title: VQ-D2_BM_plasma_cells_rep1

tag: cell type

value: Bone marrow donor derived plasma cells (CD138+ B220-)

tag: background strain

value: V{kappa}*MYC; Nras LSL Q61R/+; IgG1-Cre (recipient)

tag: disease state

value: Multiple myeloma


title: Patient 24 omental mets [SO1709_024; PanCancer Progression]

status: Public on Jul 02 2020

type: RNA

city: Los Angeles

first: Sandra

last: Orsulic

state: CA

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

country: USA

institute: David Geffen School of Medicine at UCLA

hyb_protocol: As per Nanostring Technologies standard protocol.

scan_protocol: NanoString cartridges were scanned on a digital analyzer under default settings set by the manufacturer.  555 field of view (FOV) were scanned for each lane and the images were processed by the digital analyzer to quantify fluorescent barcodes

data_processing: Raw data in RCC file format were downloaded from the digital analyzer and imported into nSolver software (NanoString Technologies) for further processing.  ERCC positive control probes were used to normalize lane to lane technical variations, and ERCC negative control probes were used to estimate the background noise level.  After adjusting for technical variation and background noise, data were further normalized by geometric mean of housekeeping genes to account for sample RNA input differences.  Normalized data were log2 transformed and used in downstream analyses including differential expression analysis.

label: fluorescent barcode

molecule: total RNA

organism: Homo sapiens

source_name: Omental metastasis

extract_protocol: FFPE tissue was collected at the time of surgery. Whole tissue sections from 152 tumors were profiled. Total RNA was isolated by the FFPE kit according to the manufacturer’s instruction (Qiagen). RNA quantity and quality was assessed by Nanodrop and Bioanalyser, respectively.

tag: tissue

value: Omental metastasis

tag: age at diagnosis

tag: height

value: nd

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IV

tag: pfs

tag: os


title: Patient 17 omental mets [SO1709_017; PanCancer Progression]

label_protocol: As per Nanostring Technologies standard protocol.

tag: brca mutation status

value: W

value: WT - No Mut

value: suboptimal

value: IIIC


title: Patient 14 omental mets [SO1709_014; PanCancer Progression]

value: UNKNOWN


title: Patient 13 omental mets [SO1709_013; PanCancer Progression]


title: GC_B_cell_creControl_RNAseq_Repl3

type: SRA

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited counts per million

organism: Mus musculus

source_name: GC B-cells

extract_protocol: Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).  Library was prepared using TruSeq stranded kit as described in manuscript.

tag: genotype


type: genomic

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description:
genomic DNA methylation from sheepBloodHD909Transgenic
HD909

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: cy3, cy5

molecule: genomic DNA

organism: Ovis aries

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD847Transgenic
HD847

tag: tissue


title: GC_B_cell_creControl_RNAseq_Repl2


title: Patient 12 omental mets [SO1709_012; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight


description:
genomic DNA methylation from sheepBloodHD271Control
HD271

value: Control


title: Patient 11 omental mets [SO1709_011; PanCancer Progression]

tag: bmi

tag: race

tag: ethnicity


description:
genomic DNA methylation from sheepBloodHD1058Control
HD1058

value: male


title: Patient 10 omental mets [SO1709_010; PanCancer Progression]

tag: brca mutation description

tag: patient mutant history

tag: debulking


description:
genomic DNA methylation from sheepBloodHD889Transgenic
HD889


title: GC_B_cell_creControl_RNAseq_Repl1


description:
genomic DNA methylation from sheepBloodHD832Transgenic
HD832


title: GC_B_cell_Tbl1xr1_KO_RNAseq_Repl5


title: Patient 9 omental mets [SO1709_009; PanCancer Progression]

tag: Stage

tag: pfs

tag: os


title: Patient 8 omental mets [SO1709_008; PanCancer Progression]

value: ASIAN


description:
genomic DNA methylation from sheepBloodHD863Control
HD863

tag: genotype huntington


title: GC_B_cell_Tbl1xr1_KO_RNAseq_Repl3

tag: genotype


title: Patient 7 omental mets [SO1709_007; PanCancer Progression]

value: Omental metastasis


title: Patient 5 omental mets [SO1709_005; PanCancer Progression]

value: nd

tag: brca mutation status

value: M

value: BRCA1 185delAG


description:
genomic DNA methylation from sheepBloodHD377Transgenic
HD377

tag: age (years)

tag: Sex

tag: basename


title: Patient 3 omental mets [SO1709_003; PanCancer Progression]

tag: tissue

tag: age at diagnosis

tag: height

value: CAUCASIAN


title: Patient 2 omental mets [SO1709_002; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: HISPANIC

value: optimal


title: Patient 6 omental mets [SO1709_006; PanCancer Progression]

tag: ethnicity

tag: brca mutation description

tag: patient mutant history


title: Patient 4 omental mets [SO1709_004; PanCancer Progression]

tag: debulking

tag: Stage

tag: pfs


description:
genomic DNA methylation from sheepBloodHD357 (HD338)Control
HD357 (HD338)

tag: genotype huntington


description:
genomic DNA methylation from sheepBloodHD850Control
HD850


description:
genomic DNA methylation from sheepBloodHD838Transgenic
HD838


title: GC_B_cell_Tbl1xr1_KO_RNAseq_Repl1

tag: genotype


title: GC_B_cell_Tbl1xr1_KO_RNAseq_Repl2


title: Patient 1 omental mets [SO1709_001; PanCancer Progression]

value: NON-HISPANIC

value: IIIA

tag: os


title: Patient 153 omental mets [SO1709_153; Pancancer immune profiling]

value: IIIB


title: GC_B_cell_Tbl1xr1_KO_RNAseq_Repl4


title: Patient 152 omental mets [SO1709_152; Pancancer immune profiling]

tag: brca mutation status

value: BRCA1 exon 2 185delAG

value: IIIC


title: Patient 150 omental mets [SO1709_150; Pancancer immune profiling]

value: UNKNOWN

value: IV


title: GC_B_cell_ImuBcl6_RNAseq_R5

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

extract_protocol: Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).  Library was prepared as described in manuscript.


title: Patient 151 omental mets [SO1709_151; Pancancer immune profiling]


title: Patient 149 omental mets [SO1709_149; Pancancer immune profiling]


title: GC_B_cell_ImuBcl6_RNAseq_R4


description:
genomic DNA methylation from sheepBloodHD861Transgenic
HD861

value: Transgenic

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD808Control
HD808

value: Control

tag: tissue


description:
genomic DNA methylation from sheepBloodHD1095Control
HD1095

value: male


title: GC_B_cell_ImuBcl6_RNAseq_R3


title: GC_B_cell_ImuBcl6_RNAseq_R2


title: Patient 147 omental mets [SO1709_147; Pancancer immune profiling]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

value: W

value: WT - No Mut


title: Patient 148 omental mets [SO1709_148; Pancancer immune profiling]

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

value: M

value: BRCA2 IVS19+1G>A deleterious


description:
genomic DNA methylation from sheepBloodHD822Transgenic
HD822


title: Patient 146 omental mets [SO1709_146; Pancancer immune profiling]

value: HISPANIC

tag: brca mutation description

value: nd

tag: patient mutant history

tag: debulking

value: suboptimal

value: III


title: Patient 144 omental mets [SO1709_144; Pancancer immune profiling]

value: NON-HISPANIC

tag: Stage

tag: pfs


title: Patient 143 omental mets [SO1709_143; Pancancer immune profiling]

value: IV

tag: os


title: GC_B_cell_ImuBcl6_Tbl1xr1_mutant_RNAseq_R5

tag: genotype


title: GC_B_cell_ImuBcl6_RNAseq_R1


title: GC_B_cell_ImuBcl6_Tbl1xr1_mutant_RNAseq_R4


title: Patient 141 omental mets [SO1709_141; Pancancer immune profiling]

tag: brca mutation status

value: BRCA2 6174delT

value: optimal


title: Patient 140 omental mets [SO1709_140; Pancancer immune profiling]

value: IIIC


title: Patient 139 omental mets [SO1709_139; Pancancer immune profiling]


title: Patient 138 omental mets [SO1709_138; Pancancer immune profiling]


description:
genomic DNA methylation from sheepBloodHD1061Transgenic
HD1061

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: Blood


description:
genomic DNA methylation from sheepBloodHD899Control
HD899

value: Control

value: male

tag: tissue

tag: basename


title: Patient 137 omental mets [SO1709_137; Pancancer immune profiling]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight


description:
genomic DNA methylation from sheepBloodHD901Control
HD901


title: GC_B_cell_ImuBcl6_Tbl1xr1_mutant_RNAseq_R3


description:
genomic DNA methylation from sheepBloodHD922Transgenic
HD922

value: female


title: Patient 136 omental mets [SO1709_136; Pancancer immune profiling]

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

value: M


title: Patient 145 omental mets [SO1709_145; Pancancer immune profiling]

value: HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: IIIB


title: Patient 135 omental mets [SO1709_135; Pancancer immune profiling]

value: nd

value: BRCA1 185delAG

value: suboptimal

tag: Stage

tag: pfs

tag: os


title: GC_B_cell_ImuBcl6_Tbl1xr1_mutant_RNAseq_R2

tag: genotype


title: Patient 142 omental mets [SO1709_142; Pancancer immune profiling]

value: NON-HISPANIC

tag: brca mutation status


title: GC_B_cell_ImuBcl6_Tbl1xr1_mutant_RNAseq_R1


description:
genomic DNA methylation from sheepBloodHD1060Transgenic
HD1060

tag: genotype huntington

tag: age (years)

tag: Sex


title: Patient 133 omental mets [SO1709_133; Pancancer immune profiling]

tag: tissue

tag: age at diagnosis

value: W

value: WT - No Mut


title: GC_B_cell_WT_RNAseq_R3


title: Patient 132 omental mets [SO1709_132; Pancancer immune profiling]

tag: height

tag: weight

value: optimal

value: IIIC


title: Patient 130 omental mets [SO1709_130; Pancancer immune profiling]

tag: bmi

tag: race


title: Patient 131 omental mets [SO1709_131; Pancancer immune profiling]

value: ASIAN

tag: ethnicity

tag: brca mutation description


title: 3730CHDI_820487_RRBS

description: The provided FASTQ files are not the raw FASTQ files from the sequencer; they have been processed by adapter trimming, and further processed using a custom script to make the file suitable for alignment.

library_source: genomic

data_processing:
To analyze the sequence data, a reference genome is created that contains only the 36 base pairs adjacent to every MspI site and every C in those sequences is changed to T. A converted sequence read file is then created by changing each C in the original sequence reads to a T. The converted sequence reads are aligned to the converted reference genome, and only reads that map uniquely to the reference genome are kept. Once reads are aligned the percent methylation is calculated for each CpG using the original sequence reads. The percent methylation and number of reads is reported for each CpG.
Genome_build: mm10

source_name: Cerebellum

extract_protocol:
DNA methylation at CpG sites was assayed with a modified version of Reduced Representation Bisulfite Sequencing (RRBS; Meissner et al., 2008). RRBS was carried out by the HudsonAlpha Institute for Biotechnology. Genomic DNA is isolated from each cell line using the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations for each genomic DNA preparation are determined using fluorescent DNA binding dye and a fluorometer (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer). 1 µg of DNA was used to make an RRBS library.
RRBS library construction starts with MspI digestion of genomic DNA , which cuts at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase is then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3prime overhang. Next, a methylated version of the Illumina paired-end adapters is ligated onto the DNA. Adapter ligated genomic DNA fragments between 105 and 185 basepairs are selected using agarose gel electrophoresis and Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments are treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA is amplified in a final PCR reaction which has been optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction uracils are copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA. The sample is now ready for sequencing on the Illumina sequencing platform. These libraries were sequenced with an Illumina Genome Analyzer IIx according to the manufacturer's recommendations.

value: Cerebellum


title: Patient 129 omental mets [SO1709_129; Pancancer immune profiling]

tag: patient mutant history

tag: debulking


description:
genomic DNA methylation from sheepBloodHD916Control
HD916

value: Control

value: male

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD907Control
HD907

value: female


title: GC_B_cell_WT_RNAseq_R2


title: Patient 128 omental mets [SO1709_128; Pancancer immune profiling]

value: Omental metastasis

value: CAUCASIAN

value: M

value: BRCA1 187delAG

tag: Stage

tag: pfs

tag: os


title: Patient 134 omental mets [SO1709_134; Pancancer immune profiling]

value: BLACK

value: nd


title: GC_B_cell_WT_RNAseq_R1

tag: genotype


description:
genomic DNA methylation from sheepBloodHD335Control
HD335

tag: genotype huntington

tag: age (years)


title: Patient 127 omental mets [SO1709_127; Pancancer immune profiling]

tag: tissue

value: NON-HISPANIC

value: suboptimal


title: GC_B_cell_Tbl1xr1_mutant_RNAseq_R5


title: Patient 126 mental mets [SO1709_126; Pancancer immune profiling]

tag: age at diagnosis

tag: brca mutation status

value: BRCA2 (nd)


title: Patient 125 omental mets [SO1709_125; Pancancer immune profiling]

tag: height

tag: weight

value: W

value: WT - No Mut

value: optimal


description:
genomic DNA methylation from sheepBloodHD383 (HD378)Transgenic
HD383 (HD378)

value: Transgenic

tag: Sex


title: GC_B_cell_Tbl1xr1_mutant_RNAseq_R4


description:
genomic DNA methylation from sheepBloodHD834Transgenic
HD834


title: Patient 123 omental mets [SO1709_123; Pancancer immune profiling]

tag: bmi

tag: race

tag: ethnicity

value: BRCA1 5385insC

value: IIIC


title: Patient 124 omental mets [SO1709_124; Pancancer immune profiling]

tag: brca mutation description

tag: patient mutant history

tag: debulking


title: Patient 122 omental mets [SO1709_122; Pancancer immune profiling]

tag: Stage

tag: pfs


title: GC_B_cell_Tbl1xr1_mutant_RNAseq_R3

tag: genotype


title: Patient 121 omental mets [SO1709_121; Pancancer immune profiling]

value: ASIAN

value: IV

tag: os


title: GC_B_cell_Tbl1xr1_mutant_RNAseq_R2


title: Patient 119 omental mets [SO1709_119; Pancancer immune profiling]

value: Omental metastasis


title: Patient 118 omental mets [SO1709_118; Pancancer immune profiling]

value: CAUCASIAN


description:
genomic DNA methylation from sheepBloodHD327Transgenic
HD327

tag: genotype huntington

tag: age (years)

value: male

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD830Control
HD830

value: Control

value: female

tag: tissue


title: Patient 117 omental mets [SO1709_117; Pancancer immune profiling]

tag: age at diagnosis

tag: height

value: NON-HISPANIC

value: nd

value: III


title: GC_B_cell_Tbl1xr1_mutant_RNAseq_R1


description:
genomic DNA methylation from sheepBloodHD852Control
HD852

tag: Sex


description:
genomic DNA methylation from sheepBloodHD931Control
HD931


title: Patient 112 omental mets [SO1709_112; Pancancer immune profiling]

tag: weight

tag: bmi

value: UNKNOWN

tag: brca mutation status

value: W


title: Released-rep2

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
All RNA-seq data were mapped to the mm10 genome for mouse using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Genome_build: mm10
Supplementary_files_format_and_content: expression Count and FPKM data

source_name: embryo

growth_protocol: mESCs were maintained 2i/LIF medium containing Ndiff227 (Clontech, #40002) supplemented with PD0325901 (SIGMA ALDRICH, #PZ0162, 1 µM), CHIR99021 (SIGMA ALDRICH, #SML1046, 3 µM) and LIF (Millipore, #ESG1106, 1000 U/ml)

extract_protocol:
RNA isolation and DNase treatment were according to instructions of RNeasy Mini Kit, QIAGEN
RNA libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol for RNA-seq libraries.
Single end RNA-Seq

treatment_protocol: 1) Treatment of Ethanol or 4-Hydroxytamoxifen (4-OHT, 100nM) in mESCs for 3 days in 2i/LIF medium; 2) Treatment H2O (control) or ETO in 14 mESCs for 4 days in 2i/LIF medium. ETO-treated E14 mESCs were then released from ETO for another 4 days.

tag: cell type

value: embryonic stem cell , blastocyst derived

tag: cell line

tag: treatment

value: ETO-released (Released)


description:
genomic DNA methylation from sheepBloodHD1098Transgenic
HD1098

value: Transgenic


title: ETO-rep2

value: Etomoxir treatment (ETO, FAO inhibition)


title: Patient 114 omental mets [SO1709_114; Pancancer immune profiling]

tag: race

tag: ethnicity

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC


description:
genomic DNA methylation from sheepBloodHD927Transgenic
HD927

tag: genotype huntington

tag: age (years)

tag: basename


title: Released-rep1


title: Patient 111 omental mets [SO1709_111; Pancancer immune profiling]

tag: tissue

value: Omental metastasis

tag: age at diagnosis

tag: height

value: M

value: BRCA2 6174delT

tag: pfs

tag: os


title: Patient 120 omental mets [SO1709_120; Pancancer immune profiling]

tag: weight

tag: bmi

value: CAUCASIAN

tag: brca mutation status

value: WT - No Mut


title: Patient 109 omental mets [SO1709_109; Pancancer immune profiling]

tag: race

value: ASIAN

value: IV


title: Patient 110 omental mets [SO1709_110; Pancancer immune profiling]

tag: ethnicity

value: nd


title: Patient 108 omental mets [SO1709_108; Pancancer immune profiling]

value: NON-HISPANIC

tag: brca mutation description


description:
genomic DNA methylation from sheepBloodHD882Control
HD882

value: Control

tag: Sex

value: female

value: Blood


title: ETO-rep1

tag: cell type

value: embryonic stem cell , blastocyst derived

tag: cell line

tag: treatment


title: Patient 106 omental mets [SO1709_106; Pancancer immune profiling]

value: W

tag: patient mutant history

tag: debulking

tag: Stage


title: Control-rep2

value: H2O (control)


title: Patient 107 omental mets [SO1709_107; Pancancer immune profiling]

tag: tissue

tag: age at diagnosis

value: optimal


title: Patient 105 omental mets [SO1709_105; Pancancer immune profiling]

tag: height

value: BRCA1 E730X (2307G>T) deleterious

value: IIIC

tag: pfs


title: Patient 116 omental mets [SO1709_116; Pancancer immune profiling]

value: Omental metastasis

tag: weight

value: suboptimal

tag: os


title: Patient 103 omental mets [SO1709_103; Pancancer immune profiling]

tag: bmi

value: CAUCASIAN

tag: brca mutation status


title: Patient 115 omental mets [SO1709_115; Pancancer immune profiling]

tag: race

tag: ethnicity

value: WT - No Mut


title: Patient 102 omental mets [SO1709_102; Pancancer immune profiling]

tag: brca mutation description


title: Patient 104 omental mets [SO1709_104; Pancancer immune profiling]


title: Control-rep1

tag: cell type


description:
genomic DNA methylation from sheepBloodHD1089Transgenic
HD1089

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: male

tag: basename


description:
genomic DNA methylation from sheepBloodHD1076Control
HD1076


description:
genomic DNA methylation from sheepBloodHD845Control
HD845


description:
genomic DNA methylation from sheepBloodHD827Transgenic
HD827


title: KO-rep2

tag: strain

value: Mof fl/fl; Cre-ER TM; C57BL/6J

tag: genotype/variation

value: Mof-KO


description:
genomic DNA methylation from sheepBloodHD819Transgenic
HD819

tag: tissue


title: Patient 101 omental mets [SO1709_101; Pancancer immune profiling]

tag: age at diagnosis

tag: height

value: NON-HISPANIC

value: nd

tag: patient mutant history

tag: debulking

tag: Stage


title: KO-rep1


title: WT-rep2

value: wild type


title: Patient 100 omental mets [SO1709_100; Pancancer immune profiling]

tag: weight

tag: bmi

value: HISPANIC

value: IV

tag: pfs

tag: os


title: Patient 99 omental mets [SO1709_099; Pancancer immune profiling]

tag: race

tag: ethnicity

tag: brca mutation status

value: W

tag: brca mutation description


title: WT-rep1

tag: cell type

value: embryonic stem cell , blastocyst derived


title: Patient 98 omental mets [SO1709_098; Pancancer immune profiling]

value: optimal


title: RAG--Replicate 2 DSP as bait

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: WT IgH locus

data_processing:
Paired-end reads (2X250) were generated by Illumina HiSeq 2500 sequencer.
Samples were separated using barcodes present in Read-1.
Adapters, if present, were removed by cutadapt and bad quality bases (< Q33) were trimmed from Read-2 keeping a minimum length of 80 bases.
The reads (Read-2 only) were aligned to 1500 bp (for VH81X) and 2767 bp (for JHs) using bowtie2.
Reads which aligned to VH81X (Inv) or JHs (Del) with an alignment quality > 20 were counted.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_bait_R2.readcounts.txt: Immunoglobulin heavy chain (IgH) locus comprises variable (V), diversity (D) and joining (J) gene segments. The main contents of the processed data files reflects to the utilization of VD and DJ recombination at the WT or intergenic control region 1 (IGCR1) deficient IgH locus. Four WT IgH locus processed files (RAG--Rep1_DQ52_as_bait_R2, RAG--Rep1_DSP_as_bait_R2, RAG--Rep2_DQ52_as_bait_R2 and RAG--Rep2_DSP_as_bait_R2) demonstrate that majority of D gene segments (at least 99%) recombine to J gene segment at the WT IgH locus, leading to deletional recombination. Other eight IGCR1 deficient IgH locus processed files (CBE--1_Rep1_DQ52_as_bait_R2, CBE--1_Rep1_DSP_as_bait_R2, CBE--1_Rep2_DQ52_as_bait_R2, CBE--1_Rep2_DSP_as_bait_R2, CBE--2_Rep1_DQ52_as_bait_R2, CBE--2_Rep1_DSP_as_bait_R2, CBE--2_Rep2_DQ52_as_bait_R2 and CBE--2_Rep2_DSP_as_bait_R2) support that D gene segments can recombine to both V and J at the IGCR1 deficient IgH locus, resulting in both inversional and deletional recombination.

source_name: Pro-B cell line

growth_protocol: Pro-B cell lines (kindly provided by Frederick W. Alt, Harvard Medical School) were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol).

extract_protocol:
Genomic DNA was collected with DNeasy Blood & Tissue Kit (Qiagen, #69506).
Briefly, 80ng genomic DNA from each sample was sonicated to an average size of 750 bp. Sonicated DNA was hybridized with Bio-DQ52 or Bio-DSP2 primer, purified with Dynabeads C1 streptavidin beads (Thermo Fisher Scientific, #65002), and used for library generation as described (Lin et al., 2016). Restriction enzyme Sacl-HF (NEB, R3156S) and BseYI (NEB, R0635S) were used to digest germline DNA with DQ52 and DSP2 as bait, respectively.

treatment_protocol: RAG2-deficient pro-B cell lines, WT, CBE-/-(1) and CBE-/-(2), were infected with RAG2-expressing lentivirus, and were cultured in complete medium with puromycin (2μg/ml). After 14 days selection with puromycin, cells were harvested.

tag: strain

value: Pro-B cell line

value: Bone marrow

tag: genotype


title: Patient 97 omental mets [SO1709_097; Pancancer immune profiling]

tag: tissue

value: Omental metastasis

value: IIIC


title: Patient 95 omental mets [SO1709_095; Pancancer immune profiling]

tag: age at diagnosis

value: CAUCASIAN


title: Patient 96 omental mets [SO1709_096; Pancancer immune profiling]

tag: height

value: WT - No Mut


description:
genomic DNA methylation from sheepBloodHD913Transgenic
HD913

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


title: Patient 92 omental mets [SO1709_092; Pancancer immune profiling]

tag: weight

tag: bmi

value: NON-HISPANIC

tag: patient mutant history

tag: debulking

tag: Stage


description:
genomic DNA methylation from sheepBloodHD812Control
HD812

value: Control


title: Patient 94 omental mets [SO1709_094; Pancancer immune profiling]

tag: race

tag: ethnicity

tag: brca mutation status

tag: pfs

tag: os


title: RAG--Replicate 2 DQ52 as bait

description: WT IgH locus

tag: strain

tag: cell type

tag: tissue

tag: genotype


title: Patient 91 omental mets [SO1709_091; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: brca mutation description


description:
genomic DNA methylation from sheepBloodHD1000Transgenic
HD1000

tag: genotype huntington

tag: age (years)

tag: Sex

value: male

tag: basename


description:
genomic DNA methylation from sheepBloodHD813Control
HD813


title: Patient 90 omental mets [SO1709_090; Pancancer immune profiling]

tag: weight

tag: bmi

value: ASIAN

tag: patient mutant history

tag: debulking

tag: Stage


description:
genomic DNA methylation from sheepBloodHD872Control
HD872


description:
genomic DNA methylation from sheepBloodHD1068Transgenic
HD1068


title: Patient 89 omental mets [SO1709_089; Pancancer immune profiling]

tag: race

tag: ethnicity

tag: brca mutation status

value: IV

tag: pfs

tag: os


title: Patient 93 omental mets [SO1709_093; Pancancer immune profiling]

tag: tissue

tag: age at diagnosis

value: nd


title: Patient 88 omental mets [SO1709_088; Pancancer immune profiling]

tag: height

value: HISPANIC

tag: brca mutation description


title: Patient 87 omental mets [SO1709_087; Pancancer immune profiling]

value: optimal


title: Patient 86 omental mets [SO1709_086; Pancancer immune profiling]

value: W


description:
genomic DNA methylation from sheepBloodHD798Control
HD798

tag: genotype huntington

tag: age (years)


title: CBE--2 Replicate 2 DSP as bait

description: IGCR1 deficient IgH locus

tag: strain

tag: cell type

value: Pro-B cell line

value: Bone marrow

tag: genotype

value: IGCR1-/- and RAG2-/-


title: CBE--2 Replicate 2 DQ52 as bait

description: IGCR1 deficient IgH locus


title: Patient 83 omental mets [SO1709_083; Pancancer immune profiling]

value: Omental metastasis

tag: weight

tag: bmi

value: BLACK

tag: patient mutant history

value: suboptimal

value: IIIC


title: Patient 84 omental mets [SO1709_084; Pancancer immune profiling]

tag: race

value: CAUCASIAN

value: M

value: BRCA 1 and 2

value: BRCA 1 and 2 (nd)

tag: debulking

tag: Stage


title: Patient 81 omental mets [SO1709_081; Pancancer immune profiling]

tag: ethnicity

value: NON-HISPANIC

tag: pfs


title: Patient 80 omental mets [SO1709_080; Pancancer immune profiling]

tag: tissue

tag: brca mutation status

value: WT - No Mut

value: IV

tag: os


title: Patient 82 omental mets [SO1709_082; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: brca mutation description

value: nd


title: RAG--Replicate 1 DSP as bait

description: WT IgH locus

tag: strain


title: CBE--2 Replicate 1 DQ52 as bait

description: IGCR1 deficient IgH locus

tag: cell type


title: Patient 78 omental mets [SO1709_078; Pancancer immune profiling]

value: HISPANIC

value: optimal


title: CBE--1 Replicate 2 DSP as bait

description: IGCR1 deficient IgH locus

value: Pro-B cell line

tag: genotype


description:
genomic DNA methylation from sheepBloodHD914Control
HD914

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


title: Patient 76 omental mets [SO1709_076; Pancancer immune profiling]

value: Omental metastasis

tag: weight

tag: bmi

tag: race

value: W

tag: patient mutant history

tag: debulking


title: Patient 77 omental mets [SO1709_077; Pancancer immune profiling]

tag: tissue

tag: ethnicity

tag: Stage

value: IIIC

tag: pfs


description:
genomic DNA methylation from sheepBloodHD862Control
HD862


title: RAG--Replicate 1 DQ52 as bait

description: WT IgH locus

value: Bone marrow


title: Patient 85 omental mets [SO1709_085; Pancancer immune profiling]

tag: age at diagnosis

tag: height

value: CAUCASIAN

tag: brca mutation status

value: M

tag: brca mutation description

value: BRCA1 187delAG

tag: os


title: Patient 75 omental mets [SO1709_075; Pancancer immune profiling]

value: NON-HISPANIC

value: BRCA2 6174delT


description:
genomic DNA methylation from sheepBloodHD858Transgenic
HD858

tag: genotype huntington

value: Transgenic

tag: age (years)


title: CBE--1 Replicate 2 DQ52 as bait

description: IGCR1 deficient IgH locus

tag: strain

tag: cell type

tag: genotype

value: IGCR1-/- and RAG2-/-


description:
genomic DNA methylation from sheepBloodHD849Transgenic
HD849

tag: Sex

tag: basename


title: Patient 74 omental mets [SO1709_074; Pancancer immune profiling]

tag: weight

tag: bmi

tag: race

value: nd

tag: patient mutant history

tag: debulking


title: CBE--2 Replicate 1 DSP as bait

description: IGCR1 deficient IgH locus

tag: tissue


title: CBE--1 Replicate 1 DSP as bait

description: IGCR1 deficient IgH locus


description:
genomic DNA methylation from sheepBloodHD933Control
HD933

value: male


title: Patient 79 omental mets [SO1709_079; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: ethnicity

value: WT - No Mut

value: optimal

tag: Stage

tag: pfs


title: Patient 73 omental mets [SO1709_073; Pancancer immune profiling]

tag: brca mutation description

tag: os


description:
genomic DNA methylation from sheepBloodHD828Transgenic
HD828

tag: genotype huntington

tag: age (years)

value: female


title: Patient 72 omental mets [SO1709_072; Pancancer immune profiling]

value: ASIAN

tag: brca mutation status


title: CBE--1 Replicate 1 DQ52 as bait

description: IGCR1 deficient IgH locus

tag: strain

tag: cell type

value: Pro-B cell line

tag: genotype


title: Patient 71 omental mets [SO1709_071; Pancancer immune profiling]

value: Omental metastasis

tag: weight

tag: bmi

tag: race

value: W


description:
genomic DNA methylation from sheepBloodHD985Transgenic
HD985

tag: Sex

tag: tissue

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodHD811Control
HD811

value: Control


title: NHD13/Setd2 KO -AML (ChIP-seq)

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Clean sequenced reads were alignmented to mm10 by bowtie2(2.2.9) with parameters: -N 1; alignmented SAM files were handled using samtools(1.7); peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set; BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing CPM.(ChIP-seq)
Clean sequenced reads were alignmented to mm10 by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Htseq(0.9.1) with default parameters; FPKM were calculated by R script on its defination, differential genes were generated by R package Deseq2(1.22.2).(RNA-seq)
Raw reads were filtered by trimmomatic with parameter: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, ILLIMINACLIP:adaper.fa:2:30:7:1:true, HEADCROP:10; clean sequenced reads were alignmented to mm10 by bismark(0.19.0) with parameters: deduplicated alignments were removed by deduplicate_bismark(bismark 0.19.0); coverage files were extracted by bismark_methylation_extractor(bismark 0.19.0); DMR regions were generated by R package DSS(2.26.0). (Bisulfite-Seq)
Genome_build: mm10
Supplementary_files_format_and_content: coverage files, bed, bigwig, peak, FPKMs, raw counts

source_name: Spleen

extract_protocol:
Fluorescence activated Cell Sorting
(For ChIP-seq): Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).  (For RNA-seq): Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  (For Bisulfite-Seq): A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR.

value: Spleen

value: C-Kit+ cells

tag: chip antibody


title: Patient 67 omental mets [SO1709_067; Pancancer immune profiling]

tag: age at diagnosis

tag: height

value: BLACK

tag: ethnicity

value: NON-HISPANIC

tag: patient mutant history

tag: debulking

tag: Stage

value: IV


title: Patient 70 omental mets [SO1709_070; Pancancer immune profiling]

value: CAUCASIAN

value: HISPANIC

tag: brca mutation status

tag: brca mutation description

value: IIIC

tag: pfs

tag: os


title: NHD13 - AML (ChIP-seq)

tag: strain

tag: cell type

tag: genotype

value: NHD13 - AML


description:
genomic DNA methylation from sheepBloodHD843Control
HD843

tag: genotype huntington

tag: age (years)

tag: Sex


title: Patient 66 omental mets [SO1709_066; Pancancer immune profiling]

tag: tissue

tag: weight

tag: bmi

tag: race

value: WT - No Mut

value: optimal


title: Patient 65 omental mets [SO1709_065; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: ethnicity

value: M

tag: patient mutant history

value: BRCA2 6174delT


title: Patient 64 omental mets [SO1709_064; Pancancer immune profiling]

value: Omental metastasis

tag: brca mutation status

tag: brca mutation description

tag: debulking

tag: Stage


title: NORMAL 9

city: Nanjing

first: Zeyi

last: Zhou

state: JiangSu province

address: Zhongshan Road No.321

institute: Cardiothoracic surgery department

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: ascending aorta smooth muscle

extract_protocol:
Ascending aorta tissue was removed, quickly frozen in liquid nitrogen, and RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ascending aorta

tag: disease

value: normal


title: Patient 68 omental mets [SO1709_068; Pancancer immune profiling]

value: W

tag: pfs

tag: os


title: NORMAL 10


title: NORMAL 8


title: NORMAL 7


title: Patient 69 omental mets [SO1709_069; Pancancer immune profiling]

value: nd


title: Patient 58 omental mets [SO1709_058; Pancancer immune profiling]

value: UNKNOWN

value: IIC


title: Patient 59 omental mets [SO1709_059; Pancancer immune profiling]


title: Patient 62 omental mets [SO1709_062; Pancancer immune profiling]

value: NON-HISPANIC

value: BRCA2 exon11 6174delT


title: Patient 63 omental mets [SO1709_063; Pancancer immune profiling]

value: CAUCASIAN


title: Patient 60 omental mets [SO1709_060; Pancancer immune profiling]


title: Patient 61 omental mets [SO1709_061; Pancancer immune profiling]


title: NORMAL 6


description:
genomic DNA methylation from sheepBloodHD855Transgenic
HD855

tag: genotype huntington

value: Transgenic

tag: age (years)

value: female

value: Blood

tag: basename


description:
genomic DNA methylation from sheepBloodREP_HD1099Control
REP_HD1099

value: Control

tag: Sex

value: male

tag: tissue


description:
genomic DNA methylation from sheepBloodHD892Transgenic
HD892


description:
genomic DNA methylation from sheepBloodHD896Transgenic
HD896


description:
genomic DNA methylation from sheepBloodREP_HD1078Control
REP_HD1078


title: Patient 56 omental mets [SO1709_056; Pancancer immune profiling]

tag: weight

tag: bmi

tag: race

value: optimal

value: IIIC


description:
genomic DNA methylation from sheepBloodHD1055Transgenic
HD1055


title: Patient 54 omental mets [SO1709_054; Pancancer immune profiling]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: ethnicity

value: suboptimal


title: NORMAL 4

value: ascending aorta

value: normal


title: Patient 52 omental mets [SO1709_052; Pancancer immune profiling]

value: nd

tag: brca mutation description

tag: patient mutant history


title: Patient 57 omental mets [SO1709_057; Pancancer immune profiling]

value: UNKNOWN

tag: debulking

tag: Stage


title: NORMAL 3

tag: disease


title: Patient 53 omental mets [SO1709_053; Pancancer immune profiling]

tag: pfs

tag: os


description:
genomic DNA methylation from sheepBloodHD376Transgenic
HD376

tag: genotype huntington

tag: age (years)


description:
genomic DNA methylation from sheepBloodREP_HD870Control
REP_HD870

tag: Sex

tag: basename


title: Patient 50 omental mets [SO1709_050; Pancancer immune profiling]

tag: tissue

tag: weight


title: Patient 51 omental mets [SO1709_051; Pancancer immune profiling]

tag: bmi

tag: race


title: NORMAL 2


title: Patient 49 omental mets [SO1709_049; Pancancer immune profiling]

tag: age at diagnosis

tag: height


title: Patient 55 omental mets [SO1709_055; Pancancer immune profiling]

tag: ethnicity

tag: brca mutation description


title: NORMAL 5


title: Patient 47 omental mets [SO1709_047; Pancancer immune profiling]

tag: patient mutant history

tag: debulking


title: Patient 48 omental mets [SO1709_048; Pancancer immune profiling]

tag: brca mutation status

value: W

value: WT - No Mut

tag: Stage

value: IV


description:
genomic DNA methylation from sheepBloodREP_HD928Control
REP_HD928


description:
genomic DNA methylation from sheepBloodREP_HD818Control
REP_HD818


title: NORMAL 1

tag: disease


title: TAAD 10

value: TAAD


description:
genomic DNA methylation from sheepBloodHD841Transgenic
HD841

tag: genotype huntington

value: Transgenic


title: Patient 43 omental mets [SO1709_043; Pancancer immune profiling]

value: CAUCASIAN

value: NON-HISPANIC

value: III

tag: pfs

tag: os


title: TAAD 9


description:
genomic DNA methylation from sheepBloodHD856Transgenic
HD856

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


title: Patient 42 omental mets [SO1709_042; Pancancer immune profiling]

tag: tissue

tag: weight

tag: bmi

value: IIIC


description:
genomic DNA methylation from sheepBloodREP_HD935Control
REP_HD935

value: Control


title: Patient 44 omental mets [SO1709_044; Pancancer immune profiling]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: race

value: optimal


title: TAAD 8

value: ascending aorta


title: Patient 46 omental mets [SO1709_046; Pancancer immune profiling]

value: ASIAN

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history


title: Patient 41 omental mets [SO1709_041; Pancancer immune profiling]

tag: brca mutation status

value: M

value: BRCA1 187delAG

tag: debulking

tag: Stage


description:
genomic DNA methylation from sheepBloodHD317Transgenic
HD317

tag: genotype huntington

value: male


title: Patient 40 omental mets [SO1709_040; Pancancer immune profiling]

value: IV

tag: pfs

tag: os


title: Patient 45 omental mets [SO1709_045; Pancancer immune profiling]

value: IIC


title: TAAD 7

tag: disease

value: TAAD


title: Patient 38 omental mets [SO1709_038; Pancancer immune profiling]

value: CAUCASIAN

value: UNKNOWN


title: TAAD 5


title: TAAD 6


title: Patient 36 omental mets [SO1709_036; Pancancer immune profiling]


title: Patient 39 omental mets [SO1709_039; Pancancer immune profiling]

value: NON-HISPANIC

value: W

value: WT - No Mut


title: TAAD 4


title: Patient 35 omental mets [SO1709_035; Pancancer immune profiling]

value: BLACK

value: IIIC


title: Patient 33 omental mets [SO1709_033; Pancancer immune profiling]

value: Omental metastasis

value: optimal

value: IIA


title: Patient 37 omental mets [SO1709_037; Pancancer immune profiling]

value: nd


description:
genomic DNA methylation from sheepBloodHD816Transgenic
HD816

value: Transgenic

tag: age (years)

tag: Sex

value: female

value: Blood

tag: basename


title: Patient 34 omental mets [SO1709_034; Pancancer immune profiling]

tag: tissue

tag: weight

tag: bmi

value: ASIAN


title: Patient 32 omental mets [SO1709_032; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: race


title: Patient 31 omental mets [SO1709_031; Pancancer immune profiling]

tag: ethnicity

value: M

tag: brca mutation description

tag: patient mutant history

value: BRCA1 5382insC


description:
genomic DNA methylation from sheepBloodREP_HD817Control
REP_HD817

value: Control

value: male


description:
genomic DNA methylation from sheepBloodREP_HD1072Control
REP_HD1072


title: TAAD 3

value: ascending aorta

value: TAAD


description:
genomic DNA methylation from sheepBloodHD900Transgenic
HD900


title: Patient 30 omental mets [SO1709_030; Pancancer immune profiling]

value: NON-HISPANIC

tag: brca mutation status

value: BRCA2 5193delC

tag: debulking

tag: Stage


title: Patient 29 omental mets [SO1709_029; Pancancer immune profiling]

value: CAUCASIAN

value: BRCA2 6174delT

value: IIIC

tag: pfs

tag: os


title: Patient 28 omental mets [SO1709_028; Pancancer immune profiling]

value: Omental metastasis

value: UNKNOWN


title: TAAD 2

tag: disease


description:
genomic DNA methylation from sheepBloodHD805Transgenic
HD805

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex


description:
genomic DNA methylation from sheepBloodREP_HD842Control
REP_HD842

value: female

tag: tissue

tag: basename


title: 1_om_met

first: Ye

last: Hu

state: California

address: 8635 W. 3rd Street, Suite 290W

institute: Cedars Sinai Medical Center

data_processing:
The Human samples sequencing was done using Illumina HiSeqX platform
Alignment using STAR (2.4.1) aligner
The raw read counts were estimated using HTSeq-0.6.1.
Read count data were normalized using DESeq2.
Hierarchical clustering analysis is performed for normalized counts of all the protein coding genes for all the samples.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: xlsx files for Raw.Read.Count and Normalized.Read.Count(using DESeq2 for normalization)

source_name: human omental metastasis

growth_protocol: Formalin-fixed paraffin-embedded (FFPE) blocks were retrieved from the pathology archives at Cedars-Sinai Medical Center under an approved IRB protocol.

extract_protocol:
Total RNA was isolated using the miRNeasy FFPE kit (cat # 217504) according to the manufacturer’s   instruction (Qiagen).
RNA libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2

treatment_protocol: FFPE blocks were sectioned onto uncharged glass slides. One 4 µm section was used for H&E   staining and delineating tumor areas by a pathologist. Depending on the tumor size, 1 to 3 unstained 10 µm sections were macrodissected (removal of non-tumor areas based on the H&E template) with a clean razor blade.

tag: organ site

value: omentum

value: human omental metastasis


title: 2_om_met


title: TAAD 1


title: Patient 27 omental mets [SO1709_027; Pancancer immune profiling]

tag: age at diagnosis

tag: height

value: nd

tag: weight

tag: bmi

value: W

value: WT - No Mut

value: optimal


title: Patient 25 omental mets [SO1709_025; Pancancer immune profiling]

tag: race

value: BLACK

tag: ethnicity

tag: brca mutation description

tag: patient mutant history


title: Patient 23 omental mets [SO1709_023; Pancancer immune profiling]

tag: debulking

value: suboptimal

tag: Stage

tag: pfs


title: 3_om_met


title: Patient 21 omental mets [SO1709_021; Pancancer immune profiling]

tag: brca mutation status

tag: os


title: Patient 22 omental mets [SO1709_022; Pancancer immune profiling]


title: Patient 20 omental mets [SO1709_020; Pancancer immune profiling]

value: NON-HISPANIC

value: IV


title: Patient 26 omental mets [SO1709_026; Pancancer immune profiling]

value: CAUCASIAN


title: 4_om_met


description:
genomic DNA methylation from sheepBloodREP_HD801Control
REP_HD801

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: Blood


title: Patient 18 omental mets [SO1709_018; Pancancer immune profiling]

tag: tissue

value: Omental metastasis

value: IIIC


title: 9_om_met

tag: organ site


description:
genomic DNA methylation from sheepBloodHD853Transgenic
HD853

value: Transgenic

value: male

tag: basename


title: Patient 19 omental mets [SO1709_019; Pancancer immune profiling]

tag: age at diagnosis

tag: height

tag: weight


description:
genomic DNA methylation from sheepBloodREP_HD897Control
REP_HD897

value: female


description:
genomic DNA methylation from sheepBloodHD869Transgenic
HD869


title: 10_om_met

value: omentum

value: human omental metastasis


title: Patient 24 omental mets [SO1709_024; Pancancer immune profiling]

value: nd

tag: bmi

tag: race

tag: ethnicity


title: 8_om_met


title: 6_om_met


title: 7_om_met


title: 5_om_met


title: 10_ov

source_name: human primary ovarian cancer

value: ovary

value: human primary ovarian cancer


title: 10_met

source_name: human  non-omental metastasis

value: bladder peritoneum

value: human  non-omental metastasis


title: Patient 7 omental mets [SO1709_007; Pancancer immune profiling]

value: UNKNOWN

tag: brca mutation description

tag: patient mutant history

tag: debulking


title: Patient 10 omental mets [SO1709_010; Pancancer immune profiling]

value: optimal

tag: Stage

tag: pfs


title: Patient 11 omental mets [SO1709_011; Pancancer immune profiling]

value: CAUCASIAN

tag: os


title: Patient 8 omental mets [SO1709_008; Pancancer immune profiling]

value: ASIAN


title: Patient 9 omental mets [SO1709_009; Pancancer immune profiling]

value: IV


title: Patient 13 omental mets [SO1709_013; Pancancer immune profiling]

value: Omental metastasis

value: suboptimal


title: Patient 12 omental mets [SO1709_012; Pancancer immune profiling]

value: IIIC


title: Patient 153 omental mets [SO1709_153; PanCancer Progression]

value: NON-HISPANIC

value: IIIB


title: Patient 16 omental mets [SO1709_016; Pancancer immune profiling]


title: Patient 17 omental mets [SO1709_017; Pancancer immune profiling]

tag: brca mutation status

value: W

value: WT - No Mut


title: Patient 15 omental mets [SO1709_015; Pancancer immune profiling]

value: nd


title: Patient 14 omental mets [SO1709_014; Pancancer immune profiling]


title: Patient 4 omental mets [SO1709_004; Pancancer immune profiling]


title: Patient 6 omental mets [SO1709_006; Pancancer immune profiling]


title: 9_ov

value: ovary


title: 9_met

value: cul de sac soft tissue


title: Patient 151 omental mets [SO1709_151; PanCancer Progression]


title: Patient 152 omental mets [SO1709_152; PanCancer Progression]

value: M

value: BRCA1 exon 2 185delAG


title: 8_ov

value: human primary ovarian cancer


title: Patient 1 omental mets [SO1709_001; Pancancer immune profiling]

value: optimal

value: IIIA


title: Patient 3 omental mets [SO1709_003; Pancancer immune profiling]

value: CAUCASIAN

value: UNKNOWN


title: Patient 2 omental mets [SO1709_002; Pancancer immune profiling]

value: Omental metastasis

value: HISPANIC


title: Patient 149 omental mets [SO1709_149; PanCancer Progression]

value: IIIC


title: Patient 150 omental mets [SO1709_150; PanCancer Progression]

value: IV


title: 8_met

value: rectosigmoid serosa

value: human  non-omental metastasis


title: 7_ov


title: Patient 146 omental mets [SO1709_146; PanCancer Progression]

value: suboptimal

value: III


title: Patient 147 omental mets [SO1709_147; PanCancer Progression]

value: NON-HISPANIC

value: W

value: WT - No Mut


description:
genomic DNA methylation from sheepBloodREP_HD988Transgenic
REP_HD988

tag: genotype huntington

value: Transgenic

tag: age (years)

tag: Sex

value: female

value: Blood


title: Patient 148 omental mets [SO1709_148; PanCancer Progression]

tag: tissue

value: M

value: BRCA2 IVS19+1G>A deleterious

value: optimal


title: Patient 5 omental mets [SO1709_005; Pancancer immune profiling]

value: Omental metastasis

tag: age at diagnosis

value: nd

value: CAUCASIAN

value: BRCA1 185delAG


description:
genomic DNA methylation from sheepBloodHD824Transgenic
HD824

tag: basename


description:
genomic DNA methylation from sheepBloodHD1078Control
HD1078

value: Control

value: male


description:
genomic DNA methylation from sheepBloodHD935Control
HD935


description:
genomic DNA methylation from sheepBloodREP_HD1059Transgenic
REP_HD1059


description:
genomic DNA methylation from sheepBloodHD818Control
HD818


description:
genomic DNA methylation from sheepBloodHD1099Control
HD1099


title: 7_met

tag: organ site

value: cul de sac soft tissue

value: human  non-omental metastasis


title: 6_ov

value: ovary

value: human primary ovarian cancer


title: Patient 143 omental mets [SO1709_143; PanCancer Progression]

tag: height

tag: weight

tag: bmi

value: NON-HISPANIC

value: W

value: WT - No Mut

value: suboptimal

value: IV


title: Patient 142 omental mets [SO1709_142; PanCancer Progression]

tag: race

tag: ethnicity

value: M

tag: brca mutation description

value: BRCA2 6174delT

value: IIIC


title: Patient 145 omental mets [SO1709_145; PanCancer Progression]

value: Omental metastasis

value: HISPANIC

value: nd

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIB


title: Patient 141 omental mets [SO1709_141; PanCancer Progression]

value: CAUCASIAN

tag: brca mutation status

tag: pfs

tag: os


description:
genomic DNA methylation from sheepBloodHD928Control
HD928

tag: genotype huntington

value: Control

tag: age (years)

tag: Sex

value: female

value: Blood


description:
genomic DNA methylation from sheepBloodHD817Control
HD817

value: male

tag: tissue

tag: basename


description:
genomic DNA methylation from sheepBloodHD988Transgenic
HD988

value: Transgenic


title: Patient 144 omental mets [SO1709_144; PanCancer Progression]

tag: age at diagnosis

tag: height

value: NON-HISPANIC

value: W

value: WT - No Mut


title: 6_met

tag: organ site

value: sigmoid serosa

value: human  non-omental metastasis


title: Patient 140 omental mets [SO1709_140; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: IIIC


title: 5_ov

value: ovary

value: human primary ovarian cancer


title: 5_met

value: bladder peritoneum


description:
genomic DNA methylation from sheepBloodREP_HD807Transgenic
REP_HD807


title: Patient 138 omental mets [SO1709_138; PanCancer Progression]

value: Omental metastasis

tag: ethnicity

value: HISPANIC

tag: brca mutation description

tag: patient mutant history

value: optimal


title: Patient 139 omental mets [SO1709_139; PanCancer Progression]

value: CAUCASIAN

tag: brca mutation status

tag: debulking

tag: Stage


title: Patient 137 omental mets [SO1709_137; PanCancer Progression]

value: nd

tag: pfs

tag: os


description:
genomic DNA methylation from sheepBloodHD880Transgenic
HD880

tag: genotype huntington

tag: age (years)

tag: Sex

value: female

value: Blood


description:
genomic DNA methylation from sheepBloodREP_HD859Transgenic
REP_HD859

value: Transgenic

value: male

tag: tissue

tag: basename


description:
genomic DNA methylation from sheepBloodHD870Control
HD870

value: Control


title: Patient 136 omental mets [SO1709_136; PanCancer Progression]

tag: age at diagnosis

tag: height

value: NON-HISPANIC

value: M

value: BRCA2 6174delT


title: Patient 134 omental mets [SO1709_134; PanCancer Progression]

tag: weight

tag: bmi

value: BLACK

value: IIIC


description:
genomic DNA methylation from sheepBloodHD1059Transgenic
HD1059


description:
genomic DNA methylation from sheepBloodHD842Control
HD842


title: Patient 132 omental mets [SO1709_132; PanCancer Progression]

tag: race

tag: ethnicity


title: 4_met

tag: organ site

value: small intestine serosa

value: human  non-omental metastasis


title: 3_ov

value: ovary

value: human primary ovarian cancer


title: 4_ov


title: Patient 133 omental mets [SO1709_133; PanCancer Progression]

value: Omental metastasis

tag: brca mutation status

value: W

tag: brca mutation description

value: WT - No Mut

tag: patient mutant history

value: optimal


title: Patient 130 omental mets [SO1709_130; PanCancer Progression]

value: nd

value: CAUCASIAN

tag: debulking

tag: Stage

tag: pfs


description:
genomic DNA methylation from sheepBloodHD897Control
HD897

tag: genotype huntington

tag: age (years)

value: female

value: Blood


description:
genomic DNA methylation from sheepBloodHD1072Control
HD1072

value: Control

tag: Sex

tag: tissue


title: Patient 129 omental mets [SO1709_129; PanCancer Progression]

tag: age at diagnosis

value: NON-HISPANIC

value: M

value: BRCA1 185delAG

value: suboptimal

tag: os


title: Patient 135 omental mets [SO1709_135; PanCancer Progression]

tag: height

tag: weight

value: IIIC


title: 2_ov

value: small intestine mesentery


title: Patient 128 omental mets [SO1709_128; PanCancer Progression]

tag: bmi

tag: race

value: BRCA1 187delAG


title: 2_met

tag: organ site

value: omentum

value: human  non-omental metastasis


title: Time point 24 hour

city: CHICAGO

first: Fabien

last: Dachet

state: IL

address: 912 S. Wood Street

department: Department of NEurology

institute: UIC

data_processing:
Concatenate Read 1
Concatenate Read 2
Trim Galore! (V 0.6)
Generate index STAR (V2.7.0) with annotation GenCode V30
Maping Star (V2.7.0)
Genome_build: GenCode V30
Supplementary_files_format_and_content: FPKM and Quantile normalization

source_name: Brain

growth_protocol: A freshly isolated region of human neocortex was obtained from a temporal lobe epilepsy adult, female patient.  At time zero, a portion of the neocortical tissue was frozen on dry ice (0H). The remaining tissue was placed at 24°C and sealed in plastic wrap. At each designated time point (1, 2, 4, 8, 12 and 24 Hours), an additional sample was removed from the tissue block, the white matter is discarded and the grey matter frozen on dry ice . When all the samples are withdraw total RNA is extracted.

extract_protocol:
Total RNA from each time point was isolated using Qiagen RNAeasy columns (mini kit, RNeasy lipid kit, Qiagen) following the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions accompanying the 'SureSelect(XT) RNA Direct' kit

treatment_protocol: The tissue is placed at 24°C and sealed in plastic wrap, then multiple resection of the tissue are done in fonction of time: the original time point used a reference (0H), then time point 1 hours, 2 hours, 4 hours, 8 hours, 12 hours and 24 hours.

tag: time

value: 24 hour

value: Grey Matter

value: Female

tag: diagnosis

value: Epilepsy


title: Patient 127 omental mets [SO1709_127; PanCancer Progression]

value: Omental metastasis

value: CAUCASIAN

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history


description:
genomic DNA methylation from sheepBloodHD801Control
HD801

value: Control

value: female

value: Blood

tag: basename


title: 3_met

value: diaphragm


title: 1_ov

value: ovary

value: human primary ovarian cancer


description:
genomic DNA methylation from sheepBloodHD807Transgenic
HD807

tag: genotype huntington

value: Transgenic


title: Patient 131 omental mets [SO1709_131; PanCancer Progression]

value: ASIAN

value: NON-HISPANIC

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs


title: Time point 12 hour

value: 12 hour

tag: tissue

value: Grey Matter

tag: Sex


description:
genomic DNA methylation from sheepBloodHD859Transgenic
HD859

tag: age (years)

value: male


title: 1_met

value: left pelvic lymph node

value: human  non-omental metastasis


title: Time point 8 hour

value: 8 hour

value: Female

value: Epilepsy


description:
genomic DNA methylation from mouse3523-cblWT
3523-cbl

growth_protocol: DNA extracted from mouse tissue

tag: strain background

tag: age

value: F

tag: genotype

value: WT

value: Cerebellum


title: Patient 125 omental mets [SO1709_125; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: brca mutation status

value: W

value: WT - No Mut

tag: os


description:
genomic DNA methylation from mouse3586-cblQ175
3586-cbl

tag: basename


description:
genomic DNA methylation from mouse3507-cblWT
3507-cbl


description:
genomic DNA methylation from mouse3516-cblWT
3516-cbl


description:
genomic DNA methylation from mouse3533-cblQ175
3533-cbl

value: M


title: PEFs_CTCF-input

city: Beijing

first: Feifei

last: Li

address: Chaoyang West Road, No.1

institute: Beijing Institute of Genomics

data_processing:
All ChIP-Seq reads were mapped using bowtie2
Peaks were called using the MACS2 callpeak command with a q value of 0.01. Narrow peaks were called for all libraries.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: peak text files

organism: Sus scrofa

growth_protocol: Porcine embryo fibroblast (PEF) were isolated from 35-day-old fetuses of Large White pigs, which was mechanically dissociated and digested in DMEM supplemented with 0.5 mg/mL collagenase IV for 2.5 h at 38 ℃. Isolated PFFs were cultured in the Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 15% fetal bovine serum (FBS, Gibco), 2 mM GlutaMAX (Gibco) and 1% nonessential amino acids (NEAA, Gibco) for 24 h.

extract_protocol: ChIP-seq was conducted according to previously described protocols devoloped by Zhu et al.with few modifications. PMID: 30922236

tag: breed

value: Large White pigs

tag: cell type

value: pig embryonic fibroblasts (PEFs)

tag: chip antibody


title: Time point 4 hour

tag: time

value: 4 hour

tag: tissue

value: Grey Matter

tag: diagnosis


title: Time point 2 hour

value: 2 hour

tag: Sex


title: PEFs_CTCF_rep2

value: Abclonal, A1133


title: Patient 123 omental mets [SO1709_123; PanCancer Progression]

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

value: BRCA1 5385insC

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs


title: Time point 1 hour

value: 1 hour

value: Female

value: Epilepsy


title: Patient 124 omental mets [SO1709_124; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

value: nd


title: Patient 121 omental mets [SO1709_121; PanCancer Progression]

value: ASIAN

value: suboptimal

value: IV

tag: os


title: Patient 122 omental mets [SO1709_122; PanCancer Progression]


title: PEFs_H3K27ac_rep2

tag: breed

value: Large White pigs

tag: cell type

value: pig embryonic fibroblasts (PEFs)

tag: chip antibody

value: Abcam, ab4729


title: Reference time point   (0 hour)

tag: time

value: 0 hour

tag: tissue

value: Grey Matter

tag: diagnosis


title: PEFs_CTCF_rep1

value: Abclonal, A1133


description:
genomic DNA methylation from mouse3538-cblQ175
3538-cbl

tag: basename

tag: strain background

tag: age

tag: Sex

value: M

tag: genotype

value: Cerebellum


title: Patient 120 omental mets [SO1709_120; PanCancer Progression]

tag: age at diagnosis

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation status

value: W

tag: brca mutation description

value: WT - No Mut

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs


title: PEFs_H3K27ac_rep1

tag: breed

tag: cell type

tag: chip antibody


title: dko_H2B

city: Pasadena

first: Yandong

address: 1200 E. California Blvd

institute: California Institute of Technology

data_processing:
library strategy: synthesized oligo sequencing
The sequencing reads were filtered based on the constant fixed region in the oligo (the constant region includes the PCR handle(Position 1-20), the first T7 ligation site(Position 21-30), second T7 ligation site(Position 51-84) and reverse PCRhandle PCR handle(Position 93-100)). Reads that had more than one mismatch against the constant region were disregarded.
The 1st round cell barcode (Position 43-50) and 2nd round cell barcode (Position 85-92) were connected together to generate the full cell barcode.
The number of reads for each barcode was then calculated and the real-cell barcodes were identified from spurious cell barcodes as the former have a much higher number of reads than the latter.
The protein copy numbers in single cells were quantified by counting the UMIs (Position 31-42) associated with the cell barcodes.
Supplementary_files_format_and_content: Matrix table with protein counts for H2B and H2Bub from wt and dko sample

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Fresh colonies of yeast strain were grown in YPD until OD600 of ~0.5 (10 mL culture).

extract_protocol:
The protein-oligo conjugate bands were excised from the SDS-PAGE gel, and the protein-oligo complex were recovered from gel slab.
Two rounds of PCR amplification were carried out for next-generation sequencing library preparation. 10% of the materials recovered from the gel was used for PCR amplification. First, the DNA part of the protein-DNA conjugate was amplified using its PCR handle. Thensequencing adapters were appended using NEB Next Multiplex Oligos for Illumina (NEB) in second-round PCR. After each round of PCR, PCR amplicons were separated on 3% agarose gel and purified using gel extraction kit (Thermo Scientific, K210012) without heating.

tag: background strain

value: BY4741 (MATa his3 leu2 met15 ura3)


title: Patient 119 omental mets [SO1709_119; PanCancer Progression]

tag: tissue

value: Omental metastasis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: os


description:
genomic DNA methylation from mouse3531-cblQ175
3531-cbl

tag: basename

tag: strain background

tag: age

tag: Sex

tag: genotype


title: Patient 118 omental mets [SO1709_118; PanCancer Progression]

tag: age at diagnosis

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history

tag: debulking

tag: Stage


title: PEFs_H3K4me3_rep2

tag: breed

value: Large White pigs

tag: cell type

tag: chip antibody

value: Abcam, ab8580


description:
genomic DNA methylation from mouse3614-cblQ175
3614-cbl

value: F

tag: tissue


title: wt_H2Bub

tag: background strain

value: wt


description:
genomic DNA methylation from mouse3527-cblQ175
3527-cbl


description:
genomic DNA methylation from mouse3695-cblWT
3695-cbl

value: WT


description:
genomic DNA methylation from mouse3640-cblQ175
3640-cbl


title: wt_H2B


description:
genomic DNA methylation from mouse3714-cblWT
3714-cbl


title: PEFs_H3K4me3_rep1

value: pig embryonic fibroblasts (PEFs)


description:
genomic DNA methylation from mouse3677-cblWT
3677-cbl

value: M


title: dko_H2Bub


title: AG_murula_rep2

data_processing:
The quality of all libraries were assessed using FastQC
Pig Hi-C reads were processed using a Juicer pipeline. The data was aligned against the Sscrofa11.1 reference genome.
We used HOMER software to obtain the PC1 value and A/B compartment status.
TADs were called using deDoc at best resolution for each chromosome.
We used Fithic software to identified loops in PEFs and MEFs at 10 kb resolution
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: The files including all the valid interaction pairs were created by juicer ( described as Durand NC et al., 2016). The valid pairs are stored using a whitespace separated file that contains, on each line : <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <cigar1> <sequence1> <mapq2> <cigar2> <sequence2> <readname1> <readname2>.

growth_protocol: MII oocytes were enucleated through gentle aspiration of the first polar body and adjacent cytoplasm, containing chromosomes, with a beveled pipette (17-20 μm) in manipulation medium supplemented with 7.5 mg/ml cytochalasin B. Enclosed cytoplasts were transferred to mTBM until IVF. After being stained with Hoechst, the presence of the maternal genome was examined under a fluorescence microscope. Completely enucleated oocytes were selected and then subjected to IVF. Zygotes (PN4), 4-cell embryos and morula were collected 18.5 h, 48 h and 120 h after adding the sperm.

extract_protocol: All the embryos were treated with pronase to remove polar bodies, zona pellucida and excess sperm. The sisHi-C was conducted according to previously described protocols developed by Ke et al.Cell. 2017. PMID: 28709003

tag: tissue/cell type

tag: restriction enzyme

value: MboI


title: AG_morula_rep1


title: rnp-6 SA 3

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Biology of Ageing

description:
MTIF_REP_3
MTIF: rnp6 infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

data_processing:
Trimming: flexbar 2.5; -n 18 -ao 10 -u 5 -q 20 -m 20 -f i1.8 -ae ANY
Alignment: Hisat version 2.0.4
Removed duplicates using samtools version 1.3.1
Guided assembly: StringTie 1.0.4; -p 18 -G ORIGINAL_GTF -f 0.99
Merging assemblies: Cuffmerge 2.2.1; --min-isoform-fraction 1.0
Quantification: Cuffquant 2.2.1
Differential analysis: Cuffdiff 2.2.1; --dispersion-method per-condition
Supplementary_files_format_and_content: tab-separated values or excel table of gene expression and splicing data
for kiss-splice
Alignment: STAR version 2.5.2b
Splicing analysis: kissplice version 2.4.0 (https://doi.org/10.1186/1471-2105-13-S6-S5)
Differential splicing with R package kissDE
Supplementary_files_format_and_content: Excel table of differential splicing
for SAJR (https://doi.org/10.1038/msb.2012.67)
Alignment: STAR version 2.5.2b
followed protocol for differential splicing using SAJR (https://protocolexchange.researchsquare.com/article/nprot-6093/v1)
Supplementary_files_format_and_content: Excel tables of differential splicing
Genome_build: WBcel235

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were cultured at 20°C. Nematodes were cultured using standard techniques on nematode growth medium agar plates with the Escherichia coli strain OP50.

extract_protocol:
Samples were isolated using mRNAeasy Mini Kit (QIAGEN)
Illumina TruSeq stranded RiboZero

treatment_protocol: DAY1 adults of respective genotypes were transferred to tryptic soy plates seeded with either heat killed OP50 or live S. aureus.  After 4 hours of incubation at 25°C, the animals were harvested.

tag: diet

value: Live S. aureus

tag: developmental stage

value: Day 1

value: whole organism


title: Patient 117 omental mets [SO1709_117; PanCancer Progression]

tag: height

tag: weight

tag: bmi

tag: race

value: NON-HISPANIC

value: optimal

value: III

tag: pfs

tag: os


title: N2 SA 3

description:
WTIF_REP_3
WTIF: wt infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: strain

tag: genotype

value: wild type


title: Patient 116 omental mets [SO1709_116; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

value: CAUCASIAN

tag: ethnicity

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: suboptimal

tag: Stage

value: IV


title: Patient 115 omental mets [SO1709_115; PanCancer Progression]

tag: tissue

value: nd

tag: brca mutation status

value: W

value: WT - No Mut

value: IIIC


description:
genomic DNA methylation from mouse3510-cblWT
3510-cbl

tag: basename

tag: strain background

tag: age

tag: Sex

value: F

value: WT

value: Cerebellum


title: rnp-6 OP50 3

description:
MTN2_REP_3
MTN2: rnp6 mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: diet

value: Heat killed E. coli OP50

tag: developmental stage

value: Day 1


title: AG_4cell_rep2

tag: breed

value: Large White pigs

tag: tissue/cell type

tag: restriction enzyme

value: MboI


title: Patient 114 omental mets [SO1709_114; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: NON-HISPANIC

value: optimal

tag: pfs

tag: os


title: AG_4cell_rep1


title: rnp-6 SA 2

description:
MTIF_REP_2
MTIF: rnp6 infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: genotype

value: Live S. aureus

tag: tissue

value: whole organism


description:
genomic DNA methylation from mouse3631-cblQ175
3631-cbl

tag: basename

tag: strain background


title: Patient 112 omental mets [SO1709_112; PanCancer Progression]

value: Omental metastasis

value: CAUCASIAN

tag: ethnicity

value: UNKNOWN

tag: brca mutation status

tag: brca mutation description

tag: patient mutant history

tag: debulking

tag: Stage


description:
genomic DNA methylation from mouse3708-cblWT
3708-cbl

tag: age

tag: Sex

value: M


title: AG_zygote_rep2

tag: breed

tag: tissue/cell type

tag: restriction enzyme


title: Patient 111 omental mets [SO1709_111; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: BRCA2 6174delT

tag: pfs


description:
genomic DNA methylation from mouse3695-strWT
3695-str

tag: basename

tag: strain background

tag: genotype

tag: tissue

value: Striatum


title: PEFs_histone-input

tag: cell type

value: pig embryonic fibroblasts (PEFs)

tag: chip antibody


title: AG_zygote_rep1


description:
genomic DNA methylation from mouse3640-strQ175
3640-str

tag: age

value: F


title: Patient 110 omental mets [SO1709_110; PanCancer Progression]

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history

tag: debulking

tag: Stage

value: IV

tag: os


title: N2 SA 2

description:
WTIF_REP_2
WTIF: wt infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: strain

value: wild type

tag: diet

tag: developmental stage

value: Day 1


title: PA_murula_rep2

growth_protocol: Oocytes were activated with two direct current pulses at 1.2 kV/cm for 30 μs provided by a BTX Electro-cell Manipulator 200 (BTX) in activation medium. Then the activated oocytes were transferred into 500 μL porcine zygote medium-3 (PZM3) and cultured at 38.5 °C in humidified 5% CO2. Zygotes (PN4) were collected 16 h after electrical stimulation, 4-cell embryos were collected 48 h after electrical stimulation and the morula were collected 120 h after electrical stimulation.

tag: breed

value: Large White pigs

tag: tissue/cell type

tag: restriction enzyme

value: MboI


title: rnp-6 OP50 2

description:
MTN2_REP_2
MTN2: rnp6 mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: genotype

value: Heat killed E. coli OP50


title: Patient 109 omental mets [SO1709_109; PanCancer Progression]

tag: tissue

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: ASIAN

value: NON-HISPANIC

value: optimal

tag: pfs


title: N2 OP50 2

description:
WTN2_REP_2
WTN2: wt mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

value: whole organism


title: PA_morula_rep1


title: PA_4cell_rep2


title: N2 OP50 3

description:
WTN2_REP_3
WTN2: wt mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx


title: rnp-6 SA 1

description:
MTIF_REP_1
MTIF: rnp6 infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

value: Live S. aureus


title: Patient 107 omental mets [SO1709_107; PanCancer Progression]

value: Omental metastasis

value: CAUCASIAN

tag: ethnicity

tag: brca mutation status

value: W

tag: brca mutation description

value: WT - No Mut

tag: patient mutant history

tag: debulking

value: IIIC


title: Patient 108 omental mets [SO1709_108; PanCancer Progression]

value: nd

tag: Stage

tag: os


description:
genomic DNA methylation from mouse3631-strQ175
3631-str

tag: basename

tag: strain background

tag: age

tag: Sex

value: F

value: Striatum


description:
genomic DNA methylation from mouse3614-strQ175
3614-str

tag: genotype

tag: tissue


title: N2 SA 1

description:
WTIF_REP_1
WTIF: wt infected
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: strain

value: wild type

tag: diet

tag: developmental stage

value: Day 1


title: Patient 106 omental mets [SO1709_106; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

tag: pfs


description:
genomic DNA methylation from mouse3708-strWT
3708-str

value: M

value: WT


title: PA_zygote_rep2

tag: breed

value: Large White pigs

tag: tissue/cell type

tag: restriction enzyme

value: MboI


title: Patient 105 omental mets [SO1709_105; PanCancer Progression]

value: ASIAN

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation status

tag: brca mutation description

tag: patient mutant history

value: BRCA1 E730X (2307G>T) deleterious

tag: debulking

value: optimal

tag: Stage

tag: os


description:
genomic DNA methylation from mouse3714-strWT
3714-str

tag: basename

tag: strain background

tag: age

tag: Sex

tag: genotype

tag: tissue


title: N2 OP50 1

description:
WTN2_REP_1
WTN2: wt mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: strain

tag: diet

value: Heat killed E. coli OP50

tag: developmental stage

value: whole organism


title: IVF_murula_rep2

growth_protocol: MII oocytes were co-incubated with sperm for 5 h. After fertilization, oocytes were transferred into 500 μL PZM3 medium and cultured in four-well dishes at 38.5 ℃ in 5% CO2 humidified air. Zygotes, 4-cell embryos and morula were collected 18.5 h, 48 h and 120 h after adding the sperm suspension to the fertilization droplets.

tag: breed

tag: tissue/cell type

tag: restriction enzyme


description:
genomic DNA methylation from mouse3677-strWT
3677-str


title: Patient 104 omental mets [SO1709_104; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

tag: brca mutation description

tag: pfs


description:
genomic DNA methylation from mouse3586-strQ175
3586-str

tag: basename

tag: strain background

tag: age

tag: Sex


title: Patient 103 omental mets [SO1709_103; PanCancer Progression]

tag: tissue

value: nd

tag: brca mutation status

value: W

value: WT - No Mut

tag: patient mutant history

tag: debulking

tag: Stage

value: IV

tag: os


title: IVF_morula_rep1

tag: breed

tag: tissue/cell type

tag: restriction enzyme


description:
genomic DNA methylation from mouse3531-strQ175
3531-str

tag: genotype

value: Striatum


title: PA_4cell_rep1


title: rnp-6 OP50 1

description:
MTN2_REP_1
MTN2: rnp6 mock
geneexp_ALL.tsv
diff_sig_geneexp.xlsx
diff_sig_splic.xlsx
kissDE_anot_all (1).xlsx
SAJR WTIF_vs_MTIF.results.xlsx
SAJR WTN2_vs_WTIF.results.xlsx

tag: diet

tag: developmental stage

value: Day 1


title: PA_zygote_rep1


title: IVF_zygote_rep2


title: IVF_4cell_rep1


title: IVF_zygote_rep1


title: IVF_4cell_rep2


title: Patient 102 omental mets [SO1709_102; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

tag: ethnicity

tag: brca mutation description

value: IIIC

tag: pfs


title: PEFs_HiC_rep2

source_name: PEFs

value: Large White pigs

value: PEFs


title: Patient 126 mental mets [SO1709_126; PanCancer Progression]

tag: tissue

tag: brca mutation status

value: M

tag: patient mutant history

value: BRCA2 (nd)

tag: debulking


title: PEFs_HiC_rep1

tag: breed

tag: tissue/cell type

value: MboI


title: Patient 97 omental mets [SO1709_097; PanCancer Progression]

value: NON-HISPANIC

value: optimal

tag: Stage

tag: os


title: Patient 96 omental mets [SO1709_096; PanCancer Progression]


title: Patient 100 omental mets [SO1709_100; PanCancer Progression]

value: HISPANIC


title: Patient 98 omental mets [SO1709_098; PanCancer Progression]

value: Omental metastasis


title: Patient 101 omental mets [SO1709_101; PanCancer Progression]

value: CAUCASIAN


title: Patient 99 omental mets [SO1709_099; PanCancer Progression]


description:
genomic DNA methylation from mouse3527-strQ175
3527-str

tag: basename

tag: strain background

tag: age

tag: Sex

tag: genotype


title: Zoey

first: Jeffrey

last: Kidd

address: 1241 Catherine St

hyb_protocol: Hybridization buffer and components recommended by Agilent were mixed with samples and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridization oven according to manufacturer’s instructions. After hybridization, slides were washed sequentially according to manufaturer’s instructions.

scan_protocol: Scanned on an NimbleGen MS 200 Microarray Scanner with multi TIFF option and 2um resolution Images were quantified using Agilent Feature Extraction Software 12.0.2.2.

data_processing: Agilent Feature Extraction Software 12.0.2.2 was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

label_protocol: 1ug of gDNA was labeled using the direct method without restriction digest according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: gDNA was extracted with phenol chloroform methods or DNeasy Blood & Tissue Kits (Qiagen, Germantown, MD)

treatment_protocol: not applicable

value: lymphocytes

value: Great Dane Zoey


description:
genomic DNA methylation from mouse3640-ctxQ175
3640-ctx

value: F

value: Cortex


title: Patient 95 omental mets [SO1709_095; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: nd


title: VN76

tag: tissue


title: NGSD2


title: Penelope

organism: Canis lupus

value: Wolf


description:
genomic DNA methylation from mouse3510-strWT
3510-str

value: WT

value: Striatum


description:
genomic DNA methylation from mouse3516-strWT
3516-str


description:
genomic DNA methylation from mouse3533-strQ175
3533-str


title: Patient 94 omental mets [SO1709_094; PanCancer Progression]

tag: ethnicity

tag: brca mutation status

value: W

tag: brca mutation description

value: WT - No Mut

tag: patient mutant history

value: IIIC

tag: pfs


description:
genomic DNA methylation from mouse3538-strQ175
3538-str

value: M


title: Patient 93 omental mets [SO1709_093; PanCancer Progression]

value: NON-HISPANIC

tag: debulking

tag: Stage

tag: os


description:
genomic DNA methylation from mouse3523-strWT
3523-str

tag: basename

tag: strain background

tag: age


title: HEK293T cells, SpACE_RNF2_Rep3

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). Cells were used for experiments until passage 20. Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s  NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep), using 37.5ug of base editor plasmid co-translationally encoding P2A-EGFP or variants thereof and 12.5ug of gRNA plasmids. 6-7x10E6 HEK293T cells were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). GFP positive cells were sorted 36-40h after transfection after doublet-exlusion and gating for the cell population on a BD FACSARIA II.

tag: cell line

tag: treatment

value: SpACE

tag: guide rna (grna)

tag: gfp

value: All GFP

tag: replicate


title: HEK293T cells, ABEmax_RNF2_Rep3

value: ABEmax


title: HEK293T cells, Target-AID_RNF2_Rep3

value: Target-AID


title: HEK293T cells, miniABEmax-V82G_RNF2_Rep3


description:
genomic DNA methylation from mouse3531-ctxQ175
3531-ctx

tag: Sex

tag: genotype

tag: tissue


title: NIH_23356

value: lymphocytes

tag: breed

value: Breed _Breed


title: NIH_2972

value: Great Dane Zoey


description:
genomic DNA methylation from mouse3507-strWT
3507-str

value: F


description:
genomic DNA methylation from mouse3631-ctxQ175
3631-ctx

value: Cortex


title: NIH_20576


description:
genomic DNA methylation from mouse3510-ctxWT
3510-ctx


description:
genomic DNA methylation from mouse3714-ctxWT
3714-ctx


description:
genomic DNA methylation from mouse3708-ctxWT
3708-ctx


title: HEK293T cells, nCas9_RNF2_Rep3


title: NIH_21270


title: NIH_16145


title: HEK293T cells, SpACE_RNF2_Rep2


title: Patient 91 omental mets [SO1709_091; PanCancer Progression]

data_processing: Raw data in RCC file format were downloaded from the digital analyzer and imported into nSolver software (NanoString Technologies) for further processing.  ERCC positive control probes were used to normalize lane to lane technical variations, and ERCC negative control probes were used to estimate the background noise level.  After adjusting for technical variation and background noise, data were further normalized by geometric mean of housekeeping genes to account for sample RNA input differences.  Normalized data were log2 transformed and used in downstream analyses including differential expression analysis.

extract_protocol: FFPE tissue was collected at the time of surgery. Whole tissue sections from 152 tumors were profiled. Total RNA was isolated by the FFPE kit according to the manufacturer’s instruction (Qiagen). RNA quantity and quality was assessed by Nanodrop and Bioanalyser, respectively.

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

tag: ethnicity

tag: brca mutation status

tag: brca mutation description

tag: patient mutant history

value: optimal


title: Patient 92 omental mets [SO1709_092; PanCancer Progression]

value: nd

tag: debulking

tag: Stage

tag: pfs

tag: os


title: NIH_14566


title: Patient 90 omental mets [SO1709_090; PanCancer Progression]

value: ASIAN

value: W

value: WT - No Mut

value: IV


title: HEK293T cells, Target-AID_RNF2_Rep2

tag: cell line

tag: treatment

tag: guide rna (grna)

tag: gfp

tag: replicate


title: HEK293T cells, miniABEmax-V82G_RNF2_Rep2


title: HEK293T cells, ABEmax_RNF2_Rep2


title: Patient 89 omental mets [SO1709_089; PanCancer Progression]

tag: tissue

tag: age at diagnosis

tag: height

value: NON-HISPANIC


title: Patient 87 omental mets [SO1709_087; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: IIIC


title: HEK293T cells, nCas9_RNF2_Rep2

value: All GFP


title: Patient 86 omental mets [SO1709_086; PanCancer Progression]

tag: ethnicity

tag: brca mutation status

tag: brca mutation description


title: NIH_14529

tag: breed


title: HEK293T cells, SpACE_RNF2_Rep1

value: SpACE


title: Patient 88 omental mets [SO1709_088; PanCancer Progression]

value: HISPANIC

tag: patient mutant history

tag: debulking

tag: Stage

tag: pfs


title: Patient 84 omental mets [SO1709_084; PanCancer Progression]

value: M

value: BRCA 1 and 2

value: BRCA 1 and 2 (nd)

tag: os


title: Patient 85 omental mets [SO1709_085; PanCancer Progression]

value: BRCA1 187delAG


title: HEK293T cells, miniABEmax-V82G_RNF2_Rep1

tag: cell line

tag: treatment

tag: guide rna (grna)

tag: gfp


title: Patient 83 omental mets [SO1709_083; PanCancer Progression]

tag: tissue

value: Omental metastasis

tag: age at diagnosis

tag: height

value: BLACK

value: suboptimal


title: NIH_1223

value: lymphocytes

value: Breed _Breed

value: Great Dane Zoey


title: Patient 82 omental mets [SO1709_082; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

value: nd


description:
genomic DNA methylation from mouse3516-ctxWT
3516-ctx

tag: basename

tag: strain background

tag: age

tag: Sex

value: F

tag: genotype

value: WT

value: Cortex


title: NIH_8542

tag: breed


description:
genomic DNA methylation from mouse3507-ctxWT
3507-ctx


title: HEK293T cells, ABEmax_RNF2_Rep1

value: ABEmax

value: All GFP

tag: replicate


description:
genomic DNA methylation from mouse3527-ctxQ175
3527-ctx

value: M


title: HEK293T cells, Target-AID_RNF2_Rep1

tag: cell line

value: Target-AID


description:
genomic DNA methylation from mouse3586-ctxQ175
3586-ctx


title: NIH_10442


description:
genomic DNA methylation from mouse3533-ctxQ175
3533-ctx


description:
genomic DNA methylation from mouse3677-ctxWT
3677-ctx


description:
genomic DNA methylation from mouse3695-ctxWT
3695-ctx


description:
genomic DNA methylation from mouse3538-ctxQ175
3538-ctx


title: HEK293T cells, nCas9_RNF2_Rep1

tag: treatment


title: NGSD1


title: NIH_6610


title: EG49


title: 1756


description:
genomic DNA methylation from mouse3631-liverQ175
3631-liver

value: Liver


title: Patient 81 omental mets [SO1709_081; PanCancer Progression]

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs

tag: os


title: NIH_13131

tag: tissue


title: PT61


description:
genomic DNA methylation from mouse3614-ctxQ175
3614-ctx

tag: basename


title: TW04


title: HEK293T cells, SpACE_HEKsite2_Rep3

value: SpACE

tag: guide rna (grna)

tag: gfp


title: Patient 80 omental mets [SO1709_080; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

tag: brca mutation status

value: W

value: WT - No Mut

value: IV


title: LB85

value: lymphocytes

tag: breed

value: Great Dane Zoey


title: HEK293T cells, GFP_Rep3

tag: cell line

tag: treatment

value: GFP

tag: replicate


title: HEK293T cells, Target-AID_HEKsite2_Rep3


description:
genomic DNA methylation from mouse3533-liverQ175
3533-liver

tag: strain background

tag: age

tag: Sex

tag: genotype


title: HEK293T cells, miniABEmax-V82G_HEKsite2_Rep3


title: Patient 77 omental mets [SO1709_077; PanCancer Progression]

tag: tissue

value: CAUCASIAN

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history

tag: debulking

tag: Stage

tag: pfs

tag: os


title: Patient 78 omental mets [SO1709_078; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: weight

tag: bmi

tag: race

value: HISPANIC

tag: brca mutation status


title: Patient 79 omental mets [SO1709_079; PanCancer Progression]


title: HEK293T cells, ABEmax_HEKsite2_Rep3

tag: cell line

tag: treatment

value: ABEmax

tag: guide rna (grna)

tag: gfp

value: All GFP

tag: replicate


description:
genomic DNA methylation from mouse3523-ctxWT
3523-ctx

tag: basename

tag: strain background

tag: age

tag: Sex

value: F

tag: genotype

value: WT

tag: tissue

value: Cortex


title: Patient 76 omental mets [SO1709_076; PanCancer Progression]

tag: age at diagnosis

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs

tag: os


title: Patient 75 omental mets [SO1709_075; PanCancer Progression]

value: Omental metastasis

tag: height

tag: weight

tag: bmi

tag: race

tag: brca mutation status

value: M

value: BRCA2 6174delT


title: HEK293T cells, nCas9_HEKsite2_Rep3

tag: cell line

tag: treatment

tag: guide rna (grna)

tag: gfp

tag: replicate


title: EG44

tag: tissue

value: lymphocytes

tag: breed


description:
genomic DNA methylation from mouse3538-liverQ175
3538-liver

tag: basename

tag: strain background

tag: age

tag: Sex

tag: genotype

value: Liver


description:
genomic DNA methylation from mouse3614-liverQ175
3614-liver


title: HEK293T cells, GFP_Rep2

value: GFP


title: Patient 74 omental mets [SO1709_074; PanCancer Progression]

tag: age at diagnosis

tag: height

value: CAUCASIAN

tag: ethnicity

tag: brca mutation description

tag: patient mutant history

tag: debulking

tag: Stage

tag: pfs

tag: os


description:
genomic DNA methylation from mouse3708-liverWT
3708-liver


title: Patient 73 omental mets [SO1709_073; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: nd


description:
genomic DNA methylation from mouse3523-liverWT
3523-liver

tag: basename

tag: tissue


title: Patient 72 omental mets [SO1709_072; PanCancer Progression]

value: ASIAN

tag: brca mutation status

value: W

value: WT - No Mut


title: VN42

tag: breed

value: Great Dane Zoey


title: HEK293T cells, Target-AID_HEKsite2_Rep2

tag: cell line

tag: treatment

value: Target-AID

tag: guide rna (grna)

tag: gfp

value: All GFP

tag: replicate


description:
genomic DNA methylation from mouse3631-bloodQ175
3631-blood

tag: strain background

tag: age

tag: Sex

value: F

tag: genotype

value: Blood


title: PG84


description:
genomic DNA methylation from mouse3640-liverQ175
3640-liver


title: QA5


title: HR93


title: HEK293T cells, SpACE_HEKsite2_Rep2

value: SpACE


title: Patient 71 omental mets [SO1709_071; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

tag: patient mutant history

tag: debulking

value: optimal

tag: Stage

value: IIIC

tag: pfs

tag: os


description:
genomic DNA methylation from mouse3533-bloodQ175
3533-blood

tag: basename

value: M

tag: tissue


description:
genomic DNA methylation from mouse3507-bloodWT
3507-blood

value: WT


title: HEK293T cells, ABEmax_HEKsite2_Rep2

tag: cell line

tag: treatment

value: ABEmax

tag: guide rna (grna)

tag: gfp


title: Patient 70 omental mets [SO1709_070; PanCancer Progression]

tag: weight

tag: bmi

tag: race

value: CAUCASIAN

value: HISPANIC

tag: brca mutation status


description:
genomic DNA methylation from mouse3527-liverQ175
3527-liver

tag: strain background

tag: age

tag: Sex

tag: genotype

value: Liver


title: HEK293T cells, nCas9_HEKsite2_Rep2

tag: replicate


title: LB79

value: lymphocytes

tag: breed


title: HEK293T cells, miniABEmax-V82G_HEKsite2_Rep2


title: Patient 69 omental mets [SO1709_069; PanCancer Progression]

tag: age at diagnosis

tag: height

tag: ethnicity

tag: brca mutation description

value: nd

tag: patient mutant history

tag: debulking

tag: Stage

tag: pfs

tag: os


title: NA63

tag: tissue

value: Great Dane Zoey


title: PT71


title: NA8

value: SubSaharan_ VillageDog


title: HEK293T cells, GFP_Rep1

tag: cell line

tag: treatment

value: GFP

tag: guide rna (grna)

tag: gfp

value: All GFP


title: Patient 68 omental mets [SO1709_068; PanCancer Progression]

tag: weight

tag: bmi

tag: race

tag: brca mutation status

value: W

value: WT - No Mut

value: IV


title: NA89

tag: breed


title: HEK293T cells, SpACE_HEKsite2_Rep1

value: SpACE

tag: replicate


title: Patient 67 omental mets [SO1709_067; PanCancer Progression]

value: Omental metastasis

tag: age at diagnosis

tag: height

value: BLACK

tag: ethnicity

value: NON-HISPANIC

tag: brca mutation description

value: optimal


title: RNA-seq on ruxolitinb+GSKLSD1 treated murine leukemia cells-3

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description:
GSKRUX3
processed data file: GSKRUX_normcounts.txt

data_processing:
Raw reads were trimmed with BBDuk and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GSKRUX_normcounts.txt: Tab-delimited text file includes gene names and normalized counts.

source_name: Bone marrow

growth_protocol: CEBPA/CSF3R murine leukemia cells were cultured in IMDM +20% FBS.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen).
Libraries were constructed by BGI.

treatment_protocol: Cells were treated with DMSO, 50 nM Ruxolitinib, 2 nM GSK-LSD1 or the combination for 24 hours.

tag: strain/background

value: BALB/c

tag: cell type

value: CEBPA/CSF3R leukemia cells


description:
genomic DNA methylation from mouse3677-bloodWT
3677-blood

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

extract_protocol: genomic DNA was extracted

tag: basename

tag: strain background

tag: age

tag: Sex

value: M

tag: genotype

value: WT

tag: tissue

value: Blood


title: HEK293T cells, Target-AID_HEKsite2_Rep1

tag: cell line

tag: treatment

value: Target-AID

tag: guide rna (grna)

tag: gfp


title: ID168

value: lymphocytes

tag: breed

value: Great Dane Zoey


title: HR85


description:
genomic DNA methylation from mouse3516-bloodWT
3516-blood

value: F


title: HEK293T cells, miniABEmax-V82G_HEKsite2_Rep1

value: All GFP

tag: replicate


title: RNA-seq on ruxolitinb+GSKLSD1 treated murine leukemia cells-2

description:
GSKRUX2
processed data file: GSKRUX_normcounts.txt


title: RNA-seq on ruxolitinb+GSKLSD1 treated murine leukemia cells-1

description:
GSKRUX1
processed data file: GSKRUX_normcounts.txt


title: HEK293T cells, ABEmax_HEKsite2_Rep1

value: ABEmax


description:
genomic DNA methylation from mouse3708-bloodWT
3708-blood


title: 1735


title: HEK293T cells, nCas9_HEKsite2_Rep1


title: RNA-seq on GSKLSD1 treated murine leukemia cells-2

description:
GSK2
processed data file: GSKRUX_normcounts.txt


description:
genomic DNA methylation from mouse3614-bloodQ175
3614-blood