gene expression profile_ALS06573

description: unique sample


title: whole blood gene expression profile_ALS06558

description: unique sample


title: S243

description: Illumina TruSeq RNA Sample Prep Kit

value: M


title: whole blood gene expression profile_ALS05278

description: unique sample


title: S262

description: Illumina TruSeq RNA Sample Prep Kit


title: whole blood gene expression profile_ALS04840

description: unique sample


title: S291

description: Illumina TruSeq RNA Sample Prep Kit


title: whole blood gene expression profile_ALS05696

description: unique sample


title: S755

description: Illumina TruSeq RNA Sample Prep Kit


title: whole blood gene expression profile_ALS06131

description: unique sample