title: cyto_0_rp1

description: cytoplasmic extract from day 0 (replicate 1)


title: nucleus_0_rp3

status: Public on Jan 31 2015

type: SRA

city: Lausanne

first: Ana

last: Marques

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

description: Nuclear extract from day 0 (replicate 3)

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse reference genome (mm9) using TopHat [version 2.0.9 (Trapnell et al. 2009)]. Splice junctions from ENSEMBL build 70 (Flicek et al. 2013) were provided to facilitate reads that map across known mouse transcript splice junctions. Pair mates read mapped to distinct chromosomes were discarded.
Gene expression-To account for differences in RNA-sequencing depth, we considered the smallest number of mapped reads (93 million, day 12) and randomly sampled the same number of mapped reads from the remaining samples. Expression levels of protein-coding transcripts and lncRNAs annotated by Guttman and colleagues (Guttman et al. 2011) and ENSEMBl build 70, (Flicek et al. 2013) were estimated using Cufflinks [version 1.3.0, (Trapnell et al. 2010)].
Genome_build: mm9
Supplementary_files_format_and_content: gene expression (FPKMs) as tab delimited file.

molecule: polyA RNA

organism: Mus musculus

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) before induction of Dicer LoF

growth_protocol: Mouse DTCM23/49 XY embryonic stem (mES) cell lines (Nesterova et al. 2008) were grown on 0.1% gelatin-coated plates in a culture medium at 37oC in a humidified atmosphere supplemented with 5% CO2, in KnockOut Dulbecco's Modified Eagle Medium (D-MEM, Invitrogen 10829-018) containing 1% antibiotic penicillin/streptomycin (Invitrogen 15140-122), supplemented with 10% Fetal Bovine Serum (FBS, Invitrogen 10108-165), 100 μM non-essential amino acids (Invitrogen 11140-076), 100 μM L-glutamine (Invitrogen 25030-024), 60 μM β-mercaptoethanol (Invitrogen 31350-010) and 0.01% leukemia inhibitory factor (LIF; Millipore; ESG1106).

extract_protocol:
Total cellular extract and cytoplasmic and nuclear fractions-fractionation using the PARIS kit (Ambion AM1921) -was extracted using the miRNeasy kit (Qiagen 217004) Genomic DNA was removed from all RNA extractions using the DNA-free kit (Ambion AM1906).
100 base paired end polyA-selected directional RNA sequencing libraries were prepared by BGI solutions (Hong Kong)

treatment_protocol: mESC cells were seeded at a density of 8.0 x 105 cells/dish were seeded in 10 cm2 dishes and grown for 24h prior to Tamoxifen treatment. In triplicate, deletion of Dicer’s RNAse III domain was induced by culturing the cells in the presence of 800nM Tamoxifen [(Z)-4-HydroxyTamoxifen (4-OHT), Sigma H7904]. Cells treated with 0.1% ethanol were used as control (3 replicates). Dicer-deficient colonies were selected and expanded from 10 cm2 to T-75 75 cm2 tissue culture flasks. Cells were passaged every 2-3 days until 70-80% confluence for 12 days.

tag: days after lof

tag: replicate

tag: subcellular localization

value: nucleus


title: nucleus_0_rp1

description: Nuclear extract from day 0 (replicate 1)


title: whole_cell_0_rp2

description: whole cell extract from day 0 (replicate 2)

value: whole cell


title: whole_cell_0_rp3

description: whole cell extract from day 0 (replicate 3)


title: nucleus_0_rp2

description: Nuclear extract from day 0 (replicate 2)


title: cyto_0_rp2

description: cytoplasmic extract from day 0 (replicate 2)

value: cytoplasm


title: whole_cell_12_rp2

description: whole cell extract from day 12 (replicate 2)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 12 days after induction of Dicer LoF


title: whole_cell_12_rp1

description: whole cell extract from day 12 (replicate 1)


title: Cont H3K4me1

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Basecalls performed using Torrent Suite (Life technologies)
All sequence data obtained from Ion Proton were merged before alignment onto the human reference genome hg19 using the BWA algorithm (CLC Genomics Workbench Software).
Duplicate reads and low read/mapping quality reads were trimmed out with the CLC Genomics Workbench Software.
Peak detection was done using the MACS algorithm in Avadis NGS software. H3K4me1 binding sites in LSD2-depleted HepG2 cells were detected based on the H3K4me1 peaks significantly enriched over H3K4me1 peaks in control HepG2 cells at a cutoff value of p=10^-5.
Genome_build: hg19
Supplementary_files_format_and_content: BED file generated using MACS algorithm in Avadis NGS software.

molecule: genomic DNA

organism: Homo sapiens

source_name: HepG2, Cont H3K4me1

growth_protocol: HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified eagle’s medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Crosslinked nuclear extracts were subjected to DNA fragmentation by Covaris S220 sonifier, and chromatin-DNA complexes were pulled down using specific antibodies.
Libraries were prepared using an Ion Plus Fragment Kit (Lifetechnologies, Part no. 4471252) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end repair enzyme, and was purified with two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. After adapter ligation, DNA was PCR amplified with Ion primers for 13 cycles. The purified DNA was checked for quality on Agilent 2100 Bioanalyzer instrument with an Agilent High Sensitivity DNA kit. The library DNA was approximately 170–220 bp in length.  Libraries ware quantified using quantitative real-time PCR with the Ion Library Quantitation Kit (Part no. 4468802). Diluted librarie DNA was subjected to emulsion PCR using Ion OneTouch System and sequenced on the Ion PGM and Ion Proton semiconductor sequencers (Lifetechnologies) according to the manufacturer's protocols.

treatment_protocol: For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Invitrogen) when they were approximately 50% confluent.

tag: cell line

tag: variation

value: control

tag: chip antibody

value: anti-H3K4me1 (abcam, ab8895)


title: Mouse Megakaryocytes, rep1-2

city: Salt Lake City

first: Jesse

middle: Worth

last: Rowley

state: Ut

department: Medicine

country: USA

institute: University of Utah

description:
This Sample represents 2 replicates.
PolyA RNA

data_processing:
Basecalls were performed with GAPipeline 1.3.2 for the human sample; CASAVA 1.7.0 for mouse samples.
Reads were aligned with the Novoalign software against hg19 for human or mm9 for mouse and including splice junction file created from Ensembl genes as detailed in http://useq.sourceforge.net/usageRNASeq.html
Reads were parsed using Useq software (http://useq.sourceforge.net).
FPKM (RPKM) expression estimates were calculated using the Useq software (http://useq.sourceforge.net) for all Ensembl gene regions with overlapping gene regions removed.
Extracted reads aligning to genetic loci of proteasome subunits matching the gene ontology term GO:0000502~proteasome complex were extracted from the Bam files using BedTools (http://bedtools.readthedocs.org/).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files contain the gene name, chromosomal coordinates, and FPKM for proteasome components matching the gene ontology term GO:0000502~proteasome complex.

molecule: total RNA

source_name: bone marrow-derived megakaryocytes

growth_protocol: For mouse samples, bone marrow was flushed from C57BL/6 mouse tibia and femur, and cells were homogenized and cultured in DMEM medium containing TPO for 4 days.

extract_protocol:
RNA was extracted with Trizol followed by DNase treatment and ethanol precipitation. Poly-A RNA was enriched using oligo dT beads following the Illumina TruSeq RNA sample preparation kit protocol.
Illumina TruSeq RNA sample preparation Kit V2 With Oligo dT selection.

tag: strain/background

tag: cell type

value: megakaryocytes

tag: tissue derivation

value: bone marrow


title: LSD2-KD input

source_name: HepG2, LSD2-KD input

value: none (input)


title: sw2

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
As an initial quality filter, all reads containing Ns were discarded.
The adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. The HD component of the adapter (first 4 and last 4 nucleotides) was subsequently removed.
The reads were mapped full length, no mis-matches or gaps allowed to the reference H. sapiens genome using PatMan [Prueffer et al, 2008]
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The computational prediction of the targets was conducted using the plant target prediction tool within the UEA sRNA Workbench.
Genome_build: Homo sapiens genome, ver 38, GRCh38
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

source_name: malignant chondrocyte

growth_protocol: SW1353 chondrosarcoma cells were cultured in Dulbecco’s modified Eagle’s medium (Life Technologies) containing 10% (volume/volume) fetal bovine serum (Sigma Aldrich), 2 mM glutamine and 1% (volume/volume) penicillin-streptomycin. Cells were fed every other day and maintained at 37oC in an atmosphere of 5% CO2.  After 21 days of culture, cells were collected for total RNA extraction.

extract_protocol:
Total RNA was extracted using the miRCURY™ RNA Isolation Kit - Tissue (Exiqon).
Total RNA (1µg) was ligated to adenylated 3’ HD adapter by using T4 RNA ligase 2 (truncated T4 RNA ligase). The ligated product was cleaned and concentrated by Zymo RNA cleaning and concentrating kit. The remaining adapter was de-adenylated by adenylase and degraded by exonuclease. Then the 3’ ligated products were ligated to 5’ HD adapter by using T4 RNA ligase 1, and the reaction product was further cleaned and concentrated by the Zymo RNA cleaning and concentrating kit. The concentrated RNA being ligated to both 5’ and 3’ HD adapters were reverse transcribed into cDNA and the cDNA was amplified by using Phusion DNA polymerase. The amplified products were run on 6-8% of PAGE gel. The band around the size of 147bp was cut and the PCR products, the library, were extracted from the gel and were sent for sequencing.

treatment_protocol: no special treatment

tag: tissue type

value: Human bone chondrosarcoma, fibroblast-like cell line

tag: molecule subtype

value: small RNA


title: Cont input

source_name: HepG2, Cont input


title: whole_cell_10_rp1

description: whole cell extract from day 10 (replicate 1)

source_name: Conditional Dicer mutant mouse Embryonic stem cell (described in Nesterova et al, 2008) 10 days after induction of Dicer LoF


title: LSD2-KD H3K4me1

source_name: HepG2, LSD2-KD H3K4me1


title: mtr2

description: Sample 2

data_processing:
As an initial quality filter, all reads containing Ns were discarded.
The adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. The HD component of the adapter (first 4 and last 4 nucleotides) was subsequently removed.
The reads were mapped full length, no mis-matches or gaps allowed to the reference M. truncatula genome using PatMan [Prueffer et al, 2008]
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The computational prediction of the targets was conducted using the plant target prediction tool within the UEA sRNA Workbench.
Genome_build: Medicago truncatula ver 3.5
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

organism: Medicago truncatula

source_name: leaf

growth_protocol: the seeds were germinated in petri dish on phytoagar and the seedlings were transferred to 3.5 inch pots. The seedlings were grown in Sanyo Versatile Environmental Test Chamber with 23°C for 18hrs and 16°C for 6hrs.

extract_protocol:
Trizol reagent was used for total RNA extraction and the low molecular weight RNA was isolated by using mirVana kit.
Total RNA (1µg) was ligated to adenylated 3’ HD adapter by using T4 RNA ligase 2 (truncated T4 RNA ligase). The ligated product was cleaned and concentrated by Zymo RNA cleaning and concentrating kit. The remaining adapter was de-adenylated by adenylase and degraded by exonuclease. Then the 3’ ligated products were ligated to 5’ HD adapter by using T4 RNA ligase 1, and the reaction product was further cleaned and concentrated by the Zymo RNA cleaning and concentrating kit. The concentrated RNA being ligated to both 5’ and 3’ HD adapters were reverse transcribed into cDNA and the cDNA was amplified by using Phusion DNA polymerase. The amplified products were run on 6-8% of PAGE gel. The band around the size of 147bp was cut and the PCR products, the library, were extracted from the gel and were sent for sequencing.

tag: developmental stage

value: two months old plants with flowers

tag: tissue

value: young leaves


title: SCC_Etop_High_spike-in_(20140617_5)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 30 microM etoposide with a spike-in of untreated budding yeast cells.

data_processing:
Library strategy:  BLESS (PMID 23503052)
After Illumina paired-end sequencing, each read (read1 and read2) in a pair was treated separately. Adaptors were removed using the program trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Then, those reads containing the series [NT]CGAGGTAGTA were selected and the sequence following it was retained. The selected reads were mapped as single-end reads against the MM9 release of the mouse genome and also against release sacCer3 of the yeast genome using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). For the mapped reads, the cleavage site was determined as the first base pair for reads mapped to the forward strand and the last base pair for reads mapped to the reverse strand. Mouse cleavage sites were normalized by first aggregating them into 25bp intervals for mouse and then multiplying the fraction of total counts in each interval by the size of the mouse genome. Yeast cleavage sites from all samples in this series were pooled and then normalized in 1bp intervals by multiplying the fraction of total counts in each interval by the size of the yeast genome.

organism:
Saccharomyces cerevisiae
Mus musculus

source_name: BLESS pull-down

extract_protocol: Treated mouse SCC cells and untreated yeast cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.

value: squamous cell carcinoma

tag: genotype/variation

value: wild-type

tag: drug

value: 30 microM etoposide

tag: yeast spike-in

value: nuclei, wild-type strain W303


title: mtr1

description: Sample 1


title: SCC_Doxo_High_spike-in_(20140617_3)

description: Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 3.0 microM doxorubicin with a spike-in of untreated budding yeast cells.

extract_protocol: Doxorubicin-treated mouse SCC cells and untreated yeast cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.

value: 3.0 microM doxorubicin


title: SCC_Etop_Low_spike-in_(20140617_4)

description: Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 3 microM etoposide with a spike-in of untreated budding yeast cells.

value: 3 microM etoposide


title: SCC_Doxo_Low_spike-in_(20140617_2)

description: Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 0.3 microM doxorubicin with a spike-in of untreated budding yeast cells.

value: 0.3 microM doxorubicin


title: SCC_Doxo_Low_(20140224_16)

description: Genome-wide double-strand breaks in squamous cell carcinoma cells after 24 hours of treatment with 0.3 microM doxorubicin.

data_processing:
Library strategy:  BLESS (PMID 23503052)
After Illumina paired-end sequencing, each read (read1 and read2) in a pair was treated separately. Adaptors were removed using the program trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Then, those reads containing the series [NT]CGAGGTAGTA were selected and the sequence following it was retained. The selected reads were mapped as single-end reads against the MM9 release of the mouse genome using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). For the mapped reads, the cleavage site was determined as the first base pair for reads mapped to the forward strand and the last base pair for reads mapped to the reverse strand. Cleavage points were normalized by first aggregating them into 25bp intervals and then multiplying the fraction of total counts in each interval by the size of the mouse genome.

extract_protocol: Doxorubicin-treated SCC cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.


title: SCC_Acla_Low_(20140224_20)

description: Genome-wide double-strand breaks in squamous cell carcinoma cells after 24 hours of treatment with 0.4 microM aclarubicin.

extract_protocol: Aclarubicin-treated SCC cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.

value: 0.4 microM aclarubicin


title: SCC_Acla_Low_spike-in_(20140617_6)

description: Genome-wide double-strand breaks in mouse squamous cell carcinoma cells after 24 hours of treatment with 0.4 microM aclarubicin with a spike-in of untreated budding yeast cells.

extract_protocol: Aclarubicin-treated mouse SCC cells and untreated yeast cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.


title: SCC_Control_(20140224_15)

description: Genome-wide double-strand breaks in non-treated squamous cell carcinoma cells.

extract_protocol: Untreated SCC cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.


title: SCC_Etop_High_(20140224_19)

description: Genome-wide double-strand breaks in squamous cell carcinoma cells after 24 hours of treatment with 30 microM etoposide.

extract_protocol: Etoposide-treated SCC cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.


title: LSD2

description:
NOTE: Sequence data were generated using two different platforms, Ion Torrent PGM and Proton.
Processed data file: LSD2_vs_Input_Peaks_detected_by_MACS.bed

data_processing:
Basecalls performed using Torrent Suite (Life technologies)
All sequence data obtained from Ion PGM and Proton were merged before alignment onto the human reference genome hg19 using the BWA algorithm (CLC Genomics Workbench Software).
Duplicate reads and low read/mapping quality reads were trimmed out with the CLC Genomics Workbench Software.
Peak detection was done using the MACS algorithm in Avadis NGS software. LSD2 binding sites were detected based on the LSD2 peaks significantly enriched over input peaks at a cutoff value of p=10^-5.
Genome_build: hg19
Supplementary_files_format_and_content: BED file generated using MACS algorithm in Avadis NGS software.

source_name: HepG2 cells in normal condition, LSD2 ChIP

extract_protocol:
Crosslinked nuclear extracts were subjected to DNA fragmentation by Covaris S220 sonifier, and chromatin-DNA complexes were pulled down using specific antibodies.
Libraries were prepared using an Ion Plus Fragment Kit (Lifetechnologies, Part no. 4471252) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end repair enzyme, and was purified with two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. After adapter ligation, DNA was PCR amplified with Ion primers for 15 cycles. The purified DNA was checked for quality on Agilent 2100 Bioanalyzer instrument with an Agilent High Sensitivity DNA kit. The library DNA was approximately 170–220 bp in length.  Libraries ware quantified using quantitative real-time PCR with the Ion Library Quantitation Kit (Part no. 4468802). Diluted librarie DNA was subjected to emulsion PCR using Ion OneTouch System and sequenced on the Ion PGM and Ion Proton semiconductor sequencers (Lifetechnologies) according to the manufacturer's protocols.

value: anti-LSD2 polyclonal antibody (raised in rabbits by administering recombinant human LSD2 protein (region 26 – 822))


title: SCC_Control_spike-in_(20140617_1)

description: Genome-wide double-strand breaks non-treated squamous cell carcinoma cells with a a spike-in of untreated budding yeast cells

data_processing:
After Illumina paired-end sequencing, each read (read1 and read2) in a pair was treated separately. Adaptors were removed using the program trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Then, those reads containing the series [NT]CGAGGTAGTA were selected and the sequence following it was retained. The selected reads were mapped as single-end reads against the MM9 release of the mouse genome and also against release sacCer3 of the yeast genome using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). For the mapped reads, the cleavage site was determined as the first base pair for reads mapped to the forward strand and the last base pair for reads mapped to the reverse strand. Mouse cleavage sites were normalized by first aggregating them into 25bp intervals for mouse and then multiplying the fraction of total counts in each interval by the size of the mouse genome. Yeast cleavage sites from all samples in this series were pooled and then normalized in 1bp intervals by multiplying the fraction of total counts in each interval by the size of the yeast genome.
Library strategy:  BLESS (PMID 23503052)

extract_protocol: Untreated mouse SCC cells and yeast cells were cross-linked at room temperature with 2% formaldehyde and incubated with 125 mM glycine. The cells were then incubated with lysis butter and nuclear break buffer for 45min at 37 degrees C for nuclei isolation. The nuclei were quickly digested by proteinase K (100 microgram/ml) at 37 degrees C for 4 min, and then washed twice with NEB buffer 2 and once with quick blunting buffer followed by end blunting using quick blunting kit (New Englan Biolabs). The nuclei where then washed and subject to ligation with biotin labeled proximal linker at 16 degrees C for 18 hours. After ligation, genomic DNA was isolated and digested with HaeIII, followed by streptavidin beads capture, ligation of distal linker, digestion of I-Scel, PCR amplification, and XhoI digestion before Illumina sequencing.


title: pUC19

status: Public on Jan 30 2015

city: Berkeley

first: James

last: Nunez

state: CA

address: 731 Stanley Hall

institute: University of California, Berkeley

description:
pUC19
Integration products

data_processing:
3' adapters were removed using Cutadapt, discarding reads shorter than 15nt
Reads containing integrated protospacer were selected using Cutadapt, requiring at least 10 nt of protospacer sequence with no errors
Reads were mapped to plasmid fasta usinig Bowtie, allowing up to 2 mismatches and requiring unique mapping
Genome_build: pCRISPR [pUC19_CrisprA.fa; see fasta file linked to Series record]
Genome_build: pUC19 [https://www.neb.com/~/media/NebUs/Page%20Images/Tools%20and%20Resources/Interactive%20Tools/DNA%20Sequences%20and%20Maps/Text%20Documents/puc19fsa.txt]
Genome_build: pUC19_CrisprI_no_BBvCI [pUC19_CrisprI_no_BBvCI.fa; see fasta file linked to Series record]
Supplementary_files_format_and_content: .xls files containing protospacer sequence, plasmid strand and location of integration, and number of reads found

organism: Cloning vector pUC19

source_name: Plasmid

extract_protocol:
Integration reactions were performed with Cas1-Cas2, protospacer, and plasmid.   The integration reaction was performed with 75 nM Cas1   Cas2, 200 nM  protospacer and 7.5 nM pCRISPR or pUC19 in 20 mM HEPES, pH 7.5, 25 mM  KCl, 10 mM MgCl2, 10% DMSO and 1 mM DTT.
The DNAs were isolated by phenol-chloroform extraction and ethanol    precipitation. The excess protospacers were removed using 100K MWCO    Amicon Ultra-0.5 mL centrifugal filters. The resulting integration    products were digested into smaller DNA fragments using dsDNA    Fragmentase (New England Biolabs) for 75 min at 37   C and quenched at    65   C for 15 min. Fragments were end repaired using T4 DNA Polymerase    (NEB), Klenow (NEB) and T4 PNK (NEB) and A-tailed with Klenow exo (3      to 5   exo minus) (NEB). Adapters were ligated onto fragments using T4    DNA ligase (NEB) and cDNA libraries were amplified by PCR using    Phusion (NEB).
Integration products were fragmented, end-repaired, adapter ligated, PCR amplified, and analyzed by Illumina sequencing. Libraries were sequenced on an Illumina HiSeq2500 on rapid run mode.

tag: protospacer

value: GCCCAATTTACTACTCGTTCTGGTGTTTCTCGT


title: pCRISPR

description:
pCrispr (which is pUC19 carrying a CRISPR locus)
Integration products


title: Human Megakaryocytes, rep1

description:
This Sample represents 1 replicate.
PolyA RNA

data_processing:
Basecalls were performed with GAPipeline 1.3.2 for the human sample; CASAVA 1.7.0 for mouse samples.
Reads were aligned with the Novoalign software against hg19 for human or mm9 for mouse and including splice junction file created from Ensembl genes as detailed in http://useq.sourceforge.net/usageRNASeq.html
Reads were parsed using Useq software (http://useq.sourceforge.net).
FPKM (RPKM) expression estimates were calculated using the Useq software (http://useq.sourceforge.net) for all Ensembl gene regions with overlapping gene regions removed.
Extracted reads aligning to genetic loci of proteasome subunits matching the gene ontology term GO:0000502~proteasome complex were extracted from the Bam files using BedTools (http://bedtools.readthedocs.org/).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files contain the gene name, chromosomal coordinates, and FPKM for proteasome components matching the gene ontology term GO:0000502~proteasome complex.

source_name: CD34+ cord blood cell-derived megakaryocytes

growth_protocol: Human CD34+ cells were extracted from cord blood using Miltenyi magnetic beads. Cells were cultured for 3 days in SCF/TPO/IL3 in XVIVO followed by 9 additional days in SCF/TPO. Following culture, cells were placed on fibrinogen-coated plates overnight to enrich for megakaryocytes.

value: megakaryocytes

value: cord blood


title: whole_cell_0_rp1

description: whole cell extract from day 0 (replicate 1)

tag: days after lof

value: whole cell


title: pCrisprI_no_BBvCI (Protospacer A/T)

description:
pCrisprI_no_BBvCI is equivalent to the pCrispr plasmid with a missing restriction enzyme site.
Integration products

value: ACGAGAAACACCAGAACGAGTAGTAAATTGGGA


title: RNA extracted from leaves of plants

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

description: short RNA

data_processing:
Removed adaptors. Sequences without adaptor matches were discarded.
Sequences were counted and ordered
Supplementary_files_format_and_content: Tabular format. Counts of each species of sRNA in the library

organism: Cicer arietinum

source_name: Cicer arietinum variety "Red Chickpea of Cassano delle Murgie”

growth_protocol: For Cicer arietinum sample were from plant population (=variety) grown in the field whereas a Nicotiana benthamiana CymRSV infected was grown in the grow chamber at 21°C

extract_protocol:
Size fractionated small RNA from total RNA extracts of Cicer arietinum leaves and from Nicotiana benthamiana infected by Cymbidium ringspot virus were mixed in a ratio of 1000 to 1 in amount, respectively.  Total RNA was obtained using TriReagent (Sigma) following manual indications and fractionation was done running total RNAthrough a high resolution polyacrilamide gel electrophoresis. RNA 20nt to 30 nt in size was eluted and used for librariy generation. The RNA was  ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing.
The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.

treatment_protocol: For Cicer arietinum leaves were collected from 2 plants for each row and from 30 rows of the experimental plot. For Cymbidiom ringspot virus-infected N. benthamiana, RNA was extracted from systemic leaves with symptoms.

tag: protocol

value: Leaves from Cicer arietinum and leaves from Cymbidium ringspot virus-infected Nicotiana benthamiana were mixed in a 1000:1 ratio

tag: tissues used

value: leaves

tag: sampling

value: bulk of leaves from plant population


title: WT Cul_Input_ChIPSeq

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using Bowtie (Langmead B, et.al 2009) , and TopHat(Trapnell C, et.al 2009) for RNA-Seq
H4K16ac data peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05, Sirt1 ChIP were analyzed using MACS ( Zhang et al, 2008), with pvalue of 10^-5, --gsize mm, and the rest were defualt setting, input data reads were shuffled and down sampled to adujst for difference in read coverage.
FPKM (RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq processed data files are bigWig format and in text format generated from Cuffdiff, and for ChIP-Seq data wig files were generated using filtered reads residing in enriched regions

source_name: Satellite cells

growth_protocol: FACS isolated satellite cells were grown in Hams F-10 media (Gibco), 20% fetal bovine serum (FBS, Gibco), bFGF (12.5ng/mL), Penicillin/streptomycin (1x, Gibco).

extract_protocol:
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with H4K16ac antibody (Millipore, CS204361) or Sirt1 antibody (Upstate, 07-131) Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed.

treatment_protocol: For differentiation, cells were placed in Hams F-10 media (Gibco) with 2% horse serum (Gibco) for 24 hrs.

value: proliferating satellite cells

tag: strain

value: C57Bl/6 background

value: WT


title: SIRT1mKO FI_Input_ChIPSeq

value: quiescent satellite cells

tag: chip antibody


title: WT FI_Input_ChIPSeq


title: WT Cul_SIRT1_ChIPSeq2

description: Chromatin IP against Sirt1

value: Anti-Sirt1 (Upstate, 07-131)


title: WT FI_SIRT1_ChIPSeq2

description: Chromatin IP against Sirt1


title: WT Cul_SIRT1_ChIPSeq1

description: Chromatin IP against Sirt1


title: WT FI_SIRT1_ChIPSeq1

description: Chromatin IP against Sirt1


title: SCC_Doxo_High_(20140224_18)

description: Genome-wide double-strand breaks in squamous cell carcinoma cells after 24 hours of treatment with 3.0 microM doxorubicin.

value: squamous cell carcinoma

value: wild-type

value: 3.0 microM doxorubicin


title: SIRT1mKO FI_H4K16ac_ChIPSeq

description: Chromatin IP against H4K16ac

value: Anti-H4K16ac (Millipore, CS204361)


title: pCrisprI_no_BBvCI (Protospacer C/C)

value: GCCCAATTTACTACTCGTTCTGGTGTTTCTCGC


title: WT FI_H4K16ac_ChIPSeq

description: Chromatin IP against H4K16ac


title: input

source_name: HepG2 cells in normal condition, input

tag: cell line


title: SIRT1mKO Diff_RNASeq2

description: PolyA RNA sequencing

tag: cell type

value: satellite cells


title: SIRT1mKO Diff_RNASeq1

description: PolyA RNA sequencing


title: WT Cul_RNASeq4

description: PolyA RNA sequencing


title: SIRT1mKO Cul_RNASeq1

description: PolyA RNA sequencing


title: WT Diff_RNASeq1

description: PolyA RNA sequencing


title: WT Cul_RNASeq3

description: PolyA RNA sequencing


title: Nippostrongylus brasiliensis Sample 7

status: Public on Feb 01 2015

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-33nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: sequence id + number of reads + sequence

organism: Nippostrongylus brasiliensis

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

value: Adult

tag: blaxter clade

value: V


title: WT Cul_RNASeq2

description: PolyA RNA sequencing


title: SIRT1mKO FI_RNASeq3

description: PolyA RNA sequencing


title: WT Cul_RNASeq1

description: PolyA RNA sequencing


title: WT FI_RNASeq5

description: PolyA RNA sequencing


title: UC Male (CCFA_Risk_322)

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
CCFA_Risk_322
Male diagnosed at age 14.16666667 with UC.

data_processing:
Illumina HiSeq 2000 for sequencing.
Reads were aligned using TopHat, using hg19 as the reference genome and mapping reads per kilobase per million mapped reads (RPKM) as output.
RPKM were normalized using the DESeq algorithm using Avaids NGS software, where normalized counts were log2-transformed and base-lined to the median expression of control samples.
Normalized expression values were baselined to the median of all samples.
We removed all transcripts that did not have at least 5 RPKM in at least 5 different samples.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files contain normalized and baselined RPKM values for each sample.

source_name: Ileal biopsy in treatment-naïve patient, UC

growth_protocol: Ileal biopsies were stored in RNAlater at -80C.

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DNA Mini Kit, RNA quality and concentration were measured by Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2000 with single-end 50-bp reads (Illumina, San Diego, CA).

value: Ileal biopsy

tag: Sex

value: Male

tag: age at diagnosis

tag: paris age

tag: diagnosis

value: UC

tag: l2 type

tag: histopathology

tag: deep ulcer


title: WT FI_RNASeq1

description: PolyA RNA sequencing

tag: genotype/variation


title: WT FI_RNASeq2

description: PolyA RNA sequencing


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_320)

description:
CCFA_Risk_320
Female diagnosed at age 15.75 with CD characterized with normal and no deep ulcer.

source_name: Ileal biopsy in treatment-naïve patient, CD

tag: tissue

value: Female

value: CD

value: cCD

value: Normal

value: No


title: WT Cul_H4K16ac_ChIPSeq

description: Chromatin IP against H4K16ac

value: proliferating satellite cells

value: C57Bl/6 background

value: WT


title: UC Female (CCFA_Risk_318)

description:
CCFA_Risk_318
Female diagnosed at age 4.5 with UC.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_317)

description:
CCFA_Risk_317
Male diagnosed at age 10.5 with CD characterized with Microscopic inflammation and no deep ulcer.

value: Microscopic inflammation


title: UC Male (CCFA_Risk_319)

description:
CCFA_Risk_319
Male diagnosed at age 11 with UC.


title: UC Female (CCFA_Risk_316)

description:
CCFA_Risk_316
Female diagnosed at age 16.92 with UC

source_name: Ileal biopsy in treatment-naïve patient


title: UC Female (CCFA_Risk_315)

description:
CCFA_Risk_315
Female diagnosed at age 14.91666667 with UC.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_314)

description:
CCFA_Risk_314
Male diagnosed at age 11 with CD characterized with normal and no deep ulcer.


title: SIRT1mKO Cul_RNASeq2

description: PolyA RNA sequencing


title: WT Diff_RNASeq2

description: PolyA RNA sequencing


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_313)

description:
CCFA_Risk_313
Female diagnosed at age 5.416666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: iCD

value: Macroscopic inflammation


title: SIRT1mKO FI_RNASeq2

description: PolyA RNA sequencing

value: quiescent satellite cells


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_312)

description:
CCFA_Risk_312
Male diagnosed at age 10.66666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_311)

description:
CCFA_Risk_311
Male diagnosed at age 13.83 with CD characterized with Microscopic inflammation and no deep ulcer


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_309)

description:
CCFA_Risk_309
Female diagnosed at age 13.66666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_307)

description:
CCFA_Risk_307
Male diagnosed at age 11.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: UC Female (CCFA_Risk_306)

description:
CCFA_Risk_306
Female diagnosed at age 16.33333333 with UC.


title: UC Male (CCFA_Risk_305)

description:
CCFA_Risk_305
Male diagnosed at age 13.58333333 with UC.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_310)

description:
CCFA_Risk_310
Female diagnosed at age 13.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_308)

description:
CCFA_Risk_308
Male diagnosed at age 15.75 with UC.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_304)

description:
CCFA_Risk_304
Male diagnosed at age 10.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_321)

description:
CCFA_Risk_321
Female diagnosed at age 9.583333333 with CD characterized with normal and no deep ulcer.


title: UC Male (CCFA_Risk_302)

description:
CCFA_Risk_302
Male diagnosed at age 17.08333333 with UC.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_303)

description:
CCFA_Risk_303
Male diagnosed at age 15.33 with CD characterized with Microscopic inflammation and no deep ulcer


title: UC Famale (CCFA_Risk_301)

description:
CCFA_Risk_301
Female diagnosed at age 16.67 UC


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_300)

description:
CCFA_Risk_300
Male diagnosed at age 13.00 with Macroscopic inflammation and deep ulcer

value: Yes


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_299)

description:
CCFA_Risk_299
Male diagnosed at age 12.75 with CD characterized with normal and no deep ulcer.


title: UC Male (CCFA_Risk_298)

description:
CCFA_Risk_298
Male diagnosed at age 15.91666667 with UC.


title: UC Male (CCFA_Risk_297)

description:
CCFA_Risk_297
Male diagnosed at age 15.83333333 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_296)

description:
CCFA_Risk_296
Male diagnosed at age 10.58333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Male (CCFA_Risk_295)

description:
CCFA_Risk_295
Male diagnosed at age 9.416666667 with UC.


title: UC Male (CCFA_Risk_292)

description:
CCFA_Risk_292
Male diagnosed at age 10.83333333 with UC.


title: UC Male (CCFA_Risk_294)

description:
CCFA_Risk_294
Male diagnosed at age 15.08 with UC


title: UC Male (CCFA_Risk_291)

description:
CCFA_Risk_291
Male diagnosed at age 7.416666667 with UC.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_293)

description:
CCFA_Risk_293
Female diagnosed at age 12.5 with CD characterized with Microscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_290)

description:
CCFA_Risk_290
Male diagnosed at age 13.75 with UC.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_289)

description:
CCFA_Risk_289
Female diagnosed at age 14.08333333 with CD characterized with normal and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_286)

description:
CCFA_Risk_286
Male diagnosed at age 6.583333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_287)

description:
CCFA_Risk_287
Female diagnosed at age 16.25 with CD characterized with normal and no deep ulcer.


title: UC Male (CCFA_Risk_288)

description:
CCFA_Risk_288
Male diagnosed at age 13.75 with UC.


title: UC Male (CCFA_Risk_284)

description:
CCFA_Risk_284
Male diagnosed at age 15.33333333 with UC.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_285)

description:
CCFA_Risk_285
Female diagnosed at age 12.66666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_283)

description:
CCFA_Risk_283
Male diagnosed at age 15.5 with UC.


title: UC Male (CCFA_Risk_282)

description:
CCFA_Risk_282
Male diagnosed at age 16.5 with UC.


title: UC Female (CCFA_Risk_280)

description:
CCFA_Risk_280
Female diagnosed at age 16.58333333 with UC.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_281)

description:
CCFA_Risk_281
Male diagnosed at age 16.5 with CD characterized with normal and no deep ulcer.


title: UC Male (CCFA_Risk_277)

description:
CCFA_Risk_277
Male diagnosed at age 7.25 with UC.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_275)

description:
CCFA_Risk_275
Female diagnosed at age 10.83 with CD characterized with Macroscopic inflammation and deep ulcer


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_273)

description:
CCFA_Risk_273
Male diagnosed at age 16.91666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_271)

description:
CCFA_Risk_271
Male diagnosed at age 11.66666667 with CD characterized with normal and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_270)

description:
CCFA_Risk_270
Male diagnosed at age 16.75 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_276)

description:
CCFA_Risk_276
Male diagnosed at age 13.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: WT FI_RNASeq4

description: PolyA RNA sequencing


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_268)

description:
CCFA_Risk_268
Male diagnosed at age 15.75 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_265)

description:
CCFA_Risk_265
Male diagnosed at age 12.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_264)

description:
CCFA_Risk_264
Male diagnosed at age 15.5 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_266)

description:
CCFA_Risk_266
Male diagnosed at age 15.91666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_262)

description:
CCFA_Risk_262
Male diagnosed at age 15.66666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_261)

description:
CCFA_Risk_261
Male diagnosed at age 10.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_269)

description:
CCFA_Risk_269
Male diagnosed at age 13.91666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Female (CCFA_Risk_272)

description:
CCFA_Risk_272
Female diagnosed at age 12 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_263)

description:
CCFA_Risk_263
Male diagnosed at age 12 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_274)

description:
CCFA_Risk_274
Female diagnosed at age 12.33333333 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_260)

description:
CCFA_Risk_260
Male diagnosed at age 12.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_279)

description:
CCFA_Risk_279
Female diagnosed at age 14.25 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_255)

description:
CCFA_Risk_255
Male diagnosed at age 14.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_257)

description:
CCFA_Risk_257
Male diagnosed at age 11.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_258)

description:
CCFA_Risk_258
Male diagnosed at age 11.91666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_259)

description:
CCFA_Risk_259
Male diagnosed at age 16.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_253)

description:
CCFA_Risk_253
Male diagnosed at age 15.08333333 with CD characterized with normal and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_256)

description:
CCFA_Risk_256
Female diagnosed at age 12.83333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Female (CCFA_Risk_249)

description:
CCFA_Risk_249
Female diagnosed at age 16.91666667 with UC.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_252)

description:
CCFA_Risk_252
Female diagnosed at age 14.91666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Female (CCFA_Risk_251)

description:
CCFA_Risk_251
Female diagnosed at age 16.83333333 with UC.


title: UC Male (CCFA_Risk_250)

description:
CCFA_Risk_250
Male diagnosed at age 6.916666667 with UC.


title: UC Female (CCFA_Risk_248)

description:
CCFA_Risk_248
Female diagnosed at age 13.66666667 with UC.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_267)

description:
CCFA_Risk_267
Female diagnosed at age 13.66666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_278)

description:
CCFA_Risk_278
Male diagnosed at age 15.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_254)

description:
CCFA_Risk_254
Female diagnosed at age 13.16666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Female (CCFA_Risk_247)

description:
CCFA_Risk_247
Female diagnosed at age 6.333333333 with UC.


title: UC Male (CCFA_Risk_238)

description:
CCFA_Risk_238
Male diagnosed at age 5.75 with UC.


title: UC Male (CCFA_Risk_233)

description:
CCFA_Risk_233
Male diagnosed at age 14 with UC.


title: UC Female (CCFA_Risk_244)

description:
CCFA_Risk_244
Female diagnosed at age 15.58333333 with UC.


title: UC Male (CCFA_Risk_246)

description:
CCFA_Risk_246
Male diagnosed at age 14.91666667 with UC.


title: UC Female (CCFA_Risk_245)

description:
CCFA_Risk_245
Female diagnosed at age 14.91666667 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_229)

description:
CCFA_Risk_229
Male diagnosed at age 15.5 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_231)

description:
CCFA_Risk_231
Female diagnosed at age 10.16666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Male (CCFA_Risk_242)

description:
CCFA_Risk_242
Male diagnosed at age 13.25 with UC.


title: UC Female (CCFA_Risk_241)

description:
CCFA_Risk_241
Female diagnosed at age 12 with UC.


title: UC Female (CCFA_Risk_240)

description:
CCFA_Risk_240
Female diagnosed at age 11.83333333 with UC.


title: UC Female (CCFA_Risk_226)

description:
CCFA_Risk_226
Female diagnosed at age 11.91666667 with UC.


title: UC Male (CCFA_Risk_243)

description:
CCFA_Risk_243
Male diagnosed at age 11.58333333 with UC.


title: UC Male (CCFA_Risk_232)

description:
CCFA_Risk_232
Male diagnosed at age 8.5 with UC.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_237)

description:
CCFA_Risk_237
Male diagnosed at age 12.58333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_236)

description:
CCFA_Risk_236
Female diagnosed at age 12.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_230)

description:
CCFA_Risk_230
Male diagnosed at age 16.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_228)

description:
CCFA_Risk_228
Male diagnosed at age 10.83333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_239)

description:
CCFA_Risk_239
Male diagnosed at age 15 with UC.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_227)

description:
CCFA_Risk_227
Male diagnosed at age 13.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_225)

description:
CCFA_Risk_225
Female diagnosed at age 15.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_223)

description:
CCFA_Risk_223
Female diagnosed at age 10.66666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_224)

description:
CCFA_Risk_224
Male diagnosed at age 12.08333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_222)

description:
CCFA_Risk_222
Female diagnosed at age 16.5 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_220)

description:
CCFA_Risk_220
Male diagnosed at age 12.66666667 with CD characterized with normal and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_218)

description:
CCFA_Risk_218
Female diagnosed at age 15.83333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_221)

description:
CCFA_Risk_221
Female diagnosed at age 10.75 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_219)

description:
CCFA_Risk_219
Male diagnosed at age 13.58333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Male (CCFA_Risk_234)

description:
CCFA_Risk_234
Male diagnosed at age 13.75 with UC.


title: UC Female (CCFA_Risk_235)

description:
CCFA_Risk_235
Female diagnosed at age 16.58333333 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_217)

description:
CCFA_Risk_217
Male diagnosed at age 11.91666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_216)

description:
CCFA_Risk_216
Male diagnosed at age 12.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_209)

description:
CCFA_Risk_209
Male diagnosed at age 11.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_204)

description:
CCFA_Risk_204
Female diagnosed at age 16.91666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_207)

description:
CCFA_Risk_207
Male diagnosed at age 16.5 with CD characterized with Macroscopic inflammation and no deep ulcer


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_214)

description:
CCFA_Risk_214
Female diagnosed at age 15.58333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_215)

description:
CCFA_Risk_215
Male diagnosed at age 13.83333333 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_203)

description:
CCFA_Risk_203
Male diagnosed at age 16.83333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_202)

description:
CCFA_Risk_202
Female diagnosed at age 14.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_200)

description:
CCFA_Risk_200
Female diagnosed at age 15.58333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_210)

description:
CCFA_Risk_210
Male diagnosed at age 15.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_201)

description:
CCFA_Risk_201
Female diagnosed at age 15 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_208)

description:
CCFA_Risk_208
Male diagnosed at age 12.75 with CD characterized with Macroscopic inflammation and no deep ulcer


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_211)

description:
CCFA_Risk_211
Male diagnosed at age 15 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_199)

description:
CCFA_Risk_199
Female diagnosed at age 14.33333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_205)

description:
CCFA_Risk_205
Female diagnosed at age 15.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_195)

description:
CCFA_Risk_195
Male diagnosed at age 14.33333333 with CD characterized with normal and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_198)

description:
CCFA_Risk_198
Male diagnosed at age 13.75 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_197)

description:
CCFA_Risk_197
Male diagnosed at age 11.25 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: mRNA-Seq data from pregnant armadillo endometrium

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

department: Human Genetics

institute: The University of Chicago

description: mRNA

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were mapped to appropriate ENSEMBL Gene builds using bowtie with parameters allowing two mismatches and discarding reads that mapped to more than one gene. Uniquely mapped reads for each gene were counted.
Genome_build: Dasnov2.0 (armadillo)
Supplementary_files_format_and_content: Armadillo.txt contains mapped mRNA-Seq data as the number of unique reads  (Mapped_Reads) that map to ENSEMBL genes (Ensembl_Gene_ID) and the associated gene name for each ENSEMBL gene (Assocaited_Gene_Name).

organism: Dasypus novemcinctus

source_name: Pregnant armadillo endometrium

extract_protocol:
Qiagen RNeasy followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pregnant endometrium


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_194)

description:
CCFA_Risk_194
Female diagnosed at age 9.5 with CD characterized with normal and no deep ulcer.

value: Ileal biopsy


title: CD Male with Undetermined and No Deep Ulcer (CCFA_Risk_192)

description:
CCFA_Risk_192
Male diagnosed at age 15.16666667 with CD characterized with Undetermined and no deep ulcer.

value: Male

value: Undetermined


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_193)

description:
CCFA_Risk_193
Female diagnosed at age 15.25 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Female


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_191)

description:
CCFA_Risk_191
Female diagnosed at age 14.5 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: CD


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_189)

description:
CCFA_Risk_189
Female diagnosed at age 8 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_190)

description:
CCFA_Risk_190
Male diagnosed at age 7.166666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_188)

description:
CCFA_Risk_188
Female diagnosed at age 6.166666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_213)

description:
CCFA_Risk_213
Female diagnosed at age 16.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_212)

description:
CCFA_Risk_212
Female diagnosed at age 12 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_206)

description:
CCFA_Risk_206
Female diagnosed at age 15.33333333 with CD characterized with normal and no deep ulcer.

value: cCD


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_187)

description:
CCFA_Risk_187
Male diagnosed at age 8 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_186)

description:
CCFA_Risk_186
Male diagnosed at age 9.25 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_183)

description:
CCFA_Risk_183
Male diagnosed at age 7.33 with CD characterized with Macroscopic inflammation and deep ulcer


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_196)

description:
CCFA_Risk_196
Female diagnosed at age 13.91666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_181)

description:
CCFA_Risk_181
Male diagnosed at age 8.416666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_184)

description:
CCFA_Risk_184
Male diagnosed at age 5.666666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_174)

description:
CCFA_Risk_174
Male diagnosed at age 7.916666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: Not IBD Female (CCFA_Risk_180)

description:
CCFA_Risk_180
Female diagnosed at age 12.66666667 with not IBD.

source_name: Ileal biopsy in treatment-naïve patient, not IBD

value: Not IBD


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_176)

description:
CCFA_Risk_176
Male diagnosed at age 8.916666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_182)

description:
CCFA_Risk_182
Male diagnosed at age 9.166666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: No


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_179)

description:
CCFA_Risk_179
Male diagnosed at age 8.833333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_173)

description:
CCFA_Risk_173
Female diagnosed at age 8.92 with CD characterized with Macroscopic inflammation and no deep ulcer


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_171)

description:
CCFA_Risk_171
Male diagnosed at age 16.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_177)

description:
CCFA_Risk_177
Male diagnosed at age 9.583333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_175)

description:
CCFA_Risk_175
Male diagnosed at age 7.92 with CD characterized with Macroscopic inflammation and no deep ulcer


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_168)

description:
CCFA_Risk_168
Male diagnosed at age 9.25 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_178)

description:
CCFA_Risk_178
Male diagnosed at age 6.75 with CD characterized with Macroscopic inflammation and no deep ulcer


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_172)

description:
CCFA_Risk_172
Male diagnosed at age 16.08333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_167)

description:
CCFA_Risk_167
Male diagnosed at age 9.583333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_165)

description:
CCFA_Risk_165
Female diagnosed at age 9.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_166)

description:
CCFA_Risk_166
Male diagnosed at age 9.583333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_169)

description:
CCFA_Risk_169
Male diagnosed at age 9.083333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_164)

description:
CCFA_Risk_164
Female diagnosed at age 8.833333333 with CD characterized with normal and no deep ulcer.

value: Normal


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_163)

description:
CCFA_Risk_163
Female diagnosed at age 9.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_161)

description:
CCFA_Risk_161
Female diagnosed at age 8.833333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_160)

description:
CCFA_Risk_160
Male diagnosed at age 12.58333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_159)

description:
CCFA_Risk_159
Female diagnosed at age 11.91666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_158)

description:
CCFA_Risk_158
Female diagnosed at age 7.833333333 with CD characterized with normal and no deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_157)

description:
CCFA_Risk_157
Female diagnosed at age 8.833333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_156)

description:
CCFA_Risk_156
Female diagnosed at age 6.75 with CD characterized with normal and no deep ulcer.


title: UC Female (CCFA_Risk_154)

description:
CCFA_Risk_154
Female diagnosed at age 14.41666667 with UC.

value: UC


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_170)

description:
CCFA_Risk_170
Male diagnosed at age 9 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Male (CCFA_Risk_152)

description:
CCFA_Risk_152
Male diagnosed at age 9.666666667 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_150)

description:
CCFA_Risk_150
Male diagnosed at age 10.66666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Female (CCFA_Risk_155)

description:
CCFA_Risk_155
Female diagnosed at age 13.16666667 with UC.


title: UC Female (CCFA_Risk_144)

description:
CCFA_Risk_144
Female diagnosed at age 13.08333333 with UC.


title: UC Female (CCFA_Risk_151)

description:
CCFA_Risk_151
Female diagnosed at age 6.75 with UC.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_143)

description:
CCFA_Risk_143
Female diagnosed at age 10.66666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_145)

description:
CCFA_Risk_145
Female diagnosed at age 11.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_149)

description:
CCFA_Risk_149
Male diagnosed at age 11.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_142)

description:
CCFA_Risk_142
Male diagnosed at age 6.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_147)

description:
CCFA_Risk_147
Male diagnosed at age 11.08333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_136)

description:
CCFA_Risk_136
Female diagnosed at age 11.58333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_140)

description:
CCFA_Risk_140
Female diagnosed at age 11 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_137)

description:
CCFA_Risk_137
Male diagnosed at age 15.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_162)

description:
CCFA_Risk_162
Female diagnosed at age 9.75 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_139)

description:
CCFA_Risk_139
Male diagnosed at age 11.5 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_135)

description:
CCFA_Risk_135
Male diagnosed at age 14.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_138)

description:
CCFA_Risk_138
Female diagnosed at age 11.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_133)

description:
CCFA_Risk_133
Male diagnosed at age 13.66666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_132)

description:
CCFA_Risk_132
Male diagnosed at age 9.166666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: UC Female (CCFA_Risk_131)

description:
CCFA_Risk_131
Female diagnosed at age 8.25 with UC.


title: UC Male (CCFA_Risk_153)

description:
CCFA_Risk_153
Male diagnosed at age 8.5 with UC.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_148)

description:
CCFA_Risk_148
Male diagnosed at age 8.833333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_146)

description:
CCFA_Risk_146
Female diagnosed at age 7.25 with CD characterized with Macroscopic inflammation and deep ulcer.


title: UC Male (CCFA_Risk_129)

description:
CCFA_Risk_129
Male diagnosed at age 11.83333333 with UC.


title: UC Male (CCFA_Risk_130)

description:
CCFA_Risk_130
Male diagnosed at age 15.5 with UC.


title: UC Female (CCFA_Risk_128)

description:
CCFA_Risk_128
Female diagnosed at age 11.5 with UC.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_141)

description:
CCFA_Risk_141
Female diagnosed at age 12.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: UC Female (CCFA_Risk_127)

description:
CCFA_Risk_127
Female diagnosed at age 14.5 with UC.


title: UC Male (CCFA_Risk_125)

description:
CCFA_Risk_125
Male diagnosed at age 5.75 with UC.


title: UC Female (CCFA_Risk_124)

description:
CCFA_Risk_124
Female diagnosed at age 11.66666667 with UC.


title: UC Male (CCFA_Risk_126)

description:
CCFA_Risk_126
Male diagnosed at age 5.5 with UC.


title: Not IBD Male (CCFA_Risk_120)

description:
CCFA_Risk_120
Male diagnosed at age 8 with Not IBD

source_name: Ileal biopsy in treatment naïve patient


title: UC Female (CCFA_Risk_122)

description:
CCFA_Risk_122
Female diagnosed at age 10.5 with UC.


title: DCM_S32

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adapters.
Resulting reads were mapped on the human transcriptome (UCSC gene-build hg19.v65) using RSEM v1.2.3.
Data were normalized using TMM with the Bioconductor package EdgeR
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: UCSC.hg19.65
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

extract_protocol:
Extract protocol: Ventricular samples from 6 patients with medically refractory dilated cardiomyopathy (DCM), excluding specifically those patients with evidence of ischaemic cardiomyopathy or myocarditis were immediately frozen in liquid nitrogen. Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score: 7.9) and quantity were determined on the Agilent 2100 Bioanalyzer. RNA samples were analyzed in the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subject status

value: DCM-diagnosed patients who had undergone heart transplant (hDCM)

value: heart


title: UC Female (CCFA_Risk_123)

description:
CCFA_Risk_123
Female diagnosed at age 8.5 with UC.


title: DCM_S48


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_134)

description:
CCFA_Risk_134
Male diagnosed at age 11.5 with CD characterized with Macroscopic inflammation and no deep ulcer

value: iCD


title: Not IBD Male (CCFA_Risk_118)

description:
CCFA_Risk_118
Male diagnosed at age 9.666666667 with not IBD.


title: Not IBD Male (CCFA_Risk_117)

description:
CCFA_Risk_117
Male diagnosed at age 7.833333333 with not IBD.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_115)

description:
CCFA_Risk_115
Female diagnosed at age 14.08333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: Macroscopic inflammation


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_116)

description:
CCFA_Risk_116
Male diagnosed at age 11.33333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: Not IBD Female (CCFA_Risk_121)

description:
CCFA_Risk_121
Female diagnosed at age 10.66666667 with not IBD.


title: UC Male (CCFA_Risk_114)

description:
CCFA_Risk_114
Male diagnosed at age 9.916666667 with UC.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_185)

description:
CCFA_Risk_185
Male diagnosed at age 8.75 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: DCM_S30


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_113)

description:
CCFA_Risk_113
Female diagnosed at age 13.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: DCM_S26


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_111)

description:
CCFA_Risk_111
Male diagnosed at age 14.5 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_112)

description:
CCFA_Risk_112
Female diagnosed at age 14.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_110)

description:
CCFA_Risk_110
Male diagnosed at age 11.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CTR_S6a

value: control


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_108)

description:
CCFA_Risk_108
Male diagnosed at age 15 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CTR_S4a


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_107)

description:
CCFA_Risk_107
Male diagnosed at age 15.75 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_119)

description:
CCFA_Risk_119
Male diagnosed at age 12.66666667 with UC.


title: CTR_S3b


title: CTR_S1a


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_103)

description:
CCFA_Risk_103
Male diagnosed at age 14.83333333 with CD characterized with Microscopic inflammation and no deep ulcer.

value: Microscopic inflammation


title: CD Female with Undetermined and No Deep Ulcer (CCFA_Risk_102)

description:
CCFA_Risk_102
Female diagnosed at age 11.58333333 with CD characterized with Undetermined and no deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_101)

description:
CCFA_Risk_101
Female diagnosed at age 2.25 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_100)

description:
CCFA_Risk_100
Female diagnosed at age 12.83333333 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_098)

description:
CCFA_Risk_098
Male diagnosed at age 14.83333333 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Yes


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_099)

description:
CCFA_Risk_099
Female diagnosed at age 15.5 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Ileal biopsy


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_097)

description:
CCFA_Risk_097
Female diagnosed at age 14.16666667 with CD characterized with Microscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_096)

description:
CCFA_Risk_096
Female diagnosed at age 13.08333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_094)

description:
CCFA_Risk_094
Female diagnosed at age 9.75 with CD characterized with normal and no deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_095)

description:
CCFA_Risk_095
Male diagnosed at age 14.75 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Male


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_093)

description:
CCFA_Risk_093
Male diagnosed at age 5.75 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_109)

description:
CCFA_Risk_109
Male diagnosed at age 13.58333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_091)

description:
CCFA_Risk_091
Male diagnosed at age 14.75 with CD characterized with Microscopic inflammation and no deep ulcer.


title: UC Male (CCFA_Risk_092)

description:
CCFA_Risk_092
Male diagnosed at age 9.833333333 with UC.


title: Not IBD Female (CCFA_Risk_090)

description:
CCFA_Risk_090
Female diagnosed at age 9.916666667 with not IBD.


title: Not IBD Female (CCFA_Risk_086)

description:
CCFA_Risk_086
Female diagnosed at age 14.75 with not IBD.


title: Not IBD Male (CCFA_Risk_089)

description:
CCFA_Risk_089
Male diagnosed at age 15.75 with not IBD.


title: Not IBD Female (CCFA_Risk_088)

description:
CCFA_Risk_088
Female diagnosed at age 10.33333333 with not IBD.


title: Not IBD Male (CCFA_Risk_084)

description:
CCFA_Risk_084
Male diagnosed at age 10.25 with not IBD.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_105)

description:
CCFA_Risk_105
Male diagnosed at age 15.91666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: Not IBD Male (CCFA_Risk_082)

description:
CCFA_Risk_082
Male diagnosed at age 15.58333333 with not IBD.


title: Not IBD Male (CCFA_Risk_083)

description:
CCFA_Risk_083
Male diagnosed at age 11.41666667 with not IBD.


title: Not IBD Male (CCFA_Risk_080)

description:
CCFA_Risk_080
Male diagnosed at age 14.16666667 with not IBD.


title: CD Male with Undetermined and No Deep Ulcer (CCFA_Risk_104)

description:
CCFA_Risk_104
Male diagnosed at age 14.08333333 with CD characterized with Undetermined and no deep ulcer.

value: Undetermined


title: Not IBD Male (CCFA_Risk_081)

description:
CCFA_Risk_081
Male diagnosed at age 15.83333333 with not IBD.


title: Not IBD Male (CCFA_Risk_079)

description:
CCFA_Risk_079
Male diagnosed at age 8.5 with not IBD.


title: Not IBD Male (CCFA_Risk_078)

description:
CCFA_Risk_078
Male diagnosed at age 12.83333333 with not IBD.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_106)

description:
CCFA_Risk_106
Female diagnosed at age 13.16666667 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Female


title: Not IBD Male (CCFA_Risk_077)

description:
CCFA_Risk_077
Male diagnosed at age 7.25 with not IBD.


title: DCM_S27


title: Not IBD Female (CCFA_Risk_076)

description:
CCFA_Risk_076
Female diagnosed at age 11 with not IBD.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_075)

description:
CCFA_Risk_075
Male diagnosed at age 16.5 with CD characterized with Macroscopic inflammation and deep ulcer.

value: CD


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_073)

description:
CCFA_Risk_073
Female diagnosed at age 8.583333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: Not IBD Female (CCFA_Risk_072)

description:
CCFA_Risk_072
Female diagnosed at age 13.08333333 with not IBD.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_074)

description:
CCFA_Risk_074
Female diagnosed at age 5.416666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: DCM_S24


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_071)

description:
CCFA_Risk_071
Male diagnosed at age 10.66666667 with CD characterized with normal and no deep ulcer.

value: cCD


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_070)

description:
CCFA_Risk_070
Female diagnosed at age 8.583333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: Not IBD Female (CCFA_Risk_085)

description:
CCFA_Risk_085
Female diagnosed at age 6.583333333 with not IBD.

value: Not IBD


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_069)

description:
CCFA_Risk_069
Female diagnosed at age 12.08333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: Castrate Resistant Met (matched) (RS-01580060)

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences reads were trimmed with adaptor sequence and mapped to ensembl GRCm38 reference with anntation GTF version 71 using tophat 2.0
Reads counts are calculated by R scripts with Rsamtools and GenomicRanges package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample.

source_name: Orthotopic Tumor

growth_protocol: Myc-CaP AS or CR cell lines were injected into anterior prostate lobes of FVB male mice eith intact or surgically precastrated. Resulting primary and met tumors were utilized for RNA extraction

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor type

value: metastatic

tag: phenotype

value: castrate resistant


title: Not IBD Male (CCFA_Risk_067)

description:
CCFA_Risk_067
Male diagnosed at age 12.91666667 with not IBD.


title: Not IBD Female (CCFA_Risk_087)

description:
CCFA_Risk_087
Female diagnosed at age 11.58333333 with not IBD.


title: Castrate Resistant Primary Orthotopic Tumor (RS-01580059)

value: primary


title: Not IBD Female (CCFA_Risk_065)

description:
CCFA_Risk_065
Female diagnosed at age 12.33333333 with not IBD.


title: Not IBD Male (CCFA_Risk_064)

description:
CCFA_Risk_064
Male diagnosed at age 14.25 with not IBD.


title: Androgen Sensitive Primary Orthotopic Tumor (RS-01574311)

value: androgen sensitive


title: Castrate Resistant Primary Orthotopic Tumor (RS-01580057)


title: Androgen Sensitive Met (matched) (RS-01574312)


title: Androgen Sensitive Primary Orthotopic Tumor (RS-01574309)


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_063)

description:
CCFA_Risk_063
Female diagnosed at age 8.5 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_062)

description:
CCFA_Risk_062
Male diagnosed at age 10.66666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_057)

description:
CCFA_Risk_057
Male diagnosed at age 7.583333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: No


title: Androgen Sensitive Met (matched) (RS-01574310)


title: STAT1_BXH2_IFNG_1h

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

institute: Istituto Clinico Humanitas

description: Chromatin IP against STAT1

data_processing:
Reads pooled: Sample 19 and Sample 20; Sample 21 and Sample 22; Sample 24 and Sample 25; Sample 26 and Sample 27; Sample 28 and Sample 29.
Reads quality filtered according to the Illumina pipeline.
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and --gsize=2.72e9, --tsize=36. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *-peaks.bed: list of the peaks called by MACS having -10*log10(pvalue) >= 100

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 or BXH2/TyJ mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 5-10ug of antibody. Antibodies were pre-bound overnight to 50-100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: Macrophages were subjected to different treatment (see individual samples for details)

tag: strain

value: BMDM cells (7th day of differentiation)

tag: antibody

value: STAT1 (santa cruz, sc-592)

tag: treatment

value: IFNgamma 100U/ml for 1 hour


title: SIRT1mKO FI_RNASeq1

description: PolyA RNA sequencing

tag: cell type

value: quiescent satellite cells

value: C57Bl/6 background


title: CD Male with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_060)

description:
CCFA_Risk_060
Male diagnosed at age 13.58333333 with CD characterized with Microscopic inflammation and no deep ulcer.

value: Ileal biopsy

value: Microscopic inflammation


title: Not IBD Male (CCFA_Risk_055)

description:
CCFA_Risk_055
Male diagnosed at age 11.41666667 with not IBD.

value: Male


title: STAT1_BXH2_IFNG_4h

description: Chromatin IP against STAT1

value: IFNgamma 100U/ml for 4 hour


title: STAT1_WT_IFNG_4h

description: Chromatin IP against STAT1


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_068)

description:
CCFA_Risk_068
Male diagnosed at age 10.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: CD

value: iCD

value: Macroscopic inflammation


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_058)

description:
CCFA_Risk_058
Male diagnosed at age 16.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_061)

description:
CCFA_Risk_061
Male diagnosed at age 10.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_053)

description:
CCFA_Risk_053
Female diagnosed at age 9.166666667 with CD characterized with Microscopic inflammation and no deep ulcer.

value: Female

value: cCD


title: STAT1_WT_IFNG_1h

description: Chromatin IP against STAT1


title: WT FI_RNASeq3

description: PolyA RNA sequencing

value: WT


title: STAT1_BXH2_IFNG_2h

description: Chromatin IP against STAT1

value: IFNgamma 100U/ml for 2 hour


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_052)

description:
CCFA_Risk_052
Male diagnosed at age 16.08333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: No


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_051)

description:
CCFA_Risk_051
Male diagnosed at age 8.75 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Yes


title: STAT1_WT_IFNG_2h

description: Chromatin IP against STAT1

value: BMDM cells (7th day of differentiation)

value: STAT1 (santa cruz, sc-592)


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_066)

description:
CCFA_Risk_066
Male diagnosed at age 8.416666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Microscopic inflammation and Deep Ulcer (CCFA_Risk_059)

description:
CCFA_Risk_059
Male diagnosed at age 9.42 with CD characterized with Microscopic inflammation and deep ulcer


title: STAT1_WT_IFNG_UT

description: Chromatin IP against STAT1

value: No treatment


title: STAT1_BXH2_IFNB_2h

description: Chromatin IP against STAT1

value: IFNbeta 100U/ml for 2 hour


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_050)

description:
CCFA_Risk_050
Male diagnosed at age 13.41666667 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Ileal biopsy


title: STAT1_BXH2_IFNB_1h

description: Chromatin IP against STAT1

value: IFNbeta 100U/ml for 1 hour


title: Castrate Resistant Met (matched) (RS-01580058)

value: metastatic

value: castrate resistant


title: STAT1_BXH2_IFNG_UT

description: Chromatin IP against STAT1


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_056)

description:
CCFA_Risk_056
Female diagnosed at age 13.25 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: CD


title: STAT1_BXH2_IFNB_4h

description: Chromatin IP against STAT1

value: IFNbeta 100U/ml for 4 hour


title: STAT1_BXH2_IFNB_UT

description: Chromatin IP against STAT1


title: STAT1_WT_IFNB_4h

description: Chromatin IP against STAT1


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_046)

description:
CCFA_Risk_046
Female diagnosed at age 15.16666667 with CD characterized with Macroscopic inflammation and deep ulcer.

value: iCD

value: Macroscopic inflammation


title: STAT1_WT_IFNB_2h

description: Chromatin IP against STAT1


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_045)

description:
CCFA_Risk_045
Male diagnosed at age 5.416666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: Male


title: STAT1_WT_IFNB_1h

description: Chromatin IP against STAT1


title: Not IBD Male (CCFA_Risk_054)

description:
CCFA_Risk_054
Male diagnosed at age 2.333333333 with not IBD.

value: Not IBD


title: Not IBD Male (CCFA_Risk_044)

description:
CCFA_Risk_044
Male diagnosed at age 9.166666667 with not IBD.


title: STAT1_WT_IFNB_UT

description: Chromatin IP against STAT1


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_043)

description:
CCFA_Risk_043
Female diagnosed at age 12.08333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: Female


title: IRF1_WT_LPS_2h

description: Chromatin IP against IRF1

value: IRF1 (santa cruz, sc-640)

value: LPS 10ng/ml for 2 hours