title: Mut-Sulcus-NO-drug-rep1

city: Seattle

first: Kimberly

middle: A

last: Aldinger

state: WA

address: 1900 Nineth Ave

institute: Seattle Children's Research Institute

library_source: transcriptomic

data_processing:
Illumina FASTQ Generation v1.0.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm10 transcriptome using salmon aligner v0.11.3
Counts per million (CPM) were calculated using edgeR v3.22.3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including logCPM values for each sample

source_name: Mut-Sulcus-NO-drug

extract_protocol:
Whole forebrains were dissected, embedded in OCT, frozen at -80°C, cryo-sectioned at 16mm in the coronal plane onto PEN Membrane Glass Slides (Applied Biosystems, USA). Laser capture microdissection was performed using Leica DM LMD-6000 Laser Microdissection system to capture tissue containing the hippocampal CA1 ventricular lining. Total RNA was isolated from LCM-enriched samples pooled across ~6 slides per genotype using the Qiagen RNeasy Micro Kit and RNA quality was assessed using the Agilent Bioanalyzer 6000 Pico Kit [RNA Integrity Number (RIN) = 7.68±0.26 (mean±s.d.)].
SMART-Seq v4

treatment_protocol: All Pregnant dams were given doxycycline from embryonic day (E)13.5to E15.5 to induce activating Pik3ca mutation. Drug (verteporfin) was administred intraperitoneally, once daily from E13.5 to E18.5. Pups were harvested at birth (P0) and genotyped.

tag: strain background

value: FVB/mixed

tag: age

value: Postnatal day 0

tag: genotype/variation

value: Pik3ca mutant

tag: treatment

value: none (control)

value: Hippocampal CA1 ventricular zone cells


title: Mut-Sulcus-NO-drug-rep2

status: Public on May 15 2019

type: SRA

country: USA

molecule: total RNA

organism: Mus musculus

tag: cell type


title: Mut-Sulcus-NO-drug-rep3


title: Mut-Gyrus-NO-drug-rep3

source_name: Mut-Gyrus-NO-drug


title: PAPCTS blood 1

type: genomic

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

hyb_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

data_processing: IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array versions HumanHap550 v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: neuroblastoma

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: usi

value: PAPCTS

tag: tissue

value: blood

tag: gender

value: male

tag: cog risk

value: high

tag: inss stage

tag: mycn status

value: amp

tag: ploidy

value: diploid (=1.0)

tag: ploidy value


title: PAKGMY blood 1

scan_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PAKGMY


title: Mut-Gyrus-NO-drug-rep2


title: PAKIVG blood 1

label_protocol: Standard Illumina HumanHap550 Genotyping BeadChip v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1 BeadChip protocol

value: PAKIVG

value: female

value: non-amp


title: PAKEKY blood 1

value: PAKEKY

value: low

value: hyperdiploid (>1.0)


title: 1_(HTA-2_0)

type: RNA

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Microarray data analysis was performed using ArrayStudio software package version 10.0.1.75 (Omicsoft). For this raw data from Affymetrix microarrays were processed with robust multi-array (RMA) as normalization method.

label: Biotin

source_name: liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Biological samples are first lysed and homogenized in Trizol, separation of phases is done. Sample is then applied to an RNeasy Mini spin column (Qiagen), DNAse treatment is performed.

value: Liver

tag: statin treatment

value: No Statin

tag: statin

value: Male

tag: bmi

tag: height (cm)

tag: waist circonference (cm)

tag: diastolic blood pressure (mmhg)

tag: systolic blood pressure (mmhg)

tag: fasting blood glucose (mmol/l)

tag: fasting insulin (mui/l)

tag: hba1c (%)

tag: cholest total (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: triglycerides (mmol/l)


title: PAIXJX blood 1

tag: usi

value: PAIXJX

tag: tissue

tag: gender

tag: cog risk

value: intermediate

tag: inss stage

tag: mycn status


title: Mi2b_proB_ATAC_rep2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

library_source: genomic

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 assembly of the mouse genome using the genome mappers Bowtie2 for ATAC and STAR for RNASeq.
ATAC peaks call was perfomed with MACS2 call peaks  with --nomodel--shift 37 --extsize 73
findPeaks (HOMER) algorithm was used for ChIP peak calling with -factor for CTCF and- histone for Mi-2b ChIP-seq data sets
mergePeaks (HOMER) was used to find overlaping ATAC peaks in Mi-2bKOvsWT proB and LtrpreB cell ATAC datasets
Normalization and differential expression of RNAseq data sets was performed by HOMER implementation of DeSeq2 with analyzeRepeats.pl,  getDiffExpression.pl and addGeneAnnotation.pl
Genome_build: mm10
Supplementary_files_format_and_content: xls, txt

source_name: Adult bone marrow

extract_protocol:
Erythroid, myeloid, T cells, NK cells and mature B lineage (Lin) cells were depleted from BM cell suspensions, and Lin–cKitloCD19+CD43+were sorted as pro-B cells by FACS.
Nextera DNA sample prep kit (Illumina)

tag: strain

value: bone marrow

tag: cell type

value: Pro-B

tag: genotype


title: PAKMBX blood 1

value: PAKMBX

value: blood

tag: ploidy


title: Mut-Sulcus-Drug-rep2

source_name: Mut-Sulcus-Drug

tag: strain background

value: FVB/mixed

tag: age

value: Postnatal day 0

tag: genotype/variation

value: Pik3ca mutant

tag: treatment

value: Drug (verteporfin)

value: Hippocampal CA1 ventricular zone cells


title: Mut-Gyrus-NO-drug-rep1

value: none (control)


title: Mut-Sulcus-Drug-rep1


title: Mut-Gyrus-Drug-rep3

source_name: Mut-Gyrus-Drug


title: PANCYF blood 1

value: PANCYF

value: female

value: high

value: amp

value: diploid (=1.0)

tag: ploidy value


title: PAMYXR tumor 1

value: PAMYXR

value: neuroblastoma


title: WT_proB_ATAC_rep1

value: bone marrow

value: WT


title: PAKGEJ blood 1

value: PAKGEJ

value: male

value: non-amp

value: hyperdiploid (>1.0)


title: PAMZYP tumor 1

value: PAMZYP


title: Mut-Gyrus-Drug-rep1

value: FVB/mixed

value: Postnatal day 0

value: Pik3ca mutant

value: Drug (verteporfin)


title: PAPBJE blood 1

value: PAPBJE

value: blood


title: Mut-Gyrus-Drug-rep2

value: Hippocampal CA1 ventricular zone cells


title: Ctrl-NO-drug-rep3

source_name: Ctrl-NO-drug

value: wildtype

value: none (control)


title: PAKGGW blood 1

value: PAKGGW

value: female

value: low


title: Ctrl-NO-drug-rep1


title: PAPCHV blood 1

value: PAPCHV

value: high

value: amp


title: Ctrl-Drug-rep3

source_name: Ctrl-Drug


title: Mut-Sulcus-Drug-rep3


title: PAMWHM blood 1

value: PAMWHM

value: male

value: non-amp

value: hyperdiploid (>1.0)


title: Ctrl-NO-drug-rep2

value: FVB/mixed

value: Postnatal day 0


title: PAMZMG tumor 1

value: PAMZMG

value: neuroblastoma

value: diploid (=1.0)


title: PAPHGF blood 1

value: PAPHGF

value: blood


title: Ctrl-Drug-rep2

value: wildtype

value: Drug (verteporfin)

value: Hippocampal CA1 ventricular zone cells


title: 823ckoPTUt3

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: PBDB RM 4332

department: Internal Medicine

institute: University of Iowa

data_processing:
Illumina basespace used for analysis
Base trimming to 125 bp was performed using Fastq toolkit (V2.2.0)  10 bases were trimmed from the 5' end, and 16 bases were trimmed from the 3' end
Alignment was performed using RNAseq Alignment (v1.1.0) and Bowtie2 to align to Mus musculus/mm10
Transcripts were assembled and differential gene expression was performed using Cufflinks Assembly and DE (Version 2.1.0)
Genome_build: mm10

molecule: polyA RNA

source_name: Heart

extract_protocol:
Hearts were removed and flash frozen in liquid nitrogen, RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using TruSeq RNA Library prep kit  V2

treatment_protocol: WT and Med13 cardiac-specific knockout mice (Med13cKO) were put on a normal chow or PTU diet at 8 weeks of age for a duration of 4 weeks.  A third group was put on a PTU diet for 4 weeks followed by 3 daily injections of T3.

value: heart

value: 12 weeks

value: Med13 cKO

value: PTU + T3


title: PANFVP tumor 1

value: PANFVP

value: female

value: high

value: amp


title: 824ckoPTUt3


title: Ctrl-Drug-rep1

value: FVB/mixed

value: Postnatal day 0


title: PANCBZ tumor 1

value: PANCBZ

value: neuroblastoma

value: non-amp

value: hyperdiploid (>1.0)


title: 820ckoPTUt3


title: PAMZZZ tumor 1

value: PAMZZZ


title: 812ckoPTU

value: PTU


title: 832cKOPTU


title: PANAKY tumor 1

value: PANAKY

value: male

value: diploid (=1.0)


title: PAKHAV blood 1

value: PAKHAV

value: blood

value: low


title: PANRRW blood 1

value: PANRRW


title: 834ckoPTU

value: heart

value: 12 weeks

value: Med13 cKO


title: PAKLAM blood 1

value: PAKLAM

value: female


title: PAKGCI blood 1

value: PAKGCI


title: 828ckoNC

value: NC


title: PANANV tumor 1

value: PANANV

value: neuroblastoma

value: high

value: amp


title: PANVDL blood 1

value: PANVDL


title: 830ckoNC


title: PAIXRK blood 1

value: PAIXRK

value: male

value: diploid (=1.0)


title: PAIRLN blood 1

value: PAIRLN

value: blood

value: hyperdiploid (>1.0)


title: 826ckoNC

value: heart

value: 12 weeks


title: 818wtPTUt3

value: WT

value: PTU + T3


title: PAIXNV blood 1

value: PAIXNV

value: female

value: non-amp


title: PAIXIF blood 1

value: PAIXIF


title: 819wtPTUt3


title: 821wtPTUt3


title: PANKVF blood 1

value: PANKVF

value: high


title: PANLET blood 1

value: PANLET


title: PANRUV blood 1

value: PANRUV


title: 813wtPTU

value: PTU


title: PANWBG blood 1

value: PANWBG

value: amp


title: 827wtNC

value: NC


title: 833wtPTU


title: 811wtPTU


title: PAIVZR blood 1

value: PAIVZR

value: blood

value: diploid (=1.0)


title: PAKXNY blood 1

value: PAKXNY

value: low

value: hyperdiploid (>1.0)


title: PALTXM blood 1

value: PALTXM

value: female

value: intermediate


title: 831wtNC

value: heart

value: 12 weeks

value: WT


title: 825wtNC


title: PALURF blood 1

value: PALURF

value: male

value: high

value: non-amp


title: PAKRZV blood 1

value: PAKRZV


title: PANYHH blood 1

value: PANYHH


title: PAMPWJ blood 1

value: PAMPWJ

value: blood


title: PANKFE blood 1

value: PANKFE

value: diploid (=1.0)


title: BMDM_TcESLPS_003

city: Tlalnepantla de Baz

first: Luis

middle: Ignacio

last: Terrazas Valdes

state: Estado de Mexico

address: Av. de los Barrios 1, colonia Los Reyes Iztacala

country: Mexico

institute: UNAM

data_processing: Analysis of the NanoString data was done in R 3.2.5. Raw NanoString data was imported to R using NanoStringQCPro and normalized using NanoStringNorm. For technical variation was adjusted using the sum of positive controls, we then substracted the backgroung using the mean of negative controls and finally, we normalized RNA content using the geometric mean of the housekeeping genes.

label: nanostring fluorescence barcode

growth_protocol: Bone marrow derived macrophages (BMDMs) were grown from bone marrow precursors incubated with M-CSF for 7 days.

extract_protocol: After a period of 4 or 24 h incubation with previously mention treatments, 500ul of Qiazol reagent (Qiagen) were added into the wells and upon 5 minutes at RT supernatants were transferred into new tubes with fresh cold chloroform (300 ul) gently mixed and left additional 10 min at RT. After samples were centrifugated (12,000 rpm 15 min), supernatants were mixed with 500 ul of ice cold isopropil alcohol and a final round of centrifugation conducted (12,000 rpm 5 min) pellets were left to dry, quantified by using nanodrop and normalized to 10 ng each sample. Quality was ensure with BioAnalyzer

treatment_protocol: BMDMs were exposed to LPS (1mg/ml), TcES (25ng/ml) or TcES plus LPS for 4 or 24 h. After these time points, total RNA was extracted using Qiazol and following the manufacters protocol.

tag: Sex

value: adult

value: bone marrow derived macrophages (BMDM)

value: T. crassiceps excreted/secreted products (25ug/ml) + LPS


title: BMDM_TcES_005

value: female

value: T. crassiceps excreted/secreted products (25ug/ml)


title: BMDM_TcESLPS_006


title: BMDM_LPS_004

value: LPS (1 ug/ml) for 24hrs


title: BMDM_TcES_002


title: PAMXGF blood 1

value: PAMXGF

value: amp

value: hyperdiploid (>1.0)


title: PAMBAC blood 1

value: PAMBAC

value: male

value: high


title: BMDM_PBS_000

value: PBS for 4hrs


title: PALAJR blood 1

value: PALAJR

value: intermediate

value: non-amp


title: PALZHF blood 1

value: PALZHF

value: blood

value: low


title: pwr-r3

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: duplicate biological replicate 2

data_processing:
Fastq data were aligned via Tophat2 to the TAIR10 genome allowing only alignment to the Tair10 transcriptome (TAIR10.gff) . Transcripts were assembled using cufflinks and allowing only transcripts with known structure to the TAIR10.gff file. Differentially expressed genes were called using Cuffdiff using standard parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values were separated from each cuffdiff gene_exp.diff file in each experiment and combined into the processed .csv file

organism: Arabidopsis thaliana

source_name: 7-day-old whole seedling

growth_protocol: Arabidopsis plants were grown on 1/2 MS, 0.8% agar media at 23 degrees C under long day light conditions (16 hrs light: 8 hrs dark) for 7 days

extract_protocol:
RNA was extracted from as in Du et al, Cell, 2012,  151(1): 167–180.
RNA libraries were constructed using the illumina TruSeq Stranded mRNA LT kit (ref no15032612) following manufacterers instructions

treatment_protocol: Harvested at ZT +12

value: pwr SALK_071811C

value: 7-day-old whole seedling


title: hos15-r3

description: duplicate biological replicate 2


title: PALYVF blood 1

value: PALYVF

value: diploid (=1.0)


title: hos15-r2

description: duplicate biological replicate 1


title: PALWEV blood 1

value: PALWEV

value: female


title: PANRRN blood 1

value: PANRRN

value: hyperdiploid (>1.0)


title: hda9-r3

description: duplicate biological replicate 2


title: hda9-r2

description: duplicate biological replicate 1


title: hda9-hos15-r3

description: duplicate biological replicate 2


title: PANXFX blood 1

value: PANXFX


title: PAITFA blood 1

value: PAITFA


title: hda9-hos15-r2

description: duplicate biological replicate 1


title: PANZHT blood 1

value: PANZHT

value: male

value: high


title: PALLWA blood 1

value: PALLWA

value: amp


title: Col-r3

description: duplicate biological replicate 2

value: Wildtype, ecotype Colombia-0


title: Col-r2

description: duplicate biological replicate 1


title: PAKTEA blood 1

value: PAKTEA

value: blood

value: low

value: non-amp


title: pwr-r2

description: duplicate biological replicate 1

value: pwr SALK_071811C

value: 7-day-old whole seedling


title: PAKVFT blood 1

value: PAKVFT

value: diploid (=1.0)


title: BMDM_LPS_001

value: female

value: adult

value: bone marrow derived macrophages (BMDM)

value: LPS (1 ug/ml) for 4hrs


title: PAKUXT blood 1

value: PAKUXT

value: male


title: PAKZRE blood 1

value: PAKZRE

value: high


title: PALWVJ blood 1

value: PALWVJ

value: hyperdiploid (>1.0)


title: PAKJZE blood 1

value: PAKJZE

value: blood


title: PALFPI blood 1

value: PALFPI

value: non-amp


title: PALFSZ blood 1

value: PALFSZ

value: low


title: PALPNM blood 1

value: PALPNM

value: intermediate


title: PALKNC blood 1

value: PALKNC

value: female

value: diploid (=1.0)


title: PAKJBX blood 1

value: PAKJBX


title: PALHCB blood 1

value: PALHCB


title: PAKWUV blood 1

value: PAKWUV


title: PAIXPL blood 1

value: PAIXPL

value: male


title: PAIWWN blood 1

value: PAIWWN

value: hyperdiploid (>1.0)


title: PALFTD blood 1

value: PALFTD

value: blood


title: Ref.cRNA.for.MS3.6

city: Amsterdam

first: Inge

last: Huitinga

address: Meibergdreef 47

department: Neuroimmunology

country: Netherlands

institute: Netherlands Institute for Neuroscience

hyb_protocol: Samples were hybridized to an Agilent Human Gene Expression 4x44K v2 Microarray (Part Number G4845A) for 17 h at 65°C in a rotating hybridization chamber. Arrays were washed in 6 x saline sodium phosphate–EDTA (SSPE)/0.005% N-lauroylsarcosine (Sigma-Aldrich, St. Louis, MO, USA) for 5 min, then in 0.06 x SSPE/0.005% N-lauroylsarcosine for 1 min, and finally in acetonitrile (Sigma-Aldrich) for 30 sec, followed by drying in a nitrogen flow

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner at 5 mm resolution and 100% photomultiplier tube setting

data_processing: Microarray scans were quantified using Agilent Feature Extraction software (version 9.5.3.1) and normalized using loess (LIMMA), which was followed by a between-array normalization using the Gquantile algorithm in LIMMA

source_name: Pooled MS and control brain material and tonsil

label_protocol: The Low Input Quick Amp Labeling Kit (Agilent Technologies) was used for sample amplification and fluorescent labeling according to manufacturer’s instructions. 100 ng experimental RNA input and 50 ng reference pool RNA input was used for linear amplification and fluorescent labeling. Experimental samples were labeled with Cy5-CTP, and the reference pool was labeled with Cy3-CTP (Perkin Elmer, Waltham, MA, USA)

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

treatment_protocol: Series of 10 cryostat sections (20 μm each) of subcortical normal-appearing white matter were obtained

tag: sample type

value: reference sample


title: Ref.cRNA.for.MS4.3


title: Ref.cRNA.for.MS4.2


title: Ref.cRNA.for.MS4.1


title: Ref.cRNA.for.MS3.4


title: Ref.cRNA.for.MS3.7


title: Ref.cRNA.for.MS2.1


title: Ref.cRNA.for.MS3.2


title: PALADE blood 1

tag: usi

value: PALADE

value: non-amp


title: Ref.cRNA.for.MS3.3


title: Ref.cRNA.for.MS3.5


title: Ref.cRNA.for.MS2.2


title: PAMFHC blood 1

value: PAMFHC

tag: tissue


title: Ref.cRNA.for.MS3.1


title: PAKZRF blood 1

value: PAKZRF

tag: gender

value: high


title: Ref.cRNA.for.MS1.4


title: Ref.cRNA.for.MS1.6


title: Ref.cRNA.for.MS1.5


title: PAMYGL tumor 1

value: PAMYGL

value: neuroblastoma

value: female

tag: cog risk

value: amp


title: PAKNXW blood 1

value: PAKNXW

tag: inss stage

value: diploid (=1.0)


title: Ref.cRNA.for.CTR.9


title: Ref.cRNA.for.MS1.3


title: Ref.cRNA.for.MS1.1


title: PANRLC blood 1

value: PANRLC

value: male

value: intermediate

tag: mycn status


title: Ref.cRNA.for.MS1.2


title: PANJVU blood 1

value: PANJVU


title: PALKST blood 1

value: PALKST

value: blood


title: PAMLMY blood 1

value: PAMLMY

value: hyperdiploid (>1.0)


title: Ref.cRNA.for.CTR.8

value: reference sample


title: Ref.cRNA.for.CTR.7


title: PALXTB blood 1

value: PALXTB

value: non-amp


title: PANAET blood 1

value: PANAET


title: PAKGAB blood 1

value: PAKGAB

value: high


title: Ref.cRNA.for.CTR.6


title: PALZZV blood 1

value: PALZZV

value: female

value: amp


title: PAKFNB blood 1

value: PAKFNB

value: low

value: diploid (=1.0)


title: PANATD blood 1

value: PANATD


title: Ref.cRNA.for.CTR.4


title: PALCUZ blood 1

value: PALCUZ


title: PALXTE blood 1

value: PALXTE

value: blood


title: Ref.cRNA.for.CTR.5


title: Ref.cRNA.for.CTR.3


title: PAKINP blood 1

value: PAKINP

value: hyperdiploid (>1.0)


title: PALJFH blood 1

value: PALJFH

value: male

value: intermediate


title: PAKHHB blood 1

value: PAKHHB


title: PAIWEH blood 1

value: PAIWEH

value: high

value: non-amp


title: PAIWLL blood 1

value: PAIWLL

value: hypodiploid


title: Ref.cRNA.for.CTR.1

value: reference sample


title: PAIVRB blood 1

value: PAIVRB

value: low


title: Ref.cRNA.for.CTR.2


title: White_matter_MS4.2

source_name: MS donor subcortical normal appearing white matter

tag: nbb no.

tag: ms/control

value: MS

tag: cortisol level

tag: mild or severe disease

value: mild

value: F


title: White_matter_MS4.1


title: White_matter_MS3.6


title: White_matter_MS4.3


title: White_matter_MS3.7


title: White_matter_MS3.5


title: PAKSSK blood 1

value: PAKSSK

value: blood

value: female

tag: ploidy


title: PALWSJ blood 1

value: PALWSJ

value: hyperdiploid (>1.0)


title: PAMIYK blood 1

value: PAMIYK


title: White_matter_MS3.4

tag: age


title: PALRGM blood 1

value: PALRGM

value: male


title: White_matter_MS3.3

value: high


title: PALPIN blood 1

value: PALPIN

value: non-amp


title: White_matter_MS3.2


title: White_matter_MS3.1


title: PAMSYI blood 1

value: PAMSYI

value: amp

value: diploid (=1.0)


title: PAKYZE blood 1

value: PAKYZE

value: low


title: PAKIMK blood 1

value: PAKIMK


title: PAKTXL blood 1

value: PAKTXL


title: PALAKM blood 1

value: PALAKM

value: blood


title: PAMBPH blood 1

value: PAMBPH

value: female


title: White_matter_MS2.1

value: MS

value: severe

value: F


title: PAIWHU blood 1

value: PAIWHU

value: male

value: hyperdiploid (>1.0)


title: PAKMVG blood 1

value: PAKMVG

value: intermediate

value: non-amp


title: White_matter_MS1.6


title: White_matter_MS1.4


title: White_matter_MS1.5


title: PAKYMV blood 1

value: PAKYMV

value: high

value: diploid (=1.0)


title: White_matter_MS1.3

value: low


title: PALWNI blood 1

value: PALWNI


title: White_matter_CTR.7

source_name: Control donor subcortical white matter

value: CTR


title: White_matter_MS1.1


title: PALFYS blood 1

value: PALFYS

value: blood

value: amp


title: AbdB+Hth_input (transient)

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads were aligned to the dm6 genome assembly (excluding Scaffolds) using bowtie version 1.2.2 with the -m1 option.
Peaks were called using macs2 version 2.1.1.20160309 using single tags and q-value thresholds of q1e-2 and q1e-10.
Genome_build: dm6
Supplementary_files_format_and_content: Bed files contain the union peak regions across both replicates at macs2 thresholds q1e-2 and q1e-10, locations of plasmid sequence matches to the genome were excluded. Bedgraph files are 20 bp bins of reads from both replicates, scaled to reads-per-million of reads overlapping peak regions.

organism: Drosophila melanogaster

source_name: Transiently transfected Kc167 cells

growth_protocol: Drosophila Kc167 cells were cultured in Schneider’s medium supplemented with 5% fetal calf serum and antibiotics at 25°C.

extract_protocol:
Cells were harvested and fixed using 1% formaldehyde in PBS for 10 min at 23°C in an Eppendorf Thermomixer at 700 rpm, then sorted using a MoFlo FACS machine (Beckman Coulter) to standardise levels of Hox-GFP proteins across experiments, and finally sonicated to provide chromatin fragments of approximately 500 bp in length. Fragmented chromatin was immunoprecipitated using an anti-GFP antibody (SIGMA, G1544) and DNA was purified using a standard phenol-chloroform extraction.
Sequencing libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara Bio Inc.) in accordance with the sample preparation guide.

treatment_protocol: Cells harvested in log phase were used to seed 10 cm dishes at a density of 2.5 × 10^7 cells per dish and let to adhere. Transfection was performed using FuGENE 6 Transfection Reagent (Promega E2691) according to the manufacturer’s instructions. Dishes were then incubated at 25°C for ~14 hours. After this period, gene expression was induced for 4 hours using CuSO4 at final concentration of 1mM.

tag: cell line

value: Kc167 cells

tag: plasmid

tag: chip antibody


title: White_matter_CTR.9

tag: Sex

value: F


title: White_matter_MS2.2

value: MS

value: severe


title: White_matter_MS1.2


title: PALIDE blood 1

value: PALIDE

value: male

tag: ploidy value


title: White_matter_CTR.6


title: White_matter_CTR.1


title: White_matter_CTR.4


title: AbdB+Hth_56 (transient)

description:
AbdB_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz

value: Anti-GFP (Sigma, G1544)


title: PALXVY blood 1

tag: usi

value: PALXVY

value: non-amp


title: White_matter_CTR.8


title: White_matter_CTR.5


title: White_matter_CTR.3


title: White_matter_CTR.2


title: PALEAC blood 1

value: PALEAC

tag: tissue

value: hyperdiploid (>1.0)


title: PAKHCF blood 1

value: PAKHCF

tag: gender

value: female

value: high


title: AbdB+Hth_55 (transient)


title: PAIXLC blood 1

value: PAIXLC

tag: cog risk

value: low


title: PALJXU blood 1

value: PALJXU

value: blood

tag: inss stage


title: AbdB_51 (transient)

description:
AbdB.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz

value: Kc167 cells

value: pMT-eGFP-AbdB


title: PALETJ blood 1

value: PALETJ

tag: mycn status


title: PALBFW blood 1

value: PALBFW

value: diploid (=1.0)


title: AbdA_input (transient)

value: pMT-eGFP-AbdA


title: AbdA+Hth_53 (transient)

description:
AbdA_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz

value: Anti-GFP (Sigma, G1544)


title: PAKYAY blood 1

value: PAKYAY

value: amp


title: AbdA_49 (transient)

description:
AbdA.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz


title: AbdA_50 (transient)


title: PAMKGY blood 1

value: PAMKGY

value: male

value: non-amp

value: hyperdiploid (>1.0)


title: Ubx+Hth_input (transient)


title: AbdB_input (transient)


title: PAKUAW blood 1

value: PAKUAW


title: PALJUV blood 1

value: PALJUV

value: female

value: high


title: PALAPJ blood 1

value: PALAPJ

value: blood


title: Ubx_2 (transient)

description:
Ubx.bedgraph.gz
Hox_macs_q1e-2.bed.gz
Hox_macs_q1e-10.bed.gz

value: Kc167 cells


title: Ubx_input (transient)


title: PALBDS blood 1

value: PALBDS


title: AbdB_52 (transient)

value: pMT-eGFP-AbdB


title: PAKFRB blood 1

value: PAKFRB

value: intermediate

value: diploid (=1.0)


title: PALBEB blood 1

value: PALBEB


title: AbdA+Hth_input (transient)


title: AbdA+Hth_54 (transient)

value: Anti-GFP (Sigma, G1544)


title: PALBCY blood 1

value: PALBCY

value: male

value: low


title: Ubx_1 (transient)


title: PAIXAY blood 1

value: PAIXAY

value: non-amp

value: hyperdiploid (>1.0)


title: Ubx+Hth_2 (transient)

description:
Ubx_Hth.bedgraph.gz
Hox_Hth_macs_q1e-2.bed.gz
Hox_Hth_macs_q1e-10.bed.gz


title: PANHVF blood 1

value: PANHVF

value: high


title: PALVRB blood 1

value: PALVRB

value: blood

value: female


title: PAMEZB blood 1

value: PAMEZB


title: Ubx+Hth_1 (transient)

value: Kc167 cells


title: PALZMR blood 1

value: PALZMR


title: PAMXFC blood 1

value: PAMXFC

value: intermediate


title: huc2_p5_sti_50 [T5_95]

city: shanghai

first: Yufang

last: Shi

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Science

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 containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie and single-end clean reads were aligned to the reference genome using TopHat. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. For unigene DGE, Bowtie was used to aligned single-end clean reads to the unigene sequences.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilo base of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazaviet al., 2008). For unigene DGE, we used RSEM to count the reads numbers mapped to each unigene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.10.1). DESeq provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.
A signed network was constructed by using any gene that was expressed at an FPKM value of 0.1 or higher in at least one of the samples. Soft power parameter was estimated and used to derive a pairwise distance matrix for selected genes using the topological overlap measure, and the dynamic hybrid cut method was used to detect clusters. The node centrality, defined as the sum of within-cluster connectivity measures, was used to rank genes for ‘‘hub-ness’’ within each cluster. For visual analysis of the constructed networks by hard thresholding of edge distances, the closest 150 edges were represented using Cytoscape 3.0.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited table includes raw read counts for all samples

growth_protocol: Umbilical cord was harvested from fetus with natural labor from Changzhou Maternal and Child Health Care Hospital, temporally preserved in saline added with 100 U/mL penicillin, 100 U/mL streptomycin and 0.54% sodium citrate anticoagulant. Cells were isolated as described below. Umbilical cord was washed with saline supplement with antibiotics. After the blood vessels were removed, the tissue was excised into pieces with diameter around 1 cm. The tissue clumps were cultured in the petri dish with low glucose DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 U/mL streptomycin. Half of culture medium was changed at day 4. At day 12, all the clumps were removed and cells were cultured for one more week. When cells reached around 80% confluency, cell can be passaged and cultured under the condition mentioned above. Samples are all qualified for microbiology and virology tests.

extract_protocol:
MSCs were captured on a large microfluidic chip (designed for cells from 17–25 μm) using the Fluidigm C1 Autoprep System. Capturing efficiency was evaluated by microscopic observation, each capture site was manually confirmed with single cell and processed further. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated. These procedures were achieved by Novogene company.

treatment_protocol: those samples labeled with "sti" were cultured under normal medium plus 10ng/ml IFNγ plus TNFα

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

tag: treatment

value: IFNγ+TNFα


title: PAMEVI blood 1

value: PAMEVI

value: male

tag: ploidy


title: PAIXNC blood 1

value: PAIXNC


title: PAIXMM blood 1

value: PAIXMM

value: low

value: non-amp


title: PALNFE blood 1

value: PALNFE

value: hyperdiploid (>1.0)


title: huc2_p5_sti_49 [T5_94]


title: HU8110

city: Philadelphia

first: Daniel

middle: J

last: Rader

state: PA

address: 3400 Civic Center Blvd

department: ITMAT

institute: University of Pennsylvania

description: For RNA-seq analysis, primary human hepatocytes from each vial (Thermo Fisher Scientific) were thawed and spun down and then immediately processed for RNA isolation

data_processing:
Quality control for raw fastq files were assessed using FastQC
Adaptor trimming for Illumina paired-end libraries was applied using TrimGalore!
Sequenced reads were aligned with reference genome using STAR aligner
RNA-seq quantified as transcripts per million (TPMs) using RSEM
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: TPM measurements

source_name: Primary hepatocytes

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Human plateable hepatocytes, Metabolism qualified


title: huc2_p5_sti_48 [T5_93]


title: huc2_p5_sti_47 [T5_92]


title: HU8148

growth_protocol: For RNA-seq analysis, primary human hepatocytes from each vial (Thermo Fisher Scientific) were thawed and spun down and then immediately processed for RNA isolation


title: PAMYCE blood 1

value: PAMYCE

value: blood

value: female

value: high

value: diploid (=1.0)


title: HU8116


title: input_4xUAS

city: Vienna

first: Vanja

last: Haberle

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

description: PCR amplified cDNA (STAP-seq transcript); polyA+ RNA

data_processing:
Library strategy: STAP-seq
Basecalls where performed using CASAVA 1.9.1
Paired-end COF-STAP-seq reads were trimmed to 46 bp, with the first 10 bp of the forward read as the unique molecular barcode identifier (UMI). The reads were mapped using the remaining 36 bp as paired-end to a reference containing 133bp long sequences of all 12,000 CP candidates and to M. musculus (mm9) genome (for spike-in controls) using Bowtie version 0.12.9 allowing 2 mis-matches. The spike-in control M. musculus CP sequences were selected from their H. sapiens orthologs such that the reads could unambiguously be mapped to mm9 genome with the same mapping parameters. Multi-mapping was allowed and only mappings with reverse reads mapping to the end of the oligo sequence were kept ensuring they correspond to reporter transcripts transcribed from that particular cloned CP candidate. Read pairs that still mapped to more than one oligo sequence were randomly assigned to one position. For paired-end reads that mapped to the same positions, we collapsed those that have identical UMIs as well as those for which the UMIs differed by 1 nucleotide to ensure the counting of unique reporter transcripts. Tag counts at each position represent the sum of the 5′-most position of collapsed fragments.
Unique tags mapping to any position within the CP candidate were summed to obtain tag count per CP candidate. We did the same for the 9 spike-in M. musculus CPs, and the counts were used to calculate normalization factors between the datasets. For each spike-in CP we first assigned factor 1 to the dataset with the lowest count and then calculated down-scaling factors for all other datasets based on their counts for that CP. Final normalization factors were calculated as median of factors for individual spike-in CPs and were used to normalize raw tag counts for each sample. For each cofactor, normalized tag counts across the 3 biological replicates were averaged.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of 12,000 core promoter candidates from the human genome and tag counts at those 12,000 candidates as follows: 1) Raw tag counts in each individual replicate of 5 cofactors and 2 controls is provided in All_reps_raw_tagcounts_per_oligo.txt file and 2) Normalized counts (normalized to spike-in) of merged replicates per cofactor are provided in the Merged_reps_spikein_normalized_tagcounts_per_oligo.txt file. BigWig files contain normalized tag count per genomic position averaged across 3 biological replicates for each cofactor and separated by strand.

source_name: HCT116 cells

extract_protocol: The UAS STAP-seq screening vector was generated from pSTAP-seq_fly-ctrl (Addgene ID 86380) by cloning an array of 4 upstream activating sequences (UAS) (obtained from pSGE_91_4xUAS_dCP (Addgene ID 71169)) upstream of the library insertion site (position of the core promoter) between the XhoI and BglII restriction sites. The core promoter candidate library was cloned from a pool of 12,000 synthesized 200-mer oligonucleotides obtained from Twist Biosciences Inc. The CP candidates spanned 133bp total, centered on the candidates major (+1) TSS, flanked by the Illumina i5 (33bp) and i7 (34bp) adapter sequences upstream and downstream, respectively, serving as constant linkers for amplification and cloning. To comprehensively amplify the oligonucleotide pool (diluted to 1ng/µl) and thereby create the CP candidate library insert we performed 20 PCR reactions (98°C for 45 seconds (s); followed by 15 cycles of 98°C for 15s, 65°C for 30s, 72°C for 10s) with 1µl diluted oligonucleotide pool as template, using KAPA Hifi Hot Start Ready Mix (KAPA Biosystems; cat. no. KK2602) and primers (fw: TAGAGCATGCACCGGACACTCTTTCCCTACACGACGCTCTTCCGATCT and rev: GGCCGAATTCGTCGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) that add extra 15bp to each of the adapters, serving as homology arms for directional cloning of the CP candidate library insert using In-Fusion HD (Clontech; cat. no. 639650). All PCR reactions were pooled and purified with Agencourt AMPureXP DNA beads (ratio beads/PCR 1.4; cat. no. A63881). Directional cloning of the library insert (amplified oligonucleotide pool) into the UAS-STAP-seq screening vector was performed using In-Fusion HD (Clontech; cat. no. 639650) recombination.

value: HCT116 cells

tag: cofactor

tag: experimental procedure

value: STAP-Seq


title: PAMHPN blood 1

value: PAMHPN


title: IL-1β 4 h 2_HCAEC

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

description: Human coronary artery endothelial cells (HCAEC) treated with IL-1β for 4 h

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.5.1.1. Spot values were normalized using the default linear-lowess normalization.

label: Cy3 (green signal)

source_name: Human Coronary Artery Endothelial Cells

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Human Coronary Artery Endothelial Cells (HCAEC) obtained from Lonza were cultured in EBM-2 medium (Clonetics, Lonza) supplemented with EGM-2MV Single Quots (Clonetics, Lonza) and 5% FBS.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >9.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: HCAEC were treated with recombinant (rec.) human (h) IL1β (20 U/mL; PeproTech, USA) for 4 h. Treatment was performed by replacing culture medium containing 5% FBS by one with 2% FBS added with suitable stimuli.

value: no treatment

tag: incubation time

value: 4 h

label: Cy5 (red signal)

source_name: HCAEC

value: IL-1β 20 U/mL


title: huc2_p5_sti_46 [T5_90]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p5_sti_45 [T5_89]


title: PAKYSH blood 1

source_name: neuroblastoma

value: PAKYSH

value: male

value: low

value: non-amp


title: huc2_p5_sti_44 [T5_88]


title: HU8164

value: Human plateable hepatocytes, Metabolism qualified


title: PALWKV blood 1

value: PALWKV

value: blood

value: hyperdiploid (>1.0)


title: PAMBKU blood 1

value: PAMBKU

value: female

value: high


title: PALIIN blood 1

value: PALIIN


title: PAMJXC blood 1

value: PAMJXC

value: diploid (=1.0)


title: huc2_p5_sti_43 [T5_87]


title: huc2_p5_sti_42 [T5_86]


title: PAKMRM blood 1

value: PAKMRM

value: amp


title: PAMDXC blood 1

value: PAMDXC


title: IL-1β 4 h 3_HCAEC

value: no treatment

value: 4 h

value: IL-1β 20 U/mL


title: huc2_p5_sti_41 [T5_85]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PANUVK blood 1

value: PANUVK

value: non-amp


title: PAMZMV blood 1

value: PAMZMV

value: blood

value: low

value: hyperdiploid (>1.0)


title: PAMMTK blood 1

value: PAMMTK

value: female

value: high


title: PAIWTE blood 1

value: PAIWTE

value: male

value: intermediate


title: huc2_p5_sti_39 [T5_82]


title: PAMUFZ blood 1

value: PAMUFZ

value: amp

value: diploid (=1.0)


title: PAMIEV blood 1

value: PAMIEV


title: PALAKC blood 1

value: PALAKC


title: huc2_p5_sti_37 [T5_80]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p5_sti_40 [T5_83]


title: huc2_p5_sti_38 [T5_81]


title: PANGHY blood 1

value: PANGHY

value: non-amp


title: huc2_p5_sti_36 [T5_79]


title: PAKPJE blood 1

value: PAKPJE

value: blood


title: PAKIPY blood 1

value: PAKIPY

value: hyperdiploid (>1.0)


title: huc2_p5_sti_35 [T5_77]


title: PALWRG blood 1

value: PALWRG

value: low


title: PAMZUE blood 1

value: PAMZUE

value: female

value: high


title: PAIXHH blood 1

value: PAIXHH

value: male


title: huc2_p5_sti_34 [T5_76]


title: PAMKBM blood 1

value: PAMKBM


title: PAKJBA blood 1

value: PAKJBA

value: amp


title: Cold+1d+Wounding-3

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

country: Germany

institute: Freie Universität Berlin

description:
Gene expression in leaves after 'treatment'
5d 4°C + 1d 20°C + 2d Wounding

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 (Agilent) at 23°C and 1 minute with GE Wash buffer 2 (Agilent) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2600D) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_1105_Oct12 (Read Only) and Grid_Name 049286_D_F_20130524). The resulting processed signals of all individual hybridizations were normalized and log2-converted as described in Firtzlaff V, Oberländer J, Geiselhardt S, Hilker M and Kunze R, 2016, Sci. Rep. 6, 28544.

label_protocol: Cy3-labeled cRNA was synthesized with the Agilent Quick Amp Labeling Kit one-cCy3-labeled cRNA was synthesized with the Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-0442) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from frozen and ground tissue according to Verwoerd et al. (1989. Nucleic Acids Res. 17, 2362) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For cold treatment, Arabidopsis thaliana Col-0 plants were grown for 7 weeks on soil under short day conditions (8-h/16-h light/dark cycle, 120 μmol m−2 sec−1 light intensity, 50% relative humidity) and then transferred for five days to 4°C under short day conditions (8-h/16-h light/dark cycle, 120 μmol m−2 sec−1 light intensity, 50% relative humidity). Subsequently plants were retransferred to 20°C. Control plants were kept constantly at 20°C.  For larval feeding, P. brassicae or M. brassicae larvae were transferred to leaves of untreated ánd chilling-treated plants and allowed to gregariously feed for two days. Mechanical wounding was applied twice per day for two days on leaves of untreated and chilling-treated plants.

value: 5d 4C + 1d 20C + 2d Wounding

tag: accession

value: rosette leaf 17


title: PAMVAG blood 1

value: PAMVAG

value: non-amp

value: diploid (=1.0)


title: Cold+1d+Wounding-2


title: Cold+1d+Wounding-1


title: Cold+1d+Mamestra-2

description:
Gene expression in leaves after 'treatment'
5d 4°C + 1d 20°C + 2d Mamestra larval feeding

value: 5d 4C + 1d 20C + 2d Mamestra larval feeding


title: huc2_p5_sti_32 [T5_71]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p5_sti_33 [T5_75]


title: Cold+1d+Mamestra-1


title: PALTYS blood 1

value: PALTYS

value: blood


title: Cold+1d+Pieris-3

description:
Gene expression in leaves after 'treatment'
5d 4°C + 1d 20°C + 2d Pieris larval feeding

value: 5d 4C + 1d 20C + 2d Pieris larval feeding


title: PAMTPS blood 1

value: PAMTPS

value: high


title: huc2_p5_sti_31 [T5_48]


title: PAIXNG blood 1

value: PAIXNG

value: male


title: PALFPS blood 1

value: PALFPS


title: huc2_p5_sti_30 [T5_47]


title: PALCBW blood 1

value: PALCBW

value: female


title: PAMBMJ blood 1

value: PAMBMJ

value: amp

value: hyperdiploid (>1.0)


title: PAICAI blood 1

value: PAICAI

value: non-amp


title: Cold+1d+Mamestra-3

value: 5d 4C + 1d 20C + 2d Mamestra larval feeding

value: rosette leaf 17


title: huc2_p5_sti_29 [T5_46]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PAMUBS blood 1

value: PAMUBS

value: blood

value: low


title: T Wounding-3

description:
Gene expression in leaves after 'treatment'
6d 20°C + 2d Wounding

source_name: T Wounding-3

value: 6d 20C + 2d Wounding


title: Cold+1d+Pieris-1

value: 5d 4C + 1d 20C + 2d Pieris larval feeding


title: PAKYJX blood 1

value: PAKYJX


title: T Wounding-2

source_name: T Wounding-2


title: Cold+1d+Pieris-2


title: PAMVLG blood 1

value: PAMVLG

value: male

value: high


title: T Wounding-1

source_name: T Wounding-1


title: PALBWZ blood 1

value: PALBWZ

value: female


title: PAKIZR blood 1

value: PAKIZR

value: hyperdiploid (>1.0)


title: PAMVRA blood 1

value: PAMVRA

value: non-amp


title: huc2_p5_sti_27 [T5_42]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: huc2_p5_sti_28 [T5_45]

value: IFNγ+TNFα


title: PAMSSZ blood 1

value: PAMSSZ


title: huc2_p5_sti_26 [T5_40]


title: huc2_p5_sti_25 [T5_39]


title: PANBSP blood 1

value: PANBSP

value: blood

value: diploid (=1.0)


title: PANGNK blood 1

value: PANGNK

value: low


title: huc2_p5_sti_24 [T5_33]


title: huc2_p5_sti_23 [T5_32]


title: PAIXJX tumor 1

value: PAIXJX

value: neuroblastoma

value: intermediate


title: PAMNLH blood 1

value: PAMNLH

value: high


title: PAMXCN blood 1

value: PAMXCN

value: female


title: PAMRAA blood 1

value: PAMRAA

value: male

value: amp

value: hyperdiploid (>1.0)


title: huc2_p5_sti_22 [T5_31]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PAMNYX blood 1

value: PAMNYX

value: blood

value: non-amp


title: PAMNCL blood 1

value: PAMNCL


title: PAIVMJ blood 1

value: PAIVMJ

value: low


title: PAIXHH tumor 1

value: PAIXHH

value: neuroblastoma


title: PAKIAP blood 1

value: PAKIAP

value: high


title: T Mamestra-2

description:
Gene expression in leaves after 'treatment'
6d 20°C + 2d Mamestra larval feeding

source_name: T Mamestra-2

value: 6d 20C + 2d Mamestra larval feeding

value: rosette leaf 17


title: T Pieris-2

description:
Gene expression in leaves after 'treatment'
6d 20°C + 2d Pieris larval feeding

source_name: T Pieris-2

value: 6d 20C + 2d Pieris larval feeding


title: T Mamestra-1

source_name: T Mamestra-1


title: T Mamestra-3

source_name: T Mamestra-3


title: T Pieris-1

source_name: T Pieris-1


title: T Pieris-3

source_name: T Pieris-3


title: PAMMXF blood 1

value: PAMMXF

value: male

value: amp


title: PAMNXD blood 1

value: PAMNXD

value: female

value: hyperdiploid (>1.0)


title: PAMNAL blood 1

value: PAMNAL

value: blood

value: non-amp


title: huc2_p5_sti_21 [T5_30]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: Cold+3d-2

description:
Gene expression in leaves after 'treatment'
5d 4°C + 3d 20°C


title: huc2_p5_sti_19 [T5_28]


title: PAMPFJ blood 1

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

value: PAMPFJ


title: PANHZS blood 1

value: PANHZS

value: low

value: diploid (=1.0)


title: Cold+3d-1

value: rosette leaf 17


title: huc2_p5_sti_18 [T5_27]


title: PANBCI blood 1

value: PANBCI

value: high


title: PALKXX blood 1

value: PALKXX

value: male

value: intermediate


title: huc2_p5_sti_20 [T5_29]


title: Control 2-2

description:
Gene expression in leaves after 'treatment'
8d 20°C

source_name: Control 2-2


title: Control 2-1

source_name: Control 2-1


title: Control 2-3

source_name: Control 2-3


title: PALEBK blood 1

value: PALEBK


title: PALRCT blood 1

value: PALRCT

value: hyperdiploid (>1.0)


title: huc2_p5_sti_16 [T5_25]


title: PANUIF blood 1

value: PANUIF

value: blood

value: female


title: PALFXR blood 1

value: PALFXR

value: amp


title: huc2_p5_sti_15 [T5_24]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PALFVJ blood 1

value: PALFVJ

value: non-amp

value: diploid (=1.0)


title: PALWVX blood 1

value: PALWVX

value: high


title: PALGXF blood 1

value: PALGXF

value: male


title: Cold-3

description:
Gene expression in leaves after 'treatment'
5d 4°C

value: 5d 4C

value: rosette leaf 17


title: huc2_p5_sti_14 [T5_22]


title: huc2_p5_sti_13 [T5_21]


title: PANZRV blood 1

value: PANZRV

value: low

value: hyperdiploid (>1.0)


title: PANSIC blood 1

value: PANSIC

value: blood

value: intermediate


title: PANRVJ blood 1

value: PANRVJ


title: huc2_p5_sti_17 [T5_26]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PAIWNT blood 1

value: PAIWNT

value: non-amp


title: huc2_p5_sti_11 [T5_16]


title: PALNTJ blood 1

value: PALNTJ


title: PAPBJT blood 1

value: PAPBJT

value: high

value: diploid (=1.0)


title: huc2_p5_sti_10 [T5_14]


title: PAKFVB blood 1

value: PAKFVB

value: male


title: Cold+3d-3

value: rosette leaf 17


title: Cold-1

value: 5d 4C


title: PAKZHI blood 1

value: PAKZHI


title: Control 1-3

description:
Gene expression in leaves after 'treatment'
5d 20°C

source_name: Control 1-3


title: huc2_p5_sti_9 [T5_13]


title: huc2_p5_sti_8 [T5_12]


title: PAICAK blood 1

value: PAICAK

value: female

value: hyperdiploid (>1.0)


title: PALWXP blood 1

value: PALWXP

value: blood

value: low


title: huc2_p5_sti_7 [T5_11]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PALWIP blood 1

value: PALWIP

value: non-amp


title: PAPEVV blood 1

value: PAPEVV

value: high

value: amp


title: Control 1-1

source_name: Control 1-1


title: huc2_p5_sti_6 [T5_10]


title: PANSBN blood 1

value: PANSBN

value: male

value: diploid (=1.0)


title: huc2_p5_sti_12 [T5_18]


title: PAKYMG blood 1

value: PAKYMG

value: intermediate


title: huc2_p5_sti_5 [T5_8]


title: PAPAKS blood 1

value: PAPAKS

value: female


title: PANWRR blood 1

value: PANWRR


title: PAKPBK blood 1

value: PAKPBK

value: blood

value: hyperdiploid (>1.0)


title: Control 1-2

source_name: Control 1-2

value: rosette leaf 17


title: PAPBFP blood 1

value: PAPBFP


title: PALPKZ blood 1

value: PALPKZ

value: non-amp


title: PALHKS blood 1

value: PALHKS


title: PALYLZ blood 1

value: PALYLZ

value: low


title: huc2_p5_ctrl_50 [C5_89]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc2_p5_ctrl_51 [C5_91]


title: huc2_p5_sti_4 [T5_6]

value: IFNγ+TNFα


title: huc2_p5_sti_3 [T5_5]


title: huc2_p5_sti_2 [T5_4]


title: PALNVP blood 1

value: PALNVP

value: high


title: huc2_p5_sti_1 [T5_3]


title: PAPGJR blood 1

value: PAPGJR

value: female

value: amp

value: diploid (=1.0)


title: PALHTR blood 1

value: PALHTR

value: blood

value: hyperdiploid (>1.0)


title: PANNMS blood 1

value: PANNMS


title: PANHEU blood 1

value: PANHEU

value: male

value: non-amp


title: PALLJJ blood 1

value: PALLJJ

value: low


title: huc2_p5_ctrl_47 [C5_84]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc2_p5_ctrl_49 [C5_87]


title: huc2_p5_ctrl_48 [C5_85]


title: Cold-2

value: 5d 4C

value: rosette leaf 17


title: TGF-β [AR3032]

city: Tokyo

first: Yasuhiro

last: Yoshimatsu

address: M&D tower N-707, 1-5-45 Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

description: Dish culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TGF-β

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

growth_protocol: TEC were maintained in basal EGM-2MV medium (CC-3202, Lonza, Basel, Switzerland) containing 5% fetal bovine serum (FBS)

extract_protocol: RNA fractions were prepared using Nucleo Spin  (TaKaRaBio, Otsu, Japan) following the manufacturer's recommendations.

treatment_protocol: Tumor endothelial cells were cultured in the absence or presence of 1 ng/mL of TGF-β2 in combination with 50 ng/mL of FGF2  or 3 mM infigratinib for 72 h.

value: Tumor endothelial cell (TEC) -derived from melanoma

tag: agent

value: TGF-beta


title: PAMREY blood 1

source_name: neuroblastoma

value: PAMREY

tag: ploidy value


title: PANVZF blood 1

tag: usi

value: PANVZF


title: PALXHW blood 1

value: PALXHW

tag: tissue

value: female

value: high

value: diploid (=1.0)


title: PAPCDN blood 1

value: PAPCDN

value: blood

tag: gender

value: hyperdiploid (>1.0)


title: PANLPX blood 1

value: PANLPX

value: male

tag: cog risk

value: non-amp


title: PALNHR blood 1

value: PALNHR

tag: inss stage

value: amp


title: huc2_p5_ctrl_46 [C5_83]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: C8.LPS.6.2

city: Phiadelphia

first: Corbett

middle: T

last: Berry

address: 3800 Spruce St

data_processing:
Fastq files were mapped to the mouse transcriptome (Ensembl, mouse cDNA GRCh38) using Kallisto
Reads were annotated with EnsemblDB and EnsDb.Mmusculus.v79, and Tximport was used to summarize transcripts to genes.
Data were log2 transformed and scaled using weighted trimmed mean of M-values with edgeR
Data were filtered to remove unexpressed and lowly expressed (>1 count per million (cpm) across 2 or more all samples) genes.
Differentially expressed genes (false discovery rate < 0.05 and absolute log2 fold change >= 0.59) were identified using limma
Genome_build: mouse cDNA GRCh38
Supplementary_files_format_and_content: tab delimited text with estimated counts and cpm (CPM)

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were grown as previously described (Brodsky IE, et al., 2010) in a 37°C 5% CO2 humidified incubator in DMEM supplemented with 10% FBS, HEPES, sodium pyruvate (complete-DMEM) and 30% L929 supernatant for 7–9 days.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions. Samples were run on Illumina NextSeq 500 to generate 75-base pair, single-end reads with a Q30 score of ~80%, resulting in 25–50 million fragments/sample.

treatment_protocol: BMDMs were prepared as described above, and 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37°C incubator for 16 hours. BMDMs were stimulated with LPS (100 ng/mL) or CpG (1μM) for 0, 2, or 6 hrs.

tag: strain

tag: genotype/variation

tag: agonist

value: LPS

tag: time point

value: 6 hrs

tag: biological replicate


title: C8.CPG.6.1

value: CpG


title: C8.LPS.6.1


title: R3.LPS.6.2


title: R3.CPG.6.2


title: C8.CPG.6.2


title: B6.CPG.6.1

value: Wild-type


title: R3.CPG.6.1


title: B6.CPG.6.2


title: R3.LPS.6.1


title: huc2_p5_ctrl_45 [C5_80]

tag: donor id

tag: cell type

tag: passage

tag: treatment


title: huc2_p5_ctrl_44 [C5_78]


title: B6.LPS.6.2


title: TGF-β+infigratinib [AR3032]

description: Dish culture

source_name: TGF-β+infigratinib

value: Tumor endothelial cell (TEC) -derived from melanoma

value: TGF-beta+infigratinib


title: B6.LPS.6.1


title: PALWUM blood 1

value: PALWUM

value: intermediate

tag: mycn status

tag: ploidy


title: C8.CPG.2.2


title: PAIWMI blood 1

value: PAIWMI

value: blood

value: high

tag: ploidy value


title: C8.CPG.2.1


title: PAMANU blood 1

tag: usi

value: PAMANU

value: female

value: hyperdiploid (>1.0)


title: huc2_p5_ctrl_43 [C5_76]


title: huc2_p5_ctrl_41 [C5_74]


title: huc2_p5_ctrl_42 [C5_75]


title: PANRPS blood 1

value: PANRPS

tag: tissue

value: male

value: non-amp

value: diploid (=1.0)


title: PANYUG blood 1

value: PANYUG

tag: gender


title: R3.CPG.2.2

value: CpG


title: PANGXK blood 1

value: PANGXK

tag: cog risk


title: TGF-β+FGF2

description: Dish culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The file Second_array_normalized_data.txt includes raw, normalized values and detection flags.

treatment_protocol: Tumor endothelial cells were cultured in the absence or presence of 1 ng/mL of TGF-β2 in combination with 50 ng/mL of FGF2  for 72 h.

value: Tumor endothelial cell (TEC) -derived from melanoma


title: TGF-β+FGF2 [AR3032]

description: Dish culture

tag: agent


title: huc2_p5_ctrl_40 [C5_73]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: R3.CPG.2.1

tag: strain


title: PANANV blood 1

value: PANANV

tag: inss stage

value: amp


title: B6.CPG.2.2

tag: genotype/variation

value: Wild-type

tag: agonist


title: PALUDH blood 1

value: PALUDH

value: blood

value: high


title: PAIDJS blood 1

value: PAIDJS

value: low

value: hyperdiploid (>1.0)


title: B6.CPG.2.1

tag: time point

tag: biological replicate


title: huc2_p5_ctrl_37 [C5_64]

tag: donor id

tag: cell type


title: PALVFV blood 1

value: PALVFV

value: female

value: non-amp


title: C8.LPS.2.2

value: LPS


title: huc2_p5_ctrl_36 [C5_62]

tag: passage

tag: treatment


title: FGF2

description: Dish culture


title: Control [AR3032]

description: Dish culture

source_name: Control

value: Control


title: huc2_p5_ctrl_39 [C5_68]


title: huc2_p5_ctrl_38 [C5_67]


title: C8.LPS.2.1


title: Control

description: Dish culture

value: Tumor endothelial cell (TEC) -derived from melanoma


title: PALTPM blood 1

value: PALTPM

value: intermediate

tag: mycn status

tag: ploidy


title: acinary (sample 33)

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description:
Methylation data from lung adenocarcinoma.
SAMPLE 33

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'
Matrixprocessed.txt reports Average Beta (normalized and filtered data).

label: biotin/DNP

source_name: lung adenocarcinoma

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: acinary


title: acinary (sample 34)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 34


title: papillary (sample 38)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 38

value: papillary


title: normal (sample 35)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 35

value: normal


title: lepidic (sample 37)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 37

value: lepidic


title: normal (sample 39)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 39


title: solid (sample 36)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 36

value: solid


title: PAPEAV blood 1

data_processing: IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array versions HumanHap550 v1, v3, v3duo, Human610-Quad v1.0 & HumanOmniExpress-12v1

tag: usi

value: PAPEAV

value: blood

value: high

tag: ploidy value


title: TGF-β

description: Dish culture


title: R3.LPS.2.1


title: PANZPV blood 1

value: PANZPV

tag: tissue

tag: gender

value: diploid (=1.0)


title: B6.LPS.2.2

value: Wild-type


title: huc2_p5_ctrl_35 [C5_61]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: micropapillary (sample 31)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 31

value: micropapillary


title: R3.LPS.2.2

value: LPS


title: huc2_p5_ctrl_32 [C5_53]


title: huc2_p5_ctrl_34 [C5_56]


title: huc2_p5_ctrl_33 [C5_55]


title: normal (sample 32)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 32


title: acinary (sample 30)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 30


title: PAIWKK blood 1

value: PAIWKK

value: male

tag: cog risk

value: non-amp

value: hyperdiploid (>1.0)


title: PALIFG blood 1

value: PALIFG


title: lymph node (sample 29)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 29

value: lymph node


title: PALXUM blood 1

value: PALXUM

value: female

value: low


title: acinary (sample 40)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 40

value: acinary


title: huc2_p5_ctrl_30 [C5_51]


title: huc2_p5_ctrl_31 [C5_52]


title: normal (sample 28)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 28

value: normal


title: C8.untreated.6.2

tag: strain

value: 6 hrs


title: PALRDI blood 1

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

value: PALRDI

value: blood

tag: inss stage

value: diploid (=1.0)


title: B6.LPS.2.1

tag: genotype/variation

value: Wild-type


title: huc2_p5_ctrl_29 [C5_49]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PAMAJT blood 1

value: PAMAJT


title: solid (sample 26)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 26

value: solid


title: R3.untreated.6.2

tag: agonist


title: PANFLF blood 1

value: PANFLF

value: intermediate

value: non-amp

value: hyperdiploid (>1.0)


title: huc2_p5_ctrl_27 [C5_45]


title: huc2_p5_ctrl_28 [C5_47]


title: C8.untreated.6.1

tag: time point


title: papillary (sample 25)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 25

value: papillary


title: B6.untreated.6.2

tag: biological replicate


title: micropapillary (sample 24)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 24

value: micropapillary


title: PALUYS blood 1

value: PALUYS

value: female

value: high


title: B6.untreated.6.1

value: 6 hrs


title: lepidic (sample 23)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 23

value: lepidic


title: huc2_p5_ctrl_25 [C5_39]

tag: donor id


title: PANENB blood 1

value: PANENB

value: blood


title: huc2_p5_ctrl_24 [C5_38]

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)


title: PAMAMR blood 1

value: PAMAMR

value: male


title: lymph node (sample 22)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 22

value: lymph node


title: PANWAT blood 1

value: PANWAT


title: PANUKV blood 1

value: PANUKV

value: amp

value: diploid (=1.0)


title: huc2_p5_ctrl_23 [C5_34]

tag: passage

value: naïve


title: PAPBZI blood 1

value: PAPBZI

value: non-amp

value: hyperdiploid (>1.0)


title: huc2_p5_ctrl_22 [C5_33]

tag: treatment


title: PANZVU blood 1

value: PANZVU

value: high

tag: mycn status


title: huc2_p5_ctrl_21 [C5_30]


title: acinary (sample 19)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 19

value: acinary


title: solid (sample 20)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 20

value: solid


title: micropapillary (sample 18)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 18

value: micropapillary


title: R3.untreated.6.1

value: 6 hrs


title: normal (sample 17)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 17

value: normal


title: huc2_p5_ctrl_19 [C5_27]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: PAKFUY blood 1

value: PAKFUY

value: blood

value: male

tag: ploidy


title: PAMMMS blood 1

tag: usi

value: PAMMMS

value: amp


title: huc2_p5_ctrl_18 [C5_25]

value: naïve


title: micropapillary (sample 27)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 27


title: lepidic (sample 16)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 16

value: lepidic


title: BA0177_17_a

first: Naofumi

last: Miwa

institute: Toho University

hyb_protocol: Illumina Infinium HD methylation assay, Manual protocol

scan_protocol: Scan was performed using iScan (version 3.2.45).

data_processing: Data was processed by GenomeStudio (v2011.1) and methylation module (1.9.0).

source_name: Excised endometrial tissue

extract_protocol: Genomic DNA was prepared according to a standard protocol using commercially available kit (NucleoSpin, Takara Bio).

value: endometrial tissue

tag: phenotype

value: control

value: female


title: papillary (sample 15)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 15

tag: tissue

value: papillary


title: huc2_p5_ctrl_17 [C5_24]


title: PAMRKI blood 1

first: Gonzalo

last: Lopez

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

value: PAMRKI

tag: gender

value: intermediate

value: non-amp

value: diploid (=1.0)

tag: ploidy value


title: acinary (sample 14)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 14

value: acinary


title: PAKRKL blood 1

value: PAKRKL

tag: cog risk

value: low

value: hyperdiploid (>1.0)


title: PANCCG blood 1

value: PANCCG

value: blood

tag: inss stage


title: PAKWGF blood 1

value: PAKWGF

value: high


title: huc2_p5_ctrl_14 [C5_18]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc2_p5_ctrl_15 [C5_22]


title: huc2_p5_ctrl_16 [C5_23]


title: normal (sample 12)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 12

value: normal


title: BA0177_18_a

label_protocol: Illumina Infinium HD methylation assay, Manual protocol

value: endometrial tissue

value: control

value: female


title: lymph node (sample 21)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 21

value: lymph node


title: PAKHAE blood 1

value: PAKHAE

value: male

value: non-amp


title: solid (sample 13)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 13

value: solid


title: huc2_p5_ctrl_13 [C5_17]


title: PALUST blood 1

description: Genomic DNA extracted from primary neuroblastoma and matched blood samples

value: PALUST

value: low


title: solid (sample 11)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 11


title: papillary (sample 10)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 10

value: papillary


title: huc2_p5_ctrl_12 [C5_15]


title: BA0177_21_a

value: obese


title: BA0177_22_b


title: huc2_p5_ctrl_11 [C5_14]


title: PAMRIZ blood 1

value: PAMRIZ

value: blood

value: intermediate

value: hyperdiploid (>1.0)


title: acinary (sample 9)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 9

value: acinary


title: lepidic (sample 8)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 8

value: lepidic


title: PAKSWB blood 1

value: PAKSWB


title: lymph node (sample 7)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 7


title: PAMSUE blood 1

value: PAMSUE

value: female


title: huc2_p5_ctrl_10 [C5_13]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc2_p5_ctrl_9 [C5_12]


title: huc2_p5_ctrl_8 [C5_11]


title: solid (sample 6)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 6

value: UJEPRQ


title: BA0177_14_b

value: endometrial tissue

value: control


title: PAKRBA blood 1

value: PAKRBA

value: male

value: low

value: non-amp


title: PALSAE blood 1

value: PALSAE

value: blood

value: high


title: huc2_p5_ctrl_7 [C5_10]


title: BA0177_24_a

value: obese


title: BA0177_15_a


title: PALGFF blood 1

value: PALGFF

value: hyperdiploid (>1.0)


title: huc2_p5_ctrl_6 [C5_9]


title: acinary (sample 4)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 4

value: acinary


title: micropapillary (sample 5)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 5

value: micropapillary


title: PAMYBA blood 1

value: PAMYBA

value: diploid (=1.0)


title: huc2_p5_ctrl_5 [C5_8]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: lymph node (sample 3)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 3

value: lymph node

value: UJEPRQ


title: BA0177_16_a

value: endometrial tissue

value: control

value: female


title: lymph node (sample 2)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 2


title: huc2_p5_ctrl_4 [C5_7]


title: PAMFLZ blood 1

value: PAMFLZ

value: male

value: intermediate

value: non-amp


title: PAKYMW blood 1

value: PAKYMW

value: blood


title: normal (sample 1)

description:
Methylation data from lung adenocarcinoma.
SAMPLE 1

value: normal


title: huc2_p5_ctrl_3 [C5_4]


title: huc2_p5_ctrl_2 [C5_3]


title: PALPIA blood 1

value: PALPIA

value: high

value: amp


title: PAMAFV blood 1

value: PAMAFV

value: low

value: hyperdiploid (>1.0)


title: dcl2 [MethylC-seq]

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Sequencing reads were processed to remove adapters and low-quality reads as in Panda et al., PMID: 27506905. PCR duplicated reads were removed, and only uniquely mapping reads were used to assay methylation.
The weighted methylation level of genomic features (TE, gene, or DMR) was calculated as described previously in Schultz et al., PMID: 23131467.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file showing total number of reads (total) and reads reporting methylation (mc_count) for each cytosine in the genome.

growth_protocol: Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.

extract_protocol:
DNA was isolated from each sample using fractional precipitation followed by phenol-chloroform extraction and RNaseA treatment.
1 µg of isolated DNA was used to prepare libraries as previously described in Urich et al., PMID: 25692984.
Single-end Illumina sequencing of 150 bp was performed at the University of Georgia Genomics Facility.

tag: ecotype

value: Columbia


title: dcl2/dcl3/dcl4 [MethylC-seq]

source_name: inflorescence (stage 1-12) immature flower buds


title: PALVSG blood 1

city: New York

address: 1399 Park avenue

institute: Mount Sinai School of Medicine

value: PALVSG


title: huc2_p2_sti_50 [T2_96]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p5_ctrl_1 [C5_2]

value: naïve


title: aly1-2/ddm1 [MethylC-seq]

description: MethylC-seq

data_processing:
Sequencing reads were processed to remove adapters and low-quality reads as in Panda et al., PMID: 27506905. PCR duplicated reads were removed, and only uniquely mapping reads were used to assay methylation.
The weighted methylation level of genomic features (TE, gene, or DMR) was calculated as described previously in Schultz et al., PMID: 23131467.
Genome_build: TAIR10
Supplementary_files_format_and_content: *tsv: Tab-delimited text files showing total number of reads (total) and reads reporting methylation (mc_count) for each cytosine in the genome.

tag: ecotype/background

tag: genotype/variation

value: inflorescence (stage 1-12) immature flower buds


title: cmt3 [MethylC-seq]

description: MethylC-seq


title: met1 [MethylC-seq]

description: MethylC-seq


title: huc2_p2_sti_48 [T2_94]


title: aly1-2 [MethylC-seq]

description: MethylC-seq


title: PAMIYK tumor 1

value: PAMIYK

value: neuroblastoma

value: female


title: PAMACS blood 1

value: PAMACS

value: blood

value: male

value: non-amp

value: diploid (=1.0)


title: PALZBH tumor 1

value: PALZBH

value: high


title: PALNAP blood 1

value: PALNAP

value: low

value: hyperdiploid (>1.0)


title: huc2_p2_sti_46 [T2_92]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: wt Col - rep3 [MethylC-seq]

description: MethylC-seq

value: Columbia

value: wt


title: huc2_p5_ctrl_26 [C5_43]

value: naïve


title: huc2_p2_sti_44 [T2_90]

value: IFNγ+TNFα


title: huc2_p2_sti_45 [T2_91]


title: PAMXYU blood 1

value: PAMXYU


title: wt Col - rep2 [MethylC-seq]

description: MethylC-seq

value: inflorescence (stage 1-12) immature flower buds


title: PAMAKZ tumor 1

value: PAMAKZ

value: neuroblastoma

value: female

value: intermediate


title: pol V [MethylC-seq]

description: MethylC-seq

value: pol


title: PALZSL tumor 1

value: PALZSL

value: male

value: amp


title: huc2_p2_sti_43 [T2_89]


title: PAMAKZ blood 1

value: blood

value: non-amp

value: diploid (=1.0)


title: PALZRG tumor 1

value: PALZRG

value: high

value: hyperdiploid (>1.0)


title: huc2_p2_sti_49 [T2_95]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: cmt2 [MethylC-seq]

description: MethylC-seq

value: Columbia

value: inflorescence (stage 1-12) immature flower buds


title: wt Col - rep1 [MethylC-seq]

description: MethylC-seq

value: wt


title: PALKUC blood 1

value: PALKUC

value: female


title: PAMMWD blood 1

value: PAMMWD


title: huc2_p2_sti_40 [T2_85]


title: huc2_p2_sti_42 [T2_88]


title: huc2_p2_sti_41 [T2_86]


title: huc2_p2_sti_39 [T2_46]


title: PALPSY blood 1

value: PALPSY

value: low


title: huc2_p2_sti_38 [T2_45]


title: huc2_p2_sti_47 [T2_93]


title: PAMHMK tumor 1

value: PAMHMK

value: neuroblastoma


title: huc2_p2_sti_37 [T2_44]


title: huc2_p2_sti_36 [T2_43]


title: huc2_p2_sti_35 [T2_42]


title: PALVKK tumor 1

value: PALVKK

value: non-amp


title: PAMLNB blood 1

value: PAMLNB

value: blood

value: male


title: PAMIIU blood 1

value: PAMIIU

value: high

value: diploid (=1.0)


title: huc2_p2_sti_34 [T2_41]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p2_sti_33 [T2_40]


title: PAMHMK blood 1

value: hyperdiploid (>1.0)


title: huc2_p2_sti_32 [T2_39]


title: huc2_p2_sti_31 [T2_38]


title: PAIWUF tumor 1

value: PAIWUF

value: female

value: intermediate


title: PAMZLY blood 1

value: PAMZLY


title: PAMAFV tumor 1

value: PAMAFV

value: low


title: PALNRP blood 1

value: PALNRP


title: huc2_p2_sti_30 [T2_36]


title: huc2_p2_sti_29 [T2_35]


title: N243Quit_24wk

city: Boston

first: Kahkeshan

last: Hijazi

address: 715 Albany Street

institute: Boston University

description: RNA was extracted from the cells using miRNeasy mini kit (Qiagen) according to manufacturer's protocol

hyb_protocol: Affymetrix Suggest Protocol

scan_protocol: Affymetrix Suggest Protocol

data_processing: RMA generated expression value using affy library in R using the custom CDF HuGene10stv1_Hs_ENTREZG_14.1.0 from brainarray.

source_name: Nasal Epithelium

label_protocol: Affymetrix Suggest Protocol

value: nasal epithelium

tag: patient id

tag: time in weeks

tag: rna integrity number (rin)

tag: age

value: F


title: N265smoker_0wk

extract_protocol: RNA was extracted from the cells using miRNeasy mini kit (Qiagen) according to manufacturer's protocol

value: M


title: huc2_p2_sti_28 [T2_33]

tag: donor id

tag: cell type

tag: passage

tag: treatment


title: huc2_p5_ctrl_20 [C5_28]

value: naïve


title: N265Quit_4wk


title: N243Quit_8wk


title: N265Quit_8wk


title: PAKIRR blood 1

tag: usi

value: PAKIRR

value: blood

tag: mycn status

value: amp

tag: ploidy


title: PALVVH blood 1

value: PALVVH

tag: tissue

tag: gender

value: male

value: non-amp

tag: ploidy value


title: N265Quit_16wk


title: N243Quit_4wk


title: N227smoker_0wk


title: N243Quit_16wk


title: N227Quit_4wk


title: PAMZYP blood 1

value: PAMZYP

tag: cog risk

value: high

tag: inss stage

value: hyperdiploid (>1.0)


title: N243smoker_0wk


title: huc2_p2_sti_27 [T2_32]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc2_p2_sti_26 [T2_31]


title: huc2_p2_sti_25 [T2_30]


title: N208Quit_24wk


title: N227Quit_24wk


title: N227Quit_8wk


title: PAMZZZ blood 1

value: PAMZZZ

value: female


title: PAIWWN tumor 1

value: PAIWWN

value: neuroblastoma

value: intermediate


title: huc2_p2_sti_24 [T2_29]


title: huc2_p2_sti_23 [T2_28]


title: N208Quit_16wk

value: nasal epithelium

value: F


title: huc2_p2_sti_22 [T2_27]


title: N208Quit_8wk


title: PALVUC blood 1

value: PALVUC

value: blood

value: low


title: PAMXSL blood 1

value: PAMXSL

value: diploid (=1.0)


title: huc2_p2_sti_21 [T2_26]


title: PAMZCY blood 1

value: PAMZCY

value: non-amp


title: huc2_p2_sti_20 [T2_25]


title: PALZZV tumor 1

value: PALZZV

value: high

value: amp

value: hyperdiploid (>1.0)


title: PANAYF blood 1

value: PANAYF

value: male


title: huc2_p2_sti_19 [T2_24]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PAMIZA tumor 1

value: PAMIZA

value: neuroblastoma

value: female


title: huc2_p2_sti_17 [T2_21]


title: huc2_p2_sti_16 [T2_19]


title: PAMBNU blood 1

value: PAMBNU

value: blood

value: intermediate


title: PAMZGT blood 1

value: PAMZGT

value: diploid (=1.0)


title: N208smoker_0wk

value: nasal epithelium

value: F


title: PAMXWF blood 1

value: PAMXWF

value: high

value: non-amp


title: N208Quit_4wk


title: N206Quit_24wk

value: M


title: PAMFHC tumor 1

value: PAMFHC

value: male

value: hyperdiploid (>1.0)


title: N205Quit_16wk


title: huc2_p2_sti_14 [T2_17]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: N206Quit_16wk


title: N205smoker_0wk


title: N205Quit_24wk


title: N206smoker_0wk


title: huc2_p2_sti_13 [T2_16]


title: huc2_p2_sti_18 [T2_22]


title: N206Quit_4wk


title: PALVFV tumor 1

value: PALVFV

value: neuroblastoma

value: female


title: PAMYCK blood 1

value: PAMYCK

value: blood

value: amp


title: huc2_p2_sti_11 [T2_11]


title: huc2_p2_sti_12 [T2_13]


title: PAMEEH tumor 1

value: PAMEEH

value: intermediate


title: N206Quit_8wk

value: nasal epithelium


title: huc2_p2_sti_10 [T2_10]


title: N116Quit_8wk

value: F


title: N116smoker_0wk


title: huc2_p2_sti_9 [T2_9]


title: PAMEZH tumor 1

value: PAMEZH

value: high


title: PAMBPH tumor 1

value: PAMBPH

value: low

value: non-amp


title: N116Quit_4wk


title: huc2_p2_sti_15 [T2_18]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: PAMZMG blood 1

value: PAMZMG

value: diploid (=1.0)


title: PAMAJT tumor 1

value: PAMAJT

value: neuroblastoma

value: hyperdiploid (>1.0)


title: huc2_p2_sti_7 [T2_7]

value: IFNγ+TNFα


title: huc2_p2_sti_8 [T2_8]


title: N107Quit_16wk


title: N107Quit_8wk


title: PAMFBR tumor 1

value: PAMFBR

value: male

value: amp


title: PAMEVI tumor 1

value: PAMEVI


title: N107smoker_0wk

value: nasal epithelium

value: F


title: huc2_p2_sti_6 [T2_6]


title: PAMYXR blood 1

value: PAMYXR

value: blood

value: female

value: high


title: N107Quit_24wk


title: huc2_p2_sti_5 [T2_5]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: PAMXJT blood 1

value: PAMXJT

value: low

value: non-amp


title: huc2_p2_sti_3 [T2_3]


title: huc2_p2_sti_4 [T2_4]


title: PAMYGL blood 1

value: PAMYGL

value: diploid (=1.0)


title: PAIXPU blood 1

value: PAIXPU

value: hyperdiploid (>1.0)


title: huc2_p2_sti_2 [T2_2]

value: IFNγ+TNFα


title: PALPGL blood 1

value: PALPGL

value: intermediate


title: huc2_p2_sti_1 [T2_1]


title: 35 Clone_hif(1/2)-4

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized and log2 transformed

label: biotin

source_name: cell line LNCaP

label_protocol: biotin

growth_protocol: The LNCaP/Empty and LNCaP/HIF1a cell lines were grown in charcoal stripped serum for 96 hours

extract_protocol: Total RNA was extracted using Trizol and isopropanol precipitation, according to the manufacturers instructions. Quality control was performed with an Agilent Bioanalyser

treatment_protocol: 1 nM R1881 or 0.01% ethanol

tag: clone

value: Normal


title: huc2_p2_ctrl_50 [C2_96]

value: naïve


title: PALXMM blood 1

value: PALXMM

value: male


title: 34 Clone_empty-1

value: Empty


title: PAMZCE blood 1

value: PAMZCE

value: blood

value: high

value: amp


title: huc2_p2_ctrl_49 [C2_95]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: 36 Clone_empty-2

value: Androgen


title: 33 Clone_hif(1/2)-2

value: Vehicle


title: huc2_p2_ctrl_48 [C2_94]


title: 31 Clone-empty-6


title: 32 Clone_hif(4/9)-3


title: 30 Clone_empty-2


title: huc2_p2_ctrl_46 [C2_86]


title: huc2_p2_ctrl_47 [C2_87]


title: huc2_p2_ctrl_45 [C2_85]


title: 28 Clone_empty-4


title: PAIXFZ blood 1

value: PAIXFZ

value: female

value: non-amp

value: diploid (=1.0)


title: PAIXFT blood 1

value: PAIXFT

value: low

value: hyperdiploid (>1.0)


title: huc2_p2_ctrl_43 [C2_83]

value: naïve


title: PAKLTE blood 1

value: PAKLTE

value: intermediate


title: huc2_p2_ctrl_42 [C2_82]


title: 27 Clone_hif(1/2)-3


title: PALFSE blood 1

value: PALFSE

value: male


title: PAKJYZ blood 1

value: PAKJYZ

value: blood


title: huc2_p2_ctrl_41 [C2_75]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: PAIWUJ blood 1

value: PAIWUJ


title: huc2_p2_ctrl_40 [C2_74]


title: PALXAF blood 1

value: PALXAF


title: 29 Clone_hif(1/2)-1

value: Normal


title: 26 Clone_empty-5

value: Empty


title: PAKPUT blood 1

value: PAKPUT

value: female

value: non-amp


title: PAKJZD blood 1

value: PAKJZD

value: low


title: huc2_p2_ctrl_39 [C2_73]

value: naïve


title: 24 Clone_hif(1/2)-5

value: Vehicle


title: 23 Clone_empty-4


title: huc2_p2_ctrl_44 [C2_84]


title: huc2_p2_ctrl_38 [C2_66]


title: PAKNZZ blood 1

value: PAKNZZ

value: hyperdiploid (>1.0)


title: huc2_p2_ctrl_37 [C2_65]


title: PAKJFU blood 1

value: PAKJFU

value: intermediate

value: diploid (=1.0)


title: 25 Clone_hif(1/2)-2

value: Androgen


title: 22 Clone_hif(1/2)-5


title: huc2_p2_ctrl_36 [C2_64]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: 20 Clone_hif(1/2)-4


title: 19 Clone_hif(4/9)-1


title: 21 Clone_empty-2


title: 18 Clone_hif(1/2)-4


title: 16 Clone_hif(4/9)-5


title: PAMZSH blood 1

value: PAMZSH

value: blood

value: male


title: PAKEIY blood 1

value: PAKEIY


title: PAIXVH blood 1

value: PAIXVH

value: female

value: high


title: huc2_p2_ctrl_33 [C2_61]


title: PAKXDZ blood 1

value: PAKXDZ

value: amp


title: huc2_p2_ctrl_35 [C2_63]

value: naïve


title: huc2_p2_ctrl_34 [C2_62]


title: huc2_p2_ctrl_32 [C2_54]


title: PAKSCM blood 1

value: PAKSCM

value: non-amp


title: ethanol exposure with lipopolysaccharide injection 4hr prior to sacrifice, replicate 1

city: Louisville

first: Michael

last: Merchant

state: KY

address: 570 South Preston Street, Room 102S Donald Baxter Research Building

department: Medicine

institute: University of Louisville

data_processing:
Illumina FastQ Generation version 1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1. The FastQC results indicated that all sequences were of high quality (Q32), with the exception of the final base.
Sequences were directly aligned to the Mus musculus  reference genome assembly (mm10.fa). A gene annotation file for mm10, was downloaded from Ensembl. The analysis was performed using Tophat (version 2.0.4), generating alignment files in bam format.
The aligned RNA-seq reads were assembled according to the mm10 gtf annotation file using Cufflinks V2.2.1.
Differentially expressed genes were identified for five pairwise comparisons (PF4hLPS vs. PF; EtOH4hLPS vs EtOH; EtOH4hLPS vs PF4hLPS; EtOH vs PF, and EtOH AND EtOH4hLPS vs PF AND PF4hLPS) using Cuffdiff (version 2.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited cuffnorm normalized FPKM values

source_name: whole kidney

growth_protocol: 8-week-old male C57BL6/J mice (Jackson Laboratory, Bar Harbor, ME) were housed in a pathogen free barrier facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.  Procedures were approved by the Institutional Animal Care and Use Committee (UofL IACUC number 15148).

extract_protocol:
At the time of sacrifice, kidneys were collected and cortex sections were separated and snap frozen.  Tissues were stored at -80° C and then incubated in RNAlater-ICE (Life Technologies, Carlsbad, CA) at -20° C for 72 hours prior to RNA extraction.  RNA was isolated using the mirVana kit (Life Technologies, Carlsbad, CA) according to manufacturer’s instructions for total RNA isolation.  RNA quality was evaluated by Nanodrop ND-1000 (Thermo Fisher Scientific, Grand Island, NY) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) analysis.
Libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit-Set A (Cat # RS-122-2301) with Ribo-Zero Gold.

treatment_protocol: Mice were fed alcohol-containing Lieber DeCarli diet ad libitum or pair fed iso-caloric maltose-dextrin control diet for 6 weeks.   The Lieber DeCarli diet contained the following ethanol concentrations: 0% for two days, 1% for two days, 2% for two days, 4% for 1 week, 5% for one week, and 6% for three weeks.  Animals were injected with lipopolysaccharide (LPS, E. coli; 10 mg/kg i.p Sigma, St. Louis, MO) or vehicle (saline), 4 hours prior to sacrifice.

value: kidney

tag: tissue region

value: cortex

tag: lps dosing

value: 10 mg/Kg I.P.

tag: strain


title: ethanol exposure with lipopolysaccharide injection 4hr prior to sacrifice, replicate 3


title: PAKYMN blood 1

value: PAKYMN

value: low

value: hyperdiploid (>1.0)


title: ethanol exposure, replicate 3

value: 0 mg/Kg I.P.


title: PAKWCJ blood 1

value: PAKWCJ

value: blood


title: PALKXJ blood 1

value: PALKXJ


title: huc2_p2_ctrl_30 [C2_52]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: ethanol exposure with lipopolysaccharide injection 4hr prior to sacrifice, replicate 2


title: 15 Clone_empty-3

value: Empty

value: Androgen


title: huc2_p2_ctrl_31 [C2_53]


title: 12 Clone_hif(4/9)-4

value: Normal


title: 17 Clone_empty-3


title: 13 Clone_empty-1

value: Vehicle


title: 10 Clone_empty-3


title: 14 Clone_hif(1/2)-2


title: ethanol exposure, replicate 1


title: 8 Clone_empty-5


title: huc2_p2_ctrl_28 [C2_50]

value: naïve


title: 9 Clone_hif(1/2)-5


title: pair fed control with lipopolysaccharide injection 4hr prior to sacrifice, replicate 3


title: huc2_p2_ctrl_29 [C2_51]


title: 11 Clone_hif(1/2)-1


title: PALLDC blood 1

value: PALLDC

value: male

value: high

value: non-amp

value: diploid (=1.0)


title: PALNIE blood 1

value: PALNIE

value: intermediate


title: pair fed control with lipopolysaccharide injection 4hr prior to sacrifice, replicate 2

value: kidney

value: cortex

value: 10 mg/Kg I.P.


title: PALAKE blood 1

value: PALAKE

value: blood

value: amp


title: ethanol exposure, replicate 2

value: 0 mg/Kg I.P.


title: huc2_p2_ctrl_26 [C2_48]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: huc2_p2_ctrl_27 [C2_49]


title: PALKXL blood 1

value: PALKXL


title: huc2_p2_ctrl_25 [C2_47]

value: naïve


title: PALLDU blood 1

value: PALLDU

value: female


title: pair fed control with lipopolysaccharide injection 4hr prior to sacrifice, replicate 1


title: 7 Clone_hif(1/2)-1

value: Vehicle


title: pair fed control, replicate 3


title: pair fed control, replicate 2


title: PAKXDF blood 1

value: PAKXDF

value: male

value: high

value: non-amp

value: hyperdiploid (>1.0)


title: pair fed control, replicate 1

value: kidney

value: cortex


title: 6 Clone_empty-4

value: Empty

value: Normal


title: 5 Clone_hif(1/2)-3

value: Androgen


title: huc2_p2_ctrl_23 [C2_39]


title: huc2_p2_ctrl_22 [C2_38]


title: PAKYAZ blood 1

value: PAKYAZ

value: blood


title: CTCF_WT_LpreB_ChIPseq

city: Charlestown

first: Katia

last: Georgopoulos

address: 1st and 13th St

institute: Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 assembly of the mouse genome using the genome mappers Bowtie2 for ATAC and STAR for RNASeq.
ATAC peaks call was perfomed with MACS2 call peaks  with --nomodel--shift 37 --extsize 73
findPeaks (HOMER) algorithm was used for ChIP peak calling with -factor for CTCF and- histone for Mi-2b ChIP-seq data sets
mergePeaks (HOMER) was used to find overlaping ATAC peaks in Mi-2bKOvsWT proB and LtrpreB cell ATAC datasets
Normalization and differential expression of RNAseq data sets was performed by HOMER implementation of DeSeq2 with analyzeRepeats.pl,  getDiffExpression.pl and addGeneAnnotation.pl
Genome_build: mm10
Supplementary_files_format_and_content: xls, txt

source_name: Adult bone marrow

extract_protocol:
Erythroid, myeloid , T cells, NK cells and mature B lineage (Lin) cells were depleted from BM cell uspensions, and Lin–CD19+CD43+BP1+ were sorted as large pre-B (LpreB) cells by FACS.Cells were expanded on OP9 stroma with IL-7, and stromal adherent phase was harvested for further analysis.
As detailed in Hu et al. Genes Dev (2016)

value: bone marrow

value: Large pre-B

tag: genotype

value: WT


title: huc2_p2_ctrl_21 [C2_37]

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 containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie and single-end clean reads were aligned to the reference genome using TopHat. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. For unigene DGE, Bowtie was used to aligned single-end clean reads to the unigene sequences.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilo base of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazaviet al., 2008). For unigene DGE, we used RSEM to count the reads numbers mapped to each unigene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.10.1). DESeq provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.
A signed network was constructed by using any gene that was expressed at an FPKM value of 0.1 or higher in at least one of the samples. Soft power parameter was estimated and used to derive a pairwise distance matrix for selected genes using the topological overlap measure, and the dynamic hybrid cut method was used to detect clusters. The node centrality, defined as the sum of within-cluster connectivity measures, was used to rank genes for ‘‘hub-ness’’ within each cluster. For visual analysis of the constructed networks by hard thresholding of edge distances, the closest 150 edges were represented using Cytoscape 3.0.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited table includes raw read counts for all samples

tag: donor id

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PALUKI blood 1

value: PALUKI


title: Mi2b_WT_LpreB_ChIPseq

tag: cell type


title: 4 Clone_empty-5

value: Vehicle


title: huc2_p2_ctrl_20 [C2_36]

tag: passage