title: EBF1_LpreB_rep2

extract_protocol:
Erythroid, myeloid , T cells, NK cells and mature B lineage (Lin) cells were depleted from BM cell suspensions, and Lin–CD19+CD43+BP1+ were sorted as large pre-B (LpreB) cells by FACS.
Trueseq stranded mRNA sample prep kit (Illumina) wtith Trizol

value: large pre-B


title: huc2_p2_ctrl_19 [C2_35]

status: Public on May 15 2019

type: SRA

city: shanghai

first: Yufang

last: Shi

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Chinese Academy of Science

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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: naïve


title: PALNGL blood 1

type: genomic

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

country: USA

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

source_name: neuroblastoma

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: usi

value: PALNGL

tag: tissue

value: blood

tag: gender

value: female

tag: cog risk

value: high

tag: inss stage

tag: mycn status

value: non-amp

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: huc2_p2_ctrl_24 [C2_46]


title: PAKZRH blood 1

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

value: PAKZRH

value: male

value: intermediate

value: diploid (=1.0)


title: 3 Clone_hif(4/9)-2

type: RNA

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

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: 2 Clone_empty-1

value: Empty

value: Androgen


title: WT_LpreB_rep3

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

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

organism: Mus musculus

source_name: Adult bone marrow

tag: strain

value: bone marrow

tag: genotype

value: WT


title: FER095: CL28_CL14_PlateRep4

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

data_processing:
bcl2fastq 2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC version 0.11.7
Trimmomatic version 0.36 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2 version 2.1.0 with default parameters
The program featureCounts from the Subread package was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: All seeds were surface-sterilized with 70% bleach, 0.2% Tween-20 for 8 min, and rinsed three times with sterile distilled water to eliminate any seed-borne microbes on the seed surface. Seeds were stratified at 4 °C in the dark for two days. Plants were germinated on vertical square 10 X 10 cm agar plates with JM containing 0.5% sucrose, for 7 days. Then, 10 plants were transferred to each of the bacteria-inoculated agar plates  containg JM without sucrose.

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: All strains were grown in separate tubes, then washed, and OD was adjusted to 0.02 before mixing and spreading over the plates were the germinated seedlings were transferred to.

tag: ecotype

value: whole seedling

tag: bacteria


title: transformant D10

city: Xianyang

first: Xiaoping

last: Li

state: Shaanxi

address: Yangling,

department: College of Plant protection

institute: Northwest A&F University,

data_processing:
bcl2fastq software were used for base-calling
Sequenced reads were trimmed for adaptor sequence,  masked for low-complexity or low-quality sequence,  and removed ribosome RNA reads, then mapped to Fusarium graminerarum PH-1 whole genome using Hisat2  with spliced mapping method.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM)  were calculated using a protocol from Kim, et al. Nat Methods, 2015. In short, the number of fragments from each gene were counted with Stringtie software, then normalized with trimmed mean of M values (TMM). After that the FPMK value of each gene was caculated with Perl script.
Genome_build: Fusarium graminerarum PH-1
Supplementary_files_format_and_content: Excel sheets include FPMK values and counts for the introns and genes of each sample.

organism: Fusarium graminearum PH-1

source_name: hyphae

growth_protocol: The vegetative hyphae of the PH-1, S139, and D10 were harvested from 16h liquid YEPD cultures.

extract_protocol:
Total RNAs was extracted using RNeasy Mini Kit (QIAGEN, US) following the manufacturer’s instructions.
Library construction and sequencing with an Illumina Hiseq 2000 sequencer were performed at Shanghai Biotechnology Corporation (Shanghai, China).

value: hyphae

tag: growth medium

value: 16hours in YEB medium

tag: genotype/variation

value: transformant D10


title: wild type PH-1

value: wild type PH-1


title: FER096: CL28_CL14_PlateRep5


title: PALKKV blood 1

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

value: PALKKV

value: blood

value: low


title: 1 Clone_hif(1/2)-3


title: PALJZV blood 1

value: PALJZV

value: high

value: amp


title: sector S139

value: sector S139


title: huc2_p2_ctrl_17 [C2_27]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

value: naïve


title: PAKLWT blood 1

tag: usi

value: PAKLWT

tag: tissue

value: female

value: diploid (=1.0)


title: WT_LpreB_rep2

value: bone marrow

value: large pre-B

value: WT


title: FER094: CL28_CL14_PlateRep3

value: whole seedling


title: huc2_p2_ctrl_16 [C2_26]

tag: treatment


title: WT_LpreB_rep1


title: PAKMVJ blood 1

value: PAKMVJ

tag: gender

tag: cog risk

tag: inss stage

value: non-amp


title: EBF1_LpreB_rep1


title: huc2_p2_ctrl_18 [C2_34]


title: FER093: CL28_CL14_PlateRep2


title: huc2_p2_ctrl_15 [C2_25]


title: PAMDAL blood 1

value: PAMDAL

value: blood

tag: mycn status


title: PAKMDB blood 1

value: PAKMDB

value: male

value: low

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: huc2_p2_ctrl_14 [C2_18]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: Mi2b_LTrpreB_rep1

extract_protocol:
Erythroid, myeloid, T cells, NK cells and mature B lineage (Lin) cells were depleted from BM cell suspensions, and Lin–cKit–/loCD19+CD43+or–CD2– were sorted as large transitional (LTr) pre-B cells by FACS.
Trueseq stranded mRNA sample prep kit (Illumina) wtith Trizol

tag: strain

value: Large transitional pre-B

tag: genotype


title: huc2_p2_ctrl_13 [C2_17]

value: naïve


title: FER090: CL14_PlateRep4

tag: ecotype

tag: bacteria


title: PALRFJ blood 1

value: PALRFJ

value: female

value: high


title: huc2_p2_ctrl_12 [C2_16]


title: PALKER blood 1

value: PALKER


title: Mi2b_proB_rep2

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.
Trueseq stranded mRNA sample prep kit (Illumina) wtith Trizol

value: bone marrow

value: Pro-B


title: PAKWUV tumor 1

value: PAKWUV

value: neuroblastoma


title: FER089: CL14_PlateRep3

value: whole seedling


title: WT_LTrpreB_rep1

value: WT


title: huc2_p2_ctrl_11 [C2_15]


title: huc2_p2_ctrl_10 [C2_14]


title: huc2_p2_ctrl_9 [C2_13]


title: Mi2b_proB_rep1


title: Mi2b_LTrpreB_rep2


title: WT_proB_rep2


title: FER087: CL14_PlateRep1


title: PAKSSK tumor 1

value: PAKSSK

value: non-amp


title: FER092: CL28_CL14_PlateRep1


title: FER086: CL28_PlateRep5


title: PALWNI tumor 1

value: PALWNI

value: intermediate


title: WT_LTrpreB_rep2


title: PALBFW tumor 1

value: PALBFW

value: male

value: diploid (=1.0)


title: FER091: CL14_PlateRep5


title: PAIXNC tumor 1

value: PAIXNC

value: hyperdiploid (>1.0)


title: FER085: CL28_PlateRep4


title: WT_proB_rep1


title: huc2_p2_ctrl_8 [C2_9]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: FER084: CL28_PlateRep3


title: 10FASD [4_23]

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

description: Male

library_source: genomic

data_processing:
Convert BAM files to FASTQ files using picard-toolds-1.108, SamToFastq.jar
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Placenta

extract_protocol:
Genomic DNA was extracted from tissues using DNeasy Blood & Tissue Kit (Qiagen) as per manufacturer protocols
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.

treatment_protocol: CF1 female mice (ART donors and recipients) were placed on Control diets (CD), 4x folic acid supplemented diets (4FASD) ) or 10x folic acid supplemented diets (10FASD) diets for 6 weeks prior to assisted reproduction and throughout gestation.  ART included superoverlation of donor females, in vitro fertilization and embryo culture.  Blastocyst stage embryos were then transfered non-surgically to pseudo pregnant mice (recipients) and mid gestation embryos were collected 8 days later.

value: CF1 x B6SJF1/J cross

tag: diet

value: 10x folic acid diet

tag: reproduction method

value: ART

value: Normal Placenta


title: PAIXST tumor 1

value: PAIXST

value: neuroblastoma

value: high


title: huc2_p2_ctrl_6 [C2_6]

tag: donor id

tag: cell type


title: FER088: CL14_PlateRep2

value: whole seedling


title: 10FASD [4_24]

description: Male


title: huc2_p2_ctrl_7 [C2_8]

tag: passage


title: 10FASD [4_22]

description: Male

tag: tissue


title: PALHVD tumor 1

tag: usi

value: PALHVD

value: female

value: non-amp


title: huc2_p2_ctrl_5 [C2_5]

tag: treatment


title: huc2_p2_ctrl_4 [C2_4]


title: FER083: CL28_PlateRep2


title: 4FASD [4_21]

description: Male

value: 4x folic acid diet


title: PALEZI tumor 1

value: PALEZI

tag: gender

value: male

tag: cog risk

value: amp

value: diploid (=1.0)


title: FER082: CL28_PlateRep1


title: huc2_p2_ctrl_3 [C2_3]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: FER081: NB_PlateRep3

value: NB


title: FER079: NB_PlateRep1


title: FER080: NB_PlateRep2


title: huc2_p2_ctrl_2 [C2_2]


title: PAKIVG tumor 1

value: PAKIVG

tag: inss stage

tag: mycn status


title: huc2_p2_ctrl_1 [C2_1]


title: 4FASD [4_20]

description: Male

value: CF1 x B6SJF1/J cross

value: ART

value: Normal Placenta


title: CD [4_18]

description: Male

value: Control diet


title: 4FASD [4_19]

description: Male


title: PAKRFK tumor 1

value: PAKRFK

value: neuroblastoma

value: high

tag: ploidy

tag: ploidy value


title: huc2_p0_ctrl_50 [C0_96]


title: CD [4_17]

description: Male

tag: strain


title: FER077: Full_PlateRep2

treatment_protocol: The entire SynCom, excluding all 10 Variovorax isolates and all five Burkholderia isolates was grown and prepared as described above (Materials and Methods 1a). The Variovorax and Burkholderia isolates were grown in separate tubes, washed and added to the rest of the SynCom to a final OD of 0.001 (the calculated OD of each individual strain in a 185-Member SynCom at a total of OD of 0.2), to form the following five mixtures: (i) Full community – all Variovorax and Burkholderia isolates added to the SynCom; (ii) Burkholderia drop-out – only Variovorax isolates added to the SynCom; (iii) Variovorax drop-out – only Burkholderia isolates added to the SynCom; (iv) Variovorax and Burkholderia drop-out – no isolates added to the SynCom; (v) Uninoculated plants – no SynCom

tag: ecotype

value: whole seedling

value: Full


title: PAKNXW tumor 1

value: PAKNXW


title: PALIFG tumor 1

value: PALIFG

value: male

value: non-amp

value: hyperdiploid (>1.0)


title: PALFSZ tumor 1

value: PALFSZ

value: low


title: CD [4_16]

description: Male


title: NAT-CD [4_15]

description: Male

value: Natural Mating


title: huc2_p0_ctrl_48 [C0_92]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PALFKG tumor 1

value: PALFKG

value: female

value: intermediate


title: FER076: Full_PlateRep1

tag: bacteria


title: FER075: DOB_PlateRep3

value: DropoutBurkholderia


title: huc2_p0_ctrl_47 [C0_90]


title: NAT-CD [4_14]

description: Male

value: CF1 x B6SJF1/J cross

tag: diet

value: Control diet

value: Normal Placenta


title: FER074: DOB_PlateRep2

value: whole seedling


title: PAKWCJ tumor 1

value: PAKWCJ

value: neuroblastoma


title: huc2_p0_ctrl_46 [C0_89]


title: PALFXR tumor 1

value: PALFXR

value: male

value: high

value: amp


title: FER073: DOB_PlateRep1


title: huc2_p0_ctrl_45 [C0_86]


title: FER078: Full_PlateRep3

value: Full


title: PALGFF tumor 1

value: PALGFF

value: low

value: non-amp

value: hyperdiploid (>1.0)


title: PALFPS tumor 1

value: PALFPS

value: diploid (=1.0)


title: huc2_p0_ctrl_49 [C0_95]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: FER072: DOV_PlateRep3

value: DropoutVariovorax


title: FER071: DOV_PlateRep2

value: whole seedling


title: FER070: DOV_PlateRep1


title: 10FASD [4_12]

description: Male

value: CF1 x B6SJF1/J cross

value: 10x folic acid diet

tag: reproduction method

value: ART

value: Normal Placenta


title: 10FASD [4_10]

description: Male


title: huc2_p0_ctrl_42 [C0_79]

tag: donor id


title: PALBFV tumor 1

value: PALBFV

value: neuroblastoma

value: female

value: high


title: huc2_p0_ctrl_43 [C0_80]

tag: cell type


title: 4FASD [4_9]

description: Male

value: 4x folic acid diet


title: FER069: DOVB_PlateRep3

value: DropoutVariovoraxBurkholderia


title: PALKUC tumor 1

value: PALKUC

value: amp


title: huc2_p0_ctrl_41 [C0_78]

tag: passage


title: 4FASD [4_8]

description: Male

tag: tissue


title: NAT-CD [4_13]

description: Male

value: Control diet

value: Natural Mating


title: 10FASD [4_11]

description: Male


title: huc2_p0_ctrl_40 [C0_75]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: 4FASD [4_7]

description: Male


title: PALWVJ tumor 1

tag: usi

value: PALWVJ

value: male

value: non-amp

value: hyperdiploid (>1.0)


title: FER068: DOVB_PlateRep2

value: whole seedling


title: FER067: DOVB_PlateRep1


title: huc2_p0_ctrl_39 [C0_73]

tag: treatment


title: huc2_p0_ctrl_44 [C0_83]


title: FER066: NB_PlateRep3

value: NB


title: huc2_p0_ctrl_38 [C0_72]


title: PAKHHZ tumor 1

value: PAKHHZ

value: neuroblastoma

tag: gender


title: FER065: NB_PlateRep2


title: PAKYMG tumor 1

value: PAKYMG

value: female

tag: cog risk

value: intermediate

value: diploid (=1.0)


title: CD [4_6]

description: Male

value: CF1 x B6SJF1/J cross

value: ART

value: Normal Placenta


title: CD [4_5]

description: Male

value: Control diet


title: huc2_p0_ctrl_37 [C0_71]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: CD [4_4]

description: Male


title: PALBCY tumor 1

value: PALBCY

value: male

value: low

tag: inss stage


title: PALPSY tumor 1

value: PALPSY

tag: mycn status

value: non-amp

value: hyperdiploid (>1.0)


title: huc2_p0_ctrl_35 [C0_67]


title: huc2_p0_ctrl_36 [C0_68]


title: PALADE tumor 1

value: PALADE

value: neuroblastoma

tag: ploidy


title: PAKZRE tumor 1

value: PAKZRE

value: female

value: high

value: amp

tag: ploidy value


title: huc2_p0_ctrl_33 [C0_60]


title: huc2_p0_ctrl_34 [C0_64]


title: huc2_p0_ctrl_32 [C0_59]


title: huc2_p0_ctrl_31 [C0_58]


title: FER064: NB_PlateRep1

value: whole seedling

value: NB


title: huc2_p0_ctrl_30 [C0_57]


title: RNAPII spt6l rep2 IP

city: Guangzhou

first: Chen

last: Chen

state: Guangdong

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

data_processing:
The reads were aligned to the TAIR10 assembly using the Bowtie2 program with default settings.
unmapped reads and PCR duplicates were removed by using Samtools (verion1.7)
peaks were called by using MACS2 program with following setting: -g 135000000, -broad, and -broad-cutoff 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files were generated by using bamCoverage (deeptools2) with following settings: -bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 300 --samFlagExclude 1796

source_name: seedlings

growth_protocol: Plants were grown on half strength of Murashige and Skoog (½ MS) medium (0.5XMS salts, 1.5% [w/v] sucrose, and 0.8% agar [pH 5.8]) or soil under 16h/8h light/dark cycle at 23°C

extract_protocol:
ChIP was performed as previously described (Chen et al., 2017) with some modifications. Five grams of 10-day-old Arabidopsis seedlings grown on ½ MS medium were collected. Protein A Dynabeads (Invitrogen) was pre-incubated with antibody (5 µL for 50 µL beads) at 4 degree in a rotor at least 6h. After removing excess or unbound antibodies, the pre-cleaned chromatins (cleaned by incubating with Dynabeads alone) were add into antibody bound Dynabeads.
NEBNext® Ultra™ DNA Library Prep Kit (E7370S)

treatment_protocol: 10 µM flavopiridol or DMSO was sprayed on 10 days old seedlings for 1h

value: seedlings

tag: age

value: 10 days

tag: chip antibody

value: anti-PolII (ab817, abcam)


title: Spt6L-GFP Treat Input

description: treat with 10 µM flavopiridol 1h

tag: ecotype


title: Spt6L-GFP Mock IP rep2

description: treat with DMSO 1h

value: anti-GFP (ab290, abcam)


title: Spt6L-GFP Treat IP rep1

description: treat with 10 µM flavopiridol 1h


title: Spt6L-GFP Mock IP rep1

description: treat with DMSO 1h


title: Spt6L-GFP Mock Input

description: treat with DMSO 1h


title: Spt6L-GFP Treat IP rep2

description: treat with 10 µM flavopiridol 1h


title: spt6l Input


title: huc2_p0_ctrl_29 [C0_55]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PALNGL tumor 1

value: PALNGL


title: PALTPM tumor 1

value: PALTPM

value: intermediate

value: non-amp


title: PALKKL tumor 1

value: PALKKL

value: neuroblastoma

value: male

value: low

value: hyperdiploid (>1.0)


title: PALKDE tumor 1

value: PALKDE

value: female

value: high


title: PALPKZ tumor 1

value: PALPKZ

value: diploid (=1.0)


title: huc2_p0_ctrl_28 [C0_54]


title: PAMWSV blood 1

value: PAMWSV

value: blood


title: huc2_p0_ctrl_27 [C0_53]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: SPT6L-GFP IP rep2

value: seedlings

value: 10 days

value: anti-GFP (ab290, abcam)


title: SPT6L-GFP IP rep1


title: PALUDH tumor 1

value: PALUDH

value: non-amp


title: huc2_p0_ctrl_26 [C0_44]


title: PALYLZ tumor 1

value: PALYLZ

value: neuroblastoma

value: male


title: PALRGM tumor 1

value: PALRGM

value: hyperdiploid (>1.0)


title: Spt6LΔSH2 spt6l Input


title: huc2_p0_ctrl_25 [C0_41]


title: PALPGL tumor 1

value: PALPGL

value: female

value: intermediate


title: NAT-CD [4_2]

description: Male

tag: strain

value: CF1 x B6SJF1/J cross

tag: diet

value: Control diet

value: Natural Mating

value: Normal Placenta


title: NAT-CD [4_3]

description: Male

tag: reproduction method


title: NAT-CD [3_12]

description: Female

source_name: Embryo

value: Delayed Embryo


title: NAT-CD [4_1]

description: Male


title: huc2_p0_ctrl_24 [C0_40]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: 10FASD [3_7]

description: Female

value: 10x folic acid diet

value: ART

tag: tissue


title: 4FASD [3_4]

description: Female

value: 4x folic acid diet


title: 10FASD [3_9]

description: Female


title: NAT-CD [3_11]

description: Female


title: 4FASD [3_6]

description: Female


title: CD [3_3]

description: Female


title: NAT-CD [3_10]

description: Female


title: 4FASD [3_5]

description: Female


title: PALWXP tumor 1

tag: usi

value: PALWXP

value: neuroblastoma

value: low

value: non-amp


title: Spt6LΔHtH-GFP spt6l heterozygous Input

value: seedlings

value: 10 days


title: PALYEC tumor 1

value: PALYEC

value: male

value: high

value: amp

value: hyperdiploid (>1.0)


title: huc2_p0_ctrl_23 [C0_38]

tag: passage

tag: treatment


title: CD [3_2]

description: Female

value: CF1 x B6SJF1/J cross

value: Control diet

value: Delayed Embryo


title: 10FASD [3_8]

description: Female

value: 10x folic acid diet


title: huc2_p0_ctrl_22 [C0_33]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: CD [3_1]

description: Female

value: ART


title: Spt6LΔYqgF-GFP spt6l heterozygous IP rep2

value: anti-GFP (ab290, abcam)


title: Spt6LΔHtH-GFP spt6l heterozygous IP rep2


title: PALKXL tumor 1

value: PALKXL

value: neuroblastoma

tag: gender

tag: cog risk

value: intermediate

value: diploid (=1.0)


title: huc2_p0_ctrl_21 [C0_32]


title: 10FASD [2_36]

description: Female

value: Normal Embryo


title: Spt6LΔHtH-GFP spt6l heterozygous IP rep1

value: seedlings

value: 10 days


title: PALIIN tumor 1

value: PALIIN

value: male

value: high

tag: inss stage

tag: mycn status

value: non-amp


title: Spt6LΔYqgF-GFP spt6l heterozygous IP rep1


title: 4FASD [2_35]

description: Female

value: CF1 x B6SJF1/J cross

value: 4x folic acid diet


title: Spt6LΔYqgF-GFP spt6l heterozygous Input


title: PAKYSH tumor 1

value: PAKYSH

value: low

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: huc2_p0_ctrl_19 [C0_28]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PADAEC tumor 1

value: PADAEC

value: neuroblastoma


title: Spt6LSHΔ2-GFP spt6l heterozygous IP rep2

tag: age

tag: chip antibody

value: anti-GFP (ab290, abcam)


title: huc2_p0_ctrl_17 [C0_26]


title: huc2_p0_ctrl_18 [C0_27]


title: huc2_p0_ctrl_16 [C0_25]


title: huc2_p0_ctrl_15 [C0_24]


title: 10FASD [2_31]

description: Female

tag: strain

value: 10x folic acid diet

value: ART

value: Normal Embryo


title: PADLNM tumor 1

value: PADLNM

value: amp


title: PALAKC tumor 1

value: PALAKC

value: female

value: intermediate


title: 10FASD [2_33]

description: Female

value: CF1 x B6SJF1/J cross

tag: diet


title: 10FASD [2_32]

description: Female

tag: reproduction method


title: Spt6LΔHtHΔSH2-GFP spt6l heterozygous IP rep1

value: seedlings

value: 10 days

tag: ecotype


title: Spt6LSHΔ2-GFP spt6l heterozygous Input


title: Spt6LSHΔ2-GFP spt6l heterozygous IP rep1


title: Spt6LΔHtHΔSH2-GFP spt6l heterozygous IP rep2


title: PADLKJ tumor 1

value: PADLKJ

value: male

value: high


title: huc2_p0_ctrl_20 [C0_31]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: 4FASD [2_30]

description: Female

value: 4x folic acid diet

tag: tissue


title: PADKXS tumor 1

tag: usi

value: PADKXS

value: neuroblastoma


title: CD [2_34]

description: Female

value: Control diet

value: ART

value: Normal Embryo


title: Spt6LΔHtHΔSH2-GFP spt6l heterozygous Input


title: PADKYP tumor 1

value: PADKYP

value: amp


title: 4FASD [2_28]

description: Female


title: Spt6LΔYqgFΔSH2-GFP spt6l heterozygous IP rep1

value: anti-GFP (ab290, abcam)


title: CD [2_27]

description: Female

value: CF1 x B6SJF1/J cross


title: PACZPX tumor 1

value: PACZPX

value: non-amp


title: Spt6LΔYqgFΔSH2-GFP spt6l heterozygous IP rep2

value: seedlings

value: 10 days


title: PADIEY tumor 1

value: PADIEY

value: female

value: high


title: PADIBM tumor 1

value: PADIBM


title: Spt6LΔYqgFΔSH2-GFP spt6l heterozygous Input


title: huc2_p0_ctrl_11 [C0_17]

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

tag: treatment

value: naïve


title: huc2_p0_ctrl_13 [C0_21]


title: huc2_p0_ctrl_12 [C0_20]


title: CD [2_26]

description: Female

value: Control diet


title: SPT6LΔSH2-GFP spt6l IP rep2


title: huc2_p0_ctrl_14 [C0_22]


title: CD [2_25]

description: Female

value: ART


title: SPT6LΔSH2-GFP spt6l IP rep1


title: huc2_p0_ctrl_9 [C0_15]


title: 10FASD [2_23]

description: Female

value: 10x folic acid diet

value: Normal Embryo


title: huc2_p0_ctrl_10 [C0_16]


title: 10FASD [2_24]

description: Female


title: 4FASD [2_29]

description: Female

value: 4x folic acid diet


title: PADENF tumor 1

value: PADENF

value: neuroblastoma

tag: gender

value: male

tag: cog risk


title: PADFLI tumor 1

value: PADFLI

tag: inss stage

tag: mycn status

value: non-amp


title: huc2_p0_ctrl_8 [C0_13]


title: RNAPII spt6l rep1 IP

value: seedlings

value: 10 days

value: anti-PolII (ab817, abcam)


title: PADLES tumor 1

value: PADLES

value: female

value: high


title: 4FASD [2_22]

description: Female

value: CF1 x B6SJF1/J cross


title: RNAPII spt6l SPT6LΔSH2 IP rep2


title: PADLBE tumor 1

value: PADLBE


title: huc2_p0_ctrl_7 [C0_12]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc2_p0_ctrl_6 [C0_11]


title: 4FASD [2_21]

description: Female

value: ART

value: Normal Embryo


title: RNAPII spt6l SPT6LΔSH2 IP rep1


title: PADPEY tumor 1

value: PADPEY

value: amp


title: huc2_p0_ctrl_5 [C0_9]


title: PADPCI tumor 1

value: PADPCI

value: neuroblastoma

value: male


title: PACRZM tumor 1

value: PACRZM

value: non-amp


title: huc2_p0_ctrl_4 [C0_4]


title: aly1-1 - rep 2 [RIP-seq]

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: RNA

data_processing:
Demultiplexed RNA-seq paired-end reads were processed to remove adapter sequences from both 3' and 5' ends using BBDuk2 program from BBTools package (https://jgi.doe.gov/data-and-tools/bbtools/) with the following parameters: “k=23 mink=11 hdist=1 tbo”. Adapter-trimmed reads were further processed to remove bases below the Phred quality score Q30 at both 3' and 5' ends by using BBDuk2.
For each sample, processed reads from multiple runs were first merged, then aligned to reference TAIR10 Arabidopsis thaliana genome using STAR version 2.5.1b (Dobin et al., PMID: 23104886) with the parameters “--outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100”.
Read alignments against Arabidopsis genes and TEs (Araport11 release) were counted using featureCounts (Liao et al., PMID: 24227677) from the Subread package version 1.6.1 with the parameters “ -p -B -C -g gene_id -M --fraction -s 2”. The resulting read counts were used for all subsequent analyses.
Genome_build: TAIR10
Supplementary_files_format_and_content: Raw counts of reads for each gene as calculated using featureCounts (described in data processing above), is provided.

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:
ALY1-GFP protein was isolated from cell lysates by immunoprecipitation using Protein G Dynabeads (Invitrogen) which were pre-incubated with ⍺GFP (Abcam, ab290). RNA was subsequently isolated using Trizol LS (Invitrogen).
RNA isolated from IP underwent rRNA-depletion (RiboMinus Plant Kit for RNA seq, Invitrogen) or was directly used as input to prepare libraries with the NEBNext Ultra II Directional RNA library prep kit and was dual-indexed.
Multiplexed libraries were sequenced on a HiSeq2500

value: Columbia


title: huc2_p0_ctrl_3 [C0_3]


title: 10FASD [2_18]

description: Female

value: 10x folic acid diet

value: Normal Placenta


title: PACPJG tumor 1

value: PACPJG

value: female

value: high


title: CD [2_19]

description: Female

value: CF1 x B6SJF1/J cross

value: Control diet


title: huc2_p0_ctrl_2 [C0_2]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PADPHP tumor 1

value: PADPHP


title: 10FASD [2_17]

description: Female

value: ART


title: PADNNX tumor 1

value: PADNNX


title: aly1-1 - rep 1 [RIP-seq]

description: RNA

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


title: huc2_p0_ctrl_1 [C0_1]


title: wt Col - rep 2 rRNA depleted [RIP-seq]

description: RiboMinus RNA


title: huc1_p5_sti_58 [sti_s_49]

value: IFNγ+TNFα


title: 4FASD [2_15]

description: Female

value: 4x folic acid diet


title: PADKRU tumor 1

value: PADKRU

value: neuroblastoma


title: wt Col - rep 1 [RIP-seq]

description: RNA

value: Columbia


title: CD [2_14]

description: Female


title: CD [2_20]

description: Female

value: Normal Embryo


title: PADKNE tumor 1

value: PADKNE

value: amp


title: aly1-1 - rep 4 rRNA depleted [RIP-seq]

description: RiboMinus RNA


title: EV-B3 Rep 4

city: East Lansing

first: Thomas

last: Sharkey

state: MI

address: 612 Wilson Rd, Rm 210 Plant Biology Building

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: Alterations in Gene Expresion in Arabidopsis thalliana Expressing ISPS.csv

data_processing:
Sequencing reads were cleaned and trimmed using Trimmomatic version 0.32 (Bolger et al., 2014)
Cleaned reads were examined with FASTQC (Andrews, 2012) for quality control
Reads were mapped to the reference genome, Arabidopsis thaliana (TAIR10)
To calculate read counts for each gene, Rsubread version 3 (Liao et al., 2013) tool (featureCounts function) was used to build read count matrix.
Read count matrix was analyzed using the linear-model based Limma::Voom package (Law et al., 2014) to calculate the gene expression values (RPKM) and perform gene DE statistical analyses
Genome_build: TAIR10
Supplementary_files_format_and_content: CSV file includes RPKM values for each sample

source_name: leaves

growth_protocol: T3 plants were grown on Sure-Mix growing medium under a 12 h photoperiod, 120 μmol•m-2•s-1 light intensity, 23oC day-time and 20oC night-time temperatures, and 60 % relative humidity

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA) following the manufacturer's recommendations

treatment_protocol: EV-B3 does not emit isoprene; B2 emits isoprene

value: 51/2 weeks since seeding

tag: isoprene emission

value: Non-emitting

value: leaves


title: huc1_p5_sti_56 [sti_s_16]


title: CD [2_13]

description: Female

value: CF1 x B6SJF1/J cross

value: Control diet

value: Normal Placenta


title: EV-B3 Rep 3

tag: age


title: aly1-1 - rep 3 rRNA depleted [RIP-seq]

description: RiboMinus RNA


title: PAAPFA tumor 1

value: PAAPFA

value: male

value: high

value: non-amp


title: huc1_p5_sti_55 [sti_s_13]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PADXAS tumor 1

value: PADXAS

value: neuroblastoma

value: female


title: 4FASD [2_11]

description: Female

value: 4x folic acid diet

value: ART


title: B2 Rep 4

value: 51/2 weeks since seeding

value: Isoprene emitting


title: 4FASD [2_16]

description: Female


title: 10FASD [2_12]

description: Female

value: 10x folic acid diet


title: huc1_p5_sti_54 [sti_s_6]


title: PADWVR tumor 1

value: PADWVR


title: PADLPR tumor 1

value: PADLPR


title: PADLPZ tumor 1

value: PADLPZ


title: B2 Rep 3

value: leaves


title: B2 Rep 2


title: huc1_p5_sti_52 [sti_n_69]


title: huc1_p5_sti_53 [sti_n_70]


title: huc1_p5_sti_57 [sti_s_18]


title: 10FASD [2_9]

description: Female

value: CF1 x B6SJF1/J cross

value: Normal Placenta


title: CD [2_10]

description: Female

value: Control diet


title: 10FASD [2_8]

description: Female


title: huc1_p5_sti_51 [sti_n_68]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: 10FASD [2_7]

description: Female


title: huc1_p5_sti_49 [sti_n_63]

value: IFNγ+TNFα


title: PADSMF tumor 1

value: PADSMF

value: high

value: non-amp


title: PADSEC tumor 1

value: PADSEC

value: neuroblastoma

value: female


title: huc1_p5_sti_48 [sti_n_62]


title: PADBUM tumor 1

value: PADBUM

value: male


title: dcl2 [small RNA-seq]

description: Total small RNA

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_normalized_counts.tsv: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

extract_protocol:
Inflorescence small RNA was isolated with Trizol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on a HiSeq2500.

tag: ecotype/background

value: Columbia

tag: genotype/variation

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


title: aly1-2 [small RNA-seq]

description: Total small RNA


title: pol V [small RNA-seq]

description: Total small RNA

value: pol V


title: EV-B3 Rep 2

value: 51/2 weeks since seeding

value: Non-emitting

value: leaves


title: wt Col - rep3 [small RNA-seq]

description: Total small RNA

value: wt


title: pol IV [small RNA-seq]

description: Total small RNA

value: pol IV


title: huc1_p5_sti_47 [sti_n_61]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: 4FASD [2_5]

description: Female

tag: strain

value: CF1 x B6SJF1/J cross

tag: diet

value: 4x folic acid diet

value: ART

value: Normal Placenta


title: huc1_p5_sti_50 [sti_n_65]


title: huc1_p5_sti_46 [sti_n_58]


title: PADRWY tumor 1

value: PADRWY

value: neuroblastoma

value: high

value: non-amp


title: PADRLI tumor 1

value: PADRLI

value: female


title: huc1_p5_sti_45 [sti_n_56]


title: 4FASD [2_6]

description: Female

tag: reproduction method


title: wt Col - rep2 [small RNA-seq]

description: Total small RNA

value: Columbia

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


title: WT Input

data_processing:
The reads were aligned to the TAIR10 assembly using the Bowtie2 program (Langmead and Salzberg, 2012) with default settings. After removing unmapped reads and PCR duplicates, peaks were called by using MACS2 program (Zhang et al., 2008) with following setting (-g 135000000, -broad, and -broad-cutoff 0.01). The coverage files (BigWig files) for all the samples were converted from bam files by using bamCoverage (from deeptools2) (Ramirez et al., 2016) with following settings (-bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 300).
Genome_build: TAIR10
Supplementary_files_format_and_content: BIgWig

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 12 days under 16h light/ 8h dark condition

extract_protocol: ChIP was performed as previously described (Chen et al., 2017) with some modifications. Five grams of 10-day-old Arabidopsis seedlings grown on ½ MS medium were collected. Protein A Dynabeads (Invitrogen) was pre-incubated with antibody (5 µL for 50 µL beads) at 4 ֯C in a rotor at least 6h. After removing excess or unbound antibodies, the pre-cleaned chromatins (cleaned by incubating with Dynabeads alone) were add into antibody bound Dynabeads. The ChIP libraries were prepared as the instructions of NEBNext® Ultra™ DNA Library Prep Kit (E7370S) and used for Illumina single-end sequencing.

value: seedlings

tag: developmental

value: 10 days

tag: chip antibody

tag: ecotype


title: CD [2_1]

description: Female

value: Control diet

tag: tissue


title: PADLJN tumor 1

tag: usi

value: PADLJN


title: CD [2_2]

description: Female


title: huc1_p5_sti_44 [sti_n_51]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

tag: treatment

value: IFNγ+TNFα


title: PADLIC tumor 1

value: PADLIC

tag: gender

value: male

tag: cog risk

tag: inss stage

tag: mycn status


title: huc1_p5_sti_43 [sti_n_50]


title: wt Col - rep1 [small RNA-seq]

description: Total small RNA

tag: ecotype/background

tag: genotype/variation

value: wt


title: PADKWZ tumor 1

value: PADKWZ


title: PADKVV tumor 1

value: PADKVV

value: neuroblastoma


title: NAT-CD [1_11]

description: Female

tag: strain

value: CF1 x B6SJF1/J cross

tag: diet

value: Natural Mating

value: Normal Placenta


title: NAT-CD [1_12]

description: Female

tag: reproduction method


title: PADBHZ tumor 1

value: PADBHZ

value: female

value: high

value: non-amp


title: RNAPII WT rep1

data_processing:
The reads were aligned to the TAIR10 assembly using the Bowtie2 program (Langmead and Salzberg, 2012) with default settings. After removing unmapped reads and PCR duplicates, peaks were called by using MACS2 program (Zhang et al., 2008) with following setting (-g 135000000, -broad, and -broad-cutoff 0.01). The coverage files (BigWig files) for all the samples were converted from bam files by using bamCoverage (from deeptools2) (Ramirez et al., 2016) with following settings (-bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 300)
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 10 days under 16h light/ 8h dark condition

extract_protocol: ChIP was performed as previously described (Chen et al., 2017) with some modifications. Five grams of 10-day-old Arabidopsis seedlings grown on ½ MS medium were collected. Protein A Dynabeads (Invitrogen) was pre-incubated with antibody (5 µL for 50 µL beads) at 4 ֯C in a rotor at least 6h. After removing excess or unbound antibodies, the pre-cleaned chromatins (cleaned by incubating with Dynabeads alone) were add into antibody bound Dynabeads. The ChIP libraries were prepared as the instructions of NEBNext® Ultra™ DNA Library Prep Kit (E7370S) and used for Illumina single-end sequencing

value: seedlings

tag: developmental

value: 10 days

tag: chip antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (ab817, Abcam)


title: huc1_p5_sti_41 [sti_n_4]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: RNAPII WT rep2

data_processing:
The reads were aligned to the TAIR10 assembly using the Bowtie2 program (Langmead and Salzberg, 2012) with default settings. After removing unmapped reads and PCR duplicates, peaks were called by using MACS2 program (Zhang et al., 2008) with following setting (-g 135000000, -broad, and -broad-cutoff 0.01). The coverage files (BigWig files) for all the samples were converted from bam files by using bamCoverage (from deeptools2) (Ramirez et al., 2016) with following settings (-bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 300)
Genome_build: TAIR10
Supplementary_files_format_and_content: BIgWig

tag: tissue

tag: ecotype


title: huc1_p5_sti_42 [sti_n_7]

tag: donor id


title: 4FASD [2_4]

description: Female

value: 4x folic acid diet

value: ART


title: PADNXC tumor 1

tag: usi

value: PADNXC

value: amp


title: huc1_p5_sti_40 [sti_n_3]

tag: cell type

tag: passage


title: CD [2_3]

description: Female

value: Control diet


title: BMDM_TcESLPS_miRNA_007

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

tag: age

value: adult

value: bone marrow derived macrophages (BMDM)

tag: treatment

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


title: PADNFT tumor 1

value: PADNFT

value: neuroblastoma

tag: gender

value: male

tag: cog risk

tag: inss stage

tag: mycn status


title: NAT-CD [1_8]

description: Female

tag: strain

value: CF1 x B6SJF1/J cross

tag: diet

value: Natural Mating

value: Normal Placenta


title: PADMGA tumor 1

value: PADMGA

value: high

value: non-amp


title: NAT-CD [1_9]

description: Female

tag: reproduction method


title: huc1_p5_sti_38 [r5_96]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: NAT-CD [1_7]

description: Female


title: huc1_p5_sti_39 [sti_n_1]


title: BMDM_TcES_miRNA_006

value: female

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


title: PADKFS tumor 1

value: PADKFS


title: huc1_p5_sti_37 [r5_95]


title: PADLTD tumor 1

value: PADLTD

value: amp


title: NAT-CD [1_6]

description: Female

value: Control diet

value: Normal Embryo


title: BMDM_LPS_miRNA_005

value: adult

value: bone marrow derived macrophages (BMDM)

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


title: huc1_p5_sti_36 [r5_93]


title: NAT-CD [1_10]

description: Female

value: CF1 x B6SJF1/J cross

value: Natural Mating


title: PADMVB tumor 1

value: PADMVB

value: neuroblastoma

value: male


title: NAT-CD [1_5]

description: Female


title: PADIHC tumor 1

value: PADIHC

value: high

value: non-amp


title: huc1_p5_sti_34 [r5_89]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: huc1_p5_sti_35 [r5_90]


title: BMDM_PBS24_miRNA_004

value: female

value: PBS for 24hrs


title: NAT-CD [1_4]

description: Female

value: Control diet


title: BMDM_TcESLPS_miRNA_003

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


title: NAT-CD [1_3]

description: Female

value: Normal Embryo


title: BMDM_LPS_miRNA_001

value: adult

value: bone marrow derived macrophages (BMDM)

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


title: BMDM_PBS4_miRNA_000

value: PBS for 4hrs


title: NAT-CD [1_2]

description: Female

value: CF1 x B6SJF1/J cross

value: Natural Mating


title: huc1_p5_sti_33 [r5_88]


title: PAMLNB tumor 1

value: PAMLNB

value: neuroblastoma

value: male

value: low

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: huc1_p5_sti_32 [r5_84]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: NAT-CD [1_1]

description: Female

tag: tissue


title: PADWIM tumor 1

value: PADWIM

value: female

value: high

value: non-amp


title: PAKIAP tumor 1

value: PAKIAP


title: huc1_p5_sti_31 [r5_83]

tag: donor id


title: 87M

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

description:
LD
COUNTS_gem_andreas_macrophages.txt

data_processing:
RNA-seq were aligned with the RNA-seq GEM pipeline (http://gemtools.github.io/)
Genes annotated (gencode M2) were quantified with Flux Capacitor (http://sammeth.net/confluence/display/FLUX/Home)
Gene counts were normalized with the TMM method of the edgeR R package
Genome_build: GRCm38
Supplementary_files_format_and_content: Gencode M2 anntotated genes with raw counts

molecule: polyA RNA

source_name: Monocytic cells

growth_protocol: Six week-old C57BL/6 (male) mice were infected intraperitoneally with either 2x10E2 or 2x10E6 plaque forming units (pfu) of the strain Docile of LCMV to induce an acute or chronic infection, respectively.

extract_protocol:
Spleens were harvested and immersed in RNAlater prior to total RNA extraction by RNeasy Mini kit (Qiagen). Total RNA from splenic monocytic cells was directly extracted after cell sorting by RNeasy Micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Monocytic cells

tag: viral strain

value: LCMV 'Docile'

tag: infection dose

tag: day post-infection


title: MCF7KT80_rep3

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description:
total-RNA-seq
Library type: Unstranded

data_processing:
Paired-end reads were pseudo-aligned to the reference transcriptome using Kallisto v0.44.0 (PMID: 27043002).
Genome_build: cDNA Human Gencode v28 (GRCh38)
Supplementary_files_format_and_content: *.tsv: Transcripts abundances inferred using Kallisto.

source_name: ERα positive breast cancer cells

growth_protocol: MCF7 breast adenocarcinoma cell line and MCF7 overexpressing KRT80 were cultured in DMEM (Sigma-Aldrich) supplemented with 10% FCS (Foetal Calf Serum, First Link UK), 2 mM L-Glutamine, 100 units/mL penicillin, and 0.1 mg/mL streptomycin (Sigma) and further supplemented with 10-8 M Estradiol (Sigma).

extract_protocol:
Cells were washed with PBS and harvested using a cell lifter (Corning) in RLT buffer supplemented with 1% b-mercaptoethanol. Cell lysate was homogenized using QIAshredder columns (QIAGEN) and RNA extraction was performed with RNeasy Mini Kit (QIAGEN) following manufacturer´s instructions.
RNA-seq library preparation using NEBNext rRNA Depletion Kit (NEB #E6310) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following the manufacturer’s instructions.

treatment_protocol: Transfected MCF7 K80 cells, carrying Neomycin resistance, were selected with G418 (SIGMA), used at a final concentration of 1 mg/mL.

tag: cell line

tag: cell type

value: Breast adenocarcinoma cell line

tag: overexpression


title: huc1_p5_sti_30 [r5_81]

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

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.

tag: passage

tag: treatment


title: MCF7KT80_rep2

description:
total-RNA-seq
Library type: Unstranded


title: 86M

description:
LD
COUNTS_gem_andreas_macrophages.txt

tag: Sex


title: PADVWW tumor 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

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: usi

value: PADVWW

tag: gender

tag: cog risk

tag: inss stage

tag: mycn status


title: MCF7KT80_rep4

description:
total-RNA-seq
Library type: Unstranded


title: MCF7KT80_rep1

description:
total-RNA-seq
Library type: Unstranded


title: MCF7_rep4

description:
total-RNA-seq
Library type: Unstranded


title: huc1_p5_sti_29 [r5_80]


title: 91M

description:
HD
COUNTS_gem_andreas_macrophages.txt

tag: strain


title: BMDM_TcES_miRNA_002

tag: age

value: adult

value: bone marrow derived macrophages (BMDM)

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


title: PADTRV tumor 1

value: PADTRV

tag: tissue

value: neuroblastoma


title: huc1_p5_sti_27 [r5_77]

tag: donor id


title: 90M

description:
HD
COUNTS_gem_andreas_macrophages.txt

value: male

tag: viral strain

tag: infection dose


title: PADTTB tumor 1

value: PADTTB


title: PADMTD tumor 1

value: PADMTD

value: amp


title: MCF7_rep3

description:
total-RNA-seq
Library type: Unstranded

tag: cell line


title: PADUYJ tumor 1

value: PADUYJ

value: female


title: MCF7_rep2

description:
total-RNA-seq
Library type: Unstranded

tag: cell type


title: huc1_p5_sti_26 [r5_74]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: PADUWR tumor 1

value: PADUWR

value: high

value: non-amp


title: MCF7_rep1

description:
total-RNA-seq
Library type: Unstranded

value: Breast adenocarcinoma cell line


title: 80M

description:
HD
COUNTS_gem_andreas_macrophages.txt

value: Monocytic cells

value: LCMV 'Docile'

tag: day post-infection


title: huc1_p5_sti_25 [r5_73]

tag: passage


title: PADTJJ tumor 1

value: PADTJJ


title: 84M

description:
LD
COUNTS_gem_andreas_macrophages.txt


title: 125d31

description:
HD
COUNTS_gem_andreas_spleens.txt

source_name: Spleens

value: Spleens


title: huc1_p5_sti_28 [r5_78]

tag: treatment


title: 120d31

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: Sex


title: 124d31

description:
HD
COUNTS_gem_andreas_spleens.txt


title: PADTJY tumor 1

tag: usi

value: PADTJY

value: neuroblastoma


title: 118d31

description:
LD
COUNTS_gem_andreas_spleens.txt

value: male


title: PADKGF tumor 1

value: PADKGF

tag: gender


title: huc1_p5_sti_23 [r5_71]


title: PADKFU tumor 1

value: PADKFU

tag: cog risk


title: huc1_p5_sti_22 [r5_47]


title: PADRYN tumor 1

value: PADRYN

tag: inss stage

value: amp


title: huc1_p5_sti_20 [r5_44]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: 84d9

description:
HD
COUNTS_gem_andreas_spleens.txt


title: huc1_p5_sti_21 [r5_46]

value: IFNγ+TNFα


title: D2 PC9GR after Apatinib treatment

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

data_processing:
The data are processed by Annoroad RNA-seq pipeline. low quality reads are filtered, adaters are removed; cleaned reads are mapped to hg38 by HISAT2 v2.1.0.; Ensembl annotation (Homo_sapiens.GRCh38.89.chr) is used for gene expression quantification (HTSeq v0.6)  and the data is normalized by FPKM method
Genome_build: HG.GRCh38
Supplementary_files_format_and_content: fpkm.xls, FPKM expression

source_name: Human lung cancer cell line

growth_protocol: RPMI-1640 complete medium (BI, Israel) containing 10% FBS (5% CO2, 37°C) and cultured according to the protocol

extract_protocol:
Total RNA extraction was performed using Exiqon’s miRCURY RNA Isolation Kit.
PolyA enriched mRNA sequencing from both end; the pair end sequencing was carried out using the Illumina HiSeq X Ten sequencer at 150bps.

treatment_protocol: 8 μM Apatinib treatment for 48hrs

value: Gefitinib-resistant lung cancer cell line

tag: group

value: PC9GR after apatinib treatment


title: 81d9

description:
HD
COUNTS_gem_andreas_spleens.txt

tag: strain


title: D3 PC9GR after Apatinib treatment


title: D1 PC9GR after Apatinib treatment


title: PADPRJ tumor 1

value: PADPRJ

value: high

tag: mycn status

value: non-amp


title: huc1_p5_sti_19 [r5_42]


title: huc1_p5_sti_24 [r5_72]


title: C3 PC9GR cells


title: PADSXU tumor 1

value: PADSXU

tag: tissue

value: female


title: huc1_p5_sti_18 [r5_41]

tag: donor id


title: 77d9

description:
LD
COUNTS_gem_andreas_spleens.txt

value: Spleens

tag: viral strain

value: LCMV 'Docile'


title: C2 PC9GR cells


title: PADSXE tumor 1

value: PADSXE

value: neuroblastoma


title: PAKINP tumor 1

value: PAKINP

value: low

tag: ploidy

value: hyperdiploid (>1.0)

tag: ploidy value


title: huc1_p5_sti_17 [r5_40]

tag: cell type


title: 64d7

description:
HD
COUNTS_gem_andreas_spleens.txt

value: male

tag: infection dose

tag: day post-infection


title: exposure to AB-Fe complex

city: Padua

first: Karina

last: Fincati

address: V.le G. Colombo, 3

department: Department of Biology, University of Padua

country: Italy

institute: CNR-Institute for Biomedical Technologies

description: In all hybridizations SH-SY5Y cell culture was used as control for direct comparison to the experimental conditions: expoure to AB-Fe

hyb_protocol: Labeled aRNA was dissolved in 90 ul of hybridization buffer, denaturated at 90ºC for 3 min and applied directly to microarray slides. Microarray hybridization was carried out in an ArrayBooster Hybridization Station. The reaction was carried out overnight at 42ºC. Posthybridization washing was performed according to the microarray slides manufacturer’s instructions.

scan_protocol: The microarrays slides were scanned using a GenePix 4000B laser scanner  and images were processed using Genepix 6.0 software.

data_processing: Data analysis  were performed using Acuity 4.0 software. Initial results were normalized using Lowess algorithm and filtered to exclude extreme outliers and flags. We also excluded any spots that had no detectable response on all slides. The log-ratios of expression were calculated as the base 2 logarithm of the ratios of background-corrected intensity medians of red dye over green dye intensities. In order to obtain a single expression value for each gene, the internal replicates (1 to 14) were plotted versus the technical replicates (6 for exposure to AB and 2 for exposure to AB-Fe complex and Fe ). The X-Y scatterplot confirmed that the data were generally reproducible but we observed the presence of extreme outliers values. Then we excluded the outliers and the values of spots replicates within and among arrays were averaged using a trimmed mean. We excluded any spot that had no detectable response in all three treatments. Consequently, the final dataset was composed of 2814 genes.

label: Alexa Fluor 555, Alexa Fluor 647

source_name: human neuroblastoma cells culture

label_protocol: 1 ug of total RNA was amplified following the SuperscriptTM Indirect RNA Amplification System Kit (InvitrogenTM): total RNA was reverse transcribed into single-stranded complementary DNA (cDNA) using oligo(dT) primer containing a T7 promoter and Superscript III reverse transcriptase. RNase H was then added together with E. coli DNA polymerase I and E. coli DNA ligase, followed by a short incubation in order to achieve synthesis of the second-strand cDNA. The purified double-strand cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase. This step generated antisense RNA (aRNA) molecules complementary to the original mRNA targets, incorporating amino-allyl UTP (aa-UTP) into the aRNA. 10 ug of purified aRNA was coupled with Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen) according to the manufacturer’s instructions.

growth_protocol: SH-SY5Y human neuroblastoma cells were purchased from ECACC. SH-SY5Y human neuroblastoma cells were maintained in Dulbecco’s modified Eagle’s medium (1: 1) with L-Glutamine and 15 mM Hepes at 37 °C with 5% CO2 in a humidified atmosphere (90 % humidity). The medium was replaced every 2 days. Penicillin (100 units/ml) and streptomycin (100 ug/ml), 15 % fetal bovine serum, and MEM non-essential amino acids (100x) were added to the medium. 0.25% Trypsin-EDTA solution and phosphate buffered saline (PBS) were obtained from Sigma Aldrich. SHSY5Y cells were plated onto 6-well plates.

extract_protocol: Total RNA of SH-SY5Y human neuroblastoma cells exposed to AB,  AB-metal complexes (AB-Fe) and Fe was isolated using the Qiagen RNA/DNA Mini Kit following the manufacturer’s instructions.

treatment_protocol: The day after this plating, the culture medium was replaced with the same medium with 2 % FBS containing AB or AB-metal complexes at 0.5 uM peptide concentration. The cells were incubated with different AB or AB-metal complexes for 24h. The cell treatment was also performed in the presence of metals (Fe) at a concentration 10-fold higher than the peptide concentration.

tag: cell line

tag: treatment

value: B-amyloid aluminum complex and Fe

source_name: human neuroblastoma cells exposed to AB-Zn complex

value: control


title: PAKANZ tumor 1

tag: usi

value: PAKANZ


title: 63d7

description:
HD
COUNTS_gem_andreas_spleens.txt

tag: Sex


title: huc1_p5_sti_16 [r5_39]

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

value: IFNγ+TNFα


title: B3 PC9 after Apatinib treatment

value: Gefitinib-sensitive lung cancer cell line

value: PC9 after apatinib treatment


title: exposure to Fe

description: In all hybridizations SH-SY5Y cell culture was used as control for direct comparison to the experimental conditions: expoure to Fe

value: Fe

source_name: human neuroblastoma cells exposed to Zn


title: exposure to AB for AB-Fe dataset

description: In all hybridizations SH-SY5Y cell culture was used as control for direct comparison to the experimental conditions: expoure to AB

value: B-amyloid aluminum complex

source_name: human neuroblastoma cells exposed to AB


title: huc1_p5_sti_15 [r5_38]


title: B2 PC9 after Apatinib treatment


title: 62d7

description:
LD
COUNTS_gem_andreas_spleens.txt

value: Spleens


title: PACVXN tumor 1

source_name: neuroblastoma

value: PACVXN

tag: gender

tag: cog risk

value: high

tag: inss stage

value: non-amp


title: huc1_p5_sti_14 [r5_37]


title: 61d7

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: strain

value: LCMV 'Docile'


title: PACVNB tumor 1

value: PACVNB

tag: tissue

value: neuroblastoma

value: female

tag: mycn status


title: B1 PC9 after Apatinib treatment

tag: group


title: A3 PC9 cells


title: huc1_p5_sti_13 [r5_36]

tag: donor id


title: 55d6

description:
HD
COUNTS_gem_andreas_spleens.txt

value: male

tag: viral strain


title: 78d9

description:
LD
COUNTS_gem_andreas_spleens.txt


title: PACYGY tumor 1

value: PACYGY


title: PACXHH tumor 1

value: PACXHH


title: A2 PC9 cells

tag: cell type


title: huc1_p5_sti_12 [r5_35]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: 54d6

description:
HD
COUNTS_gem_andreas_spleens.txt

tag: infection dose


title: 51d6

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: day post-infection


title: huc1_p5_sti_11 [r5_33]

value: IFNγ+TNFα


title: A1 PC9 cells

tag: cell line

value: Gefitinib-sensitive lung cancer cell line


title: PACUGP tumor 1

value: PACUGP


title: 49d6

description:
LD
COUNTS_gem_andreas_spleens.txt


title: C1 PC9GR cells

value: Gefitinib-resistant lung cancer cell line


title: huc1_p5_sti_9 [r5_29]

tag: treatment


title: 141_8h

city: Beijing

first: Zongmin

last: Du

address: No. 20, Fengtai Dongdajie Street

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
BWA (Burrows-Wheeler Aligner) (Li et al., 2009) was used to map clean reads to the mouse reference genome (NCBI37/mm9) and Bowtie1 (Langmead et al., 2009) was used to map clean reads to reference gene.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tar archives with text files that contain FPKM values and differential expression statistics.

source_name: human peripheral  lymphocytes

growth_protocol: Human peripheral lymphocytes were isolated from the whole blood collected from 5 healthy donors using Ficoll-Paque Plus. The purified lymphocytes were maintained in RPMI-1640 supplemented with 10% FBS and 2 mmol/L L-glutamine at 37 C in a 5% CO2 incubator.

extract_protocol:
Total RNA were purified from the lymphocytes infected with 201  or 141 strain using a TRIzol reagent (Invitrogen, USA) and treated with RNAse free DNase I (Thermo Fisher Scientific, USA).  Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano kit were used to detect RNA integrity number, rRNA ratio (28S/18S), and the concentration of the total RNA samples.
Sequencing libraries were prepared using Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol. In brief, the first-strand cDNA was generated by First Strand Master Mix and SuperScript II (Invitrogen) reverse transcription using random primers and the second-strand cDNA was synthesized by using DNA polymerase I and RNase H. The fragmented cDNA molecules were end-repaired and purified and ligated with PloyA adaptor.

treatment_protocol: Human peripheral lymphocytes were infected with 201 or 141 bacteria at MOI of 10. The infected lymphocytes as well as the uninfectecd cells were  collected at  2, 4 and 8 hours post infection.

tag: bacterial strain used in infection

value: Antiqua strain

tag: hours post infection

value: peripheral lymphocytes


title: Normal

value: No infection


title: PACRYY tumor 1

tag: usi

value: PACRYY

value: high


title: huc1_p5_sti_8 [r5_28]

tag: passage


title: 43d5

description:
HD
COUNTS_gem_andreas_spleens.txt

value: Spleens

tag: Sex

value: LCMV 'Docile'


title: PACSAS tumor 1

value: PACSAS

value: neuroblastoma

tag: gender


title: 41d5

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: strain

value: male


title: huc1_p5_sti_6 [r5_26]


title: 141_4h


title: PALVKK blood 1

value: PALVKK

tag: tissue

value: blood

value: female

tag: cog risk

tag: inss stage

value: non-amp

tag: ploidy

value: diploid (=1.0)

tag: ploidy value


title: huc1_p5_sti_7 [r5_27]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: 201_8h

value: Microtus strain


title: 26d3

description:
HD
COUNTS_gem_andreas_spleens.txt

tag: viral strain

tag: infection dose

tag: day post-infection


title: huc1_p5_sti_5 [r5_25]

tag: treatment


title: PALVDR blood 1

value: PALVDR

value: low

tag: mycn status

value: hyperdiploid (>1.0)


title: 38d5

description:
LD
COUNTS_gem_andreas_spleens.txt


title: PALXSU blood 1

tag: usi

value: PALXSU

value: intermediate


title: 141_2h

tag: bacterial strain used in infection

value: Antiqua strain

tag: hours post infection

value: peripheral lymphocytes


title: huc1_p5_sti_4 [r5_24]

tag: passage


title: huc1_p5_sti_10 [r5_32]


title: 201_2h


title: huc1_p5_sti_3 [r5_23]


title: PALYPW blood 1

value: PALYPW

tag: gender

value: high


title: 201_4h


title: huc1_p5_sti_2 [r5_22]


title: 22d3

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: tissue

value: Spleens

tag: strain

tag: Sex

value: male

value: LCMV 'Docile'


title: 46d5

description:
HD
COUNTS_gem_andreas_spleens.txt


title: PALJVX tumor 1

value: PALJVX

value: neuroblastoma

tag: cog risk

tag: inss stage

value: non-amp

tag: ploidy


title: AN-h-input

data_processing:
Aligned with bwa 0.5.9
Peaks called with Macs 1.4.1
Genome_build: GRch37
Supplementary_files_format_and_content: bed files; scores represent enrichments for given peaks

source_name: cell line LNCaP

growth_protocol: Cells were cultured in phenol red-free RPMI media supplemented with 10% charcoal dextran-stripped FBS for 72 hours before adding 1 nM R1881 or 0.01% ethanol (vehicle control) for 4 hours.

extract_protocol:
Genomic DNA was isolated using phenol:chloroform:isopropanol (25:24:1, Invitrogen), back-extracted with 200ul of TE, precipitated with isopropanol, washed with 75% ethanol, air-dried and resuspended in 60ul 10mM Tris-HCl pH 8.
TruSeq ChIP kit from Illumina

treatment_protocol: For hypoxic experiments, cells were placed in a hypoxic incubator at 1% oxygen for 12 hours prior to the addition of R1881 or ethanol.

tag: input?

value: input


title: huc1_p5_sti_1 [r5_19]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

value: IFNγ+TNFα


title: AN-n-input


title: 2_2d0

description:
non-infected
COUNTS_gem_andreas_spleens.txt

tag: viral strain

tag: infection dose

tag: day post-infection


title: ET-H-ME3

value: N

value: Y

tag: chip antibody

tag: target protein


title: ET-N-ME3


title: huc1_p5_ctrl_52 [r6_96]

tag: treatment

value: naïve


title: PAIXLC tumor 1

tag: usi

value: PAIXLC

value: low

tag: mycn status

value: hyperdiploid (>1.0)

tag: ploidy value


title: PALLJJ tumor 1

value: PALLJJ

tag: tissue

tag: gender

value: female


title: 25d3

description:
HD
COUNTS_gem_andreas_spleens.txt

value: Spleens

tag: strain

tag: Sex


title: 1_2d0

value: male


title: AN-H-ME3


title: PALKKV tumor 1

value: PALKKV

tag: cog risk

tag: inss stage

tag: ploidy


title: huc1_p5_ctrl_50 [r6_90]

tag: donor id

tag: cell type

tag: passage


title: Mst1/2 liver-dKO (replicate 2)

city: Boston

first: Wantae

last: Kim

state: Massachusetts

address: 188 Longwood Ave.

institute: Harvard School of Dental Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
All reads were delivered, including those that did not pass-filter.
Genome_build: mm9 using ELAND
Supplementary_files_format_and_content: tab-delimited text files for each sample

source_name: Mst1/2 liver-dKO_liver

extract_protocol:
Total RNA from mouse liver tissue was prepared using Rneasy mini kit (Qiagen) according to the manufacturer's protocol. Six total RNA samples were submitted to NIH Intramural Sequencting Center (NISC) for Sequencing using established Illumina TruSeq RNA Sample Prep Kit protocols. RNA libraries were prepared for sequencing using standard Illumina protocols.
Poly-A enrichment of mRNA was performed from 1 microgram of total RNA using the mRNA Purification Kit (Invitrogen). The mRNA was sheared to ~200 bases using a Covaris E210.  First strand synthesis was performed using random hexamers and SuperScript II (Invitrogen) followed by second strand synthesis with DNA polymerase I, dNTPs and RNAseH.  cDNAs were cleaned up using QIAquick PCR Clean Up kit (Qiagen). Illumina libraries were constructed using the SPRI-TE robot and reagents (Beckman) and paired-end Illumina adapters.  The libraries were size-selected for ~400 bp fragments on a Pippin Prep (Sage Science) followed by PCR amplification using Phusion PCR Master Mix (New England Biolabs). The libraries were cleaned up using QIAquick PCR Clean Up kit.

tag: strain background

tag: genotype/variation

value: Mst1-/-; Mst2fl/fl; alb-Cre+/+

tag: age

value: Liver


title: huc1_p5_ctrl_49 [r6_83]

city: shanghai

first: Yufang

last: Shi

address: 320 Yueyang Road

institute: Chinese Academy of Science

tag: treatment


title: 23d3

description:
LD
COUNTS_gem_andreas_spleens.txt

tag: viral strain

value: LCMV 'Docile'

tag: infection dose

tag: day post-infection


title: Mst1/2 liver-dKO (replicate 3)

tag: tissue


title: AN-N-ME3

tag: chip antibody

tag: target protein


title: PALUST tumor 1

city: New York

first: Gonzalo

last: Lopez

address: 1399 Park avenue

institute: Mount Sinai School of Medicine

tag: usi

value: PALUST

value: neuroblastoma

tag: gender

tag: mycn status

value: non-amp

tag: ploidy value


title: Mst1/2 liver-dKO (replicate 1)


title: PALVUC tumor 1

value: PALVUC

tag: cog risk

tag: inss stage

tag: ploidy


title: ET-H-ME1

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

value: N

value: Y


title: PAKHAV tumor 1

value: PAKHAV


title: control (replicate 3)

tag: strain background

value: Mst1-/-; Mst2fl/fl; alb-Cre-/-


title: ET-N-ME1


title: huc1_p5_ctrl_47 [r6_73]

tag: donor id

tag: cell type

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

value: naïve


title: PAMHDM tumor 1

value: PAMHDM

value: high

value: hyperdiploid (>1.0)


title: huc1_p5_ctrl_48 [r6_80]

tag: treatment


title: control (replicate 2)

tag: genotype/variation

tag: age


title: AN-H-ME1


title: huc1_p5_ctrl_46 [r6_47]


title: huc1_p5_ctrl_51 [r6_95]


title: huc1_p5_ctrl_45 [r6_45]


title: AN-N-ME1


title: control (replicate 1)

tag: tissue


title: ET-H-HIF

tag: chip antibody


title: NSC-derived tumour cells - NF1_3

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

data_processing:
Alignment: STAR 2.5.2a
Transcript quantification: htseq-count
Differential expression: DESeq2 (1.8.2)
GAGE gene set analysis: GAGE (2.18.0)
Genome_build: GRCm38/mm10

source_name: Subventricular Zone

growth_protocol: Cells were cultured in NSC standard culture for up to 10 passages

extract_protocol:
RNA was isolated by using RNAeasy Plus Mini Kit (Qiagen).
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

value: NSC-derived tumour cells

tag: genotype


title: PALNFE tumor 1

tag: usi

value: PALNFE

value: female

value: low


title: huc1_p5_ctrl_44 [r6_44]

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.


title: PALEBK tumor 1

value: PALEBK

tag: gender

value: male


title: NSC-derived tumour cells - NF1_1


title: AN-H-HIF

tag: target protein


title: huc1_p5_ctrl_43 [r6_43]


title: ET-N-HIF


title: NSC-derived tumour cells - LTR3

value: lgT/Ras


title: huc1_p5_ctrl_42 [r6_41]


title: PALXUM tumor 1

value: PALXUM

value: neuroblastoma

tag: mycn status

value: non-amp

tag: ploidy value


title: PALFSE tumor 1

value: PALFSE

tag: cog risk

tag: inss stage


title: huc1_p5_ctrl_41 [r6_40]


title: NSC-derived tumour cells - LTR2


title: PALVVH tumor 1

value: PALVVH

tag: ploidy


title: AN-N-HIF

value: Y

value: N


title: NSC-derived tumour cells - LTR1


title: ET-H-AR

value: AR N20

value: AR


title: ET-N-AR


title: PALPIN tumor 1

value: PALPIN

value: hyperdiploid (>1.0)


title: PALFIT tumor 1

value: PALFIT

value: high

value: diploid (=1.0)


title: PAIVRB tumor 1

value: PAIVRB

value: low


title: huc1_p5_ctrl_39 [r6_36]

tag: donor id

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: PAIVMJ tumor 1

value: PAIVMJ

value: neuroblastoma

value: male


title: NSC-derived tumour cells - NF1_2

tag: cell type

value: NSC-derived tumour cells


title: huc1_p5_ctrl_38 [r6_32]

tag: passage


title: PAKPLH tumor 1

value: PAKPLH

value: female

value: non-amp


title: AN-H-AR

value: Y

value: AR N20

value: AR


title: primary NSC - 3

value: primary NSC

value: wild type


title: huc1_p5_ctrl_37 [r6_27]

tag: treatment


title: primary NSC - 5


title: PAKRKL tumor 1

value: PAKRKL

value: hyperdiploid (>1.0)


title: primary NSC - 1


title: H3K9me2_shKDM3A_ChIPSeq

city: Merced

first: Fabian

middle: Volker

last: Filipp

state: California

address: 5200 North Lake Road

department: Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology

institute: University of California Merced

data_processing:
Sequenced regions were aligned to the reference human genome 19 using the Bowtie alignment program that utilizes an extended Burrows-Wheeler indexing for an ultrafast memory efficient alignment. Peak calling utilized a model-based analysis of ChIP-Seq (MACS) algorithm. The overlap analysis, plot of genomic location, sequence extraction, motif identification, and peak filtering were performed using ChIPseek: a web-based analysis for ChIP data. ChIPseek also employs scripts from BEDtools using a genome binning algorithm used by the UCSC genome browser to sort genomic regions into groups along the length of chromosome. Data visualization was carried out using the integrative genomics viewer.
ChIP-Seq reads were aligned to the hg19 genome assembly using bowtie version 1.1.2 with the following configurations: -q -S -m 1 -n 2
ChIP-Seq peaks were called using MACS version 1.4.4 with default settings
Genome_build: HG19
Supplementary_files_format_and_content: wig files and xls files were generated using MACS 1.4.4; wig scores represent fragment pileup. Xls active peak files contain number of tags, -10*log10(pvalue) for the peak region, fold enrichment, and FDR

growth_protocol: CWR22Rv1 is a human prostate carcinoma epithelial cell line derived from a xenograft that was serially propagated in mice after castration-induced regression and relapse of the parental, androgen-dependent CWR22 xenograft (CRL-2505, American Type Culture Collection, Manassas, VA). The CWR22Rv1 prostate cancer cell line was kindly provided by Dr. James Jacobberger (Case Western Reserve University, Cleveland, OH), and are maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and antibiotics. Cell cultures are regularly tested to ensure absence of mycoplasma. The CWR22Rv1 prostate cancer cell line expresses AR full-length with a duplicated DNA binding domain in exon 3 and AR splice variants, for example AR-v7, lacking a ligand binding domain. Thus, the CWR22Rv1 cell line displays constitutively active AR even in the absence of androgen. In the ChIP-Seq study ChIP-grade antibodies against H3K9me1 (ab9045, Abcam, Cambridge, MA), H3K9me2 (07-441, Sigma EMD Millipore, Darmstadt, Germany), KDM3A (A301-539A, Bethyl Laboratories, Montgomery, TX), or AR (PG21, 06-680, Sigma EMD Millipore, Darmstadt, Germany) were used. The AR antibody recognizes both forms of the AR. All experimental protocols were approved by the Institutional Review Board at the University of California Merced. The study was carried out as part of IRB UCM13-0025 of the University of California Merced and as part of dbGap ID 5094 on somatic mutations in cancer and conducted in accordance with the Helsinki Declaration of 1975.

extract_protocol:
Cells were crosslinked using 1% formaldehyde for 10 min at 298 K. Formaldehyde was removed and cells were incubated with 125 mM glycine for 5 min at 298 K. Nuclear extracts were collected and sonicated to obtain 300 bp chromatin fragments using the Covaris S2 ultrasonicator (Covaris, Woburn, MA). 100 µg of chromatin was incubated with 5 µg of AR (PG21, 06-680, Sigma EMD Millipore, Darmstadt, Germany), 5 µg of KDM3A (A301-538A, Bethyl Laboratories, Montgomery, TX), 2 µg of H3K9me1 (ab9045, Abcam, Cambridge, MA), or 2 µg of H3K9me2 (07-441, Sigma EMD Millipore, Darmstadt, Germany) antibodies overnight at 277 K followed by incubation with 30 µl of protein A/G beads for 4 hours. After four washes, crosslinking was reversed. Chromatin was digested with ribonuclease A followed by proteinase K. Then the DNA was purified using spin columns. The size of the DNA was confirmed by a bioanalyzer (Agilent Biotechnologies, Savage, MD).
The purified DNA library was sequenced using an Illumina HighSeq2000 at the Sanford-Burnham Medical Research Institute at Lake Nona, National Genome Library Core Facility.

treatment_protocol: Lentiviral vectors encoding KDM3A small hairpin RNA (shRNA), AR shRNA or lentiviral pLKO.1 control shRNA were purchased from Open Biosystems (GE Healthcare Dharmacon, Lafayette, CO), and packaged in human embryonic kidney 293T cells (CRL-3216, American Type Culture Collection, Manassas, VA) by calcium phosphate transfection. The supernatant containing lentiviral particles were collected 48 hours after transfection. CWR22Rv1 cells were transduced with the supernatant of lentiviral particles in the presence of polybrene (8 µg/ml) for 24 hours before replacement with the fresh growth media. Cells were analyzed at 72 hours post-transduction. The knockdown efficiency was confirmed by quantitative real time polymerase chain reaction (qRT-PCR) and Western-blot analysis.

tag: cell line

tag: antibody


title: AN-N-AR

value: N


title: huc1_p5_ctrl_40 [r6_38]

value: umbilical cord derived mesenchymal stem cell (MSC)


title: huc1_p5_ctrl_36 [r6_24]

value: naïve


title: PALWSJ tumor 1

value: PALWSJ

tag: tissue

value: low


title: huc1_p5_ctrl_35 [r6_22]


title: huc1_p5_ctrl_34 [r6_20]


title: AR_shKDM3A_ChIPSeq

source_name: human prostate carcinoma epithelial cell line

value: AR (PG21, 06-680, Sigma EMD Millipore, Darmstadt, Germany)


title: PAKWMT tumor 1

value: PAKWMT

value: neuroblastoma

value: high


title: PALWRG tumor 1

value: PALWRG

value: male

value: non-amp


title: H3K9me1_shKDM3A_ChIPSeq

value: H3K9me1 (ab9045, Abcam, Cambridge, MA)


title: huc1_p5_ctrl_33 [r6_19]


title: RNA_tgILC1_infected_rep5

city: Saint Louis

first: Eugene

last: Park

state: MO

address: 4616 Lindell Blvd, Apt 201

institute: Washington University

data_processing:
Basecalls performed with CASAVA
ATAC-seq: reads were aligned to mm10 using Bowtie2, samtools was used to filter reads with q<30, and PicardTools was used to remove duplicate reads. Peaks were called with default commands in MACS2 and -q 0.05
RNA-seq: pseudoalignments to mm10 and abundance measurements with kallisto
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq: bigwig files; RNA-seq: abundance tsv files

source_name: splenic ILC1

extract_protocol: the RNA was extracted from 50,000 sorted cells using Trizol. Libraries were prepared using the Clontech SMARTer Kit. Sequencing was with 1x50 single end reads on an Illumina HiSeq 3000 instrument.

value: spleen

tag: strain

tag: infection status

value: infected d35


title: RNA_tgILC1_infected_rep4


title: Control_shKDM3A_ChIPSeq


title: KDM3A_shKDM3A_ChIPSeq

value: KDM3A (A301-538A, Bethyl Laboratories, Montgomery, TX)


title: PAKSWB tumor 1

tag: usi

value: PAKSWB

value: hyperdiploid (>1.0)


title: RNA_tgILC1_infected_rep3


title: RNA_tgILC1_infected_rep2


title: PAMVAG blood 2

value: PAMVAG

value: blood

tag: gender

value: diploid (=1.0)


title: H3K9me1_pLKO.1_ChIPSeq


title: RNA_tgILC1_infected_rep1


title: huc1_p5_ctrl_30 [r6_16]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc1_p5_ctrl_29 [r6_15]


title: AR_pLKO.1_ChIPSeq

value: AR (PG21, 06-680, Sigma EMD Millipore, Darmstadt, Germany)


title: PAKWWF tumor 1

value: PAKWWF

value: neuroblastoma


title: KDM3A_pLKO.1_ChIPSeq


title: RNA_cNK_infected_rep5

source_name: splenic cNK

value: cNK


title: PAKYRJ blood 1

value: PAKYRJ

value: male

value: low


title: PACSNL tumor 1

value: PACSNL

value: female

value: high

value: non-amp


title: RNA_cNK_infected_rep4

value: spleen

value: infected d35


title: PAKXIA blood 1

value: PAKXIA

value: blood

value: hyperdiploid (>1.0)


title: Control_pLKO.1_ChIPSeq


title: PAMJKM blood 1

value: PAMJKM


title: 377746

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

hyb_protocol: Hybridization was performed at 42 °C for at least 40 hours after pooling of Cy5- and Cy3-labeled samples for each array. Subsequent to hybridization, the slides were washed in three SDS/SSC wash buffers of stepwise lower stringency.

scan_protocol: Microarrays were scanned using the Axon GenePix 4400A microarray scanner (MDS Analytical Technologies, Sunnyvale, California)

data_processing: Manual processing of data was carried out in GenePix Pro 6.1 to identify possible major issues. Subsequent analysis was carried out in the R environment using the following packages: Bioconductor bundle, Limma, Aroma, KTH. Print-tip lowess was used for normalization and empirical Bayes t-test for statistical analysis.

label_protocol: Labeling was carried out with aminoallyl-modified dUTP incorporated during cDNA synthesis using Superscript III (Invitrogen). Incubation with Cy3 or Cy5 monoreactive NHS-ester for 30 min.

growth_protocol: HC11 mammary epithelial cells were grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, 5mg/mL insulin, 10ng/mL epidermal growth factor (EGF) and 50mg/mL gentamicin; all cell culture reagents were purchased from Sigma.

extract_protocol: Total RNA was extracted using Trizol precipitation and purified using Qiagen RNeasy Mini Kit followed by an on-column DNase1 digestion (Qiagen, Valencia, CA). Quantitative and qualitative analysis of RNA was performed on the NanoDrop 1000 spectrophotometer (Thermoscientific) and the Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: HC11 mammary epithelial cells were grown in RPMI 1640 supplemented with 10% FBS, L-glutamine, 5mg/mL insulin, 10ng/mL epidermal growth factor (EGF) and 50mg/mL gentamicin. Proliferating cells were transfected with either 25nM miRNA206 mimic or NC mimic twice with 24 hour intervals, cells collected 24h after second transfection

value: mouse mammary stem-like cells

tag: differentiation stage

value: proliferation stage

tag: treated with

source_name: HC11_NC mimic

value: NC mimic


title: RNA_cNK_infected_rep2

value: cNK


title: huc1_p5_ctrl_26 [r6_10]

value: umbilical cord derived mesenchymal stem cell (MSC)

value: naïve


title: huc1_p5_ctrl_32 [r6_18]


title: 377745


title: huc1_p5_ctrl_27 [r6_11]


title: RNA_cNK_infected_rep3


title: H3K9me2_pLKO.1_ChIPSeq

value: H3K9me2 (07-441, Sigma EMD Millipore, Darmstadt, Germany)


title: PAIDJS tumor 1

value: PAIDJS

value: neuroblastoma

value: male

value: low

tag: mycn status

tag: ploidy value


title: PALNLU blood 1

value: PALNLU

tag: cog risk

value: high

tag: inss stage

value: non-amp


title: huc1_p5_ctrl_31 [r6_17]

tag: donor id


title: huc1_p5_ctrl_25 [r6_9]

tag: cell type


title: PALEND blood 1

value: PALEND

value: blood

value: amp

tag: ploidy

value: diploid (=1.0)


title: RNA_cNK_infected_rep1

value: spleen

value: infected d35


title: RNA_cNK_uninfected_rep3

value: cNK

value: uninfected


title: huc1_p5_ctrl_24 [r6_7]

value: umbilical cord derived mesenchymal stem cell (MSC)

tag: passage

tag: treatment

value: naïve


title: huc1_p5_ctrl_28 [r6_14]


title: RNA_cNK_uninfected_rep2


title: RNA_cNK_uninfected_rep1


title: 3T3-p53-Q3

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Basecalls performed using CASAVA version 1.8
The RNA-seq sequence reads were mapped to mouse genome assembly mm10 using open source RNA-seq alignment tool HISAT2 (ver 2.0.4)
The alignment results were converted to RNA-seq gene expression measurement as RPKM (reads/kilo base of total exon length/million mapped) using Partek Genome Suite (version 6.6) with NCBI RefSeq database.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

source_name: MEF p53 null_Glutamine-free

growth_protocol: Cell lines cultured in standard (25 mM glucose, 2 mM L-glutamine) DMEM

extract_protocol:
RNA from cell culture was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit V2 was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared with TruSeq SR Cluster V3 kits (Illumina).

treatment_protocol: Cell lines were cultured in two conditions using DMEM without L-glutamine (glutamine-free) or with 2 mM L-glutamine added into the DMEM (control) for 18 hours

tag: cell line

value: mouse embryonic fibroblast (MEF)

tag: genotype/variation

tag: culture condition


title: PAMKHK blood 1

value: PAMKHK

tag: tissue

value: female

value: hyperdiploid (>1.0)


title: 3T3-p53-Q2

value: DMEM without L-glutamine (glutamine-free)


title: PAKSFV blood 1

tag: usi

value: PAKSFV

value: male

value: high


title: huc1_p5_ctrl_21 [r6_4]


title: 3T3-p53-Com3

source_name: MEF p53 null_complete

value: DMEM + 2 mM L-glutamine


title: PAMKZW blood 1

value: PAMKZW

value: blood

tag: gender

value: amp


title: huc1_p5_ctrl_19 [ctr_s_60]


title: huc1_p5_ctrl_20 [ctr_s_66]


title: mMSC shlSLR no.1

city: Nagoya

first: Yasuyuki

last: Mizutani

state: Aichi

address: showa-ku, turumai-cho, 65

department: Gastroenterology

country: Japan

institute: Nagoya University Graduate School of Medicine

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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D).

data_processing: The scanned images were analyzed with  Agilent Feature Extraction (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: mMSC shlSLR no.1

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, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using RLT buffer (Qiagen) and an RNeasy Mini Kit (Qiagen) and was treated with RNase-free DNase (Qiagen).

treatment_protocol: Three different target sequences used for shRNA-mediated knockdown of mouse Meflin. These Meflin shRNAs were transduced to primary cultured mouse MSCs by a retroviral expression system

value: primary MSCs


title: mMSC shlSLR no.3

source_name: mMSC shlSLR no.3


title: mMSC shControl

source_name: mMSC_ISLR　shControl


title: 3T3-p53-Com2