title: Adult SPF Female Replicate 1

description:
SMARTseq + Nextera XT
A2M_SPF_Female


title: Adult ABX Female Replicate 2

status: Public on Dec 14 2017

type: SRA

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
SMARTseq + Nextera XT
A2M_ABX_Female

library_source: transcriptomic

data_processing:
reads were mapped to mouse reference genome GRCm38 using STAR. Reads per gene were counted using featureCounts. Mouse reference genome .fasta file and gene annotation .gtf file were downloaded from Gencode version M9
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Mus musculus

source_name: Brain microglia

extract_protocol: RNA libraries were prepared for sequencing using SMART-Seq (TAKARA) protocole and Nextera XT DNA library (Illumina)

tag: strain

tag: age

value: Adult (2 months)

tag: antibiotics treatment

value: Specfic-pathogen-free (SPF) treated with ABX


title: Adult SPF Female Replicate 3

description:
SMARTseq + Nextera XT
A2M_SPF_Female

value: Specfic-pathogen-free (SPF)


title: Pop2Plate2_H08_S380

city: Cambridge

first: Andrew

last: Navia

state: MA

address: 77 Massachusetts Ave

department: IMES

country: USA

institute: MIT

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generat .fastq files from .bcl files.
tophat2.0.10 was used to align the scRNA-seq data
rsem-1.2.3 generated an expression matrix in psuedocounts
Dimensional reduction, clustering and differential expression performed using Seurat v1.4.0.16 implimented in R v3.3.2
Genome_build: mm10
Supplementary_files_format_and_content: log transformed TPM matrix filtered on cells with all genes

source_name: GFP+_Tet+_IL-4 producing cell

extract_protocol:
Lysates were treated as single cells in an adapted SMART-Seq II protocol (Trombetta et al., Current Protocols in Molecular Biology, 2014, 107:II:4:22). Briefly, mRNA was extracted from lystates using SPRI beads and then reverse transcribed and amplified using a poly-adenylated RT primer and template switching SMART oligo.
Library construction followed from the protocol above (Trombetta et al.,).

treatment_protocol: Cells were sorted into RLT buffer by FACS, spun down, and snap frozen on dry ice.

tag: strain background

tag: mouse strain

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse

tag: infected with

value: 200 PFU of Influenza A virus PR8 strain

tag: tissue

value: Lymph Node

tag: cell type

value: GFP+ cells

tag: cd1d tet pos

value: yes

tag: gfp pos

value: Il-4 Producing


title: Pop2Plate2_H04_S376


title: Pop2Plate2_H06_S378


title: Pop2Plate2_H03_S375


title: Pop2Plate2_H12_S384


title: Pop2Plate2_G05_S365


title: Pop2Plate2_G03_S363


title: Pop2Plate2_H10_S382


title: at-endosperm-BS_replicate1_ler_wt_x_col_wt

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Arabidopsis thaliana F1-endosperm of Landsberg-0 (female) crossed with Columbia-0 (male)

library_source: genomic

data_processing:
Bisulfite-seq: For each mutant, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were merged and trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the TAIR10 Arabidopsis genome using the Bismark read mapper (Krueger and Andrews, 2011) allowing up to one mismatch per read. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
genome build: TAIR10
processed data files format and content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: AT F1-Endosperm Landsberg x Columbia

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
Genomic DNA of hand-dissected endosperm  from 18-28 siliques was purified using MagJET Plant Genomic DNA kit (Thermo Fisher Scientific) and sonicated in Bioruptor (Diagenode) for 30 cycles (30 sec ON, 30 sec OFF at high power) using a Bioruptor (Diagenode). The bisulfite conversion was done using the EpiTect Fast DNA Bisulfite Kit (Qiagen) during the library preparation.
Bisulfite libraries were generated using Ovation Ultralow Methyl-Seq Library Systems (NuGEN) following the manufacturer's protocol using 20 ng of starting DNA.

treatment_protocol: Material was generated by manually crossing of emasculated wt (Ler) with pollen of wt (Col) plants.

value: endosperm

tag: genotype

value: Ler x Col


title: Pop2Plate2_C12_S324


title: Pop2Plate2_F01_S349


title: Pop2Plate2_C11_S323


title: Pop2Plate2_H07_S379


title: Pop2Plate2_C09_S321


title: Pop2Plate2_C07_S319


title: Pop2Plate2_C05_S317


title: Pop2Plate2_G12_S372


title: Pop2Plate2_C04_S316


title: Pop2Plate2_H02_S374


title: Pop2Plate2_G02_S362


title: Pop2Plate2_F12_S360


title: Pop2Plate2_B12_S312


title: Pop2Plate2_B09_S309


title: Pop2Plate2_F10_S358


title: Pop2Plate2_F09_S357


title: Pop2Plate2_B07_S307


title: Pop2Plate2_B05_S305


title: Pop2Plate2_B06_S306


title: Pop2Plate2_C10_S322


title: Pop2Plate2_F08_S356


title: Pop2Plate2_B04_S304


title: Pop2Plate2_B03_S303


title: Pop2Plate2_A09_S297


title: Pop2Plate2_C03_S315


title: Pop2Plate2_C08_S320


title: Pop2Plate2_A05_S293


title: Pop2Plate2_C01_S313


title: Pop2Plate1_H06_S282


title: Pop2Plate1_H10_S286


title: Pop2Plate2_B10_S310


title: Pop2Plate2_F02_S350


title: Pop2Plate1_H01_S277


title: Pop2Plate1_H03_S279


title: Pop2Plate1_G12_S276


title: Pop2Plate1_G10_S274


title: Pop2Plate1_G09_S273


title: Pop2Plate1_G08_S272


title: Pop2Plate2_A10_S298


title: Pop2Plate1_G01_S265


title: Pop2Plate1_G03_S267


title: Pop2Plate2_A03_S291


title: Pop2Plate1_H09_S285


title: Pop2Plate2_B02_S302


title: Pop2Plate2_A08_S296


title: Pop2Plate2_A06_S294


title: Pop2Plate2_A02_S290


title: Pop2Plate2_C06_S318


title: Pop2Plate1_F04_S256


title: Pop2Plate1_F05_S257


title: Pop2Plate1_G06_S270


title: Pop2Plate1_H05_S281


title: Pop2Plate1_F08_S260


title: Pop2Plate2_B08_S308


title: Pop2Plate1_G05_S269


title: Pop2Plate1_F12_S264


title: Pop2Plate1_H04_S280


title: Pop2Plate1_F10_S262


title: Pop2Plate1_F07_S259


title: Pop2Plate1_F09_S261


title: Pop2Plate1_E05_S245


title: Pop2Plate1_E10_S250


title: Pop2Plate1_F11_S263


title: Pop2Plate1_D12_S240


title: Pop2Plate1_F06_S258


title: Pop2Plate1_F03_S255


title: Pop2Plate1_E06_S246


title: Pop2Plate1_F01_S253


title: Pop2Plate1_E07_S247


title: Pop2Plate1_F02_S254


title: Pop2Plate1_E04_S244


title: Pop2Plate2_A12_S300


title: Pop2Plate1_E03_S243


title: Pop2Plate1_E02_S242


title: Pop2Plate1_D02_S230


title: Pop2Plate1_D08_S236


title: Pop2Plate1_D09_S237


title: Pop2Plate1_D05_S233


title: Pop2Plate1_C07_S223


title: Pop2Plate1_C09_S225


title: Pop2Plate1_E01_S241


title: Pop2Plate1_D07_S235


title: Pop2Plate1_C04_S220


title: Pop2Plate1_C05_S221


title: Pop2Plate1_C01_S217


title: Uninfected cells

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

data_processing:
Alignment, barcode assignation, and generation of cell-gene-count matrices all performed using cellranger 2.0.0 from 10x genomics
Additional analyses described at https://github.com/jbloomlab/flu_single_cell
Genome_build: GRCh38 and custom A/WSN/1933 derived from plasmids used for reverse genetics. Sequences provided at https://github.com/jbloomlab/flu_single_cell
Supplementary_files_format_and_content: HDF5 Gene-Barcode Matrix format containing UMI counts of each gene for individual cells. Can be deconvoluted to tsv and mtx files using cellranger reanalyze

molecule: polyA RNA

organism: Homo sapiens

source_name: continuous cell line derived from human lung carcinoma

growth_protocol: Cells were infected (or for uninfected sample grown) in influenza growth media as described in Bloom et al. 2011

extract_protocol:
Cells were trypsonized, washed, and processed using the 10x Genomics Chromium Single Cell 3' Solution v1 kit following manufacturer's instructions
10x Chromium Single Cell 3' Solution v1 kit following manufacturer's instructions.
3' RNAseq with single cell barcodes

treatment_protocol: Cells were infected with an intended biologically active MOI of 0.1 as measured by flow cytometry and infection was permitted to proceed for the indicated time

tag: cell line

tag: infection time

value: Not infected

tag: influenza strain


title: Pop2Plate1_C02_S218


title: Pop2Plate1_B11_S215


title: Pop2Plate1_D10_S238


title: MA9.3RAS FTO-PBS input

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the hg19 genome assembly using Tophat 2.1.1
peaks were called using MACS2 and exomePeak. Only the peaks called by both the two tools are retained for further analysis.
the m6A peaks were annotated using an ad hoc perl script.
GSEA and DAVID tool were used to perform pathway enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocals (Dan et al., 2012)

tag: tumor

value: acute monocytic leukemia

value: peripheral blood

tag: antibody

tag: treatment

value: FTO-PBS


title: MA9.3RAS FTO-R-2HG m6A-seq

value: m6A antibody


title: MA9.3RAS Ctrl-R-2HG m6A-seq


title: Pop2Plate1_B06_S210


title: Pop2Plate1_B05_S209


title: MA9.3RAS Ctrl-R-2HG input


title: Pop2Plate1_B04_S208


title: MA9.3RAS Ctrl-PBS m6A-seq

value: Ctrl-PBS


title: Pop2Plate1_D01_S229


title: Pop2Plate1_B03_S207


title: Pop2Plate1_B02_S206


title: MA9.3ITD shFTO-1-R-2HG m6A-seq


title: Pop2Plate1_B01_S205


title: MA9.3ITD shFTO-1-R-2HG input


title: Pop2Plate1_A12_S204


title: Pop2Plate1_A11_S203


title: MA9.3ITD shNS-1-R-2HG m6A-seq


title: MA9.3RAS FTO-R-2HG input


title: MA9.3ITD shFTO-1-PBS m6A-seq

value: shFTO-PBS


title: Pop2Plate1_A09_S201


title: Pop2Plate1_A06_S198


title: Pop2Plate1_B08_S212


title: Pop2Plate1_A07_S199


title: MA9.3ITD shNS-1-PBS m6A-seq

value: shNS-PBS


title: Pop2Plate1_A05_S197


title: MA9.3ITD shFTO-1-PBS input


title: MA9.3ITD shNS-1-PBS input


title: MA9.3ITD shNS-1-R-2HG input


title: MA9.3RAS FTO-PBS m6A-seq


title: Pop2Plate1_A03_S195


title: NOMO-1 R-2HG m6A-seq


title: Pop2Plate1_A01_S193


title: Pop2Plate1_A02_S194


title: MA9.3RAS Ctrl-PBS input


title: NOMO-1 R-2HG input


title: NOMO-1 PBS m6A-seq

value: PBS


title: Pop1Plate2_G12_S180

source_name: GFP+_Tet-_IL-4 producing cell

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse

value: no


title: NOMO-1 PBS input


title: MA9.3ITD_PBS_Rep3

description:
rep3
Drug2_vs_PBS2.all.gene.result.xls
RS41_combined.fastq.gz

data_processing:
sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: .xls file containing the expression and p value

extract_protocol:
RNA was extracted by mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with total RNA extraction protocol. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).
Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced to 50 bp using TruSeq SBS kit on Illumina HiSeq system.


title: MA9.3ITD_R-2HG_Rep3

description:
rep3
Drug2_vs_PBS2.all.gene.result.xls
RS42_combined.fastq.gz


title: Pop1Plate2_G11_S179

value: 200 PFU of Influenza A virus PR8 strain

value: Lymph Node


title: Pop1Plate2_G10_S178

value: GFP+ cells

value: yes


title: Pop1Plate2_G08_S176

value: Il-4 Producing


title: Pop1Plate2_G07_S175


title: Pop1Plate2_G05_S173


title: MA9.3ITD_PBS_Rep1

description:
rep1
Drug2_vs_PBS2.all.gene.result.xls
RS33_GTCCGC_R1.fastq.gz


title: MA9.3ITD_R-2HG_Rep1

description:
rep1
Drug2_vs_PBS2.all.gene.result.xls
RS34_GTGAAA_R1.fastq.gz


title: Pop1Plate2_G06_S174


title: Pop1Plate2_G03_S171


title: NOMO-1_R-2HG_Rep3

description:
rep3
Drug1_vs_PBS1.all.gene.result.xls
RS38_combined.fastq.gz


title: Pop1Plate2_G04_S172


title: NOMO-1_R-2HG_Rep2

description:
rep2
Drug1_vs_PBS1.all.gene.result.xls
RS36_combined.fastq.gz


title: Pop1Plate2_F12_S168


title: NOMO-1_PBS_Rep3

description:
rep3
Drug1_vs_PBS1.all.gene.result.xls
RS37_combined.fastq.gz


title: NOMO-1_PBS_Rep2

description:
rep2
Drug1_vs_PBS1.all.gene.result.xls
RS35_combined.fastq.gz


title: Pop1Plate2_G02_S170


title: Pop1Plate2_F09_S165


title: NOMO-1_R-2HG_Rep1

description:
rep1
Drug1_vs_PBS1.all.gene.result.xls
RS30_ATGTCA_R1.fastq.gz


title: Pop1Plate2_F11_S167


title: NOMO-1_PBS_Rep1

description:
rep1
Drug1_vs_PBS1.all.gene.result.xls
RS29_AGTTCC_R1.fastq.gz


title: Pop1Plate2_F07_S163


title: Pop1Plate2_F06_S162


title: MA9.3ITD_R-2HG_Rep2

description:
rep2
Drug2_vs_PBS2.all.gene.result.xls
RS40_combined.fastq.gz


title: Pop1Plate2_F05_S161


title: MNC-#1 Sample 11 RNA Seq-1

description:
Healthy control
Group2_vs_Group3.all.gene.result.xls
JC26_AGTTCC_R1.fastq.gz

data_processing:
sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: .xls file containing the expression

extract_protocol:
RNA was extracted by mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with total RNA extraction protocol. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by PrepX mRNA Library kit (WaferGen) combined Apollo 324 NGS automated library prep system.
Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced to 50 bp using TruSeq SBS kit on Illumina HiSeq system.

value: healthy control


title: CD34+ HSPC-#2 Sample 12 RNA Seq-1

description:
Healthy control
Group2_vs_Group3.all.gene.result.xls
JC27_ATGTCA_R1.fastq.gz

source_name: CD34+ HSPC-#2


title: MNC-#2 Sample 13 RNA Seq-1

description:
Healthy control
Group2_vs_Group3.all.gene.result.xls
JC28_ATCACG_R1.fastq.gz


title: Pop1Plate2_F04_S160


title: Pop1Plate2_F03_S159


title: MA9.3ITD Sample 9 RNA Seq-1

description:
Sensitive cell lines
Group2_vs_Group3.all.gene.result.xls
JC24_GCCAAT_R1.fastq.gz


title: U937 Sample 8 RNA Seq-1

description:
Sensitive cell lines
Group2_vs_Group3.all.gene.result.xls
JC23_GGTAGC_R1.fastq.gz


title: Pop1Plate2_F01_S157


title: Pop1Plate2_F02_S158


title: ML-2 Sample 6 RNA Seq-1

description:
Sensitive cell lines
Group2_vs_Group3.all.gene.result.xls
JC21_CGTACG_R1.fastq.gz


title: Pop1Plate2_E12_S156


title: K562 Sample 5 RNA Seq-1

description:
Resistant cell lines
Group1_vs_Group2.all.gene.result.xls
JC20_GTTTCG_R1.fastq.gz


title: Pop1Plate2_E10_S154


title: MA9.3RAS Sample 4 RNA Seq-1

description:
Resistant cell lines
Group1_vs_Group2.all.gene.result.xls
JC19_GTGGCC_R1.fastq.gz


title: Pop1Plate2_E07_S151


title: Pop1Plate2_E08_S152


title: TF-1 Sample 2 RNA Seq-1

description:
Resistant cell lines
Group1_vs_Group2.all.gene.result.xls
JC16_TAGCTT_R1.fastq.gz


title: Pop1Plate2_E06_S150


title: Pop1Plate2_E05_S149


title: MA9.3ITD_PBS_Rep2

description:
rep2
Drug2_vs_PBS2.all.gene.result.xls
RS39_combined.fastq.gz


title: Pop1Plate2_D10_S142


title: Pop1Plate2_D07_S139


title: CD34+ HSPC-#1 Sample 10 RNA Seq-1

description:
Healthy control
Group2_vs_Group3.all.gene.result.xls
JC25_CAGATC_R1.fastq.gz

source_name: CD34+ HSPC-#1


title: Pop1Plate2_D12_S144


title: Pop1Plate2_D03_S135


title: Pop1Plate2_D04_S136


title: Pop1Plate2_D02_S134


title: Pop1Plate2_D05_S137


title: Pop1Plate2_B09_S117


title: NOMO-1 Sample 7 RNA Seq-1

description:
Sensitive cell lines
Group2_vs_Group3.all.gene.result.xls
JC22_GTAGAG_R1.fastq.gz


title: Pop1Plate2_D01_S133


title: Pop1Plate2_B08_S116


title: Pop1Plate2_B07_S115


title: Pop1Plate2_E09_S153


title: Pop1Plate2_B03_S111


title: Pop1Plate2_B04_S112


title: HEL Sample 3 RNA Seq-1

description:
Resistant cell lines
Group1_vs_Group2.all.gene.result.xls
JC18_GTGAAA_R1.fastq.gz

source_name: HEL


title: Pop1Plate2_B02_S110


title: Pop1Plate2_B01_S109


title: KO_12h

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

country: China

institute: SMMU

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files with whole genomic peaks

source_name: Mouse peritoneal macrophage cells

growth_protocol: Mouse peritoneal macrophages (PM) from wild type (WT) and IFN-I receptor deficient (Ifnar-/-) mice were obtained 3 days after i.p. injected with the thioglycolate and were cultured in DMEM medium with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For 2×107 cells, 10ul VSV were added to cell culture medium for 12 hours or not.

tag: passages

value: ≤7

tag: strain

tag: genotype/variation

value: IFN-I receptor deficient (Ifnar-/-)

tag: infection

value: with VSV infection


title: NB4 Sample 1 RNA Seq-1

description:
Resistant cell lines
Group1_vs_Group2.all.gene.result.xls
JC15_ACAGTG_R1.fastq.gz

value: acute monocytic leukemia

value: peripheral blood


title: KO_0h

value: without VSV infection


title: Pop1Plate2_E04_S148

tag: strain background

tag: mouse strain


title: SEV_total

value: wild type


title: Pop1Plate2_A10_S106

tag: infected with

tag: tissue


title: Pop1Plate2_A08_S104

tag: cell type

tag: cd1d tet pos


title: Pop1Plate2_B10_S118

tag: gfp pos


title: GOT2 RIP-seq rep2

data_processing:
Raw reads were aligned to the reference genome (mm10) using TopHat (v2.0.14) (Kim et al. 2013) after removing adapter.
RPKM were calculated by Cuffnorm.
The mm10 genome annotation (RefSeq gene) is download form UCSC. tdf files are generated by IGVtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files with whole genomic peaks

source_name: Mouse embryonic fibroblast (MEF) cells

growth_protocol: Mouse embryonic fibroblast (MEF) cells were prepared from mouse embryos at embryonic day 13.5, and cultured in DMEM medium. Then the primary, low passage(≤7) cultured cells were analyzed as described.

treatment_protocol: 2×10^7 cells were transfected with pcDNA 3.1 (-)B Got2 flag plasmid and lysed with 1ml iCLIP lysis buffer (50mM Tris-HCl pH7.0, 100mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:200 P.I.). And the lysate was sonicated at high level, in 4℃ bath, for 5min, 30s on/30s off. 2μl Turbo DNase (Ambion) and 0.4μl RNase I were added then the mixture was vortexed at 37℃ for 5min exactly. Immediately added 20μl RRI, mixed thoroughly. And centrifuged to obtain the clear lysate. Then added 20μl Anti-flag M2 Magnetic Beads (SIGMA Aldrich) and incubated at 4℃ for 5 hrs to capture the Protein-RNA complex. After that, beads were washed twice with cold high salt wash buffer (50mM Tris-HCl pH7.0, 1M NaCl, 1mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and once with cold wash buffer (20mM Tris-HCl pH7.0, 10mM MgCl2, 0.2% Tween-20). And resuspended the beads in 200μl P.K. buffer (100mM Tris-HCl pH7.0, 50mM NaCl, 10mM EDTA) vortexed at 12000rpm, 37℃, for 20min, and added 200μl Urea/P.K. buffer, vortexed for another 20min.

value: 7 or fewer

value: embryonic fibroblast (MEF)

tag: rip antibody & beads


title: ribosome profiling 0h

data_processing:
Library strategy: Ribosome profiling
Raw reads were aligned to the reference genome (mm10) using TopHat (v2.0.14) (Kim et al. 2013) after removing adapter.  RPKM were calculated by Cuffnorm. The mm10 genome annotation (RefSeq gene) is download form UCSC. tdf files are generated by IGVtools.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files with whole genomic peaks

growth_protocol: Mouse peritoneal macrophages (PM) were obtained 3 days after i.p. injected with the thioglycolate and were cultured in DMEM medium with 10% fetal bovine serum.

treatment_protocol: 2×10^7 cells Add harringtonine to cell culture medium to a final concentration of 2 μg ml − 1. Mix quickly and return it to the incubator. After Cell lysis, proform nuclease footprinting and ribosome recovery, and finally footprint fragment purification.

value: peritoneum

value: macrophage


title: Pop1Plate2_A06_S102

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse

value: 200 PFU of Influenza A virus PR8 strain

value: no


title: Pop1Plate2_A09_S105

value: Lymph Node

value: GFP+ cells

value: yes


title: GOT2 RIP-seq rep1

value: Anti-flag M2 Magnetic Beads (SIGMA Aldrich)


title: ribosome profiling 12h

value: ≤7


title: NC_total


title: Pop1Plate2_A04_S100

value: Il-4 Producing


title: Pop1Plate2_A07_S103


title: Pop1Plate2_A05_S101


title: Pop1Plate2_A03_S99


title: Pop1Plate2_A02_S98


title: Pop1Plate2_A01_S97


title: Pop1Plate1_H04_S88


title: Pop1Plate1_H07_S91


title: Pop1Plate2_A11_S107


title: Pop1Plate2_A12_S108


title: Pop1Plate1_H01_S85


title: Pop1Plate1_H11_S95


title: 6_C4_Input_2

city: Smithville

first: Li

last: Wang

state: TX

address: 1808 Park Rd 1C

department: Epigenetics and molecular carcinogenesis

institute: UT-MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
Sequenced DNA reads were mapped to mouse genome mm10 using bowtie (version 1.1.2) with at most 2 mismatches allowed and only the reads that were mapped to unique position were retained. To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
H3K9Ac peaks were detected by MACS (version 1.4.2). The window size was set as 500 bp and the p-value cutoff was 1e-5. H3K9Ac peaks were initially called by comparing to the corresponding total H3. Then the peaks that overlapped ENCODE blacklisted regions or were not called by comparing to the corresponding total input were removed.
Genome_build: mm10
Supplementary_files_format_and_content: The peak locations in bed format

source_name: Embryoid body cells

extract_protocol:
Lysates were clarifed from the sonicated nuclei of day 5 EBs, and chromatin fragments were isolated with antibodies indicated.
ChIP libraries were prepared using a Kapa Hyper Preparation kit (KAPA Biosystems, Wilmington, MA) protocol for Illumina Platforms. Briefly, for each library, 5ng of ChIP DNA was end-repaired and 3’-adenylated using a proprietary master mix, then ligated to the specific NexTflex adaptors from Bioo Scientific (Bioo Scientific, Austin, TX). The adaptor-ligated DNA was enriched using a KAPA Hyper Library Preparation kit (KAPA Biosystems, KK8502) with 5 cycles of PCR (1 cycle at 98°C for 45 seconds; 4 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds; 1 cycle at 72°C for 1 minute), then purified with AmpureXP beads (Beckman Coulter, A63881). The library quality was validated on a 2200 TapeStation from Agilent Technologies (Agilent, Santa Clara, CA). Concentrations of the libraries were determined using a Kapa Library Quantification Kit (KAPA Biosystems, KK4933) and loaded on cBOT (Illumina) at final concentration of 1.5nM for cluster generation, then sequenced with 50bp single-read on a HiSeq3000 sequencer (Illumina).

tag: differentiation stage

value: ES-derived embryoid bodies at day 5

tag: genotype

tag: chip antibodies


title: 6_C4_Input_1


title: Pop1Plate1_G11_S83


title: 6_C4_CHIP_K9ac_1

value: H3K9ac (Millipore, 07-352)


title: 6_C4_CHIP_K9ac_2


title: 6_C4_CHIP_H3_1

value: H3 (Abcam, ab1791)


title: 6_C4_CHIP_H3_2


title: 6_1_Input_2


title: 6_1_Input_1


title: Pop1Plate1_G04_S76


title: Pop1Plate1_G10_S82


title: 6_1_CHIP_K9ac_2


title: Pop1Plate1_G06_S78


title: 6_1_CHIP_K9ac_1


title: 6_1_CHIP_H3_1


title: Pop1Plate1_F02_S62


title: 4_C2_Input_2


title: 6_1_CHIP_H3_2


title: Pop1Plate1_F06_S66


title: 4_C2_CHIP_K9ac_1


title: 4_C2_CHIP_K9ac_2


title: 4_C2_CHIP_H3_2


title: Pop1Plate1_E12_S60


title: Pop1Plate1_G12_S84


title: Pop1Plate1_E11_S59


title: 4_C2_CHIP_H3_1


title: 4_1_Input_2


title: Pop1Plate1_E09_S57


title: Pop1Plate1_E10_S58


title: 4_1_Input_1


title: 4_1_CHIP_H3_2


title: 4_1_CHIP_K9ac_1


title: 4_1_CHIP_H3_1


title: Pop1Plate1_E08_S56


title: Pop1Plate2_E02_S146


title: 4_C2_Input_1


title: Pop1Plate1_E07_S55


title: Pop1Plate1_E05_S53


title: Dog_PWD0093_Sperm BS-seq library1

city: Los Angeles

middle: D

last: Smith

state: California

address: 1050 Childs way

institute: University of Southern California

data_processing:
Bisulfite-Seq reads were mapped to reference genome by rmapbs with default parameters
Methylation levels at all cytosine sites and hmr calls were made by methpipe with default parameters
Genome_build: gorGor3; rn5; canFam3
Supplementary_files_format_and_content: .meth files contain 6 columns: chromosome, start position, strand, base context, methylation level, coverage

organism: Canis lupus familiaris

source_name: Sperm

extract_protocol:
Standard Illumina genomic library
PE Illumina adaptors were used, ligated libraires were amplified according the maunfacturers instruction.

treatment_protocol: Bisulfite treated genomic DNA

tag: individual

tag: breed

value: portuguese water dog

tag: library


title: Rat_R2_Sperm BS-seq

organism: Rattus norvegicus


title: Dog_PWD0093_Sperm BS-seq library2


title: Dog_LAB0026_Sperm BS-seq library2

value: labrador


title: Dog_DOB0027_Sperm BS-seq library2

value: doberman


title: Rat_R1_Sperm BS-seq


title: Dog_DOB0027_Sperm BS-seq library1


title: Pop1Plate1_E03_S51


title: Pop1Plate1_D08_S44


title: Pop1Plate1_E01_S49


title: Pop1Plate1_E02_S50


title: 4_1_CHIP_K9ac_2

tag: strain


title: Dog_LAB0026_Sperm BS-seq library1


title: Pop1Plate1_E04_S52


title: Dog_DOB0024_Sperm BS-seq library2


title: Pop1Plate1_D06_S42


title: Dog_DOB0024_Sperm BS-seq library1


title: Pop1Plate1_D12_S48


title: Pop1Plate1_D03_S39


title: Pop1Plate1_D07_S43


title: Pop1Plate1_D09_S45


title: 4C2_d5_3

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M8 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.

extract_protocol:
Day 3 and day 5 EBs were harvested and total RNA was isolated using an RNeasy mini plus kit (Qiagen, 74134) following the manufacturer’s instructions.
The libraries were prepared using the Illumina TruSeq stranded total RNA kit according to the manufacturer’s protocol, except that the PCR amplification was reduced to 8 cycles.

tag: differentiation stages


title: 4C2_d5_2


title: Pop1Plate1_D05_S41


title: 4C2_d5_1


title: Pop1Plate1_D02_S38


title: 4C2_d3_2

value: ES-derived embryoid bodies at day 3


title: Pop1Plate1_C11_S35


title: 4_1_d5_2


title: 4_1_d5_1


title: 4_1_d5_3


title: 4_1_d3_3


title: Pop1Plate1_C10_S34


title: 4_1_d3_2


title: Pop1Plate1_C09_S33


title: WB_Liver_90d_BS-seq

city: Wuhan

first: Yuhua

last: Fu

state: Hubei

address: No.1, Shizishan Street, 430070, Wuhan, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

data_processing:
Raw GA sequencing data were processed by Illumina base-calling pipeline (SolexaPipeline-1.0).
BS-seq reads were deduplicated and aligned against the bisulfite-converted Sscrofa10.2 reference sequence by using Bismark (v0.15.0), with the Bismark command of “--phred33-quals --non_bs_mm --gzip -N 1 --score_min L,0,-0.6”.
Methylation status was determined using the bismark_methylation_extractor script and only uniquely aligned reads, the number of methylated and unmethylated CpG and non-CpG (CHG and CHH, H representing A/C/T) sites was counted for each individual cytosine.
R package “DSS” (v 2.12.0) was used to identify the differently methylated CpGs (DMCs) and differently methylated regions (DMRs)
Genome_build: Sus scrofa (Sscrofa10.2)
Supplementary_files_format_and_content: Identified DMCs and DMRs

organism: Sus scrofa

growth_protocol: The liver tissues were obtained from three male pigs at Postnatal day 90.

extract_protocol:
Genomic DNA from liver collected was extracted using the DNeasy Blood & Tissue Kit (Qiagen)
The bisulfite conversion of liver DNA was carried out using a modified NH4SO4-based protocol and amplified by 12 cycles of PCR. Ultra-high-throughput pair-end sequencing was carried out using the Illumina Genetic Analyzer (GA2) according to manufacturer instructions.

value: Chinese wild boar

tag: age

value: Postnatal day 90

tag: Sex

value: male

value: liver


title: 4_1_d3_1


title: LW_Liver_90d_BS-seq

value: Large White pig


title: Pop1Plate1_C08_S32

tag: strain background

tag: mouse strain

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse

value: 200 PFU of Influenza A virus PR8 strain

value: Lymph Node

value: GFP+ cells

value: no


title: ES_Liver_90d_BS-seq

value: Enshi black pig

tag: tissue


title: Pop1Plate1_C06_S30

tag: infected with

tag: cell type

value: yes

value: Il-4 Producing


title: Pop1Plate1_C02_S26

tag: cd1d tet pos

tag: gfp pos


title: L-WT-5

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
processed data file:
Lung_Count.csv

data_processing:
Illumina CASAVA softeware used for basecalling
Sequences were aligned using Tophat2 to the mm10 UCSC genome
Features were counted and a count table produced using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: CSV files containg table of counts for all samples from either Lung or Ileum.

extract_protocol:
For RNA extraction the post-caval lobe of the lung or a small section of the terminal ileum was collected into RNALater (Ambion). Tissue was retrieved from the storage solution, placed in Purelink RNA mini kit lysis buffer (Ambion) and homogenized using a Precellys homogenizer (Bertin). RNA was extracted using a Purelink RNA mini kit (Ambion).
mRNA was purified from 1mg of total RNA extracted as above using a NEBNext Poly(A) mRNA Magnetic isolation module (New England Biolabs). First and second strand DNA was synthesized using NEBNext synthesis modules (New England Biolabs), purified using Agencourt AMPure XP beads (Beckman Coulter), and quantified using Quant-it-pico-green dsDNA assay (Life Technologies). Libraries were prepared from 10ng ds-cDNA using an Ovation SP ultralow library system (Nugen) in combination with a Mondrian SP work station (Nugen). Libraries were amplified by PCR for 15 cycles, quantified, denatured and 10pmol of each library were pooled and sequenced.
RNA-Seq - Sequencing was carried out in 3 batches as detailed in the sample chracteristics column.

tag: genotype/variation

value: WT; TL1A expressed under the control of the CD2 promoter

value: F

value: Lung (Post Caval love)

tag: batch

value: Batch 1


title: L-WT-4

description:
processed data file:
Lung_Count.csv

value: M


title: 4C2_d3_3

value: ES-derived embryoid bodies at day 3

tag: genotype


title: L-WT-3

description:
processed data file:
Lung_Count.csv


title: Pop1Plate1_C01_S25


title: Pop1Plate1_B11_S23


title: L-WT-2

description:
processed data file:
Lung_Count.csv

value: Batch 2


title: 4C2_d3_1


title: Pop1Plate1_C12_S36


title: L-WT-1

description:
processed data file:
Lung_Count.csv


title: L-Mem+sol-4

description:
processed data file:
Lung_Count.csv

value: Mem+Sol; overexpression of both membrane bound and soluble forms of TL1A


title: L-Mem+sol-3

description:
processed data file:
Lung_Count.csv


title: Pop1Plate1_B08_S20


title: Pop1Plate1_B02_S14


title: Pop1Plate1_A12_S12


title: Pop1Plate1_B06_S18


title: L-Mem+sol-1

description:
processed data file:
Lung_Count.csv


title: Pop1Plate1_A11_S11


title: L-Mem+sol-2

description:
processed data file:
Lung_Count.csv


title: L-Mem-5

description:
processed data file:
Lung_Count.csv

value: Mem; overexpressed membrane restricted TL1A Delta 69-93


title: L-Mem-4

description:
processed data file:
Lung_Count.csv


title: Pop1Plate1_A08_S8

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse


title: Pop1Plate1_A06_S6

value: 200 PFU of Influenza A virus PR8 strain


title: I_WT-5

description:
processed data file:
Ileum_Count.csv

source_name: teminal Ileum_WT

value: Terminal Ileum

value: Batch 3


title: I_WT-4

description:
processed data file:
Ileum_Count.csv


title: I_WT-3

description:
processed data file:
Ileum_Count.csv


title: Pop1Plate1_A02_S2

value: Lymph Node

value: GFP+ cells

value: no


title: Pop1Plate1_A05_S5

value: yes

value: Il-4 Producing


title: L-Mem-3

description:
processed data file:
Lung_Count.csv


title: L-Mem-1

description:
processed data file:
Lung_Count.csv


title: L-Mem-2

description:
processed data file:
Lung_Count.csv

value: F


title: Pop1Plate1_A01_S1


title: I_WT-2

description:
processed data file:
Ileum_Count.csv

value: WT; TL1A expressed under the control of the CD2 promoter


title: Mock_IP_rep2

city: Stockholm

first: kun

last: wang

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholms Universitet

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Sequence reads were mapped to the  Sulfolobus acidocaldarius DSM639 genome (NC_007181.1) with Burrows-Wheeler Aligner (BWA 0.7.10) with default parameters
peaks were called using MACS2 with following parameters: --nomodel --extsize 200
Genome_build: Sulfolobus acidocaldarius DSM639 genome (NC_007181.1)
Supplementary_files_format_and_content: bedGraph files were generated with MACS2

organism: Sulfolobus acidocaldarius DSM 639

source_name: cell

growth_protocol: Sulfolobus acidocaldarius DSM639 were cultivated in Brock basal salts medium supplemented with 0.1% tryptone at 80 Celsius degree and pH 2.

extract_protocol:
cell pellets fragmented by sonication. Then the cleared lysate were mixed with Saci_1107 specific antibody, pre-immune serum, respectively. Immunoprecipitated DNA is extracted by IPure kit (Diagenode) according to the manufacturer’s instructions.
Sequencing libraries were prepared using the ThruPLEX®-FD Prep Kit (Rubicon Genomics) under instructions from the manufacturer.
Clustered using onboard clustering and sequenced on MiSeq (MCS 2.4.1.3/RTA 1.18.54) with a 1x51 setup in High Output mode.

treatment_protocol: Upon reaching the early exponential growth phase (an OD600 between 0.2 and 0.3), formaldehyde was added to the culture at a final concentration of 1%. After a 5-minute incubation, glycine was added to a final concentration of 125 mM. Fixed cells were harvested by centrifugation at 8000 x g during 10 minutes

value: DSM 639

value: wild type

tag: chip antibody

value: pre-immune serum


title: I_WT-1

description:
processed data file:
Ileum_Count.csv


title: 3_Tr48

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

country: Germany

institute: Medical Center Freiburg

data_processing:
The resulting 74 bp paired-end reads were quality-checked with FastQC. Sequencing data were mapped to the human genome (hg19, UCSC, https://genome.ucsc.edu) with STAR (https://github.com/alexdobin/STAR). (--quantMode GeneCounts –sjdbOverhang n-1). Followed by the alignment, transcripts with less than 10 reads were removed. The given RNA counts were normalized by DESeq2 based on a negative binomial distribution model (28). Data were Log2 transformed and median centered across samples.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read count

source_name: Treatment 48h

growth_protocol: Brain tumor tissue was obtained during the neurosurgical tumor resection and further processed in sterile conditions under a tissue culture hood. First, the tissue was fragmented to very small pieces and resuspended in cell-dissolving solution. The tissue fragments were centrifuged at 1000 rpm for 5 minutes and subsequently resuspended with 5ml ACK Lysing Buffer to remove blood cells. The cells were finally resuspended in medium and transferred into a tissue culture flask.

extract_protocol:
RNA was extracted by All Prep Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. RNA integrity was measured using the Agilent RNA Nano Assay Agilent Bioanalyser 2100 (http://www.home.agilent.com) according to the manufacturer’s instructions. Sequencing libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina HiSeq4000 sequencer.
Sequencing libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina HiSeq4000 sequencer

treatment_protocol: For metabolic treatment, different metabolites were supplemented into the medium. Creatine-enriched environment was simulated by 15 mMol creatine supplementation. Cells were cultured under normoxic (21% O2) or hypoxic (3% O2) conditions.

value: primary cell line-Brain tumor

tag: treatment

value: creatine 48h


title: I_Mem+sol-6

description:
processed data file:
Ileum_Count.csv

source_name: teminal Ileum_Mem+sol

value: Mem+Sol; overexpression of both membrane bound and soluble forms of TL1A

value: M


title: Mock_IP_rep1


title: 2_Tr48


title: I_Mem+sol-5

description:
processed data file:
Ileum_Count.csv


title: 1_Tr48


title: I_Mem+sol-4

description:
processed data file:
Ileum_Count.csv


title: Pop1Plate1_A10_S10

value: IL-4/GFP- enhanced transcript (4Get) reporter mouse

value: 200 PFU of Influenza A virus PR8 strain


title: input DNA_rep1


title: I_Mem+sol-3

description:
processed data file:
Ileum_Count.csv

value: Terminal Ileum

value: Batch 3


title: input DNA_rep2


title: Saci_1107_ChIPSeq_rep1


title: Pop1Plate1_A07_S7

value: Lymph Node

value: GFP+ cells


title: Pop1Plate1_A04_S4

value: no

value: yes


title: I_Mem+sol-2

description:
processed data file:
Ileum_Count.csv

value: F


title: 2_NO

source_name: Normoxia

value: normoxia


title: 3_HO

source_name: Hypoxia

value: hypoxia


title: 10 hour infection

organism:
Homo sapiens
Influenza A virus (A/WSN/1933(H1N1))

tag: cell line

tag: infection time

value: 10 hours

tag: influenza strain


title: I_Mem+sol-1

description:
processed data file:
Ileum_Count.csv


title: 8 hour infection replicate #1

value: 8 hours


title: I_Mem-5

description:
processed data file:
Ileum_Count.csv

source_name: teminal Ileum_Mem

value: Mem; overexpressed membrane restricted TL1A Delta 69-93


title: I_Mem-4

description:
processed data file:
Ileum_Count.csv


title: 2_HO

value: primary cell line-Brain tumor


title: 1_HO


title: 6 hour infection

value: 6 hours


title: I_Mem-3

description:
processed data file:
Ileum_Count.csv


title: Gorilla_Sperm BS-seq library2

organism: Gorilla gorilla

tag: individual

value: Ivan

tag: library


title: I_Mem-2

description:
processed data file:
Ileum_Count.csv

tag: strain background

tag: Sex

value: M


title: 3_Tr24

source_name: Treatment 24h

tag: tissue

value: creatine 24h


title: 3_NO


title: I_Mem-1

description:
processed data file:
Ileum_Count.csv

value: Terminal Ileum


title: 2_Tr24


title: Gorilla_Sperm BS-seq library1


title: 1_Tr24


title: fvb-LAP-MYC;Arid1a Het-T-MYC-rep3

status: Public on Dec 13 2017

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university

data_processing:
Sequencing reads were aligned to mouse genome (mm10) by bowtie2 (version 2.2.3)
After mapping reads to mouse genome (mm10) by bowtie2 (version 2.2.3) with parameter “--sensitive”,perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard Mark Duplicates (version 1.92, http://broadinstitute.github.io/picard).
The enriched regions (peaks) were identified using MACS2 (version 2.0.10.20131216), with a q-value cut-off of 0.05.For the occupancy-based analysis, common peaks of replicates were used. Peak regions was annotated by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, and peak file

source_name: frozen liver tumor tissue

extract_protocol:
Frozen liver tumor tissues were minced quickly with a razorblade into small pieces which less than 0.5 cm3. Crosslink tissue in 1% formaldehyde for 20 min at room temperature.Dounce tissue in ice-cold PBS first with the loose and later with the tight pestle. Rinse tissue with PBS. genomic DNA were isolated and performed for ChIP-seq.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit, and sequenced on Illumina NEXTseq 500 using High  Output kit v2 reagents at CRI Sequencing Facility at UT Southwestern.

treatment_protocol: When take off dox water, LAP-tta-Arid1aflfl; TRE-MYC (LAP-MYC WT) and LAP-tta-Arid1afl/+;Alb-cre;TRE-MYC (LAP-MYC Arid1a Het) and LAP-tta-Arid1aflfl;Alb-cre;TRE-MYC (LAP-MYC Arid1a Homo) mice generate tumor. Collect tumor tissue at time of death for Chip-seq.

tag: stain

value: FVB

value: liver tumor

tag: age

value: about 70 days-old

tag: genotyping

value: MYC (Santa Cruz, sc-764x)


title: fvb-LAP-MYC;Arid1a Het-T-MYC-rep2


title: fvb-LAP-MYC;Arid1a Homo-T-MYC-rep3

value: about 100 days-old


title: fvb-LAP-MYC;Arid1a Homo-T-MYC-rep1


title: fvb-LAP-MYC;Arid1a Homo-T-MYC-rep2


title: fvb-LAP-MYC;WT-T-MYC-rep2

value: about 55 days-old


title: fvb-LAP-MYC;Arid1a Het-T-MYC-rep1


title: 1_NO

value: normoxia


title: fvb-LAP-MYC;WT-T-MYC-rep3


title: fvb-LAP-MYC;Arid1a Homo-T-input-rep3


title: fvb-LAP-MYC;Arid1a Het-T-input-rep3


title: 8 hour infection replicate #2

source_name: continuous cell line derived from human lung carcinoma


title: fvb-LAP-MYC;Arid1a Het-T-input-rep2


title: fvb-LAP-MYC;Arid1a Het-T-input-rep1


title: fvb-LAP-MYC;WT-T-input-rep3


title: fvb-LAP-MYC;Arid1a Homo-T-input-rep1


title: fvb-LAP-MYC;WT-T-input-rep2


title: s51510_M5CRe-

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: samples were aligned to mm10 with GSNAP (v2014-12-17); splice site were supported by using Ensembl version 75
fragment count: fragments were counted with featureCounts v1.4.6 and gtf annotation from of Ensembl version 75 was used
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (bfx564.mm10.e75.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 12 samples
Supplementary_files_format_and_content: tab delimited file from DESeq2 output (bfx564.deseq.csv.gz); columns are according to the DESeq2 output (EnsemblID, log2Foldchange, lfcSE, stat, pvalue and padj), followed by the normalised counts for the 12 samples, the mean of the two conditions and annotation from Ensembl (Gene Symbol, chromosom, chromosom start and end, strand, biotype and description)

growth_protocol: B16 cells (10e5) were injected i.d. into body flanks of MC-proficient and MC-deficient animals. Tumors were dissected 16 d.p.i.

extract_protocol:
CD45+ Ly6G– CD11b+ F4/80+ cells were sorted into cold PBS containing 5% BSA and were sedimented by centrifugation. An aliquot of the sorted cells was subjected to reanalysis to determine the degree of sorting purity. Cells were resuspended in 350 μl of RLT+b-ME buffer (RNeasy Micro Kit, Qiagen), stored at -80°C and used for Illumina-based sequencing. RNA quantity and quality was determined by measurement on the Qubit device as well as using the Agilent BioAnalyzer 2100. Only the samples with the RNA integrity number above 8 were sequenced.
SMARTer Ultra Low Input RNA for Illumina Sequencing Kit - HV from Clontech was used to reverse transcribe the RNA and amplify full-length cDNA according to the user manual. It was followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

tag: host strain background

value: FVB/n

tag: host strain genotype/variation

value: cre-negative littermate

tag: injected with

value: B16 cells

tag: cell type

value: B16F10 TAMs (tumor-associated macrophages)

tag: cell subtype

value: CD45+ Ly6G- CD11b+ F4/80+ cells


title: s51511_M5CRe+

value: Mcpt5-Cre+ R26DTA


title: fvb-LAP-MYC;WT-T-input-rep1

tag: chip antibody


title: s51044_M5CRe-


title: s91932_M5CRe-


title: s51929_M5CRe+


title: s51930_M5CRe-


title: fvb-LAP-MYC;WT-T-MYC-rep1


title: s91931_M5CRe-


title: s51267_M5CRe+


title: s51042_M5CRe+


title: Rag1-LAP-MYC;WT-adARID1A-N-rep3

description: rag_adcre7 in rag.normalized.logCPM.txt

data_processing:
Raw sequencing reads were trimmed to remove adaptor and low quality sequences (Phred score < 20) using trim_galore package. Trimmed reads were aligned to mouse reference genome GRCm38/mm10 with HiSAT2.
After duplicates removal by SAMtools, read counts were generated for the annotated genes based GENCODE V20, using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file of gene RPKM values, txt file of gene CPM value.

extract_protocol:
Frozen liver tumor tissues or normal tissues RNA were harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Nugen library protocols.

treatment_protocol: When take off dox water, LAP-tta-Arid1aflfl; TRE-MYC (LAP-MYC WT) or LAP-tta-Arid1aflfl;Alb-cre;TRE-MYC (LAP-MYC Arid1a Het) or LAP-tta-Arid1aflfl;Alb-cre;TRE-MYC (LAP-MYC Arid1a Homo) mice generate tumor. Collect tumor tissue at time of death. For ARID1A overexpression experiment,adeno-hARID1A or adeno-Cre are injected into Rag1-/-;-LAP-MYC;WT mice, and liver tissues are collected 14 days after virus injection.

value: liver

value: about 42 days-old


title: s51509_2_M5CRe+


title: s51043_M5CRe+


title: s51041_M5CRe-


title: Rag1-LAP-MYC;WT-adARID1A-N-rep2

description: rag_adcre6 in rag.normalized.logCPM.txt


title: Rag1-LAP-MYC;WT-adARID1A-N-rep1

description: rag_adcre5 in rag.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Homo-T-input-rep2


title: Rag1-LAP-MYC;WT-adCre-N-rep2

description: rag_adcre3 in rag.normalized.logCPM.txt

value: LAP-tta-WT;TRE-MYC+adCre


title: fvb-LAP-MYC;Arid1a Homo-T-rep4

description: myc_KO_T46 myc_T.normalized.logCPM.txt


title: Rag1-LAP-MYC;WT-adCre-N-rep3

description: rag_adcre4 in rag.normalized.logCPM.txt


title: Rag1-LAP-MYC;WT-adCre-N-rep1

description: rag_adcre1 in rag.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Homo-T-rep1

description: myc_KO_T42 in myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Homo-T-rep2

description: myc_KO_T43 myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Het-T-rep4

description: myc_HET_T50 in myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Het-T-rep2

description: myc_HET_T48 in myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;Arid1a Het-T-rep1

description: myc_HET_T47 in myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;WT-T-rep4

description: myc_WT_T41 in myc_T.normalized.logCPM.txt


title: fvb-LAP-MYC;WT-T-rep3

description: myc_WT_T40 in myc_T.normalized.logCPM.txt


title: mix-LAP-MYC;Arid1a Het-T-rep8

description: S13 in Arid1aHetMycVSMyc_RPKM.csv

value: C57/B6 and 129 , FVB mix

value: about 90 days-old


title: fvb-LAP-MYC;WT-T-rep1

description: myc_WT_T38 in myc_T.normalized.logCPM.txt

value: FVB

value: liver tumor


title: mix-LAP-MYC;Arid1a Het-T-rep6

description: S11 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;Arid1a Het-T-rep7

description: S12 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;WT-T-rep2

description: myc_WT_T39 in myc_T.normalized.logCPM.txt


title: mix-LAP-MYC;Arid1a Het-T-rep3

description: S3 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;Arid1a Het-T-rep2

description: S2 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;Arid1a Homo-T-rep3

description: myc_KO_T45 myc_T.normalized.logCPM.txt


title: mix-LAP-MYC;WT-T-rep4

description: S9 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;WT-T-rep6

description: S14 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;Arid1a Het-T-rep5

description: S5 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;Arid1a Het-T-rep3

description: myc_HET_T49 in myc_T.normalized.logCPM.txt

value: about 70 days-old


title: mix-LAP-MYC;WT-T-rep3

description: S8 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;WT-T-rep2

description: S7 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;Arid1a Homo-T-ATAC-rep3

data_processing:
Sequences were aligned with Bowtie2. Using 3 to 4 replicates for each genotypic condition, we obtained an average of 27 uniquely mapped fragments. Peaks were called using MACS2 with p-value = 1e-5 cuttoff in 200 bps smoothing window. Replicate concordance for each condition were measured by calculating IDR (Irreproducibility Discovery Rate) by IDR R package. Overlapping peaks were identified and annotated using ChIPpeakAnno package. Normalized bigwig files for browser tracks visualization and heatmaps were generated by deepTools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file, and peak file

extract_protocol:
Frozen liver tumor tissue nuclears were harvested and genomic DNA were tagged following the ATAC-seq protocol.
ATAC-seq libraries were prepared for sequencing using standard ATAC-seq protocol.

treatment_protocol: When take off dox water, LAP-tta-Arid1aflfl; TRE-MYC (LAP-MYC WT) and LAP-tta-Arid1afl/+;Alb-cre;TRE-MYC (LAP-MYC Arid1a Het) and LAP-tta-Arid1aflfl;Alb-cre;TRE-MYC (LAP-MYC Arid1a Homo) mice generate tumor. Collect tumor tissue at time of death for ATAC-seq.

value: about 100 days-old


title: fvb-LAP-MYC;Arid1a Homo-T-ATAC-rep1


title: mix-LAP-MYC;WT-T-rep7

description: S15 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;Arid1a Homo-T-ATAC-rep2


title: fvb-LAP-MYC;Arid1a Het-T-ATAC-rep3


title: fvb-LAP-MYC;Arid1a Het-T-ATAC-rep2


title: mix-LAP-MYC;WT-T-rep1

description: S6 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;WT-T-ATAC-rep4

value: about 55 days-old


title: fvb-LAP-MYC;Arid1a Het-T-ATAC-rep1


title: mix-LAP-MYC;Arid1a Het-T-rep1

description: S1 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;Arid1a Het-T-rep4

description: S4 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;WT-T-ATAC-rep2


title: fvb-LAP-MYC;WT-T-ATAC-rep3


title: mix-LAP-MYC;WT-T-rep5

description: S10 in Arid1aHetMycVSMyc_RPKM.csv


title: mix-LAP-MYC;WT-T-rep8

description: S16 in Arid1aHetMycVSMyc_RPKM.csv


title: fvb-LAP-MYC;WT-T-ATAC-rep1


title: K562-C11-N2-Inp

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Reads were demultiplexing stage by the bacl2fastq2 software (v2.15, Illumina) and trimmed for adapter and low quality squence with the Trimmotative software
ChIP-Seq Reads were mapped to the human genome with Bowtie2 v.2.1.0 (Langmead & Salzberg, 2012) with default parameters.
Peak calling was performed with SICER (v1.1) (Zang et al., 2009), with a window size of 200bp and a gap size of 600bp. For each ChIP sample, peak calling was performed relative to the respective input sample. Bigwig format signal tracks were generated with deeptools  (Ramirez et al., 2016), normalizing for sequencing depth.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain peaks called
Supplementary_files_format_and_content: BW files contain depth-normalized read counts

growth_protocol: K562 cells (American Type Culture Collection, ATCC) were cultured in RPMI-1640 (Gibco) supplemented with 10% BCS (Hyclone), BJ (ATCC) and IMR90 fibroblasts (Coriell) were cultured in MEM (Gibco), supplemented with 10% FBS (Gemini), 2 mM L-Glutamine (Gibco), 1 mM sodium pyruvate (Sigma), 10 mM Non-Essential Amino Acids (NEAA, Gibco), with or without 1% penicillin-streptomycin (Gibco). HCT116 H2AX KO cell lines (gift from W. Bonner) were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin. U2OS cells with stably integrated LacO arrays (gift from T. Misteli) were cultured in DMEM supplemented with 10% FBS and 200 µg/ml hygromycin. Cells were maintained at 37 °C in a humidified incubator containing 5% CO2. Cell lines were negative for mycoplasma.

extract_protocol:
Sequencing libraries were constructed from DNA samples with the Illumina TruSeq V3 library construction protocol.
Cells were treated as indicated, crosslinked with 1% formaldehyde in PBS for 10 min, followed by quenching with 125 mM glycine. Cells were then resuspended in lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% nonidet P-40) to isolate nuclei. Nuclei were resuspended in micrococcal nuclease (MNase) digestion buffer (10 mM Tris pH 7.4, 15 mM NaCl, 60 mM KCl, 0.15 mM spermine, 0.5 mM spermidine) and 1.2 U/µl MNase was added for 30-45 min at 37 °C. The reaction was stopped by adding 50 mM EDTA and nuclear pellets were resuspended in 10mM Tris-HCl (pH8.0), 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine. Lysates were sonicated briefly to disrupt nuclear membranes using an ultra sonicator water bath (Bioruptor, Diagenode). Diluted lysates were incubated o/n at 4 °C with the indicated antibodies after addition of 1% Triton X-100. IPs were performed using 30 µl Protein A/G magnetic beads (Pierce). Eluted DNA was purified with QIAquick PCR purification (Qiagen) according to the manufacturer instructions. Purified ChIP DNA was analyzed by qPCR using a LightCycler 480 II (Roche).
Sequencing libraries were constructed from DNA samples (ChIP and control samples) with the Illumina TruSeq V3 library construction protocol (Illumina, San Diego, USA).

treatment_protocol: Plasmid transfections were performed using Lipofectamine 2000 transfection reagent (Life Technologies), cells were analyzed 24 h to 48 h post transfection. Lentiviral infection was carried out by spin infection (2250 rpm, 90 min, Beckman-Coulter Allegra X-12R centrifuge) with 8 µg/ml polybrene (Sigma), cells were incubated overnight prior to virus removal and selection with puromycin (1-2 µg/ml). Individual MISSION shRNA-expressing lentiviral vectors were from Sigma (Table S2). SiRNAs (Dharmacon ON-TARGET, Table S2) were transfected using DF-1 reagent following the manufacturer’s instructions (Dharmacon) and analyzed 48 h - 96 h post transfection.

tag: cell line

tag: treatment

value: Untreated

tag: antibody

value: Input

tag: transfection


title: K562-F10-N2-1-2

source_name: K562 sh-RFP

value: α-macroH2A1.2 (Millipore MABE61)

value: sh-RFP


title: K562-F10-N2-Inp


title: K562-N-Inp-1


title: K562-Aph-gH2Ax-1

value: Aphidicolin

value: α-phospho-H2AX (S139) (Millipore 05-636)


title: K562-N-gH2Ax-1


title: 2A3-N-Inp-1


title: 2A3-N-gH2Ax-1


title: K562-Aph-Inp-1


title: 2A3-Aph-gH2Ax-1


title: N_2_rH2Ax


title: 2A3-Aph-Inp-1


title: K562_A3_gH2Ax


title: N_1_rH2Ax


title: K562_N1_gH2Ax


title: K562_N3_gH2Ax


title: Saci_1107_ChIPSeq_rep2

tag: strain

value: DSM 639

tag: genotype

value: wild type


title: Aph_0.5_1_rH2Ax


title: K562_A1_gH2Ax


title: K562_N1_Inp


title: K562_N1_12


title: K562-C11-N2-1-2


title: Aph_0.5_2_rH2Ax


title: K562_N3_Inp


title: K562_N3_12


title: K562_A3_Inp


title: K562_A1_Inp


title: K562_A3_12


title: U251 WT V5-rDLST

city: Houston

first: Yugang

address: 6767 Bertner Avenue

institute: MD Anderson Cancer Center

data_processing:
the paired-end RNA-seq reads were mapped to  hg19 genome version by software STAR (with default paramaters)
featureCounts was then used to count the number of fragments mapped to each gene
Genome_build: hg19
Supplementary_files_format_and_content: csv format, a matrix summarizing number of reads mapped to each gene

source_name: U251 cells

extract_protocol:
Total RNA was extracted from cells by using PureLinkTM RNA Mini Kit (Thermo Fisher Scientific, Waltham, MA).
Illumina compatible libraries were prepared by using the KAPA Stranded mRNA-Seq Library Preparation Kit for Illumina® platforms (KAPA Biosystems). In brief, 250 ng of total RNA was enriched for poly-A-tailed mRNA by using Kapa’s mRNA Capture beads. Poly-A-enriched RNA was fragmented to a median size of 150 bp by using chemical fragmentation and converted into double-stranded cDNA with dUTP incorporated into the second cDNA strand. The ends of the double-stranded cDNA were polished, 5’-phosphorylated, and 3’-A-tailed for the ligation of indexed adapters. Adapter-ligated DNA fragments were amplified by 8 cycles of PCR. The strand with incorporated dUTP was not amplified. The resulting libraries were quantified by qPCR and assessed for size distribution by using the 4200 TapeStation (Agilent Technologies), and then multiplexed, 4 per pool, and sequenced on the Illumina’s NextSeq500 by using the mid-output, 75-bp paired-end read format.

value: Brain Tumor

value: wild type DLST


title: U251 V5-rDLST R224A/K226E

value: DLST R224A/K226E mutant


title: N_2_mH2A1

value: α-macroH2A1 (Millipore 07-219)


title: U251 WT Flag-rGcn5

value: wild type Gcn5


title: U251 Flag-rGcn5 Y645A

value: Gcn5 Y645A mutant


title: N_2_mH2A1_Inp


title: Aph_0.5_1_mH2A1_Inp


title: N_1_mH2A1


title: Aph_0.5_1_mH2A1


title: Aph_0.5_2_mH2A1


title: K562_A1_12


title: H3K79succ U251 shGcn5 cells

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 with the following configurations: bowtei2 --very-sensitive -p 10
Only uniquely mapped reads  (mapq>=10) were kept for further analysis
peaks were called using MACS2 (macs2 callpeak --nomodel  --extsize 200 -p 0.001)
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generated by MACS2

growth_protocol: U251 cells were routinely cultured in DMEM supplemented with 10% BCS. The U251 shGcn5 cells were maintaned as stable cell line.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The libraries were amplified by using three cycles of PCR and then assessed for quality by using a Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, Ankeny, IA) and quantified by using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).


title: U251 cells input

value: input


title: N_1_mH2A1_Inp


title: U251 shGcn5 cells input


title: Gcn5 U251 cells


title: Aph_0.5_2_mH2A1_Inp


title: U251 V5-OGDH cells input


title: P300b_mRNASeq

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Sequences were aligned to the hg19 human genome sequence using TopHat v2.
FPKM (fragments per kb per million mapped reads) for each annotated hg19 RefSeq gene ID was determined using Cuffdiff v2 from Cufflinks RNA-Seq analysis tools at http://cufflinks.cbcb.umd.edu.
Bedgraph files were generated using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain all mapped reads; cuffdiffout_all_genes_hg19_FPKM.txt

source_name: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

growth_protocol: Human Bronchial/Tracheal Epithelial Cells (HBTEC, Lifeline Cell Technology Cat# FC-0035; lot# 02196) were grown at 37°C in BronchiaLife Medium Complete Kit (Lifeline Cell Technology catalog number: LL-0023) in a 5% CO2 incubator

extract_protocol:
1X10^6 Low-passage HBTEC were mock-infected or infected with Ad5 vectors 3 days after reaching confluence. RNA was isolated 24h p.i. using QIAGEN RNeasy Plus Mini Kit. Eluted RNA was treated with Ambion DNA-free DNA Removal Kit and then Ambion TRIzol reagent, precipitated with isopropanol, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer.
One microgram of RNA was fragmented and copied into DNA then PCR amplified with bar-coded primers for separate samples to prepare sequencing libraries using the Illumina TruSeq RNA Sample Preparation procedure.

treatment_protocol: HBTEC were grown until they reached confluence. Cells were then incubated 3 days more without addition of fresh media and were either mock infected or infected with the indicated Ad5-based vectors for 24h in the conditioned medium.

tag: passage

tag: Sex

value: Male


title: DCAF7b_mRNASeq

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)


title: CtBPb_mRNASeq


title: FOXKb_mRNASeq


title: e1aWT_mRNASeq


title: mock_mRNASeq


title: RBb_mRNASeq


title: dl312_mRNASeq


title: CtBPb_INP

description: genomic DNA and viral DNA

data_processing:
Reads were mapped to the hg19 human genome reference using Bowtie2 software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled into 50 base pair windows and each read was extended by 150 bases and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other.
Wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19
Supplementary_files_format_and_content: wiggle

extract_protocol:
1x10^7 low-passage HBTEC were mock-infected or infected with indicated Ad vector 3 days after reaching confluence. 24h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and 2ug of anti-Pol2, -H3K27ac or 5uL of H3K18ac anti-rabbit sera. 50uL of protein A dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.


title: DCAF7b_Pol2_ChIPSeq

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-Pol2 (N20) Santa Cruz Cat#sc-899


title: e1aWT_INP

description: genomic DNA and viral DNA


title: FOXKb_INP

description: genomic DNA and viral DNA


title: CtBPb_Pol2_ChIPSeq

description: genomic DNA and viral DNA


title: α-KGDH U251 V5-OGDH cells

value: alpha-KGDH


title: H3K79succ U251 cells


title: FOXKb_Pol2_ChIPSeq

description: genomic DNA and viral DNA


title: mock_INP

description: genomic DNA and viral DNA


title: FOXKb_H3K18ac_ChIPSeq

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-H3K18ac (814) Grunstein/Kurdistani laboratories (Suka et al., 2001)


title: e1aWT_H3K27ac_ChIPSeq

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-H3K27ac Active Motif Cat#39133 Lot#31814008


title: mock_Pol2_ChIPSeq

description: genomic DNA and viral DNA


title: e1aWT_Pol2_ChIPSeq

description: genomic DNA and viral DNA


title: mock_H3K18ac_ChIPSeq

description: genomic DNA and viral DNA


title: e1aWT_H3K18ac_ChIPSeq

description: genomic DNA and viral DNA


title: DCAF7b_H3K18ac_ChIPSeq

description: genomic DNA and viral DNA


title: YF-HW-11-066_D1277.5_Tet

city: Palo Alto

first: Bin

last: Hu

address: 3801 Miranda Avenue

department: School of Medicine

institute: Stanford University

data_processing:
Reads were aligned to hg19 using bowtie2, discarding pairs with mapping quality less than 20. The reads from all samples were pooled, and a peak file was generated using MACS2.
Peaks that overlapped with repetitive regions or low complexity DNA regions, such as satellite DNA or retrotransposons, were removed from the analysis.
Peaks were visualized using IGV, with the y-axis set at the scale of reads per base pair. Gene and TSS annotations were based on the RefSeq database. ChIP-seq results in GM12878 were downloaded from the ENCODE project. The ability of the peaks to discriminate between subpopulations was assessed by calculating Spearman correlation coefficients on the 5,000 peaks with the greatest overall variance following a regularized-log transform.
To assess differential openness, we ran DESeq2 on the matrix of insertions in peaks by sample. Peaks were considered to be differentially open if the Wald test was less than 0.05, following multiple hypothesis correction with the Benjamini-Hochberg procedure.

source_name: PBMC

extract_protocol:
DNA from the transposase reaction was purified via a Qiagen MinElute kit.
PCR amplification was performed using Nextera PCR primers. The final libraries were quantified using a KAPA Library Quantification Kit and sequenced on an Illumina HiSeq 2500 by ELIM Biopharm.

treatment_protocol: YFV tetramer- positive and naïve CD8 T cells were sorted from PBMC at indicated time points after vaccination. Pellets from 20,000 cells were washed with cold PBS, then with RSB buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) and lastly with lysis buffer (RSB buffer + 0.1% NP40 + 0.1% Tween 20). The pellet obtained was then resuspended in the transposase reaction mix (25μL 2× TD buffer, 1μL Illumina transposase and 24μL nuclease-free water) and incubated at 37oC for 30 min.

tag: donor

tag: days post yfv-17d

value: sorted A2-NS4B214 tetramer+ CD8 T cells

tag: tissue

value: PBMC


title: YF-M15-660_D180_Tet


title: YF-M15-640_D150_Tet


title: YF-X-14-009-002_D2555_Tet


title: YF-M15-677-D90_Tet


title: YF-M15-675_D90_Tet


title: DCAF7b_INP

description: genomic DNA and viral DNA


title: FOXKb_H3K27ac_ChIPSeq

description: genomic DNA and viral DNA


title: YF-M15-675_D28_Tet


title: CtBPb_H3K27ac_ChIPSeq

description: genomic DNA and viral DNA


title: YF-M15-678_D90_Tet


title: DCAF7b_H3K27ac_ChIPSeq

description: genomic DNA and viral DNA


title: mock_H3K27ac_ChIPSeq

description: genomic DNA and viral DNA


title: CtBPb_H3K18ac_ChIPSeq

description: genomic DNA and viral DNA


title: YF-M15-653_D28_Tet


title: YF-M15-677_D14_Tet


title: YF-M15-661_D28_Tet


title: YF-M15-679_D21_Tet


title: YF-M15-678_D21_Tet


title: YF-Ig-E07(TAD)_D3285_Tet

value: YF Ig E07 (TAD)


title: EV_Ctrl_rep1_RNAseq

first: Ritwick

last: Sawarkar

address: 51 Stubeweg

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed and mapped to Ensembl annotation release 78 with TopHat2
Unique reads were counted with featureCounts and DESeq2 was used for differential gene expression analysis.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample, differential gene expression analysis

growth_protocol: Human HEK293T cells were cultured in Dulbecco's Modified Eagle's medium (DMEM; Biochrom) supplemented with 10% FBS (Gibco), 1% Penicillin-streptomycin (Gibco) and 1% L-glutamine (Gibco) at 37C in an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted in using the RNA Clean & Concentrator kit (Zymo Research, cat. no. R1013) according to the manufacturer’s protocol.
TruSeq Stranded mRNA library prep kit (Illumina cat. no. RS-122-2101)

treatment_protocol: HEK293T cells were transfected with a total of 1ug in 6-well plates using FuGene 6 tranfection reagent (Promega) following the manufacturer's protocol.

tag: genotype/variation

value: control


title: ERbeta_rep2_RNAseq

source_name: ERbeta

value: ERbeta expression


title: input_DNA_embryo

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
genomic DNA
s5

data_processing:
Basecalling was performed using CASAVA version 1.9
Illumina FastQ files for ChIPseq data on IP and input samples were aligned against the Drosophila melanogaster dm3 genome using Bowtie2 in local mode allowing for 1 mismatch in the read seed (-N 1) and reporting at most 1 alignment per read (-k 1).
Duplicated reads (i.e. PCR over-amplification artifacts) were detected and removed using sambamba 0.5.1.
Quality assessment of ChIPseq data was performed with the htSeqTools package v1.4.0 (Planet et al., 2012) and FastQC version 0.10.
Unless otherwise specified, all downstream analyses were performed using R version 2.15 and Bioconductor (Huber et al., 2015). For visualization, genome-wide tracks of smoothed mean log2 normalized coverage ratio IP/Input were generated in R using a bin size of 50bp.
To determine dBigH1 content for all genes in the Drosophila melanogaster dm3 genome (Ensembl April 2014), gene-level log2 RPKM fold-change of IP/Input samples was computed using Mean and Variance normalization (Shao et al., 2012).
Genome_build: dm3
Supplementary_files_format_and_content: Processed Excel XLSX file contains Flybase gene level information, log2RPKM sample quantification and log2 MAnorm fold-change IP/Input for all genes in the dm3 genome.

organism: Drosophila melanogaster

source_name: Early Embryo

extract_protocol:
Embryos were collected in peach juice plates at 0-2 hours after fertilization (for details see Materials and Methods section in Pérez-Montero et al., 2013).
ChIP-seq, library construction, cluster generation and Sequencing analysis were performed using the Illumina HiSeq2000, sequencing type SR50, following manufacture’s protocols (www.illumina.com). In brief, libraries were prepared using Illumina’s ChIP-Seq Sample Prep Kit from 3.5 ng of ChIP/Input DNA. Samples were size selected to ̴300-350 bp using DNA magnetic beads. Adaptor-modified DNA fragments were subjected to limited PCR amplification (18 cycles). Using Illumina’s Cluster Generation Kit, libraries were subject to cluster generation for subsequent sequencing.

tag: stock

tag: developmental stage

value: early 0-2 hpf embryos


title: input_DNA_testes

source_name: whole testes

growth_protocol: No growth protocol

extract_protocol:
2000 testes from w1118 males were dissected and fixed (see Materials and Methods section for details). Fixed testes were stored at 4°C in wash B. Testes were hand-dissected in wash B to remove the accessory glands. Pools of 1000 testes were transferred in 700ul of sonication buffer dissected in wash B to remove the accessory glands. Pools of 1000 testes were transferred in 700ml of sonication buffer. Conditions were established to obtain chromatin fragments 200-500 bp in length.
ChIP-seq, library construction, cluster generation and Sequencing analysis were performed using the Illumina HiSeq2000, sequencing type SR50, following manufacture’s protocols (www.illumina.com). In brief, libraries were prepared using Illumina’s ChIP-Seq Sample Prep Kit from 3.5 ng of ChIP/Input DNA. Samples were size selected to ̴300-350 bp using DNA magnetic beads. Adaptor-modified DNA fragments were subjected to limited PCR amplification (18 cycles). Using Illumina’s Cluster Generation Kit, libraries were subject to cluster generation for subsequent sequencing.

treatment_protocol: No treatment

value: adult

value: whole testes


title: dBigH1_ChIPseq_embryo

description:
genomic DNA
s1

value: anti-dBigH1 (Perez-Montero et al., 2013)


title: Input DNA naïve CD8

city: Atlanta

first: Rama

middle: S

last: Akondy

state: GA

address: 1462 CLifton Rd

department: Emory Vaccine Center

institute: Emory University

data_processing:
Methylated DNA was aligned to the genome using BWA and differentially methylated regions were identified using the Bioconductor package MeDIPS and custom R scripts. Significantly different regions of DNA methylation were identified using the built in exact test for negative binomial distribution at a significance level of p<0.0005. Shared regions of methylation between effector and memory cells were defined as regions that were significantly different in effector compared to naïve cells, but not significantly different when comparing effector and memory cells. Secondary data analysis and figures were plotted using custom R scripts. The processed datafile lists the differentially methylated regions in the three samples.
Genome_build: Hg19
Supplementary_files_format_and_content: Excel file containing differentially methylated regions relative to naïve CD8 sample

source_name: FACS isolated CD8 T cells

extract_protocol:
Cells were sorted and DNA was extracted using the Qiagen blood and tissue kit
MeDIP-seq services by Activ motif

tag: donor id

value: YFHW1B-077 day 166

tag: ip antibody

tag: phenotype

value: CD45RA+ CCR7+

tag: days after yfv-17d


title: YFV early memory

value: 5-methyl cytosine

value: YFV-A2NS4B 214 tetramer


title: Total Naïve CD8


title: YFV Effector

value: YFTCR-180 day 14


title: hu_Th1.4

first: Klaus

last: Ley

address: 9420 Athena Circle

department: Inflammation Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, and adapters using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10 for mouse samples
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: peripheral blood mononuclear cell

growth_protocol:
Mouse: Naïve CD4 T cells were stimulated with anti-mouse CD3ε and anti-mouse CD28 for 72 h in the presence of recombinant mouse IL-12, recombinant mouse IL-2 and anti-mouse IL-4 for Th1 differentiation, recombinant mouse IL-4, recombinant mouse IL-2, anti-mouse IL-12 and anti-mouse IFNγ for Th2 differentiation, recombinant mouse IL-6, recombinant human TGFβ, anti-mouse IL-4 and anti-mouse IFNγ for Th17 differentiation, and recombinant human TGFβ and recombinant mouse IL-2 for Treg differentiation.
Human: Naïve or Th1 cells were directly isolated from fresh blood peripheral blood mononuclear cell without in vitro culture

extract_protocol:
Mouse CD4 T-cells: Naïve CD4 T cells were isolated from spleens of 8-12 week old mice using EasySep™ Mouse CD4+ T Cell Isolation Kit (STEMCELL Technologies, Vancouver, Canada). Following isolation, purified CD4 T cells were differentiated in vitro in 24-well plate coated with 8 μg/ml anti-mouse CD3ε  (145-2C11) and 8 μg/ml anti-mouse CD28 (37.51) for 72 h in the presence of 25 ng/ml recombinant mouse IL-12, 20 ng/ml recombinant mouse IL-2 and 1 μg/ml anti-mouse IL-4 (11B11) for Th1 differentiation, 50 ng/ml recombinant mouse IL-4, 20 ng/ml recombinant mouse IL-2, 1 μg/ml anti-mouse IL-12 and  1 μg/ml anti-mouse IFN-γ (XMG1.2) for Th2 differentiation, 50 ng/ml recombinant mouse IL-6, 5 ng/ml recombinant human TGF-β1, 1 μg/ml antimouse  IL-4 and 1 μg/ml anti-mouse IFN-γ for Th17 differentiation, and 5 ng/ml recombinant human TGF-β1 and 20 ng/ml recombinant mouse IL-2 for Treg differentiation.
Neutrophils and Promyelocytes: Bone marrow cells were stained with anti-mouse surface markers PerCP-CD45 (30-F11), FITC-Ly6G (1A8), APC-CD115 (AFS98), PE-F4/80 (BM8), PE/Cy7-CD11c (N418), PE/Cy7- TER119 (TER119), PE/Cy7-CD19 (6D5), eFluor®450-CD11c (M1/70), PE-CD4 (GK1.5), PE Siglec-F (E50-2440). Neutrophils were CD45+CD11c+Ly6Ghi and promyelocytes were CD45+CD11c+Ly6Glo. Promyelocytes were further distinguished from monocytes as SSChiCD115-. Cell sorting was done by BD FACSAriaTM II (BD Biosciences, San Diego, CA).
Human Cd4 T cells: Human peripheral blood mononuclear cells were obtained from healthy donors through the LJI Clinical Core in accordance with the La Jolla Institute for Allergy and Immunology Normal Blood Donor Program (VD-057). PBMCs were isolated using SepMate tubes (STEMCELL Technologies). Then, PBMCs were stained by the anti-human surface markers Alexa Fluor® 700 CD3 (UCHT1), eFluor®450 CD4 (OKT4), PE/Cy7-CD25 (BC96), PerCPCy5.5-CD45RA (HI100), Brilliant VioletTM 605-CD45RO (UCHL1), PE-CXCR3 (CEW33D), APC-CCR4 (D8SEE), FITC-CCR6 (R6H1). The CD4 T cell  subsets were sorted by BD FACSAriaTM Fusion (BD Biosciences) based on chemokine receptors expression. Live  CD3+CD4+CD25- cells were further gated using CD45RA and CD45RO  surface markers to differentiate between naïve and memory T cell subsets, respectively. Within the memory T cell subset, Th1 cells were CXCR3+CCR4-CCR6-.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: peripheral blood mononuclear cell

tag: age

value: 29 years

tag: disease state

value: Healthy donor

tag: gender

value: female


title: hu_Th1.3

institute: La Jolla Institute for Allergy and Immunology

value: 32 years

value: male


title: hu_Th1.2

value: 38 years


title: PI_2

city: Cambridge

first: Karsten

last: Bach

address: Tennis Court Road

department: Department of Pharmacology

data_processing:
Fastq files were processed using the standard 10x Genomics pipeline. In brief the propiertary software uses the STAR aligner to align against the reference genome and transcriptome. Reads are then grouped by the cellular barcode. Gene-level counts are finally computed based on unique molecular indentifiers.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain barcodes and genes for each sample, the combined files contain the merged data from all samples
Supplementary_files_format_and_content: mtx files contain UMI counts per gene and cell for each sample, the combined files contain the merged data from all samples

source_name: Mammary epithelial cells

extract_protocol:
Single cell suspensions were incubated in HF medium (Hank’s balanced salt solution (Gibco) + 1% foetal bovine serum, Gibco) + 10% normal rat serum (Sigma) for 20 min on ice to pre-block before antibody staining. All antibody incubations were performed for 10 min on ice in HF media. Mammary cells were stained with the following primary antibodies: CD31-biotin (eBioscience, clone 390); CD45-biotin (eBioscience, clone 30F11); Ter119-biotin (eBioscience, clone Ter119) and EpCAM-PE (Biolegend, clone G8.8). Cells were then stained with streptavidin-PE-CF594 (BD-Biosciences). Propidium Iodide (PI, ; Sigma) was used to detect dead cells. Cells were filtered through a cell strainer (Partec) before sorting. Sorting of cells was done using a SH800Z sorter (SONY). Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. Chip alignment and sorting calibration was performed with automatic setup beads (SONY) immediately prior to sorting. Doublets, dead cells and contaminating haematopoietic, endothelial and stromal cells were gated out and EpCAM positive cells were sorted in LoBind microcentrifuges tubes (Eppendorf) with HF. After sorting cells were spun down and resuspended in of HF. Samples were manually counted using an improved Neubauer chamber and the cell concentration was normalized by addition of HF. Equal numbers of cells per sample were processed for scRNA library preparation. Samples were processed for scRNA library preparation within 9 hours from tissue isolation.
For droplet-based scRNA-seq, sorted cells were encapsulated into droplets, and libraries were prepared using the ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics).

value: Post-involution

value: Mammary gland

tag: strain


title: YF-M15-660_D14_Tet

value: sorted A2-NS4B214 tetramer+ CD8 T cells

value: PBMC


title: YF-M15-658_D14_Tet


title: hu_Th1.1

city: San Diego

value: 35 years


title: PI_1


title: hu_Tn.4

value: Tn


title: hu_Tn.3


title: L_2

value: Lactation


title: G_2

value: Gestation


title: hu_Tn.1


title: hu_Tn.2


title: NP_1

value: Nulliparous


title: dBigH1_ChIPseq_testes

value: adult

value: whole testes

tag: chip antibody

value: anti-dBigH1 (Pérez-Montero et al., 2013)


title: G_1


title: DCAF7b_IRF3_INP

description: genomic DNA and viral DNA

extract_protocol:
1x10^7 low-passage HBTEC were mock-infected or infected with indicated Ad vector 3 days after reaching confluence. 24h p.i. cells double crosslinked with 4mM DSG in PBS for 30min then 1% formaldehyde for 10 min, crosslinking was quenched in 500mM Tris pH7.9 for 20min and cell pellets were lysed in 1mL lysis buffer 1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche complete protease inhibitors) for 10min on ice. Lysate was pelleted at 3000 rpm 5min 4C then resuspended in 1mL lysis buffer 2 (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, Roche complete protease inhibitors) and placed on nutator 10min 4C and pelleted as before, then resuspended in 125uL of lysis buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, Roche complete protease inhibitors) and sonicated at 4C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 4X lysis dilution buffer (16.7 mM Tris-HCl, 1% Triton X-100, 1.2mM EDTA, 167mM NaCl, 0.1% SDS) and precleared for 1h 4C with 30uL of protein A dynabeads washed and blocked in 0.5% BSA in PBS on nutator. IPs were performed O/N at 4C on nutator with precleared chromatin and 5ug of anti-IRF3 (Cat#sc-9082). 50uL of protein A dynabeads were added for 4h on nutator at 4C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65C. Samples were RNase A treated for 1h at 37¡C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

tag: passage

tag: Sex

value: Male


title: CtBPb_IRF3_INP

description: genomic DNA and viral DNA


title: 23_M5CreMinus_MC_6mo

data_processing:
basecalling: bcl2fastq 1.8.4
alignment: samples were aligned to mm10 with GSNAP (v2014-12-17); splice site were supported by using Ensembl version 75
fragment count: fragments  were counted with featureCounts v1.4.6 and gtf annotation from of Ensembl version 75 was used
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (bfx319.mm10.e75.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; followed by counts from the samples
Supplementary_files_format_and_content: tab delimited file from DESeq2 output (bfx319.*month.table*.csv.gz); columns are according to the DESeq2 output (EnsemblID, log2Foldchange, lfcSE, stat, pvalue and padj), followed by the normalised counts for the samples, the mean of the two conditions and annotation from Ensembl (Gene Symbol, chromosom, chromosom start and end, strand, biotype and description)

growth_protocol: cells were purified from 2 month and 6 month old mice.

extract_protocol:
CD45 cells excluding mast cells (CD117 high, FceR1 high) were sorted from digested skin. Total RNA was solated using the Qiagen RNeasy Micro Kit+
SMARTer Ultra Low Input RNA for Illumina Sequencing Kit - HV from Clontech was used to reverse transcribe the RNA and amplify full-length cDNA according to the user manual. It was followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: no treatment

tag: strain background

value: FVB/n

value: 6 months

value: K14HPV16 Mcpt5-Cre-

value: Skin-inflitrating leucocytes

tag: cell subtype

value: CD45+ cells


title: FOXKb_IRF3_INP

description: genomic DNA and viral DNA


title: 19_M5CrePlus_woMC_6mo

tag: genotype/variation

value: K14HPV16 Mcpt5-Cre+

value: CD45+ cells excluding mast cells


title: mock_IRF3_INP

description: genomic DNA and viral DNA


title: 22_M5CreMinus_MC_6mo


title: e1aWT_IRF3_INP

description: genomic DNA and viral DNA


title: CtBPb_IRF3_ChIPSeq

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-IRF3 (FL-425) Santa Cruz Cat#sc-9082 Lot#31515


title: FOXKb_IRF3_ChIPSeq

description: genomic DNA and viral DNA


title: DCAF7b_IRF3_ChIPSeq

description: genomic DNA and viral DNA


title: 20_M5CreMinus_woMC_6mo


title: 17_M5CrePlus_woMC_6mo


title: 16_M5CrePlus_woMC_6mo


title: 18_M5CreMinus_woMC_6mo


title: PxylX-dnaKJ, rpoHD252G, 6 h of DnaKJ depletion

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

institute: Stockholm University

description:
Sample_5_GTACCACA
An overnight culture was grown in PYE supplemented with 0.3 % xylose. To start the depletion of DnaKJ cells were washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE supplemented with 0.2 % glucose. The culture was sampled after 6 h.

data_processing:
Data processing was performed by Genewiz.
Sequence reads were trimmed to remove low quality bases at ends, mapped to the reference genome (C. crescentus NA1000), hit counts were calculated and RPKM values for genes determined
Samples were compared to determine relative changes in gene expression (fold changes)
Genome_build: ASM2200v1
Supplementary_files_format_and_content: File containing expression values, normalized expression values, unique gene reads, total gene reads, RPKM and the chromosome region.

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus NA1000

growth_protocol: Cultures were grown in mid-log phase in rich medium (PYE) at 30 °C while shaking.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (done by Genewiz)

value: KJ839 (PxylX-dnaKJ, rpoHD252G)

tag: treatment protocol

value: 6 h of DnaKJ depletion


title: 13_M5CreMinus_woMC_6mo


title: PxylX-dnaKJ, rpoHD252G, 9 h of DnaKJ depletion

description:
Sample_6_GGTATAGG
An overnight culture was grown in PYE supplemented with 0.3 % xylose. To start the depletion of DnaKJ cells were washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE supplemented with 0.2 % glucose. The culture was sampled after 9 h.

value: 9 h of DnaKJ depletion


title: 12_M5CrePlus_woMC_6mo


title: PxylX-dnaKJ, ∆rpoH::tetR, 6 h of DnaKJ depletion

description:
Sample_7_CGAGAGAA
An overnight culture was grown in PYE supplemented with 0.3 % xylose. To start the depletion of DnaKJ cells were washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE supplemented with 0.2 % glucose. The culture was sampled after 6 h.

value: KJ844 (PxylX-dnaKJ, deltarpoH::tetR)


title: NP_2

tag: developmental stage

value: Nulliparous

tag: tissue

value: Mammary gland


title: 10_M5CrePlus_woMC_2mo

value: 2 months


title: PxylX-dnaKJ, undepleted

description:
Sample_2_GCGTTAGA
Cells were grown in PYE supplemented with 0.3 % xylose.

value: SG400 (PxylX-dnaKJ)

value: undepleted


title: PxylX-dnaKJ, 6 h of DnaKJ depletion

description:
Sample_3_ATCTGACC
An overnight culture was grown in PYE supplemented with 0.3 % xylose. To start the depletion of DnaKJ cells were washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE supplemented with 0.2 % glucose. The culture was sampled after 6 h.


title: PxylX-dnaKJ, 9 h of DnaKJ depletion

description:
Sample_4_AACCAGAG
An overnight culture was grown in PYE supplemented with 0.3 % xylose. To start the depletion of DnaKJ cells were washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE supplemented with 0.2 % glucose. The culture was sampled after 9 h.


title: 9_M5CrePlus_woMC_2mo

value: FVB/n


title: 7_M5CreMinus_woMC_2mo


title: mock_IRF3_ChIPSeq

description: genomic DNA and viral DNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: Male


title: 4_M5CreMinus_MC_2mo

value: K14HPV16 Mcpt5-Cre-

value: Skin-inflitrating leucocytes


title: Promyelocyte.3

source_name: Bone marrow

value: Promyelocyte

value: Bone marrow

value: 8 weeks

value: female


title: 5_M5CreMinus_woMC_2mo

value: CD45+ cells excluding mast cells


title: 1_M5CrePlus_woMC_2mo

value: K14HPV16 Mcpt5-Cre+


title: 2_M5CrePlus_woMC_2mo


title: Neutrophil.2

value: Neutrophil


title: Promyelocyte.1


title: Neutrophil.3


title: AR-52117_M5CRe-

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: samples were aligned to mm10 with GSNAP (v2014-12-17); splice site were supported by using Ensembl version 75
fragment count: fragments  were counted with featureCounts v1.4.6 and gtf annotation from of Ensembl version 75 was used
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (bfx564.mm10.e75.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 12 samples
Supplementary_files_format_and_content: tab delimited file from DESeq2 output (bfx564.deseq.csv.gz); columns are according to the DESeq2 output (EnsemblID, log2Foldchange, lfcSE, stat, pvalue and padj), followed by the normalised counts for the 12 samples, the mean of the two conditions and annotation from Ensembl (Gene Symbol, chromosom, chromosom start and end, strand, biotype and description)

growth_protocol: MB49 cells (10e5) were injected i.d. into body flanks of MC-proficient and MC-deficient animals. Tumors were dissected 20 d.p.i.

extract_protocol:
CD45+ Ly6G– CD11b+ F4/80+ cells were sorted into cold PBS containing 5% BSA and were sedimented by centrifugation. An aliquot of the sorted cells was subjected to reanalysis to determine the degree of sorting purity. Cells were resuspended in 350 μl of RLT+b-ME buffer (RNeasy Micro Kit, Qiagen), stored at -80°C and used for Illumina-based sequencing. RNA quantity and quality was determined by measurement on the Qubit device as well as using the Agilent BioAnalyzer 2100. Only the samples with the RNA integrity number above 8 were sequenced.
Samples were prepped accordingly to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

tag: host strain background

tag: host strain genotype/variation

value: cre-negative littermate

tag: injected with

value: MB49 cells

value: MB49 TAMs (tumor-associated macrophages)

value: CD45+ Ly6G- CD11b+ F4/80+ cells


title: AR-52116_M5CRe-

tag: cell type


title: Neutrophil.1

tag: age


title: AR-51922_M5CRe+

value: Mcpt5-Cre+ R26DTA


title: 21_M5CreMinus_woMC_6mo

value: FVB/n

value: 6 months


title: Tn.3

source_name: Spleen

value: Tn

value: Spleen


title: Tn.1


title: AR-51921_M5CRe-


title: AR-52115_M5CRe+


title: Tn.2


title: AR-52114_M5CRe+


title: 2 h rpoHV56A overexpression

description:
Sample_1_GGAAGAGA
Cells were grown in PYE supplemented with 1 µg ml-1 tetracycline and 2 μg ml−1 chloramphenicol. Overexpression of rpoHV56A was induced by adding 500 µM vanillate two hours prior to sampling.

value: KJ874 (PdnaK::Tn5 (-66), pJS14-rrnB1B2-PvanR-VanR-PvanA-rpoHV56A-T500, pDel1)

value: overexpression of rpoHV56A


title: e1aWT_IRF3_ChIPSeq

description: genomic DNA and viral DNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: Male

value: Rabbit polyclonal anti-IRF3 (FL-425) Santa Cruz Cat#sc-9082 Lot#31515


title: Treg.3

value: Treg

value: 8 weeks

value: female


title: AR-51920_M5CRe+


title: Promyelocyte.2

value: Promyelocyte

value: Bone marrow


title: Treg.2


title: Treg.1


title: 6_M5CreMinus_MC_2mo

value: 2 months

value: K14HPV16 Mcpt5-Cre-

value: Skin-inflitrating leucocytes

value: CD45+ cells


title: 15_M5CreMinus_woMC_6mo

value: FVB/n

value: 6 months

value: CD45+ cells excluding mast cells


title: AR-51859_M5CRe-

value: cre-negative littermate

value: MB49 cells

value: MB49 TAMs (tumor-associated macrophages)

value: CD45+ Ly6G- CD11b+ F4/80+ cells


title: Th17.2

value: Spleen


title: Th17.1


title: Th2.2


title: AR-51919_M5CRe-


title: Th2.1


title: L_1

value: Lactation

value: Mammary gland


title: AR-51857_M5CRe+

value: Mcpt5-Cre+ R26DTA


title: Th1.1

value: 8 weeks

value: female


title: Th1.2