title: Natural_Adult HCMV Low

description:
Clinical samples pooled from four adults (avg. age 31) with low HCMV ab titers
Raw_natural.txt
FPKM13.txt

source_name: peripheral blood mononuclear cells, Clinical samples pooled from four adults (avg. age 31) with low HCMV ab titers


title: F1-FB-Input

status: Public on Dec 04 2017

type: SRA

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

country: USA

institute: Stanford University School of Medicine

library_source: genomic

data_processing:
ChIP-seq: bowtie -p 4 -q -m 1 -v 3 --sam --best --strata /data/bowtie_index/hg38
RNA-seq: hisat -x hg38 -1 R1.fq.gz -2 R2.fq.gz  -S R.sam
Genome_build: hg38
Supplementary_files_format_and_content: Text files. ChIP-seq: Raw read counts for specific loci. RNA-seq: DESeq2 normalized log2 transformed reads.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human induced pluripotent stem cells (iPSCs) were maintained in mTeSR-1 medium (STEMCELL Technologies) on Matrigel-coated plates. Endothelial cells (ECs) were maintained on 0.1% gelatin-coated plates with EGM-2 medium (Lonza). Cardiac progenitor cells (CPCs) were cultured on 0.1% gelatin-coated dishes in M199 (Gibco)/EGM-2  (3:1) medium supplemented with 10% FBS, 10 ng/ml basic fibroblast growth factor (bFGF, PeproTech), 5 ng/ml epithelial growth factor (EGF, PeproTech), 5 ng/mL insulin-like growth factor (IGF-1, PeproTech), and 5 ng/ml hepatocyte growth factor (HGF, PeproTech). Fibroblast cells (FBs) were cultured in DMEM medium (Gibco) supplemented with 10% FBS (Hyclone) and GlutaMax (Gibco).

extract_protocol:
Total RNAs were extracted by RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were generated using the NuGEN Encore Complete RNA-seq Library Systems (Part No. 0311, NuGEN). Chromatin immunoprecipitation were performed using approximately 1x10^7 cells of human iPSCs, fibroblasts, endothelial cells, and cardiac progenitor cells. Cells were first cross-linked with 1% formaldehyde for 10 min at RT, and formaldehyde was quenched by glycine with a final concentration of 0.125 M. Chromatin was broken into small pieces with an average size of 0.5-2 kb using the Bioruptor (Diagenode). The sonicated chromatin was then incubated with 3-5 μg of primary antibodies overnight at 4°C. A small portion (10%) of chromatin without antibody incubation was kept as input DNA for each ChIP reaction. Subsequently, 75 μl of Dynabeads Protein A or Protein G were added and incubator for 4 h at 4°C with overhead shaking. Magnetic beads were then washed away and chromatin was eluted. Crosslink was then reversed and precipitated DNA was purified and resuspended in nuclease-free water. Sequencing libraries of immunoprecipitated DNA and input DNA were constructed according to an Illumina DNA library preparation protocol.

treatment_protocol: Different human cell types: CiPSCs, EiPSCs, FiPSCs, CPCs, ECs, and FBs.

tag: cell type

value: Fibroblast cells (FBs)

tag: passage


title: Donor 3_∆UL135 6dpi SS

city: Tucson

first: Janko

last: Nikolich-Zugich

state: AZ

address: 1656 E. Mabel St.

institute: University of Arizona

description:
∆UL135 HCMV infected 6 days
Raw_donor_NSSS14.txt

library_source: transcriptomic

data_processing:
Raw sequencing data was de-multiplexed and fastq files generated using either built-in software (MiSeq) or CASAVA (HiSeq).
Raw sequence data were first evaluated using FastQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and preprocessed for quality through a combination of  trimming and filtering using Trim Galore (v0.4.0, 15 bases were trimmed off from the 5'-end of the reads and 5 bases were trimmed off from the 3'-end, Phred score threshold of 20 and minimum length of 50 bp, Paired, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Quality reads were then uniquely mapped to HHCMV (strain TB40/E, GenBank: EF999921.1) and human (GRCh38) genomes, respectively, both using Tophat2 (v2.1.1) with strand-specific alignment of fr-firststrand. For HHCMV alignment, the maximum intron size was set to 5kb as described on Tophat2 manual, and the uniquely mapped HCMV, but not human, reads were used for all subsequent analyses.
Raw read counts for each sample were obtained by mapping reads at the gene-level using HTSeq-count tool from the Python package HTSeq, with a stranded-reverse setting. DESeq2 R-package (v1.8.2) was then used to perform differential expression (DE) and statistical analysis, with a biological sample from  SS and NS libraries of same cell donor grouped.
Raw read counts for genes over a group of six biological samples of fibroblast or CD34+ HPC infection were normalized through a regularized logarithm transformation (rlog) implemented in DESeq2, and kernel density estimates (KDE) were then obtained using the density R function with default parameters. The six density curves were overlaid on one plot. The featured density variation, associated with fibroblast or CD34+ HPC infection, was further evaluated using an extended group comprised of total four time points of post infection in fibroblasts (12, 24, 48, 72hpi, total 12 samples) and all NS/SS replicates from different cell donors of CD34+ HPC infection (total 24 samples).  Density variation across samples was accessed by different bandwidth settings (0.5, 0.75, 1 and 1.25), which determine the degree of smoothing in the estimate of the density function of statistical software package R (http://www.r-project.org/). In addition, density variation across samples was assessed by the comparison between real and random samples, where raw read count for each gene in each sample was the mean value of 100 permutations of involved real samples and rlog normalization was performed.
Variability with respect to transcriptomes from infection in fibroblasts or CD34+ HPCs was assessed by the squared coefficient of variation (CV2), i.e., the variance in expression of rlog normalized counts (σ2) divided by the squared mean expression (μ2) and then multiplied by 100.  The cumulative CV2 was also obtained as a final squared coefficient of variation representing the variability in different cell types.
In addition to rlog normalized counts, we quantified expression level of genes by merging annotated isoforms' FPKM values from Cufflinks (v2.2.1).
Genome_build: EF999921.1 (HCMV), GRCh38 (Human)
Supplementary_files_format_and_content: [Raw_Fb16.txt] Raw HCMV reads counts for fibroblast infection
Supplementary_files_format_and_content: [Raw_NSSS12.txt] Raw HCMV reads counts for CD34+ HPC infection from donor 1
Supplementary_files_format_and_content: [Raw_donor_NSSS14.txt] Raw HCMV reads counts for CD34+ HPC infection from donor 2 and donor 3
Supplementary_files_format_and_content: [Raw_natural.txt] Raw HCMV reads counts for natural infection
Supplementary_files_format_and_content: [FPKM13.txt] Abundance measurements of HCMV genes for CD34+ HPC infection (donor 1) and natural infection

molecule: total RNA

organism: Human betaherpesvirus 5

source_name: Hematopoietic Stem Cells, ∆UL135 HCMV infected 6 days

growth_protocol: MRC-5 lung fibroblasts were maintained with DMEM (Gibco) supplemented with 10% FBS, 100 U/mL penicillin and streptomycin, 2mM L-alanyl-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, and 10 mM HEPES

extract_protocol:
RNA was extracted using a ZR-Duet DNA/RNA miniprep kit (Zymo Research, Irvine, CA)
RNA libraries were prepared for Illumina sequencing using either Agilent's SureSelect Strand Specific RNA Library Preparation Kit or Kapa Biosystem's KAPA Stranded mRNA-seq kit

tag: host cell type

value: CD34+ Hematopoietic Stem Cells

tag: isolate

value: initial isolate

tag: selection

value: SureSelect Targeted enrichment


title: F1-FB-Pol2

description:
F1-FB-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

tag: chip antibody

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

tag: chip antibody vendor

value: EMD Millipore

tag: chip antibody cat. #


title: Donor 3_∆UL135 2dpi SS

description:
∆UL135 HCMV infected 2 days
Raw_donor_NSSS14.txt

source_name: Hematopoietic Stem Cells, ∆UL135 HCMV infected 2 days


title: F1-EiPSC-Pol2

description:
F1-EiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Induced pluripotent stem cells (iPSCs)


title: PVC6

city: New York

first: Karen

last: Duff

state: NY

address: 630 West 168th Street, P & S 12-440

department: Pathology and Cell Biology

institute: Columbia University Medical Center

data_processing:
generated 149bp single end sequences using an Illumina Hi-Seq sequencer
aligned the fastq files to the mm9 mouse reference genome using Tophat (v2.0.6) and Bowtie (v2.0.2.0)
annotated and quantified the reads to specific genes using Python module HT-SEQ with a modified NCBIM37.61 (containing only protein coding genes) gtf to provide reference boundaries
compared aligned reads across samples using the R/Bioconductor package DESeq2 (v1.10.1)
Genome_build: mm9
Supplementary_files_format_and_content: text file with DESeq2 output. Each tissue analyzed individually.

organism: Mus musculus

source_name: Primary Visual Cortex

extract_protocol:
Trizol
TruSeq RNA Sample Prep Kit v2

tag: tissue

value: brain

tag: tissue compartment

value: Primary Visual Cortex

tag: genotype

tag: gender

value: Male

tag: strain

tag: age

value: 14-15 months


title: F1-FB-p300

description:
F1-FB-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: PVC5

description: same library run multiple times for depth


title: PVC14


title: F1-EiPSC-p300

description:
F1-EiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt


title: Donor 3_WT 2dpi SS

description:
Wildtype HCMV infected 2 days
Raw_donor_NSSS14.txt

source_name: Hematopoietic Stem Cells, Wildtype HCMV infected 2 days


title: PVC4


title: Natural_Old HCMV High

description:
Clinical samples pooled from four elderly adults (avg. age 75) with high HCMV ab titers
Raw_natural.txt
FPKM13.txt

source_name: peripheral blood mononuclear cells, Clinical samples pooled from four elderly adults (avg. age 75) with high HCMV ab titers

value: Total PBMC

value: Clinical isolates


title: F1-EiPSC-K4me3

description:
F1-EiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

value: Active Motif


title: F1-EiPSC-K4me1

description:
F1-EiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F1-EiPSC-K27me3

description:
F1-EiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)


title: Donor 3_∆UL138 2dpi SS

description:
∆UL138 HCMV infected 2 days
Raw_donor_NSSS14.txt

source_name: Hematopoietic Stem Cells, ∆UL138 HCMV infected 2 days

value: CD34+ Hematopoietic Stem Cells

value: initial isolate

value: SureSelect Targeted enrichment


title: Donor 1_∆UL138 6dpi SS

description:
∆UL138 HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt

source_name: Hematopoietic Stem Cells, ∆UL138 HCMV infected 6 days


title: PVC3


title: PVC2


title: PVC38


title: Donor 1_∆UL135 6dpi SS

description:
∆UL135 HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt


title: F1-EiPSC-K27ac

description:
F1-EiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Induced pluripotent stem cells (iPSCs)

value: Histone H3K27ac antibody (pAb)


title: F1-EiPSC-Input


title: PVC7

value: brain

value: Primary Visual Cortex


title: Donor 1_WT 6dpi SS

description:
Wildtype HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt

source_name: Hematopoietic Stem Cells, Wildtype HCMV infected 6 days


title: PVC37

value: Male

value: 14-15 months


title: Donor 1_∆UL138 2dpi SS

description:
∆UL138 HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt


title: PVC36


title: Donor 3_WT 6dpi SS

description:
Wildtype HCMV infected 6 days
Raw_donor_NSSS14.txt


title: Donor 1_∆UL135 2dpi SS

description:
∆UL135 HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt


title: F1-EC-Pol2

description:
F1-EC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Endothelial cells (ECs)

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

value: EMD Millipore


title: F1-EC-p300

description:
F1-EC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: Donor 1_WT 2dpi SS

description:
Wildtype HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt


title: F1-EC-K4me3

description:
F1-EC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

value: Active Motif


title: UT_RIP_IP Replicate 2

city: University Park

middle: C.

last: Reese

state: PA

address: North Frear Laboratory

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

description: Replicate 2

data_processing:
All samples were downloaded separately by barcode and mapped to the 2007 S. cerevisiae reference genome (sg7) using SHRiMP version 2.2.2. Reads were trimmed 15 bp from the 3’ end as a quality control measure. During mapping, SHRiMP2 calculated a score for each read based upon mismatches, and reads with less than 90% of the maximum possible score were filtered out (a 90% threshold is similar to allowing for 3 mismatches).
The reads per gene was tabulated after aligning reads to TSS and TTS from a published source (David et al. 2006).
To calculate enrichment, two of three replicates were processed at a time in all three combinations (i.e. rep 1 v. rep 2, rep 2 v. rep 3, and rep 1 v. rep 3) then averaged if the false discovery rate (FDR) was less than 1%. Enrichment was calculated in edgeR for each gene by dividing reads in the IP by reads in the mock IP while controlling for differences in library size among samples.
To calculate enrichment per third of a gene, reads per gene was split into reads that align to the first third, middle third and last third of each gene before calculating enrichment.
Genome_build: 2007 S. cerevisiae reference genome (sg7)
Supplementary_files_format_and_content: Tab-delimited text files that include read mapping statistics, read count per gene for each replicate or RIP-seq enrichment per gene for sample, relative to UT IP.

organism: Saccharomyces cerevisiae

source_name: Wild type yeast cells

growth_protocol: Normal growth conditions were 30°C shaking at 200 rpm in YPAD media. Yeast cultures were grown in rich media at 30°C to an OD600 ~0.9, crosslinked with formaldehyde (1%) and then quenched with glycine. To induce oxidative stress (OS) hydrogen peroxide was added to 0.3 mM for 25 minutes prior to crosslinking.

extract_protocol:
Cross-linked cells were harvested, then extract was made using multiple rounds of bead beating and sonication. After treatment with DNase, the IP samples were incubated with protein A-sepharose anti c-myc antibody complex. UT Input samples were treated with DNase, however they were not incubated with protein A-sepharose anti c-myc antibody complex.
Whole transcriptome cDNA libraries were synthesized using the SOLiD Total RNA-Seq Kit (PN 4445374).

tag: temperature and stress

tag: rip antibody

value: myc


title: UT_RIP_Input Replicate 2

description: Replicate 2


title: UT_RIP_IP Replicate 3

description: Replicate 3


title: WT2_10dpi+GCV SS

description: fpkmGW.txt

data_processing:
Raw sequencing data was de-multiplexed and fastq files generated using CASAVA (HiSeq).
Raw sequence data were first evaluated using FastQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and preprocessed for quality through a combination of  trimming and filtering using Trim Galore (v0.4.0, 15 bases were trimmed off from the 5'-end of the reads and 5 bases were trimmed off from the 3'-end, Phred score threshold of 20 and minimum length of 50 bp, Paired, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Quality reads were then uniquely mapped to HCMV (strain TB40/E, GenBank: EF999921.1) genome using Tophat2 (v2.1.1) with strand-specific alignment of fr-firststrand and the maximum intron size was set to 5kb as described on Tophat2 manual.
Raw read counts for each sample were obtained by mapping reads at the gene-level using HTSeq-count tool from the Python package HTSeq, with a stranded-reverse setting. DESeq2 R-package (v1.8.2) was then used to perform differential expression (DE) analysis.
In addition to rlog normalized counts, we quantified expression level of genes by merging annotated isoforms' FPKM values from Cufflinks (v2.2.1).
Besides DE, variability with respect to ∆UL135 and ∆UL138 transcriptomes across different cell donors and different infections was evaluated by kernel density estimation and dispersion metric in DESeq2.
EF999921.1 (HCMV), GRCh38 (Human)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts or FPKM values for each Sample

source_name: Hematopoietic Stem Cells

treatment_protocol: GCV samples were treated with 27 µM of the antiviral

tag: treatment

value: Wildtype CMV infected 10 days and treated with ganciclovir


title: F1-EC-K4me1

description:
F1-EC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

tag: cell type

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: PVC26

description: same library run multiple times for depth


title: WT1_10dpi+GCV SS

description: fpkmGW.txt

value: initial isolate

value: SureSelect Targeted enrichment


title: UT_RIP_IP Replicate 1

description: Replicate 1


title: PVC28

value: brain


title: F1-EC-K27me3

description:
F1-EC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

tag: passage

value: Histone H3K27me3 antibody (clone:7B11)


title: PVC25

value: Primary Visual Cortex

value: Male


title: Puf5_RIP_IP Replicate 2

description: Replicate 2


title: WT2_10dpi SS

description: fpkmGW.txt

tag: host cell type

value: Wildtype CMV infected 10 days


title: WT1_10dpi SS

description: fpkmGW.txt

tag: isolate


title: F1-EC-Input

value: Endothelial cells (ECs)


title: PVC24

value: 14-15 months


title: UT_RIP_Input Replicate 1

description: Replicate 1


title: PVC23


title: Puf5_RIP_IP Replicate 3

description: Replicate 3


title: F1-CPC-Pol2

description:
F1-CPC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Cardiac progenitor cells (CPCs)

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

value: EMD Millipore


title: Donor 2_Uninfected 6dpi NS

description:
Uninfected 6 days
Raw_donor_NSSS14.txt

source_name: Hematopoietic Stem Cells, Uninfected 6 days

value: CD34+ Hematopoietic Stem Cells

tag: selection


title: Puf5_RIP_IP Replicate 1

description: Replicate 1

value: myc


title: Donor 2_Uninfected 2dpi NS

description:
Uninfected 2 days
Raw_donor_NSSS14.txt

source_name: Hematopoietic Stem Cells, Uninfected 2 days


title: Dhh1_RIP_IP Replicate 3

description: Replicate 3


title: PVC29


title: Donor 2_∆UL138 6dpi NS

description:
∆UL138 HCMV infected 6 days
Raw_donor_NSSS14.txt


title: PVC22


title: F1-CPC-p300

description:
F1-CPC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

tag: chip antibody

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: Dhh1_RIP_IP Replicate 2

description: Replicate 2


title: EC39

source_name: Entorhinal Cortex

value: Entorhinal Cortex


title: Dhh1_RIP_IP Replicate 1

description: Replicate 1


title: F1-CPC-K4me3

description:
F1-CPC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)

tag: chip antibody vendor

value: Active Motif


title: F1-EC-K27ac

description:
F1-EC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Histone H3K27ac antibody (pAb)

tag: chip antibody cat. #


title: EC35

tag: tissue

value: brain


title: F1-CPC-K4me1

description:
F1-CPC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: Donor 2_WT 6dpi NS

value: initial isolate


title: Ccr4_RIP_IP Replicate 3

description: Replicate 3


title: EC33

tag: tissue compartment

value: Male


title: F1-CPC-K27ac

description:
F1-CPC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt


title: F1-CPC-K27me3

description:
F1-CPC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)


title: Donor 2_∆UL138 2dpi NS

description:
∆UL138 HCMV infected 2 days
Raw_donor_NSSS14.txt


title: EC20

tag: genotype

value: 14-15 months


title: Donor 2_∆UL135 2dpi NS

description:
∆UL135 HCMV infected 2 days
Raw_donor_NSSS14.txt


title: Ccr4_RIP_IP Replicate 1

description: Replicate 1


title: EC19

tag: gender


title: F1-CPC-Input

value: Cardiac progenitor cells (CPCs)


title: MCSF3

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
Illumina’s bcl2fastq software v1.19 was used for obtaining data files (fastq) for downstream analyses
The expression levels of mouse transcripts were estimated using salmon (v0.7.2) . Human GENCODE gene set (release v25) was used as transcriptome  annotation. The transcript abundances were converted into gene-level read counts by using the Bioconductor package, tximport.
Statistical analyses were done with edgeR (Bioconductor), and the differentially expressed genes were identified as those with false-discovery rates < 0.05, absolute fold change > 2 and averaged CPM (counts per million) > 1 in the samples. The heatmap was built using Cluster3 and JavaTreeView. Functional analysis of the differentially expressed genes was performed using Ingenuity Pathway Analysis software (Ingenuity Systems Inc.).
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with separate tabs for raw counts, Transcripts per Million (TPM) values for each Sample, and list of differentially expressed genes for two comparisons “B1 vs Negative_Control” and “CMCSF vs Negative_Control” included.

source_name: CD34 positive hemapoietic stem cells

growth_protocol: Human CD34+ cells (All-Cells) and mouse bone marrow cells were cultured in StemSpan serum-free media with cytokine cocktail 100 (STEMCELL Technologies), only serum-free media, or RPMI 1% FBS.

extract_protocol:
Total RNAs were isolated in replicates of three from untreated human CD34+ cells, human CD34+ cells treated with B1 Ab, and human CD34+ cells treated with M-CSF.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hemapoietic stem cell

value: M-CSF


title: MCSF2


title: Donor 1_∆UL138 6dpi NS

description:
∆UL138 HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt

value: CD34+ Hematopoietic Stem Cells


title: EC17

tag: strain


title: Donor 2_WT 2dpi NS

description:
Wildtype HCMV infected 2 days
Raw_donor_NSSS14.txt


title: EC16

tag: age


title: MCSF1


title: F1-CiPSC-Pol2

description:
F1-CiPSC-Pol2
processed data file:
ChIP-seq_enhancer_Pol2_vsd_exp.txt
ChIP-seq_promoter_Pol2_counts.txt

value: Induced pluripotent stem cells (iPSCs)

value: Anti-RNA Polymerase II antibody, CTD (clone 8WG16)

value: EMD Millipore


title: F1-CiPSC-p300

description:
F1-CiPSC-p300
processed data file:
ChIP-seq_enhancer_p300_vsd_exp.txt
ChIP-seq_promoter_p300_counts.txt

value: p300 antibody (C-20)

value: Santa Cruz Biotechnology


title: EC34

value: Entorhinal Cortex


title: Ccr4_RIP_IP Replicate 2

description: Replicate 2

tag: temperature and stress

value: myc


title: Donor 2_∆UL135 6dpi NS

description:
∆UL135 HCMV infected 6 days
Raw_donor_NSSS14.txt


title: Control3

value: untreated


title: Donor 1_WT 6dpi NS

description:
Wildtype HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt


title: Donor 1_∆UL135 6dpi NS

description:
∆UL135 HCMV infected 6 days
Raw_NSSS12.txt
FPKM13.txt


title: EC15

value: brain


title: EC14


title: F1-CiPSC-K4me1

description:
F1-CiPSC-K4me1
processed data file:
ChIP-seq_enhancer_K4me1_vsd_exp.txt
ChIP-seq_promoter_K4me1_counts.txt

value: Anti-histone H3 (mono methyl K4) antibody

value: Abcam


title: F1-CiPSC-K27me3

description:
F1-CiPSC-K27me3
processed data file:
ChIP-seq_enhancer_K27me3_vsd_exp.txt
ChIP-seq_promoter_K27me3_counts.txt

value: Histone H3K27me3 antibody (clone:7B11)

value: Active Motif


title: Control1


title: Control2


title: Donor 1_∆UL135 2dpi NS

description:
∆UL135 HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt

value: initial isolate


title: F1-CiPSC-K27ac

description:
F1-CiPSC-K27ac
processed data file:
ChIP-seq_enhancer_K27ac_vsd_exp.txt
ChIP-seq_promoter_K27ac_counts.txt

value: Histone H3K27ac antibody (pAb)


title: EC9

value: Male

value: 14-15 months


title: Donor 1_WT 2dpi NS

description:
Wildtype HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt

value: CD34+ Hematopoietic Stem Cells


title: Fibro_Uninfected 72hpi

description:
Uninfected isolated at 72 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Uninfected isolated at 72 hours

value: Fetal Lung Fibroblast MRC-5 (ATCC)


title: B1Ab2

value: hemapoietic stem cell

value: B1 Ab


title: B1Ab1


title: EC7


title: F1-CiPSC-Input

value: Induced pluripotent stem cells (iPSCs)


title: F1-CiPSC-K4me3

description:
F1-CiPSC-K4me3
processed data file:
ChIP-seq_enhancer_K4me3_vsd_exp.txt
ChIP-seq_promoter_K4me3_counts.txt

value: Histone H3K4me3 antibody (pAb)


title: P3-donor 3

city: Paris

first: Violaine

last: Saint-André

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Sequencing reads were aligned to the human genome hg19 build using Tophat (Trapnell et al., 2009) (version 2.0.6) with parameters -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 -p 12 --library-type fr-firststrand -g 2.
Gene level counts were computed using htseq-count (Anders et al., 2015) (version 0.6.1p1) with parameters -t exon -s reverse -m intersection-nonempty.
Genes annotated as protein coding in Gencode V15 were analyzed separately as coding genes.
Differential gene expression analysis was performed in R (version 3.1.3) using the DEseq2 package (Love et al.,2014).
Genes that had a mean of reads per kilobase per million (RPKM) across all samples under 2 RPKM were filtered out.
For each pDC population, genes that show absolute log2 fold change > 1, and Benjamini-Hochberg adjusted p-value < 0.01 as estimated using a Wald test, with respect to at least one other pDC population, were considered differentially expressed.
Genome_build: hg19
Tables display the log-transformed centered-reduced counts for either the coding or the non-coding genes.

source_name: plasmacytoid dendritic cells

extract_protocol:
Treated cells were sorted as P1, P2, and P3 subsets depending on extra-cellular markers: P1 (PD-L1+CD80-), P2 (PD-L1+CD80+) and P3 (PD-L1-CD80+). 1 micro-gram Total RNA-seq was extracted for library preparation.
Libraries were constructed using the "TruSeq Stranded Total RNA-seq" for paired-end sequencing.

treatment_protocol: Ex-vivo plasmacytoid pre-dendritic cells from the blood of healthy human donors were treated for 24h with influenza virus.

tag: stimulation

value: influenza virus stimulation

tag: surface markers

value: PD-L1-CD80+ sorted

value: plasmacytoid dendritic cells


title: EC8

value: brain

value: Entorhinal Cortex


title: P3-donor 2

tag: cell type


title: EC5


title: Fibro_Uninfected 48hpi

description:
Uninfected isolated at 48 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Uninfected isolated at 48 hours

tag: passage


title: Donor 1_∆UL138 2dpi NS

description:
∆UL138 HCMV infected 2 days
Raw_NSSS12.txt
FPKM13.txt

tag: host cell type


title: Fibro_Uninfected 24hpi

description:
Uninfected isolated at 24 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Uninfected isolated at 24 hours


title: EC10


title: EC6


title: P3-donor 1


title: Fibro_Uninfected 12hpi

description:
Uninfected isolated at 12 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Uninfected isolated at 12 hours


title: Ovary_Female1_1700sTS

city: Lausanne

first: Diego

last: Cortez

address: Rue de Lausanne

country: Switzerland

institute: Univerity of Lausanne - CIG

description: cDNA

data_processing:
Basecalls performed using CASAVA version 1.8.
DNA-Seq reads were aligned to the AnoCar2.0 genome assembly using bowtie v2.2.8 with default parameters.
PCR duplicates and reads mapping to multiple genome positions were filered out from the alignments.
Genome_build: RNA-Seq reads were aligned to the AnoCar2.0 genome assembly using HISATv2.0.4
Genome_build: AnoCar2.0
Supplementary_files_format_and_content: VCF files were produced using bcftools v1.3.1

organism: Anolis carolinensis

source_name: Ovary

extract_protocol:
The DNA was purified using Qiaquick PCR Purification columns (Qiagen) according to manufacturer’s instructions.
SMARTer Ultra Low Input RNA kit
DNA-Seq
RNA-Seq

tag: Sex

value: Female

tag: Stage

value: Adult


title: Ovary_Female2_1707sTS

description: cDNA


title: P2-donor 2

value: PD-L1+CD80+ sorted


title: Liver_Female3_1266sTS

description: cDNA

source_name: Liver


title: EC4


title: B1Ab3

tag: treatment


title: EC3


title: Liver_Female2_1705sTS

description: cDNA


title: Fibro_WT 48hpi

description:
Wildtype HCMV infected 48 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Wildtype HCMV infected 48 hours

tag: selection


title: P2-donor 1


title: EC38


title: Fibro_WT 24hpi

description:
Wildtype HCMV infected 24 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Wildtype HCMV infected 24 hours


title: EC2


title: Liver_Female1_1698sTS

description: cDNA


title: P1-donor 3

value: PD-L1+CD80- sorted


title: Kidney_Female3_1267sTS

description: cDNA

source_name: Kidney


title: P1-donor 2


title: Fibro_WT 12hpi

description:
Wildtype HCMV infected 12 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Wildtype HCMV infected 12 hours


title: P2-donor 3


title: P1-donor 1


title: EC36

value: Male


title: Fibro_WT 72hpi

description:
Wildtype HCMV infected 72 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, Wildtype HCMV infected 72 hours


title: Fibro_∆UL138 48hpi

description:
∆UL138 HCMV infected 48 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL138 HCMV infected 48 hours


title: Fibro_∆UL138 72hpi

description:
∆UL138 HCMV infected 72 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL138 HCMV infected 72 hours


title: Kidney_Female1_1699sTS

description: cDNA


title: EC37

description: same library run multiple times for depth

value: 14-15 months


title: Medium-donor 2

value: no stimulation

value: unsorted


title: EC29


title: EC28


title: Medium-donor 3


title: Heart_Female3_1269sTS

description: cDNA

source_name: Heart


title: Fibro_∆UL138 24hpi

description:
∆UL138 HCMV infected 24 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL138 HCMV infected 24 hours

value: Fetal Lung Fibroblast MRC-5 (ATCC)


title: Fibro_∆UL138 12hpi

description:
∆UL138 HCMV infected 12 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL138 HCMV infected 12 hours


title: Heart_Female2_1704sTS

description: cDNA


title: Medium-donor 1


title: EC25

source_name: Entorhinal Cortex


title: Ex-vivo-donor 3

source_name: plasmacytoid dendritic cells


title: Fibro_∆UL135 48hpi

description:
∆UL135 HCMV infected 48 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL135 HCMV infected 48 hours


title: Fibro_∆UL135 72hpi

description:
∆UL135 HCMV infected 72 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL135 HCMV infected 72 hours


title: Kidney_Female2_1706sTS

description: cDNA


title: Brain_Female3_1268sTS

description: cDNA

source_name: Brain


title: Fibro_∆UL135 24hpi

description:
∆UL135 HCMV infected 24 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL135 HCMV infected 24 hours


title: Fibro_∆UL135 12hpi

description:
∆UL135 HCMV infected 12 hours
Raw_Fb16.txt

source_name: Fetal Lung Fibroblast, ∆UL135 HCMV infected 12 hours


title: EC24


title: Heart_Female1_1697sTS

description: cDNA


title: Ex-vivo-donor 1


title: EC23


title: Brain_Female1_1696sTS

description: cDNA


title: EC22


title: 35LI - treatment 3 - cymopol low dose

status: Public on Dec 03 2017

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

description: cymopol - low dose

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p4 using STAR 2.4.0j
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuflinks 2.2.0 package.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: large intestine

growth_protocol: The mice were maintained under approved standard conditions

extract_protocol:
12 h following the final treatment, the mice were euthanized in 100% CO2.  The tissues were harvested immediately, frozen on dry ice, and kept at -80 ºC until analyzed.
RNA libraries were prepared for sequencing using standard Illumina protocols.    Illumina RNA library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF). Quantitation was done on a NanoDrop Spectrophotometer (NanoDrop Technologies, Inc.), and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc).  rRNAs first were removed started with 90ng of total RNA by ClonTech RiboGone –Mammalian-Low input ribosomal RNA removal kit for Human, Mouse and Rat Samples (cat#: 634848) following the manufacturer’s protocol, then the depleted RNA were used for library construction with SMARTer Universal Low input RNA kit for sequencing (cat#: 634940) combined with Illumina Nextera DNA Library Preparation Kit (cat#: FC-121-1030) according to the user guide.

treatment_protocol: Cymopol (low dose: 0.3 mmol/kg, high dose: 1.4 mmol/kg) and the non-polar extract (low dose: 0.3 g/kg, high dose: 1.0 g/kg) were dissolved in Chremophor EL (Sigma) containing 10% DMSO and administered via oral gavage for 3 consecutive days, with 24 h between each treatment.  No apparent toxicity was observed for the animals

value: large intestine

value: male

value: 4 weeks


title: 33LI - treatment 3 - cymopol low dose

description: cymopol - low dose


title: 29LI - treatment 1 - NP low dose

description: algal extract - low dose


title: EC26


title: Brain_Female2_1703sTS

description: cDNA


title: 2376g.Female

description: genomic dna


title: 27LI - treatment 1 - NP low dose

description: algal extract - low dose


title: 25LI - treatment 2 - NP high dose

description: algal extract - high dose


title: 14LI - treatment 4 - cymopol high dose

description: cymopol - high dose


title: 21LI - treatment 2 - NP high dose

description: algal extract - high dose


title: 26LI - treatment 1 - NP low dose

description: algal extract - low dose


title: 34LI - treatment 3 - cymopol low dose

description: cymopol - low dose


title: 12LI - treatment 4 - cymopol high dose

description: cymopol - high dose


title: Ex-vivo-donor 2


title: 4LI - Control

description: vehicle control


title: 11LI - treatment 4 - cymopol high dose

description: cymopol - high dose


title: 5LI - Control

description: vehicle control


title: 2LI - Control

description: vehicle control


title: RNA-seq_TAC_d21_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

data_processing:
Sequencing reads were aligned to human genome assembly hg19 by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene RPKM values

source_name: Mouse left ventricle, TAC day 21.

growth_protocol: Heart tissues were harvested at indicated time. Left ventricles were dissected and immediately frozen in liquid nitrogen.

extract_protocol: For RNA-seq analysis using the Illumina NextSeq500, 0.1-2 ug of total RNA was processed for library generation using the NuGEN Ovation RNA-seq library prep kit following the manufacturer’s protocol.

value: Heart


title: RNA-seq_TAC_d21_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d21_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, sham day 21.


title: RNA-seq_sham_d21_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d7_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, TAC day 7.


title: RNA-seq_sham_d7_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, sham day 7.


title: RNA-seq_TAC_d7_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: 23LI - treatment 2 - NP high dose

description: algal extract - high dose


title: RNA-seq_sham_d7_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d7_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d7_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d21_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d4_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, TAC day 4.


title: RNA-seq_TAC_d4_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d4_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d4_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, sham day 4.


title: RNA-seq_TAC_d2_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, TAC day 2.


title: RNA-seq_sham_d4_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d2_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_TAC_d2_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d2_rep1

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt

source_name: Mouse left ventricle, sham day 2.


title: RNA-seq_sham_d2_rep3

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d21_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: RNA-seq_sham_d2_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: BirA-only_ChIPSeq_rep2

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan University

data_processing:
Samples were aligned to the mm9 genome using bowtie1.1.2 (-m 1 -n 2 -e 70 -k 1 --best  -l 75).
sam files were converted to bam with the samtools version 1.2 and low quailty reads were filtered (MAPQ < 10).
PCR duplicates were removed using Picard.
peaks were called for each samples using MACS2 callpeak with the default parameters except q = 0.01, --broad, --broad-cutoff 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using bedtools genomecov: reads were extended to 300bp and coverage were scaled to RPM.

growth_protocol: AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.

extract_protocol:
BirA-ChIP seq experiments were performed as described (PMID: 22412018). Briefly, 1*10^7 cells were fixed with 4% formaldehyde for 10min at RT, and then the cells were divided into six part equally. Cells were lysed at 25°C in 200ul lysis buffer for 5 min.After cell lysis, the chromatin was sonicated by the Bioruptor sonicator. The cell lysate was centrifuged at 17,000g for 15min at 4°C. Supernatants were incubated with 30 μl High Capacity Streptavidin Agarose (Thermo Fisher Scientific) overnight. Beads were washed twice for 5 min with buffer 1 (2% SDS) at 25°C,once with buffer 2,once with buffer 3 and twice with buffer 4. Lastly, adding 60μl Elution buffer to the beads, and then placed in a 70°C water bath overnight with shaking.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The BirA HNRNPU stable cell line was obtained through 1μg/ml puromycin, and then the protein was induced for three days with 0.5μg/ml DOX, and 50μM Biotin treated the cells for one day.

tag: cell line

tag: genotype/variation

value: BirA HNRNPU

tag: chip antibody

value: Biotin


title: Input_rep2

source_name: Input

value: Input


title: Input_rep1


title: BirA-only_ChIPSeq_rep1


title: shCtrl_Input_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.4.
Samples were aligned to the mm9 genome using bowtie1.1.2 (-m 1 -n 2 -e 70 -k 1 --best  -l 75).
sam files were converted to bam with the samtools version 1.2 and low quailty reads were filtered (MAPQ < 10).
PCR duplicates were removed using Picard.
peaks were called for each samples using MACS2 callpeak with the default parameters except q = 0.01.
we also remove the peaks if  they are discordant between biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using bedtools genomecov: reads were extended to 300bp and coverage were scaled to RPM.

extract_protocol:
ChIP experiments were performed with 1X10e7 AML12 cells as previously described (Wen et al., 2008).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.

tag: tissue

value: AML12 cells

value: none (input)


title: BirA-HNRNPU_ChIPSeq_rep2


title: shU_RAD21_ChIPSeq_rep1


title: shCtrl_RAD21_ChIPSeq_rep2


title: shCtrl_RAD21_ChIPSeq_rep1


title: shU_Input_ChIPSeq


title: RNA-seq_sham_d4_rep2

description:
RNA-seq_read_count.txt
RNA-seq_RPKM.txt


title: shU_CTCF_ChIPSeq_rep2

value: CTCF


title: AML12_HiC_shU_biological_replicate2

description: HiC Library digested with MboI

data_processing:
Raw HiC data were processed through the HiC-Pro pipeline (MID: 26619908) (including read mapping/binning/ICE correction).
hic files were generated using HiC-Pro script: hicpro2juicebox.sh
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.

extract_protocol:
Hi-C was carried out according to the protocol (PMID: 25497547). Briefly, Five million cells were crosslinked with 1% formaldehyde for 10min at room temperature, and then the cells were divided into two tubes, taking one tube for the subsequent experiments, the cells were permeabilized with 0.2% Igepal CA630, and then the pelleted nuclei were treated with 0.5% SDS. The chromatin was digested with 100 units of MboI overnight, the DNA ends were marked by biotinylated nucleotides, After reversal of crosslinks, the DNA was sheared to a size of 300-500bp, and then the ligated DNA was pull-down by streptavidin magnetic beads.
Illumina sequencing library were prepared according to the standard Illumina protocol.

treatment_protocol: For shRNA-based knockdown, shRNA lentiviruses were then prepared as previously described (PMID: 26603343). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.

tag: condition

value: HNRNPU KD (shU)


title: shU_RAD21_ChIPSeq_rep2


title: AML12_HiC_shU_biological_replicate1

description: HiC Library digested with MboI


title: shU_CTCF_ChIPSeq_rep1


title: shCtrl_CTCF_ChIPSeq_rep1


title: AML12_HiC_shCtrl_biological_replicate2

description: HiC Library digested with MboI

value: shCtrl


title: AML12_HiC_shCtrl_biological_replicate1

description: HiC Library digested with MboI


title: shU_RNAseq_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm9 reference assembly by the Tophat2 software.
We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
For differential gene expression analysis, we analyzed raw read counts for GENCODE M1 gene models using HTSeq (Anders et al., 2015), and then calculated statistics of differential expression via DESeq2 version 1.8.2 (Love et al., 2014) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each replicate.

source_name: HNRNPU KD (shU)

extract_protocol:
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).


title: shU_RNAseq_rep1


title: shCtrl_RNAseq_rep2

source_name: shCtrl


title: shCtrl_RNAseq_rep1


title: BirA-HNRNPU_ChIPSeq_rep1


title: GRO-seq at ZT22 (ROR LDKO)

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Up_Regulated_eRNAs.bed
Down_Regulated_eRNAs.bed
nascent RNA

data_processing:
Library strategy: GRO-seq
Bowtie 1 was used to align GRO-seq samples to mm9 genome, followed by generation of ucsc visualization files using HOMER. eRNAs were detected using an in-house pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, bed
Genome_build: mm9

source_name: liver

growth_protocol: C57BL/6 mice were grown on normal chow on normal light/dark schedule

extract_protocol:
DNA or RNA is extracted using Qiagen kits
Library contruction follows illumina kits
Standard illumina method was used

treatment_protocol: no specific treatment was performed

tag: strain

value: 12 weeks old male

value: ROR LDKO


title: ΔluxR 2

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Reads were quality and adapter trimmed using Trimmomatic v0.33 with the following parameters ILLUMINACLIP:adapters.file:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Mapping was accomplished with bowtie2 version 2.1.0 (default parameters) by mapping to Vibrio harveyi ATCC BAA-1116
Counts were determined for genes and 100bp intergenic intervals using a custom perl script
Differential gene expression was identified using the program DESeq2 with default parameters
Genome_build: NC_009784.1, NC_009783.1, and NC_009777.1
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest including genes and intergenic regions for each fastq file; intergenic regions are identified as follows Inter.<molecule>.<strand>.<basepair_begin>.<basepair_end>

organism: Vibrio harveyi

source_name: ΔluxR_kate-exponential cultures

growth_protocol: 15 mL test tubes containing 5 mL LM were inoculated with overnight culture to an OD600 = 0.005. Cultures were grown to OD600 = 1.0 at 30 °C.

extract_protocol:
Cells grown to OD600=1.0 were pelleted by centrifuging and snap frozen in N2. Total RNA was isolated from cells using a Trizol/cholorform extraction protocol from a previous study (Rutherford et al., 2011). RNA was cleaned up using an Rneasy kit (Qiagen)
cDNA libraries were prepared from total RNA by the Indiana University Center for Genomics and Bioinformatics. mRNA was enriched from one microgram total RNA using RiboZero rRNA Removal (Bacteria) Kit (Illumina, Inc., San Diego, CA, USA). rRNA-depleted mRNA samples were purified by Agencourt AMPure® XP beads (Beckman Coulter, Indianapolis IN, USA) and viewed using Agilent High Sensitivity RNA ScreenTape (Agilent Technologies, Inc., Santa Clara, CA, USA). Double stranded cDNA synthesis was performed using Illumina TruSeq Stranded mRNA Library Prep Kit in accordance with the manufacturer’s standard protocol. Enriched mRNA was fragmented using divalent cations via incubation for 8 min at 94oC. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers. Second-strand synthesis was performed by subsituting dTTP with dUTP followed by digestion using Uracil-DNA-Glycosylase (UDG). A-tailing and adapter ligation was performed  followed by PCR amplification for 12 cycles using polymerase provided in kit. This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using an Agilent DNA1000 ScreenTape (Agilent Technologies, Inc., Santa Clara, CA, USA) and Picogreen assay kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were made single-stranded and diluted to 1.8pM, as per Illumina manufacturer's instructions. Cluster generation and sequencing was performed on an Illumina NextSeq500 using NextSeq 500/550 High Output v2 kit (75 cycles).
Single-end 80bp sequencing was performed on an Illumina NextSeq500 using NextSeq 500/550 High Output v2 kit (75 cycles).

tag: mutation

value: ΔluxR

tag: growth phase

value: Late-exponential cultures


title: ΔihfA ΔihfB 3

source_name: ΔihfA ΔihfB_kate-exponential cultures

value: ΔihfA ΔihfB


title: ΔihfA ΔihfB 2


title: shCtrl_CTCF_ChIPSeq_rep2


title: ΔluxR 1


title: GRO-seq at ZT22 (Control)

tag: age

value: Control


title: ΔihfA ΔihfB 1


title: RORg ChIP-seq at ZT22 (Control)

description:
RORg_Peaks_ZT22_ChIPseq.bed
RORag_Overlapped_Peaks_ZT22_ChIPseq.bed

data_processing:
Bowtie 1 was used to align ChIP-seq samples to mm9 genome, followed by peak-calling and generation of ucsc visualization files using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, bed
Genome_build: mm9

tag: antibody

value: RORg


title: ΔluxR 3


title: RORg ChIP-seq at ZT22 (ROR LDKO)


title: 4 hr 1% O2_DNase-seq

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
Hypoxia 4h
Cells under hypoxia condition for 24hrs.
DNase-seq

data_processing:
Fastq files were mapped to hg19 using bwa.
DNase peaks were called using macs with p=0.001 by comparing hypoxia samples to normoxia control.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files generated based on bam files for all samples.

source_name: Neuroblastoma cells

growth_protocol: SK-N-BE(2)c cells were maintained in RPMI1620 supplemented with 10% FBS.

extract_protocol:
DNase-seq was performed as described previously (Winter et al., 2013). Briefly, SK-N-BE(2)c cells were resuspended in RSB buffer (10 mM Tris pH 7.4, 10 mM NaCl, and 3 mM MgCl2) and lysed by slowly adding lysis buffer (0.1% IGEPAL CA-630 in cold RSB buffer). The nuclei were collected by centrifugation at 500 g for 5 min and were then digested with optimal concentration of DNase I (Roche) at 37°C. After 15 min, the digestion was stopped by adding EDTA. To remove the RNA, the samples were treated with RNase A at 37°C for 30 min, followed by proteinase K treatment at 55°C overnight. Subsequently, the DNA was purified by phenol-chloroform extraction and ethanol precipitation.
The DNase I ends were blunted and ligated to biotinylated linkers containing an MmeI restriction site. After digestion with MmeI, the DNase I digested ends were enriched using streptavidin magnetic beads (Dynabeads M-280, Life Technologies) and ligated to a second set of linkers. Subsequently, the DNA fragments were lightly amplified by PCR and sequenced using HiSeq technology (Illumina).

treatment_protocol: The cells were cultured either in normoxia (21% O2) or under hypoxic conditions (1% O2) for 4 hrs or 24 hrs. The hypoxia treated cells were placed in a hypoxia chamber (InVivo 400, Ruskinn) in which the oxygen concentration was maintained at 1% by controlling the nitrogen gas input.

value: hypoxia for 24hr


title: RORa ChIP-seq at ZT22 (Control)

description:
RORa_Peaks_ZT22_ChIPseq.bed
RORag_Overlapped_Peaks_ZT22_ChIPseq.bed

value: RORa


title: RORa ChIP-seq at ZT22 (ROR LDKO)


title: 24 hr 1% O2_DNase-seq

description:
Hypoxia 24h
Cells under hypoxia condition for 4hrs.
DNase-seq

value: hypoxia for 4hr


title: WT 2

source_name: WT_kate-exponential cultures

tag: gentoype/variation

value: wild type


title: Vec_2

status: Public on Dec 02 2017

city: Wuhan

first: Xin Yao

last: Qiu

state: Hubei

address: Hangkong Road 13

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.8
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 STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: Text files includes raw readcounts for all samples or normalized readcounts for all  samples.

source_name: glioblastoma cell line U251

growth_protocol: U251/PD-L1 or U251/Vec were normally cultured in DMEM supplemented with 10% FBS. And 12 h after the passage, 6 culture dished were subject to total RNA isolation.

extract_protocol:
Total RNA were extracted. RNA degradation and contamination was monitored on 1% agarose gels.
RNA purity was checked using the NanoPhotometer® 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).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: comparative vector only control

tag: vector

value: Lentivirus

tag: passage


title: Vec_1


title: WT 3


title: CD274_3

value: stable transfected cell line with PD-L1 overexpression


title: CD274_1


title: Normoxia_DNase-seq

description:
Normoxia
Cells under normoxia condition.
DNase-seq

value: normoxia


title: CD274_2


title: Vec_3


title: TG02-TMZ 1

city: Bethesda

first: Jing

state: Maryland

address: 9030 Old Georgetown Rd

department: Center for Cancer Research

institute: National Cancer Institute, NIH

data_processing:
CCBR Pipeliner (https://github.com/CCBR/Pipeliner) was used for processing of raw sequences with default settings.
EdgeR, DESeq2 and limma/voom were used for normalization and differentially-expressed gene identification.  The significant genes were identified across three methods using thresholds of FDR < 0.05 and fold changes greater than 2.
Ingenuity pathway analysis was used for functional annotation of gene functions based on EdgeR normalized counts.
Genome_build: hg19
Supplementary_files_format_and_content: tsv, edgeR_normalized counts abundance measurements

growth_protocol: Cells were grown in NBE medium, composed of Neurobasal-A medium, N2 and B27 supplements (Invitrogen) and recombinant human basic fibroblast growth factor (bFGF), epidermal growth factor (EGF) and 1 mM of L-Glutamine, at 37°C with 5% CO2

extract_protocol:
Total RNA was purified using PureLink@RNA Mini Kit per manufacturer’s instructions and the integrity of the RNA was assessed using an RNA600 Pico LabChip kit on a 2100 Bioanalyzer (Agilent Technologies). RNA samples with RNA Integrity Number (RIN) greater than 9.0 were submitted to ACGT, Inc (http://www.acgtinc.com/) for sequencing and paired-end sequencing was performed with 125 bp read length
Library and sequencing was done by ACGT Inc (http://www.acgtinc.com/).

treatment_protocol: Cell were treated with 0.1% of DMSO (control), TG02 (50 nM), TMZ (100 µM), or the combination for 48 hours

tag: cell type

value: Glioblastoma stem cells

tag: passages


title: TG02-TMZ 2


title: TMZ 1


title: Control 1


title: TG02 2


title: WT 1


title: Control 2


title: LAN1.GSK126.day5.rep2

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: Sample name: Sample 16

data_processing:
Samples were sequenced using Illumina TruSeq strand specific library. The pool of sixteen samples was sequenced on two lanes of an Illumina HiSeq, generating single end reads of 32-76 bp length.
Quality control tests for the mapped reads were performed using the FASTQC software (Babraham Lab, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read coverage per sample ranged between 17 Mbp to 24 Mbp.
The sequenced reads were aligned to the GRCh37/hg19 human genome  by using the tophat2  mapper  for single end alignment. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al, 2012) and the SARTools (Hugo Varet, 2015) pipelines. The average percentage of uniquely mapped reads in the aligned data was 86.50% with a standard deviation 2.3%.
Transcript abundance (reads and FPKM scores) at the GRCh37/hg19 RefSeq  gene level was computed with the Feature Counts method implemented in the Bioconductor v3.2 Rsubread package (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include the gene level  reads for each sample.

extract_protocol:
RNA was extracted from cells with the RNeasy Kit  (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Kelly and LAN-1 cells were treated in duplicate with 2 uM GSK126 (Excess Biosciences M60071-2) or DMSO for 2 or 5 days.

tag: treatment

tag: time

value: 5 days

tag: replicate


title: Kelly.GSK126.day2.rep1

description: Sample name: Sample 5

tag: cell line

value: Kelly

value: 2 days


title: Kelly.DMSO.day5.rep2

description: Sample name: Sample 4

value: DMSO


title: LAN1.GSK126.day2.rep1

description: Sample name: Sample 13


title: LAN1.GSK126.day5.rep1

description: Sample name: Sample 15


title: LAN1.GSK126.day2.rep2

description: Sample name: Sample 14


title: LAN1.DMSO.day2.rep2

description: Sample name: Sample 10


title: Kelly.GSK126.day5.rep2

description: Sample name: Sample 8


title: LAN1.DMSO.day5.rep1

description: Sample name: Sample 11


title: Kelly.GSK126.day2.rep2

description: Sample name: Sample 6


title: LAN1.DMSO.day5.rep2

description: Sample name: Sample 12


title: Kelly.DMSO.day5.rep1

description: Sample name: Sample 3


title: LAN1.DMSO.day2.rep1

description: Sample name: Sample 9


title: Kelly.DMSO.day2.rep1

description: Sample name: Sample 1


title: TG02 1


title: Kelly.GSK126.day5.rep1

description: Sample name: Sample 7


title: LAN1.input

data_processing:
Samples were sequenced using Illumina TruSeq strand specific library. The pool of eight samples was sequenced on two lanes of an Illumina HiSeq, generating single end reads of 50 bp length.
Quality control tests for the mapped reads were performed using the FastQC software (Babraham Lab, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
All of the ChIP-Seq data sets were aligned using Bowtie v2.2.3 (Langmead, 2010; Langmead and Salzberg, 2012) to the build version NCBI37/hg19 of the human genome. Quality control tests were performed based on the ChIPQC library available from Bioconductor v3.2 (Carroll et al., 2014).
The ChIP-Seq peaks for EZH2 and H3K4me3 were identified using MACS v1.4.3, and the ChIPSeq broad peaks for H3K27me3 were identified using MACS v.2.0.10 (Feng et al., 2012) with the cut-off 1e-05 for the P-value. The peaks were annotated by using the Annotate Peaks function available in the Homer v4.7 package (Heinz et al., 2010).
The genome-wide ChIP occupancy signal was expressed in units of reads per million mapped reads per bp (rpm/bp) and it was computed for each mark by using the  bamCoverage function available from the DeepTools v2.2.3 software package (Ramirez et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files present the genome-wide ChIP signal for each mark.

extract_protocol:
Precipitates were washed sequentially with ice cold low salt wash (0.1% SDS, 1% Triton-X- 100, 2 mM EDTA, 20 mM Tris-HCl, pH8.1, 150 mM NaCl), high salt wash (0.1% SDS, 1% Triton-X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), LiCl wash (0.25M LiCl, 1% IGEPALCA-630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1) and then twice with TE (1 mM EDTA, 10 mM Tris-HCl, pH 8.1). They were then eluted and reverse cross-linked in elution/reverse cross-linking buffer (1% SDS, 0.1 M NaHCO3, 0.2 M NaCl) for 5 hours.
Eluted DNA fragments were barcoded with a NEBNext DNA library preparation kit (NEB, Ipswich, MA) and subjected to sequencing on Illumina HiSeq 2000 platform.

treatment_protocol: ChIP-Seq experiments were performed on Kelly and LAN-1 cells by using the following antibodies:  anti-EZH2 (Cell Signaling 5246S); anti-MYCN (Santa  Cruz sc-53993); anti-H3K27me3 (Millipore 07-449); anti-H3K4me3 (Abcam ab8580). Crosslinking was performed in fresh cell culture medium containing 1% formaldehyde with gentle rotation for 5 mins in room temperature. Fixation was stopped by the addition of glycine (125 mM final concentration). Fixed cells were trypsinized, washed  twice in ice-cold PBS, and then resuspended in 3-x106 cells/130 l SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1, supplemented with fresh Complete mini protease inhibitor cocktail (Roche, Indianapolis, IN)). Chromatin was sheared to about 200bp fragments by Covaris ultrasonication. Centrifugation was used to remove debris at 4°C for 10 mins at top speed. The supernatant was diluted 1:10 using ice-cold ChIP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl pH 8.1, supplemented with fresh Complete mini protease inhibitor cocktail). Five percent of the diluted sample was saved as input controls and the  remainder of the diluted sample was used for immunoprecipitation with antibodies overnight at 4°C.

tag: chip antibody

value: none (input)


title: LAN1.EZH2

value: anti-EZH2 (Cell Signaling 5246S)


title: LAN1.H3K27me3

value: anti-H3K27me3 (Millipore 07-449)


title: Kelly.DMSO.day2.rep2

description: Sample name: Sample 2


title: TMZ 2


title: OligoPrecursorCell_αsynucletin-3

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

country: Japan

institute: KAN Research Institute Inc.

data_processing:
All raw sequencing reads were trimmed using Trimmomatic software.
Bases and QC were generated by FastQC.
The abundance of transcripts was then estimated using an Expectation-Maximization algotithm implicated in the software package Cufflink v2.2,1
Genome_build: Rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

organism: Rattus norvegicus

growth_protocol: Mixed glial culture cells was prepared from 1-2 day old rat and maintained in DMEM conatining 20% FBS. Then oligodendrocyte precursor cells were collected as non-adherent cells and cultured in Neurobasal medium containing 2 mM glutamine, 1% penicillin/streptomycin, 10 ng/ml PDGF, 10 ng/ml FGF, and 2% B27 supplement on poly-DL-ornithine-coated plates for 4-5 days.

extract_protocol:
total RNA was harvested using RNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using Agilent SureSelect Strand Specific RNA prep kit (G9691A)

treatment_protocol: Cultured oligopdendrocyte precursor cells were treated with preformed human alpha-synuclein fibrils for 72 hours.

value: Sprague-Dawley

tag: tissue

value: Cerebral cortex

value: Primary cultured oligodendrocyte precursor cells

value: preformed alpha-synclein fibrils


title: OligoPrecursorCell_αsynucletin-1


title: KELLY.H3K27me3


title: LAN1.H3K4me3

value: anti-H3K4me3 (Abcam ab8580)


title: OligoPrecursorCell_control-3

value: Control


title: KELLY.EZH2


title: OligoPrecursorCell_control-1


title: KELLY.input

value: input


title: 3M_GV_WT_6

status: Public on Dec 01 2017

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Sequencing adapters were trimmed using Cutadapt and low quality reads were pre-filtered by FASTX-Toolkit before mapping.  The quality of reads after filtering was examined using fastQC.
All filtered reads were aligned to mouse reference genome (GRCm38/mm10) by Tophat (v2.0.10) using SAMtools (v0.1.18) and Bowtie (v2.1.0) with default parameters
Individual mapped reads were fed to Cufflinks (v1.2.1) to contruct transcriptome models and any novel genes and transcripts that did not fit the supplied gene models were also assembled.
Cuffmerge was used to converge individual transcriptome to produce a master gene model.
Cufflinks was run to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) by using RefSeq genes as reference
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig

source_name: GV (germinal vesicle) oocytes

extract_protocol:
cDNA synthesis and amplification was performed using 5 oocytes per sample and Smart-Seq2 protocol.
Sequencing libraries were constructed using the amplified cDNA and Nextera® XT DNA Library Preparation Kit (Illumina, San Diego, CA) and indexed using Nextera® XT Index Kit (Illumina). Library quality was confirmed using DNA 1000 kit on Tapestation 2200 (Aglilent Technologies), and the libraries were then sequenced on Illumina’s Hiseq 2500 platform with 75bp pair-end reads.

treatment_protocol: Mature female mice were superovulated by intra-peritoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG; Sigma, St. Louis, MO) to stimulate follicle development. To collect oocytes arrested at GV (germinal vesicle) stage, mice were euthanized 44 h later by CO2 inhalation, the ovaries removed, and GV oocytes were isolated by puncturing the ovaries with a 26-1/2 G needle under the dissecting microscope (Olympus SZH-ILLK).

value: GV oocytes

tag: genotype/variation

value: wild type

value: 3 months


title: 3M_GV_KO_1

tag: strain

value: ClpP-/-


title: 6M_GV_KO_3

value: 6 months


title: 6M_GV_KO_1


title: 6M_GV_KO_2


title: 6M_GV_WT_5


title: 3M_GV_KO_3


title: 3M_GV_WT_5


title: OligoPrecursorCell_αsynucletin-2


title: KELLY.H3K4me3

value: Kelly


title: 6M_GV_WT_4


title: MEL1_TKO1

first: Nipun

last: Verma

address: 430 East 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: ERRBS

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format

source_name: MEL1 human embryonic stem cells

growth_protocol: HUES8 (NIHhESC-09-0021) hESCs were cultured on irradiated mouse embryonic fibroblasts (iMEFs) feeder layers in DMEM/F12 medium (Life Technologies, 12500-062) supplemented with 20% KnockOut Serum Replacement (Life Technologies, 10828028), 1X MEM Non-Essential Amino Acids (Life Technologies, 11140050), 1X GlutaMAX (Life Technologies, 35050079), 100U/ml Penicillin and 100 μg/ml Streptomycin (Gemini, 15070063), 0.055 mM 2-mercaptoethanol (Life Technologies, 21985023) and 10 ng/ml recombinant human bFGF (EMD Millipore, GF003AF). Cells were incubated at 37 °C with 5% (vol/vol) CO2, and media was changed daily. Cultures were passaged at a 1:6 - 1:12 split ratio every 4 - 6 days using TrypLE (Life Technologies, 12563-029). 5 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells are regularly confirmed to be mycoplasma-free by the MSKCC Antibody & Bioresource Core Facility.

extract_protocol:
For RRBS genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines.
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: No treatments were applied prior to genomic DNA extraction

value: MEL1 hESCs

tag: genotype

value: Inactivating mutations in TET1, TET2 and TET3


title: MEL1_TKO2

description: ERRBS


title: MEL1_WT2

description: ERRBS

value: Wild type sequence


title: MEL1_WT1

description: ERRBS


title: 6M_GV_WT_6


title: OligoPrecursorCell_control-2


title: 3M_GV_WT_4


title: ATP7B_1_K0243

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description:
Sample 5
all_samples_counts.txt
DEgenesKOvsWT.txt

data_processing:
Reads from each sample were mapped to mus musculus genome assembly GRCm38 using STAR v 2.4 with default parameters. STAR was provided with both fasta and GTF files for the reference genome downloaded from Ensembl.
Genes and exons read counts were calculated using featureCounts from the R package Rsubread version 1.16
Gene differential expression of KO vs WT samples was calculated using the R package edgeR version 3.8. To do this edgeR quasi-likelihood pipeline was used. First; only genes with a count-per-million above 1 in at least  three samples were retained. Then TMM normalization was performed. A Negative Binomial model extended with quasi-likelihood  was considered to take into account the different sequencing techniques used as well as samples type (KO or WT). Differentially expressed genes (DE) were determined through the QL F-test and multiple testing correction was carried out using the Benjamini-Hochberg method. Genes with adjusted p-values < 0.05 were considered DE.
Genome_build: mus musculus GRCm38
Supplementary_files_format_and_content: all_samples_counts.txt: text file with all samples read counts (tab separated) ; differential_expression_results.xlsx: excel file with the list of differentially expressed genes between KO and WT samples;

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and cleanup with the Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: Sex

value: male


title: ATP7B_1_K0204

description:
Sample 4
all_samples_counts.txt
DEgenesKOvsWT.txt


title: WT2_wild_type

description:
Sample 2
all_samples_counts.txt
DEgenesKOvsWT.txt

value: female


title: FARI_1508_C5

city: NEW YORK

first: Cecilia

last: Berin

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
processed data file:
peanut_gene_raw_counts
peanut_1r1c_RLE_normalized_RPKM

data_processing:
RNAseq reads were aligned to hg38 using star
Genes were quantified using featurecount
Cells with reads<5e5 were removed and genes with counts<1 in <cell were removed.
RPKM were calcuated after RLE normalizaiton within EdgeR
Genome_build: hg38
Supplementary_files_format_and_content:
peanut_gene_raw_counts: raw counts for each Sample
peanut_1r1c_RLE_normalized_RPKM: normalized RPKM for each Sample

growth_protocol: PBMCs were isolated by density centrifugation with Ficoll-Paque Plus (GE Healthcare) and cultured in AIM V® medium (Gibco) with 2.5% autologous plasma.

extract_protocol:
Sorted Tregs and CD154+ T cells were resuspended and loaded onto a Fluidigm C1TM Single-Cell Auto Prep IFC for Fluidigm C1TM processing as per manufacturer protocols (Fluidigm). Single-cells were visualized by microscopy and wells containing >1 cell were noted and excluded from further steps. cDNA was generated according to Fluidigm C1TM protocols with SMARTer® UltraTM Low RNA Kit for the Fluidigm C1TM System reagents (Clontech Laboratories). Resultant cDNA from Fluidigm C1TM processing was subsequently assessed for quantity and quality using a Qubit Fluorometer 3.0 (Thermo Fisher Scientific) and 2100 Bioanalyzer or 2200 TapeStation (Agilent Technologies).
cDNA which passed QC were subsequently processed for library construction using the Nextera XT DNA Library Prep and Nextera XT Index Kits (all from Illumina).

treatment_protocol: PBMCs were stimulated with 100 μg/mL crude peanut extract (CPE) or 5μL/mL anti-CD3/CD28 beads (Invitrogen) for 18 hours. For surface CD154 staining (sorting), blocking anti- CD40 antibody (Miltenyi Biotec) was added to the culture to maintain CD154 at the surface. PBMCs stimulated for 18h were harvested and enriched for CD154+ cells using the CD154 MicroBead Kit (Miltenyi Biotec). Enriched cells were stained with CD3 APC-Cy7 (Clone SK7, eBioscience), CD4 Alexa Fluor 488 (Clone OKT4, BioLegend) and CD154 streptavidin PE (Clone 24-31, eBioscience). CD3+CD4+CD154+ T cells were sorted on the BD FACSAria IIu (BD Biosciences) in Mount Sinai’s Flow Cytometry Core Facility, and resuspended according to manufacturer protocols (Fluidigm, South San Francisco, CA).

tag: subject id

tag: allergies

value: Peanut

tag: stimulation

tag: tissue/cell type

value: blood; peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: Tregs


title: FARI_1508_G4


title: WT3_wild_type

description:
Sample 3
all_samples_counts.txt
DEgenesKOvsWT.txt


title: FARI_1508_F8


title: FARI_1511_A6

source_name: polyclonally activated T cells_peanut allergic subject_FARI_1511


title: FARI_1511_A11


title: 3M_GV_KO_2

tag: cell type

tag: passage

tag: age


title: FARI_1511_C3


title: FARI_1511_B6


title: FARI_1511_B12


title: FARI_1511_D2


title: FARI_1511_E2


title: FARI_1511_E10


title: FARI_1511_D9plus4


title: FARI_1511_F12


title: FARI_1511_H2


title: FARI_1511_H9


title: FARI_1511_H7


title: FARI_1504_B7

source_name: peanut-responsive T cells_peanut allergic subject_FARI_1504


title: FARI_1504_B5


title: FARI_1504_D7


title: FARI_1504_C10


title: FARI_1504_E10


title: FARI_1504_E11


title: FARI_1504_E12


title: FARI_1504_F1


title: FARI_1504_H2


title: FARI_1508_H6


title: FARI_1511_D1


title: FARI_1508_D11


title: FARI_1508_B9


title: FARI_1511_E11


title: FARI_1511_B7


title: FARI_1511_D12plus2


title: FARI_1511_G9


title: FARI_1511_F6


title: FARI_1511_E12plus2


title: FARI_1504_E2plus2


title: FARI_1504_D4


title: FARI_1511_G10


title: FARI_1504_G10


title: FARI_1504_G12


title: FARI_1504_H9


title: FARI_1508_A12


title: FARI_1504_H4


title: FARI_1504_D12


title: FARI_1504_B11


title: FARI_1511_D3


title: FARI_1508_C11


title: FARI_1508_G10


title: FARI_1511_B1


title: FARI_1508_F10


title: FARI_1511_C11


title: FARI_1504_H12


title: FARI_1504_E4


title: FARI_1511_E4


title: FARI_1511_C10


title: FARI_1504_B1


title: FARI_1508_C1


title: FARI_1504_C12


title: FARI_1504_C4


title: FARI_1504_D1


title: FARI_1504_F10


title: FARI_1511_G12


title: FARI_1504_G3


title: FARI_1508_A9


title: FARI_1508_E4


title: FARI_1508_D3


title: FARI_1508_B1


title: FARI_1511_B5


title: FARI_1508_G11


title: FARI_1511_G8


title: FARI_1511_A10plus2


title: FARI_1511_C4plus2


title: FARI_1511_F1


title: FARI_1511_G2plus2


title: FARI_1504_A11


title: FARI_1504_F6


title: FARI_1511_H4


title: FARI_1504_A10


title: FARI_1504_B12


title: FARI_1511_H5


title: FARI_1504_C11


title: FARI_1511_H12


title: FARI_1504_D9


title: FARI_1504_F2


title: FARI_1504_F12


title: FARI_1504_H10


title: FARI_1504_H5


title: HD64_A12_S16

source_name: Tregs_healthy control_HD64


title: FARI_1504_D3


title: HD64_E11_S31


title: HD64_E3_S26


title: FARI_1511_H11


title: HD64_B1_S6


title: HD64_B8_S16


title: HD64_F6_S28


title: HD64_C1_S13


title: FARI_1511_F3


title: HD64_H9_S8


title: FARI_1504_G9


title: HD64_E9_S27


title: HD64_E4_S8


title: HD64_F12_S19


title: HD64_H5_S2


title: HD64_D7_S31


title: HD64_D6_S20


title: HD64_C2_S32


title: HD64_G10_S1


title: HD64_F11_S15


title: HD64_F10_S10


title: 1403-A3_AGGCAGAA-GCGTAAGA_L003

source_name: peanut-responsive T cells_peanut allergic subject_1403

value: Peanut & Egg & Milk


title: 1402-B11_AAGAGGCA-CTCTCTAT_L005

source_name: polyclonally activated T cells_peanut allergic subject_1402


title: HD64_A10_S7


title: 1401-G8_CAGAGAGG-AAGGAGTA_L002

source_name: peanut-responsive T cells_peanut allergic subject_1401


title: 1375-B5_GGACTCCT-CTCTCTAT_L001

source_name: peanut-responsive T cells_peanut allergic subject_1375


title: 1407-G7_CTCTCTAC-AAGGAGTA_L004

source_name: peanut-responsive T cells_peanut allergic subject_1407


title: 1375-B11_AAGAGGCA-CTCTCTAT_L001


title: HD64_H6_S23


title: 1401-E1_TAAGGCGA-GTAAGGAG_L002


title: 1402-A9_GCTACGCT-GCGTAAGA_L005


title: HD53-D4_TCCTGAGC-AGAGTAGA_L007

source_name: Tregs_healthy control_HD53


title: HD64_A9_S11


title: 1434-F8_CAGAGAGG-ACTGCATA_L008


title: 1430-E11_AAGAGGCA-GTAAGGAG_L006

source_name: polyclonally activated T cells_peanut allergic subject_1430


title: 1375-C1_TAAGGCGA-TATCCTCT_L001


title: HD64_G11_S26


title: 1430-G4_TCCTGAGC-AAGGAGTA_L006


title: 1375-D9_GCTACGCT-AGAGTAGA_L001


title: 1403-C2_CGTACTAG-TATCCTCT_L003


title: 1402-D6_TAGGCATG-AGAGTAGA_L005


title: 1402-A7_CTCTCTAC-GCGTAAGA_L005


title: 1403-C5_GGACTCCT-TATCCTCT_L003


title: 1436-C6_TAGGCATG-TATCCTCT_L007


title: 1375-A10_CGAGGCTG-GCGTAAGA_L001


title: 1403-D2_CGTACTAG-AGAGTAGA_L003


title: 1430-F3_AGGCAGAA-ACTGCATA_L008


title: 1402-B2_CGTACTAG-CTCTCTAT_L007


title: 1436-C3_AGGCAGAA-TATCCTCT_L007


title: 1430-F5_GGACTCCT-ACTGCATA_L006


title: 1407-E4_TCCTGAGC-GTAAGGAG_L004


title: 1402-C6_TAGGCATG-TATCCTCT_L005


title: 1401-G4_TCCTGAGC-AAGGAGTA_L002


title: 1430-F12_GTAGAGGA-ACTGCATA_L006


title: 1401-G11_AAGAGGCA-AAGGAGTA_L002


title: 1401-E12_GTAGAGGA-GTAAGGAG_L002


title: 1401-G2_CGTACTAG-AAGGAGTA_L002


title: 1430-G6_TAGGCATG-AAGGAGTA_L006


title: 1434-F7_CTCTCTAC-ACTGCATA_L008


title: 1401-E6_TAGGCATG-GTAAGGAG_L002


title: 1403-A1_TAAGGCGA-GCGTAAGA_L003


title: 1375-A7_CTCTCTAC-GCGTAAGA_L001


title: 1402-C4_TCCTGAGC-TATCCTCT_L005


title: 1430-H7_CTCTCTAC-CTAAGCCT_L006


title: HD53-D3_AGGCAGAA-AGAGTAGA_L007


title: HD51-G7_CTCTCTAC-AAGGAGTA_L008

source_name: Tregs_healthy control_HD51


title: 1407-E12_GTAGAGGA-GTAAGGAG_L004


title: 1430-H8_CAGAGAGG-CTAAGCCT_L006


title: HD53-D2_CGTACTAG-AGAGTAGA_L007


title: 1407-H6_TAGGCATG-CTAAGCCT_L004


title: 1407-H5_GGACTCCT-CTAAGCCT_L004


title: 1401-E8_CAGAGAGG-GTAAGGAG_L002


title: 1401-H1_TAAGGCGA-CTAAGCCT_L002


title: 1401-F6_TAGGCATG-ACTGCATA_L002


title: 1430-G12_GTAGAGGA-AAGGAGTA_L006


title: 1402-A8_CAGAGAGG-GCGTAAGA_L005


title: 1375-A6_TAGGCATG-GCGTAAGA_L001


title: HD51-G11_AAGAGGCA-AAGGAGTA_L008


title: 1401-F2_CGTACTAG-ACTGCATA_L002


title: 1401-F10_CGAGGCTG-ACTGCATA_L002


title: 1407-H3_AGGCAGAA-CTAAGCCT_L004


title: 1403-A11_AAGAGGCA-GCGTAAGA_L003


title: 1401-F11_AAGAGGCA-ACTGCATA_L002


title: 1435-F12_GTAGAGGA-ACTGCATA_L008


title: HD51-G8_CAGAGAGG-AAGGAGTA_L008


title: 1430-G8_CAGAGAGG-AAGGAGTA_L006


title: 1401-G5_GGACTCCT-AAGGAGTA_L002


title: 1403-B1_TAAGGCGA-CTCTCTAT_L003


title: 1375-B8_CAGAGAGG-CTCTCTAT_L001


title: 1435-B11_AAGAGGCA-CTCTCTAT_L007


title: 1401-H8_CAGAGAGG-CTAAGCCT_L002


title: 1403-A7_CTCTCTAC-GCGTAAGA_L003


title: 1401-H2_CGTACTAG-CTAAGCCT_L002


title: 1375-C12_GTAGAGGA-TATCCTCT_L001


title: 1375-C3_AGGCAGAA-TATCCTCT_L001


title: HD54-H5_GGACTCCT-CTAAGCCT_L008

source_name: Tregs_healthy control_HD54


title: c - high weight of loin - 10hp

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

description: c - high weight of loin

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa  genome  as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw.genes.*.csv.gz - raw genes counts
Supplementary_files_format_and_content: res.genes.*.csv.gz - DESeq2 results for differential expressed gene analysis

organism: Sus scrofa

source_name: Hampshire_high weight loin_muscle tissue

extract_protocol:
Immediately after slaughter, tissue samples were collected into RNAlater solution (Ambion, ThermoFisher) and stored at -20°C. The total RNA was isolated from muscle tissue with the use of Direct-zol RNA Mini Prep (ZymoResearch). The quality and quantity of obtained RNA were checked on NanoDrop 2000 spektrofotometer  (Thermo Scientific; Wilmington, USA) and on TapeStation 2200 (RNAScreen Tape, Agilent, Perlan Technologies, Poland). Samples with RIN above 7.5 were used to libraries construction.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.

tag: breed

value: Hampshire pigs

tag: gender

value: 6 month

tag: loin weight group

value: high weight of loin

value: longissimus lumborum


title: c - high weight of loin - 9hp

description: c - high weight of loin


title: 1375-C10_CGAGGCTG-TATCCTCT_L001


title: b - low weight of loin - 8p

description: b - low weight of loin

source_name: Pietrain_low weight loin_muscle tissue

value: Pietrain pigs

value: low weight of loin


title: 1430-F10_CGAGGCTG-ACTGCATA_L006


title: c - high weight of loin - 8hp

description: c - high weight of loin


title: 1407-G6_TAGGCATG-AAGGAGTA_L004


title: HD53-C12_GTAGAGGA-TATCCTCT_L007


title: a - high weight of loin - 7p

description: a - high weight of loin

source_name: Pietrain_high weight loin_muscle tissue


title: 1401-F12_GTAGAGGA-ACTGCATA_L002


title: b - low weight of loin - 5p

description: b - low weight of loin


title: 1375-B10_CGAGGCTG-CTCTCTAT_L001


title: b - low weight of loin - 3p

description: b - low weight of loin


title: 1403-C3_AGGCAGAA-TATCCTCT_L003


title: a - high weight of loin - 6p

description: a - high weight of loin


title: 1401-G1_TAAGGCGA-AAGGAGTA_L002


title: 1434-B6_TAGGCATG-CTCTCTAT_L007


title: 1401-G12_GTAGAGGA-AAGGAGTA_L002


title: d - low weight of loin - 3hp

description: d - low weight of loin

source_name: Hampshire_low weight loin_muscle tissue


title: 1402-A2_CGTACTAG-GCGTAAGA_L005


title: a - high weight of loin - 2p

description: a - high weight of loin


title: 1403-A8_CAGAGAGG-GCGTAAGA_L003


title: 1436-G3_AGGCAGAA-AAGGAGTA_L008


title: 1407-F11_AAGAGGCA-ACTGCATA_L004


title: 1430-H6_TAGGCATG-CTAAGCCT_L006


title: a - high weight of loin - 1p

description: a - high weight of loin


title: 1401-E5_GGACTCCT-GTAAGGAG_L002


title: d - low weight of loin - 2hp

description: d - low weight of loin


title: 1407-G1_TAAGGCGA-AAGGAGTA_L004


title: d - low weight of loin - 1hp

description: d - low weight of loin


title: 1375-A2_CGTACTAG-GCGTAAGA_L001


title: 1430-G10_CGAGGCTG-AAGGAGTA_L006


title: 20SKB_1

city: Waurn Ponds

first: Sanna

last: Barrand

state: VIC

address: 75 Pigdon Rd

department: Faculty of Health, School of Medicine

country: Australia

institute: Deakin University

description: femaleDifferentialCounts0_50_topTable_edgeR xls tabular_processed data

data_processing:
quality control using fastQC
alignment using tophat suite
normalisation and differential expression edgeR
Genome_build: rn6
Supplementary_files_format_and_content: Excel file contains raw and normalized read count and statistics

source_name: Hypothalamic RNA

extract_protocol:
At postnatal day 10, the offspring was humanely culled, hypothalamus was dissected, snap frozen in liquid nitrogen and stored at -80 degrees until RNA extraction. RNA was extracted using manufactures protocol (Allprep RNA/DNA mini kit (cat.no 80204 Qiagen, Hilden, Germany) and send to library prep and sequencing at Macrogen Inc., Korea, in RNAstable tubes.
TruSeq RNA Library Prep Kit

treatment_protocol: Maternal High fat diet (43% digestible energy from lipids) or control diet (12% digestible energy from lipids) exposure during pregnancy and postnatal life until postnatal day 10

value: Sprague Dawley

value: Hypothalamus

value: Postnatal day 10

tag: diet

value: high fat diet


title: 21SKB_1

description: maleDifferentialCounts0_50_topTable_edgeR.xls.tabular_processed data

tag: tissue


title: 1402-C11_AAGAGGCA-TATCCTCT_L005


title: 19SKB_1


title: 1402-D3_AGGCAGAA-AGAGTAGA_L005


title: 1401-G3_AGGCAGAA-AAGGAGTA_L002


title: HD53-H2_CGTACTAG-CTAAGCCT_L008


title: 23SKB_1


title: 24SKB_1


title: 1436-G2_CGTACTAG-AAGGAGTA_L008


title: 1430-E10_CGAGGCTG-GTAAGGAG_L006


title: 15SKB_1


title: 1402-C5_GGACTCCT-TATCCTCT_L005


title: 18SKB_1


title: 1407-G8_CAGAGAGG-AAGGAGTA_L004


title: 17SKB_1


title: HD51-C7_CTCTCTAC-TATCCTCT_L007


title: 16SKB_1


title: 12SKB_1

value: control diet


title: HD54-D6_TAGGCATG-AGAGTAGA_L007


title: 22SKB_1


title: HD54-D8_CAGAGAGG-AGAGTAGA_L007


title: 11SKB_1

value: male


title: 1375-B6_TAGGCATG-CTCTCTAT_L001


title: 10SKB_1

value: female


title: 14SKB_1


title: 1430-E12_GTAGAGGA-GTAAGGAG_L008

value: Peanut


title: 9SKB_1


title: 1403-D8_CAGAGAGG-AGAGTAGA_L003

value: blood; peripheral blood mononuclear cells (PBMCs)


title: 1407-F1_TAAGGCGA-ACTGCATA_L004


title: 1401-H6_TAGGCATG-CTAAGCCT_L002


title: 13SKB_1


title: 1430-E2_CGTACTAG-GTAAGGAG_L006


title: 1375-A3_AGGCAGAA-GCGTAAGA_L001


title: 8SKB_1


title: 6SKB_1


title: 1403-B3_AGGCAGAA-CTCTCTAT_L003


title: 1435-F11_AAGAGGCA-ACTGCATA_L008

value: Tregs


title: 1375-A9_GCTACGCT-GCGTAAGA_L001


title: HD53-H1_TAAGGCGA-CTAAGCCT_L008


title: 1430-E1_TAAGGCGA-GTAAGGAG_L006


title: 5SKB_1


title: 4SKB_1


title: 1SKB_1


title: 3SKB_1


title: 2SKB_1


title: 1402-B9_GCTACGCT-CTCTCTAT_L005


title: 1403-D9_GCTACGCT-AGAGTAGA_L003

value: Peanut & Egg & Milk


title: 1430-F4_TCCTGAGC-ACTGCATA_L006


title: HD54-H8_CAGAGAGG-CTAAGCCT_L008


title: 1375-C2_CGTACTAG-TATCCTCT_L001


title: 1375-D1_TAAGGCGA-AGAGTAGA_L001


title: 1430-H9_GCTACGCT-CTAAGCCT_L006


title: 1402-D7_CTCTCTAC-AGAGTAGA_L005


title: 1375-D7_CTCTCTAC-AGAGTAGA_L001


title: 1403-B5_GGACTCCT-CTCTCTAT_L003


title: 1430-G2_CGTACTAG-AAGGAGTA_L006


title: 1402-D5_GGACTCCT-AGAGTAGA_L005


title: HD51-G10_CGAGGCTG-AAGGAGTA_L008


title: 1403-D1_TAAGGCGA-AGAGTAGA_L003


title: 7SKB_1


title: 1430-F9_GCTACGCT-ACTGCATA_L006


title: 1403-A4_TCCTGAGC-GCGTAAGA_L003


title: 1375-D8_CAGAGAGG-AGAGTAGA_L001


title: 1436-G4_TCCTGAGC-AAGGAGTA_L008


title: 1375-B2_CGTACTAG-CTCTCTAT_L001


title: HD51-C9_GCTACGCT-TATCCTCT_L007


title: 1402-A6_TAGGCATG-GCGTAAGA_L005


title: 1375-B7_CTCTCTAC-CTCTCTAT_L001


title: 1436-C4_TCCTGAGC-TATCCTCT_L007


title: 1403-D3_AGGCAGAA-AGAGTAGA_L003


title: 1430-F2_CGTACTAG-ACTGCATA_L008


title: 1401-E3_AGGCAGAA-GTAAGGAG_L008


title: 1430-H1_TAAGGCGA-CTAAGCCT_L006


title: 1375-C11_AAGAGGCA-TATCCTCT_L001


title: 1430-H5_GGACTCCT-CTAAGCCT_L006


title: 1403-B4_TCCTGAGC-CTCTCTAT_L003


title: 1401-G9_GCTACGCT-AAGGAGTA_L002


title: 1407-G10_CGAGGCTG-AAGGAGTA_L004


title: 1403-C9_GCTACGCT-TATCCTCT_L003


title: 1401-E9_GCTACGCT-GTAAGGAG_L002


title: 1430-F7_CTCTCTAC-ACTGCATA_L006


title: 1434-F4_TCCTGAGC-ACTGCATA_L008


title: 1407-H4_TCCTGAGC-CTAAGCCT_L004


title: 1435-D10_CGAGGCTG-AGAGTAGA_L007


title: 1434-F5_GGACTCCT-ACTGCATA_L008


title: 1401-G10_CGAGGCTG-AAGGAGTA_L002


title: 1430-E3_AGGCAGAA-GTAAGGAG_L006


title: 1401-F9_GCTACGCT-ACTGCATA_L002


title: 1402-B12_GTAGAGGA-CTCTCTAT_L005


title: HD51-G9_GCTACGCT-AAGGAGTA_L008


title: 1407-F6_TAGGCATG-ACTGCATA_L004


title: 1403-B6_TAGGCATG-CTCTCTAT_L003


title: 1401-E7_CTCTCTAC-GTAAGGAG_L002


title: 1430-F8_CAGAGAGG-ACTGCATA_L006


title: 1402-B5_GGACTCCT-CTCTCTAT_L005


title: 1403-B8_CAGAGAGG-CTCTCTAT_L003


title: 1403-C11_AAGAGGCA-TATCCTCT_L003


title: 1430-G3_AGGCAGAA-AAGGAGTA_L006


title: 1434-B4_TCCTGAGC-CTCTCTAT_L007


title: 1407-H9_GCTACGCT-CTAAGCCT_L004


title: 1403-A12_GTAGAGGA-GCGTAAGA_L003


title: 1375-A1_TAAGGCGA-GCGTAAGA_L001


title: 1401-F8_CAGAGAGG-ACTGCATA_L002


title: 1401-E4_TCCTGAGC-GTAAGGAG_L008


title: 1407-E8_CAGAGAGG-GTAAGGAG_L004


title: 1403-C4_TCCTGAGC-TATCCTCT_L003


title: 1402-A10_CGAGGCTG-GCGTAAGA_L005


title: 1401-G6_TAGGCATG-AAGGAGTA_L002


title: 1430-E9_GCTACGCT-GTAAGGAG_L006


title: 1435-G1_TAAGGCGA-AAGGAGTA_L008


title: HD54-H7_CTCTCTAC-CTAAGCCT_L008


title: 1402-A1_TAAGGCGA-GCGTAAGA_L005


title: 1434-B7_CTCTCTAC-CTCTCTAT_L007


title: 1401-F1_TAAGGCGA-ACTGCATA_L002


title: 1430-F1_TAAGGCGA-ACTGCATA_L006


title: 1401-G7_CTCTCTAC-AAGGAGTA_L002


title: 1375-C6_TAGGCATG-TATCCTCT_L001


title: 1401-F7_CTCTCTAC-ACTGCATA_L002


title: 1401-F4_TCCTGAGC-ACTGCATA_L002


title: 1403-C12_GTAGAGGA-TATCCTCT_L003


title: 1403-A9_GCTACGCT-GCGTAAGA_L007


title: 1403-B2_CGTACTAG-CTCTCTAT_L003


title: 1434-B8_CAGAGAGG-CTCTCTAT_L007


title: 1436-C5_GGACTCCT-TATCCTCT_L007


title: 1430-H4_TCCTGAGC-CTAAGCCT_L006


title: 1375-D5_GGACTCCT-AGAGTAGA_L001


title: 1430-E4_TCCTGAGC-GTAAGGAG_L006


title: 1403-D4_TCCTGAGC-AGAGTAGA_L003


title: 1430-F2_CGTACTAG-ACTGCATA_L006


title: 1403-A9_GCTACGCT-GCGTAAGA_L003


title: 1407-E10_CGAGGCTG-GTAAGGAG_L008


title: 1407-F3_AGGCAGAA-ACTGCATA_L004


title: 1436-C2_CGTACTAG-TATCCTCT_L007


title: 1407-H1_TAAGGCGA-CTAAGCCT_L004


title: 1407-G11_AAGAGGCA-AAGGAGTA_L004


title: 1401-F3_AGGCAGAA-ACTGCATA_L002


title: 1430-G1_TAAGGCGA-AAGGAGTA_L006


title: 1407-E9_GCTACGCT-GTAAGGAG_L004


title: 1402-A12_GTAGAGGA-GCGTAAGA_L007


title: 1434-B5_GGACTCCT-CTCTCTAT_L007


title: 1407-G2_CGTACTAG-AAGGAGTA_L004


title: 1402-B3_AGGCAGAA-CTCTCTAT_L007


title: 1403-C8_CAGAGAGG-TATCCTCT_L003


title: HD53-H3_AGGCAGAA-CTAAGCCT_L008


title: 1430-G9_GCTACGCT-AAGGAGTA_L006


title: HD54-D5_GGACTCCT-AGAGTAGA_L007


title: 1403-A5_GGACTCCT-GCGTAAGA_L003


title: 1430-E5_GGACTCCT-GTAAGGAG_L006


title: HD53-H4_TCCTGAGC-CTAAGCCT_L008


title: 1435-B12_GTAGAGGA-CTCTCTAT_L007


title: 1403-C6_TAGGCATG-TATCCTCT_L003


title: HD53-G12_GTAGAGGA-AAGGAGTA_L008


title: 1403-C10_CGAGGCTG-TATCCTCT_L003


title: HD54-D9_GCTACGCT-AGAGTAGA_L007


title: 1430-H3_AGGCAGAA-CTAAGCCT_L006


title: 1430-E11_AAGAGGCA-GTAAGGAG_L008


title: 1407-H8_CAGAGAGG-CTAAGCCT_L004


title: 1435-F9_GCTACGCT-ACTGCATA_L008


title: 1403-B12_GTAGAGGA-CTCTCTAT_L003


title: 1430-F1_TAAGGCGA-ACTGCATA_L008


title: HD51-C10_CGAGGCTG-TATCCTCT_L007


title: 1401-E1_TAAGGCGA-GTAAGGAG_L008


title: 1407-H7_CTCTCTAC-CTAAGCCT_L004


title: 1402-D1_TAAGGCGA-AGAGTAGA_L005


title: 1375-A5_GGACTCCT-GCGTAAGA_L007


title: 1403-A2_CGTACTAG-GCGTAAGA_L003


title: 1436-G5_GGACTCCT-AAGGAGTA_L008


title: 1375-D6_TAGGCATG-AGAGTAGA_L001


title: 1403-D5_GGACTCCT-AGAGTAGA_L003


title: 1401-H7_CTCTCTAC-CTAAGCCT_L002


title: HD54-H6_TAGGCATG-CTAAGCCT_L008


title: 1375-C5_GGACTCCT-TATCCTCT_L001


title: 1402-A11_AAGAGGCA-GCGTAAGA_L007


title: 1375-C9_GCTACGCT-TATCCTCT_L001


title: 1403-A10_CGAGGCTG-GCGTAAGA_L007


title: 1/12 mutations

city: Baltimore

first: Daniel

last: Goldman

address: 725 N. Wolfe St.

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

data_processing:
adaptor removed with Cutadapt
reads mapped to lamin locus with Bowtie 2
low quality (Q < 35) and incompletely mapping reads removed (custom code)
read "anchored" by using the first diagnostic position to score the identity of the template as wild-type or mutated (custom code)
reads parsed for template switches by counting the number of times two consecutive diagnostic positions indicated a switch in template identity (custom code)
Genome_build: custom build (see supplementary WT_template.fa file)
Supplementary_files_format_and_content: for each dataset, a tab-separated file of processed reads, in which each row represents one processed read and the first column indicates the number of template switches, the second column indicates the nucleotide position(s) of template switches, the third column is the read seqeunce, the fourth column is an array of 0s and 1s representing WT or mutated template identity for each nucleotide, the fifth column is the array of 0s and 1s as in the previous column except now with the initial identity of the template "anchored" by the first diagnostic position (as indicated in the publication methods), the sixth column indicates whether the sequence is wild-type at all non-diagnostic positions ("true" or "false"), and the seventh column indicates whether the read is entirely wild-type in sequence ("WT") or entirely mutated ("mut") or a hybrid ("chimera)

source_name: HEK293T cells

growth_protocol: HEK293T cells grown in DMEM + 10% FBS

extract_protocol:
60h after nucleofection, cells were trypsinized, washed in PBS, and 500000 cells were lysed in 40µl of QuickExtract DNA Extraction Solution. 40µl of H2O was added to each lysis.
PCR amplicons were purified on a 10% non-denaturing TBE/PAGE gel and the band corresponding to the PCR product was cut from the gel, eluted over-night, and precipitated with isopropanol. After resuspension, sample concentrations were quantified on a bioanalyzer, and the barcoded samples were pooled to a concentration of 0.4µM per sample in 10µl.

treatment_protocol: HEK293T (GFP1-10) were nucleofected with different combinations of repair ssODNs.

tag: cell line

tag: genotype/variation

value: 1/12 mutations


title: 1402-D4_TCCTGAGC-AGAGTAGA_L005


title: 1430-F3_AGGCAGAA-ACTGCATA_L006


title: 1/6 mutations

value: 1/6 mutations


title: 1402-C1_TAAGGCGA-TATCCTCT_L005


title: 1401-H5_GGACTCCT-CTAAGCCT_L002


title: 1375-A8_CAGAGAGG-GCGTAAGA_L001


title: 1401-E10_CGAGGCTG-GTAAGGAG_L002


title: 1/3 mutations

value: 1/3 mutations


title: PCR control

value: PCR control


title: 1375-A12_GTAGAGGA-GCGTAAGA_L001


title: 1407-E5_GGACTCCT-GTAAGGAG_L004


title: 1430-E7_CTCTCTAC-GTAAGGAG_L006


title: 1375-B3_AGGCAGAA-CTCTCTAT_L001


title: No mutation

value: No mutation


title: 1407-G9_GCTACGCT-AAGGAGTA_L004


title: 1434-F6_TAGGCATG-ACTGCATA_L008


title: 1403-A10_CGAGGCTG-GCGTAAGA_L003


title: HD54-H9_GCTACGCT-CTAAGCCT_L008


title: 1435-B10_CGAGGCTG-CTCTCTAT_L007


title: 1375-C4_TCCTGAGC-TATCCTCT_L001


title: 1430-F11_AAGAGGCA-ACTGCATA_L006


title: 1375-B9_GCTACGCT-CTCTCTAT_L001


title: 1403-B11_AAGAGGCA-CTCTCTAT_L003


title: 1402-A11_AAGAGGCA-GCGTAAGA_L005


title: HD51-C8_CAGAGAGG-TATCCTCT_L007


title: 1407-G12_GTAGAGGA-AAGGAGTA_L004


title: 1403-C1_TAAGGCGA-TATCCTCT_L003


title: 1403-D6_TAGGCATG-AGAGTAGA_L003


title: 1375-C7_CTCTCTAC-TATCCTCT_L001


title: 1402-B1_TAAGGCGA-CTCTCTAT_L005


title: 1403-B9_GCTACGCT-CTCTCTAT_L003


title: 1430-H2_CGTACTAG-CTAAGCCT_L006