title: CD4_A_n_41

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: BRD3170N-CTCF_ChIP-seq

status: Public on Aug 24 2020

type: SRA

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

library_source: genomic

data_processing:
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
processed data files format and content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal colon

extract_protocol: ChIP-seq was performed as described previously (Liau et al., 2016).  In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments.  Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335).  ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3‚Ä≤ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.

tag: tissue

value: Normal colon

tag: biological sample

tag: treatment


title: CD4_E_g_39

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

description:
rawReadsData.csv
Counts_Normalization_cd4.csv

library_source: transcriptomic

data_processing:
Reads were mapped, using STAR software (version 2.6.0a), to human reference genome GrCh38 (v83), obtaining 60,675 annotated genes.
The number of reads (counts) for each gene was determined using HTSeq python package (version 0.9.0)
Between-lane normalization from EDASeq R package (version 2.18.0) was performed to force the upper quartile of reads in each lane to be the same.
Normalized data not available for five samples that did not not pass QC (PBMC_A_g_09, CD14_E_g_32, CD14_E_g_39, CD4_A_m_63, CD4_E_g_32).
Genome_build: GrCh38 (v83)
Supplementary_files_format_and_content: Raw read counts; normalized counts

molecule: total RNA

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Paque™ (GE healthcare life Sciences, Little Chalfont, United Kingdom). The PBMCs were subsequently sorted using Magnetic Cell Isolation and Cell Separation (AutoMACS Pro 360; Miltenyi Biotec, Bergisch Gladbach, Germany), positively selected for monocytes using CD14 MicroBeads, human, and negatively selected for CD4+ T cells using the CD4+ T Cell Isolation Kit, human (both from Miltenyi Biotec), according to the manufacturer’s protocol. RNA was extracted using the RNeasy Mini Kit (Qiagen) and tested for quantity and purity by Nanodrop (Thermo Scientific) and quality by RIN-value with Agilent 2100 Bioanalyzer (Agilent technologies, Inc., Santa Clara, Ca, USA). All Samples were aliquoted and stored per 1.5-2.0 µg at -80°C until use.
Total RNA was sent to GenomeScan B.V. (Leiden, Netherlands) for library preparation and sequencing. Before sequencing, the RNA sample preparation was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s protocol. Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed.

tag: sequencingid

tag: cell type

value: CD4+ T cells

tag: Sex

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: good

tag: height

value: stopped

value: Positive


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD007_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOs

value: male

tag: strain


title: BRD3162-WCE_ChIP-seq

source_name: Colon tumor

value: Colon tumor


title: 2304B-08-6B

type: genomic

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

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

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

data_processing:
R 3.4.2, minfi 1.24
Unmethylated and methylated signal intensities and detection p-value
normalized Average Beta by minfi stratified quantile normalization, cross-reactionary probes and probes with bad quality were removed

label: Cy3, Cy5

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Whole blood was collected for session 1 (28 subjects) at pre exposure, session 2 (31 subjects) at both pre- and post- exposure, using PAXgene blood DNA tubes and stored at -80˚C. Genomic DNA was isolated using PAXgene Blood DNA kit

treatment_protocol: Subjects went throught a 3-day explosive breaching training course where they were exposed to controlled, low-level blast

value: Whole blood

tag: session

value: Session 1 (site 8)

tag: time

value: post

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD006_indexed


title: CD4_A_m_49

value: Adalimumab

value: moderate

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD4_E_n_38

tag: sequencingid

tag: cell type

tag: Sex

value: m

tag: disease state

tag: age

tag: studysubjectid

value: no

value: never


title: BRD3162-K27Ac_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: CD4_A_n_37

value: CD4+ T cells

tag: drug

tag: response

tag: height


title: 2304B-08-5B

tag: session

tag: time

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD004_indexed

tag: brain region

tag: strain


title: 2304B-08-7B


title: BRD3162-CTCF_ChIP-seq


title: 2304B-08-4B


title: CD4_A_g_36

tag: sequencingid

tag: cell type

value: f

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD4_E_g_35

tag: Sex

tag: disease state

tag: age

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: good

value: stopped


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD012_indexed

tag: brain region

value: MOs

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C2_AD001_indexed

tag: strain


title: 2304B-08-2B

tag: tissue

value: Whole blood

tag: session

tag: time

tag: tbi

tag: breaching history


title: 323_colon2 [re-analysis]

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
323-AS-2_S2
reanalysis of GSM3131536

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis.
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: colon

growth_protocol: primary cells/cell line mix

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNAse dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

tag: mouse strain


title: 323_colon3 [re-analysis]

description:
323-AS-3_S3
reanalysis of GSM3131537


title: wt+antibiotics2

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods (the filtering code available at: https://github.com/KenLauLab/scRNAseqQC).
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: wt+antibiotics

growth_protocol: primary cells

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

treatment_protocol: Microbiome depletion was performed by pre-treatment of Lrig1CreERT2/+;Atoh1fl/fl animals with a broad-spectrum antibiotic cocktail containing kanamycin (4.0 mg/ml), metronidazole (2.15 mg/ml), gentamicin (0.35 mg/ml), colistin sulfate (8500 U/ml), and vancomycin (0.45 mg/ml) in their drinking water for seven days prior to tamoxifen treatment. Mid-dose antibiotics and low-dose antibiotics were 0.75x and 0.25x of the original 1x concentration, respectively. Following tamoxifen administration, Lrig1CreERT2/+;Atoh1fl/fl received either standard or antibiotic-supplemented drinking water for an additional fourteen days.

tag: strain background

tag: genotype/variation

value: wild type

tag: treatment

value: antibiotics

value: terminal ileum

tag: cell type

value: primary epithelial cells


title: CD4_E_m_33

tag: sequencingid

tag: Sex

value: m

tag: disease state

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-1B

tag: tissue

tag: session

value: Session 1 (site 8)

tag: time

value: post

tag: age

tag: tbi

tag: breaching history


title: 2304B-08-37A

value: pre


title: 2304B-08-3B


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD010_indexed

tag: brain region

tag: strain


title: AtohKO+antibiotics2

source_name: AtohKO+antibiotics

tag: strain background

tag: genotype/variation

value: AtohKO

tag: treatment

tag: cell type


title: CD4_E_g_32

tag: sequencingid

value: CD4+ T cells

tag: Sex

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD008_indexed

value: MOs

tag: age


title: CD4_A_m_34

value: Adalimumab

value: yes

tag: anti-ccp

value: Negative

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-36A

tag: tissue

value: Whole blood

tag: session

tag: time

value: male

tag: tbi

tag: breaching history


title: AtohKO+antibiotics1

tag: strain background

tag: genotype/variation

tag: treatment

value: antibiotics

value: terminal ileum

tag: cell type

value: primary epithelial cells


title: CD4_E_n_31

tag: sequencingid

tag: Sex

value: m

tag: disease state

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: stopped

value: Positive


title: 2304B-08-35A

tag: tissue

value: Session 1 (site 8)

value: pre

tag: age


title: CD4_A_n_30

value: CD4+ T cells

value: rheumatoid arthritis (RA)

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD004_indexed

tag: brain region

value: MOs

tag: strain


title: TNFdARE3

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods  (the filtering code available at: https://github.com/KenLauLab/scRNAseqQC).
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: TNFdARE_terminal ileum

tag: strain background

tag: genotype/variation

value: TNFdARE

tag: cell type


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD002_indexed

tag: Sex


title: 2304B-08-32A

tag: session

tag: time

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C3_AD001_indexed

tag: age


title: TNFdARE2

tag: tissue


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD001_indexed


title: CD4_A_g_28

tag: sequencingid

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: TNFdARE1

tag: strain background

tag: genotype/variation

tag: cell type


title: CD4_A_m_29

tag: Sex

value: moderate

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD4_E_n_27

tag: sequencingid

tag: age

value: Etanercept

value: never


title: 2304B-08-30A

tag: tissue

value: Whole blood

tag: session

tag: time

value: male

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD004_indexed

tag: brain region

tag: strain


title: CD4_E_n_26

tag: disease state

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Negative


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD007_indexed

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD007_indexed

tag: age


title: AtohKO2_reseq

source_name: AtohKO_terminal ileum

tag: strain background

tag: genotype/variation

value: AtohKO

tag: tissue

value: terminal ileum

tag: cell type

value: primary epithelial cells


title: 2304B-08-31A

tag: session

value: Session 1 (site 8)

tag: time

value: pre

tag: tbi

tag: breaching history


title: CD4_A_n_25

tag: sequencingid

value: CD4+ T cells

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: anti-ccp

value: Positive

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C1_AD006_indexed

tag: brain region

value: MOs

tag: Sex

tag: strain


title: wt+antibiotics1

tag: strain background

tag: genotype/variation

value: wild type

tag: treatment

value: antibiotics


title: 2304B-08-29A

tag: tissue

tag: session

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD010_indexed


title: 2304B-08-33A

tag: time

tag: tbi

tag: breaching history


title: 2304B-08-28A


title: CD4_A_g_24

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf


title: CD4_E_n_23

tag: Sex

value: Etanercept

value: no

value: yes

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-27A

tag: tissue

value: Whole blood

tag: session

tag: time

tag: age

value: male

tag: tbi


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD012_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_D10_AD001_indexed


title: wt7

source_name: wild type_terminal ileum

tag: strain background

tag: genotype/variation

value: terminal ileum

tag: cell type

value: primary epithelial cells


title: CD4_A_n_22

tag: sequencingid

value: CD4+ T cells

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight


title: wt6

tag: tissue


title: AtohKO3

value: AtohKO


title: CD4_A_g_21

tag: Sex

value: rheumatoid arthritis (RA)

value: never

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD4_A_n_20

tag: age


title: wt5

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type


title: 2304B-08-26A

tag: session

value: Session 1 (site 8)

tag: time

value: pre

tag: tbi

tag: breaching history


title: AtohKO2


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD007_indexed

tag: brain region

value: MOs

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD008_indexed


title: 2304B-08-23A

tag: tissue


title: CD4_A_m_19

tag: sequencingid

tag: Sex

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Negative


title: wt3

tag: strain background

tag: genotype/variation

tag: cell type


title: 2304B-08-22A

value: Whole blood

tag: session

tag: time

tag: age

tag: tbi


title: wt4

tag: tissue


title: CD4_E_n_18

tag: sequencingid

value: Etanercept

value: no

value: yes

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD004_indexed

tag: brain region

tag: Sex

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD006_indexed


title: AtohKO1

tag: strain background

value: AtohKO

value: terminal ileum

value: primary epithelial cells


title: 2304B-08-25A

tag: breaching history


title: wt2

tag: genotype/variation

tag: cell type


title: wt1


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD012_indexed


title: 2304B-08-20A

tag: session

tag: time


title: 2304B-08-21A

tag: age

tag: tbi


title: CD4_A_n_15

tag: sequencingid

value: CD4+ T cells

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

value: never

tag: weight

value: Positive


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD002_indexed

tag: brain region

value: MOs

tag: Sex

tag: strain


title: 2304B-08-19A

tag: tissue

value: Session 1 (site 8)

value: pre

tag: breaching history


title: J3_KO6

city: Montreal

first: Nathalie

last: Labrecque

state: QC

address: 5415, boul. de l’Assomption Montréal (Québec)

department: Microbiology and Immunology

country: Canada

institute: Université de Montréal

data_processing:
Illumina NextSeq was used for peak calling
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b
Gene expressions are obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries.
DESeq2 version 1.22.2 was used to normalize gene readcounts and compute differential expression between the various experimental conditions.  Sample clustering based on normalized log readcounts produces a hierarchy of samples. A principal component analysis is also used to validate that samples correlate as expected.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include readcounts values for each Sample

molecule: polyA RNA

source_name: CD8+ T cells (OT-I)

extract_protocol:
Day 3 in vivo activated OT-I (Nr4a3 deficient or sufficient; Viable_CD44hi_CD45_2+ CD8+ cells) and sorted directly in TRIzol were stored at -80˚C and then RNA was extracted usind a TRIzol protocol.
Library preparation was done with the KAPA RNA HyperPrep PolyA library preparation kit (Roche). RNA libraries were prepared for sequencing using 100ng of RNA

tag: activating condition

value: Day3_In vivo_activated_OT-I_CD44hi

tag: activation details

value: Adoptively transferred_OT-I_into B6.SJL_and then activated by Lm-OVA infection

tag: genotype

value: Nr4a3 KO OT-I


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD010_indexed

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C12_AD008_indexed


title: 2304B-08-17A

value: Whole blood

tag: session

tag: time

tag: tbi


title: CD4_A_n_14

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

value: no

value: stopped

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-12A

tag: tissue

tag: Sex

value: male

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD001_indexed

tag: brain region

tag: age

tag: strain


title: J3_KO5

tag: activating condition

tag: activation details

tag: genotype


title: J3_KO4


title: CD4_E_m_13

tag: sequencingid

tag: cell type

tag: disease state

value: Etanercept

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Negative


title: CD4_A_g_17

value: CD4+ T cells

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: good

value: never

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C11_AD002_indexed

tag: brain region

value: MOs

tag: Sex

tag: age

tag: strain


title: J3_WT6

tag: activating condition

value: Day3_In vivo_activated_OT-I_CD44hi

tag: activation details

tag: genotype

value: Nr4a3 WT OT-I


title: 2304B-08-24A

tag: tissue

tag: session

value: Session 1 (site 8)

tag: time

value: pre

tag: tbi

tag: breaching history


title: J3_WT5

value: Adoptively transferred_OT-I_into B6.SJL_and then activated by Lm-OVA infection


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD008_indexed


title: 2304B-08-11A

value: Whole blood


title: CD4_E_n_11

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive


title: 2304B-08-10A

tag: age

tag: Sex

value: male


title: CD4_A_m_16

value: Adalimumab

value: moderate

value: yes

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD012_indexed

tag: brain region

tag: strain


title: CD4_A_n_12

tag: sequencingid

tag: cell type

value: CD4+ T cells

value: m

value: rheumatoid arthritis (RA)


title: CD4_A_g_10

tag: disease state

tag: studysubjectid

value: good


title: 2304B-08-9A

tag: tissue

tag: session

tag: time

tag: tbi

tag: breaching history


title: J3_KO3

tag: activating condition

value: Day3_In vivo_activated_OT-I_CD44hi

tag: activation details

tag: genotype

value: Nr4a3 KO OT-I


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD006_indexed

value: MOs

tag: Sex

tag: age


title: 2304B-08-8A

value: Session 1 (site 8)

value: pre


title: J3_WT4

value: Adoptively transferred_OT-I_into B6.SJL_and then activated by Lm-OVA infection

value: Nr4a3 WT OT-I


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD010_indexed


title: J3_KO1


title: 2304B-08-7A

value: Whole blood


title: CD4_A_g_09

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD007_indexed

tag: brain region

value: male

tag: strain


title: 2304B-08-6A

tag: tissue

tag: session

tag: time

tag: tbi

tag: breaching history


title: CD4_E_m_07

tag: sequencingid

tag: cell type

tag: Sex

value: f

tag: disease state

tag: age

tag: studysubjectid

tag: drug

value: Etanercept

value: moderate

value: never


title: J3_WT3

tag: activating condition

tag: activation details

tag: genotype


title: CD4_A_n_08

value: CD4+ T cells

value: rheumatoid arthritis (RA)

value: Adalimumab

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 2304B-08-5A

tag: tissue

tag: session

value: Session 1 (site 8)

tag: time

tag: Sex

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD002_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: J3_WT2

tag: activating condition

value: Day3_In vivo_activated_OT-I_CD44hi

tag: activation details

value: Adoptively transferred_OT-I_into B6.SJL_and then activated by Lm-OVA infection

tag: genotype


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_C10_AD004_indexed


title: CD4_E_g_05

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: CD4_A_n_06

tag: Sex

value: yes

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD012_indexed

tag: brain region

tag: age

tag: strain


title: 2304B-08-3A

tag: tissue

value: Whole blood

tag: session

tag: time

value: pre

tag: tbi

tag: breaching history


title: J3_WT1

tag: activating condition

tag: activation details

tag: genotype

value: Nr4a3 WT OT-I


title: 2304B-08-4A

value: male


title: 2304B-08-2A


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD008_indexed


title: 2304B-08-1A


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD010_indexed


title: MS_12 [3-7275]

city: Chicago

first: John

last: Crispino

address: 300 Superior St

institute: Northwestern University

data_processing:
RNA-seq: Sequencing data was analyzed using the protocol by Anders et al.(Anders et al., 2013). Briefly, raw reads were aligned by TopHat2 (Kim et al., 2013). Aligned reads were counted by HTSeq (Anders et al., 2015). Data normalization and differential gene expression were done by DESeq2 (Love et al., 2014). Clustering and PCA were performed in matlab. GSEA(Subramanian et al., 2005) was used to find groups of enriched genes between different groups of samples.
Genome_build: hg38
Supplementary_files_format_and_content: CountsMatrix.txt

growth_protocol: All cells were grown in RPMI supplemented with IL-3

extract_protocol:
RNA was extracted using the Direct-Zol RNA MIniPrep Kit on MDS-L cell populations described above that were harvested and immediately lysed in Trizol.
To generate RNA sequencing libraries, RNA quality was determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of > 7 and quantified using Qubit. Directional mRNA libraries were prepared using Illumina TruSeq mRNA Sample Preparation Kits per manufacturer’s instructions. Briefly, polyadenylated mRNAs were captured from total RNA using oligo-dT selection. Next, samples were converted to cDNA by reverse transcription, and each sample was ligated to Illumina sequencing adapters containing unique barcode sequences. Barcoded samples were then amplified by PCR and the resulting cDNA libraries by quantified using qPCR. CUT&RUN-sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina complemented with NEBNext Multiplex Oligos for Illumina. The dA-tailing temperature was decreased to 50oC, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. Next, 2.1x AMPure XP beads (Beckman) were added for cleanup of adaptor-ligated DNA without size selection. After PCR amplification, the reaction was cleaned up with AMPure XP beads. Libraries were validated using the Agilent High Sensitivity DNA Kit on Bioanalyzer.

treatment_protocol: No treatment

tag: cell type

value: MDSL cells

tag: condition

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 4 cDNA


title: MS_11 [3-6263]

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA


title: CD4_A_m_02

tag: sequencingid

value: CD4+ T cells

tag: Sex

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

value: never

tag: weight

tag: rf

tag: anti-ccp

value: Positive


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD007_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: 2304B-03-27A

tag: tissue

tag: session

value: Session 1 (site 3)

tag: time

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD002_indexed

tag: Sex


title: 2304B-03-28A


title: MS_09 [3-Lenti]

tag: cell type

tag: condition

value: parent MDS-L cells expressing Cas9 - effectively a control


title: MS_07 [2-6263]


title: CD14_A_g_80

description:
rawReadsData.csv
Counts_Normalization_cd14.csv

tag: sequencingid

value: Monocytes

value: m

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: good

value: stopped

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD4_E_n_01

tag: age

value: Etanercept

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp


title: 2304B-03-26A

tag: tissue

value: Whole blood

tag: session

tag: time

value: pre

tag: Sex

value: male

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B9_AD001_indexed

tag: brain region

tag: strain


title: 2304B-03-25A


title: CD14_E_m_79

tag: sequencingid

tag: cell type

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

value: yes

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD012_indexed

tag: age


title: MS_05 [2-Lenti]

value: MDSL cells

tag: condition


title: CD4_E_n_03

value: CD4+ T cells

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive

tag: anti-ccp

value: Negative

tag: leucocytencount

tag: trombocytencount


title: 2304B-03-24A

tag: tissue

tag: session

value: Session 1 (site 3)

tag: time

tag: Sex

tag: tbi

tag: breaching history


title: MS_06 [2-910]

tag: cell type

value: MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout


title: MS_10 [3-910]


title: CD4_A_n_04

tag: sequencingid

value: m

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD010_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: CD14_A_g_78

value: Monocytes

value: f

value: Adalimumab

value: good

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: 2304B-03-23A

tag: tissue

value: Whole blood

tag: session

tag: time

tag: Sex

tag: tbi

tag: breaching history


title: CD14_E_n_77

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: no

value: never

tag: hemoglobinecount


title: CD14_E_n_76

value: rheumatoid arthritis (RA)

tag: age

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: 2304B-03-22A

tag: tissue

tag: session

value: pre

value: male


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD007_indexed

tag: brain region

tag: Sex

tag: strain


title: MS_03 [1-6263]

value: MDSL cells

tag: condition

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA


title: MS_04 [1-7275]

tag: cell type

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 4 cDNA


title: MS_08 [2-7275]


title: CD14_E_n_75

tag: sequencingid

tag: disease state

value: Positive

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD006_indexed

tag: age


title: 2304B-03-20A

value: Session 1 (site 3)

tag: time

tag: tbi

tag: breaching history


title: CD14_A_n_74

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

value: Negative

tag: hemoglobinecount


title: MS_01 [1-Lenti]

tag: cell type

tag: condition

value: parent MDS-L cells expressing Cas9 - effectively a control


title: 2304B-03-21A

tag: tissue

tag: session

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD002_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD008_indexed


title: MS_02 [1-910]

value: MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B8_AD001_indexed


title: CD14_E_m_72

tag: sequencingid

value: Monocytes

value: f

tag: disease state

value: moderate

value: stopped

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: 2304B-03-19A

value: Whole blood

tag: time

tag: tbi

tag: breaching history


title: CD14_E_n_71

value: m

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: hemoglobinecount


title: 2304B-03-18A

tag: tissue

tag: session

value: pre

tag: age

tag: Sex

value: male


title: Xrcc4-/- p53-/- Released rep6

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
library strategy: linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS)
Sequencing reads in FASTQ files were decoded and adaptor sequence trimmed using by ea-utils tool. Paired-end reads with less than 20 nucleotides bait sequence in the 5’ end of read1 were filtered out. Paired-end reads were mapped to the mouse mm9 reference genome using BWA mem with default settings.
Paired-end reads with a mapping quality less than 10 and multiple mapped reads were filtered out. Mapped reads were then further analyzed using read2.
Among non-split mapped, those with more than three quarters length of mapped sequence were defined as mapped with >=75% sequence reads. Among them, those that were not split mapped and mapped within the IgkJ4 bait to IgkJ2 regions were defined as germline.
The rest of non-germline sequence and read2 split mapped with breakpoint sequence with were further classified according to prey genomic location: trans-joins with antigen receptor (AgR) genes (Igh, Igl, Tcra, Tcrd, Tcrg, Tcrb), cis-joins with Igk V region and trans-joins with non AgR loci (else).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files contain all captured prey sequence with both cis-rearrangement and trans-rearrangement

source_name: Xrcc4-/- p53-/- Released

extract_protocol:
Genomic DNA was extracted with proteinase K digestion overnight and phenol/chloroforme extraction.
Briefly, DNA was purified and sonicated (Bioruptor, Diagenode) into 500–1,000 bp fragments. LAM-PCR was performed using bait primer coupled with biotin, 1U Phusion polymerase (Thermo Scientific) and the following cycles: 1x (98 °C for 120 s); 80x (95 °C for 30 s; 58 °C for 30 s; 72 °C for 90 s); and 1x (72 °C for 360 s). Biotinylated PCR fragments were incubated with MyOne streptavidin C1 beads (Invitrogen) and rotated for 4 h in 1 M NaCl and 5 mM EDTA buffer at room temperature. After washes with B&W buffer (1 M NaCl; 5 mM Tris-HCl, 0.5 mM EDTA), on-bead ligation was performed using 2.5 mM bridge adaptor, 1 mM hexamine cobalt chloride (Sigma), 15 U T4 DNA ligase (Promega), 15% PEG-8000 (Sigma) and the following cycles: 25 °C for 1 h; 22°C for 2 h; and 16°C O/N. After washing three times with B&W buffer (1 M NaCl, 5 mM Tris-HCl (pH 7.4) and 0.5 mM EDTA (pH 8.0)), the on-bead ligated products were subjected to nested PCR using Phusion polymerase, locus-specific and adaptor primers and the following cycles: 1x (95 °C for 300 s); 15x (95 °C for 60 s; 72 °C 60 s); and 1x (72 °C 600 s). Blocking digestion was then performed with I-SceI for 1 h to remove uncut germline DNA. After purification using a Qiagen column, recovered DNA was PCR-amplified using Illumina primers, Phusion polymerase and the following cycles: 1x (95°C for 180 s); 10x (95°C for 30 s; 60°C for 30 s; 72°C for 60 s); and 1x (72°C for 360 s). The tagged PCR products were size-selected for DNA fragments between 500–1000 bp on a 1% agarose gel and purified using a Qiagen column before loading onto an Illumina Miseq machine for paired-end 2X250 bp sequencing.

treatment_protocol: 1 million/ml v-abl pro-B cells were treated with 3uM v-abl kinase inhibitor (STI571) for 3 days. After washing off inhibitor, cells were released into fresh medium.

tag: genotype/cell type

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

tag: treatment

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD012_indexed

tag: brain region

tag: strain


title: Xrcc4-/- p53-/- Released rep5

description: linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS)


title: CD14_E_g_69

tag: sequencingid

tag: cell type

tag: disease state

value: good

value: Positive

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD008_indexed

value: MOs


title: 2304B-03-17A

value: Session 1 (site 3)

tag: time

tag: tbi

tag: breaching history


title: CD14_A_m_70

value: Monocytes

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: hemoglobinecount


title: CD14_E_n_68

tag: sequencingid

tag: Sex

value: f

tag: age

value: Negative


title: Xrcc4-/- p53-/- Released rep3

tag: genotype/cell type

tag: treatment


title: Xrcc4-/- p53-/- Released rep4


title: 2304B-03-16A

tag: tissue

value: Whole blood

tag: session


title: CD14_A_m_73

tag: cell type

tag: disease state

value: moderate

value: yes

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD010_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD007_indexed


title: CD14_E_n_67

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight


title: 2304B-03-14A

tag: time

value: pre

tag: age

tag: Sex

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD006_indexed

value: male


title: Xrcc4-/- p53-/- ABLKi rep3

source_name: Xrcc4-/- p53-/- ABLKi

tag: genotype/cell type

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

tag: treatment

value: v-abl kinease inhibitor STI571(ABLKi) for 3 days


title: Xrcc4-/- p53-/- Released rep2

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: Xrcc4-/- p53-/- Released rep1


title: 2304B-03-13A

tag: tissue

tag: session


title: Xrcc4-/- p53-/- ABLKi rep2


title: CD14_E_n_66

tag: sequencingid

tag: cell type

tag: disease state

value: no

value: stopped

tag: rf

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD14_E_n_65

value: Monocytes

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight


title: 2304B-03-12A

value: Session 1 (site 3)

tag: time

tag: age

tag: Sex

tag: tbi

tag: breaching history


title: 2304B-03-11A

tag: tissue

tag: session


title: SW480-2_RNA-seq

data_processing:
RNA-seq data was mapped to the reference transcriptome (hg19) using salmon (Patro et al, 2017) and differential expression analyses were done as described in Bioconductor’s RNA-seq workflow by Love et al., 2015.
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

source_name: Cell line

extract_protocol: Whole RNA was extracted using the QIAGEN RNeasy kit according to the manufacturer’s protocol. For RNA-seq library preparation, Poly(A) RNA was enriched using magnetic oligo(dT)-beads (Life Technologies) and then ligated to RNA adaptors for sequencing. RNA-seq was performed with two biological replicates per colon cancer line and in singlicate for tumor samples. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.

tag: sample type

value: Cell line

tag: biological sample


title: 2304B-03-20A


title: CD14_E_n_71

tag: sequencingid

tag: cell type

value: m

tag: disease state

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD012_indexed

tag: brain region

value: MOs

tag: strain


title: RKO-2_RNA-seq


title: SW480-1_RNA-seq


title: 2304B-03-15A

value: Whole blood

tag: time

tag: age


title: CD14_A_m_70

tag: Sex

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: trombocytencount


title: 2304B-03-19A

tag: tissue

tag: session

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD010_indexed


title: 2304B-03-16A


title: CD14_E_n_67

tag: sequencingid

tag: cell type

value: f

tag: disease state

value: rheumatoid arthritis (RA)

value: Etanercept

value: yes

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD008_indexed

tag: brain region

tag: Sex

value: male

tag: age

tag: strain


title: 2304B-03-18A

tag: time

value: pre


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD004_indexed


title: Xrcc4-/- p53-/- ABLKi rep1

tag: genotype/cell type

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

tag: treatment

value: v-abl kinease inhibitor STI571(ABLKi) for 3 days


title: MGH5328_RNA-seq

tag: sample type

value: Colon tumor

tag: biological sample


title: CD14_E_n_68

value: Monocytes

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

value: Negative

value: Positive

tag: trombocytencount


title: CD14_E_n_66

tag: sequencingid

tag: cell type

tag: disease state

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B7_AD002_indexed

tag: brain region

value: MOs

tag: Sex

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD004_indexed


title: MGH3535-WCE_ChIP-seq

data_processing:
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

extract_protocol: ChIP-seq was performed as described previously (Liau et al., 2016).  In brief, crosslinked cells were lysed and DNA was sheared to between 400 and 2,000 base pair fragments.  Antibodies were as follows: CTCF (Cell signaling #3418), H3K27ac (Active Motif #39133), H3K9me3 (Abcam #8898), H3K27me3 (Cell Signaling #97335).  ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3′ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 38-base paired-end reads on an Illumina NextSeq500 instrument.

tag: sample type

tag: biological sample


title: MGH8416_RNA-seq


title: CD14_A_n_64

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height


title: 2304B-03-14A

tag: tissue

value: Whole blood

tag: session

value: Session 1 (site 3)

tag: time

tag: tbi

tag: breaching history


title: 2304B-03-17A


title: CD14_E_n_65

tag: sequencingid

tag: cell type

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 2304B-03-13A

tag: age

tag: Sex


title: MGH3535-K36me3_ChIP-seq

tag: sample type

tag: biological sample


title: RKO-1_RNA-seq

value: Cell line


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD012_indexed

tag: brain region

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD002_indexed


title: CD14_E_g_69

value: m

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: good

tag: height

tag: leucocytencount


title: 2304B-03-11A

tag: tissue

tag: session

tag: time

value: pre

tag: tbi

tag: breaching history


title: MGH29208-WCE_ChIP-seq

value: Colon tumor


title: MGH29208-K27me3_ChIP-seq


title: CD14_A_m_63

tag: sequencingid

tag: cell type

value: Monocytes

tag: disease state

value: moderate

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD006_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: MGH28891-WCE_ChIP-seq

tag: sample type

tag: biological sample


title: CD14_E_n_62

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

value: never

value: Negative

tag: leucocytencount


title: CD14_E_m_61

tag: sequencingid

tag: cell type

tag: disease state

tag: alcoholuseunitsweek

value: Positive


title: MGH2834-WCE_REP4_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD008_indexed

value: MOs


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD007_indexed


title: 2304B-03-9A

tag: tissue

value: Whole blood

tag: session

value: Session 1 (site 3)

tag: time

tag: tbi

tag: breaching history


title: 2304B-03-10A

tag: age

tag: Sex


title: 2304B-03-8A


title: CD14_A_n_60

value: rheumatoid arthritis (RA)

value: Adalimumab

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: MGH2834-K36me3_ChIP-seq

tag: sample type

tag: biological sample


title: MGH28891-K36me3_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD006_indexed

tag: brain region

value: male

tag: strain


title: CD14_A_g_59

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: leucocytencount


title: CD14_A_n_58

tag: Sex

tag: age

tag: weight

tag: rf


title: 2304B-03-12A

tag: tissue

tag: session

tag: time

value: pre

tag: tbi

tag: breaching history


title: MGH2834_RNA-seq

tag: sample type

value: Colon tumor

tag: biological sample


title: 2304B-03-6A


title: CD14_E_m_57

tag: sequencingid

tag: cell type

value: Monocytes

value: m

tag: disease state

tag: studysubjectid

value: Etanercept

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: LS174T-2_RNA-seq

value: Cell line


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B2_AD001_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD010_indexed


title: 2304B-03-7A

tag: tissue

tag: session


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD002_indexed


title: CD14_E_n_56

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: leucocytencount


title: LS174T-1_RNA-seq

tag: sample type

tag: biological sample


title: 2304B-03-4A

tag: time

tag: tbi

tag: breaching history


title: 2304B-03-5A

tag: Sex


title: CD14_E_g_55

tag: sequencingid

tag: cell type

tag: disease state

tag: age

tag: studysubjectid

value: good

value: never

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: HCT116-DMSO-24h-2_RNA-seq

tag: treatment

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: HCT116-DMSO-24h-1_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD001_indexed

tag: brain region

value: MOs

tag: strain


title: CD14_E_n_54

value: rheumatoid arthritis (RA)

tag: drug

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive

tag: leucocytencount


title: 2304B-03-2A

tag: tissue

value: Whole blood

tag: session

value: Session 1 (site 3)

tag: time

tag: Sex

value: male

tag: tbi

tag: breaching history


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B1_AD004_indexed

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD008_indexed


title: HCT116-5AZA-24h-1_RNA-seq

tag: sample type

tag: biological sample

tag: treatment


title: CD14_E_m_53

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: moderate

value: stopped

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 2304B-03-1A

tag: tissue

tag: session

value: pre


title: HCT116-5AZA-24h-2_RNA-seq


title: 2304B-03-3A

tag: time

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD004_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD006_indexed

tag: age


title: HCT116-2_RNA-seq

tag: sample type

tag: biological sample


title: CD14_E_n_52

tag: sequencingid

value: Monocytes

value: m

value: Etanercept

tag: response

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD001_indexed


title: HCT116-1_RNA-seq

value: Cell line


title: CD14_E_g_50

tag: cell type

tag: disease state

tag: studysubjectid

tag: drug

value: good

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD012_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: FHC-2_RNA-seq

tag: sample type

tag: biological sample


title: CD14_A_m_49

tag: sequencingid

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD010_indexed

value: MOs


title: FHC-1_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD010_indexed


title: BRD3409N-K36me3_ChIP-seq

value: Colon tumor


title: CD14_E_g_48

tag: cell type

value: rheumatoid arthritis (RA)

tag: weight

tag: rf

value: Positive

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD007_indexed


title: CD14_E_g_47

tag: disease state

tag: studysubjectid

tag: drug

tag: anti-ccp


title: BRD3187N_RNA-seq

value: Normal colon


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD006_indexed

tag: brain region

tag: Sex

value: male


title: CD14_A_g_46

tag: age

value: never

value: Negative

tag: hemoglobinecount

tag: trombocytencount


title: BRD3187_RNA-seq

tag: sample type

tag: biological sample


title: CD14_E_g_51

tag: sequencingid

value: f

tag: response

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD008_indexed

tag: strain


title: CD14_A_n_45

tag: cell type

value: no

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf


title: BRD3179_RNA-seq


title: CD14_E_g_44

value: Monocytes

tag: disease state

tag: studysubjectid

tag: drug

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B12_AD012_indexed

tag: brain region

tag: Sex

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD002_indexed


title: CD14_E_n_43

value: Etanercept

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: BRD3174_RNA-seq

tag: sample type

tag: biological sample


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD001_indexed

tag: strain


title: BRD3162N-WCE_ChIP-seq


title: CD14_A_n_42

tag: sequencingid

tag: cell type

tag: response

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD012_indexed


title: BRD3162N-K36me3_ChIP-seq


title: BRD3162_RNA-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B11_AD004_indexed


title: CD14_A_n_41

tag: disease state

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: CD14_E_n_40

tag: studysubjectid

tag: drug

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD010_indexed

tag: brain region

tag: Sex

tag: age


title: CD14_E_g_39

tag: anti-ccp

tag: hemoglobinecount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD008_indexed

tag: strain


title: right colon CD

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

extract_protocol:
Human epithelial cell suspensions were obtained by EDTA extraction and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

value: Crohn's Disease (remission with mild disease index)

tag: tissue

value: colon

tag: biopsy

value: right colonic biopsy


title: left colon CD

value: left colonic biopsy


title: CD14_E_n_38

tag: sequencingid

tag: cell type

value: m

tag: response

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD006_indexed

value: MOs


title: MGH8416-WCE_REP2_ChIP-seq

value: Colon tumor

tag: biological sample

tag: treatment


title: CD14_A_n_37

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Adalimumab

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive


title: MGH8416-WCE_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD002_indexed

tag: brain region

tag: Sex

value: male

tag: age


title: MGH8416-K9me3_ChIP-seq

tag: tissue


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD007_indexed

tag: strain


title: CD14_E_g_35

tag: sequencingid

value: good

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD001_indexed


title: CD14_A_m_34

tag: cell type

tag: response

value: moderate

tag: height

value: yes


title: MGH8416-K27me3_ChIP-seq

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_B10_AD004_indexed


title: CD14_A_g_36

value: Monocytes

value: f

tag: disease state

tag: studysubjectid

tag: drug

tag: alcoholuseunitsweek

value: stopped

tag: weight


title: CD14_E_m_33

tag: Sex

tag: age

value: Etanercept

tag: rf


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD010_indexed

tag: brain region

tag: strain


title: MGH8416-K27Ac_ChIP-seq

tag: tissue


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD007_indexed


title: CD14_E_g_32

tag: sequencingid

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: MGH5328-CTCF_ChIP-seq

tag: biological sample

tag: treatment


title: MGH5328-K27Ac_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD008_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD006_indexed


title: CD14_A_n_30

tag: cell type

tag: disease state

tag: studysubjectid

tag: response

value: no

tag: height


title: CD14_E_n_31

tag: Sex

tag: age

tag: drug

tag: alcoholuseunitsweek

tag: weight


title: CD14_A_m_29

tag: sequencingid

tag: rf


title: MGH5238-WCE_ChIP-seq

tag: tissue


title: MGH2834-WCE_REP2_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD002_indexed

tag: brain region

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A9_AD001_indexed


title: CD14_A_g_28

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: MGH2834-WCE_ChIP-seq

tag: biological sample

tag: treatment


title: DNA methylation_Etanercept_moderateResponse_79

hyb_protocol: Genome-wide DNA methylation profiling was performed at the GenomeScan B.V (Leiden, Netherlands). DNA was subjected to quality control analysis using a PicoGreen assay (ThermoFisher) and bisulfite treated with an EZ DNA Methylation Kit (Zymo Research) before being subjected to whole genome amplification and subsequently hybridized to the Infinium MethylationEPIC BeadChip array (Illumina).

scan_protocol: Beadchip images were scanned on the iScan system

data_processing:
Infinium MethylationEPIC BeadChip images were scanned on the iScan system and the data quality was checked using minfi (version 1.30.0) R package35 with default settings, which shows every sample has a high quality of data. Raw data were read by ChAMP package (version 2.14.0) from IDAT files and converted to beta values, which is the ratio of methylated (M) intensity to the sum of methylated and unmethylated (U) intensity, i.e. β= M/(M+U +100). Probes that meet any one of the following criteria were excluded for further analyses: (1) probes with detection p-value (detPcut) > 0.01; (2) probes with bead count < 3 in at least 5% of samples; (3) probes targeting non-CpG positions; (4) probes targeting SNP sites; and (5) probes that aligned to multiple locations as described [36]. Finally, 735,297 probes were retained. Beta-mixture quantile normalization (BMIQ) was then applied to beta values to reduce the bias between Type I and Type II probes, followed by identification of differential methylation positions (DMPs) between responders and non-responders to either ADA or ETN, using the same ChAMP package.
MatrixSignal.csv:  Unmethylated and methylated signal intensities
MatrixProcessed_Raw.csv:  Average Beta.
The filtered and normalized (Beta-mixture quantile normalization) average Betas are represented in the Sample Data table.

label: Cy5 and Cy3

extract_protocol: DNA was isolated from frozen PBMCs using a Qiacube (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s protocols.

tag: disease state

tag: cell type

value: PBMC

value: Etn

tag: response

tag: height

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg


title: CD14_E_n_27

tag: sequencingid

tag: Sex

tag: age

tag: studysubjectid

tag: drug

tag: alcoholuseunitsweek

value: never

tag: weight

tag: rf


title: DNA methylation_Adalimumab_goodResponse_80

value: rheumatoid arthritis (RA)

value: m

value: Ada

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Adalimumab_goodResponse_78

tag: disease state

tag: cell type


title: CD14_E_n_26

tag: response

tag: height

tag: anti-ccp


title: MGH2834-K9me3_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD010_indexed

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: MGH2834-K27Ac_ChIP-seq


title: CD14_A_n_25

tag: sequencingid

tag: studysubjectid

tag: drug

value: Adalimumab

tag: alcoholuseunitsweek

tag: weight

value: Negative

value: Positive


title: DNA methylation_Adalimumab_noResponse_74

tag: disease state

value: f

tag: smokingstatus

value: yes

tag: rfposneg

value: n

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD012_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD008_indexed


title: DNA methylation_Etanercept_noResponse_76

tag: cell type

tag: response

value: no

tag: height


title: CD14_A_g_24

value: Monocytes

tag: Sex

tag: age

value: good

value: stopped

tag: rf

tag: anti-ccp


title: DNA methylation_Etanercept_noResponse_75

value: PBMC

tag: drug

value: Etn

value: never

value: y


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD007_indexed

tag: brain region

tag: strain


title: DNA methylation_Etanercept_moderateResponse_72

tag: disease state

value: rheumatoid arthritis (RA)

value: moderate

tag: alcoholuseunitsweek

tag: weight


title: DNA methylation_Etanercept_noResponse_67

tag: smokingstatus

tag: rfposneg

tag: anticcpposneg


title: MGH1904-WCE_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: DNA methylation_Adalimumab_noResponse_64

tag: cell type

value: Ada

tag: response

tag: height

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD14_E_n_23

tag: sequencingid

tag: Sex

tag: age

tag: studysubjectid

tag: drug

value: Etanercept

tag: rf

tag: anti-ccp


title: DNA methylation_Etanercept_noResponse_71

tag: disease state

value: m

tag: smokingstatus

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

tag: anticcpposneg


title: DNA methylation_Etanercept_noResponse_65

tag: cell type

value: f

tag: response

tag: height


title: DNA methylation_Adalimumab_moderateResponse_63

value: yes

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: CD14_A_n_22

tag: sequencingid

tag: Sex

tag: age

value: Adalimumab

value: Positive


title: DNA methylation_Etanercept_noResponse_68

tag: drug

value: no

value: n


title: DNA methylation_Etanercept_moderateResponse_61


title: DNA methylation_Adalimumab_moderateResponse_70

value: stopped


title: HCT116-DMSO-24h-WCE-2_ChIP-seq

tag: tissue

value: HCT116 Cell line

tag: biological sample

tag: treatment

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: DNA methylation_Adalimumab_moderateResponse_73

tag: disease state

value: PBMC

tag: smokingstatus

tag: alcoholuseunitsweek


title: DNA methylation_Etanercept_noResponse_66

value: Etn

tag: weight

tag: rfposneg

value: y

tag: anticcpposneg


title: CD14_A_g_21

tag: cell type

value: Monocytes

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: response

value: good

tag: height

value: never

tag: rf

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD012_indexed

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: DNA methylation_Etanercept_noResponse_77

value: f

tag: drug

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Adalimumab_goodResponse_59

tag: disease state

value: Ada

tag: smokingstatus

tag: alcoholuseunitsweek

tag: weight


title: CD14_A_n_20

tag: sequencingid

tag: cell type

tag: studysubjectid

value: Adalimumab

value: yes

value: Positive


title: CD14_A_m_19

tag: response

value: moderate

tag: height

tag: rf

value: Negative


title: BRD3328N-WCE_ChIP-seq

tag: tissue

value: Normal colon

tag: biological sample

tag: treatment


title: DNA methylation_Adalimumab_noResponse_60

value: PBMC

tag: Sex

value: m

tag: age

tag: drug

value: no

tag: rfposneg

value: n

tag: anticcpposneg


title: DNA methylation_Etanercept_goodResponse_69

tag: disease state

value: rheumatoid arthritis (RA)

value: Etn

tag: smokingstatus

value: stopped

value: y

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Etanercept_noResponse_62

tag: cell type

value: never

tag: alcoholuseunitsweek

tag: weight


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD007_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: DNA methylation_Adalimumab_noResponse_58

value: f

value: Ada

tag: response

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD010_indexed

tag: Sex


title: CD14_E_n_18

tag: sequencingid

value: Monocytes

tag: age

tag: studysubjectid

value: Etanercept

value: yes

tag: rf

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD001_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD006_indexed


title: BRD3328N-CTCF_ChIP-seq

tag: tissue

value: Normal colon

tag: biological sample

tag: treatment


title: MGH1904-CTCF_ChIP-seq

value: Colon tumor


title: MGH2834-CTCF_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A8_AD004_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD004_indexed


title: BRD3187N-WCE_ChIP-seq


title: BRD3187-WCE_REP2_ChIP-seq


title: DNA methylation_Etanercept_moderateResponse_57

tag: disease state

value: PBMC

value: m

tag: drug

value: moderate

tag: smokingstatus

tag: rfposneg

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: HCT116-DMSO-24h-K27me3_ChIP-seq

value: HCT116 Cell line

value: 5-azacytidine was obtained from SelleckChem (S1782) and HCT116 cells were cultured in the presence of 5 uM or 1:2000 DMSO control.  Cells were plated in media containing 5-aza or DMSO and harvested at 24 h and 7 days.  Media was refreshed with fresh 5-aza every 2nd day for the 7 day culture.


title: BRD3187N-K27me3_ChIP-seq


title: DNA methylation_Etanercept_noResponse_54

value: rheumatoid arthritis (RA)

tag: cell type

tag: Sex

value: Etn

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight


title: CD14_A_g_17

tag: sequencingid

tag: age

tag: studysubjectid

value: Adalimumab

value: good

value: never

tag: rf

value: Negative

tag: anti-ccp


title: DNA methylation_Etanercept_noResponse_56

tag: disease state

value: f

tag: drug

tag: smokingstatus

value: stopped

value: y


title: DNA methylation_Etanercept_moderateResponse_53

tag: rfposneg

tag: anticcpposneg

tag: hemoglobinecount


title: CD14_A_n_15

tag: cell type

value: Monocytes

value: Positive

tag: leucocytencount

tag: trombocytencount


title: CD14_E_m_13

tag: Sex

value: Etanercept

tag: response

tag: height


title: BRD3187-WCE_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: CD14_A_m_16

tag: sequencingid

tag: age

tag: studysubjectid

value: moderate

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD001_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A7_AD002_indexed


title: DNA methylation_Etanercept_goodResponse_55

tag: disease state

value: rheumatoid arthritis (RA)

tag: cell type

value: PBMC

tag: drug

value: Etn

tag: smokingstatus

tag: rfposneg

value: n

tag: anticcpposneg

tag: hemoglobinecount


title: DNA methylation_Etanercept_noResponse_52

tag: Sex

value: m

tag: response

value: no

tag: height

tag: leucocytencount

tag: trombocytencount


title: CD14_E_n_11

tag: sequencingid

value: f

tag: age

tag: studysubjectid

tag: alcoholuseunitsweek

value: never

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD007_indexed

tag: brain region

tag: strain


title: BRD3187-K9me3_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: CD14_A_n_14

tag: cell type

tag: disease state

tag: drug

value: Adalimumab

value: stopped

tag: weight

tag: rf


title: BRD3179-WCE_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD012_indexed

tag: Sex


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD002_indexed


title: BRD3187-K27me3_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD008_indexed


title: DNA methylation_Etanercept_goodResponse_51

tag: response

value: good

tag: height

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Adalimumab_moderateResponse_49

tag: age

value: Ada

tag: alcoholuseunitsweek


title: BRD3179N-WCE_REP3_ChIP-seq

tag: tissue

value: Normal colon

tag: biological sample

tag: treatment


title: CD14_A_n_12

tag: sequencingid

tag: cell type

value: Monocytes

tag: disease state

tag: studysubjectid

tag: drug

value: yes

value: Positive

tag: anti-ccp


title: BRD3187-K27Ac_ChIP-seq

value: Colon tumor


title: BRD3179N-WCE_REP2_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD006_indexed

tag: brain region

value: MOs

tag: Sex

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD001_indexed


title: CD14_A_g_10

value: rheumatoid arthritis (RA)

tag: response

tag: height

tag: weight

tag: rf

tag: hemoglobinecount


title: BRD3179N-WCE_ChIP-seq

tag: tissue


title: CD14_E_m_07

tag: age

value: Etanercept

value: moderate

tag: alcoholuseunitsweek

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD012_indexed


title: DNA methylation_Etanercept_goodResponse_50

tag: disease state

tag: cell type

value: PBMC

value: f

value: Etn

tag: smokingstatus

tag: rfposneg

tag: anticcpposneg


title: BRD3179N-K27me3_ChIP-seq

tag: biological sample

tag: treatment


title: BRD3187-CTCF_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A6_AD004_indexed

tag: brain region

tag: Sex

tag: strain


title: BRD3179N-K27Ac_ChIP-seq


title: CD14_A_n_08

tag: sequencingid

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: no

tag: height

value: never

tag: weight

tag: rf

value: Negative

tag: anti-ccp


title: CD14_A_g_09

tag: cell type

value: m

tag: disease state

tag: age

value: good

tag: alcoholuseunitsweek

value: stopped

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: BRD3179N-CTCF_REP2_ChIP-seq

tag: tissue

value: Normal colon

tag: biological sample

tag: treatment


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD010_indexed

tag: brain region

tag: Sex

tag: strain


title: CD14_E_g_05

tag: sequencingid

value: Monocytes

tag: studysubjectid

tag: drug

tag: response

tag: height


title: BRD3179N-CTCF_ChIP-seq


title: DNA methylation_Etanercept_goodResponse_47

tag: disease state

tag: cell type

tag: smokingstatus

tag: weight

tag: rfposneg

value: y

tag: anticcpposneg


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD008_indexed

value: MOs

value: male

tag: age


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD007_indexed


title: CD14_A_n_06

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

value: yes

tag: rf

tag: anti-ccp

value: Positive

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Etanercept_goodResponse_44

value: PBMC

tag: Sex

value: f


title: CD14_A_n_04

tag: sequencingid

tag: studysubjectid

tag: drug

value: Adalimumab


title: CD14_E_n_03

tag: disease state

value: Etanercept

tag: response

value: no

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD006_indexed

tag: brain region

tag: strain


title: CD14_A_m_02

tag: cell type

value: moderate

value: never

tag: weight

value: Negative


title: BRD3179-K27Ac_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: CD14_E_n_01

tag: age

tag: alcoholuseunitsweek

value: stopped

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD004_indexed

tag: Sex


title: BRD3179-CTCF_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A5_AD002_indexed


title: BRD3170N-WCE_ChIP-seq

value: Normal colon


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD012_indexed


title: PBMC_E_m_79

description:
rawReadsData.csv
Counts_Normalization_PBMC.csv

tag: sequencingid

value: m

tag: studysubjectid

tag: drug

tag: leucocytencount

tag: trombocytencount


title: BRD3170N-K9me3_ChIP-seq


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD010_indexed

tag: brain region

value: MOs

tag: strain


title: PBMC_A_g_78

tag: cell type

tag: disease state

tag: response

value: good

tag: height

tag: weight


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD008_indexed

value: male

tag: age


title: BRD3170N-CTCF_ChIP-seq

tag: tissue

tag: biological sample

tag: treatment


title: BRD3162-WCE_ChIP-seq


title: PBMC_E_n_77

tag: Sex

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD007_indexed


title: DNA methylation_Adalimumab_noResponse_45

tag: drug

value: Ada

tag: smokingstatus

tag: rfposneg

value: n

tag: anticcpposneg

tag: leucocytencount

tag: trombocytencount


title: PBMC_E_n_76

tag: sequencingid

tag: cell type

value: PBMC

value: f

tag: disease state

tag: studysubjectid

tag: response

tag: height

value: Positive


title: DNA methylation_Adalimumab_goodResponse_46

tag: Sex

tag: age

tag: weight


title: DNA methylation_Etanercept_goodResponse_48

value: Etn

tag: alcoholuseunitsweek

value: y


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD006_indexed

tag: brain region

tag: strain


title: DNA methylation_Etanercept_noResponse_38

tag: drug

value: no

tag: smokingstatus

value: never

tag: hemoglobinecount


title: BRD3162-K27Ac_ChIP-seq

tag: tissue

value: Colon tumor

tag: biological sample

tag: treatment


title: PBMC_A_g_80

tag: sequencingid

tag: cell type

value: Adalimumab

value: stopped

tag: rf

tag: anti-ccp

tag: leucocytencount

tag: trombocytencount


title: BRD3162-CTCF_ChIP-seq


title: PBMC_E_n_75

tag: Sex

tag: disease state

tag: age

tag: studysubjectid

value: Etanercept

tag: response

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD004_indexed

tag: brain region

value: MOs

tag: strain


title: DNA methylation_Etanercept_noResponse_43

tag: drug

tag: smokingstatus

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

tag: anticcpposneg

tag: hemoglobinecount


title: DNA methylation_Adalimumab_goodResponse_36

tag: cell type

value: good

tag: leucocytencount


title: MS_12 [3-7275]

value: MDSL cells

tag: condition

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 4 cDNA


title: DNA methylation_Etanercept_goodResponse_35

tag: disease state

value: rheumatoid arthritis (RA)

tag: Sex

tag: trombocytencount


title: PBMC_A_n_74

tag: sequencingid

tag: age

tag: studysubjectid

tag: response

value: yes

tag: rf

value: Negative

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A4_AD001_indexed

tag: brain region

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD012_indexed


title: PBMC_A_m_73

value: PBMC

value: f

tag: drug

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Positive


title: MS_11 [3-6263]

tag: cell type

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA


title: DNA methylation_Adalimumab_noResponse_42

value: Ada

value: no

tag: smokingstatus

value: never

tag: rfposneg

value: n

tag: anticcpposneg

value: y

tag: hemoglobinecount

tag: leucocytencount


title: DNA methylation_Etanercept_goodResponse_39

tag: disease state

tag: Sex

tag: age

value: Etn

value: good

value: stopped

tag: trombocytencount


title: MS_10 [3-910]

value: MDSL cells

tag: condition

value: MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout


title: DNA methylation_Adalimumab_noResponse_37

value: rheumatoid arthritis (RA)

value: m

tag: response


title: PBMC_E_n_71

tag: sequencingid

value: PBMC

tag: studysubjectid

value: Etanercept

value: yes

tag: rf

tag: anti-ccp


title: DNA methylation_Adalimumab_moderateResponse_34

tag: drug

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD008_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: PBMC_E_m_72

tag: cell type

value: f

value: Positive

tag: hemoglobinecount

tag: leucocytencount


title: PBMC_A_m_70

tag: Sex

tag: disease state

tag: age

value: Adalimumab


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD007_indexed


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD010_indexed


title: DNA methylation_Adalimumab_noResponse_41

value: Ada

tag: response

value: no

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: trombocytencount


title: PBMC_E_g_69

tag: sequencingid

tag: studysubjectid

tag: drug

value: good

value: stopped

tag: rf

tag: anti-ccp


title: DNA methylation_Etanercept_noResponse_40

value: Etn

tag: height

tag: alcoholuseunitsweek

tag: weight


title: DNA methylation_Etanercept_goodResponse_32

value: rheumatoid arthritis (RA)

tag: cell type

tag: hemoglobinecount

tag: leucocytencount


title: MS_07 [2-6263]

value: MDSL cells

tag: condition

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA


title: MS_06 [2-910]

value: MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout


title: PBMC_E_n_68

value: PBMC

tag: Sex

tag: disease state

tag: age

value: Etanercept

tag: response

value: Negative


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD004_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD006_indexed


title: DNA methylation_Adalimumab_noResponse_30

value: m

tag: smokingstatus

tag: rfposneg

value: n

tag: anticcpposneg

tag: trombocytencount


title: DNA methylation_Etanercept_moderateResponse_33

tag: drug

value: moderate

tag: height


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD002_indexed


title: PBMC_E_n_67

tag: sequencingid

value: f

tag: studysubjectid

value: no

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

value: Positive

tag: anti-ccp


title: MS_05 [2-Lenti]

tag: cell type

tag: condition

value: parent MDS-L cells expressing Cas9 - effectively a control


title: PBMC_E_n_66

tag: Sex

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

tag: response

value: stopped

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A3_AD001_indexed

tag: brain region

tag: strain


title: MS_04 [1-7275]

value: MDSL cells

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 4 cDNA


title: DNA methylation_Adalimumab_goodResponse_28

value: PBMC

tag: drug

value: Ada

value: good

tag: height

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: trombocytencount


title: PBMC_E_n_65

tag: sequencingid

tag: studysubjectid

value: Etanercept

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Negative

tag: anti-ccp


title: PBMC_A_n_64

tag: cell type

tag: Sex

tag: disease state

tag: age

value: Adalimumab

tag: response


title: MS_03 [1-6263]

tag: condition

value: FBXO11 knockout cells with overexpression of FBXO11 isoform 1 cDNA


title: MS_08 [2-7275]


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD012_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: PBMC_A_m_63

value: f

tag: drug

value: moderate

tag: height

value: yes

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD008_indexed


title: MS_01 [1-Lenti]

value: parent MDS-L cells expressing Cas9 - effectively a control


title: DNA methylation_Adalimumab_moderateResponse_29

value: rheumatoid arthritis (RA)

tag: smokingstatus

value: stopped

tag: rfposneg

tag: anticcpposneg

tag: trombocytencount


title: DNA methylation_Etanercept_noResponse_31

value: m

value: Etn

value: no

tag: alcoholuseunitsweek

tag: weight


title: MS_09 [3-Lenti]

tag: cell type

value: MDSL cells


title: DNA methylation_Etanercept_noResponse_26

tag: disease state

value: PBMC

tag: Sex

value: never

value: n


title: PBMC_E_n_62

tag: sequencingid

tag: age

tag: studysubjectid

value: Etanercept

tag: response

tag: rf

value: Negative

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD007_indexed

tag: brain region

value: MOs

tag: strain


title: AB17CRE_RNA_rep3

city: Shanghai

first: Ze-Guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw sequencing reads were trimmed by Trimmomatic (v0.36) to remove adapters and low quality sequences.
The filtered reads were mapped to the mm10 genome by TopHat2, following assembled, counted and normalized with the Cufflinks.
Differentially expressed genes were analyzed by Cuffdiff in the Cufflinks suit using p value <0.05 and fold change >2 as cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file includes mRNA expression value in each sample.

source_name: AB17: immortalized primary hepatocytes with Arid1afl/fl genotype.

extract_protocol:
RNAs were isolated with TRIzol reagent (Life Technologies) and performed on three independent biological replicates. Extracted RNAs were digested with DNase I and purified using the RNeasy Mini Elute Cleanup Kit (Qiagen).
The mRNAs were separated by the NEBNext Poly(A) mRNA Magnetic Isolation Module based on the coupling of Oligo d(T)25 to paramagnetic beads which was then served as the solid support for the direct binding of poly(A)+ RNA. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit® for Illumina according to the manufacturer’s instructions, and paired-end sequenced by Illumina HiSeq-2500.

tag: treatment

value: AB17CRE cells infected by the adenoviral vector expressing Cre recombinase (Ad-Cre) to knock out Arid1a.

tag: genotype

value: Arid1a-/-, KO


title: DNA methylation_Etanercept_noResponse_27

value: f

tag: drug

tag: height

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount


title: PBMC_E_m_61

tag: sequencingid

tag: cell type

tag: Sex

tag: disease state

value: moderate

tag: alcoholuseunitsweek

tag: weight

value: Positive

tag: trombocytencount


title: MS_02 [1-910]

tag: condition

value: MDS-L cells with Cas9 and FBXO11 sgRNA - effectively FBXO11 knockout


title: AB17CRE_RNA_rep2

tag: strain

tag: treatment


title: PBMC_A_n_60

value: m

value: rheumatoid arthritis (RA)

tag: age

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: yes

tag: rf

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD006_indexed

tag: brain region

value: male


title: AB17CRE_RNA_rep1

tag: genotype


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD002_indexed


title: AB17GFP_RNA_rep3

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

value: Arid1afl/fl, WT


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD010_indexed


title: PBMC_A_n_58

tag: sequencingid

tag: cell type

value: PBMC

value: no

tag: height

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD001_indexed

value: MOs

tag: Sex


title: AB17GFP_RNA_rep2


title: DNA methylation_Adalimumab_noResponse_25

tag: disease state

value: Ada

tag: smokingstatus

value: never

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

value: n

tag: anticcpposneg

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD012_indexed

tag: age

tag: strain


title: PBMC_E_m_57

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

tag: rf

tag: anti-ccp


title: AB17GFP_RNA_rep1

tag: treatment

tag: genotype


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A2_AD004_indexed

tag: brain region

tag: Sex


title: PBMC_E_n_56

tag: sequencingid

tag: cell type

value: f

tag: disease state

tag: height

value: stopped

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD010_indexed

tag: age


title: DNA methylation_Adalimumab_goodResponse_24

value: good

tag: smokingstatus

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

value: y

tag: anticcpposneg

tag: trombocytencount


title: PBMC_A_g_59

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

tag: rf

value: Positive

tag: anti-ccp


title: PBMC_E_g_55

tag: sequencingid

tag: cell type

tag: Sex

value: Negative


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD008_indexed

tag: brain region

value: male

tag: strain


title: AB17GFP_Rad21

data_processing:
Reads were aligned to the mm10 reference genome using bowtie2;
Low-quality reads were removed by SAMtools;
PCR duplicates were removed using Picard tool (http://broadinstitute.github.io/picard)
The MACS2 with default parameters was deployed for peak calling, with corresponding inputs as background separately.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/TF-DNA complexes were isolated with antibody.
The ChIP libraries for Illumina sequencing were constructed using NEBNext® ChIP-Seq Library Prep Master Mix and sequenced on Illumina HiSeq-2500 instrument.

tag: treatment

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

tag: genotype

tag: chip antibody

value: Rad21 (Abcam, ab992)


title: PBMC_E_n_54

value: PBMC

value: m

tag: disease state

tag: age

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: hemoglobinecount

tag: leucocytencount


title: DNA methylation_Adalimumab_noResponse_20

tag: drug

tag: response

value: no

tag: smokingstatus

value: yes

tag: rfposneg

tag: anticcpposneg

tag: trombocytencount


title: DNA methylation_Etanercept_noResponse_23

tag: cell type

tag: Sex

value: Etn


title: DNA methylation_Adalimumab_goodResponse_17

value: Ada

value: never

value: n


title: DNA methylation_Adalimumab_goodResponse_21

value: f


title: DNA methylation_Adalimumab_moderateResponse_19

value: moderate