title: single mES cell treated with conventional BS, replicate 3

data_processing:
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 using the cutadapt tool, low-quality and short reads were filtered out by applying ‘-q 20 –nextseq-trim 20 –max-n 0 -m 20’ arguments. The clean reads were then aligned to the spike-in sequences (found in Extended Data Table 1) and reference genomes (mouse reference GRCm39 for mESC samples and human reference GRCh38 for cfDNA samples) using the hisat-3n tool. The ‘--base-change C,T --no-splice-alignment –bowtie2-dp 1 –score-min L,0,1’ argument was used for all DNA libraries to ensure accurate alignment. To make use of the strand-specific property of the library, the ‘--directional-mapping’ argument was applied for 10 ng / 3.3 ng mES gDNA and cfDNA libraries, while ‘--directional-mapping-reverse’ arguments were used for single cell mESC libraries. The sorted mapped reads were then processed to remove PCR duplicates using the MarkDuplicateSpark command in the GATK tool. Finally, the number of converted and unconverted reads at all C sites were counted using the hisat-3n-table command, and the methylation ratio was calculated as the number of unconverted reads divided by total coverage.
Assembly: hg38, mm10
Supplementary files format and content: For bw files, number of conversion and unconverted are counted from mapped bam files using samtools mplieup and cpup tool. Methylation level is calculated by converstion count over sequence coverage and bw files were created by bedGraphToBigWig tools.
Supplementary files format and content: For tsv files, unconversion ratio on RNA sites are detected by the hisat3n-table tools. m5C sites are filter by statatistical cutoff and annotated based of ensembl release 108.

value: WT

value: conventional BS


title: miRNA Control fibroblast C15

status: Public on Oct 13 2023

type: SRA

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

country: Italy

institute: University of Brescia

library_source: transcriptomic

data_processing:
After read trimming using cutadapt v1.18 (adapter 3' AACTGTAGGCACCATCAAT; adapter 5' GTTCAGAGTTCTACAGTCCGACGATC), quantification was performed with mirdeep2 pipeline (Friedländer et al., 2012) using as reference miRNAs and hairpins as defined in miRBase 22.1. Reads shorter than 17 nucleotides were discarded. MiRNAs with average expression across samples lower than 20 count were excluded from further analysis. Differential expression analysis was performed with DESeq2 R package v1.38.3 (Love et al., 2014). Differentially expressed miRNAs (DE-miRNAs) were selected by using an adjusted p-value ≤ 0.05 (p-value correction with Benjamini & Hochberg).
Quantification was performed with mirdeep2 pipeline (Friedländer et al., 2012) using as reference miRNAs and hairpins as defined in miRBase 22.1. Reads shorter than 17 nucleotides were discarded.  MiRNAs with average expression across samples lower than 20 count were excluded from further analysis.
Assembly: Reference miRNAs and hairpins as defined in miRBase 22.1.
Supplementary files format and content: Differential expression analysis was performed with DESeq2 R package v1.38.3 (Love et al., 2014).  Differentially expressed miRNAs (DE-miRNAs) were selected by using an adjusted p-value ≤ 0.05 (p-value correction with Benjamini & Hochberg).

molecule: total RNA

organism: Homo sapiens

source_name: dermis

growth_protocol: Control and patient fibroblasts were grown between 1st and 4th in vitro passage at 37 °C in a 5% CO2 atmosphere in Earle's Modified Eagle Medium supplemented with 2 mM L-glutamine, 10% FBS, and 100 µg/ml penicillin and streptomycin

extract_protocol:
Total RNA was purified from patient and control cells grown for 72 hours at 70-80% of confluency using the miRNeasy kit (Qiagen). Sample quality and quantity were evaluated with the QIAxcel (QIAGEN) and the Qubit fluorometer (Thermofisher Scientific), respectively.
To ensure the accuracy and reproducibility of the data, a biological replicate (BR) was prepared for each patient and control sample, resulting in a total of 72 miRNAs libraries. Reverse transcription and library preparation were achieved following the standard protocol of the QIAseq miRNA Library kit (QIAGEN). All procedures were carried out in accordance with the manufacturer's instructions. This method incorporates unique molecular indexes during cDNA synthesis, which uniquely tag each strand before amplification, resulting in a more accurate reflection of endogenous miRNA levels by controlling for library amplification bias (Wong et al., 2019). Libraries were quantified with the QIAxcel (QIAGEN) diluted to 100 pM and pooled equally, with 6 samples per pool, followed by emulsion PCR and enrichment with the Ion OneTouch2 with ES system. Libraries were then loaded onto an Ion 540 chip and sequenced on the Ion S5 instrument.

tag: tissue

value: dermis

tag: cell type

value: Skin fibroblasts

tag: genotype

value: healthy donors

tag: disease state

value: unaffected


title: WT HEK293T polyA+ RNA treated with ultrafast BS, replicate 2

city: Chicago

first: Chang

last: Ye

state: Illinois

country: USA

institute: University of Chicago

description:
RNA-HEK293T-UBS2
HEK293T-WT_sites.tsv

data_processing:
After trimming the TruSeq sequencing adapters from the 3′ ends of read 1 and read 2 using the cutadapt tool, low-quality and short reads were filtered out by applying ‘-q 20 –nextseq-trim 20 –max-n 0 -m 20’ arguments. The clean reads were then aligned to the spike-in sequences (found in Extended Data Table 1) and reference genomes (mouse reference GRCm39 for mESC samples and human reference GRCh38 for cfDNA samples) using the hisat-3n tool. The ‘--base-change C,T --no-splice-alignment –bowtie2-dp 1 –score-min L,0,1’ argument was used for all DNA libraries to ensure accurate alignment. To make use of the strand-specific property of the library, the ‘--directional-mapping’ argument was applied for 10 ng / 3.3 ng mES gDNA and cfDNA libraries, while ‘--directional-mapping-reverse’ arguments were used for single cell mESC libraries. The sorted mapped reads were then processed to remove PCR duplicates using the MarkDuplicateSpark command in the GATK tool. Finally, the number of converted and unconverted reads at all C sites were counted using the hisat-3n-table command, and the methylation ratio was calculated as the number of unconverted reads divided by total coverage.
Assembly: hg38, mm10
Supplementary files format and content: For bw files, number of conversion and unconverted are counted from mapped bam files using samtools mplieup and cpup tool. Methylation level is calculated by converstion count over sequence coverage and bw files were created by bedGraphToBigWig tools.
Supplementary files format and content: For tsv files, unconversion ratio on RNA sites are detected by the hisat3n-table tools. m5C sites are filter by statatistical cutoff and annotated based of ensembl release 108.
Library strategy: ultrafast bisulfite-seq

molecule: polyA RNA

growth_protocol: Cells were purchased from the American Type Culture Collection (ATCC). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell VIOS 160i incubator (Thermo Scientific). All cell lines were grown in DMEM medium (GIBCO, catalog no. 11995) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (Gibco).

extract_protocol: Library preparation starting from mES genomic DNA: The mixture of mES gDNA (100-200 ng/µl) and spike-in lambda DNA (0.1%) were fragmented by sonication in 100 µl tube for 11 cycles of 30 seconds on and 30 seconds off using Bioruptor® Pico (Diagenode). The fragmented genomic DNA was size selected by Agencourt AMPure XP (Beckman Coulter) to 300-500 bp and eluted with 17 µl water. 3′-Dephosphorylation was conducted by adding 2 µl 10x T4PNK buffer (NEB) and 1 µl of T4 PNK (NEB) and the mixture was incubated at 37 °C for 30 min followed by 65 °C for 20 min. After purification by DNA Clean & Concentrate kit (Zymo Research), 164 bp dsDNA oligos (0.001%) was added as spike-in.  After BS treatment, all samples were desulphonated on Zymo-Spin IC columns following manufacturer’s protocol except that final washing step was conducted for four times instead of twice. Then the samples were incubated at 95 °C for 5 min to denature DNA, and cold-shocked on ice for 2 min followed by libraries construction using xGen™ Methyl-Seq Lib Prep kit for 96rxn (IDT, catalog no: 10009824).   Library preparation starting from small number of mES cells (100-cell, 10-cell and single-cell): The DNA libraries starting from small number of mES cells were constructed following the previous method with slight modifications40,41. In brief, mES cells were sorted by fluorescence-activated cell sorting (FACS) into lysis buffer containing 20 mM Tris-HCl (pH 8.0), 2 mM EDTA, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL QIAGEN protease and 0.6 pg lambda DNA (dam-, dcm-). Genomic DNA was released under the program of 50 °C for 3 h, followed by 75 °C for 30 min. Bisulfite treatment was performed using UBS-1 and Zymo DNA Methylation-Gold kit side by side. The first-strand DNA was synthesized by random priming using 50 U Klenow exo-, 400 μM P5-N6-oligo1 (CTACACGACGCTCTTCCGATCTNNNNNN, IDT) at 37 °C for 30 min. After 4 rounds of random priming, samples were purified with 0.8x AMPure XP beads. The second strand was synthesized using P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNNN, IDT). After purification with 0.8x AMPure XP beads, the sequencing index was introduced by PCR using Multiplex Oligos for Illumina (NEB) and KAPA HiFi HotStart ReadyMix. Library preparation for human plasma cfDNA: 41 ng of plasma cfDNA either from healthy people or from patient’s sample was spiked-in with 0.1% of the 164 bp dsDNA containing four 5mC sites and water was added to give each sample total volume 25 µl. Then to each sample, End Repair & A-Tailing Buffer (3.5 µl) and End Repair & A-Tailing Enzyme Mix from KAPA HyperPlus kit (Roche, catalog no: 07962428001) were added and the mixture was incubated at 65 °C for 30 min. Then a mixture of 15 µl ligation buffer, 5 µl DNA ligase, 2.5 µl water and 2.5 µl 15 µM methylated NEBNext adaptor was added, and the mixture was incubated at 20 °C for 1 h. Then 3 µl USER enzyme (NEB, catalog no: M5505S) was added and incubated at 37 °C for 15 min. Then the ligated DNA was purified by 1.0x Ampure beads and eluted with 41 µl water and divided into 5 parts. One part equivalent to 1 ng cfDNA will be directly amplified as input library. Two parts containing 10 ng cfDNA were treated with UBS condition followed by desulphonation the same procedure as described above for mES gDNA, and the other two parts equivalent to 10 ng cfDNA were treated with the conventional BS condition following manufacture’s protocol. The purified DNA was then amplified using KAPA HiFi Uracil+ DNA polymerase (Roche, catalog no: 07959079001) and the libraries was purified by 0.7x Ampure beads.

tag: cell line

value: embryonic kidney

tag: method

value: ultrafast BS


title: single mES cell treated with conventional BS, replicate 2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

value: mESC

tag: sample amount

value: single mES cell


title: BRD4 JQ1 rep 1

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq 550 output.
ChIP-seq reads were trimmed using Cutadapt v4.0 using --nextseq-trim 25 option, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg38 genome (or mm10 genome to determine spike-in factors) using Bowtie version 2.3.5.1 with default settings.
To create ChIP-seq average profiles, coverage matrices were generated from markduped bam files using ngs.plot.r v2.61. Spike-in normalisation of average profiles was performed by multiplying the total number of reads by a factor inversely proportional to Mouse spike-in unique deduplicated reads and an average of two normalised replicas was used for average profile visualisation with R default plot functions and ggplot2.
BigWig files were generated with bamCoverage from Deeptools v3.3.2 package with --scaleFactor option for spike-in normalization.
Assembly: hg38
Supplementary files format and content: spike-in normalized bigWig

source_name: Bo103, PDAC

growth_protocol: Cells were grown in a 1:1 mix of high glucose (4.5g/L) DMEM (Thermo, 61965059) and DMEM/F12 (Thermo, 11320033) containing 10% FBS (Thermo, 10270106), 1.6μg/ml amphotericin (Sigma, A2411), 10μM Y-27632 (Selleckchem, S1049), 6.2μg/ml ciprofloxacin (Sigma, 17850), 8.4ng/ml choleratoxin (Sigma, C8052), 500ng/mL insulin (Sigma, I9278) and 20nM 1-thioglycerol (Sigma, M6145), in a 37oC incubator supplied with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde (Thermo Fisher, 28906) for 5 min. Cross-linking was stopped by the addition of glycine (125 mM) and cells were washed twice with cold PBS. After harvesting cells by scraping, the pellet was washed once with PBS plus 0.5% BSA and resuspended in RIPA buffer to a final concentration of 1x10^7 cells/ml. Samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments of 400 bps on average.
DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q33230). Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200-700bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906). The sequencing run was Single End and Dual Index with 75 bp reads.

treatment_protocol: Cells were treated (in biological duplicates for the sequencing assays) with DMSO (vehicle), SN38, JQ1 or their combination (SN38+JQ1) for 1 hour.

value: Bo103, PDAC

tag: treatment

value: Pancreatic tumor patient-derived cells

tag: chip antibody

value: BRD4 (Bethyl Laboratories, #A301985A100)


title: 100 mES cells treated with ultrafast BS, replicate 1

value: 100 mES cells


title: single mES cell treated with conventional BS, replicate 1


title: WT HEK293T polyA+ RNA treated with ultrafast BS, replicate 1

description:
RNA-HEK293T-UBS1
HEK293T-WT_sites.tsv


title: miRNA Control fibroblast C14


title: BRD4 SN38 rep 2


title: 10 mES cells treated with conventional BS, replicate 3

value: 10 mES cells


title: 10 mES cells treated with conventional BS, replicate 2


title: miRNA Control fibroblast C13_biological replicate


title: WT HeLa polyA+ RNA treated with ultrafast BS, replicate 3

description:
RNA-HeLa-UBS3
HeLa-WT_sites.tsv

source_name: HeLa

value: HeLa

value: epithelial cell


title: BRD4 SN38 rep 1


title: miRNA Control fibroblast C13


title: WT HeLa polyA+ RNA treated with ultrafast BS, replicate 2

description:
RNA-HeLa-UBS2
HeLa-WT_sites.tsv

value: WT


title: 10 mES cells treated with conventional BS, replicate 1

value: conventional BS


title: BRD4 vehicle rep 1

value: DMSO


title: miRNA Control fibroblast C12

value: dermis

value: Skin fibroblasts


title: 7ng of cfDNA treated with ultrafast BS, replicate 2

library_source: other

molecule: other

source_name: plasma

value: plasma

value: 7ng of cfDNA


title: 100 mES cells treated with conventional BS, replicate 3


title: H3K36me3 combo rep 1


title: 7ng of cfDNA treated with ultrafast BS, replicate 1

value: ultrafast BS


title: 100 mES cells treated with conventional BS, replicate 2

value: mESC


title: H3K36me3 combo rep 2


title: miRNA Control fibroblast C11_biological replicate

value: healthy donors

value: unaffected


title: BRD4 vehicle rep 2

value: Bo103, PDAC

value: Pancreatic tumor patient-derived cells


title: 7ng of cfDNA treated with conventional BS, replicate 2


title: miRNA Control fibroblast C10_biological replicate


title: 7ng of cfDNA treated with conventional BS, replicate 1


title: miRNA Control fibroblast C10


title: miRNA Control fibroblast C11


title: H3K36me3 JQ1 rep 2


title: H3K36me3 JQ1 rep 1


title: 100 mES cells treated with conventional BS, replicate 1

value: 100 mES cells


title: H3K36me3 SN38 rep 1


title: SEC62 -/- rep 2

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed of adapter sequences with Trim Galore 0.6.6 using Cutadapt 1.18 and FastQC 0.11.9 (--fastqc --nextera --clip_R1 1).
Trimmed reads were aligned with STAR 2.7.8a against the GENCODE v37 gene annotation and GRCh38 genome sequence, masked for NuMTs, and quantified with Salmon 1.3.0 (-l A --seqBias --posBias) using the GENCODE v37 transcript sequences, with customised mitochondrial sequences (properly merged bicistronic transcript sequences and corrected terminal sequences).
Transcript quantifications were summarised to gene-level with tximport 1.14.2 and analysed for differential changes between wild type and knockout genotypes with DESeq2 1.26.0, using the apeglm shrinkage estimator with an lfcThreshold of 1.
Assembly: GRCh38

source_name: breast

growth_protocol: CAL51 cells and CAL51 cells stably expressing Cas9-mCherry were cultured at 37°C in humidified 95% air: 5% CO2 in media Dulbecco’s modified essential media (DMEM) containing: glucose (4.5 g/L), foetal bovine serum (10%), sodium pyruvate (1 mM), uridine (50 µg/ml), penicillin (100 U/ml), and streptomycin sulphate (100 µg/ml).

extract_protocol:
CAL51 cells were trypsinised, and resuspended in a lysis solution containing 150 mM NaCl, 0.1% Triton X-100 and 50 mM Tris-HCl (pH 8) for 30 min at 4°C. Then, cells were centrifuged at 21,000 g for 15 min at 4°C to clarify lysates. Protein concentration was determined using a Bicinchoninic acid (BCA) assay. RNA was isolated from CAL51 cells using a miRNeast MiniKit (Qiagen) incorporating an on-column DNase digestion according to the manufacturer’s instructions.
Libraries were constructed using an Illumina Stranded mRNA preparation kit and sequenced using a NovaSeq platform by AGRF.

treatment_protocol: CAL51 cells were seeded at 60% confluency, and transfected with 1.5 ug of pD1311-AD mammalian Cas9 expression vector encoding the respective gRNA template using FuGENE HD.  For establishing stably transfected colonies, single-cell sorting was performed 3 days post transfection, where cells were selected based off GFP fluorescence signal using a FACSAria II (BD Biosciences) in PBS + 2% FBS (v/v). Editing of alleles was confirmed by Sanger sequencing performed by AGRF using primers detailed in Table S7.

value: breast

value: epithelial-like


title: miRNA Control fibroblast C9_biological replicate


title: SEC62 -/- rep 3


title: H3K36me3 SN38 rep 2


title: H3K36me3 vehicle rep 2


title: miRNA Control fibroblast C12_biological replicate


title: GOLGA8M -/- rep 3

value: GOLGA8M -/-


title: miRNA Control fibroblast C9


title: WT HeLa polyA+ RNA treated with ultrafast BS, replicate 1

description:
RNA-HeLa-UBS1
HeLa-WT_sites.tsv

value: HeLa

value: epithelial cell

value: WT


title: H3K36me3 vehicle rep 1

value: DMSO


title: miRNA Control fibroblast C8_biological replicate

value: dermis

value: Skin fibroblasts


title: SEC62 -/- rep 1


title: miRNA Control fibroblast C8


title: GOLGA8M -/- rep 2


title: H3K27ac combo rep 2


title: miRNA Control fibroblast C7


title: miRNA Control fibroblast C7_biological replicate


title: miRNA Control fibroblast C6


title: SEC61A2 -/- rep 2


title: SEC61A2 -/- rep 3


title: H3K27ac JQ1 rep 1


title: miRNA Control fibroblast C6_biological replicate


title: H3K27ac JQ1 rep 2


title: GOLGA8M -/- rep 1


title: SEC61A2 -/- rep 1


title: H3K27ac SN38 rep 2


title: miRNA Control fibroblast C5


title: H3K27ac SN38 rep 1


title: GOLGA5 -/- rep 2

value: GOLGA5 -/-


title: GOLGA5 -/- rep 3


title: miRNA Control fibroblast C4_biological replicate


title: GOLGA5 -/- rep 1


title: H3K27ac vehicle rep 1


title: H3K27ac vehicle rep 2


title: H3K27ac combo rep 1


title: miRNA Control fibroblast C3_biological replicate


title: PEX26 -/- rep 3


title: PEX26 -/- rep 2


title: TOP1 CAD 1hr SN38+JQ1 rep 1

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq 550 output.
ChIP-seq reads were trimmed using Cutadapt v4.0 using --nextseq-trim 25 option, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.3.5.1 with default settings.
To create ChIP-seq average profiles, coverage matrices were generated from markduped bam (merged duplicates) files and plotted using ngs.plot.r v2.61.
The profiles were smoothed using local polynomial regression in R.
BigWig files were generated with bamCoverage from Deeptools v3.3.2 package.
Assembly: hg38
Supplementary files format and content: library size normalized bigWig
Library strategy: CAD-Seq

extract_protocol:
Cells were immediately lysed in 2 ml of M buffer (9.3 mM Tris-HCl pH 6.5, 18.6 mM EDTA, 5.59 M guanidine thiocyanate, 0.93 % DTT, 0.93 % Sarcosyl, 3.72 % Triton X 100) and briefly sonicated with Bandelin probe sonicator at 20 % amplitude for 3 cycles with 30 sec ON, 30 sec OFF. DNA covalent adducts were precipitated with 50 % EtOH at -20°C, centrifuged at 14000 rpm and pellets were washed thrice in wash buffer (20 mM Tris-HCl pH 7.5, 50 mM NaCl, 1 mM EDTA, 50 % EtOH). Pellets were dried for 5 min and resuspended in TE-SDS 0.1 % (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1 % SDS). After 30 min incubation by gentle agitation samples were further sonicated with Covaris ME220 sonicator for 5 min at High Cell protocol in milliTUBE–1 mL with AFA Fiber to produce fragments of about 1 kb.
DNA from CAD was quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q33230). Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200-700bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906). The sequencing run was Single End and Dual Index with 75 bp reads.

treatment_protocol: Cells were treated (in biological duplicates for the sequencing assays) with DMSO (vehicle), SN38 alone or in combination with JQ1 for 1 hour. In the last 30 min MG132 (10 µM) was added to the cells treated drugs and to the MG132 sample.

value: 1hr SN38+JQ1

value: Pancreatic tumor patient-derived xenografts (PDX)


title: miRNA Control fibroblast C3

value: healthy donors


title: PEX26 -/- rep 1


title: TOP1 CAD 1hr SN38 rep 2

value: 1hr SN38


title: miRNA Control fibroblast C2_biological replicate

value: unaffected


title: Wild type rep 3

value: Wild type


title: Wild type rep 2


title: miRNA Control fibroblast C2


title: miRNA Control fibroblast C1_biological replicate


title: miRNA Control fibroblast C5_biological replicate


title: TOP1 CAD vehicle rep 2


title: TOP1 CAD 1hr SN38 rep 1


title: miRNA Control fibroblast C4


title: TOP1 CAD 1hr SN38+JQ1 rep 2


title: ShallowTS-HumanBlood_Validation_Pool3

status: Public on Oct 12 2023

city: Boston

first: Patrick

middle: T

last: Griffin

state: MA

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

description:
bisulfite converted DNA
TS-HumanBlood_Validation_Shallow.tar.gz

data_processing:
https://github.com/patricktgriffin/TIME-Seq
Assembly: mm10,hg19
Supplementary files format and content: bismark.cov
Library strategy: TIME-Seq

source_name: Whole blood

value: Whole blood

tag: strain

tag: age

value: various

tag: Sex

value: mixed


title: Wild type rep 1

value: breast

value: epithelial-like


title: ShallowTS-HumanBlood_Validation_Pool1


title: ShallowTS-HumanBlood_Validation_Pool6


title: p28_ls21_Tnai_CCPneg

type: genomic

city: La Jolla

first: Gary

last: Firestein

state: CA

address: 9500 Gilman Dr

department: Division of Rheumatology, Allergy & Immunology

institute: University of California, San Diego School of Medicine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Samples were scanned using the Illumina Infinium MethylationEPIC Kit chip based on standard Illumina protocol.

data_processing: Samples were processed using minfi R package, normalized using Dasen method with wateRmelon R package, standard quality control parameters were applied. One sample, p20_ls23_Tnai_CCPpos, failed QC. Probes that failed QC were removed from processed data.

label: Cy5, Cy3

source_name: Patient 28, Sample 21 Tnai cells

label_protocol: Standard Illumina protocol.

extract_protocol: PBMCs were separated by use of antibodies and magnetic beads into B, memory T and naïve T cell subsets for analyses.

tag: assay

value: CCPneg

tag: gender

value: Female


title: p125_ls124_Tnai_ERA

source_name: Patient 125, Sample 124 Tnai cells

value: ERA


title: p119_ls119_Tnai_CCPpos

source_name: Patient 119, Sample 119 Tnai cells

value: CCPpos


title: p83_ls89_Tnai_CCPpos

source_name: Patient 83, Sample 89 Tnai cells


title: p119_ls119_B_CCPpos

source_name: Patient 119, Sample 119 B cells


title: p66_ls57_Tnai_CCPpos

source_name: Patient 66, Sample 57 Tnai cells


title: p75_ls75_B_CCPneg

source_name: Patient 75, Sample 75 B cells


title: p119_ls119_Tmem_CCPpos

source_name: Patient 119, Sample 119 Tmem cells


title: p93_ls92_B_CCPpos

source_name: Patient 93, Sample 92 B cells


title: p43_ls35_Tnai_CCPneg

source_name: Patient 43, Sample 35 Tnai cells


title: p109_ls109_Tmem_ERA

source_name: Patient 109, Sample 109 Tmem cells


title: p114_ls114_B_ERA

source_name: Patient 114, Sample 114 B cells


title: p87_ls86_Tnai_ERA

source_name: Patient 87, Sample 86 Tnai cells


title: p62_ls61_Tnai_CCPneg

source_name: Patient 62, Sample 61 Tnai cells


title: p90_ls90_Tnai_CCPpos

source_name: Patient 90, Sample 90 Tnai cells


title: p123_ls123_Tnai_CCPpos

source_name: Patient 123, Sample 123 Tnai cells


title: ShallowTS-HumanBlood_Validation_Pool5

source_name: Whole blood


title: p28_ls21_Tmem_CCPneg

source_name: Patient 28, Sample 21 Tmem cells


title: ShallowTS-HumanBlood_Validation_Pool4


title: miRNA Control fibroblast C1

source_name: dermis

value: dermis

value: Skin fibroblasts


title: p102_ls99_Tmem_CCPpos

source_name: Patient 102, Sample 99 Tmem cells


title: p106_ls101_Tnai_CCPpos

source_name: Patient 106, Sample 101 Tnai cells


title: p88_ls88_Tmem_CCPpos

source_name: Patient 88, Sample 88 Tmem cells


title: p12_ls20_Tmem_CCPpos

source_name: Patient 12, Sample 20 Tmem cells


title: p112_ls113_B_CCPpos

source_name: Patient 112, Sample 113 B cells


title: p92_ls94_Tmem_CCPpos

source_name: Patient 92, Sample 94 Tmem cells


title: p72_ls73_B_CCPneg

source_name: Patient 72, Sample 73 B cells


title: p52_ls46_B_CCPneg

source_name: Patient 52, Sample 46 B cells


title: p22_ls22_Tmem_CCPneg

source_name: Patient 22, Sample 22 Tmem cells


title: p108_ls107_B_CCPpos

source_name: Patient 108, Sample 107 B cells


title: p96_ls105_Tnai_CCPneg

source_name: Patient 96, Sample 105 Tnai cells


title: p66_ls57_Tmem_CCPpos

source_name: Patient 66, Sample 57 Tmem cells


title: p126_ls126_Tmem_ERA

source_name: Patient 126, Sample 126 Tmem cells


title: p13_ls11_Tmem_CCPpos

source_name: Patient 13, Sample 11 Tmem cells


title: p105_ls104_Tnai_CCPneg

source_name: Patient 105, Sample 104 Tnai cells


title: p10_ls7_Tmem_CCPneg

source_name: Patient 10, Sample 7 Tmem cells


title: p31_ls24_B_CCPneg

source_name: Patient 31, Sample 24 B cells


title: p2_ls1_Tmem_CCPpos

source_name: Patient 2, Sample 1 Tmem cells


title: p90_ls90_B_CCPpos

source_name: Patient 90, Sample 90 B cells


title: p101_ls97_Tmem_CCPneg

source_name: Patient 101, Sample 97 Tmem cells


title: p25_ls25_Tnai_CCPpos

source_name: Patient 25, Sample 25 Tnai cells


title: p127_ls127_Tmem_ERA

source_name: Patient 127, Sample 127 Tmem cells


title: p130_ls130_Tnai_ERA

source_name: Patient 130, Sample 130 Tnai cells


title: p52_ls46_Tmem_CCPneg

source_name: Patient 52, Sample 46 Tmem cells


title: p12_ls20_B_CCPpos

source_name: Patient 12, Sample 20 B cells


title: p53_ls48_Tnai_CCPneg

source_name: Patient 53, Sample 48 Tnai cells


title: p75_ls75_Tnai_CCPneg

source_name: Patient 75, Sample 75 Tnai cells


title: p104_ls103_Tmem_CCPneg

source_name: Patient 104, Sample 103 Tmem cells


title: p23_ls47_B_CCPpos

source_name: Patient 23, Sample 47 B cells


title: p34_ls34_Tnai_CCPneg

source_name: Patient 34, Sample 34 Tnai cells


title: p107_ls106_Tmem_CCPneg

source_name: Patient 107, Sample 106 Tmem cells


title: p80_ls82_B_ERA

source_name: Patient 80, Sample 82 B cells


title: p46_ls41_Tnai_CCPneg

source_name: Patient 46, Sample 41 Tnai cells


title: p3_ls2_B_CCPneg

source_name: Patient 3, Sample 2 B cells


title: p115_ls115_B_CCPpos

source_name: Patient 115, Sample 115 B cells


title: p95_ls102_Tmem_CCPpos

source_name: Patient 95, Sample 102 Tmem cells


title: p82_ls85_B_CCPpos

source_name: Patient 82, Sample 85 B cells


title: p103_ls100_Tmem_ERA

source_name: Patient 103, Sample 100 Tmem cells


title: p55_ls54_B_CCPneg

source_name: Patient 55, Sample 54 B cells


title: p13_ls11_Tnai_CCPpos

source_name: Patient 13, Sample 11 Tnai cells


title: p29_ls18_Tnai_CCPneg

source_name: Patient 29, Sample 18 Tnai cells


title: p80_ls82_Tnai_ERA

source_name: Patient 80, Sample 82 Tnai cells


title: p74_ls70_B_CCPneg

source_name: Patient 74, Sample 70 B cells


title: p126_ls126_Tnai_ERA

source_name: Patient 126, Sample 126 Tnai cells


title: p86_ls83_Tmem_CCPpos

source_name: Patient 86, Sample 83 Tmem cells


title: p110_ls110_B_CCPpos

source_name: Patient 110, Sample 110 B cells


title: p93_ls92_Tmem_CCPpos

source_name: Patient 93, Sample 92 Tmem cells


title: p117_ls117_Tnai_CCPpos

source_name: Patient 117, Sample 117 Tnai cells


title: p128_ls128_Tnai_ERA

source_name: Patient 128, Sample 128 Tnai cells


title: p126_ls126_B_ERA

source_name: Patient 126, Sample 126 B cells


title: p117_ls117_B_CCPpos

source_name: Patient 117, Sample 117 B cells


title: p7_ls8_B_CCPneg

source_name: Patient 7, Sample 8 B cells


title: p112_ls113_Tmem_CCPpos

source_name: Patient 112, Sample 113 Tmem cells


title: p101_ls97_B_CCPneg

source_name: Patient 101, Sample 97 B cells


title: p59_ls56_B_CCPneg

source_name: Patient 59, Sample 56 B cells


title: p53_ls48_B_CCPneg

source_name: Patient 53, Sample 48 B cells


title: p96_ls105_B_CCPneg

source_name: Patient 96, Sample 105 B cells


title: p76_ls80_Tnai_CCPneg

source_name: Patient 76, Sample 80 Tnai cells


title: p57_ls51_Tmem_CCPneg

source_name: Patient 57, Sample 51 Tmem cells


title: p51_ls43_Tmem_CCPneg

source_name: Patient 51, Sample 43 Tmem cells


title: p116_ls116_Tmem_CCPpos

source_name: Patient 116, Sample 116 Tmem cells


title: p105_ls104_Tmem_CCPneg

source_name: Patient 105, Sample 104 Tmem cells


title: p84_ls81_B_CCPpos

source_name: Patient 84, Sample 81 B cells


title: p44_ls37_Tmem_CCPpos

source_name: Patient 44, Sample 37 Tmem cells


title: p92_ls94_Tnai_CCPpos

source_name: Patient 92, Sample 94 Tnai cells


title: p98_ls96_B_CCPneg

source_name: Patient 98, Sample 96 B cells


title: p128_ls128_Tmem_ERA

source_name: Patient 128, Sample 128 Tmem cells


title: p91_ls84_B_ERA

source_name: Patient 91, Sample 84 B cells


title: p107_ls106_B_CCPneg

source_name: Patient 107, Sample 106 B cells


title: p124_ls125_Tmem_CCPpos

source_name: Patient 124, Sample 125 Tmem cells


title: p90_ls90_Tmem_CCPpos

source_name: Patient 90, Sample 90 Tmem cells


title: p104_ls103_B_CCPneg

source_name: Patient 104, Sample 103 B cells


title: p121_ls121_B_CCPpos

source_name: Patient 121, Sample 121 B cells


title: p127_ls127_B_ERA

source_name: Patient 127, Sample 127 B cells


title: p103_ls100_B_ERA

source_name: Patient 103, Sample 100 B cells


title: p102_ls99_Tnai_CCPpos

source_name: Patient 102, Sample 99 Tnai cells


title: p106_ls101_Tmem_CCPpos

source_name: Patient 106, Sample 101 Tmem cells


title: p114_ls114_Tmem_ERA

source_name: Patient 114, Sample 114 Tmem cells


title: p3_ls2_Tnai_CCPneg

source_name: Patient 3, Sample 2 Tnai cells


title: p130_ls130_B_ERA

source_name: Patient 130, Sample 130 B cells


title: p7_ls8_Tnai_CCPneg

source_name: Patient 7, Sample 8 Tnai cells


title: p10_ls7_Tnai_CCPneg

source_name: Patient 10, Sample 7 Tnai cells


title: p120_ls120_Tnai_ERA

source_name: Patient 120, Sample 120 Tnai cells


title: p95_ls102_Tnai_CCPpos

source_name: Patient 95, Sample 102 Tnai cells


title: p108_ls107_Tnai_CCPpos

source_name: Patient 108, Sample 107 Tnai cells


title: p84_ls81_Tnai_CCPpos

source_name: Patient 84, Sample 81 Tnai cells


title: p104_ls103_Tnai_CCPneg

source_name: Patient 104, Sample 103 Tnai cells


title: p103_ls100_Tnai_ERA

source_name: Patient 103, Sample 100 Tnai cells


title: p105_ls104_B_CCPneg

source_name: Patient 105, Sample 104 B cells


title: p111_ls111_B_CCPpos

source_name: Patient 111, Sample 111 B cells


title: p87_ls86_Tmem_ERA

source_name: Patient 87, Sample 86 Tmem cells


title: p117_ls117_Tmem_CCPpos

source_name: Patient 117, Sample 117 Tmem cells


title: p116_ls116_B_CCPpos

source_name: Patient 116, Sample 116 B cells


title: p123_ls123_B_CCPpos

source_name: Patient 123, Sample 123 B cells


title: p125_ls124_B_ERA

source_name: Patient 125, Sample 124 B cells


title: p81_ls77_Tnai_ERA

source_name: Patient 81, Sample 77 Tnai cells


title: p31_ls24_Tmem_CCPneg

source_name: Patient 31, Sample 24 Tmem cells


title: p89_ls91_Tmem_CCPpos

source_name: Patient 89, Sample 91 Tmem cells


title: p107_ls106_Tnai_CCPneg

source_name: Patient 107, Sample 106 Tnai cells


title: p32_ls33_Tnai_CCPneg

source_name: Patient 32, Sample 33 Tnai cells


title: p51_ls43_Tnai_CCPneg

source_name: Patient 51, Sample 43 Tnai cells


title: p86_ls83_Tnai_CCPpos

source_name: Patient 86, Sample 83 Tnai cells


title: p125_ls124_Tmem_ERA

source_name: Patient 125, Sample 124 Tmem cells


title: p97_ls93_Tnai_ERA

source_name: Patient 97, Sample 93 Tnai cells


title: p129_ls129_B_ERA

source_name: Patient 129, Sample 129 B cells


title: p85_ls87_Tnai_CCPpos

source_name: Patient 85, Sample 87 Tnai cells


title: p26_ls15_Tnai_ERA

source_name: Patient 26, Sample 15 Tnai cells


title: p73_ls74_Tnai_CCPneg

source_name: Patient 73, Sample 74 Tnai cells


title: p88_ls88_Tnai_CCPpos

source_name: Patient 88, Sample 88 Tnai cells


title: p74_ls70_Tnai_CCPneg

source_name: Patient 74, Sample 70 Tnai cells


title: p98_ls96_Tnai_CCPneg

source_name: Patient 98, Sample 96 Tnai cells


title: p106_ls101_B_CCPpos

source_name: Patient 106, Sample 101 B cells


title: p113_ls112_B_CCPpos

source_name: Patient 113, Sample 112 B cells


title: p128_ls128_B_ERA

source_name: Patient 128, Sample 128 B cells


title: p121_ls121_Tmem_CCPpos

source_name: Patient 121, Sample 121 Tmem cells


title: p121_ls121_Tnai_CCPpos

source_name: Patient 121, Sample 121 Tnai cells


title: p43_ls35_Tmem_CCPneg

source_name: Patient 43, Sample 35 Tmem cells


title: p72_ls73_Tnai_CCPneg

source_name: Patient 72, Sample 73 Tnai cells


title: p55_ls54_Tmem_CCPneg

source_name: Patient 55, Sample 54 Tmem cells


title: p10_ls7_B_CCPneg

source_name: Patient 10, Sample 7 B cells


title: p89_ls91_B_CCPpos

source_name: Patient 89, Sample 91 B cells


title: p91_ls84_Tmem_ERA

source_name: Patient 91, Sample 84 Tmem cells


title: p89_ls91_Tnai_CCPpos

source_name: Patient 89, Sample 91 Tnai cells


title: p19_ls67_Tnai_CCPpos

source_name: Patient 19, Sample 67 Tnai cells


title: TOP1 CAD vehicle rep 1

value: DMSO


title: p12_ls20_Tnai_CCPpos

source_name: Patient 12, Sample 20 Tnai cells


title: p127_ls127_Tnai_ERA

source_name: Patient 127, Sample 127 Tnai cells


title: p29_ls18_Tmem_CCPneg

source_name: Patient 29, Sample 18 Tmem cells


title: p99_ls95_Tmem_CCPneg

source_name: Patient 99, Sample 95 Tmem cells


title: p8_ls6_Tnai_CCPpos

source_name: Patient 8, Sample 6 Tnai cells


title: p99_ls95_Tnai_CCPneg

source_name: Patient 99, Sample 95 Tnai cells


title: p22_ls22_Tnai_CCPneg

source_name: Patient 22, Sample 22 Tnai cells


title: 4435_04U

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis
Genotype Call (SNP call): AA, AB, BB, NoCall

label: Biotin

source_name: peripheral white blood cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

value: male

value: peripheral white blood cells

value: HNSqCC patient


title: 4485_04U

scan_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.


title: ShallowTS-HumanBlood_Validation_Pool2

source_name: Whole blood


title: 4418_04U


title: p19_ls67_Tmem_CCPpos

source_name: Patient 19, Sample 67 Tmem cells


title: 4470_04U


title: p130_ls130_Tmem_ERA

source_name: Patient 130, Sample 130 Tmem cells


title: p86_ls83_B_CCPpos

source_name: Patient 86, Sample 83 B cells


title: 4406_04U


title: p3_ls2_Tmem_CCPneg

source_name: Patient 3, Sample 2 Tmem cells


title: p44_ls37_B_CCPpos

source_name: Patient 44, Sample 37 B cells


title: 4355_04U


title: 4343_04U


title: 4452_04U


title: p88_ls88_B_CCPpos

source_name: Patient 88, Sample 88 B cells


title: 4342_04U


title: 4334_04U


title: p111_ls111_Tnai_CCPpos

source_name: Patient 111, Sample 111 Tnai cells


title: 4321_16


title: p87_ls86_B_ERA

source_name: Patient 87, Sample 86 B cells


title: 4295_04U


title: p26_ls15_Tmem_ERA

source_name: Patient 26, Sample 15 Tmem cells


title: 4293_04U


title: p73_ls74_B_CCPneg

source_name: Patient 73, Sample 74 B cells


title: 4317_16


title: 4292_04U


title: p118_ls118_Tmem_CCPpos

source_name: Patient 118, Sample 118 Tmem cells


title: p75_ls75_Tmem_CCPneg

source_name: Patient 75, Sample 75 Tmem cells


title: 4415_04U


title: p84_ls81_Tmem_CCPpos

source_name: Patient 84, Sample 81 Tmem cells


title: p93_ls92_Tnai_CCPpos

source_name: Patient 93, Sample 92 Tnai cells


title: p96_ls105_Tmem_CCPneg

source_name: Patient 96, Sample 105 Tmem cells


title: 4281_16

source_name: peripheral white blood cells


title: p115_ls115_Tmem_CCPpos

source_name: Patient 115, Sample 115 Tmem cells


title: p25_ls25_B_CCPpos

source_name: Patient 25, Sample 25 B cells


title: p114_ls114_Tnai_ERA

source_name: Patient 114, Sample 114 Tnai cells


title: 4320_16


title: 4340_04U


title: 4279_16


title: 4253_16


title: p83_ls89_Tmem_CCPpos

source_name: Patient 83, Sample 89 Tmem cells


title: 4278_16


title: p19_ls67_B_CCPpos

source_name: Patient 19, Sample 67 B cells


title: p115_ls115_Tnai_CCPpos

source_name: Patient 115, Sample 115 Tnai cells


title: p92_ls94_B_CCPpos

source_name: Patient 92, Sample 94 B cells


title: p2_ls1_B_CCPpos

source_name: Patient 2, Sample 1 B cells


title: 4250_16


title: p76_ls80_B_CCPneg

source_name: Patient 76, Sample 80 B cells


title: 4251_16


title: 4249_16


title: 4247_16


title: 4248_16


title: 4282_16


title: p109_ls109_B_ERA

source_name: Patient 109, Sample 109 B cells


title: p94_ls98_Tnai_CCPpos

source_name: Patient 94, Sample 98 Tnai cells


title: 4245_16


title: 4235_04U


title: p94_ls98_Tmem_CCPpos

source_name: Patient 94, Sample 98 Tmem cells


title: 4246_16


title: p81_ls77_Tmem_ERA

source_name: Patient 81, Sample 77 Tmem cells


title: 4234_16


title: 4232_16


title: 4231_16


title: 4230_16


title: p46_ls41_B_CCPneg

source_name: Patient 46, Sample 41 B cells


title: p29_ls18_B_CCPneg

source_name: Patient 29, Sample 18 B cells


title: p43_ls35_B_CCPneg

source_name: Patient 43, Sample 35 B cells


title: p52_ls46_Tnai_CCPneg

source_name: Patient 52, Sample 46 Tnai cells


title: 4229_16

source_name: peripheral white blood cells


title: 4204_16


title: p46_ls41_Tmem_CCPneg

source_name: Patient 46, Sample 41 Tmem cells


title: p81_ls77_B_ERA

source_name: Patient 81, Sample 77 B cells


title: p7_ls8_Tmem_CCPneg

source_name: Patient 7, Sample 8 Tmem cells


title: p82_ls85_Tnai_CCPpos

source_name: Patient 82, Sample 85 Tnai cells


title: 4206_16


title: p32_ls33_Tmem_CCPneg

source_name: Patient 32, Sample 33 Tmem cells


title: p82_ls85_Tmem_CCPpos

source_name: Patient 82, Sample 85 Tmem cells


title: p57_ls51_B_CCPneg

source_name: Patient 57, Sample 51 B cells


title: p100_ls108_Tmem_CCPneg

source_name: Patient 100, Sample 108 Tmem cells


title: p74_ls70_Tmem_CCPneg

source_name: Patient 74, Sample 70 Tmem cells


title: 4199_16


title: 4198_16


title: 4200_16


title: 4197_16


title: p25_ls25_Tmem_CCPpos

source_name: Patient 25, Sample 25 Tmem cells


title: 4188_16


title: 4187_16


title: 4203_16


title: p8_ls6_B_CCPpos

source_name: Patient 8, Sample 6 B cells


title: 4176_16


title: p97_ls93_Tmem_ERA

source_name: Patient 97, Sample 93 Tmem cells


title: 4186_16


title: 4185_16


title: p122_ls122_Tmem_ERA

source_name: Patient 122, Sample 122 Tmem cells


title: 4174_16


title: p95_ls102_B_CCPpos

source_name: Patient 95, Sample 102 B cells


title: p124_ls125_Tnai_CCPpos

source_name: Patient 124, Sample 125 Tnai cells


title: p59_ls56_Tmem_CCPneg

source_name: Patient 59, Sample 56 Tmem cells


title: 4143_16

source_name: peripheral white blood cells


title: 4151_16


title: 4163_16


title: 4201_16


title: p80_ls82_Tmem_ERA

source_name: Patient 80, Sample 82 Tmem cells


title: 4097_16


title: p98_ls96_Tmem_CCPneg

source_name: Patient 98, Sample 96 Tmem cells


title: p113_ls112_Tmem_CCPpos

source_name: Patient 113, Sample 112 Tmem cells


title: p99_ls95_B_CCPneg

source_name: Patient 99, Sample 95 B cells


title: p120_ls120_B_ERA

source_name: Patient 120, Sample 120 B cells


title: 4045_16


title: 4060_16


title: 4061_04U


title: 4046_04U


title: p62_ls61_B_CCPneg

source_name: Patient 62, Sample 61 B cells


title: p129_ls129_Tmem_ERA

source_name: Patient 129, Sample 129 Tmem cells


title: p124_ls125_B_CCPpos

source_name: Patient 124, Sample 125 B cells


title: p23_ls47_Tmem_CCPpos

source_name: Patient 23, Sample 47 Tmem cells


title: 4036_16


title: p59_ls56_Tnai_CCPneg

source_name: Patient 59, Sample 56 Tnai cells


title: p26_ls15_B_ERA

source_name: Patient 26, Sample 15 B cells


title: 4027_16


title: 4029_16


title: p112_ls113_Tnai_CCPpos

source_name: Patient 112, Sample 113 Tnai cells


title: p51_ls43_B_CCPneg

source_name: Patient 51, Sample 43 B cells


title: 4020_04U


title: 4028_16


title: p34_ls34_Tmem_CCPneg

source_name: Patient 34, Sample 34 Tmem cells


title: 4014_16


title: 4005_16


title: 3983_16


title: p116_ls116_Tnai_CCPpos

source_name: Patient 116, Sample 116 Tnai cells


title: p23_ls47_Tnai_CCPpos

source_name: Patient 23, Sample 47 Tnai cells


title: 4031_16

source_name: peripheral white blood cells


title: p62_ls61_Tmem_CCPneg

source_name: Patient 62, Sample 61 Tmem cells


title: 3962_16


title: p122_ls122_Tnai_ERA

source_name: Patient 122, Sample 122 Tnai cells


title: p8_ls6_Tmem_CCPpos

source_name: Patient 8, Sample 6 Tmem cells


title: 3968_16


title: 3941_16


title: 3939_16


title: p72_ls73_Tmem_CCPneg

source_name: Patient 72, Sample 73 Tmem cells


title: p57_ls51_Tnai_CCPneg

source_name: Patient 57, Sample 51 Tnai cells


title: p97_ls93_B_ERA

source_name: Patient 97, Sample 93 B cells


title: p85_ls87_B_CCPpos

source_name: Patient 85, Sample 87 B cells


title: 3899_16


title: p13_ls11_B_CCPpos

source_name: Patient 13, Sample 11 B cells


title: p34_ls34_B_CCPneg

source_name: Patient 34, Sample 34 B cells


title: 3912_16


title: p73_ls74_Tmem_CCPneg

source_name: Patient 73, Sample 74 Tmem cells


title: 3882_16


title: p110_ls110_Tnai_CCPpos

source_name: Patient 110, Sample 110 Tnai cells


title: 3921_16


title: p120_ls120_Tmem_ERA

source_name: Patient 120, Sample 120 Tmem cells


title: 3877_16


title: p129_ls129_Tnai_ERA

source_name: Patient 129, Sample 129 Tnai cells


title: 3880_16


title: 3875_16


title: p122_ls122_B_ERA

source_name: Patient 122, Sample 122 B cells


title: p108_ls107_Tmem_CCPpos

source_name: Patient 108, Sample 107 Tmem cells


title: 3872_16


title: 3873_16


title: p28_ls21_B_CCPneg

source_name: Patient 28, Sample 21 B cells


title: 3860_16

source_name: peripheral white blood cells


title: 3852_16


title: p31_ls24_Tnai_CCPneg

source_name: Patient 31, Sample 24 Tnai cells


title: 3856_16


title: p85_ls87_Tmem_CCPpos

source_name: Patient 85, Sample 87 Tmem cells


title: 3889_16


title: p109_ls109_Tnai_ERA

source_name: Patient 109, Sample 109 Tnai cells


title: p83_ls89_B_CCPpos

source_name: Patient 83, Sample 89 B cells


title: p44_ls37_Tnai_CCPpos

source_name: Patient 44, Sample 37 Tnai cells


title: p102_ls99_B_CCPpos

source_name: Patient 102, Sample 99 B cells


title: 3845_16


title: 3835_16


title: p123_ls123_Tmem_CCPpos

source_name: Patient 123, Sample 123 Tmem cells


title: 3836_16


title: 3831_16


title: 3829_16


title: p118_ls118_B_CCPpos

source_name: Patient 118, Sample 118 B cells


title: 3830_16


title: p110_ls110_Tmem_CCPpos

source_name: Patient 110, Sample 110 Tmem cells


title: 3814_16


title: p66_ls57_B_CCPpos

source_name: Patient 66, Sample 57 B cells


title: 3870_16


title: 3795_16


title: 3863_16


title: p76_ls80_Tmem_CCPneg

source_name: Patient 76, Sample 80 Tmem cells


title: p32_ls33_B_CCPneg

source_name: Patient 32, Sample 33 B cells


title: 3793_16


title: 3786_16


title: p100_ls108_B_CCPneg

source_name: Patient 100, Sample 108 B cells


title: 3772_16


title: p91_ls84_Tnai_ERA

source_name: Patient 91, Sample 84 Tnai cells


title: 3775_16


title: p111_ls111_Tmem_CCPpos

source_name: Patient 111, Sample 111 Tmem cells


title: 3785_16


title: p101_ls97_Tnai_CCPneg

source_name: Patient 101, Sample 97 Tnai cells


title: 3767_04U

source_name: peripheral white blood cells


title: p118_ls118_Tnai_CCPpos

source_name: Patient 118, Sample 118 Tnai cells


title: p94_ls98_B_CCPpos

source_name: Patient 94, Sample 98 B cells


title: 3765_16


title: p113_ls112_Tnai_CCPpos

source_name: Patient 113, Sample 112 Tnai cells


title: 3749_16


title: p53_ls48_Tmem_CCPneg

source_name: Patient 53, Sample 48 Tmem cells


title: p100_ls108_Tnai_CCPneg

source_name: Patient 100, Sample 108 Tnai cells


title: p22_ls22_B_CCPneg

source_name: Patient 22, Sample 22 B cells


title: p55_ls54_Tnai_CCPneg

source_name: Patient 55, Sample 54 Tnai cells


title: p68_ls62_Tnai_CCPneg

source_name: Patient 68, Sample 62 Tnai cells


title: p77_ls76_Tnai_ERA

source_name: Patient 77, Sample 76 Tnai cells


title: 3680_16


title: 3739_16


title: 3687_16


title: 3690_16


title: 3689_16


title: p40_ls32_Tnai_CCPpos

source_name: Patient 40, Sample 32 Tnai cells


title: p60_ls53_Tnai_ERA

source_name: Patient 60, Sample 53 Tnai cells


title: 3677_16


title: p70_ls68_Tnai_CCPpos

source_name: Patient 70, Sample 68 Tnai cells


title: p71_ls69_Tnai_CCPneg

source_name: Patient 71, Sample 69 Tnai cells


title: 3668_16


title: 3659_16


title: 3651_16


title: 3653_16


title: p61_ls55_Tnai_ERA

source_name: Patient 61, Sample 55 Tnai cells


title: p39_ls40_Tnai_CCPpos

source_name: Patient 39, Sample 40 Tnai cells


title: p69_ls64_Tnai_CCPneg

source_name: Patient 69, Sample 64 Tnai cells


title: p41_ls39_Tnai_CCPpos

source_name: Patient 41, Sample 39 Tnai cells


title: 3748_16

source_name: peripheral white blood cells


title: 3657_16


title: p36_ls65_Tnai_CCPpos

source_name: Patient 36, Sample 65 Tnai cells


title: 3637_04U


title: p63_ls59_Tnai_CCPneg

source_name: Patient 63, Sample 59 Tnai cells


title: p38_ls29_Tnai_CCPneg

source_name: Patient 38, Sample 29 Tnai cells


title: 3648_16


title: 3628_16


title: 3630_16


title: p78_ls78_Tnai_CCPpos

source_name: Patient 78, Sample 78 Tnai cells


title: 3626_16


title: p45_ls38_Tnai_ERA

source_name: Patient 45, Sample 38 Tnai cells


title: p14_ls17_Tnai_CCPneg

source_name: Patient 14, Sample 17 Tnai cells


title: 3587_16


title: 3600_16


title: 3618_04U


title: p35_ls72_Tnai_CCPpos

source_name: Patient 35, Sample 72 Tnai cells


title: 3619_16


title: 3583_16


title: p37_ls31_Tnai_CCPpos

source_name: Patient 37, Sample 31 Tnai cells


title: p48_ls45_Tnai_CCPneg

source_name: Patient 48, Sample 45 Tnai cells


title: 3577_16


title: p65_ls66_Tnai_CCPneg

source_name: Patient 65, Sample 66 Tnai cells


title: p20_ls23_Tnai_CCPpos

source_name: Patient 20, Sample 23 Tnai cells


title: 3576_16


title: 3566_16


title: 3562_16


title: 3568_16


title: p17_ls14_Tnai_CCPneg

source_name: Patient 17, Sample 14 Tnai cells


title: 3549_16


title: p4_ls9_Tnai_CCPpos

source_name: Patient 4, Sample 9 Tnai cells


title: p30_ls30_Tnai_CCPneg

source_name: Patient 30, Sample 30 Tnai cells


title: p67_ls58_Tnai_ERA

source_name: Patient 67, Sample 58 Tnai cells


title: p16_ls50_Tnai_CCPpos

source_name: Patient 16, Sample 50 Tnai cells


title: p33_ls28_Tnai_CCPneg

source_name: Patient 33, Sample 28 Tnai cells


title: p15_ls12_Tnai_CCPpos

source_name: Patient 15, Sample 12 Tnai cells


title: 3544_16

source_name: peripheral white blood cells


title: 3539_16


title: 3536_16


title: p11_ls4_Tnai_CCPneg

source_name: Patient 11, Sample 4 Tnai cells


title: p49_ls42_Tnai_CCPpos

source_name: Patient 49, Sample 42 Tnai cells


title: 3517_16


title: p79_ls79_Tnai_CCPpos

source_name: Patient 79, Sample 79 Tnai cells


title: p9_ls3_Tnai_CCPpos

source_name: Patient 9, Sample 3 Tnai cells


title: p5_ls10_Tnai_CCPneg

source_name: Patient 5, Sample 10 Tnai cells


title: p50_ls44_Tnai_CCPneg

source_name: Patient 50, Sample 44 Tnai cells


title: p27_ls26_Tnai_CCPneg

source_name: Patient 27, Sample 26 Tnai cells


title: 3489_16


title: 3482_04U


title: 3469_16


title: 3511_16


title: 3459_16


title: p54_ls71_Tnai_CCPneg

source_name: Patient 54, Sample 71 Tnai cells


title: p56_ls52_Tnai_CCPneg

source_name: Patient 56, Sample 52 Tnai cells


title: 3503_16


title: 3547_16


title: 3435_16


title: 3446_16


title: p18_ls19_Tnai_CCPneg

source_name: Patient 18, Sample 19 Tnai cells


title: 3432_16


title: p1_ls5_Tnai_CCPpos

source_name: Patient 1, Sample 5 Tnai cells


title: p21_ls16_Tnai_CCPneg

source_name: Patient 21, Sample 16 Tnai cells


title: p6_ls13_Tnai_CCPpos

source_name: Patient 6, Sample 13 Tnai cells


title: 3424_04U


title: 3500_16


title: p64_ls60_Tnai_CCPneg

source_name: Patient 64, Sample 60 Tnai cells


title: 3417_16


title: 3415_04U


title: p58_ls63_Tnai_CCPpos

source_name: Patient 58, Sample 63 Tnai cells


title: p24_ls27_Tnai_CCPneg

source_name: Patient 24, Sample 27 Tnai cells


title: p47_ls49_Tnai_CCPpos

source_name: Patient 47, Sample 49 Tnai cells


title: 3451_16

source_name: peripheral white blood cells


title: p48_ls45_Tmem_CCPneg

source_name: Patient 48, Sample 45 Tmem cells


title: p1_ls5_Tmem_CCPpos

source_name: Patient 1, Sample 5 Tmem cells


title: p6_ls13_Tmem_CCPpos

source_name: Patient 6, Sample 13 Tmem cells


title: 3420_16


title: p42_ls36_Tnai_CCPpos

source_name: Patient 42, Sample 36 Tnai cells


title: p9_ls3_Tmem_CCPpos

source_name: Patient 9, Sample 3 Tmem cells


title: p30_ls30_Tmem_CCPneg

source_name: Patient 30, Sample 30 Tmem cells


title: 3371_16


title: 3388_16


title: p38_ls29_Tmem_CCPneg

source_name: Patient 38, Sample 29 Tmem cells


title: p61_ls55_Tmem_ERA

source_name: Patient 61, Sample 55 Tmem cells


title: 3368_16


title: 3397_16


title: 3393_16


title: 3404_16


title: 3411_16


title: p68_ls62_Tmem_CCPneg

source_name: Patient 68, Sample 62 Tmem cells


title: 3385_16


title: p56_ls52_Tmem_CCPneg

source_name: Patient 56, Sample 52 Tmem cells


title: p20_ls23_Tmem_CCPpos

source_name: Patient 20, Sample 23 Tmem cells


title: p58_ls63_Tmem_CCPpos

source_name: Patient 58, Sample 63 Tmem cells


title: p33_ls28_Tmem_CCPneg

source_name: Patient 33, Sample 28 Tmem cells


title: 3412_16


title: 3361_16


title: p79_ls79_Tmem_CCPpos

source_name: Patient 79, Sample 79 Tmem cells


title: 3369_16


title: p16_ls50_Tmem_CCPpos

source_name: Patient 16, Sample 50 Tmem cells


title: 3345_16


title: 3343_16


title: 3337_16


title: 3401_16


title: 3344_16


title: p24_ls27_Tmem_CCPneg

source_name: Patient 24, Sample 27 Tmem cells


title: p5_ls10_Tmem_CCPneg

source_name: Patient 5, Sample 10 Tmem cells


title: p14_ls17_Tmem_CCPneg

source_name: Patient 14, Sample 17 Tmem cells


title: 3334_16

source_name: peripheral white blood cells


title: p78_ls78_Tmem_CCPpos

source_name: Patient 78, Sample 78 Tmem cells


title: p77_ls76_Tmem_ERA

source_name: Patient 77, Sample 76 Tmem cells


title: p36_ls65_Tmem_CCPpos

source_name: Patient 36, Sample 65 Tmem cells


title: p4_ls9_Tmem_CCPpos

source_name: Patient 4, Sample 9 Tmem cells


title: 3359_16


title: 3331_16


title: 3316_16


title: 3309_16


title: p60_ls53_Tmem_ERA

source_name: Patient 60, Sample 53 Tmem cells


title: 3306_16


title: p11_ls4_Tmem_CCPneg

source_name: Patient 11, Sample 4 Tmem cells


title: p47_ls49_Tmem_CCPpos

source_name: Patient 47, Sample 49 Tmem cells


title: 3313_16


title: 3308_16


title: 3305_16


title: 3323_16


title: 3304_16


title: 3320_16


title: p67_ls58_Tmem_ERA

source_name: Patient 67, Sample 58 Tmem cells


title: 3303_16


title: p35_ls72_Tmem_CCPpos

source_name: Patient 35, Sample 72 Tmem cells


title: p40_ls32_Tmem_CCPpos

source_name: Patient 40, Sample 32 Tmem cells


title: 3302_16


title: 3296_16


title: p70_ls68_Tmem_CCPpos

source_name: Patient 70, Sample 68 Tmem cells


title: p49_ls42_Tmem_CCPpos

source_name: Patient 49, Sample 42 Tmem cells


title: p17_ls14_Tmem_CCPneg

source_name: Patient 17, Sample 14 Tmem cells


title: 3295_16


title: p15_ls12_Tmem_CCPpos

source_name: Patient 15, Sample 12 Tmem cells


title: p45_ls38_Tmem_ERA

source_name: Patient 45, Sample 38 Tmem cells


title: 3294_16


title: p65_ls66_Tmem_CCPneg

source_name: Patient 65, Sample 66 Tmem cells


title: p50_ls44_Tmem_CCPneg

source_name: Patient 50, Sample 44 Tmem cells


title: p18_ls19_Tmem_CCPneg

source_name: Patient 18, Sample 19 Tmem cells


title: 3286_16

source_name: peripheral white blood cells


title: 3288_16


title: p54_ls71_Tmem_CCPneg

source_name: Patient 54, Sample 71 Tmem cells


title: 3291_16


title: 3289_16


title: 3287_16


title: p71_ls69_Tmem_CCPneg

source_name: Patient 71, Sample 69 Tmem cells


title: p69_ls64_Tmem_CCPneg

source_name: Patient 69, Sample 64 Tmem cells


title: p27_ls26_Tmem_CCPneg

source_name: Patient 27, Sample 26 Tmem cells


title: 3276_16


title: p64_ls60_Tmem_CCPneg

source_name: Patient 64, Sample 60 Tmem cells


title: 3275_16


title: p37_ls31_Tmem_CCPpos

source_name: Patient 37, Sample 31 Tmem cells


title: 3273_16


title: 3272_16


title: 3269_16


title: p42_ls36_Tmem_CCPpos

source_name: Patient 42, Sample 36 Tmem cells


title: 3262_16


title: p39_ls40_Tmem_CCPpos

source_name: Patient 39, Sample 40 Tmem cells


title: p41_ls39_Tmem_CCPpos

source_name: Patient 41, Sample 39 Tmem cells


title: 3285_16


title: p63_ls59_Tmem_CCPneg

source_name: Patient 63, Sample 59 Tmem cells


title: 3250_16


title: 3246_16


title: 3256_16


title: p40_ls32_B_CCPpos

source_name: Patient 40, Sample 32 B cells


title: p47_ls49_B_CCPpos

source_name: Patient 47, Sample 49 B cells


title: p56_ls52_B_CCPneg

source_name: Patient 56, Sample 52 B cells


title: p30_ls30_B_CCPneg

source_name: Patient 30, Sample 30 B cells


title: 3236_16


title: 3245_16


title: 3243_16


title: p71_ls69_B_CCPneg

source_name: Patient 71, Sample 69 B cells


title: p50_ls44_B_CCPneg

source_name: Patient 50, Sample 44 B cells


title: p45_ls38_B_ERA

source_name: Patient 45, Sample 38 B cells


title: 3235_16

source_name: peripheral white blood cells


title: 3223_16


title: 3270_16


title: p21_ls16_Tmem_CCPneg

source_name: Patient 21, Sample 16 Tmem cells


title: 3220_16


title: 3218_16


title: p15_ls12_B_CCPpos

source_name: Patient 15, Sample 12 B cells


title: 3216_16


title: p17_ls14_B_CCPneg

source_name: Patient 17, Sample 14 B cells


title: 3214_16


title: 3205_16


title: p37_ls31_B_CCPpos

source_name: Patient 37, Sample 31 B cells


title: p63_ls59_B_CCPneg

source_name: Patient 63, Sample 59 B cells


title: 3199_16


title: 3196_16


title: p79_ls79_B_CCPpos

source_name: Patient 79, Sample 79 B cells


title: 3200_16


title: p35_ls72_B_CCPpos

source_name: Patient 35, Sample 72 B cells


title: p69_ls64_B_CCPneg

source_name: Patient 69, Sample 64 B cells


title: p77_ls76_B_ERA

source_name: Patient 77, Sample 76 B cells


title: p20_ls23_B_CCPpos

source_name: Patient 20, Sample 23 B cells


title: p64_ls60_B_CCPneg

source_name: Patient 64, Sample 60 B cells


title: 3180_16


title: 3183_16


title: p36_ls65_B_CCPpos

source_name: Patient 36, Sample 65 B cells


title: p14_ls17_B_CCPneg

source_name: Patient 14, Sample 17 B cells


title: 3173_16


title: p58_ls63_B_CCPpos

source_name: Patient 58, Sample 63 B cells


title: p61_ls55_B_ERA

source_name: Patient 61, Sample 55 B cells


title: 3166_16


title: p70_ls68_B_CCPpos

source_name: Patient 70, Sample 68 B cells


title: p78_ls78_B_CCPpos

source_name: Patient 78, Sample 78 B cells


title: 3164_16

source_name: peripheral white blood cells


title: 3212_16


title: 3157_04U


title: p16_ls50_B_CCPpos

source_name: Patient 16, Sample 50 B cells


title: p68_ls62_B_CCPneg

source_name: Patient 68, Sample 62 B cells


title: p27_ls26_B_CCPneg

source_name: Patient 27, Sample 26 B cells


title: 3185_16


title: 3156_16


title: 3147_16


title: p1_ls5_B_CCPpos

source_name: Patient 1, Sample 5 B cells


title: p39_ls40_B_CCPpos

source_name: Patient 39, Sample 40 B cells


title: 3144_16


title: 3135_16


title: p18_ls19_B_CCPneg

source_name: Patient 18, Sample 19 B cells


title: 3132_16


title: p54_ls71_B_CCPneg

source_name: Patient 54, Sample 71 B cells


title: p42_ls36_B_CCPpos

source_name: Patient 42, Sample 36 B cells


title: 3112_16


title: 3122_16


title: p4_ls9_B_CCPpos

source_name: Patient 4, Sample 9 B cells


title: 3140_16


title: 3106_16


title: p24_ls27_B_CCPneg

source_name: Patient 24, Sample 27 B cells


title: p65_ls66_B_CCPneg

source_name: Patient 65, Sample 66 B cells


title: 3101_16


title: p60_ls53_B_ERA

source_name: Patient 60, Sample 53 B cells


title: 3100_16


title: p11_ls4_B_CCPneg

source_name: Patient 11, Sample 4 B cells


title: 3149_16


title: p38_ls29_B_CCPneg

source_name: Patient 38, Sample 29 B cells


title: 3086_16


title: p41_ls39_B_CCPpos

source_name: Patient 41, Sample 39 B cells


title: 3088_16


title: p6_ls13_B_CCPpos

source_name: Patient 6, Sample 13 B cells


title: 3083_16

source_name: peripheral white blood cells


title: 3077_16


title: 3068_16


title: 3073_16


title: T47D_2hr_rep2

city: Salt Lake City

first: Alexandra

last: Richey

state: UT

address: 2000 Cir of Hope Dr

department: Biomedical Engineering

institute: University of Utah

data_processing:
Sequencing reads were aligned to hg19 build of the human genome using HISAT2
SAMtools was used to convert SAM files to BAM files
Read counts were normalized and analyzed for differential expression via the DESeq2 package in R
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads that mapped to known genes were assigned with featureCounts
Assembly: hg19
Supplementary files format and content: Gene counts (raw) in a text file

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 3 days prior to  E2 treatments, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Following timed E2 treatments cells were lysed with buffer RLT plus (Qiagen) containing 1% beta-mercaptoethanol (Sigma-Aldrich). RNA was extracted and purified using a Quick RNA Mini Prep kit (Zymo Research).
NEBNext Ultra II Directional RNA Library Prep kit with poly(A) mRNA isolation was used to construct RNA-seq libraries according to the manufacturer's instructions (NEB).

treatment_protocol: Cells were treated with 10 nM 17beta-estradiol (E2) for 8, 4, 2, or 0 hours.

value: Breast; Ductal Carcinoma

value: 2 hr 10 nM E2


title: T47D_0hr_rep2

value: 0 hr 10 nM E2


title: T47D_0hr_rep1


title: T47D_2hr_rep1


title: 3066_16


title: 3057_16


title: T47D_4hr_rep2

value: 4 hr 10 nM E2


title: T47D_4hr_rep1


title: 3051_16


title: 3049_16


title: T47D_8hr_rep1

value: 8 hr 10 nM E2


title: 3047_16


title: 3040_16


title: Ishi_0hr_rep2

source_name: Ishikawa

value: Ishikawa

value: endometrioid adenocarcinoma


title: Ishi_0hr_rep1


title: Ishi_2hr_rep2


title: 3038_16


title: Ishi_2hr_rep1


title: 3034_16


title: Ishi_4hr_rep2


title: 3033_16


title: 3029_16


title: Ishi_4hr_rep1


title: 3023_16


title: Ishi_8hr_rep2


title: 3062_16


title: 3019_16


title: T47D_8hr_rep2


title: 3013_16


title: 3011_16


title: BxPC_SBKO#2_4

city: Bethesda

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description: BxPC-3 SERPINB3 knockout#2

data_processing:
For AsPC-1 ± SERPINB3 and Panc 10.05 ± SERPINB3, the samples have 22 to 29 million pass filter reads with more than 85% of bases above the quality score of Q30. For AsPC-1 SERPINB3 ± a MYC inhibitor, Panc 10.05 SERPINB3 ± a MYC inhibitor, and BxPC-3 ± SERPINB3 knockout, the samples have 86 to 130 million pass filter reads with more than 85% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Pancreatic cancer cell line

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: No treatment

value: SERPINB3 knockout#2


title: BxPC_SBKO#2_1

description: BxPC-3 SERPINB3 knockout#2


title: BxPC_SBKO#1_4

description: BxPC-3 SERPINB3 knockout#1

value: SERPINB3 knockout#1


title: BxPC_SBKO#1_3

description: BxPC-3 SERPINB3 knockout#1


title: 2998_16


title: 3003_16


title: BxPC_SBKO#1_2

description: BxPC-3 SERPINB3 knockout#1


title: 2993_16


title: 3191_16


title: 3010_16


title: BxPC_SBKO#2_3

description: BxPC-3 SERPINB3 knockout#2


title: BxPC_SBKO#1_1

description: BxPC-3 SERPINB3 knockout#1


title: 3032_16


title: BxPC_NC_4

description: BxPC-3 control

value: Control vector


title: 2980_16


title: Ishi_8hr_rep1


title: BxPC_NC_3

description: BxPC-3 control


title: 2972_16


title: 3008_16


title: BxPC_NC_2

description: BxPC-3 control


title: 2967_16


title: BxPC_NC_1

description: BxPC-3 control


title: Panc10.05_SB_MYCi_4

description: Panc 10.05 SERPINB3 transgene

value: MYC inhibitor

value: SERPINB3 expressing transgene


title: 2951_16


title: BxPC_SBKO#2_2

description: BxPC-3 SERPINB3 knockout#2


title: 2926_16


title: Panc10.05_SB_MYCi_3

description: Panc 10.05 SERPINB3 transgene


title: Panc10.05_SB_MYCi_1

description: Panc 10.05 SERPINB3 transgene


title: Panc10.05_SB_MYCi_2

description: Panc 10.05 SERPINB3 transgene


title: Panc10.05_SB_DMSO_4

description: Panc 10.05 SERPINB3 transgene

value: DMSO


title: Panc10.05_SB_DMSO_2

description: Panc 10.05 SERPINB3 transgene


title: Panc10.05_SB_DMSO_3

description: Panc 10.05 SERPINB3 transgene


title: 2902_16

value: male


title: 2913_16

value: peripheral white blood cells


title: 2908_16

value: HNSqCC patient


title: 2903_16


title: 2897_16


title: 2917_16


title: 2894_16


title: 2893_16


title: Panc10.05_SB_DMSO_1

description: Panc 10.05 SERPINB3 transgene


title: As_SB_MYCi_3

description: AsPC-1 SERPINB3 transgene


title: As_SB_MYCi_2

description: AsPC-1 SERPINB3 transgene


title: As_SB_MYCi_4

description: AsPC-1 SERPINB3 transgene


title: 2891_16


title: 2892_16


title: 2877_16


title: 2884_16


title: 2864_16


title: As_SB_MYCi_1

description: AsPC-1 SERPINB3 transgene


title: As_SB_DMSO_3

description: AsPC-1 SERPINB3 transgene


title: 2859_16


title: As_SB_DMSO_1

description: AsPC-1 SERPINB3 transgene


title: As_SB_DMSO_2

description: AsPC-1 SERPINB3 transgene


title: 2852_04U


title: HEK293T,CEP+4SU,Rep3

city: Charlottesville

first: Dina

last: Bai

state: VA

address: McCormick Rd.

department: Chemistry

institute: University of Virginia

data_processing:
Quality control
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 ploy-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.
Reads mapping to the reference genome
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level
featureCounts v1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’sapproach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Enrichment analysis of differentially expressed genes
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implementedby the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential
expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies(http://www.genome.jp/kegg/). We used cluster Profiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected P value less than0.05 were considered significantly enriched by differential expressed genes. The DisGeNETdatabase integrates human disease-related genes. DisGeNET pathways with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes. We used cluster Profiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if apre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool
http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG, Reactome, DOand DisGeNETdata sets were used for GSEA independently. SNP analysis GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD<2.0; FS > 30.0;
Assembly: Homo Sapiens(GRCh38/hg38)

growth_protocol: HEK293T were cultured with 5% CO2at 37 ºC with DMEM supplemented with 10% fetal bovine serum (FBS, U.S. Source, Omega Scientific) and 1% L-glutamine (Fisher Scientific). Cells were harvested for experimental use when they reached ∼90% confluency.

extract_protocol:
RNA was then purified from cells using the PureLink™ RNA Mini Kit (ThermoFisher, 12183018A) and frozen (-80 °C).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library ordTTP for non-directional library.

treatment_protocol: Cell media was replaced with 4SU-supplemented complete SILAC DMEM for 16 hrs. Afterwards, cells were washed with PBS and crosslinked at 312nm (1J/cm2) on ice. Serum-free DMEM containing CEP (AHL-Pu-1, 25 mM final in DMSO) was added to cells after crosslinking. Probe labeling in cells was allowed to proceed for 1 hr at 37 °C.

value: Embryonic Kidney

value: WT


title: 2846_16


title: HEK293T,CEP+4SU,Rep2


title: 2843_16


title: 2842_16


title: 2833_16


title: 2832_16


title: 2830_16


title: 2829_16


title: HEK293T,CEP+4SU,Rep1


title: HEK293T,4SU,Rep2


title: HEK293T,4SU,Rep1


title: HEK293T,CEP,Rep3

value: CEP


title: HEK293T,4SU,Rep3


title: HEK293T,CEP,Rep1


title: As_SB_DMSO_4

description: AsPC-1 SERPINB3 transgene


title: 2824_16


title: HEK293T,DMSO,Rep3


title: 2826_16


title: HEK293T,DMSO,Rep2


title: 2823_16


title: 2814_16


title: HEK293T,DMSO,Rep1


title: 2807_16


title: 2806_16


title: 2805_16


title: atac_74_CC0716

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

data_processing:
The demultiplexing, fragment counting were conducted using cellranger-arc software (v2.0.0)
Assembly: hg38
Supplementary files format and content: tsv
Library strategy: scATAC-seq

source_name: PBMCs

extract_protocol:
Single-cell ATAC and RNA-seq libraries were prepared using the Chromium Single Cell Multiome ATAC + Gene Expression platform (10X Genomics, Pleasanton, CA). Briefly, cryopreserved PBMCs were thawed and processed for single nuclei multi-omics analysis according to the manufacturer’s instructions (10x Genomics, CG000365 Rev B). Nuclei were obtained by incubating PBMCs for 3.10 minutes in freshly prepared Lysis buffer and washed and resuspended in chilled diluted nuclei buffer (10x Genomics, 2000153). About 9,000 cells were targeted for each experiment. Prepared nuclei were subjected to transposition of open chromatin regions. Next, transposed nuclei, reverse transcription Master Mix, barcoded Gel Beads, and Partitioning Oil were partitioned into single-cell GEMs (Gel Bead in EMulsions) using the 10X Chromium Controller and Next GEM Chip J. Within each GEM, Gel Beads are dissolved and poly-adenlyated (poly-A) mRNA transcripts are captured by uniquely barcoded poly(dt)VN oligos. Simultaneously, accessible chromatin fragments are captured by a separate oligo containing a spacer, unique barcode, and Illumina P5 adaptor sequence.
The GEMs were then incubated in a C1000 Touch Thermal Cycler (BioRad) to produce barcodedDNA from the transposed DNA, and full-length cDNA. GEMs are then broken to release and pool single-cell fractions within each sample. Pooled fractions are purified using silane magnetic beads and subjected to PCR amplification to generate sufficient mass for library construction. Next, P7 and a sample index are added to transposed DNA via PCR to generate ATAC libraries. Finally, cDNA is enzymatically fragmented before the addition of P5, P7, i7 and i5 indexes, and TruSeq Read 2 via End Repair, A-tailing, Adaptor Ligation, and PCR resulting in gene expression libraries. Quantitation of gene expression and ATAC libraries was performed using Bioanalyzer High Sensitivity DNA Analysis (Agilent). Libraries were combined into gene expression and ATAC pools and sequenced on an Illumina NovaSeq 6000 system using the read lengths recommended by 10X: 28bp (read 1), 90bp (read 2), 10bp (i7 index), and 10bp (i5 index) for gene expression libraries and 50bp (read 1), 49bp (read 2), 8bp (i7 index) and 24bp (i5 index) for ATAC libraries. CellRanger v.3.1.0 (10xGenomics) was used to demultiplex raw sequencing data and quantify transcript levels against the 10x Genomics GRCh38 reference v.3.0.0.

value: PBMCs

tag: subject

value: Female

tag: Stage

value: acute-omicron


title: atac_73_CC0710


title: 2802_16


title: atac_71_CC0594

value: Male


title: 2825_16


title: 2750_16


title: 2752_16


title: atac_70_CC0572


title: HEK293T,CEP,Rep2


title: 2748_16


title: atac_68_CC0443


title: atac_67_CC0407

value: acute


title: atac_66_CC0350


title: 2744_16


title: 2747_16


title: atac_64_CC0294

value: conv


title: atac_76_CC0829


title: atac_62_CC0294

value: pre


title: 2738_16


title: 2734_16


title: atac_63_CC0294


title: 2737_16


title: 2733_16


title: atac_61_CC0216

value: matched-ctrl


title: 2732_16


title: atac_72_CC0688


title: 2730_16


title: 2731_16


title: 2745_16


title: 2728_16


title: atac_57_CC0054


title: atac_58_CC0256


title: 2713_16


title: 2708_16


title: 2701_16


title: atac_54_CC0249


title: atac_60_CC0256


title: atac_51_CC0191


title: atac_50_CC0191


title: atac_52_CC0191


title: atac_59_CC0256


title: 2699_16


title: 2694_16


title: 2693_16


title: 2690_16


title: 2688_16


title: atac_47_CC0138


title: atac_56_CC0249


title: atac_46_CC0138


title: atac_48_CC0138


title: 2684_16


title: 2677_16


title: atac_43_CC0111


title: atac_44_CC0111


title: atac_55_CC0249


title: 2675_16


title: 2673_16


title: atac_41_CC0107


title: atac_45_CC0154


title: 2695_16


title: atac_49_CC0385


title: atac_42_CC0111


title: 2672_16


title: atac_40_CC0069


title: 2663_16


title: 2668_16


title: atac_39_CC0069


title: atac_37_CC0120


title: 2662_16


title: 2659_16


title: 2658_16


title: 2678_16


title: 2653_16


title: 2656_16


title: atac_34_CC0061


title: atac_33_CC0053


title: atac_32_CC0022


title: 2640_04U


title: atac_31_CC0022


title: atac_30_CC0022


title: 2638_16


title: gex_74_CC0716

library_source: transcriptomic single cell

data_processing:
The demultiplexing, fragment counting were conducted using cellranger-arc software (v2.0.0)
Assembly: hg38
Supplementary files format and content: tsv


title: gex_76_CC0829


title: 2649_16


title: 2626_16


title: gex_73_CC0710


title: atac_38_CC0069


title: 2627_16


title: gex_72_CC0688


title: 2625_16


title: 2618_16


title: atac_36_CC0061


title: 2611_16


title: gex_71_CC0594


title: atac_35_CC0061


title: gex_68_CC0443


title: gex_70_CC0572


title: 2657_16


title: 2607_16


title: gex_67_CC0407


title: gex_66_CC0350


title: 2602_16


title: 2599_16


title: gex_64_CC0294


title: 2635_16


title: gex_63_CC0294


title: 2598_16


title: gex_62_CC0294


title: gex_61_CC0216


title: 2571_16


title: gex_60_CC0256


title: gex_59_CC0256


title: 2570_16


title: 2567_16


title: 2566_16


title: 2564_16


title: gex_56_CC0249


title: gex_58_CC0256


title: gex_57_CC0054


title: gex_55_CC0249


title: 2605_16


title: 2560_16


title: 2549_16


title: 2557_16


title: gex_50_CC0191


title: gex_54_CC0249


title: 2541_16


title: gex_51_CC0191


title: 2536_16


title: gex_49_CC0385


title: 2546_16


title: gex_48_CC0138


title: 2578_16


title: 2531_16


title: 2534_16


title: 2524_16


title: gex_46_CC0138


title: gex_47_CC0138


title: 2522_16


title: 2520_16


title: gex_45_CC0154


title: 2515_16


title: 2514_16


title: gex_52_CC0191


title: gex_44_CC0111


title: gex_43_CC0111


title: gex_40_CC0069


title: gex_41_CC0107


title: 2505_16


title: 2490_16


title: 2451_16


title: 2434_16


title: gex_39_CC0069


title: 2433_16


title: gex_36_CC0061


title: 2419_16


title: gex_38_CC0069


title: gex_37_CC0120


title: 2383_16


title: gex_34_CC0061


title: 2368_16


title: 2340_16


title: gex_33_CC0053


title: 2291_16


title: gex_32_CC0022


title: gex_42_CC0111


title: gex_31_CC0022


title: 2282_04U


title: 2249_16


title: gex_30_CC0022


title: 2240_16


title: Subject CC0184 acute

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

data_processing:
Alignment was performed using STAR version 2.7.3a[1] and transcripts were annotated using a composite genome reference which included GRCh38 Ensembl release 100 and SARS-CoV-2. Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count[2]. DESeq2 was used for normalization[3], producing a both a normalized read count table and a regularized log expression table.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file; Raw counts per transcript

source_name: Whole blood

extract_protocol:
Blood was collected into Tempus Blood RNA tubes (Applied Biosystems) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with Tempus Blood RNA Tubes (ThermoFisher Scientific).
RNA quality was assessed using a TapeStation 4200 (Agilent) and then 200 nanograms of total RNA was used as input for cDNA synthesis and library preparation using the KAPA RNA HyperPrep kit with RiboErase (HMR) Globin (Roche) according to the manufacturer’s instructions.
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~60 million reads per sample on average.

value: Whole blood

tag: age, months

tag: condition


title: 2222_16

tag: cell type


title: Subject CC0146 acute-omicron

tag: tissue


title: Subject CC0261 acute-omicron


title: Subject CC0191 acute


title: Subject CC0022 acute


title: 2206_16

tag: disease state


title: Subject CC0548 acute-omicron


title: 2204_16


title: 2208_16


title: 2168_16


title: Subject CC0132 acute-omicron


title: 2150_16


title: Subject CC0037 acute-omicron


title: gex_35_CC0061


title: 2284_16


title: Subject CC0572 acute-omicron


title: Subject CC0716 acute-omicron


title: 2130_04U


title: 2128_04U


title: Subject CC0443 acute-omicron


title: Subject CC0476 acute-omicron


title: 2133_16


title: 2263_04U


title: 2075_16


title: Subject CC0294 acute


title: 2044_16


title: Subject CC0144 acute


title: 1997_16


title: 2011_16


title: Subject PC126 acute


title: Subject CC0069 acute


title: Subject CC0264 acute


title: Subject CC0082 acute-omicron


title: 1971_16


title: 1976_16


title: Subject CC0138 acute


title: 1991_16


title: Subject CC0028 acute-omicron


title: 1873_16


title: 1946_16


title: 1955_16


title: Subject CC0791 acute-omicron


title: 1869_16


title: Subject CC0283 acute


title: Subject CC0183 acute


title: Subject CC0710 acute-omicron


title: 1840_16


title: 1839_16


title: Subject CC0688 acute-omicron


title: Subject CC0829 acute-omicron


title: Subject CC0407 acute


title: 1765_16


title: 1803_16


title: Subject CC0594 acute-omicron


title: Subject CC0085 acute-omicron


title: Subject CC0350 acute-omicron


title: 1660_16


title: 1657_16


title: 1641_16


title: 1624_16


title: Subject CC0162 acute


title: Subject CC0249 acute


title: Subject CC0256 acute


title: Subject CC0490 acute


title: Subject CC0111 acute


title: 1845_16


title: 1491_16


title: 1482_16


title: Subject PC265 healthy

value: healthy


title: 1467_16


title: Subject CC0050 acute


title: Subject CC0200 healthy


title: 1465_16


title: Subject CC0508 healthy


title: 1446_16


title: 1418_16


title: 1410_16


title: 1752_16


title: Subject CC0113 healthy


title: Subject CC0299 healthy


title: Subject CC0061 acute


title: Subject CC0120 healthy


title: 1382_16


title: 1343_16


title: 1626_16


title: 1543_16


title: Subject CC0355 healthy


title: 1339_16


title: Subject CC0424 healthy


title: Subject CC0279 healthy


title: 1269_16


title: 1250_04U


title: Subject CC0197 healthy


title: Subject CC0421 healthy


title: 1247_04U


title: Subject CC0369 healthy


title: 1165_16


title: Subject CC0156 healthy


title: 1194_16


title: 1158_04U


title: Subject CC0183 healthy


title: Subject CC0016 healthy


title: 1216_16


title: Subject CC0254 healthy


title: 1152_04U


title: Subject PC018 healthy


title: 1144_16


title: Subject CC0155 healthy


title: 1108_16


title: Subject PC209 healthy


title: 1078_16


title: Subject CC0249 healthy


title: 1075_16


title: Subject CC0061 healthy


title: 1066_16


title: Subject CC0191 healthy


title: Subject CC0052 healthy


title: 1041_16


title: 1305_16


title: 1025_16


title: Subject PC126 healthy


title: 995_16


title: Subject CC0558 healthy


title: 1012_16


title: Subject CC0050 healthy


title: 963_16


title: 988_16


title: 965_16


title: Subject CC0536 healthy


title: Subject CC0385 healthy


title: Subject CC0053 healthy


title: 959_16


title: Subject CC0094 healthy


title: 958_16


title: Subject CC0270 healthy


title: Subject CC0529 healthy


title: 951_16


title: 946_16


title: Subject CC0334 healthy


title: 944_16


title: Subject CC0216 healthy


title: Subject CC0154 healthy


title: 911_04U


title: Subject CC0107 healthy


title: 914_16


title: Subject CC0182 healthy


title: Subject CC0073 healthy


title: 905_16


title: 892_16


title: Subject CC0144 healthy


title: Subject CC0383 healthy


title: 960_16


title: Subject CC0338 healthy


title: Subject CC0294 healthy


title: Subject CC0111 healthy


title: 869_16


title: 881_16


title: 868_16


title: Subject CC0264 healthy


title: 855_16


title: Subject CC0030 healthy


title: 942_16


title: Subject CC0259 healthy


title: Subject PC183 healthy


title: Subject CC0256 healthy


title: 802_16


title: 831_16


title: 811_16


title: 788_16


title: 780_16


title: Subject CC0022 healthy


title: Subject CC0138 healthy


title: 772_16


title: Subject CC0069 healthy


title: 876_16


title: Subject CC0173 healthy


title: 762_16


title: 761_16


title: 866_16


title: Subject CC0014 healthy


title: U87_VC_3

city: Durham

first: Meng

last: Jiao

address: 905 S lasalle St

institute: Duke University

data_processing:
RNA-seq data using the TrimGalore toolkit, which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3' end of the reads
Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCh38.p13 of the human genome and transcriptome using the STAR RNA-seq alignment tool
Reads were kept for subsequent analysis if they mapped to a single genomic location using the SAMtools. Gene counts were compiled using the HTSeq tool.
Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression were carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Assembly: GRCh38.p13 of the human genome
Supplementary files format and content: tab-delimited txt file with raw counts for all 6 samples.

source_name: brain tumor cell line

growth_protocol: U87 cells were maintained in MEM supplemented with 10% FBS, 1X MEM non-essential amino acids, and 1mM sodium pyruvate.

extract_protocol:
RNA was extracted using Trizol
RNA libraries were prepared for sequencing using standard Illumina Novaseq protocols

treatment_protocol: To generate COMT knockout in U87 cells, we digested the px330-mcherry (Addgene #98750) and pSpCas9(BB)-2A-GFP(PX458) (Addgene #48138) with BbsI (NEB; Cat #R0539S), and then gel-purified, and ligated the vectors with annealed oligos encoding sgRNA_1 or sgRNA_2 targeting human COMT. We transfected U87 cells with sgRNA-encoding constructs using LipofectamineTM 2000 (Thermo Fisher Scientific; Cat #11668019) and incubated them for 24h. We then cultured the cells for 6 days using a complete MEM medium [MEM base medium with 10% non-heat inactivated FBS, 1X non-essential amino acid (NEAA), 1mM sodium pyruvate, and 100U/ml penicillin-Streptomycin (GibcoTM by Life Technologies; Cat #15140122)] before sending them for FACS sorting (Duke Cancer Institute flow cytometry core facility). After obtaining GFP+ mCherry+ cells, we seeded them in 96 well plates and screened for COMT-KO single clones. Pure KO clones were verified by immunoblot analysis.

value: brain tumor cell line

tag: cell line

value: glioblastoma, adherent epithelial cells

tag: genotype

value: Lenti-CRISPR vector control


title: U87_KO_1

value: COMT-knockout


title: U87_VC_1


title: U87_KO_2


title: U87_VC_2


title: 755_16

value: male

value: peripheral white blood cells

value: HNSqCC patient


title: 737_16


title: 792_16


title: 732_16


title: 736_16


title: 717_16


title: 754_16


title: U87_KO_3


title: 716_16


title: KYSE70 treated with 20 nM mitoxantrone, replicate 1

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

data_processing:
The data quality was assessed with FastQC (version 0.11.5), low-quality reads were removed, and remaining adapter sequences were hard clipped with cutadapt (version 1.12) whenever applicable. The quality filtered reads were aligned with STAR (version 2.6.90c) to human reference genome (hg38) with its respective RefSeq annotation, at last, the expression levels of genes were obtained with FeatureCounts (version 1.5.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files for each Sample

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 1

growth_protocol: The cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in 5% CO2/95% air.

extract_protocol:
Total RNA was extracted from human esophageal squamous cell carcinoma cells (KYSE70) using RNeasy Kit (Qiagen; Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with 10 µM pyrimethamine or 20 nM mitoxantrone for 72 h.

value: 20 nM mitoxantrone


title: 767_16


title: KYSE70 treated with 20 nM mitoxantrone, replicate 4

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 4


title: KYSE70 treated with 10 µM pyrimethamine, replicate 4

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 4

value: 10 µM pyrimethamine


title: 711_16


title: 700_16


title: 689_16


title: 695_16


title: KYSE70 treated with 10 µM pyrimethamine, replicate 1

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 1


title: KYSE70 without treatment, replicate 4

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 4

value: Control


title: 750_16


title: KYSE70 without treatment, replicate 3

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 3


title: KYSE70 without treatment, replicate 2

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 2


title: 679_16


title: 670_16


title: KYSE70 treated with 20 nM mitoxantrone, replicate 3

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 3


title: 659_16


title: KYSE70 treated with 20 nM mitoxantrone, replicate 2

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 20 nM mitoxantrone, replicate 2


title: KYSE70 without treatment, replicate 1

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) without treatment, replicate 1


title: KYSE70 treated with 10 µM pyrimethamine, replicate 3

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 3


title: 649_16

source_name: peripheral white blood cells


title: 645_16


title: TS-HumanBlood_Validation_Pool6

description:
bisulfite converted DNA
TS-HumanBlood_Validation.tar.gz

value: various

value: mixed


title: KYSE70 treated with 10 µM pyrimethamine, replicate 2

source_name: Human esophageal squamous cell carcinoma cells (KYSE70) treated with 10 µM pyrimethamine, replicate 2


title: TS-HumanBlood_Validation_Pool5


title: 633_16


title: TS-HumanBlood_Validation_Pool3


title: TS-HumanBlood_Validation_Pool2


title: TS-HumanBlood_Validation_Pool1


title: 616_16


title: 618_16


title: 642_16


title: TS-HumanBlood_TrainTest_Pool8

description:
bisulfite converted DNA
TS-HumanBlood_TrainTest_AllPools.tar.gz


title: 606_16


title: 571_16


title: TS-HumanBlood_TrainTest_Pool7


title: 569_16


title: TS-HumanBlood_TrainTest_Pool5


title: 548_16


title: 559_16


title: TS-HumanBlood_TrainTest_Pool3


title: 547_16


title: 643_16


title: TS-HumanBlood_TrainTest_Pool4


title: TS-HumanBlood_Validation_Pool4


title: TS-HumanBlood_TrainTest_Pool2


title: 541_16


title: 529_16


title: TS-HumanBlood_TrainTest_Pool9


title: TS-HumanBlood_TrainTest_Pool17


title: TS-HumanBlood_TrainTest_Pool18


title: TS-HumanBlood_TrainTest_Pool15


title: TS-HumanBlood_TrainTest_Pool14


title: TS-HumanBlood_TrainTest_Pool16


title: TS-HumanBlood_TrainTest_Pool13


title: 533_16


title: 514_16


title: 512_16


title: 496_16


title: TS-HumanBlood_TrainTest_Pool12


title: 493_16


title: 509_16


title: 476_16


title: TS-HumanBlood_TrainTest_Pool6


title: TS-HumanBlood_TrainTest_Pool10


title: TS-HumanBlood_TrainTest_Pool11


title: 561_16


title: 470_16


title: 455_16


title: TS-HumanBlood_TrainTest_Pool1


title: 459_16


title: 98_64535

description: Gene expression data from PDAC tumor

data_processing:
mRNA-Seq samples were pooled and sequenced on NavoSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 51 to 122 million pass filter reads with more than 90% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM_TMM normalized values for each Sample

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NovaSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

value: classical

tag: tnm

value: IIB

tag: grading

tag: cohort

tag: serpinb3 expression (high_low)

value: H

tag: month


title: 97_63516

description: Gene expression data from PDAC tumor

value: basal


title: 92_67191

description: Gene expression data from PDAC tumor


title: 465_16


title: 452_16


title: 91_67151

description: Gene expression data from PDAC tumor

value: L


title: 451_16


title: 9_18590T

description: Gene expression data from PDAC tumor

value: unclassified


title: 449_16


title: 85_63529

description: Gene expression data from PDAC tumor


title: 437_16


title: 87_64570

description: Gene expression data from PDAC tumor

value: IIA


title: 441_16


title: 82_62081

description: Gene expression data from PDAC tumor


title: 429_16


title: 422_16


title: 419_16


title: 76_61134

description: Gene expression data from PDAC tumor


title: 409_16


title: 78_62069

description: Gene expression data from PDAC tumor


title: 402_16


title: 74_61126

description: Gene expression data from PDAC tumor


title: 8_17798T

description: Gene expression data from PDAC tumor


title: 73_57505

description: Gene expression data from PDAC tumor


title: 398_16


title: 71_57663

description: Gene expression data from PDAC tumor


title: 69_55770

description: Gene expression data from PDAC tumor

value: IB


title: 397_16


title: 396_16


title: 67_54184

description: Gene expression data from PDAC tumor


title: 394_16


title: 65_54178

description: Gene expression data from PDAC tumor


title: 393_16


title: 385_16


title: 80_62075

description: Gene expression data from PDAC tumor


title: 61_54169

description: Gene expression data from PDAC tumor


title: 60_52728

description: Gene expression data from PDAC tumor


title: 384_16


title: 6_17531T

description: Gene expression data from PDAC tumor


title: 58_52173

description: Gene expression data from PDAC tumor


title: 56_52248

description: Gene expression data from PDAC tumor


title: 378_16


title: 381_16


title: 404_16


title: 365_16


title: 363_16


title: 53_51782

description: Gene expression data from PDAC tumor

value: IA


title: 350_16

value: male


title: 52_51040

description: Gene expression data from PDAC tumor


title: 355_16

value: peripheral white blood cells


title: 358_16

value: HNSqCC patient


title: 54_51786

description: Gene expression data from PDAC tumor


title: 346_16


title: 49_50587

description: Gene expression data from PDAC tumor


title: 47_50611

description: Gene expression data from PDAC tumor


title: 63_54173

description: Gene expression data from PDAC tumor


title: 340_16


title: 46_49939

description: Gene expression data from PDAC tumor


title: 44_49924

description: Gene expression data from PDAC tumor


title: 41_49341

description: Gene expression data from PDAC tumor


title: 331_16


title: 321_16


title: 55_51791

description: Gene expression data from PDAC tumor


title: 43_49922

description: Gene expression data from PDAC tumor


title: 39_49225

description: Gene expression data from PDAC tumor


title: 325_16


title: 4_17529T

description: Gene expression data from PDAC tumor


title: 320_16


title: 315_16


title: 37_49221

description: Gene expression data from PDAC tumor

value: IV

value: GX


title: 319_16


title: 36_34435T

description: Gene expression data from PDAC tumor


title: 300_16


title: 348_16


title: 298_16


title: 296_16


title: 335_16


title: 33_32175T

description: Gene expression data from PDAC tumor


title: 31_32018T

description: Gene expression data from PDAC tumor

value: TXNXMX


title: 290_16


title: 308_E770T

description: Gene expression data from PDAC tumor


title: 289_16


title: 306_E762T

description: Gene expression data from PDAC tumor


title: 310_E780T

description: Gene expression data from PDAC tumor


title: 305_E739T

description: Gene expression data from PDAC tumor


title: 288_16


title: 287_16


title: 283_16


title: 304_E674T

description: Gene expression data from PDAC tumor


title: 38_49222

description: Gene expression data from PDAC tumor


title: 271_16


title: 270_16


title: 267_16


title: 302_E671T

description: Gene expression data from PDAC tumor


title: 266_16


title: 3_9728T

description: Gene expression data from PDAC tumor


title: 300_E656T

description: Gene expression data from PDAC tumor


title: 265_16


title: 298_E655T

description: Gene expression data from PDAC tumor

value: III


title: 263_16


title: 297_E639T

description: Gene expression data from PDAC tumor


title: 262_16


title: 294_E626T

description: Gene expression data from PDAC tumor


title: 296_E636T

description: Gene expression data from PDAC tumor


title: 261_16


title: 293_E623T

description: Gene expression data from PDAC tumor


title: 260_16


title: 291_E604T

description: Gene expression data from PDAC tumor