title: MV411.H3K79me2.DMSO.24h [ChIP-Seq]

value: H3K79me2 antibody


title: MOLM13.FlagENL.DMSO [ChIP-Seq]

status: Public on Oct 05 2022

type: SRA

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Raw reads were aligned to the UCSC Hg-19 genome sequence build from the Bsgenome.Hsapiens.UCSC.hg19 Bioconductor package using the Rsubread v 2.26 package's align function
Aligned BAM files were sorted using function sortBam from Rsubread v 2.2.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using sambamba v 0.7.1. The filtered and sorted bam files were then indexed using function indexBam from Rsubread v 2.2.6.
peaks were called using MACS v 2.2.7.1, peaks were called at P ≤ 1 × 10−8.
filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v3.5.0
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are in an indexed binary format
Supplementary_files_format_and_content: tab-delimited text files included chromosome number, start, end, width peak number, pvalue,annotation, distancetotss, symbol and genename for each peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: MOLM13 cells

growth_protocol: Human leukaemia cell lines were maintained in RPMI 1640 (Fisher scientific, #MT10040CV) supplemented with 10% FBS (HyClone, #SH30910.03) and 100 U ml−1 penicillin/streptomycin  (Fisher scientific, #15-140-122).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions.  After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). Then samples were sequenced using Illumina NextSeq 500.

treatment_protocol: Human leukemia cells were treated with DMSO or 5 uM TDI-055 for 24 hour

tag: chip antibody

value: Flag antibody

tag: treatment

value: DMSO control

tag: cell line


title: MV411.H3K79me2.TDI-055.24h [ChIP-Seq]

source_name: MV411 cells


title: MV411.DOT1L.TDI-055.24h [ChIP-Seq]

value: DOT1L antibody


title: OCI-AML3.TDI-055.5uM.24h_B

library_source: transcriptomic

data_processing:
RNA-seq samples were sequenced using Illumina NextSeq 500.
Raw reads were mapped to the human reference genome (hg19) and transcriptome using HISAT2 v 2.2.1 with default parameters.
Unmapped reads from hg19 alignment were mapped to the Spike-In ERCC control transcriptome using Kallisto v 0.46.2 as Spike-In control.
Lowly expressed genes with raw counts less than 10 in any individual sample were filtered before downstream analysis.
The size factor of Spike-In control was estimated using estimateSizeFactors from R Bioconductor DESeq2 v1.28.1 package
Then the size factor was assigned to the RNAseq result using the assignment function sizeFactors<-.
Differentially expressed genes between conditions were statistically determined using R Bioconductor DESeq2 v1.28.1 package
Gene-specific normalization factors for each sample was provided using pre-generated sizeFactors from Spike-In control, which preempts sizeFactors in DESeq2 calculations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj and DESeq2-normalized count(Median of ratios method) for each sample

molecule: polyA RNA

extract_protocol:
RNeasy plus mini kit (Qiagen, #74136) was used to extract total RNA and remove genomic DNA.
1000ng total RNA was used for library preparation using polyA mRNA magnetic Isolation module (NEB, #E7490) and RNA library prep kit (NEB, #7770) following manufacturer’s instructions. The library quality was assessed on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504). RNA-seq samples were sequenced using Illumina NextSeq 500.

value: OCI-AML3 Cells

tag: time point


title: MV411.Pol II.TDI-055.24h [ChIP-Seq]

value: Pol II antibody


title: MV411.Pol II.DMSO.24h [ChIP-Seq]


title: MV411.Pol II S2P.DMSO.24h [ChIP-Seq]

value: Pol IIS2P antibody


title: MV411.input.24h [ChIP-Seq]

value: input


title: OCI-AML3.DMSO.24h_B

value: DMSO


title: MV411.AFF1.DMSO.24h [ChIP-Seq]

value: AFF4 antibody


title: OCI-AML3.TDI-055.5uM.24h_A


title: MV411.PAF1.DMSO.24h [ChIP-Seq]

value: PAF1 antibody


title: OCI-AML3.DMSO.24h_A


title: MV4;11.TDI-055.5uM.24h_batch1_B

value: MV4;11 Cells


title: input-m71

status: Public on Sep 01 2022

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description:
Input signal
ChIPmentation

data_processing:
Cleaning with fastq-mcf.
Quality control with FastQC.
Mapping with Bowtie2, further processing with SAMTools.
Peak calling with MACS2.
Normalization with deepTools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files were generated with the deepTools software package (genome normalization).
Supplementary_files_format_and_content: narrowPeak files were generated with the MACS2 peak calling algorithm (FDR<0.01).

organism: Mus musculus

source_name: thymus

extract_protocol:
ChIP-sequencing (ChIPmentation) was performed as described in Vanden Bempt, M., Demeyer, S. et al., Cancer Cell, 2018.
ChIP libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: thymus

tag: cell type

value: MYCN-driven T cell lymphoma cells


title: MV411.Pol II S2P.TDI-055.24h [ChIP-Seq]


title: MV4;11.TDI-055.5uM.24h_batch1_A


title: MV4;11.DMSO.24h_batch1_B


title: p300

description:
ChIP on MYCN-driven T cell lymphoma cells with p300 antibody
ChIPmentation

value: Rabbit monoclonal anti-p300 [clone D2X6N] - CST 54062S


title: Suz12

description:
ChIP on MYCN-driven T cell lymphoma cells with Suz12 antibody
ChIPmentation

value: Rabbit monoclonal anti-SUZ12 [clone D39F6] - CST 3737S


title: N-MYC-CST

description:
ChIP on MYCN-driven T cell lymphoma cells with N-MYC antibody
ChIPmentation

value: Mouse polyclonal anti-MYCN - CST 9405S


title: H3K27me3

description:
ChIP on MYCN-driven T cell lymphoma cells with H3K27me3 antibody
ChIPmentation

value: Rabbit monoclonal anti-H3K27me3 [clone C36B11] - CST 9733S


title: H3K4me3

description:
ChIP on MYCN-driven T cell lymphoma cells with H3K4me3 antibody
ChIPmentation

value: Rabbit monoclonal anti-H3K4me3 [clone C42D8] - CST 9751S


title: CD4-Tcells-1

description: CD4+ T cells from spleen

data_processing:
Cleaning with fastq-mcf.
Quality control with FastQC.
Mapping with HISAT2, further processing with SAMTools.
Counting abundances with htseq-count.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all.counts.csv: Comma-separated file with the raw counts per gene and per sample.

molecule: total RNA

source_name: spleen

extract_protocol:
RNA extraction was performed using a Promega Maxwell, using the Maxwell RSC simplyRNA Cells Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: spleen

value: CD4+ T cells


title: CD4-Tcells-2

description: CD4+ T cells from spleen


title: CD4-Tcells-3

description: CD4+ T cells from spleen


title: H3K27ac

description:
ChIP on MYCN-driven T cell lymphoma cells with H3K27ac antibody
ChIPmentation

value: Rabbit polyclonal anti-H3K27ac - Abcam ab4729


title: EZH2

description:
ChIP on MYCN-driven T cell lymphoma cells with EZH2 antibody
ChIPmentation

value: Rabbit monoclonal anti-EZH2 [clone D2C9] - CST 5246S


title: m86-thymus

description: MYCN-induced T cell lymphoma cells (thymus)

value: MYCN-induced T cell lymphoma cells


title: MV411.AFF1.TDI-055.24h [ChIP-Seq]


title: m72-thymus


title: m56-thymus


title: m70-thymus


title: m53-thymus


title: m34-Thymus


title: Jmjd4, cKO, rep3

status: Public on Aug 30 2022

city: Shanghai

first: yansong

last: Tang

address: 1239 Siping Road

country: China

institute: Tongji University

description:
mouse_CKO.csv
T506

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 or mm10 whole genome using hisat2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Raw transcripts were assembled using the StringTie (v1.3.4). Counts per million (cpm) were calculated by the edgeR (v3.20.9).
Assembly: rn6 or mm10
Supplementary files format and content: csv files include FPKM values for each Sample.

source_name: heart

growth_protocol: Neonatal rat’s hearts were harvested from 1-day old SD rats. Next, the ventricles were separated and cut into pieces (1–3 mm2), then they were dissociated in 0.25% trypsin (Gibco, 15090046) at 4 °C overnight. Then the tissue was transferred to 0.1% collagenase type Ⅱ (Worthington, LS004176) to further digest at 37°C at 145 rpm, and the supernatant was collected into DMEM medium containing 10% FBS every 5 min. The digestion procedure was repeated 3-4 times. When the tissue was completely digested, the supernatant was centrifuged at 1500 rpm for 6 min. Then, the cells were plated in DMEM medium which containing 10% FBS, 100 unit/ml penicillin and 100 mg/ml streptomycin at 15 cm dishes at an atmosphere of 5% CO2 at 37℃ for 90 min, to remove cells that are easier attached the dishes than cardiomyocytes. Finally, the culture supernatant was collected, plated in the plates which were coated with collagen and then incubated 24 h in an atmosphere of 5% CO2 at 37 ℃ with the same medium. After 24 h, the medium was changed to cardiomyocyte medium: DMEM: F12 (1:1) medium containing 0.25% FBS, 3 mM sodium pyruvate, 0.1 mM Vitamin C and 2 mM L-Glu. hPSC-CMs were produced from ZSSY001 (Nuwacell) by regulating Wnt signaling pathway. hPSCs were grown on Matrigel (Corning, 354277) in Essential 8 TM Medium (Gibco, A15169-01, A15171-01). Cardiac differentiation was performed using dense monolayers of hPSCs treated with 6µM CHIR-99021 (Sellect, S1263) for 48 h and 5μM IWP-2 (Sellect, S7065) for 2 days in RPMI 1640 (Gibco, 11875-093)/B-27 minus insulin Medium (Gibco, A18956-01) previously described protocol . Spontaneously beating hPSC-CMs appeared after 7 days. Then the containing medium was replaced with RPMI 1640/B-27 Medium (Gibco, A17504-044). Metabolism selection was performed using Cardiomyocyte Selection Medium (ScienCell, 5911, 5962) for high purity cardiomyocytes.

extract_protocol:
The total RNA was extracted by TRIzol extraction reagent (Invitrogen, 15596018). Furthermore, the purity and concentration of RNA were examined by measuring the absorbance value at 260 and 280 nm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
NRVCs were treated with siRNA for 48h.
Jmjd4 cKO mice heart apex tissues were harvest 14 days after tamoxifen inducement.

value: heart

value: cardiomyocytes

tag: genotype

value: Jmjd4 knockout (MCM+ Jmjd4f/f (myh6 cre))

value: tamoxifen

tag: time

value: Day 14 after tamoxifen inducement


title: Jmjd4, cKO, rep1

description:
mouse_CKO.csv
T501


title: Jmjd4, flox, rep3

description:
mouse_CKO.csv
T568

value: control (Jmjd4f/f)


title: Jmjd4, flox, rep2

description:
mouse_CKO.csv
T561


title: Jmjd4, flox, rep1

description:
mouse_CKO.csv
T541


title: MV4;11.DMSO.24h_batch1_A

value: MV4;11 Cells

value: DMSO


title: input-m70

description:
Input signal
ChIPmentation

value: thymus

value: MYCN-driven T cell lymphoma cells


title: NRVC, si-Jmjd4, rep1

description:
NRVC_si-Jmjd4.csv
Si_1

organism: Rattus norvegicus

value: Sprague-Dawley (SD)

value: Jmjd4 knockdown


title: NRVC, si-NC, rep2

description:
NRVC_si-Jmjd4.csv
Ctrl_2

value: WT

value: si-NC


title: NRVC, si-Jmjd4, rep2

description:
NRVC_si-Jmjd4.csv
Si_2


title: NRVC, si-NC, rep3

description:
NRVC_si-Jmjd4.csv
Ctrl_3


title: NRVC, si-Jmjd4, rep3

description:
NRVC_si-Jmjd4.csv
Si_3


title: NRVC, si-NC, rep1

description:
NRVC_si-Jmjd4.csv
Ctrl_1


title: MWMH00851-3-6

status: Public on Aug 26 2022

type: genomic

city: Melbourne

first: Dale

middle: W

last: Garsed

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

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

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.

data_processing: Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated for each EPIC and 450k arrays separately. The beta values for each array were then merged by the probe ID into file "betaVals.all.txt.gz" file (i.e., union of the two arrays). To generate file "betaVals.platform_corrected_by_combat.txt.gz" (i.e., intersection of the two arrays), first only probes present in both arrays were kept and then batch corrected for platform differences using the "ComBat" function in the R package sva (v3.34.0).

label: Cy5 and Cy3

source_name: Primary Tumor

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: DNA was isolated from frozen tissue sections using either the Gentra Puregene Tissue Kit (Qiagen), DNeasy Blood and Tissue Kit (Qiagen), or AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

tag: gender

value: Female

value: Primary Tumor

tag: case id

value: high grade serous ovarian cancer


title: MWMH00351-3-7


title: MWMH00758-3-X


title: MWMH00083-3-7


title: MWMH00507-3-9


title: MAOC00665-3-X


title: MAOC02444-3-9


title: MAOC02145-3-7


title: MAOC00037-3-8


title: MAOC00562-3-7


title: Jmjd4, cKO, rep2

description:
mouse_CKO.csv
T504

value: heart


title: MAOC01475-3-X


title: MAOC01370-3-X


title: MAOC00602-3-2


title: MAOC02193-3-3


title: MAOC00673-3-5


title: MAOC01315-3-1


title: MAOC02427-3-4


title: MAOC01847-3-6


title: MAOC02394-3-0


title: MAOC00682-3-4


title: MAOC01064-3-6


title: MAOC02541-3-X


title: MAOC00623-3-1


title: MAOC01262-3-2


title: MAOC02417-3-1


title: MAOC01783-3-0


title: MAOC00944-3-6


title: MAOC00357-3-9


title: MAOC00287-3-5


title: MAOC02278-3-8


title: MAOC02410-3-6


title: MAOC01893-3-5


title: MMAY00753-3-1


title: MMAY00761-3-7


title: MMAC00102-3-3


title: MMAY00758-3-X


title: MMAY00738-3-4


title: MMAY00711-3-3


title: MMAY00363-3-7


title: MMAY00631-3-7


title: MMAY00627-3-6


title: MMAY00149-3-X


title: MMAY00621-3-4


title: MAOC01138-3-4


title: MMAY00594-3-2


title: MMAY00507-3-9


title: MMAY00981-3-6


title: MMAY00566-3-1


title: MAOC01491-3-0


title: MWMH00552-3-4


title: MWMH00475-3-9


title: Ku80_E2_1h_exp3

status: Public on Aug 04 2022

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using Bowtie2.
Genome_build: hg38
Supplementary_files_format_and_content: bed and bedgraph

source_name: MCF7 cells

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha(R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.

value: Ku80, MyBioSource, MBS8533127 (Lot#T14S11)


title: Ku80_Veh_exp3


title: ChIP-seq_Smc1_Veh_MCF7

data_processing:
Basecalls performed using CASAVA version 1.4
Seqencing reads were aligned to the hg38 genome assembly using Bowtie version 2.0.1.
Genome binding peaks were identified using the 'findPeaks' command in HOMER with setting of '-style factor': 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
To generate histograms for the average distribution of tag densities, position-corrected, normalized tags in 100 bp windows were tabulated within the indicated distance from specific sites in the genome. Clustering plots for normalized tag densities at each genomic region were generated using HOMER and then clustered using Gene Cluster 3.0.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Human breast cancers

extract_protocol:
Briefly, cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha (R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.

value: SMC1 Bethyl Laboratories A300-055A (A302-055A-6)


title: ChIP-seq_Rad21_Veh_MCF7


title: ChIP-seq_Smc1_E2_MCF7


title: ChIP-seq_PolII_siNC_Veh_MCF7

value: RNA Pol II (N20) Santa Cruz Biotechnology sc-899 (Lot# D2315)


title: ChIP-seq_PolII_siNC_DHT_LNCAP

source_name: Human prostate cancers

value: LNCAP


title: ChIP-seq_PolII_siNC_Veh_LNCAP


title: ChIP-seq_PolII_siNC_E2_MCF7


title: MMAY00176-3-7


title: ChIP-seq_PolII_siCbx3_E2_MCF7


title: ChIP-seq_PolII_siCbx3_Veh_MCF7


title: ChIP-seq_PolII_shMed26_1_E2_MCF7


title: ChIP-seq_PolII_shscramble_E2_MCF7


title: MMAY00010-3-7


title: ChIP-seq_PolII_shscramble_Veh_MCF7


title: ChIP-seq_PolII_shMed26_1_Veh_MCF7


title: ChIP-seq_Rad21_E2_MCF7


title: ChIP-seq_PolII_shMed26_2_Veh_MCF7


title: ChIP-seq_PolII_shMed26_2_E2_MCF7


title: ChIP-seq_PolIISer2P_shMed26_2_Veh_MCF7


title: ChIP-seq_PolIISer2P_shMed26_2_E2_MCF7


title: ChIP-seq_PolII_siCbx3_DHT_LNCAP


title: ChIP-seq_PolIISer2P_shscramble_Veh_MCF7


title: ChIP-seq_PolIISer2P_shMed26_1_E2_MCF7


title: ChIP-seq_PolIISer2P_shMed26_1_Veh_MCF7


title: ChIP-seq_PolIISer2P_shscramble_E2_MCF7


title: ChIP-seq_NCAPG_E2_MCF7


title: ChIP-seq_MED26_siNC_E2_MCF7

value: MED26 Cell Signaling Techn. 13641S(Lot#4)


title: ChIP-seq_NCAPG_Veh_MCF7


title: ChIP-seq_MED26_siNC_Veh_MCF7


title: ChIP-seq_MED26_siCbx3_Veh_MCF7


title: ChIP-seq_MED26_siCbx3_E2_MCF7


title: ChIP-seq_MED1_siNC_Veh_MCF7

value: Med1 Bethyl Laboratories A300-793A (Lot# A300-793A-5)


title: ChIP-seq_MED1_siCbx3_Veh_MCF7


title: ChIP-seq_H3K9me3_E2_MCF7


title: ChIP-seq_H3K4me3_E2_MCF7


title: ChIP-seq_H3K9me3_Veh_MCF7


title: ChIP-seq_H3K4me3_Veh_MCF7


title: ChIP-seq_Gata3_E2_MCF7

value: GATA3(HG3-31) Santa Cruz Biotechnology sc-268 (Lot#J0515)


title: ChIP-seq_Gata3_Veh_MCF7


title: ChIP-seq_ERa_E2_MCF7

value: ERalpha (HC20) Santa Cruz Biotechnology sc-543 (Lot# I0514)


title: ChIP-seq_FoxA1_E2_MCF7

value: FoxA1 diagenode C15410231 (Lot#39435)


title: ChIP-seq_FoxA1_Veh_MCF7


title: ChIP-seq_ERa_Veh_MCF7


title: ChIP-seq_CTCF_Veh_MCF7

value: CTCF Active Motif 61311(Lot#34614003)


title: ChIP-seq_CTCF_E2_MCF7


title: ChIP-seq_CBP_E2_MCF7

value: CBP diagenode C15410224 (Lot#39721)


title: ChIP-seq_CBP_Veh_MCF7


title: ChIP-seq_BRD4_Veh_exp2_MCF7

value: BRD4 diagenode C15410337 (Lot#A2710P)


title: ChIP-seq_BRD4_Veh_exp1_MCF7


title: ChIP-seq_BRD4_E2_exp1_MCF7


title: ChIP-seq_AP2y_Veh_MCF7

value: AP2γ(H-77) Santa Cruz Biotechnology sc-8977 (Lot#G1112)


title: 655A91, NA, Healthy, Healthy [scATAC-Seq]

status: Public on Jun 23 2022

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

description: 10x Genomics

library_source: genomic single cell

data_processing:
Sequencing data were used as input to the 10x Genomics Cell Ranger ATAC pipeline to demultiplex BCL files, generate FASTQs, and generate feature counts for each library.
For scRNA-seq and scATAC-seq integration, fragment file outputs generated using CellRanger ATAC count were analyzed using ArchR following the standard workflow and with default parameters unless otherwise specified.
Cells with a transcription start site enrichment score < 4, cells with fewer than 1000 detected fragments, and putative doublets were removed from downstream analysis.
Assembly: hg19
Supplementary files format and content: Fragment files

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were thawed and nuclei were extracted as for ATAC-seq. The single-cell suspensions of scATAC-seq samples were converted to barcoded scATAC-seq libraries using the Chromium Single Cell 5′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10x Genomics).
The Chromium Single Cell 5′ v2 Reagent (10x Genomics, 120237) kit was used to prepare single-cell ATAC libraries according to the manufacturer’s instructions. Quality was assessed using Agilent DNA tape screen assay.

value: peripheral blood mononuclear cells

tag: age

tag: Sex

value: FEMALE

tag: exposure

value: Healthy

tag: serostatus


title: ChIP-seq_BRD4_E2_exp2_MCF7


title: ChIP-seq_AP2y_E2_MCF7


title: 52BA23, NA, Healthy, Healthy [scATAC-Seq]

description: 10x Genomics

value: MALE


title: ChIP-seq_MED1_siCbx3_E2_MCF7


title: ChIP-seq_MED1_siNC_E2_MCF7


title: 3F3322, NA, Healthy, Healthy [scATAC-Seq]

description: 10x Genomics


title: Top1cc-seq_Input_MCF7

data_processing:
Library strategy: TOP1cc-seq
Basecalls performed using CASAVA version 1.4
Seqencing reads were aligned to the hg38 genome assembly using Bowtie version 2.0.1.
Genome binding peaks were identified using the ‘findPeaks’ command in HOMER with setting of ‘-style factor’: 200 bp peaks with 3-fold enrichment and 0.01 FDR significance over local tags.
To generate histograms for the average distribution of tag densities, position-corrected, normalized tags in 100 bp windows were tabulated within the indicated distance from specific sites in the genome. Clustering plots for normalized tag densities at each genomic region were generated using HOMER and then clustered using Gene Cluster 3.0.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

extract_protocol:
To perform TOP1cc-seq, approximately 2x10e6 cells were treated with 10 μM CPT (Selleckchem, Cat# S1288) for 10 mins and E2 or DHT, and then washed once with ice-cold 1x PBS with freshly added Proteinase inhibitors. The cells were directly in resuspended in Buffer A (50mM Tris-HCl, pH7.4, 1% SDS, 0.5% Empigen BB, 10 mM EDTA) with freshly added 1mM PMSF and Proteinase inhibitors at room temperature for 5 mins and incubate them in ice. Extracts were then sonicated using the Bioruptor® 300 (Diagenode) for 12 cycles [30 s “ON,” 30 s “OFF”] at high power setting for MCF7 cells, and 6 cycles [30 s “ON,” 30 s “OFF”] at high power setting for LNCAP cells. Cell lysate was centrifuged at 21,000 g for 10 min at 4°C and diluted with 9 times of Buffer B (20mM Tris-HCl, pH7.4, 100mM NaCl, 0.5% TritonX-100, 2mM EDTA) with freshly added Proteinase inhibitors. After pre-clear with 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D), 7 μg TOP1cc (TopoGEN, TG2017-2) was added and incubated with sample over night at 4°C for on a rotator. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. And then the immunoprecipitated complexes were successively washed 2 times with pre-cold Washing Buffer I (10mM Tris-HCl, pH7.4, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.1% SDS, 1% TritonX-100, freshly added Proteinase inhibitors), 2 times with pre-cold Washing Buffer II (10mM Tris-HCl, pH7.4, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 1% TritonX-100, freshly added Proteinase inhibitors), 1 time with pre-cold Washing Buffer III (10 mM Tris-HCl pH 7.4, 250 mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, freshly added Proteinase inhibitors) and 1 time with pre-cold TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA) with 100 mM NaCl and freshly added Proteinase inhibitors. All washes were performed at RT for 5 min on a rotator. SDS Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) was added 1 μl RNase A (Thermo Scientific™, Cat# EN0531) and incubated at 37°C for 2 hr and then added 10 μl Proteinase K (Invitrogen™, Cat# AM2548) and incubated overnight to digest all the proteins. After overnight digestion, DNA was incubated with 5 times volume of PB buffer for 30 mins and purified using QIAquick PCR Purification Kit (QIAGEN, Cat# 28106) according to the manufacturer’s instructions.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

value: Input

tag: ip antibody


title: E0FA1E, NA, Healthy, Healthy [scATAC-Seq]

description: 10x Genomics


title: 94D44E, NA, Healthy, Healthy [scATAC-Seq]

description: 10x Genomics


title: 0BF51C, 14, Severe, Positive [scATAC-Seq]

description: 10x Genomics

value: Severe

value: Positive


title: ChIP-seq_H3K27Ac_Veh_MCF7


title: 80A16A, 14, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics

value: Exposed


title: 0BF51C, 0, Severe, Negative [scATAC-Seq]

description: 10x Genomics

value: Negative


title: 0BF51C, 7, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: ChIP-seq_H3K27Ac_E2_MCF7


title: 80A16A, 0, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 40067F, 21, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: 40067F, 0, Severe, Negative [scATAC-Seq]

description: 10x Genomics


title: 40067F, 14, Severe, Negative [scATAC-Seq]

description: 10x Genomics


title: 61BBAD, 7, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 61BBAD, 0, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: BAAF62, 7, Mild, Positive [scATAC-Seq]

description: 10x Genomics

value: Mild


title: BAAF62, 14, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: 82CCF5, 14, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: BAAF62, 0, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 82CCF5, 7, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: 82CCF5, 0, Severe, Negative [scATAC-Seq]

description: 10x Genomics


title: 180E1A, 7, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: 180E1A, 14, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: B85D75, 7, Severe, Positive [scATAC-Seq]

description: 10x Genomics


title: 2AD75E, 7, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 7085CA, 0, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 7085CA, 7, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 2AD75E, 0, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 7085CA, 14, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: 0B943B, 0, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 0B943B, 3, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 7768E4, 0, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 7768E4, 14, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 2AD75E, 14, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: 61BBAD, 14, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 450905, 0, Mild, Negative [scATAC-Seq]

description: 10x Genomics


title: 655A91, NA, Healthy, Healthy [scRNA-Seq]

status: Public on Jun 19 2022

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were used as input to the 10x Genomics Cell Ranger pipeline to demultiplex BCL files, generate FASTQs, and generate feature counts for each library.
For dimensionality reduction and cell type annotation, gene-barcode matrices generated using CellRanger count were analyzed using Seurat 3 with the default parameters unless otherwise specified.
Cells with > 5% of reads mapping to the mitochondrial genome or > 2500 genes detected were removed from the analysis. Counts were log-normalized.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features,tsv, matrix.mtx) in tar archives.

extract_protocol:
Frozen PBMCs were thawed, and count and cell viability were measured by Countess II. The cell viability exceeded 80% for all samples except PBMC samples from CC subjects, which had viability between 70-80%. For single cell (sc) RNA-seq, 200K cells were aliquoted, spun down, resuspended in 30 uL PBS+0.04%BSA+0.2U/uL RNase inhibitor, and counted using Countess II.
GEM generation, post GEMRT cleanup, cDNA amplification, and library construction were performed following 10X Genomics Single Cell 5’ v1 chemistry and quality was assessed using Agilent DNA tape screen assay.

tag: library


title: 450905, 7, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: 7768E4, 7, Exposed, Exposed [scATAC-Seq]

description: 10x Genomics


title: 94D44E, NA, Healthy, Healthy [scRNA-Seq]

description: 10x Genomics


title: 52BA23, NA, Healthy, Healthy [scRNA-Seq]

description: 10x Genomics


title: 3F3322, NA, Healthy, Healthy [scRNA-Seq]

description: 10x Genomics


title: E0FA1E, NA, Healthy, Healthy [scRNA-Seq]

description: 10x Genomics


title: 450905, 14, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: B85D75, 0, Severe, Negative [scATAC-Seq]

description: 10x Genomics


title: 0BF51C, 14, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: 0BF51C, 7, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: 180E1A, 0, Severe, Negative [scATAC-Seq]

description: 10x Genomics


title: 0BF51C, 0, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: 80A16A, 14, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 80A16A, 0, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 40067F, 14, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: 61BBAD, 14, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 61BBAD, 0, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 0B943B, 14, Mild, Positive [scATAC-Seq]

description: 10x Genomics


title: 61BBAD, 7, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: BAAF62, 0, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 82CCF5, 14, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: 82CCF5, 7, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: 82CCF5, 0, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: 180E1A, 14, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: BAAF62, 7, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 180E1A, 7, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: B85D75, 0, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: 2AD75E, 14, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: B85D75, 7, Severe, Positive [scRNA-Seq]

description: 10x Genomics


title: 7085CA, 14, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 2AD75E, 0, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 7085CA, 7, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 2AD75E, 7, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 7085CA, 0, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 0B943B, 14, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 0B943B, 3, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 7768E4, 28, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 7768E4, 14, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 7768E4, 2, Exposed, Exposed [scRNA-Seq]

description: 10x Genomics


title: 450905, 14, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 40067F, 0, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: BAAF62, 14, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 450905, 0, Mild, Negative [scRNA-Seq]

description: 10x Genomics

data_processing:
Sequencing data were used as input to the 10x Genomics Cell Ranger pipeline to demultiplex BCL files, generate FASTQs, and generate feature counts for each library.
For dimensionality reduction and cell type annotation, gene-barcode matrices generated using CellRanger count were analyzed using Seurat 3 with the default parameters unless otherwise specified.
Cells with > 5% of reads mapping to the mitochondrial genome or > 2500 genes detected were removed from the analysis. Counts were log-normalized.
Assembly: hg19tar
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features,tsv, matrix.mtx) in tar archives.


title: E9CFE0, NA, Healthy, Healthy [ATAC-Seq]

data_processing:
FASTQ files were generated from the NovaSeq BCL outputs and used as input to the ENCODE ATAC-seq pipeline using the MACS2 peak-caller with all default parameters
Output narrowPeak files and aligned BAM files were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

extract_protocol:
Nuclei were extracted from frozen PBMCs. Briefly, 100K cells were spun down at 300 x g for 5 minutes at 4oC. The supernatant was removed, and cells were mixed with 100 uL of lysis buffer (10mM NaCl, 3mM MgCl2, 10mM Tris-HCl pH7.4, 0.1% Tween-20, 0.1% NonidetTM P40) and lysed on ice for 4 minutes. Wash buffer (1 mL; 10mM NaCl, 3mM MgCl2, 10mM Tris-HCl pH7.4, 0.1% Tween20) was added before centrifuging at 500 x g for 5 minutes at 4oC.
Transposition mix (25 μL 2× TD buffer, 2.5 μL transposase (Tn5, 100 nM final), 22.5 μL water) was added to the nuclear pellets, incubated at 37 °C for 30 minutes, and samples purified using the Qiagen MinElute PCR Purification Kit. DNA fragments were PCR amplified for a total of 10-11 cycles and resulting libraries purified using the Qiagen MinElute PCR Purification Kit.


title: E0FA1E, NA, Healthy, Healthy [ATAC-Seq]


title: DF309F, 0, Mild, Negative [ATAC-Seq]


title: DF309F, 14, Mild, Positive [ATAC-Seq]


title: CE0CE8, 14, Exposed, Exposed [ATAC-Seq]


title: 180E1A, 0, Severe, Negative [scRNA-Seq]

description: 10x Genomics


title: CE0CE8, 28, Exposed, Exposed [ATAC-Seq]


title: CE0CE8, 0, Exposed, Exposed [ATAC-Seq]


title: BAAF62, 7, Mild, Positive [ATAC-Seq]


title: BAAF62, 14, Mild, Positive [ATAC-Seq]


title: B96D3B, 14, Exposed, Exposed [ATAC-Seq]


title: BAAF62, 0, Mild, Negative [ATAC-Seq]


title: B85D75, 7, Severe, Positive [ATAC-Seq]


title: B85D75, 0, Severe, Negative [ATAC-Seq]


title: B96D3B, 0, Exposed, Exposed [ATAC-Seq]


title: 82CCF5, 0, Severe, Negative [ATAC-Seq]


title: 0B943B, 0, Mild, Negative [scRNA-Seq]

description: 10x Genomics


title: 82CCF5, 14, Severe, Positive [ATAC-Seq]


title: 80A16A, 14, Exposed, Exposed [ATAC-Seq]


title: 82CCF5, 7, Severe, Positive [ATAC-Seq]


title: 7768E4, 7, Exposed, Exposed [ATAC-Seq]


title: 80A16A, 0, Exposed, Exposed [ATAC-Seq]


title: 75A2B6, 14, Mild, Positive [ATAC-Seq]


title: 75A2B6, 7, Mild, Positive [ATAC-Seq]


title: 7768E4, 14, Exposed, Exposed [ATAC-Seq]


title: 450905, 7, Mild, Positive [scRNA-Seq]

description: 10x Genomics


title: 7768E4, 0, Exposed, Exposed [ATAC-Seq]


title: DF309F, 7, Mild, Positive [ATAC-Seq]


title: 7085CA, 14, Mild, Positive [ATAC-Seq]


title: 7085CA, 0, Mild, Negative [ATAC-Seq]


title: 6F894A, 0, Exposed, Exposed [ATAC-Seq]


title: 6F894A, 7, Exposed, Exposed [ATAC-Seq]


title: 655A91, NA, Healthy, Healthy [ATAC-Seq]


title: 7085CA, 7, Mild, Negative [ATAC-Seq]


title: 6F894A, 14, Exposed, Exposed [ATAC-Seq]


title: B96D3B, 28, Exposed, Exposed [ATAC-Seq]


title: 61BBAD, 7, Exposed, Exposed [ATAC-Seq]


title: 61BBAD, 14, Exposed, Exposed [ATAC-Seq]


title: 94D44E, NA, Healthy, Healthy [ATAC-Seq]


title: 5ABDCB, 14, Exposed, Exposed [ATAC-Seq]


title: 5ABDCB, 0, Exposed, Exposed [ATAC-Seq]


title: 5ABDCB, 28, Exposed, Exposed [ATAC-Seq]


title: 52BA23, NA, Healthy, Healthy [ATAC-Seq]


title: 450905, 14, Mild, Positive [ATAC-Seq]


title: 450905, 7, Mild, Positive [ATAC-Seq]


title: 450905, 0, Mild, Negative [ATAC-Seq]


title: 40067F, 21, Severe, Positive [ATAC-Seq]


title: 3F3322, NA, Healthy, Healthy [ATAC-Seq]


title: 40067F, 0, Severe, Negative [ATAC-Seq]


title: 40067F, 14, Severe, Negative [ATAC-Seq]


title: 2AD75E, 7, Mild, Negative [ATAC-Seq]


title: 3F05F3, 0, Severe, Negative [ATAC-Seq]


title: 75A2B6, 0, Mild, Negative [ATAC-Seq]


title: 3F05F3, 7, Severe, Positive [ATAC-Seq]


title: 3F05F3, 28, Severe, Positive [ATAC-Seq]


title: 2AD75E, 14, Mild, Positive [ATAC-Seq]


title: 1A9B20, 7, Mild, Positive [ATAC-Seq]


title: 2AD75E, 0, Mild, Negative [ATAC-Seq]


title: 1A9B20, 0, Mild, Negative [ATAC-Seq]


title: 180E1A, 7, Severe, Positive [ATAC-Seq]


title: 180E1A, 14, Severe, Positive [ATAC-Seq]


title: 1A9B20, 14, Mild, Positive [ATAC-Seq]


title: 180E1A, 0, Severe, Negative [ATAC-Seq]


title: 0BF51C, 14, Severe, Positive [ATAC-Seq]


title: 0E1F8E, 0, Severe, Negative [ATAC-Seq]


title: 61BBAD, 0, Exposed, Exposed [ATAC-Seq]


title: 0BF51C, 7, Severe, Positive [ATAC-Seq]


title: 0E1F8E, 14, Severe, Positive [ATAC-Seq]


title: 0BF51C, 0, Severe, Negative [ATAC-Seq]


title: 0B943B, 3, Mild, Negative [ATAC-Seq]


title: 0B943B, 0, Mild, Negative [ATAC-Seq]


title: 655A91, NA, Healthy, Healthy

data_processing:
FASTQ files were generated from the NovaSeq BCL outputs and quality was assessed with FASTQC
Eukaryotic rRNA sequences were removed using SortMeRNA, and the remaining reads were aligned against the hg19 human reference genome using STAR
Following alignment, the gene count matrix was generated using featureCounts
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

extract_protocol:
RNA was extracted from 300K cells using the Zymo Direct-zol miniprep kit (Cat# R2051) and RNA quality assessed using the Agilent DNA tape screen assay. The RNA Integrity Number (RIN) scores for all samples were > 7.0.
Total RNA libraries were generated using the NuGEN Ovation® SoLo RNA-Seq Library Preparation Kit


title: E9CFE0, NA, Healthy, Healthy


title: 94D44E, NA, Healthy, Healthy


title: 062CD8, NA, Healthy, Healthy


title: E0FA1E, NA, Healthy, Healthy


title: 6F894A, 7, Exposed, Exposed


title: 6F894A, 14, Exposed, Exposed


title: 3F3322, NA, Healthy, Healthy


title: 6F894A, 0, Exposed, Exposed


title: B96D3B, 14, Exposed, Exposed


title: 5ABDCB, 28, Exposed, Exposed


title: 5ABDCB, 14, Exposed, Exposed


title: 5ABDCB, 0, Exposed, Exposed


title: B96D3B, 28, Exposed, Exposed


title: B96D3B, 0, Exposed, Exposed


title: 0BF51C, 0, Severe, Negative


title: 0BF51C, 7, Severe, Positive


title: CE0CE8, 0, Exposed, Exposed


title: CE0CE8, 14, Exposed, Exposed


title: 80A16A, 0, Exposed, Exposed


title: CE0CE8, 28, Exposed, Exposed


title: 0B943B, 14, Mild, Positive [ATAC-Seq]


title: 0E1F8E, 7, Severe, Positive


title: 0E1F8E, 0, Severe, Negative


title: 80A16A, 14, Exposed, Exposed


title: 062CD8, NA, Healthy, Healthy [ATAC-Seq]


title: 0E1F8E, 14, Severe, Positive


title: 40067F, 14, Severe, Negative


title: 52BA23, NA, Healthy, Healthy


title: 40067F, 0, Severe, Negative


title: 40067F, 21, Severe, Positive


title: 61BBAD, 0, Exposed, Exposed


title: 3F05F3, 7, Severe, Positive


title: 61BBAD, 7, Exposed, Exposed


title: DF309F, 7, Mild, Positive


title: DF309F, 14, Mild, Positive


title: 0BF51C, 14, Severe, Positive


title: 3F05F3, 0, Severe, Negative


title: 61BBAD, 14, Exposed, Exposed


title: DF309F, 0, Mild, Negative


title: 75A2B6, 14, Mild, Positive


title: 75A2B6, 7, Mild, Positive


title: 75A2B6, 0, Mild, Negative


title: BAAF62, 7, Mild, Positive


title: BAAF62, 0, Mild, Negative


title: 1A9B20, 14, Mild, Positive


title: 1A9B20, 7, Mild, Positive


title: BAAF62, 14, Mild, Positive


title: 82CCF5, 0, Severe, Negative


title: 1A9B20, 0, Mild, Negative


title: 82CCF5, 7, Severe, Positive


title: 82CCF5, 14, Severe, Positive


title: 180E1A, 14, Severe, Positive


title: 180E1A, 7, Severe, Positive


title: B85D75, 7, Severe, Positive


title: 2AD75E, 7, Mild, Negative


title: 2AD75E, 14, Mild, Positive


title: B85D75, 0, Severe, Negative


title: 3F05F3, 28, Severe, Positive


title: 7085CA, 7, Mild, Negative


title: 0B943B, 3, Mild, Negative


title: 7085CA, 0, Mild, Negative


title: 0B943B, 14, Mild, Positive


title: 7768E4, 7, Exposed, Exposed


title: 0B943B, 0, Mild, Negative


title: 450905, 14, Mild, Positive


title: 7768E4, 0, Exposed, Exposed


title: 450905, 7, Mild, Positive


title: 450905, 0, Mild, Negative


title: N30_355NT_S30

status: Public on Apr 04 2022

city: Gaithersburg

first: Prabha

last: Chandrasekaran

state: Maryland

address: 8348 Hawkins Creamery Rd

institute: ehealth&Informatics, LLC

data_processing:
The sequencing reads for each sample were mapped to the respective reference genomes of Mesocricetus auratus (BCM_Maur_1.0.105) by Tophat (v2.1.2).
Cufflinks (v2.2.1) was then used to assemble transcripts, estimate abundances and test for differential expression.
Cufflinks (v2.2.1) provided various output files, and using two of its outputs, “genes.fpkm_tracking” (if Cuffnorm was used) and “gene_exp.diff” (if Cuffdiff was used), DEGs (Differentially Expressed Genes) were then identified.
The sequencing and initial data analysis using Qiagen CLC Genomics Workbench (version 21) was performed by FDA Next Generation Sequencing Core Facility
Data analysis was done using R Studio 1.4.1106 (http://www.R-project.org).  Heatmaps were constructed using pheatmap library. The gene list for signaling pathways were obtained from hallmark gene sets in Molecular Signatures Database (MSigDB) (Subramanian, Tamayo, et al. (2005, PNAS)). The figures were assembled in Adobe Photoshop.
Assembly: Mesocricetus auratus
Supplementary files format and content: Matrix table with raw gene counts and associated TPKM for every gene and every sample in .txt format

organism: Mesocricetus auratus

extract_protocol:
RNA was extracted from whole lung and nasal turbinates RNeasy mini kit (Qiagen, Gaithersburg, MD)
An aliquot (1 μg) of each sample of total RNA was used to prepare sequencing libraries using Illumina Stranded Messenger RNA Prep (ligation based)

treatment_protocol: The syrian golden hamsters were challenged with wild type or live attenuated SARS-CoV-2 virus

value: Nasal Turbinate

value: 6-12 months old

value: wild type

value: Challenge with Nsp1-N128S/K129E SARS-CoV-2 Virus


title: N32_360NT_S32

value: Challenge with Nsp1-K164A/H165A SARS-CoV-2 Virus


title: N31_353NT_S31

value: Challenge with DPRRA SARS-CoV-2 Virus


title: N29_357NT_S29


title: N28_348NT_S28

value: Challenge with WA1/2020 SARS-CoV-2 Virus


title: N27_350NT_S27


title: N26_352NT_S26


title: N25_351NT_S25


title: N24_349NT_S24


title: N22_362NT_S22

value: No Challenge


title: N20_358NT_S20


title: N21_354NT_S21


title: 180E1A, 0, Severe, Negative

value: peripheral blood mononuclear cells

value: FEMALE


title: 7085CA, 14, Mild, Positive

value: MALE


title: N19_359NT_S19


title: N17_361NT_S17


title: 2AD75E, 0, Mild, Negative


title: L16_354L_S16

value: Lung


title: L15_362L_S15


title: L14_355L_S14


title: N18_356NT_S18


title: L13_353L_S13


title: L11_349L_S11


title: L12_357L_S12


title: L9_356L_S9


title: L8_352L_S8


title: 7768E4, 14, Exposed, Exposed


title: L4_350L_S4


title: L10_347L_S10


title: L7_360L_S7


title: L3_351L_S3


title: L2_348L_S2


title: L1_361L_S1


title: N23_347NT_S23


title: M319_TAL1

status: Public on Apr 02 2022

description: Mouse with TAL1 expression (bone marrow transplant).

data_processing:
Cleaning with fastq-mcf.
Quality control with FastQC.
Mapping with HISAT2, further processing with SAMTools.
Counting abundances with htseq-count.
Assembly: mm10 (GRCm38)
Supplementary files format and content: *.all.counts.csv: Comma-separated files with the raw counts.

value: thymus

tag: condition

value: TAL1 overexpression


title: M318_TAL1


title: M317_TAL1


title: M315_empty

description: Mouse with empty vector (bone marrow transplant).

value: Empty vector


title: M312_empty


title: M311_empty


title: TALlx+40H-24h-2

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 24h.
Cell line

source_name: ProT cells

value: ProT cells

value: Induced expression of TAL1, 24h


title: TALlx+40H-24h-3


title: TALlx+40H-24h-1


title: TALlx+40H-12h-3

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 12h.
Cell line

value: Induced expression of TAL1, 12h


title: TALlx+40H-18h-2

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 18h.
Cell line

value: Induced expression of TAL1, 18h


title: TALlx+40H-6h-1

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 6h.
Cell line

value: Induced expression of TAL1, 6h


title: TALlx+40H-6h-2


title: TALlx+40H-18h-1


title: TALlx+40H-12h-1


title: TALlx+40H-18h-3


title: TALlx+40H-6h-3


title: TALlx-40H-3

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 0h.
Cell line

value: Induced expression of TAL1, 0h


title: L6_358L_S6

value: 6-12 months old

value: wild type

tag: treatment

value: Challenge with Nsp1-K164A/H165A SARS-CoV-2 Virus


title: L5_359L_S5


title: TAL1AKT-m117

description: Mouse with constitutive expression of TAL1 and AKT(E17K) (bone marrow transplant).

value: Constitutive expression of TAL1 and AKT(E17K)


title: TAL1AKT-m119


title: TALlx-40H-2


title: TAL1AKT-m116


title: AKT-m122

description: Mouse with AKT(E17K) (bone marrow transplant).


title: TALlx-40H-1


title: AKT-m124


title: Bend3 co-cultured with 4T1

status: Public on Mar 30 2022

description: Bend3 co-cultured with 4T1

data_processing:
Sequenced reads were trimmed for adaptors and low quality basecalls using Trim Galore! (v0.5.0).
High-quality reads were then mapped to the Mus musculus reference genome (GRCm38/mm10) with HISAT2 (v2.1.0) and the abundance of reads per gene was determined with HTSeq-count.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text files include raw counts.

extract_protocol:
RNA from freshly collected cells was extracted using TRIzol Reagent. Libraries were prepared using KAPA Stranded mRNA Sequencing Kit (1 ug of total RNA). For 4T1/EMT6.5 co-cultured with Bend3 cells, tumor and endothelial cells were separated by FACS sorting prior to RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
HiSeq4000 (Illumina) using a flow cell generating 1x50bp single-end reads.

tag: cell line

value: endothelial cell line

tag: culture condition

value: co-culture with 4T1


title: AKT-m121

tag: strain


title: Bend3 co-cultured with EMT6.5

description: Bend3 co-cultured with EMT6.5

value: co-culture with EMT6.5


title: EMT6.5 monocultured

description: EMT6.5 monoculture

value: breast cancer cell line

value: monoculture


title: Bend3 monocultured

description: Bend3 monoculture


title: 4T1 monocultured

description: 4T1 monoculture


title: EMT6.5 co-cultured with Bend3

description: EMT6.5 co-cultured with Bend3

value: co-culture with Bend3


title: 4T1 shPHGDH-2

description:
4T1 pLKO.1 shPHGDH replicate 2
rSMF023.190712.HiSeq4000.FCB.lane6.gcap_19_01.R1

tag: shRNA

value: shPHGDH


title: 4T1 shPHGDH-3

description:
4T1 pLKO.1 shPHGDH replicate 3
rSMF024.190712.HiSeq4000.FCB.lane6.gcap_19_01.R1

tag: cell type


title: 4T1 co-cultured with Bend3

description: 4T1 co-cultured with Bend3


title: 4T1 shSCR-3

description:
4T1 pLKO.1 shSCRAMBLE replicate 3
rSMF021.190712.HiSeq4000.FCB.lane6.gcap_19_01.R1

value: shSCR


title: 4T1 shSCR-2

description:
4T1 pLKO.1 shSCRAMBLE replicate 2
rSMF020.190712.HiSeq4000.FCB.lane5.gcap_19_01.R1


title: 4T1 shPHGDH-1

description:
4T1 pLKO.1 shPHGDH replicate 1
rSMF022.190712.HiSeq4000.FCB.lane6.gcap_19_01.R1


title: 4T1 shSCR-1

description:
4T1 pLKO.1 shSCRAMBLE replicate 1
rSMF019.190712.HiSeq4000.FCB.lane5.gcap_19_01.R1


title: MDA-MB-231 PHGDH OE-3

description: MDA-MB-231 pLHCX PHGDH replicate 3

tag: overexpression

value: PHGDH


title: MDA-MB-231 CTRL-3

description: MDA-MB-231 control replicate 3

value: control


title: MDA-MB-231 PHGDH OE-2

description: MDA-MB-231 pLHCX PHGDH replicate 2


title: MDA-MB-231 PHGDH OE-1

description: MDA-MB-231 pLHCX PHGDH replicate 1


title: MDA-MB-231 CTRL-2

description: MDA-MB-231 control replicate 2


title: Motor neuron WT - H3K27ac_rep2

status: Public on Feb 07 2022

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
To remove adapter sequences from the sequencing data, raw sequencing reads were trimmed using Trim Galore (www.bioinformatics.babraham.ac.uk/).
The raw trimmed reads were aligned to the mm10 mouse genome using the bowtie2 aligner (http://bowtie-bio.sourceforge.net/).
bigWig files were generated using Galaxy (usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig (wiggle type files using the program wigToBigWig)

source_name: Spinal motor neurons

growth_protocol: Motor neuron differentiation of mouse embryonic stem (ES) cells was performed as described previously (Rhee et al., 2016) with some modifications.

extract_protocol:
Cells were lysed and chromatin pellets were isolated, and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against the protein of interest.
ChIP-seq libraries were prepared according to the standard Illumina protocols. Briefly, DNA was end-repaired and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols.

treatment_protocol: ES cells were trypsinized and seeded at 6 x 10^4 cells per mL (day 0). 1 uM RA and 0.5 uM SAG were added to the medium on day 2. 5 uM DAPT was added on days 4 and 5.

value: ES-derived spinal motor neurons

tag: chip-seq antibody


title: Control - Rep 1

status: Public on Jan 31 2022

first: Kinsey

middle: C

last: Fisher

address: 124 Science Drive

department: Biology

data_processing:
Paired-end reads were mapped with bowtie with the following settings: bowtie -I 0 -X 500 --chunkmbs 256 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset. Count data was restricted to include only protein-coding genes (20,127), and then further restricted to include only genes with CPM>1 in at least 4 libraries (14,426 genes).
Differential expression analysis was then performed using edgeR version 3.24.3
Genome_build: WS273
Supplementary_files_format_and_content: One data file is a spreadhseet that consists of raw counts for all samples. The second data file is a spreadsheet that consists of one sheet with counts per million for each gene in each condition, and other sheets showing logFC, logCPM, P-value and FDR for each gene in comparisons between each condition using edgeR

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: All C. elegans strains used were grown and maintained at 20 °C on K-agar plates (51 mM sodium chloride, 32 mM potassium chloride, 1 mM calcium chloride, 1 mM magnesium sulfate, 10 µg/mL cholesterol, 0.25 % peptone, 2 % agar) seeded with OP50 E. coli bacteria.

extract_protocol:
After 52 hrs for control groups and 68 or 76 hours for rotenone-exposed groups worms were harvested for sample collection. Samples containing approximately 1,000 nematodes from each group were rinsed several times with K medium  until most of the bacteria were cleared out, then flash-frozen and maintained at -80°C.
Nematode samples were used for RNA extraction using 1 ml TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol with the exception that approximately 100 µL of acid-washed sand (Sigma-Aldrich), measured with a graduated 1.7 mL microcentrifuge tube, was added to each sample at the beginning of the protocol to aid homogenization. RNA was eluted in nuclease-free water and stored at -80ºC until further use. A nanodrop spectrophotometer (ThermoFisher) was used to assess the purity of the extracted RNA and the Qubit RNA HS Assay kit (ThermoFisher) was used to determine concentration. All RNA samples used for mRNA-Seq library preparation had a 260/280 absorbance ratio over 1.8. Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) starting with 500 ng total RNA per library and 9 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000 to obtain 50 bp paired-end reads.

treatment_protocol: Mixed stage plates were washed and bleached with hydroxide bleach solution to obtain synchronized embryos. Embryos were added to Erlenmeyer flasks with complete K-medium and HB101 at a density of 1 embryo/uL. 0.5uM of rotenone or 0.125% DMSO (control vehicle solution) were added to the cultures at the start. Rotenone was re-added after 24 and 48 h of exposure, while DMSO was only added after 24h of exposure.

value: Control

value: Wild Type (N2)


title: Control - Rep 2


title: Control - Rep 4


title: Rotenone- Rep 1

value: Rotenone


title: Extra_J9

status: Public on Jan 05 2022

type: RNA

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

description:
Cellline_J9, do not belong to this dataset
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_4.txt

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

source_name: PBMC

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: No cell cultures were involved.

extract_protocol: Total RNA was isolated from 2x106 PBMCs by AllPrep Plus (Qiagen). Quantity and quality of the samples was determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: PBMCs were extracted from the blood by CPT tubes.

tag: disease state

value: egg allergy

tag: tissue

value: PBMC


title: Rotenone- Rep 4

tag: age


title: Extra_J7

description:
Cellline_J7, do not belong to this dataset
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_2.txt


title: Extra_J8

description:
Cellline_J8, do not belong to this dataset
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_3.txt


title: Des_L3_80

description:
Patient_80 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_2.txt


title: Extra_J1

description:
Cellline_J1, do not belong to this dataset
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_2.txt


title: TALlx+40H-12h-2

description:
ProT cells with induced expression of TAL1 (with CreER and LoxP) - 4OH tamoxifen treatment timepoint 12h.
Cell line

value: ProT cells

value: Induced expression of TAL1, 12h


title: Extra_J3

description:
Cellline_J3, do not belong to this dataset
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_4.txt


title: Extra_J2

description:
Cellline_J2, do not belong to this dataset
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_3.txt


title: Des_L2_80

description:
Patient_80 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_4.txt


title: Des_L1_80

description:
Patient_80 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_1.txt


title: Des_L0_80

description:
Patient_80 Desensitized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_3.txt


title: Des_L3_78

description:
Patient_78 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_1.txt


title: Des_L3_77

description:
Patient_77 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_1.txt


title: Des_L2_78

description:
Patient_78 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_1.txt


title: Des_L1_78

description:
Patient_78 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_4.txt


title: Des_L1_77

description:
Patient_77 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L2_76

description:
Patient_76 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_3.txt


title: Des_L0_78

description:
Patient_78 Desensitized, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L3_76

description:
Patient_76 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_3.txt


title: Des_L2_77

description:
Patient_77 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_1.txt


title: Control - Rep 3


title: Rotenone- Rep 3


title: MDA-MB-231 CTRL-1

description: MDA-MB-231 control replicate 1


title: Rotenone- Rep 2


title: Tol_L1_76

description:
Patient_76 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_1.txt


title: Des_L2_75

description:
Patient_75 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L0_76

description:
Patient_76 Tolerized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L3_73

description:
Patient_73 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_3.txt


title: Des_L3_71

description:
Patient_71 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_75

description:
Patient_75 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L1_73

description:
Patient_73 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_4.txt


title: Des_L1_75

description:
Patient_75 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L2_73

description:
Patient_73 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_1.txt


title: Des_L1_71

description:
Patient_71 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_3.txt


title: No_L1_70

description:
Patient_70 Dropout, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L3_67

description:
Patient_67 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L2_67

description:
Patient_67 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L1_67

description:
Patient_67 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L0_67

description:
Patient_67 Tolerized, sample collected at -6 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L3_66

description:
Patient_66 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L2_66

description:
Patient_66 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L1_66

description:
Patient_66 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_4.txt


title: Des_L3_65

description:
Patient_65 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_2.txt


title: Des_L2_65

description:
Patient_65 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_1.txt


title: Des_L2_64

description:
Patient_64 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_3.txt


title: Des_L1_65

description:
Patient_65 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_64

description:
Patient_64 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_2.txt


title: Des_L2_63

description:
Patient_63 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_3.txt


title: Des_L1_64

description:
Patient_64 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_63

description:
Patient_63 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_4.txt


title: Des_L1_63

description:
Patient_63 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_1.txt


title: Des_L0_63

description:
Patient_63 Desensitized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L3_62

description:
Patient_62 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L2_62

description:
Patient_62 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_4.txt


title: Des_L3_61

description:
Patient_61 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L2_60

description:
Patient_60 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_3.txt


title: Des_L2_61

description:
Patient_61 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L3_60

description:
Patient_60 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_2.txt


title: Des_L2_71

description:
Patient_71 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L1_62

description:
Patient_62 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L1_60

description:
Patient_60 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_4.txt


title: No_L0_70

description:
Patient_70 Dropout, sample collected at -6 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_2.txt


title: Des_L1_61

description:
Patient_61 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L2_59

description:
Patient_59 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L3_58

description:
Patient_58 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L1_59

description:
Patient_59 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L0_60

description:
Patient_60 Tolerized, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L2_58

description:
Patient_58 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L1_58

description:
Patient_58 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_2.txt


title: Des_L0_65

description:
Patient_65 Desensitized, sample collected at -6 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_4.txt


title: Tol_L2_57

description:
Patient_57 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L3_57

description:
Patient_57 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L3_56

description:
Patient_56 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L1_57

description:
Patient_57 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L1_56

description:
Patient_56 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_4.txt


title: Tol_L2_55

description:
Patient_55 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L0_56

description:
Patient_56 Tolerized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L1_55

description:
Patient_55 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L3_55

description:
Patient_55 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_4.txt


title: Des_L2_54

description:
Patient_54 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_54

description:
Patient_54 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_54

description:
Patient_54 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_2.txt


title: Des_L2_53

description:
Patient_53 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_3.txt


title: Des_L3_53

description:
Patient_53 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_2.txt


title: Des_L3_51

description:
Patient_51 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_2.txt


title: Des_L2_51

description:
Patient_51 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L3_59

description:
Patient_59 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_4.txt


title: Des_L1_51

description:
Patient_51 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_4.txt


title: No_L3_48

description:
Patient_48 Dropout, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_49

description:
Patient_49 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_2.txt


title: Des_L2_49

description:
Patient_49 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_4.txt


title: No_L1_48

description:
Patient_48 Dropout, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_2.txt


title: No_L2_48

description:
Patient_48 Dropout, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_3.txt


title: No_L0_48

description:
Patient_48 Dropout, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_4.txt


title: Des_L1_49

description:
Patient_49 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L3_47

description:
Patient_47 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L1_50

description:
Patient_50 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L2_56

description:
Patient_56 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L2_50

description:
Patient_50 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L2_47

description:
Patient_47 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L1_47

description:
Patient_47 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_4.txt


title: Des_L2_45

description:
Patient_45 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_1.txt


title: Des_L3_45

description:
Patient_45 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_3.txt


title: Des_L1_53

description:
Patient_53 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_1.txt


title: No_L1_46

description:
Patient_46 Dropout, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_3.txt


title: No_L2_43

description:
Patient_43 Dropout, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_2.txt


title: No_L0_46

description:
Patient_46 Dropout, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_3.txt


title: Des_L3_42

description:
Patient_42 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L3_44

description:
Patient_44 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L2_44

description:
Patient_44 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L1_44

description:
Patient_44 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_1.txt


title: No_L1_43

description:
Patient_43 Dropout, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L3_50

description:
Patient_50 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_4.txt


title: No_L2_46

description:
Patient_46 Dropout, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_3.txt


title: Des_L2_42

description:
Patient_42 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L2_38

description:
Patient_38 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_2.txt


title: No_L0_37

description:
Patient_37 Dropout, sample collected at -6 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L3_36

description:
Patient_36 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_42

description:
Patient_42 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_4.txt


title: Des_L0_42

description:
Patient_42 Desensitized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L2_36

description:
Patient_36 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_45

description:
Patient_45 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_2.txt


title: No_L3_46

description:
Patient_46 Dropout, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_1.txt


title: Des_L2_34

description:
Patient_34 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_4.txt


title: Des_L2_39

description:
Patient_39 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_1.txt


title: Des_L0_39

description:
Patient_39 Desensitized, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_4.txt


title: Des_L3_34

description:
Patient_34 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_4.txt


title: Tol_L1_38

description:
Patient_38 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L3_38

description:
Patient_38 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_1.txt


title: Des_L1_34

description:
Patient_34 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_3.txt


title: No_L1_37

description:
Patient_37 Dropout, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_4.txt


title: Des_L2_32

description:
Patient_32 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L1_36

description:
Patient_36 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L0_44

description:
Patient_44 Tolerized, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_2.txt


title: Des_L1_32

description:
Patient_32 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_4.txt


title: Tol_L1_29

description:
Patient_29 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_1.txt


title: Des_L1_39

description:
Patient_39 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_2_3.txt


title: Tol_L3_29

description:
Patient_29 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_1.txt


title: Des_L3_32

description:
Patient_32 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_1.txt


title: Des_L3_39

description:
Patient_39 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L2_28

description:
Patient_28 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L3_28

description:
Patient_28 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L1_28

description:
Patient_28 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_3.txt


title: Des_L3_27

description:
Patient_27 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_4.txt


title: Des_L3_24

description:
Patient_24 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_24

description:
Patient_24 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327474_20190627074416_S001_GE2_1200_Dec17_1_4.txt


title: Des_L0_27

description:
Patient_27 Desensitized, sample collected at -6 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_2.txt


title: Des_L2_27

description:
Patient_27 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_4.txt


title: Des_L2_24

description:
Patient_24 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_27

description:
Patient_27 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_3.txt


title: Des_L2_21

description:
Patient_21 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_2.txt


title: Des_L3_21

description:
Patient_21 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_2.txt


title: No_L0_23

description:
Patient_23 Dropout, sample collected at -6 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_1.txt


title: No_L1_23

description:
Patient_23 Dropout, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327490_20190627072720_S001_GE2_1200_Dec17_1_3.txt


title: Des_L1_21

description:
Patient_21 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327489_20190627071024_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L3_12

description:
Patient_12 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L3_10

description:
Patient_10 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L2_10

description:
Patient_10 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L1_12

description:
Patient_12 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327488_20190626081041_S001_GE2_1200_Dec17_1_1.txt


title: Tol_L0_10

description:
Patient_10 Tolerized, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_1_4.txt


title: Tol_L1_10

description:
Patient_10 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_2_4.txt


title: Tol_L2_29

description:
Patient_29 Tolerized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L2_12

description:
Patient_12 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327494_S001_GE2_1200_Dec17_1_1.txt


title: Des_L3_8

description:
Patient_8 Desensitized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_3.txt


title: Des_L1_8

description:
Patient_8 Desensitized, sample collected at 0 months
Raw Data: 'red' channel of file: SG18209115_257236327496_S001_GE2_1200_Dec17_2_3.txt


title: Des_L2_8

description:
Patient_8 Desensitized, sample collected at 3 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_2.txt


title: Des_L3_7

description:
Patient_7 Desensitized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L3_6

description:
Patient_6 Tolerized, sample collected at 8 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_2_1.txt


title: Des_L1_7

description:
Patient_7 Desensitized, sample collected at 0 months
Raw Data: 'green' channel of file: SG18209115_257236327495_S001_GE2_1200_Dec17_2_3.txt


title: Des_L2_7

description:
Patient_7 Desensitized, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_2.txt


title: Tol_L2_6

description:
Patient_6 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L1_6

description:
Patient_6 Tolerized, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327484_20190617095400_S001_GE2_1200_Dec17_2_1.txt


title: Tol_L0_6

description:
Patient_6 Tolerized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_3.txt


title: No_L0_5

description:
Patient_5 Dropout, sample collected at -6 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_2.txt


title: Tol_L2_3

description:
Patient_3 Tolerized, sample collected at 3 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_4.txt


title: No_L1_4

description:
Patient_4 Dropout, sample collected at 0 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_3.txt


title: Tol_L1_3

description:
Patient_3 Tolerized, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_2.txt


title: No_L2_4

description:
Patient_4 Dropout, sample collected at 3 months
Raw Data: 'red' channel of file: 257236327482_20190617092002_S001_GE2_1200_Dec17_1_4.txt


title: PBS-d1-lung3

status: Public on Dec 21 2021

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Rattus norvegicus domestica

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in rn6 version 100
Genome_build: rn6 version 100
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Lung

growth_protocol: not applicable

extract_protocol: RNA was extracted from TRI Reagent (Merck) according to the manufacturer’s instructions.

treatment_protocol: Lungs were chopped, digested with collagenase and homogenized using a gentleMACS Dissociator. Lung-derived cell suspensions were further homogenized using a cell strainer. The pellet was enriched in leukocytes by Percoll gradient. Finally, fluorescently labeled MBP-reactive T cells were sorted and kept in TRI Reagent at -80° until further processing.

value: MBP-reactive T cells

value: LEW/Crl

tag: genotype

value: wild type

value: 6-8 weeks old

value: PBS

tag: time

value: Lung


title: PBS-d1-lung1

description: Rattus norvegicus domestica


title: HFHSD_Cur_1

status: Public on Nov 04 2021

description: Liver HFHSD+CUR 1

data_processing:
Sequencing was performed on Novaseq 6000 sequencing system (Illumina) ,  with 2x100bp read length.
Reads for each sample were mapped to the Mouse mm10 reference genome by Tophat(v2.0.13)
Cuffdiff provides various output files, and using one of its outputs, “gene_exp.diff”, DEGs(Differentially Expressed Genes) were identified. Cuffdiff v2.2.1 was used for FPKM calculation and DEG identification
For ontology analysis, genes with p<0.05  were picked and applied to DAVID as an input to get a comprehensive set of functional annotation.
Pathway Analysis was performed using Ingenuity Pathway Analysis (IPA, Qiagen, Version 01-12)
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted from left lateral lobe of liver. The mRNA sequencing libraries were prepared from 1 μg of RNA, according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit).
RNA libraries were prepared for sequencing using Illumina Truseq Stranded mRNA Library Prep kit

treatment_protocol: One group of mice were treated with High-fat High sugar diet, supplemented or not with curcumin

value: Liver

value: 99 weeks

value: Wild type

value: HFHSD Supplemented with Curcumin (HFHSD_Cur)


title: HFHSD_Cur_2

description: Liver HFHSD+CUR 2


title: PBS-d0-lung3

description: Rattus norvegicus domestica


title: PBS-d0-lung2

description: Rattus norvegicus domestica


title: HFHSD_3

description: Liver HFHSD 3

value: High Fat High Sugar Diet (HFHSD)


title: PBS-d1-lung2

description: Rattus norvegicus domestica


title: PBS-d0-lung1

description: Rattus norvegicus domestica


title: HFHSD_Cur_3

description: Liver HFHSD+CUR 3


title: NCD_Cur_3

description: Liver NCD+CUR 3

value: 107 weeks

value: NCD Supplemented with Curcumin (NCD_Cur)


title: HFHSD_2

description: Liver HFHSD 2


title: NCD_Cur_2

description: Liver NCD+CUR 2


title: NCD_1

description: Liver NCD 1

value: Normal Control Diet (NCD)


title: NCD_Cur_1

description: Liver NCD+CUR 1


title: HFHSD_1

description: Liver HFHSD 1


title: W12 cells - input DNA_20863_rep4

status: Public on Sep 01 2021

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

data_processing:
Reads were trimmed with Cutadapt version 1.18. All reads aligning to the ENCODE hg19 v1 blacklist regionswere identified by alignment with BWA version 0.7.17 and removed with Picard SamToFastq, https://broadinstitute.github.io/picard/. Remaining reads were aligned to an hg19 reference genome using BWA.
Reads with a mapQ score less than 6 were removed with SAMtools version 1.6 and PCR duplicates were removed with Picard MarkDuplicates.
Peaks were called by comparing each ChIP sample to its matching input sample.
For FANCD2, the mean fragment size was estimated by Phantompeakqualtools version 2.0. Peaks were called using SICER version 1.1 with the following parameters: redundancy threshold of 100, effective genome fraction of 0.75, window size of 25,000 bp, and gap size of 50,000 bp.
H3K27ac and Brd4 peaks were called using macsBroad (macs version 2.1.1 from 2016/03/09) with the following parameters: --broad-cutoff 0.01 -f "BAMPE".
Data was converted into bigwigs for viewing and normalized by reads per genomic content (RPGC) using deepTools version 3.0.1 using the following parameters: --binSize 25 --smoothLength 75 --effectiveGenomeSize 2700000000 --centerReads --normalizeUsing RPGC. RPGC-normalized input values were subtracted from RPGC-normalized ChIP values of matching cell type genome-wide using Deeptools with --binSize 25.
Genome_build: hg19
Supplementary_files_format_and_content: broadPEAK and bigwig files

source_name: Cervical keratinocytes

growth_protocol: W12 cervical keratinocytes were maintained in F-medium (3:1 [vol/vol] F-12–Dulbecco’s modified Eagle’s medium, 5% fetal bovine serum, 0.4 μg/ml hydrocortisone, 5 μg/ml insulin, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 μg/ml adenine, 100 U/ml penicillin and 100 μg/ml streptomycin) in the presence of irradiated 3T3-J2 feeder cells. C33-A and HeLa cell lines were maintained in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Cells were crossed-linked with 1% formaldehyde and chromatin was isolated and sheared to 100–500 bp DNA fragments using a Bioruptor sonicator (Diagonode) on high power settings. Chromatin samples were incubated overnight at 4°C with antibody and the resulting chromatin immunocomplexes were precipitated with blocked Dynabeads Protein G (Invitrogen), subjected to multiple wash steps and the chromatin eluted in elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS). Chromatin was reverse cross-linked overnight at 65°C in 0.2 M NaCl, followed by RNase A and proteinase K treatment, and the DNA purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Libraries were prepared using Kapa Hyper Preps (Roche) according to the manufacturer's instructions and sequenced on the Illumina HiSeq 4000 following the manufacturer's protocol.

treatment_protocol: To induce replication stress, C33-A and HeLa cells were treated for 24 hours with 0.2 µM aphidicolin (Sigma A0781).

value: Extrachromosomal HPV16 positive cervical keratinocytes

value: Untreated


title: W12 cells - input DNA_20862_rep3

value: Integrated HPV16 positive cervical keratinocytes


title: W12 cells - input DNA_20861_rep2


title: NCD_2

description: Liver NCD 2


title: Tol_L3_3

description:
Patient_3 Tolerized, sample collected at 8 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_3.txt

value: egg allergy

value: PBMC


title: NCD_3

description: Liver NCD 3


title: No_L1_5

description:
Patient_5 Dropout, sample collected at 0 months
Raw Data: 'green' channel of file: 257236327483_20190617093701_S001_GE2_1200_Dec17_1_4.txt


title: W12 cells - input DNA_20831_rep1


title: Tol_L0_3

description:
Patient_3 Tolerized, sample collected at -6 months
Raw Data: 'green' channel of file: 257236327473_20190617090302_S001_GE2_1200_Dec17_1_1.txt


title: W12 cells - H3K27ac_rep7

description: Processed data files normalised to "W12 cells - input DNA_20863_rep4"


title: W12 cells - H3K27ac_rep6

description: Processed data files normalised to "W12 cells - input DNA_20862_rep3"


title: W12 cells - H3K27ac_rep5


title: W12 cells - H3K27ac_rep8


title: W12 cells - H3K27ac_rep3

description: Processed data files normalised to "W12 cells - input DNA_20861_rep2"


title: W12 cells - H3K27ac_rep1

description: Processed data files normalised to "W12 cells - input DNA_20831_rep1"


title: W12 cells - H3K27ac_rep2


title: W12 cells - Brd4_rep3

value: Brd4 (Bethyl, A301-985A, lot 5)


title: W12 cells - Brd4_rep7


title: W12 cells - Brd4_rep4


title: W12 cells - Brd4_rep5


title: W12 cells - Brd4_rep8


title: W12 cells - Brd4_rep6


title: W12 cells - Brd4_rep2


title: W12 cells - Brd4_rep1


title: C33-A cells - FANCD2

description: Processed data files normalised to "C33-A cells - input DNA"

source_name: Cervical carcinoma cells

value: HPV negative cervical carcinoma cells

value: FANCD2 (Bethyl, A302-174A, lot 1)

value: 24 hour 0.2 uM aphidicolin treatment


title: HeLa cells - input DNA

value: Integrated HPV18 positive cervical carcinoma cells

value: HeLa


title: 3598-CY-10_Rigosertib

status: Public on Jun 15 2021

city: Nashville

first: Chi

last: Yan

state: Tennessee

address: 432A Preston Res Building, 2220 Pierce Ave

institute: Vanderbilt University

description: Bulk RNA-Seq of YUMM3.3 tumors post 17 days of treatment

data_processing:
Samples were submitted to Vanderbilt Technologies for Advanced Genomics (VANTAGE) for RNA QC, library prep and sequencing with a mean of ~30M reads/sample. Samples were sequenced on the Illumina NovaSeq 6000 using 150bp paired-end reads. Reads were then aligned to the STAR aligner for reads.
Cutadapt v1.18
FastQC v0.11.7
STAR v2.7.1a
featureCounts v1.6.4
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_mouse050120N=6.count.txt

growth_protocol: For the in vivo melanoma model, mice received 3x105 of tumor cells in 100 µl of serum-free DMEM medium by subcutaneous injection in the lower back. Mouse body weight was assessed once a week, and tumor measurements were taken twice a week with micro-calipers. Tumor volume was estimated as 0.5*length*width*width. Treatment began when tumors reached ~100mm3 volume on average and continued until tumors in the experiment exceeded 15mm in diameter or became perforated.

extract_protocol:
Tumors were collected into RNAlater. RNA was extracted using Qiagen RNAeasy plus mini Kit for three replicates from H20 and Rigosertib treated groups.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rigosertib (300mg/kg, Onconova Therapeutics) or H2O (Vehcle) were administered five days a week by oral gavage in a total volume of 100μL.

value: Melanoma tumor

value: Rigosertib


title: C33-A cells - input DNA


title: 3598-CY-8_vehicle

value: Vehcle


title: 3598-CY-11_Rigosertib


title: 3598-CY-12_Rigosertib


title: 3598-CY-9_vehicle


title: 3598-CY-7_vehicle


title: HeLa cells - FANCD2

description: Processed data files normalised to "HeLa cells - input DNA"