title: EBF1-Wt-Input

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Input for the genome-wide EBF1-wt ChIP

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 1.8.4 (RTA 1.18.64)
The reads were aligned to the mm9 genome assembly using bowtie2 with default configurations
Duplicated reads were filtered and blacklisted regions were removed using samtools and Picard.
Peaks were identified using MACS2 (v2.1.0.20150731) with q-value cutoff 0.01 and further filtered for p-value 10-7 and fold change 4
Genome_build: mm9
Supplementary_files_format_and_content: The processed bedgraph files were generated by using Homer(v4.6) with default parameters. The reads are normalized to 10 million reads.

source_name: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre), 2μM 4-hydroxy-tamoxifen (4-OHT) treated

growth_protocol: A-MuLV transformed cells were cultured without feeder cells in RPMI medium supplemented with 10% FCS, 1% PSG and 50μM β-mercaptoethanol.

extract_protocol:
Cells were crosslinked  with formaldehyde, lysed and DNA was fragmented into pieces of average 300bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.
Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles.

treatment_protocol: A-MuLV transformed Ebf1fl/fl RERTCre pro-B cells were transfected by pmys-EBF1wt-IRES-GFP or pmys-EBF1-H240A-IRES-GFP and treated with 2μM 4-hydroxy-tamoxifen (4-OHT) 24h after transduction. Five days after treatment, cells were sorted as GFP+. More than two week later, the replacement was validated by IB and the cells were used for downstream analyses. As control, mock-transduced cells were harvested four days after tamoxifen treatment before cell death was observed.


title: Cnot3(+/+) RERTCre – Replicate 1

status: Public on Nov 21 2016

type: SRA

description: RNASeq of tamoxifen treated Cnot3(+/+) RERTCre – Replicate 1

library_source: transcriptomic

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 1.8.4
The paired end RNA-Seq reads were mapped to the mouse reference genome (mm9) using Tophat (v2.0.13) and Bowtie (v2.2.3.0)
The mapped reads were further assembled by using Cufflinks (v2.2.1)
The expression level of the annotated genes (UCSC, mm9) was calculated by Cuffquant
The mouse rRNA sequences were masked from the analysis. Significantly and differentially expressed genes were filtered with the q-value cutoff<0.05
Genome_build: mm9
Supplementary_files_format_and_content: The normalized gene expression values calculated by Cuffnorm (v2.2.1) is provided in txt format

molecule: total RNA

organism: Mus musculus

source_name: B220+CD43+ pro-B cells

growth_protocol: B220+CD43+ pro-B cells were derived from the bone marrow of mice and used for the RNA extraction

extract_protocol:
The total RNA was extracted using RNeasy Mini Kit according to the protocol recommended by the manufacturer.
Library preparation for RNASeq analysis was performed with the TruSeq® Stranded mRNA Library Prep Kit from Illumina® according to the manufacturer’s protocol. The library amplification was performed using 15 PCR cycles.

treatment_protocol: Cnot3fl/flRERTCre and Cnot3+/+RERTCre mice were injected with 1mg tamoxifen on day 1, 2, 4 and 7. The mice were analyzed at day 10.

tag: cell type

value: pro-B cells (bone marrow)

tag: strain

tag: genotype


title: Cnot3(fl/fl) RERTCre – Replicate 2

description: RNASeq of tamoxifen treated Cnot3(fl/fl) RERTCre – Replicate 2


title: RNA-seq_MEF_Smarcb1I

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

country: USA

institute: Harvard Medical School

data_processing:
The sequenced reads from each sample were aligned to the mouse genome+transcriptome assembly NCBIM37.67 using TopHat v2.0.8 with default parameters except turning off novel junction search ( -G <gtf> --no-novel-juncs).
Genomic coverage was calculated in R using BioConductor packages Rsamtools and Granges
Genome_build: mm9
Supplementary_files_format_and_content: wig file showing unnormalized RNA-seq coverage

molecule: polyA RNA

growth_protocol: MEFs were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified using RNeasy MinElute Cleanup Kit (Qiagen).
2 μg of total RNA was used to make the RNA-Seq library using TruSeq Total RNA Sample Prep Kit  (Illumina) and sequenced with the Hi-Seq Illumina genome analyzer.

treatment_protocol: Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used.

tag: strain background

tag: genotype/variation

value: mouse embryonic fibroblast


title: TKO embryo, replicate 3

city: La Jolla

first: ANJANA

last: RAO

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description:
TKO_3
Processed data file: EmbryoCell_RPKM.txt

data_processing:
Bulk RNA-Seq data was mapped against the mouse mm9 reference genome using tophat43 (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome Bioinformatics Site. Sequencing read coverage per gene was counted using HTSeqcount (-m union -s yes -t exon -i gene_id, http://www-huber.embl.de/users/anders/HTSeq/).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: EmbryoCell_RPKM.txt: Tab-delimited text file includes RPKM values for each sample.

source_name: E6.75 embryo, Tet1/2/3 TKO

extract_protocol:
Single embryos were lysed and converted into double stranded cDNA using SMARTer ultra-low RNA kit for Illumina sequencing (Clontech).
For single embryo samples, 1 ng of cDNA for each sample was used for preparing libraries using Nextera XT DNA sample preparation kit (IIlumina). Libraries were sequenced on Illumina HiSeq 2500 platforms according to the manufacturer's instructions.

tag: strain/background

value: Tet1/2/3 TKO

tag: age

tag: tissue

value: Whole embryo


title: Cnot3(fl/fl) RERTCre – Replicate 1

description: RNASeq of tamoxifen treated Cnot3(fl/fl) RERTCre – Replicate 1


title: EBF1-H240A-ChIP

description: Genome-wide EBF1-H240A occupancy was performed by replacement approach

library_source: genomic

molecule: genomic DNA

value: A-MuLV transformed pro-B cells (Ebf1fl/fl;RERTCre)


title: EBF1-Wt-ChIP

description: Genome-wide EBF1-wt occupancy was performed by replacement approach


title: ChIP-seq_Smarcb1_H3K4me3input

data_processing:
The sequenced reads were aligned to the mm9 genome assembly using Bowtie 0.12.6, allowing up to 10 matches (‘-m 10 --best’ options).
1kb sized bins with more than mean+3standard deviation signal in any of the input samples were marked as noisy blacklist regions (total 287kb).
Reads on the 19 autosomal chromosomes excluding blacklisted regions were kept for downstream analysis.
For batches with low library complexity (<70% in any sample), only one read was preserved mapping to each position (denoted "PCRclean" or "clean1" in file names)
Peaks of cross-correlation profiles were identified to estimate the typical fragment size for each sample.  Each read was considered to represent a signal at half typical fragment size from the 5' end.
Genomic profiles for visualization were generated using a sigma=100bp Gaussian smoothing after library size normalization
Genome_build: mm9
Supplementary_files_format_and_content: wig files depict genomic profiles after a sigma=100bp Gaussian smoothing.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat.# IP-202-1012)

treatment_protocol: Cells were infected with retrovisur expressing Cre, and selected with puromycine. 72 hours post selection, cells were harvested and used to extract chromatin.


title: ChIP-seq_WT_H3K4me3input

value: WT


title: ATAC seq Te2/3 DKO iNKT BR2 young

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

data_processing:
Library strategy: ATAC-Seq
Raw fastq ATAC files were mapped to genome mm9 using bowtie and setting (-p 8 -m 1 --best --strata -X 2000)
Unmapped reads were processed with trim_galore and remapped using the same settings. Both results were merged together
Duplicates were removed using picards and reads mapping to the mitochondrial genome were filtered out.
Peaks were called using MACS2 with nomodel and the best peaks per condition within replicates were obtained using the Irreproducibility discovery rate from ENCODE
Reproducible peaks were filtered using ENCODE's blacklist for mm9 genome as well as regions in chrY
DEseq was used to determine differentially accessible sites between wild type and TET2/3 double knockout
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing the accessible regions for each condition.

source_name: Te2/3 DKO iNKT biological replicate (BR) 2

growth_protocol: iNKT cells were isolated from thymi of the desired genotypes after staining and FACS sorting of B220-, aGalCer tetramer+, TCRb+ cells.

extract_protocol:
50.000 iNKT cells were sorted, washed once with PBS and lysed in 100 ul of ice cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630). Then, nuclei were spun at 500g for 10 min and the pellet was resuspended in 50 ul transposase reaction mix [2.5 ul transposase (Illumina), 25 ul 2x TD buffer (Illumina) and 22.5 nuclease free water). The reaction was incubated for 30 minutes at 37. Samples were purified using MinElute kit (Qiagen).
The purified DNA was amplified using Kapa Real time library amplification kit (Kapa Biosystems). Libraries were amplified for 10-11 cycles.

value: Thymus

value: Invariant NKT (iNKT) cells

value: Tet2/3 DKO mice


title: S12601_738493_hOKT3_R_0mo_WB

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Reads were aligned using Omicsoft Sequence Aligner (OSA, v.1.7.3) with OShell (v.6.1.0.2) using default parameters and a gene models index provided for Ensembl version 66.
Read counts per Ensembl gene ID were estimated using htseq-count (v.0.5.4p3).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: log10(PF_ALIGNED_BASES)>6.5, MEDIAN_CV_COVERAGE<1 & MEDIAN_CV_COVERAGE >0.4.
Genes expressed (counts per million >1) in less than 3 samples were removed. Data normalization (TMM) and differential expression analysis were performed in R using "edgeR" package.
Genome_build: GRCh37
Supplementary_files_format_and_content: combined_ABATE_raw_counts_after_qc_063016_not_collapsed.txt is a tab-delimited matrix. The first column contains the Ensembl gene ID. The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.
Supplementary_files_format_and_content: metrics_ABATE_after_qc_063016.txt is a tab-delimited matrix. The first column contains library ID, remaining columns include RNA sequencing and alignment metrics.

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was globin reduced with GLOBINclear (Ambion, TX) according to manufacturer’s instructions.
Libraries were prepared from globin reduced RNA samples using the TruSeq RNA Sample Preparation kit v2 according to manufacturer's instructions (Illumina, San Diego, CA).

tag: samplelabel

tag: sampleID

tag: status

value: R

tag: itn name

tag: studysiteshort

value: YALE

tag: gender

value: Female

tag: treatmentgroup

tag: race

value: White; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

tag: projectid

tag: seqsite

value: BRI

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3

tag: lane


title: S12602_921524_hOKT3_NR_0mo_WB

tag: samplelabel

tag: sampleID

tag: status

value: NR

tag: age

value: White


title: RNA-seq_MEF_WTI

tag: strain background

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblast


title: RNA-seq_MEF_Smarca4I


title: ChIP-seq_Smarca4_H3K4me3input


title: ATAC seq Te2/3 DKO iNKT BR1 young

source_name: Te2/3 DKO iNKT biological replicate (BR) 1

tag: tissue

tag: genotype


title: S12600_283344_hOKT3_R_0mo_WB

tag: itn name

tag: studysiteshort

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth


title: ATAC seq WT iNKT BR3

source_name: wild type iNKT cells biological replicate (BR) 3

value: Wild Type


title: RNA-seq_MEF_WTII


title: EBF1-H240A-Input

description: Input for the genome-wide EBF1-H240A ChIP

tag: strain


title: Cnot3(+/+) RERTCre – Replicate 2

description: RNASeq of tamoxifen treated Cnot3(+/+) RERTCre – Replicate 2

value: pro-B cells (bone marrow)


title: S12599_678610_hOKT3_NR_0mo_WB

tag: samplelabel

tag: sampleID

tag: status

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: ATAC seq WT iNKT BR2

source_name: wild type iNKT cells biological replicate (BR) 2

tag: tissue

tag: cell type

tag: genotype


title: ChIP-seq_WT_input-SMAR

tag: strain background

tag: genotype/variation


title: ChIP-seq_Smarca4_inputIII


title: ATAC seq Te2/3 DKO iNKT BR3 young

source_name: Te2/3 DKO iNKT biological replicate (BR) 3


title: ATAC seq WT iNKT BR1

source_name: wild type iNKT cells biological replicate (BR) 1


title: ChIP-seq_Smarcb1_inputIII


title: S12597_618372_hOKT3_R_0mo_WB

tag: itn name

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth


title: ChIP-seq_WT_inputII


title: S12595_781179_Control_C_0mo_WB

tag: samplelabel

tag: sampleID

tag: status

value: C

value: Male

value: Control

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S12596_838213_hOKT3_R_0mo_WB

tag: itn name

tag: studysiteshort

tag: age

tag: lane


title: ChIP-seq_WT_inputI

tag: strain background

tag: genotype/variation

value: WT

tag: cell type


title: ChIP-seq_Smarcb1_input-SMAR


title: ChIP-seq_WT_inputIII


title: si-EloB_R1

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: RNAseq (EloB knock-down 1)

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: The reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIP profiles were produced by MACS in BedGraph. Peaks were reported in BED format.
Genome_build: mm9

source_name: Undifferentiated ES cells

growth_protocol: E14TG2a mouse ES cells were kept under feeder-free, 20% serum conditions with LIF on 0.1% gelatin coated dishes, as in (Morey et al., 2012)

extract_protocol:
ChIP experiments used about 20 million cells, using a protocol adapted from (Stock et al., 2007). For all ChIPs except those against EloB, cells were washed 2´ with PBS, and crosslinking was started by adding 1% formaldehyde in PBS to the plate, stopped by adding 0.125 M glycine, and cells were harvested by scraping and then pelleted. For ChIPs against EloB, cells were washed 2x with PBS, protein-protein crosslinking was performed with 40 ml ChIP Crosslink Gold (Diagenode, C01019027) or 2 mM DSP (ThermoFisher, cat 22586) in 10 ml PBS for 30 min, followed by two washes with PBS. Protein-DNA crosslinking (1% formaldehyde in PBS) was then performed on the plate for 10 min, stopped by 0.125 M glycine and cells were harvested by scraping and then pelleted. Cell pellets were resuspended and incubated for 10 min in 2 ml swelling buffer (25 mM HEPES [pH 7.9], 1.5 mM MgCl2, 10 mM KCl, 0.1% NP40, protein and phosphatase inhibitors) and the suspension was homogeneized (tight pestle, 50x). Nuclei were pelleted (3,000 g, 5 min) and resuspended in 1.3 ml sonication buffer (50 mM HEPES [pH 7.9], 140 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors). Sonication (Diagenode Bioruptor, 30 s ON/30 s OFF, high potency, 2x 8 cycles with fresh ice in between). Insoluble material was pelleted, and chromatin concentration and sonication efficiency was determined in the supernatant by DNA quantification or agarose gel after decrosslinking the extracts overnight. ChIPs were performed O.N. using 20-30 μg of DNA, 4 μg antibody (the amount of antibody for reaching full enrichment was titrated) and 25 μl of protein A dynabeads in 500 μl of sonication buffer. ChIPs were washed once with sonication buffer, once with buffer wash buffer A (50 mM HEPES [pH 7.9], 500 mM Nacl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease and phosphatase inhibitors), once with  wash buffer B (20 mM Tris-Cl [pH 8.0], 250 mM LiCl, 1 mM EDTA, 0.5% Triton MP40, 0.5% Na-deoxycholate, protease and phosphatase inhibitors) twice with 1x TE pH 8.0 and eluted in 200 μl TE pH 8.0, 1% SDS followed by decrosslinking (O.N) and RNAse treatment. DNA was finally purified over PCR (Qiagen) and eluted in 55 μl water.
Libraries were prepared according to Illumina instructions.

treatment_protocol: To generate stable cell lines expressing shRNA targeted against C17orf96 , lentivirus was produced in 293T cells by calcium phosphate-mediated transfection of 5 mg plasmid. To generate stable C17orf96 –/– cell lines, 5 ug plasmids encoding sgRNAs were transfected using Lipofectamine 2000 (Invitrogen), according to the manufacturer´s instruction. Puromycin selection was performed for 1 day at 2 mg/ml, 1000 cells were split into a 10-cm dish, and clones were picked 10 days later. Clones were expanded into 6-well dishes, and C17orf96 expression was checked by Western blot. Supernatant was harvested after 48 hr, diluted 1:4, and used to infect E14 cells. Puromycin (2 mg/ml) was added for 2 days for selection. For siRNA experiments, 100,000 cells were seeded in 6-well plates and transfected 24 hr later with 20 μM siRNA using 7 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after an additional 24 hr (i.e., 48 hr after the first transfection). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen) using protocol Appendix D. For siRNA experiments followed by ChIP, 1.2 million cells were seeded, and siRNA was transfected twice at 20 μM using using 70 μl Lipofectamine RNAimax (Invitrogen) and Optimem, according to manufacturer’s instructions. Transfections were repeated one day later, and cells were harvested after additional 24 hr (i.e. 48 hr after the first transfection).

tag: cell line

value: EloB knock-down 1


title: S12594_161201_Control_C_0mo_WB

tag: samplelabel

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth


title: SMART seq Tet2/3 DKO NKT1 BR1

description: Tet2/3 DKO NKT1 BR1

data_processing:
The reads were mapped to the mm9 genome as well as UCSC transcriptome using Tophat
The read counts for each gene were quantified using HTSeq-count tool with parameters: -m union
Differential expression analysis was performed using edgeR (Robinson et al., 2010)
Genes with RPKM less than 1 in at least two replicates in each compared condition were filtered out before differential expression calling. Dispersion was estimated as tag-wise dispersion. Genes with FDR<0.05 and at least 1.5 fold difference in expression were identified as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Estimated RPKM values (txt)

source_name: Thymus

growth_protocol: iNKT cells were isolated from thymus of the desired genotypes after staining and FACS sorting of B220-, aGalCer tetramer+, TCRb+ cells.

extract_protocol:
Total RNA was isolated from the cell types of interest using the E.Z.N.A. HP Total RNA kit (Omega) according to the manufacturer’s instructions.
we performed SMARTseq as previously described (Picelli et al., 2014). In this case, the starting total RNA for each library was 10 ng. 9 cycles of preamplification were performed.Tagmentation was carried out by using the Illumina Nextera XT DNA sample preparation kit. 8 cycles were performed for amplification of adaptor- ligated fragments. 2 biological replicates per sample were used.

tag: tissue

value: Thymus

value: Invariant NKT (iNKT) cells

tag: genotype

value: Tet2/3 DKO


title: SMART seq WT NKT1 BR1

description: WT NKT1 BR1


title: SMART seq Tet2/3 DKO NKT1 BR2

description: Tet2/3 DKO NKT1 BR2


title: SMART seq Tet2/3 DKO NKT1 BR3

description: Tet2/3 DKO NKT1 BR3


title: ChIP-seq_Smarcb1_inputII


title: SMART seq WT NKT1 BR2

description: WT NKT1 BR2


title: S12598_229085_hOKT3_NR_0mo_WB

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: YALE

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry


title: S12591_371894_hOKT3_R_0mo_WB

tag: samplelabel

value: R

value: PNRI

tag: age

tag: gender

tag: treatmentgroup

tag: race

value: Other

value: TruSeq RNA v2

tag: lane


title: S12592_604690_Control_C_0mo_WB

value: MC GEORGIA

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: BRI

value: TruSeq SBS Kit v3


title: ChIP-seq_Smarca4_inputI

tag: strain background

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblast


title: ChIP-seq_Smarca4_inputII


title: S12589_314565_Control_C_0mo_WB

tag: sampleID

tag: status

value: C

tag: itn name

tag: studysiteshort

value: Male

tag: libraryid

tag: libraryprep

tag: projectid


title: SMART seq Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR2

tag: tissue

tag: genotype


title: SMART seq Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR1


title: ChIP-seq_Smarca4_H3K4me3

tag: chip antibody

value: H3K4me3 (Millipore, 07-473)


title: SMART seq WT iNKT tetramer+TCRb+CD24-NK1.1- BR3

description: WT iNKT tetramer+TCRb+CD24-NK1.1- BR3

value: Wild Type


title: S12588_693516_hOKT3_NR_0mo_WB

tag: samplelabel

value: NR

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: SMART seq WT iNKT tetramer+TCRb+CD24-NK1.1- BR2

description: WT iNKT tetramer+TCRb+CD24-NK1.1- BR2

value: Thymus

tag: cell type

value: Invariant NKT (iNKT) cells


title: ChIP-seq_Smarcb1_H3K4me3

tag: strain background

tag: genotype/variation


title: S12593_595950_hOKT3_NR_0mo_WB

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: YALE

value: Female

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid


title: SMART seq Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR3

description: Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR2

tag: tissue

tag: genotype

value: Tet2/3 DKO


title: S12587_785228_hOKT3_R_0mo_WB

tag: samplelabel

value: R

value: BRI-VM

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: seqsite

tag: flowcellid

tag: runchemistry


title: SMART seq WT iNKT tetramer+TCRb+CD24-NK1.1- BR1

description: WT iNKT tetramer+TCRb+CD24-NK1.1- BR1

tag: cell type


title: ChIP-seq_WT_H3K4me3

tag: strain background

tag: genotype/variation

value: WT

tag: chip antibody


title: ChIP-seq_Smarcb1_inputI


title: ChIP-seq_Smarcb1_SMARCA4

value: SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)


title: S12586_555647_Control_C_0mo_WB

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: Control

value: White

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

value: BRI

tag: lane


title: SMART seq Tet2/3 DKO iNKT stage 0 BR2

description: Tet2/3 DKO stage 0 BR2

tag: tissue

tag: genotype


title: SMART seq Tet2/3 DKO iNKT stage 0 BR1

description: Tet2/3 DKO stage 0 BR1


title: SMART seq WT iNKT stage 0 BR1

description: WT stage 0 iNKT cells BR1


title: S12590_689968_Control_C_0mo_WB

tag: samplelabel

value: C

value: PNRI

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: ChIP-seq_Smarca4_H3K4me1III

tag: strain background

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblast

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: S12583_770569_hOKT3_R_0mo_WB

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: Male

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: lane


title: S12582_800847_hOKT3_R_0mo_WB

tag: samplelabel

value: COLORADO

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: projectid

tag: seqsite


title: S12585_214040_hOKT3_NR_0mo_WB

tag: sampleID

tag: status

value: NR

value: Female

value: American Indian or Alaska Native; White

tag: flowcellid

tag: runchemistry


title: ChIP-seq_Smarcb1_SMARCC1

tag: strain background

tag: genotype/variation

tag: cell type

tag: chip antibody

value: SMARCC1/BAF155 (Santa Cruz, R-8, sc-9746)


title: ChIP-seq_WT_SMARCC1

value: WT


title: SMART seq WT iNKT stage 0 BR2

description: WT stage 0 iNKT cells BR2

tag: tissue

value: Thymus

value: Invariant NKT (iNKT) cells

tag: genotype

value: Wild Type


title: SMART seq Tet2/3 DKO iNKT BR2 young

description: Tet2/3 DKO iNKT cells BR2

value: Tet2/3 DKO


title: ChIP-seq_Smarcb1_H3K4me1III


title: S12581_268024_hOKT3_R_0mo_WB

tag: samplelabel

value: R

tag: itn name

tag: studysiteshort

tag: age

value: White

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

value: BRI

tag: lane


title: SMART seq Tet2/3 DKO iNKT BR1 young

description: Tet2/3 DKO iNKT cells BR1


title: ChIP-seq_WT_H3K4me1III

value: mouse embryonic fibroblast


title: ChIP-seq_Smarca4_H3K27AcIII

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: S12580_236676_Control_C_0mo_WB

tag: sampleID

tag: status

value: C

tag: gender

value: Male

tag: treatmentgroup

value: Control

tag: race

tag: trunkbarcode

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3


title: SMART seq Tet3 KO iNKT BR2

description: Tet3 KO iNKT cells BR2

tag: tissue

tag: cell type

tag: genotype

value: Tet3 KO (Tet3flx/flx cd4cre)


title: S12579_612273_hOKT3_NR_0mo_WB

tag: samplelabel

value: NR

tag: itn name

tag: studysiteshort

value: COLORADO

tag: age

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth


title: SMART seq Tet3 KO iNKT BR1

description: Tet3 KO iNKT cells BR1

value: Thymus


title: ChIP-seq_Smarcb1_H3K27AcIII

tag: strain background

tag: genotype/variation

tag: chip antibody


title: S12578_325907_hOKT3_NR_0mo_WB

tag: sampleID

tag: status

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: libraryid

tag: libraryprep

tag: projectid

tag: lane


title: S12584_289534_hOKT3_NR_0mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

value: BRI-VM

tag: age

tag: seqsite

tag: flowcellid

tag: runchemistry


title: SMART seq WT iNKT BR2

description: WT iNKT cells BR2

tag: tissue

tag: cell type

value: Invariant NKT (iNKT) cells

tag: genotype

value: Wild Type


title: SMART seq WT iNKT BR1

description: WT iNKT cells BR1


title: ChIP-seq_WT_SMARCA4

tag: strain background

tag: genotype/variation

value: WT

tag: chip antibody

value: SMARCA4/BRG1 (Abcam, EPNCIR111A, ab110641)


title: Skin_E13_rep3

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: E13.5 wild type embryonic skin

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10) genome . The RNA-seq data were aligned using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and bedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualization and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the forward or reverse strand RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: Embryonic skin

extract_protocol:
Mammmary bud pairs 2 and 3 or andjacent area of the embryonic skin were micro-dissected  from E13.5 wild type mouse embryos and used for RNA extraction. Samples were stored in RNAlater at -80°C. Ra extraction was performed using the RNAeasy micro kit (Qiagen) according to manufacturer instructions. On-column DNase I treatment was performed during 20min at room temperature to ensure pure, DNA-free RNA extraction.
A total of 100 ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. RNA sequencing (RNA-seq) libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on a HiSeq 2500 machine, as single-end, 100 base pairs (bp) reads. The preparation of libraries and sequencing were performed by the genomic platform of the University of Geneva.

tag: strain

value: embryonic skin

value: wild type


title: S12577_156104_Control_C_0mo_WB

tag: sampleID

tag: status

tag: gender

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

value: TruSeq RNA v2

value: BRI


title: ChIP-seq_WT_H3K27AcIII

tag: cell type

value: mouse embryonic fibroblast

value: H3K27ac (Cell Signaling Technology, D5E4, 8173)


title: S12575_443762_hOKT3_NR_0mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

tag: age

value: Male

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

value: TruSeq SBS Kit v3

tag: lane


title: Skin_E13_rep2

description: E13.5 wild type embryonic skin

tag: strain

tag: tissue

tag: genotype


title: ChIP-seq_Smarcb1_H3K27AcI

tag: strain background

tag: genotype/variation

tag: chip antibody


title: ChIP-seq_WT_H3K27AcI


title: ChIP-seq_WT_H3K4me1II

value: H3K4me1 (Abcam, ab8895)


title: ChIP-seq_Smarca4_H3K4me1II


title: ChIP-seq_Smarcb1_H3K4me1II


title: S12574_692210_Control_C_0mo_WB

tag: sampleID

tag: status

value: C

value: UCSF

tag: gender

value: Female

tag: treatmentgroup

value: Control

tag: race

value: White; Asian

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep


title: S12572_464149_hOKT3_R_0mo_WB

tag: samplelabel

value: R

tag: itn name

tag: studysiteshort

tag: age

tag: projectid

tag: seqsite

tag: flowcellid

tag: runchemistry

tag: lane


title: MB_E13_rep2

description: E13.5 wild type mammary buds

source_name: Mammary buds

tag: strain

tag: tissue

value: mammary buds

tag: genotype


title: Skin_E13_rep1

description: E13.5 wild type embryonic skin

value: embryonic skin


title: S12571_479125_Control_C_0mo_WB

tag: sampleID

tag: status

tag: gender

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: siteandparticipantcode


title: ChIP-seq_Smarca4_H3K27AcI

tag: strain background

tag: genotype/variation

tag: cell type

tag: chip antibody


title: S12570_537789_Control_C_0mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

tag: age

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S12569_122083_hOKT3_NR_0mo_WB

tag: sampleID

tag: status

value: NR

tag: gender

tag: treatmentgroup

tag: race

value: Black or African American; White

tag: trunkbarcode

tag: runchemistry

tag: lane


title: JCb6-08

first: John

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8
Read alignment to the mm10 genome with DNA Nexus's RNA-Seq Analysis Pipeline v1.0.11, using Tophat and these settings: -g 1 --b2-very-fast --no-coverage-search --segment-length 25 --no-novel-juncs
Read quantitation with DNA Nexus's RNA-Seq Analysis Pipeline v1.0.11, using Cufflinks (default settings)
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated value (CSV) file containing a matrix of expression values (in FPKM) for each gene (row) and each sample (column)

source_name: neuron from arcuate hypothalamus

extract_protocol:
lysis protocol from SmartSeq2 method (Picelli et al., 2015)
mRNA amplification method from SmartSeq2 method (Picelli et al., 2015). Library preparation with NuGen's Ovation Rapid Library Kit per manufacturer's instructions.

treatment_protocol: Arcuate hypothalamus was coronally sectioned by vibratome, micro-dissected, digested with papain and then dissociated by pipette trituration. GFP+ cells were manually sorted, washed in clean buffer, then captured in separate PCR caps.

tag: cell type

value: GFP+ cell from arcuate hypothalamus of vGLUT2-IRES-Cre::loxSTOPlox-L10-GFP mouse

value: young adult

tag: strain

value: mixed background


title: JCb6-06

tag: age


title: JCb6-07


title: S12567_333398_hOKT3_R_0mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

value: White

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

value: TruSeq RNA v2

value: BRI


title: JCb6-04


title: S12568_475166_Control_C_0mo_WB

tag: sampleID

tag: libraryid

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

value: TruSeq SBS Kit v3


title: S12576_707556_Control_C_0mo_WB

tag: status

value: C

value: COLORADO

tag: gender

value: Male

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: runchemistry


title: S12565_242972_Control_C_0mo_WB

tag: samplelabel

tag: itn name

value: UCSF

tag: age

value: Control

tag: lane


title: JCb6-03

tag: cell type

tag: strain


title: S12562_406442_hOKT3_NR_0mo_WB

tag: sampleID

tag: studysiteshort

value: COLUMBIA

value: Female

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid


title: S12563_853089_Control_C_0mo_WB

tag: status

tag: gender

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S12573_676063_hOKT3_R_0mo_WB

tag: samplelabel

value: R

tag: itn name

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: runchemistry


title: S12560_209864_hOKT3_NR_0mo_WB

tag: sampleID

value: NR

tag: studysiteshort

tag: age

tag: lane


title: S12564_326726_hOKT3_NR_0mo_WB

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid


title: MB_E13_rep3

description: E13.5 wild type mammary buds

tag: strain

tag: tissue

value: mammary buds

tag: genotype

value: wild type


title: S12566_397935_hOKT3_NR_0mo_WB

tag: samplelabel

tag: status

tag: gender

value: White; Other

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S12559_137567_hOKT3_R_0mo_WB

tag: sampleID

tag: itn name

tag: studysiteshort

tag: treatmentgroup

tag: race

tag: trunkbarcode

tag: runchemistry


title: JCb6-02

tag: cell type

value: GFP+ cell from arcuate hypothalamus of vGLUT2-IRES-Cre::loxSTOPlox-L10-GFP mouse

tag: age

value: young adult

tag: strain

value: mixed background


title: JCb5.2-14


title: JCb6-01


title: JCb5.2-12


title: JCb5.2-15


title: JCb5.2-13


title: S12561_493934_hOKT3_NR_0mo_WB

tag: samplelabel

value: Black or African American

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

value: TruSeq RNA v2

value: BRI

tag: lane


title: MB_E13_rep1

description: E13.5 wild type mammary buds

tag: tissue

tag: genotype


title: S12558_505125_hOKT3_R_0mo_WB

tag: sampleID

tag: status

tag: itn name

tag: gender

value: White; White

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid

value: TruSeq SBS Kit v3


title: JCb5.2-11

tag: cell type

tag: age

tag: strain


title: S10751_209864_hOKT3_NR_12mo_WB

tag: samplelabel

tag: studysiteshort

value: Male

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: runchemistry


title: JCb5.2-10


title: JCb5.2-9


title: S10750_406442_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

tag: itn name

value: COLUMBIA

tag: visitmonth

tag: libraryid

tag: lane


title: JCb6-05

tag: cell type


title: S10741_464149_hOKT3_R_12mo_WB

value: UCSF

tag: age

tag: gender

value: Female

tag: libraryprep

tag: projectid

tag: seqsite

tag: flowcellid


title: S10739_692210_Control_C_12mo_WB

tag: samplelabel

value: C

tag: studysiteshort

tag: treatmentgroup

value: Control

tag: race

value: White; Asian

tag: trunkbarcode


title: JCb5.2-6

tag: strain


title: JCb5.2-7


title: S10738_768498_hOKT3_R_12mo_WB

tag: sampleID

tag: status

value: R

tag: itn name

tag: siteandparticipantcode

tag: visitnumber

tag: runchemistry


title: JCb5.2-8

tag: cell type

value: GFP+ cell from arcuate hypothalamus of vGLUT2-IRES-Cre::loxSTOPlox-L10-GFP mouse

tag: age


title: S10737_255654_hOKT3_R_12mo_WB

tag: gender

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: projectid

tag: lane


title: S10734_156104_Control_C_12mo_WB

tag: samplelabel

tag: studysiteshort

value: COLORADO

tag: treatmentgroup

tag: race

tag: seqsite

tag: flowcellid


title: JCb5.2-5

value: young adult

tag: strain

value: mixed background


title: JCb5.2-3


title: S10732_612273_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

value: NR

tag: itn name

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

value: TruSeq RNA v2


title: S10733_325907_hOKT3_NR_12mo_WB

tag: age

tag: gender

tag: visitmonth

tag: libraryid

value: BRI

tag: runchemistry


title: S10730_800847_hOKT3_R_12mo_WB

tag: samplelabel

tag: studysiteshort

tag: libraryprep

tag: projectid

value: TruSeq SBS Kit v3

tag: lane


title: JCb5.2-4

tag: cell type

tag: strain


title: WT 878

city: Miami

first: Han

last: Gao

state: FL

address: 1095 NW 14th Terr

department: Miami Project to Cure Paralysis

institute: University of Miami

data_processing:
reads aligned to genome using Tophat version 2.1.0 running Bowtie2 version 2.2.6
reads were counted over genomic intervals using HTSeq version 0.6.1
genomic annotation used was Ensembl mouse GRCm38 version 81
read counts per gene translated to FPKM using gene lengths provided by that Ensembl annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab delimmited text file including ensembl gene id, official gene symbol, and fpkm value of expression for each gene in each sample

source_name: Spinal cord

extract_protocol:
FACS for CD45lowCD11b+ cell population from spinal cord (1000 cells per replicate)
SMART-Seq V4 Ultra Low Input RNA Kit from Clontech Laboratories

treatment_protocol: EAE

tag: tissue

value: Spinal cord

value: EAE 17 dpi

tag: genotype


title: JCb5.2-2


title: S10731_268024_hOKT3_R_12mo_WB

tag: sampleID

tag: status

tag: itn name

value: Male

tag: treatmentgroup

tag: race

value: White

tag: trunkbarcode

tag: seqsite

tag: flowcellid


title: S10715_229085_hOKT3_NR_12mo_WB

tag: samplelabel

value: YALE

tag: age

tag: gender

tag: siteandparticipantcode

tag: visitnumber

tag: visitmonth

tag: libraryid

tag: runchemistry


title: JCb5.2-1

tag: cell type

tag: strain


title: WT 874

tag: tissue

tag: genotype


title: S10721_314565_Control_C_12mo_WB

tag: sampleID

tag: status

value: C

tag: itn name

tag: studysiteshort

value: PNRI

tag: treatmentgroup

tag: libraryprep

tag: projectid

tag: lane


title: WT 877

tag: age


title: S10713_283344_hOKT3_R_12mo_WB

tag: samplelabel

tag: gender

value: Female

tag: race

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: seqsite

tag: flowcellid


title: TNFR2 KO 887

tag: strain

tag: tissue

tag: genotype


title: S10720_689968_Control_C_12mo_WB

tag: sampleID

tag: status

tag: itn name

tag: studysiteshort

value: Control

tag: visitmonth

tag: libraryid

tag: runchemistry


title: WT 875

tag: age


title: S10719_371894_hOKT3_R_12mo_WB

tag: samplelabel

value: R

tag: gender

tag: treatmentgroup

tag: race

value: Other

tag: libraryprep

tag: projectid

tag: lane


title: TNFR2 KO 885

tag: strain

tag: tissue


title: TNFR2 KO 886

tag: genotype


title: S10710_788532_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: seqsite

tag: flowcellid


title: TNFR2 KO 884

tag: age


title: S10709_678610_hOKT3_NR_12mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

tag: gender

tag: visitmonth

tag: libraryid

tag: runchemistry


title: S10708_757437_Control_C_12mo_WB

tag: treatmentgroup

tag: race

tag: libraryprep

tag: projectid

tag: lane


title: WGBS seq WT iNKT BR2 (wt2)

data_processing:
Fastq files from sequiencing were mapped against the mm9 genome using BSmap v2.74 and the parameters -v 4 -w 2 -r 0 -q 20 -R -p 12
To remove multiple mappers as well as methylation bias, BSeQC v1.0.3 with default parameters and -l 101_101 (Read length 100)
For each CpG covered by a given sample, the levels of methylation were calculated using methratio.py, script from BSmap tool with the parameters -z -t 0 -x CG -i "correct"
The methylation calling from all samples was merged into one big table (The MasterTable) containig all CpGs covered by at least one read in any of the samples.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular format text, Mastertable, containing all the methylation info for the 6 samples (2 WT, 2 DKO Young and 2 DKO transferred). The mastertable contains the CpG coverage and the total reads indication methylation in a given CpG for all samples. If a sample does not cover this CpG this is indicated with a NA in the methylation column and with zero coverage

source_name: wild type iNKT cells BR2

growth_protocol: iNKT cells were isolated from thymi or spleens of the desired genotypes after staining and FACS sorting of B220-, aGalCer tetramer+, TCRb+ cells.

extract_protocol:
After isolation of the cells, DNA was isolated using the PureLink DNA isolation  kit (Life Technologies), according to the instructions of the manufacturer.
DNA was fragmented to an average size of 200 bp using the Adaptive Focused Acoustics Covaris S2 instrument. Briefly, fully unmethylated l (lambda) DNA (Promega) was spiked into the mouse genomic DNA at a ratio of 1:200. DNA was end-repaired using the End Repair (Illumina Epicentre) and A-tailed (using Klenow fragment, NEB). Ligation of methylated adapters (NeBNext Multiplex Oligos for Illumina, NEB) was performed using Quick Ligase Kit (NEB). DNA was bisulfite-treated using the MethylCode Bisulfite Conversion Kit (Life Technologies).  The bisulfite treated DNA was amplified for 4 cycles -so as to ensure high complexity of the libraries- using Kapa HiFi Uracil+ (Kapa Biosystems).

tag: cell type

value: iNKT cells

tag: genotype

value: Wild Type


title: S10706_838213_hOKT3_R_12mo_WB

tag: sampleID

tag: status

value: White; White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: seqsite


title: WGBS seq WT iNKT BR1 (wt1)


title: S10707_618372_hOKT3_R_12mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

tag: age

tag: gender

value: TruSeq RNA v2

tag: flowcellid


title: S10705_781179_Control_C_12mo_WB

tag: treatmentgroup

tag: race

tag: visitmonth

tag: libraryid

tag: libraryprep

value: BRI

tag: runchemistry


title: iNKT WT BR2 CMS-Seq Input

description: CMS-Seq

data_processing:
The reads of CMS-IP and input samples were mapped to the mm9 genome and lambda phage DNA using Bismark mapping tool with default parameters
Biological replicates were pooled for downstream analysis
The coverage tracks (normalized to 10^6 reads) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Coverage file (RPM) bigWig files

growth_protocol: Mice were housed in a pathogen-free animal facility at the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee

extract_protocol:
Vα14i NKT cells were isolated by FACS and DNA was isolated using the PureLink genomic DNA mini kit (Life technologies).
DNA was fragmented to an average size of 200 bp using the Adaptive Focused Acoustics Covaris S2 instrument. Library preparation, bisulphite treatment and immunoprecipitation of CMS (5hmC)-enriched DNA were performed as previously described 4,5. Briefly, fully unmethylated l (lambda) DNA (Promega) was spiked into the mouse genomic DNA at a ratio of 1:200. DNA was end-repaired using the End Repair (Illumina Epicentre) and A-tailed (using Klenow fragment, NEB). Ligation of methylated adapters (NeBNext Multiplex Oligos for Illumina, NEB) was performed using Quick Ligase Kit (NEB). DNA was bisulphite-treated using the MethylCode Bisulphite Conversion Kit (Life Technologies). 1% of bisulphite-converted DNA was kept as input and the rest was used for immunoprecipitation with anti-CMS antibody. The anti-CMS recognizes 5hmC that upon bisulphite treatment is converted to cytosine-5-methylenesulfonate (CMS), enabling thus the enrichment of 5hmC containing DNA fragments4. The immunoprecipitated DNA was amplified using Kapa HiFi Uracil+ (Kapa Biosystems).

treatment_protocol: Vα14i NKT-cell preparations for  CMS-IP seq were performed using in case of control mice a pool of cells  (isolated from thymus or spleen as indicated on each case) from C57BL/6 mice and from age- and sex-matched DKO mice. For fluorescence-activated cell sorting (FACS), cells from wild type mice were depleted of CD19+, TER-119+, CD8+, CD11c+, F4/80+ and CD11b+ cells using biotinylated antibodies (Biolegend) and subsequent binding to magnetic streptavidin beads (Life Technologies). The unbound cells were stained with αGalCer-loaded CD1d tetramers and anti-TCRβ, after which tetramer-binding, TCRβ+ cells were isolated using a FACSAria cell sorter (BD Biosciences).

tag: cell type

value: thymic iNKT

tag: genotype

value: wild type

tag: antibody


title: S10704_161201_Control_C_12mo_WB

tag: sampleID

tag: status

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: projectid

value: TruSeq SBS Kit v3

tag: lane


title: WGBS seq Tet2/3 DKO iNKT BR1 young (dkoy1)

source_name: Te2/3 DKO iNKT BR1

value: Tet2/3 double knockout


title: S10699_693516_hOKT3_NR_12mo_WB

tag: samplelabel

value: NR

tag: itn name

tag: studysiteshort

tag: age

tag: gender

value: Male

value: White

tag: seqsite

tag: flowcellid


title: iNKT WT BR2 CMS-Seq IP

description: CMS-Seq

tag: cell type

value: anti-CMS


title: iNKT WT BR1 CMS-Seq Input

description: CMS-Seq

tag: genotype


title: S10702_604690_Control_C_12mo_WB

value: C

value: MC GEORGIA

tag: treatmentgroup

tag: race

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: runchemistry


title: S10698_666079_hOKT3_R_12mo_WB

tag: sampleID

tag: status

value: R

value: PNRI

value: White; American Indian or Alaska Native

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: projectid


title: CD8 DKO BR3 TR2 RNA-Seq CD8 SP

data_processing:
The reads were mapped to the mm9 genome as well as UCSC transcriptome using Tophat
The read counts for each gene were quantified using HTSeq-count tool with parameters: -m union -s reverse
Genome_build: mm9
Supplementary_files_format_and_content: Estimated RPKM values (txt)

extract_protocol:
Total RNA from iNKT cells  and CD8 SP T cells was isolated with E.Z.N.A HP Total RNA.
The integrity of the isolated RNA was evaluated in the Bioanalyzer (Agilent Technologies Inc). Only samples with a minimum RIN value of 9 were used for library preparation. Libraries were prepared using the Truseq RNA stranded kit (Illumina). Briefly, polyA+ RNAs were selected with magnetic beads, the RNA was fragmented and cDNA was synthesized. After A-tailing and adaptor ligation, libraries were generated by amplifying the cDNA for 10-12 cycles. The quality and quantity of the amplified libraries was evaluated using Bioanalyzer (Agilent Technologies Inc) and HS Qubit (Life Technologies). The libraries were pooled in a concentration of 10 nM and sequenced using an Illumina Hiseq 2500 instrument.

treatment_protocol: Vα14i NKT-cell preparations for RNASeq analysis  were performed using in case of control mice a pool of cells  (isolated from thymus or spleen as indicated on each case) from C57BL/6 mice and from age- and sex-matched DKO mice. For fluorescence-activated cell sorting (FACS), cells from wild type mice were depleted of CD19+ (6D5), TER-119+ (TER119), CD8+ (53-6.7), CD11c+ (N418), F4/80+ ( and CD11b+ cells using biotinylated antibodies (Biolegend) and subsequent binding to magnetic streptavidin beads (Life Technologies). The unbound cells were stained with αGalCer-loaded CD1d tetramers and anti-TCRβ, after which tetramer-binding, TCRβ+ cells were isolated using a FACSAria cell sorter (BD Biosciences). To obtain DKO cells, no depletion was performed since iNKTs are massively expanded. Rather, B220-, tetramer-binding, TCRβ+ cells were isolated using a FACSAria cell sorter (BD Biosciences).

value: CD8 SP

value: Tet2/3 double knock out


title: CD8 DKO BR2 RNA-Seq CD8 SP


title: CD8 DKO BR3 TR1 RNA-Seq CD8 SP


title: S10712_738493_hOKT3_R_12mo_WB

tag: samplelabel

tag: itn name

tag: studysiteshort

value: YALE

tag: age

tag: gender

value: Female

value: White; White

value: TruSeq RNA v2

tag: lane


title: S10693_289534_hOKT3_NR_12mo_WB

value: BRI-VM

tag: treatmentgroup

tag: race

tag: seqsite

value: BRI

tag: flowcellid

value: TruSeq SBS Kit v3


title: CD8 DKO BR1 RNA-Seq CD8 SP

tag: cell type

tag: genotype


title: S10692_770569_hOKT3_R_12mo_WB

tag: sampleID

tag: status

value: Male

tag: visitmonth

tag: libraryid

tag: libraryprep

tag: runchemistry


title: CD8 WT BR3 RNA-Seq CD8 SP

value: wild type


title: WGBS seq Tet2/3 DKO iNKT BR2 young (dkoy2)

source_name: Te2/3 DKO iNKT BR2

value: iNKT cells

value: Tet2/3 double knockout


title: S10690_707556_Control_C_12mo_WB

tag: samplelabel

value: C

tag: itn name

value: COLORADO

value: Control

value: White

tag: trunkbarcode

tag: siteandparticipantcode

tag: visitnumber

tag: projectid


title: S10689_445249_Control_C_12mo_WB

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

tag: race

tag: lane


title: CD8 WT BR2 RNA-Seq CD8 SP

tag: cell type

value: CD8 SP

tag: genotype


title: S10688_443762_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

value: NR

tag: visitmonth

tag: libraryid

tag: seqsite

tag: flowcellid


title: iNKT DKO BR3 RNA-Seq iNKT

source_name: Spleen

value: iNKT

value: Tet2/3 double knock out


title: S10687_479125_Control_C_12mo_WB

tag: samplelabel

tag: itn name

value: UCSF

value: Female

tag: trunkbarcode

tag: siteandparticipantcode

tag: libraryprep

tag: runchemistry


title: iNKT DKO BR2 RNA-Seq iNKT


title: S10684_122083_hOKT3_NR_12mo_WB

tag: studysiteshort

tag: age

tag: gender

tag: treatmentgroup

value: Black or African American; White

tag: visitnumber

value: TruSeq RNA v2

tag: projectid


title: iNKT WT BR1 CMS-Seq IP

description: CMS-Seq

tag: cell type

value: thymic iNKT

tag: genotype

tag: antibody

value: anti-CMS


title: S10681_397935_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

value: Male

tag: race

value: White; Other

tag: visitmonth

tag: libraryid

tag: seqsite

value: BRI

value: TruSeq SBS Kit v3

tag: lane


title: S10683_475166_Control_C_12mo_WB

tag: samplelabel

value: C

tag: itn name

tag: trunkbarcode

tag: siteandparticipantcode

tag: libraryprep

tag: flowcellid

tag: runchemistry


title: iNKT DKO BR1 RNA-Seq iNKT

tag: cell type


title: S10697_623229_Control_C_12mo_WB

tag: studysiteshort

value: PNRI

tag: age

tag: gender

tag: treatmentgroup

value: Control

tag: visitnumber

tag: projectid


title: iNKT WT BR3 RNA-Seq iNKT

tag: genotype

value: wild type


title: iNKT DKO BR3 RNA-Seq thymic iNKT


title: S10680_242972_Control_C_12mo_WB

tag: sampleID

tag: status

tag: race

value: White

tag: visitmonth

tag: libraryid

tag: seqsite


title: S10678_853089_Control_C_12mo_WB

tag: samplelabel

tag: itn name

value: COLUMBIA

tag: trunkbarcode

tag: siteandparticipantcode

tag: libraryprep

tag: lane


title: S10695_555647_Control_C_12mo_WB

tag: studysiteshort

value: BRI-VM

tag: age

tag: gender

tag: flowcellid

tag: runchemistry


title: iNKT WT BR2 RNA-Seq iNKT

tag: cell type

value: iNKT

tag: genotype


title: iNKT WT BR1 RNA-Seq iNKT


title: S10679_326726_hOKT3_NR_12mo_WB

tag: sampleID

tag: status

value: NR

value: Female

tag: treatmentgroup

tag: race

tag: visitnumber

tag: projectid


title: S10676_505125_hOKT3_R_12mo_WB

tag: samplelabel

value: R

tag: itn name

value: White; White

tag: trunkbarcode

tag: visitmonth

tag: libraryid

value: TruSeq RNA v2

tag: seqsite


title: iNKT WT BR3 RNA-Seq thymic iNKT

value: thymic iNKT


title: S10677_493934_hOKT3_NR_12mo_WB

tag: studysiteshort

tag: age

tag: gender

value: Black or African American

tag: siteandparticipantcode

tag: libraryprep

tag: lane


title: iNKT DKO BR1 RNA-Seq thymic iNKT

tag: cell type

tag: genotype

value: Tet2/3 double knock out


title: CD8 WT BR1 RNA-Seq CD8 SP

value: CD8 SP


title: M200_rep1

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: rRNA-depleted total RNA

data_processing:
Basecalling, adaptor trimming and demultiplexing was performed using Torrent Suite v4.0.2
Sequence read ends were quality trimmed using CLC Genomics Workbench v6.5.2 (quality limit = 0.05, modified-Mott trimming algorithm), resulting short reads < 50 nt were discarded
Trimmed reads were aligned to the Mycobacterium tuberculosis H37Rv complete genome sequence (NC_000962.3) using the CLC Genomics Workbench RNA-Seq algorithm (v6.5.2). RPKM values were calculated according to Mortazavi et al., Nat Methods, 2008.
Genome_build: NC_000962.3
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample

organism: Mycobacterium tuberculosis

source_name: whole cells

growth_protocol: Cells of the conditional M. tuberculosis c-otsB2 mutant were grown from frozen stocks in 7H9 medium containing 1000 ng/ml anhydrotetracycline until OD600 nm ~1. Cells were harvested, washed and then subcultered in 7H9 medium containing 100 ng/ml anhydrotetratcycline for 7 days at 1% inoculation. Cells were subsequently harvested, washed, and used to inoculate 10 - 30 ml per replicate of 7H9 medium containing either 200 ng/ml or 30 ng/ml anhydrotetracycline, respectively, at 1% inoculation. Cells were harvested for RNA extraction after 7 days of incubation at 37°C.

extract_protocol:
Cells were harvested and cell pellets were fixed overnight in 5 ml RNA Protect reagent (Qiagen). Fixed cells were pelleted, resuspended in 1 ml RLT buffer (Qiagen) and lysed by bead beating to prepare lysates. Total RNA was extracted using the RNeasy Mini kit (Qiagen).
2 µg of bacterial total RNA were depleted for rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) according to the manufacturer´s protocol (Epicentre). After fragmentation of the rRNA depleted RNA fraction by RNAse III, barcoded cDNA libraries were constructed following the Ion Total RNA-Seq Kit (v2) User Guide (Life Technologies) using IonXpressRNA barcodes 011 (sample M30_1), 012 (sample M30_2), 013 (sample M30_3), 014 (sample M200_1), 015 (sample M200_2) and 016 (sample M200_3).

tag: strain

tag: expression level

value: fully induced


title: M200_rep2

description: rRNA-depleted total RNA


title: M200_rep3

description: rRNA-depleted total RNA


title: M30_rep3

description: rRNA-depleted total RNA

value: partially silenced


title: M30_rep2

description: rRNA-depleted total RNA


title: iNKT WT BR2 RNA-Seq thymic iNKT


title: CB-32_L002_F7

status: Public on Nov 20 2016

first: Camron

last: Bryant

state: Massachusetts (MA)

address: 72 E. Concord St. R-604

department: Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

data_processing:
Samples were run across four lanes on 4 different flow cells and 50bp reads for each sample were generated via the Illumina HiSeq 4000.
Fastq files are quality checked with FastQC (v0.11.3).
Single-end reads were mapped to the mouse genome (mm10) using R-subread (a R package).  FeatureCounts was computed from R-subread.  Count normalization was carried out with voom normalization using edgeR (v3.8.6) R package. Lane effect was adjusted by adding lane as a covariant. The gene are identified as entrezgene ensembl.  Differential gene expression was carried out using the Limma (v3.22.7) R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab Delimited file of read counts per gene from R-subread

extract_protocol:
Striatum punches were harvested on Day 24 immediately following the 5-min behavioral test on the EPM, stored in RNAlater for 48 h, blotted dry with a kimwipe, and transferred to -80ºC.
Total RNA was isolated  and shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (50 bp single-end reads). Samples were sequenced using the Illumina HiSeq 4000 with 16 samples per lane over two different lanes on 3 different days (technical quadruplicates).

tag: strain background

tag: genotype/variation

value: N/-; binge-resistant

value: 82-84 days old

tag: Sex

value: male

tag: tissue

value: Striatum

tag: cage

tag: sampleID


title: CB-30_L002_F7

value: female


title: CB-26_L002_F7

value: N/N; binge-prone


title: CB-29_L002_F7


title: CB-28_L002_F7


title: CB-25_L002_F7


title: iNKT DKO BR2 RNA-Seq thymic iNKT


title: CB-23_L002_F7


title: CB-24_L002_F7


title: CB-19_L002_F7


title: CB-20_L002_F7


title: CB-21_L002_F7


title: CB-18_L002_F7


title: CB-32_L002_F4


title: CB-17_L002_F7


title: CB-22_L002_F7


title: iNKT WT BR1 RNA-Seq thymic iNKT

value: wild type


title: CB-31_L002_F4


title: CB-30_L002_F4


title: CB-28_L002_F4


title: CB-29_L002_F4


title: CB-27_L002_F4


title: CB-26_L002_F4


title: CB-25_L002_F4


title: CB-24_L002_F4


title: M30_rep1

description: rRNA-depleted total RNA


title: CB-23_L002_F4


title: CB-22_L002_F4


title: CB-27_L002_F7


title: CB-21_L002_F4


title: CB-31_L002_F7


title: CB-18_L002_F4


title: CB-20_L002_F4


title: CB-16_L004_F6


title: CB-19_L002_F4


title: CB-17_L002_F4


title: CB-13_L004_F6


title: CB-15_L004_F6


title: CB-11_L004_F6


title: CB-14_L004_F6


title: CB-8_L004_F6


title: CB-9_L004_F6


title: CB-6_L004_F6


title: CB-12_L004_F6


title: CB-4_L004_F6


title: CB-3_L004_F6


title: CB-5_L004_F6


title: CB-2_L004_F6


title: CB-1_L004_F6


title: CB-16_L001_F7


title: CB-13_L001_F7


title: CB-14_L001_F7


title: CB-10_L001_F7


title: CB-12_L001_F7


title: CB-15_L001_F7


title: CB-11_L001_F7


title: CB-9_L001_F7


title: CB-7_L001_F7


title: CB-10_L004_F6


title: CB-8_L001_F7


title: CB-2_L001_F7


title: CB-6_L001_F7


title: CB-7_L004_F6


title: CB-3_L001_F7


title: CB-5_L001_F7


title: KCNC1

city: AMHERST

first: Stelios

middle: T

last: Andreadis

state: NY

address: 908 Furnas Hall

department: Chemical & Biological Engineering

institute: University at Buffalo

data_processing:
Sequence reads that passed the Illumina quality filtering were mapped to the reference human genome (hg19) and annotated by UCSC gene annotation using Tophat (version 2.0.11) with all default settings.
The mapping quality was examined by RSeQC 2.3.9.
Then the read counts for each gene in the accepted hits are counted by the R package qRNASeq. For each gene, total reads within the exon regions were counted and overlapped regions from different transcripts were united.
The differential expressed genes between KC and KC-NC were detected by the R package DESeq2, using a design formula considering patient variability.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing gene names and raw counts

source_name: Skin

growth_protocol: Interfollicular epidermal keratinocytes were isolated from foreskin of 1-3 day old neonates and cultured in presence of EpiLife keratinocyte serum free medium (Life Technologies).

extract_protocol:
Total RNA from KC and respective KC derived NC (n=3 human donors) was isolated using RNeasy kit (Qiagen) as per manufacturer’s instructions. Quality control analysis was performed by RNA gel and Agilent Bioanlyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For KC induction into NC fate KC were plated in 10000 cells per cm2 on collagen type 1 coated dishes (10 microgram per cm2 area) and cultured in induction medium,for 10 days, containing EBM2 basal medium (Lonza) supplemented with 2% fetal bovine serum, 10 µg per ml heparin, 100 µg per ml ascorbic acid and 0.5 µg per ml hydrocortisone, 1x entamicin/Amphotericin-B  supplemented with 10 ng/ml fibroblast growth factor 2 (FGF2, BD Biosciences), 10 ng/ml Insulin like growth factor 1 (IGF1, BD Biosciences).

value: Epidermal keratinocytes derived Neural crest

tag: passage


title: KCNC2


title: CB-4_L001_F7


title: CB-1_L001_F7


title: KC2

value: Epidermal keratinocytes


title: KC3


title: KC1


title: KCNC3


title: glia_H3K9ac

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
ChIP-seq and MNase-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters:–p 8 -t -v 2 -m 1 -5 1 --suppress 5,6
The uniquely mapped nucleosomal reads were used to identify genome-wide nucleosome positions through the peak-calling tool GeneTrack
Aligned histone modification reads were converted into Bedgraph format use bedtools genomecov, normalized by total mapped reads and sorted by their genomic location, then converted BedGraph format into Bigwig format.
Genome_build: dm3
Supplementary_files_format_and_content: Bigwig is a binary file and bed file for nucleosome positions.

organism: Drosophila melanogaster

source_name: Late glial cells

growth_protocol: Embryos of two fly lines were collected on grape juice plates with yeast paste from embryo collection cages for 2 hr, and then allowed to develop for 3 and 10 additional hours before being harvested. So the collected embryos are 5–7h and  and 12–14h old, respectively.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Embryos were dechorionated with 50% solution of bleach for 3 minutes and were cross-linked in a 1:3 mix of ChIP-fixed buffer with 1.8% formaldehyde and heptane for 15 min on a shaker with speed at 300 rpm. The aqueous and organic phase was replaced with PBST plus 0.25 mM glycine to cease cross-linked reaction, and fixed embryos were rinsed by PBST for 3 times. Whole embryonic nuclei mixture were harvested by homogenizing the cross-linked Drosophila embryo, and tagged nuclei were isolated through anti-Flag M2 magnetic beads affinity purification.

value: Late glial cells

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.

tag: Stage


title: glia_H3K4me3


title: glia_H3K27ac


title: glia_H3K27me3


title: glia_H3K4me1


title: glia_nucleosome


title: GB_H3K27me3

source_name: Early glial cells

value: Early glial cells

value: 5-7h AEL


title: GB_H3K9ac


title: GB_H3K27ac


title: GB_nucleosome

value: 5–7h after egg laying (AEL)


title: GB_H3K4me1


title: glia.RNA

description: total nuclear RNA

data_processing:
mRNA-Seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, aligned to the Drosophila genome (dm3) using Bowtie/Tophat (v1.3.1) with default parameters.
Uniquely mapped reads were assembled into transcripts guided by reference annotation (FlyBase r5.43) with Cuffdiff (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM) and identify differentially expressed genes with FDR < 0.05.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene

growth_protocol: Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 2 hr, and then allowed to develop for 3 and 10 additional hours before being harvested. So the collected embryos are 5–7h and  and 12–14h old, respectively.

extract_protocol:
Nuclei RNA was harvested used the RNeasy micro kit (Qiagen, cat. no. 74004). Contaminating genomic DNA was removed from the RNA by treating with the Turbo DNA-free kit(Ambion, cat. no. AM1907M).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nuclei mixture were harvested by homogenizing the whole cross-linked Drosophila embryo, and nuclei of interest were isolated by anti-Flag M2 magnetic beads affinity purification.


title: GB_H3K4me3


title: GB.RNA

description: total nuclear RNA


title: NSC_H3K27ac

data_processing:
ChIP-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters:–p 8 -t -v 2 -m 1 -5 1 --suppress 5,6
The uniquely mapped nucleosomal reads were used to identify genome-wide nucleosome positions through the peak-calling tool GeneTrack
Aligned histone modification reads were converted into Bedgraph format use bedtools genomecov, normalized by total mapped reads and sorted by their genomic location, then converted BedGraph format into Bigwig format.
Genome_build: dm3
Supplementary_files_format_and_content: Bigwig is a binary file. And bed.txt file for nucleosome positions includes nucleosome name, location (chromatin, start, end), the number of reads aligned on predicted nucleosme (rc), fuzziness of predicted nucleosme (fuzziness, the standard deviation of tag locations around the nucleosome dyad)

source_name: Neural stem cells

treatment_protocol: Embryos were dechorionated with 50% solution of bleach for 3 minutes and were cross-linked in a 1:3 mix of ChIP-fixed buffer with 1.8% formaldehyde and heptane for 15 min on a shaker with speed at 300 rpm. The aqueous and organic phase was replaced with PBST plus 0.25 mM glycine to cease cross-linked reaction, and fixed embryos were rinsed by PBST for 3 times. Nuclei mixture were harvested by homogenizing the whole cross-linked Drosophila embryo, and nuclei of interest were isolated by anti-Flag M2 magnetic beads affinity purification.

value: Neural stem cells


title: NSC_H3K27me3


title: NSC_H3K4me3


title: NSC_H3K9ac


title: neuron_H3K4me1

source_name: neuron

value: neuron


title: neuron_H3K27ac


title: neuron_H3K4me3


title: neuron_H3K27me3


title: Runx3-P2-/-  23.12.13

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

data_processing:
Reads were demultiplexed the reads into the different samples
Reads were aligned to the mm9 genome built using Tophat (v1.4.0)
Expression at the gene level was quantified by applying HTSeq, and using the RefSeq in gtf format as annotation.
Differential expression was calculated utilizing the DESeq2 software (version 1.2.8).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file including raw counts and DESeq2 normalized counts per gene.

extract_protocol:
Freshly isolated cervical E11.5 DRG were sortedand GFP+ neurons collected into lysis buffer of the Qiagen RNAeasy kit.  RNA was prepared using Qiagen RNAeasy mini kit.
Amplification was conducted with Smarter Ultra low RNA kit from Clontech.  Amplicons were fragmented to 100-400 bp using Covaris and processed according to ChIP-seq protocol.
Sequencing libraries were barcoded.  Between 20-24 million single -end 50 bp reads were sequenced on Illumina HiSeq 2500 instrument.

value: ICR

value: Dorsal root ganglia

value: TrkC neurons

tag: age

value: Knockout


title: neuron_nucleosome


title: Runx3-P2-/-  20.1.14


title: Runx3-P2-/-  18.11.13


title: Runx3-P2-/-  01.09.13


title: Pgsa745-XYLT1 rep2

first: Nathan

last: Lewis

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

description: Recovery of XylT activity in PgsA745, rep 2

data_processing:
Quality controls was performed using fastqc 0.11.3
Reads were trimmed using Trimmomatic 0.33. Parameters were: SLIDINGWINDOW:5:10 LEADING:15 TRAILING:10 MINLEN:36 TOPHRED33
STAR 2.4.0a was used to align reads to chok1 reference genome. All parameters were set as recommended from STAR manual.
samtools 1.0 was used to convert sam file to sorted bam file.
HTSeq 0.6.1p2 was used to get read count for each gene.
Normalized count was also got from DESeq2
cufflinks 2.2.1 was used to quantify gene expression with unit of FPKM.
Genome_build: CHOK1 reference genome from ncbi ftp site: ftp://ftp.ncbi.nlm.nih.gov/genomes/Cricetulus_griseus/CHR_Un/cgr_ref_CriGri_1.0_chrUn.fa.gz
Supplementary_files_format_and_content: normalized count data and FPKM data were in excel sheet; Differential expression results were in excel sheet;

organism: Cricetulus griseus

source_name: Ovary cells

growth_protocol: CHO cells were cultured in Ham’s F-12 growth medium (Life Technologies) supplemented with 10% (v/v) fetal bovine serum (FBS; Gemini Bioproducts), 100 µg/ml of streptomycin, and 100 Units/ml of penicillin (Life Technologies)

extract_protocol: For RNA isolation, the Untergasser's Lab protocol was followed. Cells were lysed directly using Trizol, after which chloroform was added. Following 12000x g centrifugation for 15 min at 4 °C, the transparent upper phase was transferred and an equal volume of 70 % ethanol was added. This mixture was applied to a RNeasy Mini spin column (Qiagen) and the manufacturer’s instructions were followed.

treatment_protocol: No treatment

value: Ovary

value: PgsA745 stably transfected with XylT1


title: Pgsa745-XYLT1 rep1

description: Recovery of XylT activity in PgsA745, rep 1


title: Pgsa745 rep1

description: PgsA745 is a mutant of CHOK1 and lacks XylT activity, rep 1

value: Deficient in XylT activity


title: CHOK1 rep2

description: wild type CHOK1 cell line, rep 2

value: wild type


title: neuron_H3K9ac


title: CHOK1 rep1

description: wild type CHOK1 cell line, rep 1


title: neuron.RNA

tag: molecule subtype

value: total nuclear RNA


title: NSC.RNA


title: siMef2a-2

status: Public on Nov 19 2016

city: Toronto

middle: C

last: McDermott

state: ON

address: 4700 Keele Street

country: Canada

institute: York University

description: siMef2a FPKM.txt

data_processing:
Base calls are made using the Illumina CASAVA pipeline. Base quality is encoded in phred 33.
Reads are trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters are removed from the reads, and all reads are required to have a length of at least 32 b.p. Trimming and clipping are done with the Trimmomatic software.
The filtered reads are aligned to a reference genome. The alignment is done with the combination of tophat/bowtie software. It generates a Binary Alignment Map file (.bam).
The Cufflinks program is used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundances. For rat (cardiomyocytes) NGS short reads were mapped to the rat genome with the RSEM/ Bowtie software (Dewey Lab).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: Raw read counts or FPKM

organism: Rattus norvegicus

source_name: Neonatal cardiomyocytes

growth_protocol: 1) 6-8 wk MEF2-LacZ mice underwent TAC or Sham surgery. 2) Primary cardiomyocytes: In brief, whole hearts were dissociated and digested with trypsin (Promega) and collagenase (Worthington Biochemical Corp). Cardiomyocytes were re-suspended in culture medium with (DMEM/F12 (Gibco) with 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin and 50 mg/L gentamycin sulphate). The isolated cells were plated on 10 cm dishes for 60 minutes in 37oC humidified incubator with a 5% CO2 in air to remove non-myocardial cells. The cardiomyocytes were then seeded into gelatin-coated 6-well plates. The day after, medium was removed and replaced by fresh medium.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus Universal kit
Illumina TruSeq mRNA Sample Prep Kit. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1) Six weeks later they were fed atenolol (50mg/kg/day) or solvent for an additional four weeks. 2) Primary cardiomyocytes were transfected with scr or siMEF2A (100 nM final concentration).

value: Sprague Dawley

value: 1-3 day old neonates

tag: cell type

value: cardiomyocyte

value: MEF2A depletion


title: siMef2a-1

description: siMef2a FPKM.txt


title: Runx3-P2+/-  17.11.13

value: Heterozygote


title: Runx3-P2+/- 10.1.13


title: NSC_H3K4me1

value: 5-7h AEL

value: Abcam


title: scr-1

description: siMef2a FPKM.txt

value: control


title: scr-2

description: siMef2a FPKM.txt


title: ecoli_k12_pBADsigma32I54N_30C_f_2

first: Evan

middle: Thomas

last: Powers

address: 10550 North Torrey Pines Rd

department: Chemistry

institute: The Scripps Research Institute

description:
Ribosome footprinting
Processed data file: ecoli_heatshock_rawcounts.txt
Processed data file: ecoli_heatshock_normalizedcounts.txt

data_processing:
Library strategy: Ribo-Seq
Basecalls performed using Illumina CASAVA.
Reads were trimmed and adaptors removed using the fastx_toolkit.
Reads were aligned to the MG1655 genome with Bowtie.
The number of reads at each position in the genome was counted using in-house Python scripts.
The number of reads mapping to each gene was counted and normalized using EdgeR.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names).
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli cultures

growth_protocol: E. coli were grown in defined rich media at 30C.

extract_protocol:
Cells were lysed in liquid nitrogen, then samples were taken for ribosome footprint extraction.
Polysomes were digested with MNase, monosomes were purified by sucrose gradient ultracentrifugation, and the resulting mRNA fragments were extracted with phenol chloroform and gel-purified.
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes.

treatment_protocol: Cells were induced with arabinose or heat shocked, then harvested and flash frozen.

tag: plasmid

tag: growth temperature

tag: induction

value: 0.2% arabinose

tag: treatment temperature

tag: heat shock time

tag: replicate


title: ecoli_k12_pBADsigma32I54N_30C_m_2

description:
Total mRNA
Processed data file: ecoli_heatshock_rawcounts.txt
Processed data file: ecoli_heatshock_normalizedcounts.txt

data_processing:
Basecalls performed using Illumina CASAVA.
Reads were trimmed and adaptors removed using the fastx_toolkit.
Reads were aligned to the MG1655 genome with Bowtie.
The number of reads at each position in the genome was counted using in-house Python scripts.
The number of reads mapping to each gene was counted and normalized using EdgeR.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: ecoli_heatshock_rawcounts.txt: Tab-delimited text file has raw read counts per kilobase million for each E. coli gene (EcoCyc gene names).
Supplementary_files_format_and_content: ecoli_heatshock_normalizedcounts.txt: Tab-delimited text file has EdgeR-normalized counts per kilobase million for each E. coli gene (EcoCyc gene names).

extract_protocol:
Cells were lysed in liquid nitrogen, then samples were taken for total RNA.
Total RNA was extracted with phenol chloroform and alkaline fragmented, then fragments (20-40 nt) were gel-purified.
RNA was dephosphorylated, ligated to an adaptor, reverse transcribed, circularized then amplified with Illumina adaptors and barcodes.


title: ecoli_k12_pBADsigma32I54N_30C_m_1


title: Runx3-P2+/-  27.10.13

tag: strain

value: ICR

tag: tissue

value: Dorsal root ganglia

tag: genotype/variation


title: NSC_nucleosome

value: Neural stem cells

value: 5–7h after egg laying (AEL)


title: Pgsa745 rep2

description: PgsA745 is a mutant of CHOK1 and lacks XylT activity, rep 2

value: Ovary

tag: genotype


title: ecoli_k12_pBADsigma32I54N_30C_f_1


title: ecoli_k12_pBAD_30C_f_4

value: pBAD


title: ecoli_k12_pBAD_30C_m_4


title: ecoli_k12_42C_20min_f_3


title: 3Rb_1 Anti-H3.3

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

institute: McGill University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm10 genome assembly. BWA was used to align ChIP-Seq data reads to the genome.
Genome_build: mm10
Supplementary_files_format_and_content: For each Chip experiment, the associated txt contains tags distribution in 50kb window for each sample. The txt file columns are as follows: 1. chromosome 2. window start 3.window end 4.Number of tags

extract_protocol:
DNA was extracted from whole testis after sonication and precipitation with antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit by the service platform of McGill University and genome Quebec Innovation Centre

value: F1 (B6.SPRET7MOLF12 x RBF/Dnj)

value: heterozygous carriers of 3 Robertsonian translocation

tag: mouse age

value: 6 weeks

value: testis

tag: chip antibody

value: Millipore:ChIPAb+TM histone H3.3-ChIP validated antibody (cat 17-10245)


title: 3Rb_3 Anti-H3.3


title: Cg_3 Anti-H3.3


title: ecoli_k12_42C_20min_m_3


title: Cg_1 Anti-H3.3


title: 3Rb_2 Anti-H3.3


title: 1Rb_3 Anti-H3.3

value: heterozygous carriers of a single Robertsonian translocation


title: ecoli_k12_42C_10min_f_3


title: 1Rb_2 Anti-H3.3


title: ecoli_k12_42C_10min_m_3


title: ecoli_k12_30C_f_3


title: B6 Anti-gH2AX

source_name: B6 Anti-gH2AX_ChIP-seq

value: 4 weeks

value: Upstate. Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301


title: Cg Input DNA

source_name: Cg Input DNA


title: ecoli_k12_30C_m_3


title: B6 Input DNA

source_name: B6 Input DNA


title: ecoli_k12_42C_20min_f_2


title: ecoli_k12_42C_20min_m_2


title: Cg_2 Anti-H3.3


title: 3Rb_3 Anti-gH2AX

value: Millipore:anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301


title: ecoli_k12_42C_10min_m_2


title: ecoli_k12_30C_f_2


title: ecoli_k12_30C_m_2


title: ecoli_k12_42C_10min_f_2


title: 3Rb_1 Anti-gH2AX


title: ecoli_k12_42C_20min_f_1


title: 1Rb_P3 Anti-gH2AX

source_name: 1Rb_P Anti-gH2AX_ChIP-seq

value: F1(C57BL/6J x CBy.RBF-Rb(8.12)5Bnr/J)


title: 1Rb_P2 Anti-gH2AX


title: 1Rb_1 Anti-H3.3


title: ecoli_k12_42C_10min_m_1


title: ecoli_k12_42C_20min_m_1


title: 1Rb_M2 Anti-gH2AX

source_name: 1Rb_M Anti-gH2AX_ChIP-seq


title: 3Rb_2 Anti-gH2AX


title: 1Rb_M1 Anti-gH2AX


title: 1Rb_M3 Anti-gH2AX


title: ecoli_k12_30C_f_1


title: ecoli_k12_42C_10min_f_1


title: ecoli_k12_30C_m_1


title: TAC+AT (1F)

description: Aortic constriction and Beta-blocker experiment raw reads.txt

source_name: Left ventricle of the heart

value: 16-18 wk old mice

tag: treatment

value: TAC+AT

value: left ventricle of heart


title: 1Rb_M Input DNA

source_name: 1Rb_M Input DNA


title: ecoli_k12_pBADsigma32wt_30C_m_3

value: 0.2% arabinose


title: Chondrocyte_Ms8

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description: Sample 7

data_processing:
a combined transcriptome composed of both the reference and CAST versions of each transcript (based on mm10), was built using the g2gtools tool (https://g2gtools.readthedocs.io/en/latest/), the reference .gtf file, and the .vcf files for the SNPs and indels from sanger, version 5.
reads were aligned to this combined transcriptome using bowtie, with options "-q -a --best --strata --sam -v 3" and converted to .sam files using samtools (http://emase.readthedocs.io/en/latest/) and (http://samtools.sourceforge.net/)
these .sam files were converted into sparse matrices marking the locations of reads aligning to each transcript of each of the two strains using emase.
these matrices were used in conjunction with EMASE in order to quantify the number of reads aligning to each strains transcriptomes and the total number of reads aligning, regardless of strain.
Genome_build: mm10 (ref) and mm10_CAST (with CAST SNPs and indels)
Supplementary_files_format_and_content: processed data files contain effective read counts derived from the CAST and B6 strains and the total number of counts of each genes within the sample. They are text files with four columns, transcript IDs (ensembl), two columns of strain specific counts, and one column of total counts.

source_name: chondrocytes

extract_protocol:
total RNA extracted from homogenized tissue in TRIzol using mirVana miRNA isolation kit
RNA-Seq libraries constructed from 200 ng total RNA using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits. Libraries were depleted of cytoplasmic and mitochondrial rRNAs and an average of 6.7 million 2 x 75 bp paired-end reads were generated for each sample on an Illumina NextSeq 500

value: C57BL/6JxCAST/EiJ F1

tag: Sex

value: male

value: 21 days

value: growth plate chondrocyte


title: ecoli_k12_pBADsigma32wt_30C_f_3


title: Chondrocyte_Ms7

description: Sample 6

tag: age


title: TAC+AT (1E)


title: Chondrocyte_Ms4

description: Sample 4


title: ecoli_k12_pBAD_30C_f_3

value: pBAD


title: ecoli_k12_pBAD_30C_m_3


title: Chondrocyte_Ms3

description: Sample 3


title: 1Rb_P1 Anti-gH2AX


title: Sham+AT (3D)

value: Sham+AT


title: TAC+AT (1B)


title: Sham+AT (3B)


title: ecoli_k12_pBADsigma32wt_30C_f_2


title: Chondrocyte_Ms2

description: Sample 2


title: Chondrocyte_Ms1

description: Sample 1


title: ecoli_k12_pBADsigma32wt_30C_m_2


title: Sham+AT (3A)


title: ecoli_k12_pBad_30C_f_2


title: TAC+Sol (2E)

value: TAC+Solvent


title: Chondrocyte_Ms5

description: Sample 5


title: ecoli_k12_pBAD_30C_m_2


title: ecoli_k12_pBADsigma32wt_30C_f_1


title: TAC+Sol (2D)


title: ecoli_k12_pBAD_30C_f_1


title: ecoli_k12_pBADsigma32wt_30C_m_1


title: H3K27ac_mono

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

description: Sample 3

data_processing:
Data processing were performed by BGI Bioinformatics Center Version 3.0. Briefly, sequence data was filtered to get clean data firstly. Then the production of data was estimated. All of the clean data was mapped to reference genome. Only the uniquely mapped reads were used for further analysis. The distribution of uniquely mapped reads was analyzed. Meanwhile, reads enrichment region (peak) was scanned from the whole genome.
Genome_build: hg19
Supplementary_files_format_and_content: wig files (Shifted Merged MACS tag counts for every 50 bp) were generated by BGI.tech

source_name: human periphery blood monocytes

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats from Blood Center of Shanghai Changhai hospital (Shanghai, China) through Ficoll-Hypaque (Mediatech Cellgro) density gradient centrifugation. All human blood samples were collected with the informed consent of healthy donors and the experiments were approved by the Ethics Committee of the Second Military Medical University, Shanghai, China. Monocytes were purified from PBMCs using anti-CD14 microbeads (Miltenyi Biotech) and then cultured at 37°C in 24-well plates (5× 105 cells per well) in 1 mL of RPMI-1640 Medium (PAA) with 10% (vol/vol) FCS (PAA) containing 100 ng/mL human GM-CSF and 20 ng/mL human IL-4 (R&D Systems，Minneapolis, MN). Half medium was replaced by fresh medium with GM-CSF and IL-4 at day 3 and day 5. DCs were matured by 300ng/ml LPS (0111:B4, Sigma) on day 5 and harvested on day 7.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA was fragmented to 100-500bp by sonication or micrococcal nuclease digestion. DNA-end was repaired to overhang a 3’-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification. Finally we got qualified library for sequencing.

value: monocytes


title: H3K4me3_moDC

description: Sample 4

source_name: monocyte-derived DCs

value: monocyte-derived DCs


title: H3K4me3_mono

description: Sample 1


title: H3K27me3_moDC

description: Sample 5


title: H3K27me3_mono

description: Sample 2


title: ecoli_k12_pBAD_30C_m_1


title: Sham+Sol (4C)

value: Sham+Solvent


title: ChIP-Seq input in JHU-029 HNSCC

status: Public on Nov 18 2016

first: Kenneth

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: ChIP-Seq input in JHU-029 HNSCC

data_processing:
ChIP libraries were indexed, pooled, and sequenced on Illumina HiSeq-2500 sequencers.
ChIP-seq reads were aligned to the human hg19 genome assembly using bowtie version 0.12.5 with parameters 'bowtie --phred64-quals -M 1 -q -v 2 -k 1 -X 2000 --best --strata --sam'.
ChIP-seq duplicate reads were marked with samtools version number 0.1.19.
Peak calling with MACS2 version 2.0.10 and parameters '-g hs -f BAM -B -q 0.01'
Ran the IGVtools version 2.3.18 utility 'count' on aligned bam files to compute the average alignment over 25 base windows across the genome and generate binary tiled data .tdf files.
Genome_build: hg19
Supplementary_files_format_and_content: SVS_ChIPSeq_p63_tumor_peaks file is ChIP-Seq peak summary files from MACS2 in a tab delimited text file format.
Supplementary_files_format_and_content: tdf files are binary tiled data files of aligned ChIP-Seq data from the IGVtools count utility that conatin average alignment counts across the genome and can viewed in the IGV genome browser.

growth_protocol: Cells were maintained at 37°C in 5% CO2 in RPMI supplemented with 10% FBS, penicillin, and streptomycin.

extract_protocol:
JHU029 cells were subjected to additional cross-linking protein-protein interaction with 2 mM EGS followed by cross-linking with 1% (v/v) formaldehyde. Cells were then lysed in RIPA buffer  for 1-2hr at 40C. Nuclear lysates were sonicated and the sonicated chromatin was precleared with ProteinG sepharose beads (GE healthcare) pre-blocked with BSA and sonicated salmon sperm DNA. Samples were incubated with 2 μg of p63 antibody (H129, Santacruz) for overnight at 40C and with beads for additional 2 hrs. Beads were washed in wash buffer. After the wash, beads were incubated for 3 hrs at 550C, then overnight at 650C in TE buffer containing SDS, RNase A, Proteinase K. DNA was purified via Qiaquick PCR purification kit (28106, Qiagen) as per manufacturer’s instructions. Percentage of input was calculated by using 10% as standard.
Libraries were prepared for ChIP-sequencing using Illumina kit (cat number, 1005709, 1003473).

treatment_protocol: ChIP-Seq experiments used untreated JHU-029 cells.

tag: cell line


title: Sham+Sol (4E)


title: p63 ChIP-Seq in JHU-029 HNSCC

description: p63 ChIP-Seq in JHU-029 HNSCC

value: p63 (H129, Santacruz)


title: D3_coIBET_RPMI_restim_don73_10849

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation (Ensemble release 68).
Genome_build: hg19

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Tolerization was induced by treatment of monocytes with 10-100ng/mL LPS for 24 hours, followed by washout and five days culture in RPMI + 10% human serum, while trained innate immunity was induced by treatment with 5 ng/mL BG for 24 hours, followed by washout and 5 days in culture. Establishment of tolerance or training in the resulting macrophages at day 6 was determined by TNF and IL6 release at 24 hours following LPS stimulation using ELISA. For ChIP-seq, 10x106 monocytes were seeded in 10cm dishes, for RNAseq and ATAC-seq 1.5 x 106 monocytes were seeded in 6 well plates.

extract_protocol: Libraries were prepared according to Illumina's instructions.

tag: cell type

value: Monocyte

value: 5 uM IBET151 exposed 24 hours, culture media only for 2 days, LPS exposed for 4 hours.

value: Peripheral blood


title: IBET_4h_LPS_don73_10838

value: LPS and 5 uM IBET151 exposed for 4 hours


title: D3_Rescue_LPS_BGd2_don73_10845

value: LPS exposed 24 hours, BG exposed for 24 hours, culture media only for 24 hours


title: D3_RPMI_restim_don73_10846

value: Culture media for 3 days, LPS exposed for 4 hours.


title: H3K27ac_moDC

description: Sample 6


title: D3_RPMI_don73_10839

value: Culture media for 3 days


title: D3_BG_don73_10841

value: BG exposed 24 hours, culture media only for 48 hours


title: D3_BG_restim_don73_10848

value: BG exposed 24 hours, culture media only for 48 hours, LPS exposed for 4 hours.


title: Sham+Sol (4D)

value: 16-18 wk old mice

value: left ventricle of heart


title: D3_coIBET_LPS_don73_10843

value: LPS and 5 uM IBET151 exposed 24 hours, culture media only for 2 days


title: D3_coIBET_LPS_restim_don73_10850

value: LPS and 5 uM IBET151 exposed 24 hours, culture media only for 2 days, LPS exposed for 4 hours.


title: D3_Rescue_RPMI_BGd2_don73_10844

value: Culture media for 24 hours, BG exposed for 24 hours, culture media only for 24 hours


title: D3_Rescue_RPMI_BGd2_restim_don73_10851

value: Culture media for 24 hours, BG exposed for 24 hours, culture media only for 24 hours, LPS exposed for 4 hours.


title: LPS_d6_rep2_H3K27ac

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-10. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac and H3K4me3 were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: bam files sequence and quality, and BigWig files for tracks. All data have been normalized ("Normalized") to a depth per mark except few which have been marked as "NotNormalized"

source_name: LPS d6 rep2 H3K27ac

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 67µl of chromatin (1 million cells) was incubated with 229µl dilution buffer, 3µl protease inhibitor cocktail and 0.5-1µg of H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K9me3 or H3K36me3 antibodies (Diagenode) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.

tag: background strain

value: Adult Human Peripheral Blood

value: LPS-Mf (LPS exposed 24 hours, culture for 5 days to macrophage)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: LPS_4h_rep2_H3K4me1

source_name: LPS 4h rep2 H3K4me1

value: Monocyte

value: Mono_4h_LPS (LPS exposed, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: D3_LPS_restim_don73_10847

value: LPS exposed 24 hours, culture media only for 48 hours, LPS exposed for 4 hours.

value: Peripheral blood


title: D3_coIBET_RPMI_don73_10842

value: 5 uM IBET151 exposed 24 hours, culture media only for 2 days


title: BG_R_H3K9me3

source_name: BG R H3K9me3

value: BG-Mf LPS exposed (BG exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)

value: Rabbit polyclonal anti-H3K9me3 (Diagenode, cat. # pAb-193-050)


title: D3_Rescue_LPS_BGd2_restim_don73_10852

value: LPS exposed 24 hours, BG exposed for 24 hours, culture media only for 24 hours, LPS exposed for 4 hours.


title: don73_LPS_d6_24hr_BG_H3K4me1

source_name: don73 LPS d6 24hr BG H3K4me1

value: Rescue-Mf (LPS exposed 24 hours, then BG exposed 24 hours, culture for 4 days to macrophage)


title: LPS_1h_rep2_H3K4me3

source_name: LPS 1h rep2 H3K4me3

value: Mono_1h_LPS (LPS exposed, collected at 1 hour of exposure)

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: BG_4h_rep1_H3K4me1

source_name: BG 4h rep1 H3K4me1

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)


title: LPS_d1_rep2_H3K4me3

source_name: LPS d1 rep2 H3K4me3

value: Mono_day1_LPS (LPS exposed for 24 hours, collected at 24 hour of exposure)


title: BG_d1_rep1_H3K4me3

source_name: BG d1 rep1 H3K4me3

value: Adult Human Peripheral Blood

value: Mono_day1_BG (BG exposed for 24 hours, collected at 24 hour of exposure)


title: LPS_4h_rep1_H3K4me1

source_name: LPS 4h rep1 H3K4me1


title: D3_LPS_don73_10840

value: LPS exposed 24 hours, culture media only for 48 hours


title: LPS_d6_rep2_H3K4me3

source_name: LPS d6 rep2 H3K4me3

value: Monocyte

value: LPS-Mf (LPS exposed 24 hours, culture for 5 days to macrophage)


title: RPMI_d6_H3K9me3

source_name: RPMI d6 H3K9me3

value: Naïve-Mf (culture for 6 days to macrophage)


title: LPS_d6_H3K9me3

source_name: LPS d6 H3K9me3


title: BG_d1_H3K9me3

source_name: BG d1 H3K9me3


title: LPS_4h_rep1_H3K4me3

source_name: LPS 4h rep1 H3K4me3

value: Mono_4h_LPS (LPS exposed, collected at 4 hour of exposure)


title: BG_d6_rep1_H3K27me3

source_name: BG d6 rep1 H3K27me3

value: BG-Mf (BG exposed 24 hours, culture for 5 days to macrophage)

value: Rabbit polyclonal anti-H3K27me3 (Diagenode, cat. # pAb-195-050)


title: d0_rep1_H3K27ac

source_name: d0 rep1 H3K27ac

value: Monocyte (negative selected)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: BG_d1_rep2_H3K4me3

source_name: BG d1 rep2 H3K4me3


title: BG_d6_rep2_H3K4me3

source_name: BG d6 rep2 H3K4me3


title: don73_LPS_d6_24hr_BG_H3K27ac

source_name: don73 LPS d6 24hr BG H3K27ac


title: TAC+Sol (2C)

source_name: Left ventricle of the heart

value: 16-18 wk old mice

value: TAC+Solvent

value: left ventricle of heart


title: BG_d6_rep2_H3K27ac

source_name: BG d6 rep2 H3K27ac


title: don74_RPMI_d6_H3K27ac

source_name: don74 RPMI d6 H3K27ac


title: RPMI_d6_rep1_H3K4me1

source_name: RPMI d6 rep1 H3K4me1

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: LPS_d6_rep1_H3K4me3

source_name: LPS d6 rep1 H3K4me3

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: BG_d6_rep1_H3K4me1

source_name: BG d6 rep1 H3K4me1


title: BG_1h_rep2_H3K4me1

source_name: BG 1h rep2 H3K4me1

value: Mono_1h_BG (BG exposed, collected at 1 hour of exposure)


title: BG_4h_H3K9me3

source_name: BG 4h H3K9me3

value: Adult Human Peripheral Blood

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K9me3 (Diagenode, cat. # pAb-193-050)


title: RPMI_1h_rep1_H3K27ac

source_name: RPMI 1h rep1 H3K27ac

value: Monocyte

value: Mono_1h_Naive (culture only, collected at 1 hour of exposure)


title: RPMI_d6_rep1_H3K27ac

source_name: RPMI d6 rep1 H3K27ac

value: Naïve-Mf (culture for 6 days to macrophage)


title: RPMI_d1_H3K9me3

source_name: RPMI d1 H3K9me3

value: Mono_day1_Naive (RPMI media exposed 24 hours, collected at 24 hours)