title: Ishi_DMSO_ChIP_H3K27ac

data_processing:
Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 with the following arguments: bowtie --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files, pileup values for reads
Supplementary_files_format_and_content: Excel file,  Chromosome, start, stop, length, summit, pvalue, fold_enrichment, qvalue, and name values for peaks called by macs2

growth_protocol: Ishikawa cells were grown in phenol red-free RPMI-1640 media supplemented with 10% charcoal/dextran treated fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin for at least 4 days before treatment.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking.  Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009

treatment_protocol: Cells were treated with 100 nM dexamethasone, 10 nM 17-beta-estradiol, or vehicle control (DMSO) for 1 hour prior to crosslinking.

value: DMSO (vehicle) for 8 hours

tag: target protein

value: H3K27ac pAb (Active Motif 39133)


title: Ishi_Dex_ChIP_H3K27ac

status: Public on Mar 13 2018

type: SRA

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

country: USA

institute: University of Utah

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Ishikawa

tag: cell line

value: Ishikawa

tag: treatment

value: 100 nM Dexamethasone for 8 hours

tag: antibody


title: IshI_Dex_2_RNA_seq

description:
processed data files:
Ishi_RNAseq_allsets_raw.counts
Ishi_RNAseq_allsets_normalized.counts

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 build of the human genome using hisat2 V 2.0.4 with the following commands: hisat2 --dta  -t -q
counts were quantified with Subread FeatureCounts V. 1.5.1
Differential expression was determined using DESeq2 V 1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values.  These files contain raw and normalized counts for genes from the hg19 genome.

molecule: total RNA

growth_protocol: Ishikawa cells were grown in phenol red-free RPMI-1640 media supplemented with 10% charcoal/dextran treated fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin for at least 4 days before lysis.

extract_protocol:
Cells were lysed with RLT (Qiagen) plus 1% BME and total RNA was extracted from the lysis using Zymo's Quick RNA miniprep kit.
Libraries were constructed usinig the Kapa stranded mRNA-seq kit.

treatment_protocol: Cells were treated with 100 nM dexamethasone, 10 nM 17-beta-estradiol, or vehicle control (DMSO) for 1 hour prior to trypsinization.

value: 100 nM Dexamethasone 8 hr

tag: replicate


title: Ishi_Comb_Input_H3K27ac

value: IgG Control

value: none (IgG control)


title: Ishi_DMSO_ChIP_ER

value: DMSO (vehicle) for 1 hour

value: ER

value: ER HC-20 (Santa Cruz sc-543)


title: Ishi_E2_ChIP_H3K27ac

value: 10 nM Estradiol for 8 hours


title: Ishi_E2_ChIP_ER

value: 10 nM Estradiol for 1 hour


title: Ishi_E2_Dex_ChIP_H3K27ac

value: 100 nM Dexamethasone and 10 nM Estradiol for 8 hours


title: Ishi_Dex_ChIP_GR

value: 100 nM Dexamethasone for 1 hour

value: GR

value: GR E-20 (Santa Cruz sc-1003)


title: Ishi_Dex_1_RNA_seq


title: Ishi_Dex_E2_ChIP_GR

value: 100 nM Dexamethasone and 10 nM Estradiol for 1 hour


title: Ishi_DMSO_ChIP_GR


title: Ishi_DMSO_1_RNA_seq

value: DMSO 8hr


title: Ishi_Dex_E2_ChIP_ER


title: Ishi_E2_ATAC_Seq

data_processing:
Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 with the following arguments: bowtie --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files, pileup values for reads
Supplementary_files_format_and_content: Excel file,  Chromosome, start, stop, length, summit, pvalue, fold_enrichment, qvalue and name values for peaks called by macs2

extract_protocol:
Treated cells were trypsinized and purified by centrifugation before being place in nuclei isolation buffer (lysis buffer) containing 0.1% IGEPAL. Nuclei were then counted and 250,000 cells were used in ATAC-seq library preparation
Libraries were constructed as described in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al.  2015 Curr Proc Mol Biol

value: 10 nM Estradiol 1 Hr


title: Hi-ChIP_RAD21_KO

city: Beijing

first: Chenhuan

last: Xu

address: 1 Beichen West Road

country: China

institute: Beijing Institute of Genomics

description: processed file: HUES64-3BKO_RAD21.hic

data_processing:
Juicer (42) was used to analyze RAD21 Hi-ChIP data. Only interaction contacts with mapping quality score q≥5 were retained. The WT library was down-sampled to match the number of interaction contacts in the DNMT3B-KO library. Juicebox (43) was used to obtain interaction matrices at 25 kb resolution. The total interaction contacts of CTCF motif-containing 25 kb bins with each consecutive downstream or upstream 25 kb bin were retrieved from the matrix. The ratio of total interaction contacts (WT over DNMT3B-KO) was calculated for each 25 kb bin within a ±1 Mb window surrounding CTCF motif-containing bins.
Genome_build: hg38

growth_protocol: H9 human embryonic stem cells were obtained from WiCell. Cells were cultured in STEMPRO hESC SFM on cultureware coated with Geltrex Matrix at 37 °C under 5% CO2. Medium was changed every day. Cells were grown to 60-70% confluence before EdU labeling.

extract_protocol: See Rowley et al., 2017.

tag: cell type

value: HUES64 human embryonic stem cells

tag: chip antibody

value: RAD21 (abcam, ab992)


title: Hi-ChIP_RAD21_WT

description: processed file: HUES64_RAD21.hic


title: Ishi_DMSO_ATAC_Seq

value: Ishikawa

value: DMSO 1 Hr


title: Ishi_Dex_ATAC_Seq

value: 100 nM Dexamethasone 1 Hr


title: ChIP-seq_RAD21_KO

description: processed file: HUES64-3BKO_RAD21.bw

data_processing:
50 bp paired-end reads were aligned to the human genome (hg38, XX) using bowtie2. Alignment score was controlled by applying bowtie2 option --score-min L,0,-0.4. Mapping uniqueness was controlled by selecting alignments with mapping quality Q>10 using Samtools. Peak calling and read density calculation were done using MACS2 (2.1.0) with BAMPE option (38). Matrix underlying heatmaps was generated with deepTools (2.5.4) (39) and was visualized using Java Treeview (40).
Genome_build: hg38

extract_protocol: Approximately 1x107 H9 hESCs were used to make each nasChIP-seq library. Anti-CTCF (Millipore) or -SMC1A (Millipore) antibodies were pre-incubated with Dynabeads Protein A beads (Thermo Fisher). Extracted chromatin was incubated with antibody-beads complex on a rotator at 4 °C for 5 hr. Beads were washed once with Wash Buffer (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), twice with LiCl Buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA pH 8.0, 1% NP-40, 1% sodium deoxycholate), and once with 1x TE pH 8.0 with 50 mM NaCl. DNA was eluted by incubating beads in Elution Buffer at 65 °C for 30 min. Crosslinking-reversal, proteinase K digestion, phenol:chloroform:isoamyl alcohol extraction, ethanol precipitation, click chemistry, ethanol precipitation, streptavidin beads pull-down, and Illumina library preparation steps were the same as described above for nasBS-seq.


title: ChIP-seq_CTCF_KO

description: processed file: HUES64-3BKO_CTCF.bw

value: CTCF (abcam, ab70303)


title: ChIP-hairpinBS-seq_CTCF_rep1

description: processed file: H9_CTCF-hairpinCpG.bed

data_processing:
50 bp paired-end reads were first trimmed with Trimmomatic (0.36) (33) to remove any remnant adaptor sequence and bases with Phred quality score <20. Only pairs with both reads ≥20 bp were retained for subsequent analysis. Reads were aligned to the human genome (hg38, XX) using bismark (0.19.0) (34) with bowtie2 (2.2.9) (35). In rare cases of mapping rate <50%, two adjustments were made sequentially to improve the yield: 1) The 5’ end of the mate 2 reads were trimmed 5-10 bases off, which generally increased the mapping rate by 10-20%. 2) The mate 1 reads from the unmapped paired-end reads were retrieved for single-end mapping, given the fact that mate 1 reads alone could achieve >70% mapping rate under such circumstances. Alignment score was controlled by applying bowtie2 option --score-min L,0,-0.4. Mapping uniqueness was controlled by selecting alignments with mapping quality Q>10 using Samtools (1.6) (36). For each library, reads were specifically mapped to either the Watson or Crick strand, and duplicate reads were removed by bismark. Methylation of single cytosines was called from strand-specific alignments. For each strand, methylation calls from all biological replicates were pooled together unless otherwise noted. Methylation of CpGs was extracted from certain pairs of Watson/Crick strand methylation calls using bedtools (2.27.0) (37). The unmapped reads from bismark were re-aligned to the lambda genome to determine the bisulfite conversion rate of each library.
Genome_build: hg38

extract_protocol: Approximately 3x107 H9 hESCs were used to make each ChIP-hairpinBS-seq library. Anti-CTCF (Millipore) antibodies were pre-incubated with Dynabeads Protein A beads (Thermo Fisher). Extracted chromatin was incubated with antibody-beads complex on a rotator at 4 °C for 5 hr. Beads were washed once with Wash Buffer (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), twice with LiCl Buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA pH 8.0, 1% NP-40, 1% sodium deoxycholate), and once with 1x TE pH 8.0 with 50 mM NaCl. DNA was eluted by incubating beads in Elution Buffer at 65 °C for 30 min. Crosslinking-reversal, proteinase K digestion, phenol:chloroform:isoamyl alcohol extraction, ethanol precipitation, end repair reaction, and A-tailing reaction were performed. The rest of the protocol followed the method reported in (31).

value: H9 human embryonic stem cells

tag: passages


title: ChIP-seq_CTCF_WT

description: processed file: HUES64_CTCF.bw


title: Stat92E_0.7mSucrose_4_98

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "4KD+ processed data" containing normalized RPKM for each raw dataset, indexed by gene Accession (CG number)

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Wild-type males (VDRC's w1118 or 60100 control stocks) were crossed to fat body GAL4 driver line virgin females to produce so-called wild-type offspring that served as controls for the following RNAi line crosses: VDRC lines targeting dFOXO (CG3143), Stat92E (CG4257), p53 (CG33336), or Tfb1 (CG8151) as described in Musselman et al, GENETICS, 2018. Larval offspring were collected at the end of larval development (also known as the wandering third instar stage).

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared on control (0.15M) or high-sugar (0.7M or 1 M sucrose) diets using a modified Bloomington semi-defined food as previously described (J Biol Chem 288(12):8028-42). Fat bodies were isolated by fine dissection or by shearing and separation by centrifugation.

tag: tissue

value: fat body

tag: developmental stage

value: wandering third instar larva

tag: Sex

value: Female

value: 0.7m Sucrose

tag: genotype

value: VDRC's 106980 stock crossed with a UAS-Dcr2 (X); r4-GAL4) stock

tag: extraction method

value: Floated


title: Ishi_E2_Dex_ATAC_Seq

value: 100 nM Dexamethasone and 10 nM Estradiol 1 Hr


title: ctrl_0.15mSucrose_3_83

value: 0.15m Sucrose

value: VDRC's 60100 stock crossed with a UAS-Dcr2 (X); r4-GAL4 stock


title: Stat92E_0.7mSucrose_2_82


title: ChIP-seq_RAD21_WT

description: processed file: HUES64_RAD21.bw


title: nasChIP-seq_CTCF_pulse_rep2

data_processing:
50 bp paired-end reads were first trimmed with Trimmomatic to remove any remnant adaptor sequence and bases with Phred quality score <20. Only pairs with both reads ≥20 bp were retained for subsequent analysis.
Reads were aligned to the human genome (hg38) using bismark with bowtie2. Alignment score was controlled by --score-min L,0,-0.4. Mapping uniqueness was controlled by selecting alignments with mapping quality Q>10. Duplicated alignments were removed by bismark.
For each library, reads were specifically mapped to either the Watson or Crick strand, and methylation of single cytosines was called from strand-specific alignments. For each strand, methylation calls from all biological replicates were pooled together.
Methylation of CpGs were extracted from certain pairs of Watson/Crick strand methylation calls using bedtools intersect.
Genome_build: hg38
Supplementary_files_format_and_content: bdg files were generated by bismark and represent methylation frequency of cytosines in the context of CpG on each strand. bw files were normalized to counts per one million PE reads and represent occupancy frequency.

extract_protocol:
For pulse, H9 cells were transferred to medium containing 50 µM EdU and were cultured at 37 °C for 20 min before formaldehyde crosslinking. For chase, after labeling with EdU, cells were washed with DPBS twice, and cultured in medium containing 50 µM dT for 8 hr before formaldehyde crosslinking. Crosslinking with 1% formaldehyde was done in DPBS at RT for 10 min and was quenched with 0.125 M glycine. Cells were collected and washed with DPBS, and lysed in Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 10% glycerol). Pellets were collected and re-suspended in Sonication Buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.1% sodium deoxycholate, 0.5% sodium lauroylsarcosine). Sonication was done on ice using Bioruptor. Triton X-100 was added to a final concentration of 1% before centrifugation at 15,000 xg. Supernatant was collected as fraction of chromatin. Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS) was added to chromatin in a 1:1 ratio. Crosslinking reversal was done by incubation at 65 °C for 8 hr. Proteinase K was added to a final concentration of 0.2 mg/ml before incubation at 55 °C for 30 min. Phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation was done sequentially to purify genomic DNA. Click chemistry was performed in a 200 µl volume (174 µl DNA in DPBS, 2 µl 1 mM biotin-azide, 4 µl 100 mM CuSO4, 20 µl 100 mM sodium ascorbate) at 37 °C for 1 hr. After ethanol precipitation, DNA was incubated with Dynabeads Streptavidin C1 beads on a rotor for 30 min at RT, and washed according to the manufacturer’s instructions.
Beads were incubated with End Repair Enzyme Mix on a rotor for 30 min at RT. After washing, beads were incubated with Klenow Fragment (3'→5' exo-) reaction mix on a rotor for 30 min at RT. After washing, beads were incubated with T4 DNA ligase reaction mix and methylated adaptors on a rotor for 2 hr at RT. After washing, beads were incubated in 150 mM NaOH for 3 min at RT. Supernatant was collected as the fraction containing the parental strand DNA (bio-). Beads were washed 3 times with NaOH, re-suspended in 95% formamide and 10 mM EDTA pH 8.2, and incubated at 90 °C for 3 min. Supernatant was collected as the fraction containing the daughter strand DNA (bio+). Both fractions were ethanol precipitated, mixed with 1 pg of lambda DNA, and bisulfite converted with the EZ DNA Methylation-Lightning Kit. PCR amplification was done with HiFi Uracil+ polymerase. For each library, the minimal number of PCR cycles were used to yield at least 20 ng of DNA measured after purification with AMpure XP beads.

value: human embryonic stem cells

value: CTCF (Millipore, 07-729)


title: nasChIP-seq_CTCF_pulse_rep1


title: nasChIP-BS-seq_DNMT3B_chase_daughter_rep1

value: DNMT3B (Thermo, MA5-16165, lot RA2134271A)


title: nasChIP-BS-seq_DNMT3B_chase_parent_rep1


title: nasChIP-BS-seq_DNMT3B_pulse_daughter_rep1


title: nasChIP-seq_SMC1A_pulse_rep1

value: SMC1A (Bethyl, A300-055A)


title: nasChIP-BS-seq_DNMT3B_pulse_daughter_rep2


title: nasChIP-BS-seq_DNMT3A_chase_parent_rep1


title: nasChIP-BS-seq_DNMT3A_chase_daughter_rep1


title: nasChIP-BS-seq_DNMT3B_pulse_parent_rep1


title: ChIP-hairpinBS-seq_CTCF_rep2

description: processed file: H9_CTCF-hairpinCpG.bed


title: nasChIP-BS-seq_DNMT3B_pulse_parent_rep2


title: nasChIP-BS-seq_DNMT3A_pulse_daughter_rep2


title: nasChIP-BS-seq_DNMT1_chase_parent_rep1


title: nasChIP-BS-seq_DNMT3A_pulse_parent_rep1


title: nasChIP-BS-seq_DNMT1_chase_daughter_rep1


title: nasChIP-BS-seq_DNMT1_pulse_daughter_rep1


title: PTEN_Library_Plasmid

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
plasmid DNA
Targeted barcode amplification from DNA

data_processing:
Libraries were sequenced on NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software.
For TPMT, after converting from the bcl to fastq format using Illumina’s bcl2fastq version 2.18, a custom script was used to demultiplex the samples by index and call a consensus barcode from the read1 and read2 sequences. To collapse the barcode copies associated with unique UMIs, the UMI (bases 10-20 of the index read) were pasted onto the consensus barcode and unique combinations were identified (sort | uniq -c). The barcode from each unique barcode-UMI pair was used to populate a fastq file that could be used by the Enrich 2 software package to count variants. The barcode from each unique barcode-UMI pair was used to populate a fastq file that could be used by the Enrich 2 software package to count variants.
For PTEN, sequencing reads were converted to fastq format and de-multiplexed with bcl2fastq. Barcode paired sequencing reads for the plasmid library, as well as as PTEN VAMP-seq experiments 1 through 4, were joined using the fastq-join tool within the ea-utils package using the default parameters, whereas only one barcode read was collected for PTEN experiments 5 through 8. FASTQ files from these technical replicate amplification and sequencing runs were concatenated for analysis with Enrich2.
The supplied TPMT replicate bin-wise sorting data is the 15-base degenerate barcode followed by a space and the 10 base UMI.
The abundance scores for PTEN and TPMT were calculated as follows: The count for each variant in a bin was divided by the sum of counts recorded in that bin to obtain the frequency of each variant within that bin. This calculation was repeated for every bin in each replicate experiment. The summed counts of each variant in all four bins of an experiment was divided by the summed counts of all variants in all four bins of an experiment to obtain the total frequency value for each variant for each experiment. This total frequency value was used for filtering low-frequency variants out of the subsequent calculations. Next, a weighted average (w_ave) was calculated for each variant, with all weighted average values ranged from a value of 0.25 to 1. Finally, for each experiment, an abundance score for each variant was obtained by subjecting the weighted average of each variant to min-max normalization, using the weighted average value of WT, which was given a score of 1, and the median weighted average value for non-terminal nonsense variants at positions 51 through 349 for PTEN, or positions 51 through 219 for TPMT, which was given an abundance score of 0. The final abundance score for each variant was calculated by taking the mean of the min-max normalized abundance scores across the eight replicate experiments in which it could have been observed. Only variants which were scored in two or more replicate experiments were retained in the analysis. A standard error for each abundance score was calculated by dividing the standard deviation of the min-max normalized values for each variant by the square root of the number of replicate experiments in which it was observed. Lastly, the lower bound of the 95% confidence interval was calculated by multiplying the standard error with the 97.5 percentile value of a normal distribution and subtracting this product from the abundance score. The upper bound of the 95% confidence interval was calculated by instead adding the product with the abundance score.
genome build: NONE
processed data files format and content: The PTEN_barcodeInsertAssignments.tsv.gz and TPMT_barcodeInsertAssignments.tsv.gz processed data files are in gzip-compressed tab-separated text file format, containing the variant-barcode maps determined by subassembly. The TPMT_Barcode_UMI.tar file is a tar archive of gzipped text files containing the 15nt barcode attached to a 10nt unique molecular identifier (separated by a space), for each TPMT sorting bin for each experiment.

organism: Escherichia coli

source_name: Synthetic sequence

growth_protocol: HEK 293T TetBxb1BFP cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 2 μg/mL doxycycline.

extract_protocol:
Cells were transferred into a microfuge tube, pelleted and stored at -20˚C. Genomic DNA was prepared using the GentraPrep kit (Qiagen) or Dneasy kit (Qiagen).
For TPMT: for each bin, all the purified DNA was spread over eight 25 uL PCR reactions containing Kapa Robust, primers GPS-landing-f (in the genome) and BC-GPS-P7-i#-UMI (3’ of the barcode) to tag the barcodes with a unique molecular index (UMI) and add a sample index.  UMI-tagging PCR were performed using the following conditions: initial denaturation 95 ˚C 2 minutes, followed by three cycles of (95 ˚C 15 seconds, 60 ˚C 20 seconds, 72 ˚C 3 minutes). The eight PCR reactions were pooled and the PCR amplicon was purified using 1x Ampure XP (Beckman Coulter). To shorten the amplicon and add the p5 and p7 Illumina cluster-generating sequences, the UMI-tagged barcodes were then amplified with primers BC-TPMT-P5-v2 and Illumina p7. This PCR was performed with Kapa Robust and SYBR green II on a Bio-Rad mini-opticon qPCR machine, reactions were monitored and removed before saturation of the SYBR green II signal, at around 25 cycles. The amplicons were pooled and gel purified. For PTEN: .  Eight 50 μL first-round PCR reactions were each prepared with a final concentration of ~50 ng/μL input genomic DNA, 1x Kapa HiFi ReadyMix, and 0.25 μM of the KAM499/JJS_501a primers. The reaction conditions were 95 °C for 5 minutes, 98 °C for 20 seconds, 60 °C for 15 seconds, 72 °C for 90 seconds, repeat 7 times, 72 °C for 2 minutes, 4 °C hold. Eight 50 μL reactions were combined, bound to AMPure XP (Beckman Coulter), cleaned, and eluted with 40 μL water. 40% of the eluted volume was mixed with 2x Kapa Robust ReadyMix; JJS_seq_F and one of the indexed reverse primers, JJS_seq_R1a through JJS_seq_R12a were added at 0.25 μM each. Reaction conditions for the second round PCR were 95 °C for 3 minutes, 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, repeat 14 times, 72 °C for 1 minutes, 4 °C hold.  Amplicons were extracted after separation on a 1.5% TBE/agarose gel using a Quantum Prep Freeze ‘N Squeeze DNA Gel Extraction Kit (Bio-Rad).

treatment_protocol: Cells harboring variant libraries, prepared as described above, were sorted using a FACSAria III into bins according to the abundance of their expressed, EGFP tagged variant. First, live, single, recombinant cells were selected using forward and side scatter, mCherry and mTagBFP2 signals. Then, a FITC:PE-Texas Red ratiometric parameter in the BD FACSDIVA software was created. A histogram of the FITC:PE-Texas Red ratio was created and gates dividing the library into four equally populated bins based on the ratio were established.


title: nasBS-seq_chase_daughter_rep3

description:
H9_chase_dau_Wat_C(CpG).bdg.gz
H9_chase_dau_Cri_C(CpG).bdg.gz
H9_chase_intraCpG.bed.gz


title: nasBS-seq_chase_daughter_rep2


title: nasBS-seq_chase_daughter_rep4


title: nasBS-seq_chase_daughter_rep1


title: nasBS-seq_chase_parent_rep4

description:
H9_chase_par_Wat_C(CpG).bdg.gz
H9_chase_par_Cri_C(CpG).bdg.gz
H9_chase_intraCpG.bed.gz


title: nasChIP-BS-seq_DNMT1_pulse_parent_rep1


title: nasBS-seq_chase_parent_rep5


title: nasBS-seq_chase_parent_rep2


title: nasChIP-BS-seq_DNMT3A_pulse_daughter_rep1


title: nasBS-seq_chase_parent_rep3


title: nasChIP-BS-seq_DNMT3A_pulse_parent_rep2


title: nasBS-seq_chase_parent_rep1


title: nasBS-seq_pulse_daughter_rep6

description:
H9_pulse_dau_Wat_C(CpG).bdg.gz
H9_pulse_dau_Cri_C(CpG).bdg.gz
H9_pulse_intraCpG.bed.gz


title: nasBS-seq_pulse_daughter_rep5


title: nasBS-seq_pulse_daughter_rep3


title: nasBS-seq_pulse_daughter_rep2


title: nasChIP-BS-seq_DNMT1_pulse_daughter_rep2


title: nasChIP-BS-seq_DNMT1_pulse_parent_rep2


title: nasBS-seq_pulse_daughter_rep1


title: nasBS-seq_chase_daughter_rep5


title: ctrl_0.15mSucrose_2_50

value: VDRC's w1118 stock crossed with a UAS-Dcr2 (X); cg-GAL4 stock


title: nasBS-seq_pulse_parent_rep6

description:
H9_pulse_par_Wat_C(CpG).bdg.gz
H9_pulse_par_Cri_C(CpG).bdg.gz
H9_pulse_intraCpG.bed.gz


title: ctrl_1.0mSucrose_2_44

value: Male

value: 1.0m Sucrose

value: Dissected


title: nasBS-seq_pulse_parent_rep2


title: nasBS-seq_pulse_parent_rep3


title: Tfb1_0.15mSucrose_3_42

value: fat body

value: VDRC's 12580 stock crossed with a UAS-Dcr2 (X); cg-GAL4 stock


title: nasBS-seq_pulse_parent_rep5


title: MDA-MB-231_LM2_1

type: genomic

city: Melbourne

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

country: Australia

institute: Monash University

description: SAMPLE 3

hyb_protocol: Samples were hybridised to Illumina MethylationEPIC arrays for 17 hours at 48°C in an Illumina Hybridisation Oven. Single base extension and staining were performed as per the Illumina Infinium HD Protocol.

scan_protocol: Slides were scanned using an Illumina HiScan.

data_processing: Genomic DNA extracted from cell lines was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChip arrays (Illumina)

source_name: cell line

label_protocol: Bisulfite conversion of genomic DNA samples was performed using the Zymo EZ DNA Methylation kit. 200ng of bisulfite-converted DNA was then prepared for hybridisation according to the Illumina Infinium HD Assay Methylation Protocol Guide.

growth_protocol: Cells grown in DMEM 10% FBS, 1% P/S

extract_protocol: Genomic DNA was made using Qiagen DNA mini kit and concentration determined using a Nanodrop Spectrophotometer

treatment_protocol: Untreated cells

value: breast cancer cell line

tag: gfp

value: expresses GFP


title: MDA-MB-231_HM.LNm5_1

description: SAMPLE 4

value: no fluorescent proteins


title: MDA-MB-231_LNA_1

description: SAMPLE 2


title: SAMPLE 148: female_FA_P_3h_rep8

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

data_processing:
Data were analyzed in excel using Ct values for each sample, normalized to he average Ct of five miRNA housekeeping controls (SNORD61, SNORD68, SNORD72, SNORD95, SNORD96A, RNU6-2)
Matrix normalized template shows target miRNA Ct values normalized to housekeeping miRNAs as ΔCt = (Ct_Target − Ct_housekeeping)
For fold change calculations, ΔΔCt based fold-change values were obtained using sample 27 as control (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])). A fold change of 200 was considered as cutoff.

label: SYBR Green

organism: Mus musculus

source_name: female mouse exposed to filtered air

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 84 mouse miRNAs predicted to regulate inflammatory genes was assayed with the Mouse Inflammatory Response & Autoimmunity miRNA PCR Array (MIMM-105Z, Qiagen)

extract_protocol: Lung tissue was homogenized in Trizol. Total RNA was extracted with the Direct-zol (Zymo Research)

treatment_protocol: Male and female C57BL/6 mice of 8 weeks of age were exposed to 2ppm ozone (O3) or filtered air (FA) for 3 hours. Females were exposed at different stages of the estrous cycle: diestrus 1 (D1), diestrus 2 (D2), proestrus (P), estrus (E). Total RNA was extracted from whole lung homogenates and PCR arrays were used to determine the expression of 84 miRNAs associated with inflammation and immunity (3-9 animals per condition).

value: lung tissue homogenate

tag: exposure time

value: 3 hours

value: female

tag: estrous cycle stage

value: proestrus


title: SAMPLE 149: female_FA_P_3h_rep9


title: MDA-MB-231_ATCC_1

description: SAMPLE 1


title: SAMPLE 143: female_FA_P_3h_rep7


title: nasBS-seq_pulse_parent_rep1

value: human embryonic stem cells


title: SAMPLE 110: female_FA_D2_3h_rep4

value: diestrus 2


title: SAMPLE 112: female_O3_D2_3h_rep3

source_name: female mouse exposed to 2ppm ozone


title: DNAm_sample48

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: Whole blood

extract_protocol: Genomic DNA of peripheral blood was harvested with QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

tag: donor id

value: donor 48

tag: gender

value: Female

tag: disease state

value: healthy control (Ctrl)

tag: age

value: Whole blood


title: DNAm_sample44

label_protocol: Standard Infinium HD Methylation Assay protocol

value: donor 44


title: DNAm_sample47

value: donor 47


title: SAMPLE 109: female_O3_D1_3h_rep3

value: diestrus 1


title: SAMPLE 107: female_FA_D2_3h_rep3


title: DNAm_sample45

value: donor 45


title: DNAm_sample46

value: donor 46

value: Male


title: CVP_DIO_8

city: DIJON

first: Arnaud

last: BERNARD

address: Agrosup Dijon, 1 esplanade Erasme

country: France

institute: INSERM U1231

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 19 out of 23 microarrays or with a weight of 1 in all 6 microarrays from at least one experimental group. At this step, 38772 spots out of 62976 were selected. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. The resulting matrix has 35829 rows each corresponding to a unique ProbeName (provided as data Matrix) and 23 columns (individuals).

source_name: circumvallate papillae

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Dropsense™ 96 UV/VIS droplet reader (Trinean).

extract_protocol: Total RNA from CVP were extracted using total RNA purification kit (Norgen Biotek, Canada) according to the manufacturer’s instructions. Briefly, the nitrogen-frozen CVP were homogenized in the lysing buffer with a RNase free piston pellet, then RNA were selected using purification columns and treated with an amplification grade DNase (RNase-free DNase I kit, Norgen Biotek, Canada) to ensure genomic DNA removal. Purified RNA was assayed using a nanodrop spectrometer (Thermo Fischer Scientific). Transcriptomic analysis was performed by the Get-TRIX platform (INRA, Toulouse, France).

tag: condition

value: DIO

tag: strain

value: male


title: CWR22Res Nsi Rep 3

city: Glasgow

first: Rachana

middle: Ravindra

last: Patel

state: Outside the United States or Canada

address: Bearsden, Switchback Road

department: Prostate Cancer

country: United Kingdom

institute: Cancer Research UK Beatson Institute

description: Control Replicate 3

hyb_protocol: Samples for microarray were generated using Illumina sequencing reagents and HumanHT-12 v4 Expression BeadChip Kit.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lummi in R

label: Biotin

source_name: human prostate cancer cell line

growth_protocol: Cells were grown in two dimensional culture condition in RPMI with 10% FBS

extract_protocol: RNA was extracted using QIAGEN RNA extraction kit

treatment_protocol: The cells were grown till they achieve 60% confluency

tag: genotype/variation

value: Control (SPRY2 proficient)


title: DNAm_sample43

value: donor 43


title: DNAm_sample40

value: donor 40


title: SAMPLE 102: female_FA_P_3h_rep6

value: lung tissue homogenate

value: 3 hours

value: female

value: proestrus


title: CVP_Lean_3

value: Lean


title: SAMPLE 101: female_O3_P_3h_rep9


title: DNAm_sample36

value: donor 36

value: healthy control (Ctrl)

value: Whole blood


title: CVP_DIO-R_2

value: DIO-R


title: DNAm_sample37

value: donor 37


title: CWR22Res Nsi Rep 2

description: Control Replicate 2

label_protocol: Samples for microarray were generated using Illumina sequencing reagents and HumanHT-12 v4 Expression BeadChip Kit.


title: DNAm_sample42

value: donor 42

value: Female


title: DNAm_sample38

value: donor 38


title: DNAm_sample33

value: donor 33


title: CWR22Res Nsi Rep 1

description: Control Replicate 1

value: Control (SPRY2 proficient)


title: DNAm_sample41

value: donor 41

value: Male


title: DNAm_sample35

value: donor 35


title: DNAm_sample34

value: donor 34


title: CVP_DIO-R_8

value: male


title: DNAm_sample32

value: donor 32

value: osteoporosis (OP)


title: CVP_Lean_5

value: Lean


title: DNAm_sample30

value: donor 30


title: DNAm_sample25

value: donor 25

value: Whole blood


title: DNAm_sample29

value: donor 29


title: CWR22Res SPRY2 KD Pool Rep 3

description: Test Replicate 3

value: SPRY2 deficient


title: DNAm_sample31

value: donor 31


title: SAMPLE 97: female_FA_E_3h_rep4

value: lung tissue homogenate

value: 3 hours

value: female

value: estrus


title: SAMPLE 96: female_FA_D1_3h_rep4

value: diestrus 1


title: CVP_DIO-R_7

value: DIO-R


title: DNAm_sample39

value: donor 39

value: Female

value: healthy control (Ctrl)


title: SAMPLE 99: female_O3_P_3h_rep8

value: proestrus


title: DNAm_sample24

value: donor 24

value: osteoporosis (OP)


title: DNAm_sample28

value: donor 28


title: CVP_DIO_2

value: DIO

value: male


title: SAMPLE 100: female_FA_E_3h_rep6


title: CVP_DIO_3


title: DNAm_sample26

value: donor 26

value: Whole blood


title: CWR22Res SPRY2 KD Pool Rep 1

description: Test Replicate 1

value: SPRY2 deficient


title: SAMPLE 95: female_FA_D1_3h_rep3

value: lung tissue homogenate

value: 3 hours


title: MSC2_in hPL-gel_with_TN [expression]

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Raw data were quantile normalized using the GenomeStudio Software (Illumina, San Diego, USA). For comparison of gene expression of iMSCs and MSCs, all transcripts with a detection p > 0.01 were excluded.

label: biotin

source_name: MSCs, within hPL-gel with TN

label_protocol: Standard Illumina protocol.

growth_protocol: MSCs were isolated from bone marrow after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (permit number: EK128/09). For some of the profiles, the MSCs were reprogrammed into iPSCs. To this end, MSCs of three different donors (passage 2) were infected with pCXLE-based episomal plasmids (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, LIN28 and c-MYC genes. Established iPSCs were cultured on TCP coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol: RNA was isolated using the Macherey-Nagel RNA Plus kit.

treatment_protocol: To determine the impact of culture conditions on gene expression of primary MSCs, we treated the cells for three weeks in parallel with the following conditions: i) MSC were cultured on tissue culture plastic (TCP) in standard medium supplemented with 10% human platelet lysate (hPL-medium); ii) on TCP in hPL-plasma (after depletion of coagulation factors); iii) on hPL-gel generated without thrombin (TN), iv) on hPL-gel generated with TN (Sigma Aldrich, Hamburg, Germany), or iv) by trapping of the cells within hPL-gel with addition of TN. Alternatively, iPSCs were differentiated toward MSCs with the following conditions: iPSCs were either seeded on TCP with i) MSC standard medium supplemented with 10% human platelet lysate (hPL-medium) or ii) hPL-plasma (after depletion of coagulation factors); or on hPL-gel generated iii) without thrombin (TN) or iv) with TN (Sigma Aldrich, Hamburg, Germany) for a period of 35 days.

tag: donor

tag: cell type

value: mesenchymal stell cells (MSCs)

tag: passage

tag: culture condition

value: within hPL-gel with thrombin (TN)


title: DNAm_sample27

value: donor 27

tag: tissue


title: SAMPLE 93: female_FA_D1_3h_rep2

tag: Sex

value: female

value: diestrus 1


title: MSC3_in hPL-gel_with_TN [expression]


title: SAMPLE 94: female_FA_D2_3h_rep2

value: diestrus 2


title: DNAm_sample20

value: donor 20

value: Female


title: DNAm_sample21

value: donor 21

value: osteoporosis (OP)


title: CWR22Res SPRY2 KD Pool Rep 2

description: Test Replicate 2


title: CVP_DIO_10

value: DIO


title: CVP_DIO-R_10

value: DIO-R

value: male


title: CVP_DIO_6


title: SAMPLE 90: female_FA_P_3h_rep5

value: proestrus


title: CVP_DIO-R_4


title: MSC1_in hPL-gel_with_TN [expression]


title: SAMPLE 92: female_O3_D2_3h_rep2


title: MSC3_on hPL-gel_with_TN [expression]

source_name: MSCs, on hPL-gel with TN

value: hPL-gel with thrombin (TN)


title: CVP_Lean_10

value: Lean


title: DNAm_sample22

value: donor 22

value: Whole blood


title: DNAm_sample18

value: donor 18


title: MSC1_on hPL-gel_with_TN [expression]

value: mesenchymal stell cells (MSCs)


title: MSC2_on hPL-gel_with_TN [expression]


title: MSC3_on hPL-gel_without_TN [expression]

source_name: MSCs, on hPL-gel without TN

value: hPL-gel without thrombin (TN)


title: SAMPLE 89: female_FA_E_3h_rep3

value: lung tissue homogenate

value: 3 hours

value: female

value: estrus


title: SAMPLE 98: female_FA_E_3h_rep5


title: SAMPLE 88: female_O3_P_3h_rep7


title: SAMPLE 87: female_O3_E_3h_rep4


title: DNAm_sample19

value: donor 19

value: Female


title: SAMPLE 86: female_O3_D2_3h_rep1

value: diestrus 2


title: CVP_DIO-R_3

value: DIO-R


title: CVP_Lean_6

value: male


title: CVP_Lean_9


title: CVP_DIO-R_5


title: MSC1_on hPL-gel_without_TN [expression]


title: SAMPLE 84: female_O3_D1_3h_rep2

value: diestrus 1


title: MSC2_TCP_hPL-plasma [expression]

source_name: MSCs, TCP with hPL-plasma

value: tissue culture plate (TCP) with hPL-plasma


title: MSC2_on hPL-gel_without_TN [expression]


title: CVP_DIO_7

value: DIO


title: DNAm_sample17

value: donor 17

value: osteoporosis (OP)


title: SAMPLE 83: female_O3_P_3h_rep6

value: proestrus


title: CVP_Lean_4

value: Lean


title: MSC3_TCP_hPL-plasma [expression]

value: mesenchymal stell cells (MSCs)


title: MSC1_TCP_hPL-plasma [expression]


title: DNAm_sample15

value: donor 15

value: Whole blood


title: DNAm_sample16

value: donor 16


title: SAMPLE 82: female_O3_P_3h_rep5

value: lung tissue homogenate

value: 3 hours

value: female


title: MSC3_TCP_hPL-medium [expression]

source_name: MSCs, TCP with hPL-medium

value: tissue culture plate (TCP) with hPL-medium


title: SAMPLE 81: female_O3_P_3h_rep4


title: DNAm_sample14

value: donor 14

value: Male


title: DNAm_sample13

value: donor 13

value: Female


title: SAMPLE 80: female_FA_E_3h_rep2

value: estrus


title: CVP_DIO-R_6

value: DIO-R

value: male


title: SAMPLE 79: female_FA_D2_3h_rep1

value: diestrus 2


title: MSC2_TCP_hPL-medium [expression]


title: SAMPLE 78: female_FA_P_3h_rep4

value: proestrus


title: MSC1_TCP_hPL-medium [expression]

value: mesenchymal stell cells (MSCs)


title: DNAm_sample11

value: donor 11

value: osteoporosis (OP)


title: DNAm_sample8

value: donor 8

value: Whole blood


title: CVP_Lean_7

value: Lean


title: DNAm_sample9

value: donor 9


title: CVP_DIO_1

value: DIO


title: CVP_DIO_5


title: DNAm_sample23

value: donor 23


title: iMSC2_hPL-gel_with_TN [expression]

source_name: iMSCs, hPL-gel with TN

value: iPSC-derived MSCs (iMSCs)

tag: differentiation condition

value: hPL-gel with thrombin (TN)


title: SAMPLE 77: female_O3_P_3h_rep3

value: lung tissue homogenate

value: 3 hours

value: female


title: iMSC3_hPL-gel_with_TN [expression]


title: DNAm_sample10

value: donor 10

value: Female


title: iMSC1_hPL-gel_with_TN [expression]


title: DNAm_sample7

value: donor 7


title: Kiney_MN_rep2

city: Taipei

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Gene expression in kidneys from MN mice

hyb_protocol: Total Cy3 labeled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: Kidney, 6 weeks after cBSA treatment

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.  Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000.

growth_protocol: All animal procedures were performed according to IACUC approved protocol (TSGH 12-280). 6 week-old female BALB/C (National Laboratory Animal Center, Taiwan) mice were maintained in micro-isolators in pathogen-free conditions.

extract_protocol: Total RNA was extracted by commercial kit (NucleoSpin, Macherey-Nagel®). The concentration of RNA was quantified by Nanodrop 2000 spectrophotometer (Thermo Scientific) and the quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Both control and experimental groups were immunized with 0.2 mg cationic bovine serum albumin (cBSA; Chondrex, Redmond,USA) emulsified in an equal volume of complete Freund's adjuvant (Sigma, St. Louis, USA). After 2 weeks, mice from the experimental group were injected intravenously with 13 mg/kg of cBSA 3 times weekly for an additional 6 weeks. Mice from the control group received saline according to the same schedule.

value: BALB/C

value: kidney

tag: treatment

value: cBSA


title: Kiney_MN_rep1

description: Gene expression in kidneys from MN mice


title: SAMPLE 75: female_FA_E_3h_rep1

tag: exposure time

value: estrus


title: DNAm_sample12

value: donor 12

value: osteoporosis (OP)

value: Whole blood


title: Male post-secretion floral nectary 3

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.2
Reads aligned to contigs using NCBI blastn
Contigs mapped to Cucumis melo and Arabidopsis thaliana NCBI sequences
Supplementary_files_format_and_content: Squash_RNAseq_summed_analysis.xlsx (Excel file of normalized counts mapped to Cucumis melo)

organism: Cucurbita pepo

source_name: Male post-secretion floral nectary

extract_protocol:
All nectary tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-three TruSeq RNA v2 libraries were created (triplicate samples for male and female nectaries at four timepoints each, except for only duplicate samples of female ?pre-secretory #2? nectaries) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two full lanes. This generated over 240 M reads for each lane and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: Male

value: Nectary

tag: time

value: post-secretion


title: DNAm_sample6

tag: donor id

value: donor 6


title: Male post-secretion floral nectary 2

tag: gender


title: SAMPLE 73: female_O3_D1_3h_rep1

value: lung tissue homogenate

tag: estrous cycle stage

value: diestrus 1


title: SAMPLE 71: female_FA_P_3h_rep3

value: 3 hours

value: female

value: proestrus


title: SAMPLE 70: female_O3_P_3h_rep2


title: SAMPLE 69: male_O3_3h_rep8

source_name: male mouse exposed to 2ppm ozone

value: male


title: Male secretory floral nectary 3

source_name: Male secretory floral nectary

value: secretory


title: iMSC2_hPL-gel_without_TN [expression]

source_name: iMSCs, hPL-gel without TN

value: iPSC-derived MSCs (iMSCs)

value: hPL-gel without thrombin (TN)


title: DNAm_sample4

value: donor 4

value: Female

tag: disease state

tag: age


title: DNAm_sample3

value: donor 3

value: osteoporosis (OP)


title: Kiney_Ctrl_rep1

description: Gene expression in kidneys from control mice

source_name: Kidney, 6 weeks after PBS treatment

tag: strain

value: BALB/C

value: kidney

value: PBS


title: SAMPLE 67: male_O3_3h_rep7


title: Male post-secretion floral nectary 1

value: Male

value: Nectary

value: post-secretion


title: iMSC3_hPL-gel_without_TN [expression]


title: iMSC3_TCP_hPL-plasma [expression]

source_name: iMSCs, TCP with hPL-plasma

value: tissue culture plate (TCP) with hPL-plasma


title: DNAm_sample5

value: donor 5

value: Whole blood


title: Male secretory floral nectary 1


title: iMSC1_hPL-gel_without_TN [expression]


title: Kiney_Ctrl_rep2

description: Gene expression in kidneys from control mcie

value: female


title: SAMPLE 66: male_O3_3h_rep6

value: lung tissue homogenate

value: 3 hours

value: male


title: iMSC2_TCP_hPL-plasma [expression]

value: iPSC-derived MSCs (iMSCs)


title: Male secretory floral nectary 2

value: secretory


title: Male pre-secretory #2 floral nectary 3

source_name: Male pre-secretory #2 floral nectary

value: pre-secretory #2


title: Male pre-secretory #2 floral nectary 2


title: SAMPLE 64: male_FA_3h_rep6

source_name: male mouse exposed to filtered air


title: iMSC1_TCP_hPL-plasma [expression]


title: TPMT_PacBio_SMRT_Cell_6

description:
plasmid DNA
Library and barcode cassette sequencing from DNA

source_name: Synthetic sequence


title: SAMPLE 63: male_FA_3h_rep5


title: iMSC2_TCP_hPL-medium [expression]

source_name: iMSCs, TCP with hPL-medium

value: tissue culture plate (TCP) with hPL-medium


title: SAMPLE 36: female_O3_P_3h_rep1

source_name: female mouse exposed to 2ppm ozone

value: proestrus


title: TPMT_PacBio_SMRT_Cell_5


title: DNAm_sample1

source_name: Whole blood

value: donor 1

value: Female

value: osteoporosis (OP)


title: iMSC3_TCP_hPL-medium [expression]


title: TPMT_PacBio_SMRT_Cell_4


title: SAMPLE 34: female_O3_E_3h_rep3

value: estrus


title: Male pre-secretory #2 floral nectary 1

value: Male

value: Nectary


title: Male pre-secretory #1 floral nectary 3

source_name: Male pre-secretory #1 floral nectary

value: pre-secretory #1


title: iMSC1_TCP_hPL-medium [expression]


title: SAMPLE 32: female_FA_P_3h_rep2

source_name: female mouse exposed to filtered air


title: Male pre-secretory #1 floral nectary 1


title: Female post-secretion floral nectary 3

source_name: Female post-secretion floral nectary

value: post-secretion


title: TPMT_PacBio_SMRT_Cell_2


title: SAMPLE 29: female_O3_E_3h_rep2

value: female


title: iMSC1_hPL-gel_with_TN [methylation]

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol.

data_processing: Initial analysis was performed by the GenomeStudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina's standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

source_name: iMSCs, hPL-gel with TN

growth_protocol: Established iPSCs were cultured on TCP coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol: Genomic DNA was isolated using the Macherey-Nagel NucleoSpin Tissue Kit.

treatment_protocol: iPSCs were differentiated toward MSCs with the following conditions: iPSCs were either seeded on TCP with i) MSC standard medium supplemented with 10% human platelet lysate (hPL-medium) or ii) hPL-plasma (after depletion of coagulation factors); or on hPL-gel generated iii) without thrombin (TN) or iv) with TN (Sigma Aldrich, Hamburg, Germany) for a period of 35 days.

value: hPL-gel with thrombin (TN)


title: TPMT_PacBio_SMRT_Cell_3


title: SAMPLE 28: female_O3_E_3h_rep1

value: lung tissue homogenate

value: 3 hours


title: Female post-secretion floral nectary 2


title: PTEN_PacBio_SMRT_Cell_5


title: Male pre-secretory #1 floral nectary 2


title: iMSC2_hPL-gel_with_TN [methylation]

label_protocol: Standard Infinium HD Methylation Assay protocol.

value: iPSC-derived MSCs (iMSCs)


title: SAMPLE 27: female_FA_D1_3h_rep1

value: diestrus 1


title: iMSC3_hPL-gel_with_TN [methylation]


title: PTEN_PacBio_SMRT_Cell_4


title: iMSC3_TCP_hPL-plasma [methylation]

value: tissue culture plate (TCP) with hPL-plasma


title: iMSC2_TCP_hPL-plasma [methylation]


title: iMSC3_hPL-gel_without_TN [methylation]

value: hPL-gel without thrombin (TN)


title: Female post-secretion floral nectary 1


title: SAMPLE 25: female_FA_P_3h_rep1

value: proestrus


title: SAMPLE 20: male_O3_3h_rep5

value: male


title: Female secretory floral nectary 3

source_name: Female secretory floral nectary

value: Female

value: secretory


title: Bovine macrophages stimulated with FhWild-ES, replicate 3

city: Warsaw

first: Piotr

last: Bąska

state: Mazowieckie

address: Ciszewskiego 8

department: Department of Preclinical Sciences

country: Poland

institute: Warsaw University of Life Sciences WULS – SGGW

description: Technical replicate 3 of 4

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Bos taurus

source_name: BOMA, bovine macrophage cell  line

label_protocol: Quick Amp Labeling (Agilent Technologies) according to the manufacturer`s protocol

growth_protocol: The cells were cultivated in DMEM (with 5% FCS, 2 mM glutamine, 100 units/ml of penicillin, 100 µg/ml streptomycin)

extract_protocol: total RNA was extracted using RNA isolation kit (A&A Biotechnology)

treatment_protocol: Cells were stimulated in quadruplicate with FhWey-ES (10 µg/ml for 24 hours) or FhWild-ES (10 µg/ml for 24 hours)

tag: cell line

value: BOMA

value: monocytes/ macrophages

tag: agent

source_name: BOMA, bovine macrophage cell  line stimulated with FhWild-ESP

value: FhWild-ES


title: iMSC2_hPL-gel_without_TN [methylation]

tag: donor

tag: cell type


title: Bovine macrophages stimulated with FhWild-ES, replicate 1

description: Technical replicate 1 of 4


title: iMSC1_hPL-gel_without_TN [methylation]

tag: passage


title: iMSC1_TCP_hPL-plasma [methylation]


title: Bovine macrophages stimulated with FhWild-ES, replicate 2

description: Technical replicate 2 of 4


title: Bovine macrophages stimulated with FhWild-ES, replicate 4

description: Technical replicate 4 of 4


title: Female secretory floral nectary 2

tag: tissue

value: Nectary


title: PTEN_PacBio_SMRT_Cell_1


title: PTEN_PacBio_SMRT_Cell_2


title: SAMPLE 19: male_O3_3h_rep4

source_name: male mouse exposed to 2ppm ozone

tag: Sex


title: PTEN_PacBio_SMRT_Cell_3


title: Female secretory floral nectary 1


title: Female pre-secretory #2 floral nectary 3

source_name: Female pre-secretory #2 floral nectary

value: pre-secretory #2


title: SAMPLE 18: male_O3_3h_rep3


title: Bovine macrophages stimulated with FhWey-ES, replicate 4

description: Technical replicate 4 of 4

source_name: BOMA, bovine macrophage cell  line stimulated with FhWey-ESP

value: FhWey-ES


title: SAMPLE 16: male_FA_3h_rep4


title: Bovine macrophages stimulated with FhWey-ES, replicate 3

description: Technical replicate 3 of 4


title: Bovine macrophages stimulated with FhWey-ES, replicate 2

description: Technical replicate 2 of 4


title: iMSC2_TCP_hPL-medium [methylation]

tag: differentiation condition

value: tissue culture plate (TCP) with hPL-medium


title: SAMPLE 13: male_FA_3h_rep3

value: lung tissue homogenate


title: huh7 xenograft  IRA 3

city: Paris

first: Christèle

last: Desbois-Mouthon

address: 15 rue de l'école de médecine

institute: INSERM

description: Gene expression data from IR-A overexpressing Huh7-derived xenograft

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Human Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V20 was used for annotation.

source_name: Huh7 sc xenogaft expressing IRA vector

label_protocol: 500 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: Bovine macrophages stimulated with FhWey-ES, replicate 1

description: Technical replicate 1 of 4


title: Female pre-secretory #2 floral nectary 1


title: huh7 xenograft  IRA 2


title: iMSC1_TCP_hPL-medium [methylation]


title: Female pre-secretory #1 floral nectary 2

source_name: Female pre-secretory #1 floral nectary

value: pre-secretory #1


title: SAMPLE 9: male_O3_3h_rep1

value: 3 hours


title: SAMPLE 10: male_O3_3h_rep2


title: hippocampus, glyphosate-based herbicide (GBH) exposure

city: HangZhou City

first: Hua

last: Ji

state: Zhejiang

address: No.481 Bingwen road

department: Department of Basic Medicine

institute: Hangzhou medical college

description: Experimental animals were male offspring produced by ICR mice (SLAC, Shanghai, China).

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 2 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes≥2.0 and p-values＜0.05 are selected as the significantly differentially expressed.

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mouse hippocampus dissected from PND28 mouse brain

extract_protocol: The pregnant ICR mice were randomly allocated in two groups, each group consisting of 8 pregnant mice (Slac, China ). Each group were used for the circRNA microarray assay. In the control group, pregnant mice were provided with purified water. In the glyphosate treated group, pregnant mice were provided with 0.38% glyphosate in drinking water (1% Roundup®), equivalent to 50 mg of glyphosate/kg/day.

treatment_protocol: not applicable

value: ICR

tag: ages

value: 4 weeks old

value: brain (hippocampus)


title: Female pre-secretory #1 floral nectary 1


title: huh7 xenograft  control 3

description: Gene expression data from Control Huh7-derived xenograft

source_name: Huh7 sc xenogaft expressing empty vector


title: huh7 xenograft  control 2


title: huh7 xenograft  IRA 1


title: iMSC3_TCP_hPL-medium [methylation]

value: iPSC-derived MSCs (iMSCs)


title: huh7 xenograft  control 1


title: hippocampus, control

source_name: hippocampus, control

value: male


title: DNAm_sample2

value: donor 2

value: Female

value: osteoporosis (OP)

value: Whole blood


title: Female pre-secretory #1 floral nectary 3


title: SAMPLE 8: male_FA_3h_rep2

source_name: male mouse exposed to filtered air

tag: exposure time


title: N28

status: Public on Mar 12 2018

city: Basel

first: Darius

last: Juskevicius

address: Schoenbeinstr. 40

department: Molecuar Pathology

country: Switzerland

institute: Institute of Pathology

hyb_protocol: Labeled DNAs were hybridized in an ozone-free environment in a rotisserie oven at 67 C at 25 rpm for at least 24 hours then washed according to array supplier's (Agilent) protocol

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visualized and analyzed using Agilent Cytogenomics software and the ADM2 algorithm.

source_name: Sample FFPE tissue biopsy

label_protocol: A 500 nanogram aliquot of each sample and reference DNA was heat-digested to median fragment size of ~400bp then labeled with a fluorescent nucleotide (Cy3 for tumor and Cy5 for normal reference) using the BioPrime labeling kit (Invitrogen) according to manufacturer's protocol.

extract_protocol: H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted with silica column based GeneRead FFPE DNA extraction kit (Qiagen). Yields were quantified by the Qubit high sensitivity assay.

value: Nodal marginal zone lymphoma

value: female

tag: location

value: lymph node

source_name: Reference pooled 46XX

tag: reference

value: pooled normal (46,XX) reference (Promega)


title: N27

tag: gender


title: N25


title: N24


title: F2912repl

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description:
ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high
processed data file:
gene_expression_3273_samples_and_136_replicates_transformed.csv
transcript_expression_3273_samples_and_136_replicates.csv

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using TopHat2 2.0.12 or 2.0.13 (default parameters except for --mate-inner-dist X (estimated in previous step), --mate-std-dev Y (estimated in previous step), --library-type fr-firststrand, --no-coverage-search, --max-insertion-length 20, --max-deletion-length 20, --read-gap-length 20, --read-edit-dist 22) to the human genome reference GRCh38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014).
Gene expression data in FPKM were generated using cufflinks 2.2.1 (default parameters except –GTF, --frag-bias-correct GRCh38.fa, --multi-read-correct, --library-type fr-firststrand, --total-hits-norm, --max-bundle-frags 10000000). The resulting data was was post-processed by collapsing on 30,865 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, and performing a log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Single-gene classifiers (SGCs) and multi-gene classifiers (MGCs) were trained for ER, PgR, HER2, Ki67 (SGC and MGC) and NHG (MGC only) on the expression of the single underlying gene (ESR1, PGR, ERBB2 or MKI67) or multiple genes (5000 most varying genes across all samples) of a 405 sample cohort using consensus pathology scores as labels. Classifier training was performed by selecting expression thresholds that maximize prediction concordance to the consensus scores (SGCs) and nearest shrunken centroids using the pamr R package (MGCs). The classifiers were used to predict the biomarker status in a validation cohort of 3273 samples from patients enrolled in the SCAN-B study.
Genome_build: Human genome reference GRCh38/hg38.
Supplementary_files_format_and_content: Gene expression in FPKM in CSV format.

molecule: polyA RNA

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

tag: scan-b external id

tag: instrument model

value: HiSeq 2000

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: NodePositive

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

value: LumA

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F3135repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

value: NodeNegative

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

value: Basal


title: F3085repl

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

value: LumB


title: F3057repl

tag: scan-b external id

tag: instrument model

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: N21

tag: disease state

tag: gender

tag: age

tag: location

tag: reference


title: N18


title: F2911repl

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc


title: F2958repl

tag: scan-b external id

tag: instrument model

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: N22

tag: disease state

tag: gender

tag: age

tag: location

tag: reference


title: N13


title: N14


title: N10


title: N4


title: N11


title: N8


title: TPMT_PacBio_SMRT_Cell_1

source_name: Synthetic sequence

tag: cell type


title: N23


title: N1


title: F2877repl

tag: scan-b external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc


title: N6

tag: disease state

tag: gender

tag: age

tag: location

tag: reference


title: N17


title: F2841repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F2790repl

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc


title: F2860repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc


title: F2781repl

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F2755repl

tag: scan-b external id

tag: instrument model

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc


title: N9

tag: disease state

tag: gender

tag: age

tag: location

tag: reference


title: F2840repl

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event


title: N2

tag: disease state

tag: gender

tag: age


title: N12

tag: location

tag: reference


title: F2703repl

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: endocrine treated

tag: chemo treated


title: N3

tag: disease state

tag: gender

tag: age


title: F2656repl

tag: scan-b external id

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event


title: F2679repl

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: endocrine treated


title: F2691repl

tag: scan-b external id

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: chemo treated


title: F2632repl

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: ki67 status

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event


title: SAMPLE 7: male_FA_3h_rep1

tag: tissue

value: lung tissue homogenate

tag: exposure time

value: 3 hours

tag: Sex

tag: estrous cycle stage


title: F2621repl

tag: scan-b external id

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: endocrine treated


title: F2482repl

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: ki67 status

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: chemo treated


title: F2503repl

tag: scan-b external id

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc


title: F2539repl

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: ki67 status

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: endocrine treated


title: F2424repl

tag: scan-b external id

tag: lymph node status

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: overall survival event

tag: chemo treated


title: F2459repl

tag: instrument model

tag: age at diagnosis

tag: er status

tag: pgr status

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc


title: N16

tag: disease state

tag: gender

value: male

tag: age

tag: location

tag: reference


title: F2408repl

tag: scan-b external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 status

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: endocrine treated


title: F2398repl

tag: instrument model

tag: age at diagnosis

tag: er status

tag: pgr status

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: overall survival event

tag: chemo treated


title: F2390repl

tag: scan-b external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 status

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F2406repl

tag: instrument model

tag: age at diagnosis

tag: er status

tag: pgr status

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: endocrine treated


title: F2625repl

tag: scan-b external id

tag: tumor size

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: overall survival event

tag: chemo treated


title: F2277repl

tag: instrument model

tag: age at diagnosis

tag: lymph node group

tag: lymph node status

tag: ki67 status

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F2151repl

tag: scan-b external id

tag: tumor size

tag: er status

tag: pgr status

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: endocrine treated


title: F2175repl

tag: instrument model

tag: age at diagnosis

tag: her2 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: overall survival event

tag: chemo treated


title: F2174repl

tag: scan-b external id

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 status

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F2069repl

tag: instrument model

tag: age at diagnosis

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tag: her2 prediction sgc

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tag: pam50 subtype

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title: F2281repl

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title: F2018repl

tag: instrument model

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title: F1965repl

tag: scan-b external id

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title: F1923repl

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title: F1905repl

tag: scan-b external id

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tag: lymph node group

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title: F1689repl

tag: instrument model

tag: age at diagnosis

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title: F1658repl

tag: scan-b external id

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tag: her2 status

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title: F2067repl

tag: instrument model

tag: age at diagnosis

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title: F1640repl

tag: scan-b external id

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title: F1635repl

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title: F1628repl

tag: scan-b external id

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title: F2359repl

tag: instrument model

tag: age at diagnosis

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tag: ki67 prediction sgc

tag: pam50 subtype

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tag: endocrine treated


title: F1605repl

tag: scan-b external id

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tag: her2 status

tag: nhg

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tag: her2 prediction mgc

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title: F1617repl

tag: instrument model

tag: age at diagnosis

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title: F2299repl

tag: scan-b external id

tag: tumor size

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title: F1591repl

tag: instrument model

tag: age at diagnosis

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tag: overall survival event

tag: chemo treated


title: F1781repl

tag: scan-b external id

tag: tumor size

tag: lymph node group

tag: lymph node status

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tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc


title: F1587repl

tag: instrument model

tag: age at diagnosis

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tag: ki67 prediction sgc

tag: pam50 subtype

tag: overall survival days

tag: endocrine treated


title: F2287repl

tag: scan-b external id

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tag: her2 status

tag: nhg

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tag: her2 prediction mgc

tag: overall survival event

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title: F1950repl

tag: instrument model

tag: age at diagnosis

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title: F1283repl

tag: scan-b external id

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title: F1108repl

tag: instrument model

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value: Normal

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title: F934repl

tag: scan-b external id

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tag: lymph node group

tag: lymph node status

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title: F895repl

tag: instrument model

tag: age at diagnosis

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title: F912repl

tag: scan-b external id

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title: F933repl

tag: instrument model

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title: F807repl

tag: scan-b external id

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tag: scan-b external id

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title: F799repl

tag: instrument model

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title: F784repl

tag: scan-b external id

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tag: instrument model

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title: F781repl

tag: scan-b external id

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title: F777repl

tag: instrument model

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title: F1584repl

tag: scan-b external id

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title: F748repl

tag: instrument model

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title: F1582repl

tag: scan-b external id

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title: F717repl

tag: instrument model

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title: F713repl

tag: scan-b external id

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title: F679repl

tag: scan-b external id

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title: F673repl

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tag: scan-b external id

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tag: instrument model

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tag: scan-b external id

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title: F69repl

tag: instrument model

tag: age at diagnosis

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tag: scan-b external id

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tag: scan-b external id

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tag: scan-b external id

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title: F3089

tag: scan-b external id

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title: F1263

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title: F1369

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title: F1726

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title: F2872repl

tag: scan-b external id

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