title: Macrophage MCSF withdrawal

description: small RNA-seq

data_processing:
The image analysis and base calling were carried using standard Illumina pipeline.
The small RNA-seq reads were aligned to the sequences of interest by using BLAT.
Genome_build: hg18
Supplementary_files_format_and_content: the format of the output file corresponds to the standard BLAT output format.

source_name: macrophage

extract_protocol:
The bone marrow-derived macrophages were treated in M-CSF withdrawal medium and RNA was harvested using Trizol reagent. Illumina Small RNA v1.5 Sample Prep Kit (Cat#FC-930-1501) was used with 10 ug of total RNA for the construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: Doxycycline-treated sample 3 [D2-2_S5_L001]

status: Public on Sep 16 2015

type: SRA

city: Gainesville

first: Stephen

last: Sugrue

address: 1600 SW Archer Road

country: USA

institute: University of Florida

library_source: transcriptomic

data_processing:
Distinct reads were aligned as single-ended reads to sequences corresponding to splicing junctions and intron retention events using Bowtie (v0.12.9; --best –tryhard –strata -v3 -m 1)
Distinct reads were aligned as single-ended reads to the hg19 build of the human genome (GRCh37/hg19) using BWA-MEM (0.7.2) for genomic alignments
Using AceView annotations (August 2010 release), overlapping exons were combined into the maximum exonic region in a strand-dependent manner
Expression was quantified using average depth per nucleotide (APN)
Genome_build: GRCh37/hg19

molecule: total RNA

organism: Homo sapiens

source_name: Doxycycline-treated sample 3, technical replicate

growth_protocol: Doxycycline-inducible PNN knockdown HCET cell were grown in a modified DMEM media (Joo et al., 2005. Mol Vis 11:133-42)

extract_protocol:
Total RNA was extracted using Rneasy Plus Mini Kit (Qiagen) using their standard protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce shRNA expression, the cells were treated with doxycycline at a concentration of 1 μg/ml with daily change of fresh doxycycline medium for 48 to 72h.

value: HCET

tag: shRNA

value: doxycycline-inducible shRNA against PNN

tag: treatment

value: Doxycycline treated


title: SLE22

city: South San Francisco

first: Tiffany

last: hung

state: CA

address: 1 DNA Way

department: Human Genetics

institute: Genentech

description:
SAM8749922
Processed data file: SLE_Alu_counts.txt

data_processing:
Illumina software CASAVA used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for rRNA contamination, filtered for low-complexity or low-quality sequence, then mapped to hg19 whole genome using GSNAP.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: SLE_RPKMs.txt: Tab-delimited text file includes RPKM values for each patient and control.

source_name: PAXgene blood, SLE, no anti-Ro, ISM_low

extract_protocol:
RNA was extracted from PAXgene tubes.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease status

value: systemic lupus erythematosus (SLE)

tag: tissue

value: whole blood

tag: anti-ro

tag: ism


title: Doxycycline-treated sample 2 [D1-3_S8_L004]

source_name: Doxycycline-treated sample 2, technical replicate


title: Doxycycline-treated sample 1 [D1-2_S4_L003]

source_name: Doxycycline-treated sample 1, technical replicate


title: SLE17

description:
SAM8749945
Processed data file: SLE_Alu_counts.txt


title: SLE20

description:
SAM8750045
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 2 [D1-3_S8_L003]


title: Doxycycline-treated sample 2 [D1-3_S8_L002]


title: Doxycycline-treated sample 1 [D1-2_S4_L002]


title: SLE19

description:
SAM8749980
Processed data file: SLE_Alu_counts.txt


title: SLE21

description:
SAM9260118
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 1 [D1-2_S4_L004]


title: SLE18

description:
SAM9103793
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 1 [D1-2_S4_L001]


title: SLE28

description:
SAM8750005
Processed data file: SLE_Alu_counts.txt


title: Control sample 4 [C3-2_S3_L003]

source_name: Control sample 4, technical replicate

value: untreated


title: SLE12

description:
SAM8749953
Processed data file: SLE_Alu_counts.txt


title: SLE14

description:
SAM8750103
Processed data file: SLE_Alu_counts.txt


title: Doxycycline-treated sample 2 [D1-3_S8_L001]


title: SLE15

description:
SAM8750108
Processed data file: SLE_Alu_counts.txt


title: SLE35

description:
SAM8749978
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, high anti-Ro, ISM_high

value: high


title: SLE9

description:
SAM8750012
Processed data file: SLE_Alu_counts.txt


title: SLE13

description:
SAM8749967
Processed data file: SLE_Alu_counts.txt


title: SLE16

description:
SAM8750087
Processed data file: SLE_Alu_counts.txt


title: Control sample 4 [C3-2_S3_L002]


title: SLE10

description:
SAM8750002
Processed data file: SLE_Alu_counts.txt


title: Control sample 4 [C3-2_S3_L001]


title: Control sample 3 [C2-2_S2_L004]

source_name: Control sample 3, technical replicate


title: SLE8

description:
SAM8750143
Processed data file: SLE_Alu_counts.txt


title: Control sample 4 [C3-2_S3_L004]


title: Control sample 3 [C2-2_S2_L002]


title: Control sample 3 [C2-2_S2_L001]


title: SLE6

description:
SAM8749983
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, med anti-Ro, ISM_low

value: med


title: Control sample 2 [C1-3_S7_L003]

source_name: Control sample 2, technical replicate


title: SLE7

description:
SAM8750097
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, med anti-Ro, ISM_high


title: SLE11

description:
SAM8749887
Processed data file: SLE_Alu_counts.txt


title: SLE5

description:
SAM9260122
Processed data file: SLE_Alu_counts.txt


title: Control sample 2 [C1-3_S7_L002]


title: SLE2

description:
SAM8749896
Processed data file: SLE_Alu_counts.txt


title: Control sample 2 [C1-3_S7_L004]


title: SLE4

description:
SAM8749988
Processed data file: SLE_Alu_counts.txt

source_name: PAXgene blood, SLE, high anti-Ro, ISM_low


title: Control sample 1 [C1-2_S1_L003]

source_name: Control sample 1, technical replicate


title: Null 3

description:
GM12878 KO3
SAM19353346
Processed data file: GM12878submission_RPKMs.xls

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for rRNA contamination, filtered for low-complexity or low-quality sequence, then mapped to hg19 whole genome using GSNAP.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample.

source_name: GM12878, Ro60 null, untreated

growth_protocol: 15% FBS, Pen/Strep, Glutamax.

extract_protocol:
TRIZOL, RNeasy, Turbo DNase, 1 ug of RNA used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Untreated control or IFNa 1000 U/ml for 6 hours.

tag: cell line

tag: cell type

value: ENCODE EBV-immortalized B cell line

tag: genotype/variation

value: Ro60 null

tag: clone


title: Null 3 IFN

description:
GM12878 KO3 + IFNa
SAM19590766
Processed data file: GM12878submission_RPKMs.xls

source_name: GM12878, Ro60 null, IFNa

value: IFNa


title: Control sample 3 [C2-2_S2_L003]


title: SLE3

description:
SAM8750015
Processed data file: SLE_Alu_counts.txt


title: Control sample 1 [C1-2_S1_L004]


title: Control sample 1 [C1-2_S1_L002]


title: SLE1

description:
SAM8749913
Processed data file: SLE_Alu_counts.txt


title: Null 2 IFN

description:
GM12878 KO2 + IFNa
SAM19590765
Processed data file: GM12878submission_RPKMs.xls


title: Null 2

description:
GM12878 KO2
SAM19353350
Processed data file: GM12878submission_RPKMs.xls


title: Null 1 IFN

description:
GM12878 KO1 + IFNa
SAM19590764
Processed data file: GM12878submission_RPKMs.xls


title: Null 1

description:
GM12878 KO1
SAM19353342
Processed data file: GM12878submission_RPKMs.xls


title: M8

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Transcriptomic maps of single-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the University of California Santa Cruz (UCSC) hg19 reference transcriptome (2014) from the Illumina iGenomes resource using the fr-firststrand setting.
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Lucas-Brosens_Processed Data_TPMs.txt contains TPM values

source_name: Human Endometrial Pipelle Biopsy

extract_protocol:
Whole endometrial tissue pipelle biopsies were placed in RNA later immediately following biopsy (<1 min).  Following overnight incubation at 4 degrees C, samples were removed from RNA later and stored at -80 degrees C.  Total RNA was extracted using RNA STAT-60 reagent according to the manufacturer's protocol.  Purified RNA was treated using Invitrogen Amplification Grade DNase I, followed by ethanol precipitation and clean-up.  DNA-free RNA was submitted to Source Bioscience (Nottingham, UK) for library preparation and sequencing.
Library preparation was performed using Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions.  The libraries were validated on the Agilent BioAnalyser 2100 to check the size distribution of the libraries and on the Qubit High Sensitivity to check the concentration of the samples.  Samples were pooled and pools were loaded at a concentration of 8pM onto 2 lanes of an Illumina HiSeq2000 flow cell v3.

value: Endometrial pipelle biopsy

tag: cycle day

tag: live births

tag: first trimester losses

tag: age

tag: bmi


title: M9


title: M10


title: Wildtype II IFN

description:
GM12878 II + IFNa
SAM19590768
Processed data file: GM12878submission_RPKMs.xls

source_name: GM12878, wildtype, IFNa

value: wildtype

tag: replicate

value: II


title: M6


title: h2bub_KO_ChIPSeq

city: Shanghai

first: Gang

last: Wang

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology,

country: China

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

library_source: genomic

data_processing:
CASAVA version 1.6 used for base-calling
Sequencing reads were alligned to mouse genome by Bowtie version 0.12. 8 and parameters are followings:-v1, --best, --strata, -k2, -m1
Peak calling was performed independently for each sample using MACS software version 1.4.2 by p-value threshold of 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files were generated using MACS version 1.4.2. Scores represent fragments pileup at every 10 bps of ChIP-seq.

molecule: genomic DNA

organism: Mus musculus

source_name: MEFs cells knockout MED23

growth_protocol: MEFs cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (vol/vol) FBS (Hyclone)

extract_protocol:
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (Millipore, Cat. #05-1312, Lot #DAM1567819); Pol II (N20, Santa Cruz, Cat. sc-899).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic fibroblast

value: MED23 knockout

tag: chip antibody


title: Wildtype I IFN

description:
GM12878 I + IFNa
SAM19590767
Processed data file: GM12878submission_RPKMs.xls

value: I


title: M5


title: Wildtype II

description:
GM12878 II
SAM19353355
Processed data file: GM12878submission_RPKMs.xls

source_name: GM12878, wildtype, untreated


title: M7


title: h2bub_WT_ChIPSeq

source_name: MEFs cells wildtype


title: 3. PBMC

description:
SAM2707857
Processed data file: PBMC_RPKMs.xls

source_name: human blood donor peripheral blood monocyte, untreated

extract_protocol:
RNeasy purification, 1 ug of RNA used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Untreated control or IFNa 1000 U/ml for 6 hours (Sigma).

tag: disease state

value: healthy

value: peripheral blood monocytes

tag: donor id

value: C


title: 6. PBMC + IFNa

description:
SAM2707858
Processed data file: PBMC_RPKMs.xls

source_name: human blood donor peripheral blood monocyte, IFNa

tag: treatment

value: interferon-alpha


title: 5. PBMC + IFNa

description:
SAM2707861
Processed data file: PBMC_RPKMs.xls

value: A


title: M2

tag: tissue


title: 2. PBMC

description:
SAM2707863
Processed data file: PBMC_RPKMs.xls

value: B


title: M3


title: 1. PBMC

description:
SAM2707860
Processed data file: PBMC_RPKMs.xls


title: Control sample 2 [C1-3_S7_L001]

value: HCET

tag: shRNA

value: doxycycline-inducible shRNA against PNN

value: untreated


title: M4


title: M1


title: C9


title: C7


title: 4. PBMC + IFNa

description:
SAM2707864
Processed data file: PBMC_RPKMs.xls


title: C8


title: C6


title: C5


title: C2


title: C3


title: C4


title: C1


title: PER2 siRNA 2

data_processing:
Transcriptomic maps of single-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the University of California Santa Cruz (UCSC) hg19 reference transcriptome (2014) from the Illumina iGenomes resource using the fr-firststrand setting.
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Count and TPM data

source_name: Endometrial stromal cells

growth_protocol: Human Endometrial Stromal Cells were prepared and maintained in culture as described (Brosens 1999).

extract_protocol:
RNA was purified using RNA STAT-60 (AMS Bio) according to manufacturer's instructions and treated using Amplification Grade DNase I (Invitrogen) followed by ethanol precipitation and clean-up.  RNA quality was examined using the Agilent Bioanalyser 2100 and all samples had a RIN ≥8.9
Library preparation was performed using Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions.  The libraries were validated on the Agilent BioAnalyser 2100 to check the size distribution of the libraries and on the Qubit High Sensitivity to check the concentration of the samples.  Samples were pooled and pools were loaded at a concentration of 8pM onto 2 lanes of an Illumina HiSeq2000 flow cell v3.

treatment_protocol: HESCs were transfected with 50nM small interfering siRNA (PER2-siGENOME SMARTpool or siGENOME Non-Targeting siRNA Pool1 (Thermo Fisher Scientific, Waltham, MA, USA)) by jetPRIME Polyplus transfection kit (VWR Internation, Radnor, PA, USA)

tag: patient

value: Endometrial stromal cells

tag: phenotype

value: PER2 knockdown (PER2 siRNA)


title: PER2 siRNA 3

tag: cell type


title: Wildtype I

description:
GM12878 I
SAM19353354
Processed data file: GM12878submission_RPKMs.xls

tag: cell line

value: ENCODE EBV-immortalized B cell line

tag: genotype/variation


title: Non Targeting Control 2

value: Wild type (Non targeting siRNA)


title: K562 Ro60 iCLIP

data_processing:
Illumina software used for basecalling.
Reads were mapped to human genome build hg19 using STAR (https://code.google.com/p/rna-star/) with the "outFilterMultimapNmax 20" option, then PCR duplicates were removed using unique nmers in the barcode sequence. Peak calling was performed using pyicoclip (http://regulatorygenomics.upf.edu/Software/Pyicoteo/pyicoclip.html) using RefSeq genes as the region file.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Bed files include peaks.

source_name: K562, Ro60 iCLIP

growth_protocol: RPMI, 15% FBS, Pen/Strep, Glutamax.

extract_protocol:
TRIZOL, mirVANA column, Turbo DNase.
RNA libraries were prepared for sequencing using published protocol at: http://www.jove.com/video/2638/iclip-transcriptome-wide-mapping-protein-rna-interactions-with

treatment_protocol: IFNa 1000 U/ml for 6 hours.

value: ENCODE cell line lymphocyte

tag: antibody

value: anti-Ro60 (AA-3) (Santa Cruz Biotech, sc-100844)


title: Non Targeting Control 3


title: Control sample 1 [C1-2_S1_L001]


title: Non Targeting Control 1


title: GM12878 Ro60 iCLIP

source_name: GM12878, Ro60 iCLIP

value: ENCODE cell line B lymphocyte


title: Control Villus biological rep 2

status: Public on Sep 15 2015

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.9
ChIP-Seq - peak calling: MACS, version 1.4.2, considering input and local background, p<0.0001 cutoff.
RNA-Seq - normalized and differential expression: Cufflinks, version 2.1.1; settings: -b, -u, and default; Cuffmerge was used with custom 3' 1000 bp reference gtf and default settings;  Cuffnorm was used with default settings; Cuffdiff was used with -b, -u and default settings.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: Bed file for significant peaks, bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: There are two processed data matrices that apply to all the samples.  First, is the normalized expression table, prepared using Cuffnorm, which contains the normalized Log2(FPKM+1) expression values for all 9 RNA-seq samples.  The second is the differential expression table, prepared using Cuffdiff with an FDR of 5%, which contains average FPKM values for villus, control ISC and Cdx2-del ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing. The third is the custom gtf used in cuffdiff for correction of 3' bias in the RNA-seq samples.

source_name: Control mouse villus cells

growth_protocol: Epithelium from mouse jejunum was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Epithelium was frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA.
The TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 4-5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

tag: strain

value: B6;129 mixed background

value: Adult jejunum villus

tag: genotype

value: Cdx2F/F; Cre-


title: Control Villus biological rep 1


title: Control Villus biological rep 3


title: Family1263-Affected Clone5

city: New York

first: Joseph

last: Gleeson

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Reads prepped by TopHat
Alignment of fastqs via bowtie
Splice junctions called via TopHat
Transcript assembly by Cufflinks
Test for differential expression – Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: .diff files Generated from cuffdiff, represent differential gene, isoform, etc. expression comparisons between all samples
Supplementary_files_format_and_content: .bed files generated by TopHat, represent insertions, deletions and splice junctions

molecule: polyA RNA

source_name: Neural progenitor cells

growth_protocol: DMEM/F12 + .5xN2/B27 + 20ng/ml bFGF

extract_protocol:
Trizol
TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: No treatment

value: Dorsal Forebrain Equivalent

value: induced pluripotent stem cells

tag: patient diagnosis

value: Lissencephaly


title: MDS-9209-Affected Clone5


title: Family1101-Affected Clone5


title: Gp5

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Base calling was performed on instrument using real time analysis (RTA) followed by demultiplexing using CASAVA version 1.81
Reads were aligned to hg19 using TopHat version 2.0.11 with bowtie2 version 2.1.0 specifying library strategy as first-strand
Transcript abundance (reported as FPKM) was generated using cufflinks version 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Text-tab delimited file with FPKM for each Sample

source_name: colon

growth_protocol: The colon cancer cell line HCT116 was maintained in DMEM supplemented with 10% FBS and 1% antibiotics in 5% CO2

extract_protocol:
Nuclear lysates were incubated with an anti-flag antibody overnight to IP flag-DNMT1, and the entire complex was isolated using magnatic beads.  The crosslinking was reversed and RNA was isolated via trizol
RNA-seq libraries were constructed using ScriptSeq V2 (Illumina) kit as recommended by the manufacturer

treatment_protocol: Cells were crosslinked with 0.3% formaldehyde for 10 minutes to preserve RNA-protein interactions

tag: gender

value: male


title: Gp2


title: Family1101-Unaffected Clone6

value: Healthy


title: BYSMV-Small RNA

city: Beijing

first: Xian-Bing

state: Beijing

address: Yuanmingyuan West Road

institute: China Agricultural University

description: CAGATC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2
All trimmed sequences in length of 18-30nt were aligned with BYSMV genome and allowed two-mismatched reads were used for all further analysis.
the small RNA that unmatched with BYSMV represent plant reads
Supplementary_files_format_and_content: small RNA sequences and their read numbers

organism: Triticum aestivum

source_name: BYSMV-Small RNA

growth_protocol: Wheat in soil and room temperature

extract_protocol:
TRIzol reagent and seperated 18- to 30- small RNA
NEBNext Multiplex Small RNA Library Preparation kit

treatment_protocol: Mock or BYSMV infected

value: leave


title: Gp4


title: PER2 siRNA 1


title: Family1101-Affected Clone3


title: Sample_50_human_GCB_R4

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
CPM were obtained using Rsubread
Methylcall files were obtained using EERBS pipeline
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited

extract_protocol: ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

treatment_protocol: Included as additional column of SAMPLES section

value: germinal center B


title: MOCK-Small RNA

description: GATCAG

source_name: MOCK-Small RNA


title: Family1101-Unaffected Clone4


title: Sample_49_human_GCB_R3


title: Sample_46_human_NB_R4

value: naive


title: MI Sample 33

city: Framingham

first: Andrew

middle: Danner

last: Johnson

state: MASSACHUSETTS

address: The Framingham Heart Study

department: Cardiovascular Epidemiology and Human Genomics Branch

institute: National Heart, Lung and Blood Institute

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format.
Paired-end reads were aligned to RefSeq using TopHat2.
RNA reads-per-kilobase-per million mapped (RPKM) was calculated with RSeQC v2.3.9.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM and read counts were calcualted with RSeQC v2.3.9

source_name: Plalelets

extract_protocol:
Total RNA was purified from Trizol-treated samples and treated with DNase. The quality of resulting RNA was assessed by Bioanalyzer assay.
DNA-free total RNA was used as input for library construction using Ovation RNA Seq v.2 kits (NuGen, Inc., San Carlos, CA). STEMI and NSTEMI samples were batched in two groups of 16 to balance case status, age and gender across batches. After the final amplification step, libraries were size selected between 250 to 450 base pairs. The lab was blinded from case status during library preparation and sequencing.

treatment_protocol: Arterial blood samples were collected with 8mL CPT tubes (Becton Dickinson, Franklin Lakes, NJ) for RNA-seq, with sodium citrate (3.8%) from each participant at the beginning and end of their cardiac catheterization procedure.  CPT tubes were centrifuged at 1700 x g for 25 minutes at room temperature. After centrifugation, mononuclear cells and platelets were collected and centrifuged at 288 x g to obtain platelets. Platelets were pelleted by centrifugation, and lysed with RLT solution (Qiagen, Germantown, MD), and platelet lysate was kept at -80C.

tag: study id

tag: mi type

value: STEMI

tag: batch

value: F

tag: age (y)

tag: bmi (kg/m2)

tag: ht

value: Yes

tag: dyslipidemia

tag: cad

value: No

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: non-MI Sample 2

tag: mi type

value: non-myocardial infarction control


title: Input

tag: gender

tag: cell line


title: Sample_43_human_NB_R1

tag: cell type


title: Sample_45_human_NB_R3


title: MI Sample 31

tag: study id

tag: batch

value: M

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose


title: MI Sample 30

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: ca

tag: hr (bpm)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: C10

tag: tissue

value: Endometrial pipelle biopsy

tag: cycle day

tag: live births

tag: first trimester losses

tag: age

tag: bmi


title: MI Sample 32

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MDS-9209-Affected Clone3

tag: tissue

tag: cell type

tag: patient diagnosis


title: NoIP-LP-Replica2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8), default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the fission yeast ASM294v2 genome assembly using Bowtie v2.2.4 with default parameters. Aligned data were quantified using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/), reporting the average reads count for 200bp windows, with an overlap of 100bp between each window.
Genome_build: ASM294v2
Supplementary_files_format_and_content: ChIP-Seq Quantified data file is delimted and contain the following 7 columns: (1) Chromosome; (2) Start; (3) End; (4) Gene ID (Pombase) (5) Description (Pombase); (6-15) Average Reads Count

organism: Schizosaccharomyces pombe

source_name: Fission Yeast Cells

extract_protocol:
Chromatin was extracted by glass bead cell lysis. Sonicated cell lysates containing chromatin were clarified and used for the immunoprecipitation step. 40µl of GFP-Trap agarose beads (Chromotek) were incubated with 300µl of chromatin extract, overnight at 4˚C. Cross-link was reversed and DNA purified using QIAquick PCR purification column.
ChIP DNA from each sample was used undiluted for library construction. Library preparation has been performed with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs), with the following modifications: indexing was performed using the TruSeq system and for library amplification KAPA HiFi Polymerase (KAPA Biosystem) was used. Quality control was carried out by Bioanlyzer 2100 system (Agilent) and qPCR quantification by KAPA Library Quantification Kit (KAPA Biosystem). 50bp or 100bp single-end sequencing was performed on pooled libraries using respectively a MiSeq or HiSeq 2500 (Illumina) (see table).

treatment_protocol:
High Phosphate Condition: Cells were grown overnight in YES (Yeast Extract Supplemented) media to mid-log phase. Cultures were washed twice in water and resuspended in 50 ml YES media to a final concentration of 0.5 O.D./ml. After 4 hours growth at 30˚C, cell concentration was normailised to 0.5 O.D./ml, then 3% final Formaldehyde was added for 30 minutes, at 30˚C in agitation. Fixation was stopped by the additon glycine at 125mM final. Fixed cells were washed twice in water, pelleted and snap-frozen in liquid nitrogen for chromatin extraction.
Low Phosphate Condition: Cells were grown overnight in YES (Yeast Extract Supplemented) media to mid-log phase. Cultures were washed twice in water and resuspended in 50 ml YES LowPi media to a final concentration of 0.5 O.D./ml. After 4 hours growth at 30˚C, cell concentration was normailised to 0.5 O.D./ml, then 3% final Formaldehyde was added for 30 minutes, at 30˚C in agitation. Fixation was stopped by the additon glycine at 125mM final. Fixed cells were washed twice in water, pelleted and snap-frozen in liquid nitrogen for chromatin extraction.

tag: strain

value: wild-type

tag: condition

value: Low Phosphate


title: MI Sample 29

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: NoIP-LP-Replica1

tag: strain

tag: condition


title: Sample_48_human_GCB_R2

tag: cell type


title: Sample_47_human_GCB_R1


title: Myo1-GFP-LP-Replica1


title: Myo1-GFP-LP-Replica2


title: MI Sample 27

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 26

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: Sample_44_human_NB_R2

tag: cell type


title: MI Sample 22

tag: study id

tag: mi type

tag: batch

tag: gender

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 23

tag: study id

tag: mi type

value: NSTEMI

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: non-MI Sample 1

tag: mi type


title: MI Sample 34

tag: study id

tag: batch

tag: gender

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 24

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: Myo1-GFP-LP-Replica3

tag: strain

tag: condition


title: MI Sample 25

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: Myo1-GFP-HP-Replica3

tag: strain

tag: condition

value: High Phosphate


title: NoIP-HP-Replica1


title: MI Sample 20

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: Myo1-GFP-HP-Replica2

tag: strain

tag: condition


title: MI Sample 28

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 21

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: dyslipidemia

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: Myo1-GFP-HP-Replica1

tag: strain

tag: condition


title: MI Sample 19

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 18

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: dyslipidemia

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: C7-wildtype-LP-10h-Replica3

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the fission yeast ASM294v2 genome assembly using TopHat v2.0.12, guided by gene models from Pombase. Raw counts for DESeq2 analysis were generated at mRNA level using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are delimted and contain the following 7 columns: (1) Gene ID (Pombase); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Pombase); (7-30) Raw Counts

extract_protocol:
RNA was isolated using the hot acid phenol method. 1µg of RNA for each sample has been taken and digested with DNAseI (ThermoScientific), accordingly to manifacturer indication.
Poly-A fraction was isolated using theNEBNext® mRNA Isolation Module (New England Biolabs) from 1µg of DNA-free RNA. Purified mRNA was processed using NEBNext® Ultra™ RNA Library Prep Kit (New England Biolabs), with the following modifications: indexing was performed using the iPCR system and for library amplification KAPA HiFi Polymerase (KAPA Biosystem) was used. Quality control was carried out by Bioanlyzer 2100 system (Agilent) and qPCR quantification by KAPA Library Quantification Kit (KAPA Biosystem). 50bp paired-end sequencing was performed on pooled libraries using a HiSeq 2500 (Illumina) in RapidRun mode.

treatment_protocol:
High Phosphate Condition: Cells were grown overnight in YES (Yeast Extract Supplemented) media to mid-log phase. Cultures were washed twice in water and resuspended in YES media to a final concentration of 0.05 O.D./ml. Aliquotes were taken at after 4 and 10 hours, approximately 5 O.D. of cells were taken and cell pellets were snap-frozen in liquid nitrogen for RNA Extraction.
Low Phosphate Condition : Cells were grown overnight in YES (Yeast Extract Supplemented) media to mid-log phase. Cultures were washed twice in water and resuspended in phosphate depleted YES media (YES LowPi) to a final concentration of 0.05 O.D./ml. Aliquotes were taken at after 4 and 10 hours, approximately 5 O.D. of cells were taken and cell pellets were snap-frozen in liquid nitrogen for RNA Extraction.

tag: strain

tag: condition

tag: timepoint

value: 10 hours


title: MI Sample 17

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: C8-Del_myo1-LP-10h-Replica3

tag: strain

tag: condition

tag: timepoint


title: C5-wildtype-HP-10h-Replica3


title: MI Sample 16

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: MI Sample 14

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: C6-Del_myo1-HP-10h-Replica3

tag: strain

tag: condition

tag: timepoint


title: MI Sample 15

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: C4-Del_myo1-LP-4h-Replica3

tag: strain

tag: condition

tag: timepoint

value: 4 hours


title: C3-wildtype-LP-4h-Replica3


title: NoIP-HP-Replica2


title: MI Sample 11

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 9

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: B7-wildtype-LP-10h-Replica2

tag: strain

tag: condition

tag: timepoint


title: MI Sample 8

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: B8-Del_myo1-LP-10h-Replica2

tag: strain

tag: condition

tag: timepoint


title: C1-wildtype-HP-4h-Replica3


title: MI Sample 12

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: B6-Del_myo1-HP-10h-Replica2

tag: strain

tag: condition

tag: timepoint


title: B5-wildtype-HP-10h-Replica2


title: Sample_41_AicdaKO_GCB_R9

tag: cell type

tag: treatment

value: Immunized intraperitoneally with NP-CGG ratio 20-25 in alum (1:1) to induce GC formation

tag: age

value: 10- to 12-weeks


title: C2-Del_myo1-HP-4h-Replica3


title: Sample_40_AicdaKO_GCB_R8

value: germinal center B


title: MI Sample 7

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 5

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: Sample_42_AicdaKO_GCB_R10

tag: cell type

tag: treatment

tag: age


title: MI Sample 4

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: MI Sample 2

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: MI Sample 1

tag: study id

tag: mi type

tag: batch

tag: hx smoking

tag: pk/year

tag: current smoking

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: B1-wildtype-HP-4h-Replica2

tag: strain

tag: condition

tag: timepoint


title: B2-Del_myo1-HP-4h-Replica2


title: MI Sample 13

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: hx smoking

tag: pk/year

tag: current smoking

tag: sbp (mmhg)

tag: dbp (mmhg)

tag: rr

tag: asa

tag: plavix

tag: gpiib/iiia

tag: ticagrelor

tag: prasugrel

tag: statin

tag: heparin/lovenox


title: A8-Del_myo1-LP-10h-Replica1

tag: strain

tag: condition

tag: timepoint


title: MI Sample 10

tag: study id

tag: mi type

tag: batch

tag: gender

tag: age (y)

tag: bmi (kg/m2)

tag: ht

tag: dyslipidemia

tag: cad

tag: pk/day

tag: troponin (at presentation)

tag: 2nd troponin

tag: hg (g/dl)

tag: hct (%)

tag: platelets (1000s/mm3)

tag: k

tag: cl

tag: bun

tag: creatinine

tag: glucose

tag: ca

tag: hr (bpm)


title: Sample_36_AicdaKO_NB_R8

tag: cell type

value: naive

tag: treatment

tag: age


title: A4-Del_myo1-LP-4h-Replica1

tag: strain

tag: condition

tag: timepoint


title: Sample_33_WT_GCB_R10


title: Sample_35_AicdaKO_NB_R7


title: A6-Del_myo1-HP-10h-Replica1


title: A7-wildtype-LP-10_h-Replica1


title: A5-wildtype-HP-10h-Replica1


title: B4-Del_myo1-LP-4_h-Replica2


title: Sample_39_AicdaKO_GCB_R7


title: Sample_38_AicdaKO_NB_R10


title: Sample_31_WT_GCB_R8


title: A1-wildtype-HP-4h-Replica1


title: Sample_37_AicdaKO_NB_R9


title: A2-Del_myo1-HP-4_h-Replica1


title: Sample_30_WT_NB_R11


title: Sample_26_AicdaKO_GCB_R6


title: Sample_24_AicdaKO_GCB_R4


title: Sample_27_WT_NB_R8


title: Sample_25_AicdaKO_GCB_R5


title: Sample_29_WT_NB_R10


title: Sample_34_WT_GCB_R11


title: Sample_21_AicdaKO_GCB_R1


title: Sample_20_AicdaKO_NB_R6


title: Sample_32_WT_GCB_R9


title: Sample_23_AicdaKO_GCB_R3


title: Sample_17_AicdaKO_NB_R3


title: Sample_19_AicdaKO_NB_R5


title: B3-wildtype-LP-4h-Replica2


title: Sample_13_WT_GCB_R6


title: Sample_16_AicdaKO_NB_R2


title: Sample_22_AicdaKO_GCB_R2


title: Sample_11_WT_GCB_R4


title: Sample_12_WT_GCB_R5


title: Sample_18_AicdaKO_NB_R4


title: Sample_28_WT_NB_R9


title: Sample_14_WT_GCB_R7


title: Sample_10_WT_GCB_R3


title: Sample_8_WT_GCB_R1


title: Sample_9_WT_GCB_R2


title: Sample_7_WT_NB_R7


title: Sample_6_WT_NB_R6


title: Sample_3_WT_NB_R3


title: Sample_5_WT_NB_R5


title: Cdx2-del ISC biological rep 2

source_name: Cdx2-del mouse intestinal stem cells

growth_protocol: Crypts from the proximal 2/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry.

extract_protocol:
poly-A RNA was extracted with oligo dT magnetic beads (New England Biolabs) followed by DNase treatment with the RNeasy kit (Qiagen).
The Encore Complete RNA-Seq Library System (Nugen) was used, modified for 1/2 volume reactions. 200-450 bp fragments were submitted for sequencing 50 bp single-end reads on an Illumina Hi-Seq 2000 instrument.

value: B6;129 mixed background

value: Adult intestinal stem cell; proximal 2/3 of intestine

tag: genotype

value: Cdx2F/F; Lgr5-EGFP-IRES-CREERT2


title: Sample_4_WT_NB_R4


title: Cdx2-del ISC biological rep 3


title: Cdx2-del ISC biological rep 1


title: ISC Input

source_name: Control mouse intestinal stem cells

growth_protocol: Crypts from the proximal 2/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Crypts were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C and Lgr5-GFP-HI intestinal stem cells were sorted by flow cytometry. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.

extract_protocol:
Whole cell lysates were sonicated, but not immunoprecipitated.
The ThruPLEX-FD Prep Kit (Rubicon Genomics) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.

treatment_protocol: Not injected with tamoxifen.

value: Cdx2+/+; Lgr5-EGFP-IRES-CREERT2


title: Sample_1_WT_NB_R1


title: Control ISC biological rep 3


title: Control ISC biological rep 1


title: 600 Resistant 5.3S line BRD4 ChIP

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mm10 mouse genome using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed files from MACS2 for each sample

source_name: 600 Resistant 5.3S line

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: Cell lines were grown in 0.1% DMSO or 600nM of I-BET151

tag: tissue

value: haematopoietic progenitors

tag: cell line

tag: cultured in

tag: phenotype

value: BET inhibitor resistant

tag: chip antibody

tag: chip antibody vendor

value: Bethyl Labs

tag: chip antibody cat. #

tag: chip antibody lot #


title: Sensitive 5.3 line Rep 3 [RNA-seq]

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mouse genome (Ensembl Release 75, Feb 2014) using Subread
Reads were assigned to genes using featureCounts and normalised with voom. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of raw read counts and normalized expression values for all Samples

source_name: Sensitive 5.3 line

extract_protocol:
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)

value: 0.1% DMSO

value: BET inhibitor sensitive


title: Sensitive 5.3 line BRD4 ChIP


title: Sensitive 5.3 line Rep 1 [RNA-seq]


title: Sensitive 5.3 line BRD2 ChIP


title: 600 Resistant 5.3S line BRD2 ChIP


title: Sample_15_AicdaKO_NB_R1


title: 600 Resistant 5.3S line Rep 3 [RNA-seq]

source_name: Resistant 5.3S line


title: 600 Resistant 5.3S line Rep 2 [RNA-seq]


title: CDX2 ISC ChIP-Seq

extract_protocol:
Whole cell lysates were sonicated and incubated with 3 ug CDX2 antibody overnight (Bethyl Labs; A300-691A) for immunoprecipitation.
The ThruPLEX-FD Prep Kit (Rubicon Genomics) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.


title: Sensitive 5.3 line BRD3 ChIP


title: 600 Resistant 5.3S line Rep 1 [RNA-seq]


title: 600 Resistant 5.3S line BRD3 ChIP


title: Sensitive 5.3 line Rep 2 [RNA-seq]


title: cRSS-chr1-rep3

first: Jiazhi

last: Hu

address: 300 Longwood Ave

department: PCMM

institute: Children's Hospital Boston

description: aligned to mm9

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 or mm9_8653 (mm9 with modification to match DFL16.1-JH3 rearrangement) reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Merge unique and duplicated reads together, remove the ones with same bait length, prey length, and gap length
Remove background-prone junctions with gaps larger than 30nt.
Genome_build: mm9, mm9_8653
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Translocation libraries were prepared using linear-amplificate PCR-mediated HTGTS.
Linear-amplificate PCR-mediated HTGTS

treatment_protocol: 3 uM STI-571 treated for 4 days for v-Abl pro-B cells and SCF/IL7 stimulated for 4 days fro Bone Marrow pro-B cells

value: v-Abl transformed pro-B cell line

value: ATM-/-, c-Myc-DJb, Emu-Bcl2

tag: bait locus

value: cryptic RSS site in Chromosome 1

tag: treatment protocol

value: 3 uM STI-571 treated for 4 days

tag: growth protocol


title: cRSS-chr1-rep2

description: aligned to mm9

tag: cell type

value: ATM-/-, DEL-SJ, Emu-Bcl2


title: Control ISC biological rep 2


title: DAB-vAbl-Cas9-rep1

description: aligned to mm9

value: Cas9 site downsream of c-Myc

value: 3 uM STI-571 treated for 4 days, Cas9 nuclefection was done 30 hours after STI-571 treatment


title: cRSS-chr1-rep1

description: aligned to mm9

value: ATM-/-, Emu-Bcl2


title: DAB-vAbl-Cas9-rep2

description: aligned to mm9


title: RSSJ-chrX-12S-rep2

description: aligned to mm9

value: DEL-SJ


title: DAB-vAbl-Cas9-rep3

description: aligned to mm9


title: RSSJ-chr1-12S-rep2

description: aligned to mm9


title: RSSJ-chrX-12S-rep1

description: aligned to mm9


title: A3-wildtype-LP-4h-Replica1

value: wild-type

value: Low Phosphate

value: 4 hours


title: RSSJ-chr1-12S-rep1

description: aligned to mm9


title: SJ-chrX-GFP-rep2

description: aligned to mm9


title: SJ-chr1-GFP-rep1

description: aligned to mm9


title: DEL-SJ-23S-ATMi

description: aligned to mm9

value: DEL-SJ, Emu-Bcl2


title: SJ-chr1-GFP-rep2

description: aligned to mm9


title: DEL-SJ-23S-WT

description: aligned to mm9


title: SJ-chr1-GFP-rep3

description: aligned to mm9


title: DEL-SJ-12S-ATMi

description: aligned to mm9


title: DEL-SJ-12S-WT

description: aligned to mm9


title: DAB-BM-Myc-rep3

description: aligned to mm9

source_name: Bone Marrow pro-B cells

growth_protocol: Opti-MEM; 10% FBS

treatment_protocol: SCF/IL7 stimulated for 4 days

value: Bone Marrow pro-B cells

value: c-Myc-DJb

value: incubate with SCF/IL7 for 4 days

value: Opti-MEM; 10% FBS


title: DAB-BM-Myc-rep1

description: aligned to mm9


title: DAB-BM-Myc-rep2

description: aligned to mm9


title: DB-BM-Myc-rep3

description: aligned to mm9

value: c-Myc-DJb, Emu-Bcl2


title: DB-BM-Myc-rep2

description: aligned to mm9


title: DAB-vAbl-Myc-rep3

description: aligned to mm9

value: v-Abl transformed pro-B cell line

value: ATM-/-, c-Myc-DJb, Emu-Bcl2


title: DB-BM-Myc-rep1

description: aligned to mm9


title: SJ-chrX-GFP-rep3

description: aligned to mm9

value: 3 uM STI-571 treated for 4 days


title: DAB-vAbl-Myc-rep2

description: aligned to mm9


title: DB-vAbl-Myc-rep3

description: aligned to mm9


title: DEL-SJ-23S-ATM

description: aligned to mm9

value: ATM-/-, DEL-SJ, Emu-Bcl2


title: DB-vAbl-Myc-rep2

description: aligned to mm9


title: DB-vAbl-Myc-rep1

description: aligned to mm9


title: OtA0278_GP_301-432_mm9_ChIP_10M_09302013(input DNA)

first: Garyfallia

last: Papaioannou

address: Thier 1101, 50 Blossom Street

department: Medicine

institute: MGH

data_processing:
base-calling  Illumina (Otogenetics)
Reads were mapped using the DNA Nexus mapper
Regions were called using QUEST algorithm (in DNA Nexus Software)
Genome_build: mm9
Supplementary_files_format_and_content: text file with peak data

source_name: chondrocytes

growth_protocol: Chondrocytes were isolated from ribs of 11 wt mice of CD1 background age p2.5. Chondrocytes were cultured in DMEM medium, penicillin/streptomycin and 5% FCS overnight.Next day chondrocytes 90% confluent in two 10cm dishes were harvested.

extract_protocol:
Chromatin Immunoprecipitation was performed using Cell Signaling Technology SimpleChIP Plus Enzymatic Chromatin IP Kit (Magnentic Beads) #9005. For crosslinking, 260 ul  formaldehyde 37% solution was added to 10 ml medium of each 10 cm dish, then samples were prepared according to the manufacturer’s instructions. H3K27Me3 antibody (Cell signaling technologies # 9733) was used for the immunoprecipitation. After the procedure chiped DNA was retrieved at a concentration of 7.28ng/ul. As control, the 2% input sample was used. A volume of 10 microlitters of each DNA solution was submitted for chip sequencing to Otogenetics.
library construction was performed by otogenetics

value: chondrocytes

value: rib

tag: age

tag: treatment

value: overnight culture

value: none (input)


title: IgH-AB-dIGCR1-rep1

description: aligned to mm9_8653

value: ATM-/-, delta-IGCR1, Emu-Bcl2

value: IgH


title: IgH-AB-rep3

description: aligned to mm9_8653

value: ATM-/-, Emu-Bcl2


title: SJ-chrX-GFP-rep1

description: aligned to mm9

value: DEL-SJ


title: V852 DACOR1 Lentivirus 3

data_processing:
The 100 bp paired-end strand-specific sequencing reads were mapped to hg19 using TopHat with 2 mismatches allowed for full-length reads.
The raw reads were mapped to human gene annotated in RefSeq database using Cufflinks V2.0.2 and expression valued were calculated at fragment per kilobase of exon per million of mapped fragments (fpkm)
CuffDiff was used to for identifying differentially expressed genes.  P-value of < 0.05 and q-value of < 0.05 were used as cut-offs for identification of differential expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delinated text file are provided with RefSeq gene ID along with the normalized fpkm value for each sample.

source_name: Patient-derived colon cancer cell line

growth_protocol: Grown in MEM media with 2% FBS, 2.4 mM L-glutamine, 10 ug/ml insulin, 2 ug/ml human transferrin, 2 ug/ml selenium, 1 ug/ml hydrocortisone, 50 ug/ml gentamicin

extract_protocol:
RNA was isolated using RNeasy® Mini Kit (Qiagen) according to the manufacturer’s protocol.  An added DNase (Qiagen) treatment step was included after the first wash.
Library preparation as per Scriptseq Complete Gold (Human/Mouse/Rat) from Illumina

treatment_protocol: V852 cells were transduced with lentiviral supernatant and treated with 1ug/ml puromycin to target cells that were not infected with lentivirus.

tag: cancer type

value: Colorectal cancer

tag: Sex

value: Male

tag: transduction

value: DACOR1 Lentivirus


title: IgH-AB-rep2

description: aligned to mm9_8653

tag: genotype


title: IgH-AB-rep1

description: aligned to mm9_8653


title: Input

city: Utrecht

first: Janneke

last: Peeters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

description: Run 1

data_processing:
Sample demultiplexing and read quality assessment was performed using BaseSpace (Illumina) software.
Reads were mapped to the reference genome (hg19) with Bowtie 2.1.0 using default settings.
SAM files were converted to BAM files using samtools version 0.1.19.
Peaks were called using MACS-2.1.0.
Enriched regions were identified compared to the input control using MACS2 callpeak --nomodel --exttsize 300 --gsize=hs -p 1e-9.
The mapped reads were extended by 300bp and converted to TDF files with igvtools-2.3.36
Differential binding analysis was performed using the R package DiffBind version 1.8.5. In DiffBind read normalization was performed using the TMM technique using reads mapped to peaks which were background subtracted using the input control.
BEDtools v2.17.0 was used for general manipulation of peak bed-files
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

source_name: Peripheral blood

growth_protocol: CD4+CD45RO+ cells were sorted from HC peripheral blood mononuclear cells (PBMC), either in vitro activated or not, and JIA PBMC and synovial fluid mononuclear cells (SFMC).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and barcoded libraries were sequenced 75bp single-end on Illumina NextSeq500 sequencer.

treatment_protocol: To activate HC cells, HC PBMC were cultured for 16h with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads)

tag: diagnosis

value: JIA patient

tag: tissue

value: Peripheral blood

value: CD4+CD45RO+ T cells

tag: in vitro activation

value: no


title: V852 Control Lentivirus 3

tag: cell line

value: Control Lentivirus


title: JIA_D_SF_Run2

description: Run 2

source_name: Synovial Fluid

value: Synovial Fluid

tag: chip antibody

value: anti H3K27ac (ab4729; Abcam)


title: V852 DACOR1 Lentivirus 1


title: V852 DACOR1 Lentivirus 2


title: V852 Control Lentivirus 1


title: JIA_E_SF_Run2

description: Run 2


title: V852 Control Lentivirus 2


title: IgH-AB-dIGCR1-rep3

description: aligned to mm9_8653

value: v-Abl transformed pro-B cell line

value: ATM-/-,delta-IGCR1, Emu-Bcl2

value: 3 uM STI-571 treated for 4 days


title: Sample_2_WT_NB_R2

value: naive

value: Immunized intraperitoneally with NP-CGG ratio 20-25 in alum (1:1) to induce GC formation

value: 10- to 12-weeks


title: DAB-vAbl-Myc-rep1

description: aligned to mm9

value: ATM-/-, c-Myc-DJb, Emu-Bcl2

value: c-Myc-DJb


title: Control

data_processing:
100 bp paired-end DNA sequencing was performed on a HiSeq 2500 at Otogenetics Corporation.
DNA reads were mapped against human genome (hg19) using Bowtie 2.
Peak calling was performed by using MACS2.
Peak annotation was completed using ChIPpeakAnno.
Genomic hits were filtered based on a 15 or greater fold enrichment.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delinated text are provides DACOR1 ChIRP hits with genomic location, nearest gene, fold enrichment, p-value, and q-value

source_name: patient-derived colon cancer cell line

extract_protocol:
The supernatant was incubated at 65°C overnight to reverse crosslinking before extracting DNA using DNeasy Blood & Tissue Kit (Qiagen).
Illumina ChIP-seq library preparation kit

treatment_protocol: The ChIRP-seq protocol was carried out as previously described by Chu et al.  Briefly, 5 x 108 V852 cells with DACOR1 lentivirus were first crosslinked using 1% formaldehyde for 10 minutes.  The cells were spun down, suspended in Buffer A (Hepes 20mM, KCl 10mM, MgCl2 1.5 mM, DTT 0.5mM, 1% Empigen), and dounced before collecting the nuclei by centrifugation.  The nuclei were sonicated in nuclei lysis buffer (20mM Tris-HCl pH 7.5, 10mM EDTA , 1% SDS, 1mM DTT, protease inhibitor cocktail, RNaseOut  80 U/ml) to produce 100-500 bp DNA fragments.  LiCl2 was added at 0.5M to nuclear lysates. Equal amounts of nuclear lysates were incubated with either DACOR1 specific or non-specific DNA probes modified with a TEG linker and Biotin at their 5’ ends, and incubated for 24 hour at 37°C with rotation.  The next day, RiboMinus™ streptavidin-coated magnetic beads (Life Technologies) were blocked with 800 ug/ml yeast tRNA and 800 ug/ml BSA for 1 hour at 37°C in hybridization buffer (5mM Tris-HCl pH 7.5, 10mM EDTA, 500mM LiCl2) before washing and adding to nuclear lysates for 30 minutes.  The beads were then washed three times with nuclear lysis buffer, wash buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl), and PBS.  The beads were suspended in 200 ul of PBS and incubated at 75°C for 5 minutes, the supernatant was collected from the beads.

value: colorectal cancer

value: Male


title: OtA0277_GP_301-432_mm9_ChIP_10M_09302013

tag: strain

value: chondrocytes

value: rib

value: overnight culture

value: H3K27Me3 (Cell signaling technologies # 9733)


title: JIA_B_SF_Run1

description: Run 1

value: JIA patient

value: CD4+CD45RO+ T cells

value: no


title: JIA_C_PB_Run1

description: Run 1

value: Peripheral blood

value: anti H3K27ac (ab4729; Abcam)


title: shCAP-D3 infected 7 hrs 3

first: Michelle

middle: Suzanne

last: Longworth

address: 9500 Euclid Ave NE20

department: Molecular Genetics

institute: Cleveland Clinic Foundation

data_processing:
Samples were evaluated for quality and trimmed of adapters and low-quality bases using Trim Galore! v.0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default settings to produce FastQC plots and trimmed read files.
Trimmed reads were then aligned and quantified using TopHat (v.2.0.8) and Cufflinks (v2.2.0).  The Cufflinks work flow was followed using default settings but with Tophat set to "sensitive" mode (--b2-sensitive) with inner mate pair distance and standard deviation set to 100 and 30, respectively (-r 100 --mate-std-dev 30), based on library parameters.
Cuffdiff was used to assess differential expression. An adjusted P-value < 0.05 and a fold change >1.75 was deemed significant
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary Table 2.  Analysis of differentially expressed genes in uninfected control shRNA and CAP-D3 shRNA expressing HT-29 cells.  Total mRNAs from 3 different experiments per cell line were analyzed  (control shRNA experiments c_0, c_1, c_3 and CAP-D3 shRNA experiments t_0, t_1, t_3).  Normalized FPKM values (columns O-T) were averaged and used to calculate the log base 2 fold change from CAP-D3 shRNA expressing cells to control shRNA expressing cells (column J).  Adjusted p-values (q-value) are shown in column M.  Genes significantly downregulated in CAP-D3 shRNA expressing cells are highlighted in blue while genes significantly upregulated in CAP-D3 shRNA expressing cells are highlighted in red.  Genes were considered significant if the adjusted p-value was <0.05 and the log fold change was at least 1.75 fold.
Supplementary_files_format_and_content: Supplementary Table 3.  Analysis of genes that are differentially expressed in control shRNA and CAP-D3 shRNA expressing HT-29 cells as a result of infection.  Cells were infected with S. typhimurium and transcript levels were analyzed at 0.5 hours (columns E-L) and 7 hours post infection (columns M-T).  Total mRNAs from 2 different experiments per cell line were analyzed for the 0.5 hour timepoint and from 3 different experiments for the 7 hour experiment.  Normalized FPKM values were averaged and used to calculate the log base 2 fold change from uninfected to 0.5 hour infected control shRNA (sheet 1) and CAP-D3 shRNA (sheet 2) expressing cells (column H).  Adjusted p-values (q-value) are shown in column K.  Genes significantly downregulated at the 0.5 hour post-infection timepoint are highlighted in blue while genes significantly upregulated at the 0.5 hour post-infection timepoint are highlighted in red.  Genes were considered significant if the adjusted p-value was <0.05 and the log fold change was at least 1.75 fold.  There are two spreadsheets; the first contains the differentially expressed genes for the control shRNA expressing cells and the second contains the genes for the CAP-D3 shRNA expressing cells.

source_name: HT-29 cells

growth_protocol: HT-29 cells were cultured in RPMI 1640 media with L-glutamine, 10% fetal bovine serum (Gibco), and 1% penicillin/streptomycin.

extract_protocol:
TRIzol (Invitrogen) was used to harvest total RNA from tissues and cells according to manufacturer's protocol.  Samples were DNase treated and run on RNAeasy columns (Qiagen).
Directional, cDNA libraries made from cellular mRNAs were generated from the other 16 samples using the Illumina TruSeq RNA library kit and sequenced (paired-end sequencing of 100 bp reads) in the Genomics Core at the University of Chicago on an Illumina HiSeq2500, according to standard Illumina protocols.

treatment_protocol: Cells were grown to confluency and remained confluent for two days.  They were then treated for 48 hours with IPTG to induce control or CAP-D3 shRNA expression.  Cells were infected with Salmonella enterica serovar Typhimurium SL1344  in RPMI +10% FBS at a multiplicity of infection (MOI) of 10.

value: colon

value: epithelial

tag: disease

value: colon adenocarcinoma


title: IgH-AB-dIGCR1-rep2

description: aligned to mm9_8653

value: v-Abl transformed pro-B cell line

value: ATM-/-, delta-IGCR1, Emu-Bcl2

tag: bait locus

value: IgH

value: 3 uM STI-571 treated for 4 days


title: shCAP-D3 infected 0.5 hrs 2


title: shCAP-D3 uninfected 3


title: JIA_A_SF_Run1

description: Run 1

value: Synovial Fluid


title: JIA_B_PB_Run1

description: Run 1


title: Smad2 and Smad3 ChIP-seq of H345-TbRII cells

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

data_processing:
ChIP-seq reads were trimmed down to 36 bases and processed by Bowtie2 (version 2.1.0) using hg19 version of index files. Parameter used is: --local.
Peaks were called using CisGenome version 2 using default parameters except for window size (400 bp), cutoff counts (>= 10 reads (p=0.023516)), and step size (25 bp).
Genome_build: hg19
Supplementary_files_format_and_content: wig and bed files were generated using CisGenome v2.0.

growth_protocol: H345-TbRII cells were maintained in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12 #11330; Life Technologies) supplemented with insulin-transferrin-sodium selenite media supplement (5 mg/ml insulin, 5 mg/ml transferrin and 5 ng/ml sodium selenite, #I1884; Sigma-Aldrich), 10 nM b-estradiol (#E2257; Sigma-Aldrich), 10 nM hydrocortisone (#H0135; Sigma-Aldrich),  2 mM L-glutamine (#25030, Life Technologies). Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
ChIP were performed as described (Koinuma, D. et al, Mol. Cell Biol. 29, 172-186, 2009). Smad2 and Smad3-DNA complexes were isolated with antibody.
Libraries were prepared using Ion Xpress Fragment Library kit. After adaptor ligation and nick repair, 12 cycles of amplification was performed which was followed by size selection using E-Gel (475 bp). Sequencing was performed using Ion PGM OT2 400kit, Ion 318 Chip kit v2, Ion Hi-Q sequencing kit, and Ion sequencing 400 kit, following the protocol provided by the manufacturer.

treatment_protocol: Cells were treated with 1 ng/ml of TGF-b3 for 1.5 h.

value: SCLC cell line H345

tag: genotype/variation

value: wild-type TbRII positive (overexpressed)

tag: histology

value: small cell lung carcinoma

value: anti-Smad2 and Smad3 (BD, catalog# 610843, lot# unavailable)


title: JIA_A_PB_Run1

description: Run 1

value: JIA patient

tag: cell type


title: HC_C_Run2

description: Run 2

value: Healthy control

value: CD4+CD45RO+ T cells


title: HC_C_act_Run2

description: Run 2

value: Peripheral blood

value: yes


title: shCTRL infected 7 hrs 3

value: colon


title: shCTRL infected 0.5 hrs 2

value: epithelial


title: DEL-SJ-12S-ATM

description: aligned to mm9

value: ATM-/-, DEL-SJ, Emu-Bcl2

value: DEL-SJ

tag: treatment protocol

tag: growth protocol


title: JIA_C_SF_Run1

description: Run 1

value: anti H3K27ac (ab4729; Abcam)

value: no


title: shCTRL uninfected 3

value: colon adenocarcinoma


title: shCAP-D3 infected 7 hrs 2


title: DACOR1

source_name: patient-derived colon cancer cell line induced with DACOR1

tag: cancer type

value: colorectal cancer

value: Male


title: HC_B_act_Run2

description: Run 2


title: shCAP-D3 uninfected 2


title: HC_A_act_Run1

description: Run 1


title: shCTRL infected 7 hrs 2


title: JIA_C_plus

data_processing:
Sample demultiplexing and read quality assessment was performed using BaseSpace (Illumina) software.
Reads were mapped to the human reference genome (hg19) using TopHat v2.0.9 (tophat2 -p 8 --library-type fr-firststrand -G hg19.gtf).
Transcripts were assembled using CuffLinks v2.2.1 with the reference gene annotation (hg19) as a guide.
Transcriptomes were merged using Cuffmerge after which differential gene expression analysis was performed using Cuffdiff.
Reads were quartile normalized (--library-norm quartile) and reads mapping to rRNA or tRNA were masked from the quantification using the -M option. Similarly quartile normalized count and FPKM tables were generated using Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing quartile normalized FPKM values

growth_protocol: CD4+CD45RO+ cells were sorted from HC PBMC and JIA patient SFMC, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16h.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen).
Sample preparation was performed using TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and samples were sequenced 75bp single-end on Illumina NextSeq500 (Utrecht DNA sequencing facility).

treatment_protocol: Cells were cultured for 16h in the presence of 300 nM JQ1(+) or JQ1(-). Next, cells were treated for 4h with 100 ng/mL phorbol 12-myristate 13-acetate and 1 µg/mL ionomycin.

value: Synovial Fluid

tag: treatment


title: JIA_B_plus


title: JIA_C_min


title: JIA_B_min


title: JIA_A_plus


title: HC_D_plus

source_name: Peripheral Blood

value: Peripheral Blood


title: HC_D_min


title: HC_C_plus


title: JIA_A_min


title: HC_C_min


title: HC_B_min


title: HC_A_plus


title: HC_B_plus


title: HC_A_Run1

description: Run 1


title: shCAP-D3 infected 0.5 hrs 1


title: HC_B_Run2

description: Run 2


title: HC_A_min


title: CS line, 4d after Fg inoculation, rep 2

status: Public on Sep 14 2015

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from  line CS, 4 DAI
S000B43
processed data file: CS_templates.fas

data_processing:
Illumina reads from the six CS and six CS-7EL cDNA libraries were assembled following a two-step strategy to identify candidate expressed genes originating from the Th. elongatum 7EL chromosome arm in the CS ditelocentric addition line CS-7EL. At the time of the analysis, only a draft genome sequence was available for T. aestivum and very limited genomic sequences were available for Th. elongatum.  The focus of the bioinformatics analysis presented here was to identify enriched CS-7EL expressed genes that were absent in the CS samples.
All assemblies were performed using SeqMan NGen 4.0.0 (DNASTAR, Madison, WI) with the option ‘de novo’ for the first two steps and SeqMan NGen 3.1.2 (DNASTAR) with the option “small-templated” for the 3rd step.  Additional details and parameters, and a schematic summary of the assemblies are presented in the published manuscript.  In a first step, each of the twelve samples was assembled separately.  Unassembled reads were then assembled across treated and non-treated samples within each germplasm; remaining unassembled sequences were discarded.  In a second step, for CS-7EL, the de novo assembly was based on all contigs from the sub-assemblies in the first step.  For CS, all contigs from step 1 were co-assembled with publicly available EST sequences from CS (NCBI; http://www.ncbi.nlm.nih.gov/ ), to provide a broader reference base of expressed T. aestivum sequences. The resulting contigs in both assemblies were scanned for F. graminearum contaminating sequences using the F. graminearum genome database (FGDB) v3.2 open reading frames (ORFs; Wong et al., 2011) obtained from the Munich Information Center for Protein Sequences (http://mips.helmholtz-muenchen.de/genre/proj/FGDB/), and matching contigs were removed. In a third step, the CS contigs and singletons from the second step (attached file CS_templates.fas), together with F. graminearum ORFs, were used as a reference template onto which second-step contigs from CS-7EL (attached file CS_7EL_step2_contigs.fas) were assembled. The CS-7EL sequences that assembled with CS or F. graminearum sequences were discarded. The CS-7EL sequences that did not assemble onto the reference template are in the attached file CS-7EL_step3_unasm.fas and are referred to as ‘CS-7EL-enriched singletons’; in addition to Th. elongatum 7EL candidate genes, these singletons could also include T. aestivum sequences that were not present in the public databases at the time of analysis, contaminants, bad or misassembled sequences.
Genome_build: The CS contigs and singletons from the second step of the de novo assembly described above (attached file CS_templates.fas), together with F. graminearum ORFs, were used as a reference template for the templeted assembly.
Genome_build: The content of CS_templates.fas, CS_7EL_step2.fas and CS-7EL_step3_unasm.fas is described above.

source_name: rachis

growth_protocol: Plants were grown in a controlled-environment cabinet at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reach mid anthesis; then they were moved to the misting room at 25 C with the same light regime.

extract_protocol:
Total RNA from each sample was isolated using a modified form of the TRIzol (Invitrogen Canada Inc., Burlinton, Ontario) method. Isolated RNAs were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned using RNeasy Mini Kits (Qiagen) according to manufacturer’s instructions.  RNA quality and quantity was determined using a 2100 BioAnalyzer (Agilent Technologies Canada Inc, Mississauga, ON, Canada).
Multiplexed cDNA libraries for sequencing were prepared from total RNA using the TruSeq RNA Sample Preparation v2 kit (Illumina, Inc, San Diego, CA) and MID tags as described by the Manufacturer. The twelve libraries were sequenced using the short-read paired-end protocol (2 x 100 b/read) in one lane on an Illumina (San Diego, USA) HiSeq 2500 System using the Illumina HiSeq Cluster kit and following the manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of a 100,000 spores/ml suspension of the isolate Fusarium graminearum strain DAOM 180378 was point-inoculated into each of two basal florets of each developed spikelet of the wheat heads.  Water was used as a mock-inoculation treatment.  The inoculated plants were mist overhead for 30 second intervals every hour during the light period for 48 hours to maintain high humidity at a temperature of 25 oC. Following this, they were moded a to non-misted bench in the same growth room maintained at 75% humidity. Ten to twelve treated heads were used for each biological replicate, and three replicates were done per treatment.  Rachis segments from the inoculated portion of each head were sampled at 4 days after inoculation (DAI).  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: line

value: Chinese Spring

tag: tissues

value: inoculated rachis

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment

value: Fusarium graminearum


title: CS line, 4d after water inoculation, rep 1

description:
Gene expression data from water-inoculated wheat rachis from line CS, 4 DAI
S000B44
processed data file: CS_templates.fas

value: water


title: CS-7EL line, 4d after water inoculation, rep 3

description:
Gene expression data from water-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B46
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas

value: Chinese Spring with Th. elongatum chromosome 7EL


title: CS line, 4d after water inoculation, rep 3

description:
Gene expression data from water-inoculated wheat rachis from line CS, 4 DAI
S000B45
processed data file: CS_templates.fas


title: CS-7EL line, 4d after water inoculation, rep 1

description:
Gene expression data from water-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B42
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas


title: shCAP-D3 infected 7 hrs 1

tag: tissue

value: colon


title: shCTRL uninfected 2

value: epithelial


title: shCTRL uninfected 1


title: CS-7EL line, 4d after water inoculation, rep 2

description:
Gene expression data from water-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B47
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas


title: shCTRL infected 0.5 hrs 1


title: CS line, 4d after Fg inoculation, rep 1

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from line CS, 4 DAI
S000B41
processed data file: CS_templates.fas


title: shCAP-D3 uninfected 1


title: CS line, 4d after water inoculation, rep 2

description:
Gene expression data from water-inoculated wheat rachis from line CS, 4 DAI
S000B3F
processed data file: CS_templates.fas


title: CS-7EL line, 4d after Fg inoculation, rep 2

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B40
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas


title: shCTRL infected 7 hrs 1


title: CS-7EL line, 4d after Fg inoculation, rep 3

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B3C
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas


title: CS line, 4d after Fg inoculation, rep 3

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from line CS, 4 DAI
S000B3D
processed data file: CS_templates.fas


title: CS-7EL line, 4d after Fg inoculation, rep 1

description:
Gene expression data from Fusarium graminearum-inoculated wheat rachis from addition line CS-7EL, 4 DAI
S000B3E
processed data file: CS_7EL_step2_contigs.fas, CS_7EL_step3_unasm.fas


title: RL 2

city: Hangzhou

first: Youxin

last: Yang

address: Zijingang Campus, 866 Yuhangtang Road

department: Department of Horticulture

institute: Zhejiang University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by fastx_toolkit-0.0.14 and masked for low-complexity or low-quality sequence.
then mapped to tomato whole genome using Bowtie 2 version 2.0.0-beta7 with parameters -S -p 15 .
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using cuffdiff.
The number of reads falling in the genes  were counted and normalized by the size of the library.
Genome_build: SL2.31 (Annotation at: http://www.plantgdb.org/XGDB/phplib/download.php?GDB=Sl)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample,and the log2(Fold_change) normalized,_q-value,and gene annotation.

organism: Solanum lycopersicum

growth_protocol: Tomato (Solanum lycopersicum L, cv. Ailsa Craig) seeds were sown in trays filled with a mixture of peat and vermiculite (2:1, v/v) and placed in growth chambers at a temperature of 25/19C (day/night) with a photoperiod of 12 h of light (8:00 AM to 8:00 PM), a photosynthetic photon flux density (PPFD) of 200 umol m-2 s-1 from fluorescent tubes, and a relative humidity (RH) of 70%. The seedlings were watered daily and fertilised with Hoagland nutrition solution once per week.

extract_protocol:
ReverTra Ace qRT-PCR Kit (Toyobo, Japan).
The enrichment of mRNA, fragment interruption, addition of adapters, size selection, PCR amplification, and RNA-seq were performed by staff at Zhejiang Tianke (Hangzhou, China). Poly (A) mRNA was isolated using oligo dT beads and then cleaved into short fragments. A single-end RNA-seq library was prepared for 12 samples from four different treatments, and sequenced on the Illumina HiSeq 2000 platform.

treatment_protocol: Plants underwent one of four treatments: control (mock, nightly dark environment with MgCl2 treatment), RL (nightly red light treatment with MgCl2 treatment), DC3000 (nightly dark environment with DC3000 inoculation), and RL+DC3000 (nightly red light treatment with DC3000 inoculation). Leaves were collected from the plants at 5:00 AM the next day after treatment and immediately frozen in liquid nitrogen for further RNA exaction

tag: cultivar

value: Ailsa Craig

tag: development stage

value: four-leaf stage

tag: treatment group

value: RL; nightly red light treatment with MgCl2 treatment

value: leaves


title: RL+DC3000 3

value: nightly red light treatment with DC3000 inoculation


title: RL+DC3000 1


title: RL 3


title: RL 1


title: RL+DC3000 2


title: DC3000 2

value: nightly dark environment with DC3000 inoculation


title: DC3000 1


title: DC3000 3


title: Control 2

value: mock, nightly dark environment with MgCl2 treatment


title: Control 1


title: hst1Δ-KO2 rep1

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to candida lusitaniae whole genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: candida lusitaniae
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Clavispora lusitaniae

source_name: Yeast strains generated in Rusche laboratory

growth_protocol: Yeast were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) and harvested at an OD between 3.8 and 4.9

extract_protocol:
Cells were resuspended in 0.5 ml AE buffer with 10% SDS, 0.5 ml phenol, pH 5.3, and approximately 0.3 ml glass beads.  Samples were vortexed 30 min at 4°, incubated 10 min at 65°, frozen at -80°, and spun 10 min in microcentrifuge at room temperature.  The aqueous layer was extracted twice with phenol/CHCl3, and the RNA was precipitated with ethanol.  100 ug RNA was treated with DNase I for 10 min at room temp, applied to RNeasy spin column (Qiagen), treated with DNase I on the column, and eluted in water.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Duke University Sequencing core facility

treatment_protocol: 20 OD cells were collected by centrifugation, washed in AE buffer (50 mM NaOAc, pH5.3; 10 mM EDTA), and the cell pellet was stored at -20°

tag: strain

value: CL143 ura3delta  hst1delta::ClURA3


title: hst1Δ-KO1 rep2


title: Cse4_ChIPSeq

data_processing:
ChIP-seq reads were aligned to the Candida lusitaniae  genome assembly using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa aln and bwa samse
peaks were called using MACS version 2 with the following settings: -B -nomodel -extsize 200 --keep-dup 10 -q 0.01 -g 12114892
MACS2 bdgcmp was used to generate fold-enrichment and logLR track with parameters -m FE and -m logLR -p 0.00001
Supplementary_files_format_and_content: NARROWPEAK file reports peaks with FDR q <0.01

source_name: yeast cells

growth_protocol: Yeast were grown at 30°C in YPD (1% yeast extract, 2% peptone, 2% glucose). Approximately 100 OD of cells were harvested at OD600 = 3.0-4.0

extract_protocol: Crosslinked cell pellets were stored at -80°C. For lysis, cells were suspended in 100 µl ice cold lysis buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM TPCK, 1mM PMSF, 5 µg/mL chymostatin, 2 µg/mL pepstatin A, 1 mM benzamidine, and 1× complete protease inhibitors; Boehringer Mannheim) and vortexed with glass beads for 30 minutes at 4°C. The volume was brought to 800 µl and transferred away from the beads to fresh tubes. The lysate was sonicated four times for 10 seconds at setting 10 on a Sanyo Soniprep 150, and spun for 10 minutes in a microfuge at 4°C. The supernatant was collected and 160 µl was used in a final volume of 400 µl lysis buffer for each immunoprecipitation reaction. Samples were pre-cleared for 30 min with 30 µL of a 50% slurry of Protein A agarose beads and then incubated overnight with 5 µL of antibody (α-myc rabbit (Millipore-06-549).  Samples were then incubated with 10 μL Protein A agarose beads for 1 h. The beads were washed for five minutes in the following buffers:  wash 1 (150 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), wash 2 (500 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), wash 3 (0.25 M LiCl, 10 mM Tris pH 8.0,1 mM EDTA, 1% sodium deoxycholate, 1% NP40), wash 4 (10mM Tris pH 8.0, 1mM EDTA) and wash 5  (10mM Tris pH 8.0, 1mM EDTA, 20µg of RNaseA). Material was eluted from beads in 500 μL 0.1 M NaHCO3, 1% SDS. Cross-links were reversed by overnight incubation at 65°C.  DNA was then extracted with phenol:chloroform and precipitated with ethanol.

treatment_protocol: After harvesting, cells were crosslinked with 1% formaldehyde at room temperature for 45 minutes

tag: chip antibody

value: α-myc rabbit (Millipore-06-549)


title: hst1Δ-KO2 rep2

tag: genotype/variation


title: Foxd3fl/fl_2i_2

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated with Cufflinks as FPKMs.
Genome_build: mm10

source_name: mouse embryonic stem cells, Not treated with TM

growth_protocol: tetON Foxd3 and WT LF2 mESC  were grown under feeder-free conditions in Knockout-DMEM medium (KO-DMEM; Life Technologies) containing 15% FBS and LIF. Foxd3fl/fl;Cre-ER mESC (Foxd3-/- and Foxd3 fl/fl)  were grown  using two different conditions: (i)  on irradiated mouse embryonic fibroblast (MEF) feeder cells using Knockout-DMEM medium (KO-DMEM; Life Technologies) containing 15% FBS and LIF ("serum+LIF" (SL) conditions); (ii)   “2i+LIF” (2i) medium (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 (0.4 μM, Miltenyi Biotec), GSK3β inhibitor CHIR99021 (3 μM, Amsbio) and LIF).

extract_protocol:
Total RNA was isolated using Tripure reagent according to the manufacturer’s instructions (Roche). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the deletion of Foxd3, Foxd3fl/fl;Cre-ER mESC were treated with 4-Hydroxytamoxifen (TM) (2 µM, Sigma) for three days. Foxd3 overexpression  was induced by treating tetON Foxd3 mESC with doxycycline (1 µg/µl) for three days.

tag: genotype


title: mock IP


title: Mif2_ChIPSeq


title: WT_rep1

value: CL143 ura3delta


title: Control 3


title: Foxd3fl/fl_2i_1

tag: cell type


title: Foxd3-/-_2i_1

source_name: mouse embryonic stem cells, Treated with TM


title: tetON Foxd3_Dox_2

source_name: mouse embryonic stem cells, Treated with Doxycycline (Foxd3 overexpression)

value: tetON Foxd3


title: WT_Dox_1

source_name: mouse embryonic stem cells, Treated with Doxycycline

value: LF2 WT


title: tetON Foxd3_Dox_1


title: WT_rep2


title: Hst1_ChIPSeq

extract_protocol:
Crosslinked cell pellets were stored at -80°C. For lysis, cells were suspended in 100 µl ice cold lysis buffer (50 mM HEPES, pH 7.5, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1 mM TPCK, 1mM PMSF, 5 µg/mL chymostatin, 2 µg/mL pepstatin A, 1 mM benzamidine, and 1× complete protease inhibitors; Boehringer Mannheim) and vortexed with glass beads for 30 minutes at 4°C. The volume was brought to 800 µl and transferred away from the beads to fresh tubes. The lysate was sonicated four times for 10 seconds at setting 10 on a Sanyo Soniprep 150, and spun for 10 minutes in a microfuge at 4°C. The supernatant was collected and 160 µl was used in a final volume of 400 µl lysis buffer for each immunoprecipitation reaction. Samples were pre-cleared for 30 min with 30 µL of a 50% slurry of Protein A agarose beads and then incubated overnight with 5 µL of antibody (α-myc rabbit (Millipore-06-549).  Samples were then incubated with 10 μL Protein A agarose beads for 1 h. The beads were washed for five minutes in the following buffers:  wash 1 (150 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), wash 2 (500 mM NaCl, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), wash 3 (0.25 M LiCl, 10 mM Tris pH 8.0,1 mM EDTA, 1% sodium deoxycholate, 1% NP40), wash 4 (10mM Tris pH 8.0, 1mM EDTA) and wash 5  (10mM Tris pH 8.0, 1mM EDTA, 20µg of RNaseA). Material was eluted from beads in 500 μL 0.1 M NaHCO3, 1% SDS. Cross-links were reversed by overnight incubation at 65°C.  DNA was then extracted with phenol:chloroform and precipitated with ethanol.
Illumina standard sequencing protocol


title: WT_Dox_2


title: hst1Δ-KO1 rep1


title: Foxd3-/-_2i_2


title: Foxd3-/-_SL_1


title: Foxd3-/-_SL_2


title: Foxd3fl/fl_SL_2


title: A549_TPyP4-Pt-treated

city: Guangzhou

first: Yong

last: Zhao

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were filtered those adaptor contaminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample (each column represents sample's expression for genes showing abundance in all samples)

source_name: human alveolar adenocarcinoma (A549) cells

extract_protocol:
Total RNA was extracted using the Trizol reagent (Takara). A total of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations.

tag: cell line

tag: gene treatment

tag: gene expression

value: stable cell line


title: Foxd3fl/fl_SL_1


title: A549_TMPyP4-treated


title: A549_untreated

value: control


title: Control-for-Group 4

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

description: Group4_LTR.txt, Group4_Genes.txt

data_processing:
The QC of the generated libraries was performed using FastQC. Reads were mapped to mm9 genome using STAR aligner software. Reads with more than 3 mismatches were filtered out. Tag Directories of the reads of each library were created using HOMER with the option -keepOne to ensure the inclusion of repeat sequences. Reads mapping to LTR sequences and reads mapping to exons were counted using analyzeRepeats.pl script of HOMER. The output files were then subjected to DESeq for differential analysis.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files that include FPKM values for all genes or LTR sequences in each Group.

source_name: E14 cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen). Contaminating DNA was  removed by DNaseI (Ambion) treatment, and the RNA was further purified using the  QIAGEN RNeasy Kit.
The RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Catalog #: RS-122-2101) as per manufacturer's instructions.

treatment_protocol: Lipofectamine 2000 (Invitrogen) was used for transfection of shRNA plasmids according to the manufacturer’s instructions. Puromycin was added to the culture medium 16 hours post-transfection and cells were harvested for experiments after 4 days of knockdown.

value: WT