title: 31B12-A

city: Bronx

first: Liise-anne

last: Pirofski

state: New York

address: 1300 Morris Park Ave

department: Medicine - Infectious Diseases

institute: Albert Einstein College of Medicine

description:
Experiment A
GeneCounts_ExpA

data_processing:
Reads were aligned to the mouse mm10 genome using STAR v2.4.0c and mouse reads were removed before proceeding with bacterial analysis.
Reads mapping to ribosomal RNA were removed using SortMeRNA v1.9 and the Rfam 5s/5.8s, Silva archaea and bacteria 16s and 23s, and Silva eukaryotic 18s/28s databases.
Remaining reads were aligned to the ST3 genome (OXC141; GenBank FQ312027.1) using BWA 0.7.12.
Genes were quantified using FeatureCounts from the subread package (v1.4.3-p1).
Genome_build: ST3 S. pneumoniae genome (OXC141; GenBank FQ312027.1)
Supplementary_files_format_and_content: Processed files include the ID and length of each gene and read counts for each gene from each sample.  Samples are grouped by experiment (A or B) into two tables: "GeneCounts_ExpA" and "GeneCounts_ExpB"

organism: Streptococcus pneumoniae

source_name: Nasopharyngeal lavage fluid from 31B12-treated C57BL/6J mice infected with S. pneumoniae

extract_protocol:
Nasopharyngeal (NP) lavage fluid from groups of 6-8 mice were placed on ice, pooled, and centrifuged for 5 min at 7,000g, 4°C to collect cells (mouse and bacterial).  NP lavage fluid or bacterial pellets were immediately resuspended in 200 µl pre-heated Max Bacterial Enhancement Reagent (Thermo) and incubated at 95°C for 10 min.  Crude lysates were added to 1.3 ml TRIzol (Thermo) and further lysed using a BeadBeater (BioSpec) and 0.1 mm beads for 5 min.  Lysates were mixed with 280 µl ice cold chloroform and incubated at room temperature for 5 min before centrifugation for 15 min at 12,000g, 4°C.  RNA was precipitated by mixing approximately 450 µl of the upper RNA-containing layer with 600 µl cold isopropanol and centrifugation for 10 min at 15,000g, 4°C.  RNA pellets were washed twice with 75% EtOH, air dried, and resuspended in 50 µl DEPC-treated H2O.
cDNA sequencing libraries were prepared using the Nugen Ovation® RNA-Seq System V2 sample preparation kit in accordance with the manufacturer’s instructions.  Briefly, 10ng of total RNA was used for conversion to cDNA which was then amplified and purified.  Purified cDNA was sheared and size selected to remove large and small fragments.  DNA was adenylated and ligated to Illumina sequencing adapters using the KAPA Hyper Library Preparation Kit.  Final libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems), Qubit Fluorometer (Life Technologies), and Agilent 2100 BioAnalyzer.

treatment_protocol: Mice were treated with 1E2, 7A9, 31B12, or PBS 2 hours before intranasal infection with S. pneumoniae.  RNA was extracted from nasopharyngeal lavage fluid 24 hours post-infection.

tag: serotype


title: 31B12-B

status: Public on May 18 2018

type: SRA

country: USA

description:
Experiment B
GeneCounts_ExpB

library_source: transcriptomic

molecule: total RNA

tag: strain


title: Vian-2018-HIC235

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
oligomycin treated
Vian-2018-activated_B_cells_24_hours_oligomycin_30.hic

library_source: genomic

data_processing:
The paired end reads were aligned separately using BWA against the mm9 mouse build or the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse), b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

molecule: genomic DNA

organism: Mus musculus

source_name: activated B cell

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

treatment_protocol: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen); for acute ATP depletion, 20h-activated cells were shifted to glucose deficient media for 2h then, 2-Deoxy-D-glucose (5mM, Sigma) and Oligomycin (126nM, Sigma) were added to the culture for another 1.5-2h before the harvest.

tag: genotype

value: WT

tag: cell type

value: splenic B cells

tag: tissue

value: spleen

tag: age

value: 6-8 weeks old

tag: protocol

value: in situ HiC

tag: activation time

value: activated,24h, oligomycin


title: A1552-Tn (1998+ara), replicate 3

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

data_processing:
Sequencing and data processing was done by Microsynth (Balgach, Switzerland) accoridng to their standard prokaryotic differential gene expression analysis.
Reads were mapped onto the reference genome using the Bowtie2 (version 2.2.9)
Reads were counted using software htseq-count (HTSeq version 0.6.1p1)
Genome_build: Reference genome (NC_002505, NC_002506)
Supplementary_files_format_and_content: .txt files for counts

organism: Vibrio cholerae

source_name: bacterial in vitro culture

growth_protocol: V. cholerae strains were grown in 2 x 2.5 ml LB medium with 0.02% arabinose at 30C until an optical sensity at 600 nm (OD600) of 1.5-1.8 was reached. At this time, the bacteria were harvested by centrifugation at 4C.

extract_protocol:
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNAse treatment using a standard clean-up procedures. Ribodepletion was performed using a Ribo-Zero Magnetic kit (Epicentre) for Gram-negative bacteria.
Stranded Illumina TruSeq RNA libraries were prepared.

treatment_protocol: The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri reagent, and stored at -80C until their processing.

tag: genetic background

tag: transposon

value: A1552 (WT) with empty Tn transposon

tag: inducer


title: Mock-A

description:
Experiment A
GeneCounts_ExpA

source_name: Nasopharyngeal lavage fluid from PBS-treated C57BL/6J mice infected with S. pneumoniae


title: Mock-B

description:
Experiment B
GeneCounts_ExpB


title: A1552-Tn (1998+ara), replicate 2


title: Vian-2018-HIC234


title: A1552-Tn (1998+ara), replicate 1


title: 1E2-A

description:
Experiment A
GeneCounts_ExpA

source_name: Nasopharyngeal lavage fluid from 1E2-treated C57BL/6J mice infected with S. pneumoniae


title: 1E2-B

description:
Experiment B
GeneCounts_ExpB


title: Mouse Lung, Dose 0, 1day, biological replicate 2

type: RNA

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description: Taconic Biosciences Inc., Germantown, NY

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6

label: biotin

source_name: whole lung

growth_protocol: Adult male CD-1 mice were acquired from Taconic (Germantown, NY).  Animals were kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room was maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals were allowed access to Certified PicoLab Rodent 20 diet and reverse osmosis water ad libitum.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime).  Aqueous phase placed in RB(QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: Animals were placed individually in stainless-steel wire-mesh cages and exposed to styrene or air for a single 6 hour exposure.  On the morning following the last inhalation exposure, mice were euthanized by sodium pentobarbital and exsanguination.  Doses were 0 ppm (air only), 1 ppm, 5 ppm, 10 ppm, 20 ppm, 40 ppm and 120 ppm styrene.

value: adult

tag: gender

value: male

value: Whole Lung

tag: time of exposure

value: 5 day

tag: styrene dose (ppm)


title: Vian-2018-HIC238


title: Vian-2018-HIC237


title: 02 shSOX2

city: Hsinchu

first: Ming-Han

last: Kuo

address: No. 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013, R.O.C.

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by G2505C  scanner (Dye channel: R ; Scan resolution : 10 um; Tiff: 16-bit; Red PMT gain: 100%; XDR: 100 10) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

organism: Homo sapiens

source_name: endometrial adenocarcinoma

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

tag: cell line

value: Ishikawa-02 cells

tag: treatment

value: transduced with lentiviral particles encoding shSOX2


title: 02 SC

value: transduced with lentiviral particles encoding scrambled control (SC)


title: NSCLC_Tumor infiltrating CD39+ CD8 T cells 2

status: Public on May 17 2018

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v.1.5.0 and with GENCODE GRCh38 v26 gene annotation
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated in R_3.1.2 using edgeR_3.8.6 Bioconductor package with normalized.lib.sizes=TRUE option and log2 transformation
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 FPKM values for all samples

source_name: Tumor infiltrating CD39+ CD8 T cells

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit (Thermofisher, KIT0204) according to manufacturer’s protocol.
cDNA libraries were prepared using 0.5ng of total RNA and 1ul of a 1:50,000 dilution of Ambion ERCC RNA Spike-in Controls (Thermofisher, 4456740) using the SMARTSeq v2 protocol described in Nature Protocols volume 9, pages 171-181 (Picelli et al., 2014) with the following modifications: 1. Use of 20mM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Nextera XT kit (Illumina, FC-131). All samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000 (32 samples/lane).

value: Lung tumor

tag: cell population

value: CD8+ T cells

tag: phenotype


title: NSCLC_Tumor infiltrating CD39- CD8 T cells 4

source_name: Tumor infiltrating CD39- CD8 T cells


title: NSCLC_Tumor infiltrating CD39+ CD8 T cells 3


title: NSCLC_Tumor infiltrating CD39+ CD8 T cells 4


title: NSCLC_Tumor infiltrating CD39- CD8 T cells 3


title: NSCLC_Tumor infiltrating CD39- CD8 T cells 2


title: NSCLC_Tumor infiltrating CD39+ CD8 T cells 1


title: 7A9-A

description:
Experiment A
GeneCounts_ExpA

source_name: Nasopharyngeal lavage fluid from 7A9-treated C57BL/6J mice infected with S. pneumoniae

tag: serotype

tag: strain


title: SF3B1 Rep1

city: Seattle

first: Jie

last: Liu

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: UW

data_processing:
Library strategy: DNase Hi-C
Adaptor removal using cutadapt. The bride adaptor sequence is GCTGAGGGATC. After proximity ligation, the intact bridge of the valid interactions is AGCTGAGGGATCCCTCAGCT.
Mapping the reads to the reference genome with bwa mem.
Match the paired ends and remove PCR duplicates.
Remove the contacts less than 1kb apart and generate the contact maps to a given resolution (40kb or 500kb)
Genome_build: hg19
Supplementary_files_format_and_content: contactMap

source_name: Human cervical cancer

growth_protocol: HeLa cells were cultured in DMEM containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in 5% CO2

extract_protocol:
DNA samples were digested with DNase, followed by end-repair, dA-tailing, ligation of bridge adaptors, phosphorylation, and in situ ligation. After reversing crosslinks, genomic DNA was purified, sheared using a Covaris S-220 sonicator, and subjected to streptavidin-based affinity purification to recover biotinylated fragments.
NGS libraries were generated by dA tailing, ligation of sequencing adaptors, PCR amplification, and Ampure beads-based purification. Finally, libraries were sequenced on an Illumina HiSeq 4000.

treatment_protocol: HeLa cells were transfected in duplicate with either scrambled siRNA (HeLa-Rep1 and HeLa-Rep2) or SF3B1 siRNA 23850 (SF3B1-Rep1 and SF3B1-Rep2), cultured for 72 hours, and crosslinked

tag: sirna transfected

value: SF3B1 siRNA transfected-replication1

value: HeLa


title: HeLa Rep2

value: scrambled control siRNA transfected-replication2


title: SF3B1 Rep2

value: SF3B1 siRNA transfected-replication2


title: NSCLC_Tumor infiltrating CD39- CD8 T cells 1

tag: tissue


title: CRC Tumor infiltrating CD39+ CD8 T cells 8

description:
Tumor_CD8T.CD39.p_8
log2FPKM_CD8TCell_CRC.txt.gz

value: Colorectal tumor


title: CRC Tumor infiltrating CD39- CD8 T cells 4

description:
Tumor_CD8T.CD39.n_4
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39- CD8 T cells 7

description:
Tumor_CD8T.CD39.n_7
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39- CD8 T cells 6

description:
Tumor_CD8T.CD39.n_6
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 2

description:
Tumor_CD8T.CD39.p_2
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 6

description:
Tumor_CD8T.CD39.p_6
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 4

description:
Tumor_CD8T.CD39.p_4
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 1

description:
Tumor_CD8T.CD39.p_1
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 3

description:
Tumor_CD8T.CD39.p_3
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39- CD8 T cells 5

description:
Tumor_CD8T.CD39.n_5
log2FPKM_CD8TCell_CRC.txt.gz


title: HeLa Rep1

value: scrambled control siRNA transfected-replication1


title: CRC Tumor infiltrating CD39- CD8 T cells 2

description:
Tumor_CD8T.CD39.n_2
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39- CD8 T cells 3

description:
Tumor_CD8T.CD39.n_3
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Naive CD8 T cells 3

description:
PBMC_CD8T.Naive_4
log2FPKM_CD8TCell_CRC.txt.gz

source_name: Peripheral Blood Naive CD8 T cells

value: Peripheral blood

value: Naive


title: CRC Tumor infiltrating CD39- CD8 T cells 1

description:
Tumor_CD8T.CD39.n_1
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Naive CD8 T cells 4

description:
PBMC_CD8T.Naive_5
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Effector memory CD8 T cells 3

description:
PBMC_CD8T.Eff_3
log2FPKM_CD8TCell_CRC.txt.gz

value: Effector memory


title: CRC Tumor infiltrating CD39+ CD8 T cells 7

description:
Tumor_CD8T.CD39.p_7
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Effector memory CD8 T cells 5

description:
PBMC_CD8T.Eff_6
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Effector memory CD8 T cells 4

description:
PBMC_CD8T.Eff_4
log2FPKM_CD8TCell_CRC.txt.gz


title: CRC Tumor infiltrating CD39+ CD8 T cells 5

description:
Tumor_CD8T.CD39.p_5
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Naive CD8 T cells 2

description:
PBMC_CD8T.Naive_3
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Naive CD8 T cells 1

description:
PBMC_CD8T.Naive_1
log2FPKM_CD8TCell_CRC.txt.gz


title: Peripheral Blood Effector memory CD8 T cells 2

description:
PBMC_CD8T.Eff_2
log2FPKM_CD8TCell_CRC.txt.gz


title: IK6-G2_1

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

country: China

institute: Peking University

data_processing:
Clean reads were aligned to human reference hg19 using Tophat (version 2.1.1)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Cufflinks(cuffquant, cuffnorm version 2.2.1) were used  to aquire normalized expression matrix (FPKM) covering all the samples.

source_name: bone marrow xenograft of cord blood derived cell

extract_protocol:
Total RNA was respectively extracted using an RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol.
RNA products of high quality (RNA quality number > 7.0) were further used for library construction using the Illumina TruSeq RNA Prep Kit.

tag: cell type

value: CD34 positive and CD19 positive cell

tag: transformation

value: IK6 over expression


title: IK6-G3_1

value: bone marrow xenograft of cord blood derived cell

value: CD34 negative and CD19 positive cell


title: IK6-G3_0


title: IK6-G3_2


title: Peripheral Blood Effector memory CD8 T cells 1

description:
PBMC_CD8T.Eff_1
log2FPKM_CD8TCell_CRC.txt.gz


title: IK6-G2_2


title: IK6-G2_0


title: CTR-G3_0

value: empty vector


title: CTR-G3_2


title: CTR-G3_1


title: CTR-G2_1


title: CTR-G1_0

value: CD34 positive and CD19 negative cell


title: CTR-G2_0


title: CB-3438_1

source_name: cord blood

value: cord blood

value: CD34 and CD38 double positive cell


title: CB-3438_0


title: CB-19_2

value: CD19 positive cell


title: CB-19_1


title: CB-19_0


title: SPRET_BMDM_RNA_polyA_KLA_1h_rep1

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_KLA_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: SPRETEIJ_genome.tar.gz

source_name: bone marrow derived macropages (BMDM)

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
RNA-Seq: Total RNA was isolated from cells and purified using Quick RNA mini prep columns and RNase- free DNase digestion according to the manufacturer’s instructions (Zymo Research). RNA-seq libraries were prepared from poly(A)-enriched mRNA, as previously described (Oishi et al., 2017). Libraries were sequenced on HiSeq 4000 or NextSeq 500.

value: SPRET/EiJ

value: bone marrow derived macropages (BMDM)

tag: culture protocol

value: 7 day cultured BMDMs

tag: ligands in culture

value: KLA 1h

tag: chip antibody


title: SPRET_BMDM_PU1_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_PU1_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: SPRETEIJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ChIP-Seq: Chromatin immunoprecipitation (ChIP) was performed as described previously (Oishi et al., 2017). In brief, cells were resuspended in swelling buffer (10mM HEPES/KOH (pH7.9), 85mM KCl, 1mM EDTA, 0.5% IGEPAL CA-630) with protease inhibitors for 5min and then spun down and resuspended in 500μl lysis buffer (50mM Tris/HCl (pH7.4), 1% SDS, 0.5% Empigen BB, 10mM EDTA) with protease inhibitors, and chromatin was sheared using the Bioruptor (Diagenode). Lysate was diluted with 750μl dilution buffer (20mM Tris/HCl, 100mM NaCl, 0.5% TritonX-100, 2mM EDTA), 1% was taken as input DNA, and immunoprecipitation was carried out overnight with Dynabeads protein G bound to specific antibodies for PU.1 (Santa Cruz, sc- 352X), C/EBP (Santa Cruz, sc-150), H3K4me2 (Millipore, 07-030), H3K27ac (Active Motif, 39135), CJUN (Santa Cruz, sc-1694), P65 (Santa Cruz, sc-372X), USF2 (Santa Cruz, sc-862X) and RUNX1 (Santa Cruz, sc-365644). Beads were washed twice each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently eluted with elution buffer (TE, 2% SDS). DNA was reverse- crosslinked and purified using ChIP DNA Clean & Concentrator (Zymo Research) according to the manufacturer's instructions. Sequencing libraries were prepared from eluted DNA by blunting, A-tailing, adaptor ligation as previously described (Heinz et al., 2010) using NextFlex barcodes (Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected using PAGE/TBE gels for 200-400bp fragments by gel extraction and single-end sequenced on HiSeq 4000 or NextSeq 500.

value: no treatment

value: PU1 (Vendor:Santa Cruz, Cat#sc-352X)


title: SPRET_BMDM_PU1_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_PU1_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_RNA_polyA_notx_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_notx_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: SPRET_BMDM_PU1_notx_rep1


title: CTR-G2_2


title: SPRET_BMDM_PU1_KLA_1h_rep1


title: CTR-G1_1


title: SPRET_BMDM_Input_notx_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
SPRET_BMDM_Input_notx_rep2. Used for ChIP: SPRET cJun_notx_rep2, SPRET p65_notx_rep2
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: SPRETEIJ_genome.tar.gz


title: SPRET_BMDM_p65_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_p65_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: p65 (Vendor:Santa Cruz, Cat#sc-372X)


title: SPRET_BMDM_p65_notx_rep1


title: SPRET_BMDM_Input_notx_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
SPRET_BMDM_Input_notx_rep1. Used for ChIP: SPRET cJun_notx_rep1, SPRET p65_notx_rep1
Processed data file:
NA


title: CTR-G1_2


title: SPRET_BMDM_p65_KLA_1h_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_Input_KLA_1h_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
SPRET_BMDM_Input_KLA_1h_rep2. Used for ChIP: SPRET cJun_KLA_1h_rep2, SPRET p65_KLA_1h_rep2
Processed data file:
NA


title: SPRET_BMDM_Input_KLA_1h_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
SPRET_BMDM_Input_KLA_1h_rep1. Used for ChIP: SPRET cJun_KLA_1h_rep1, SPRET p65_KLA_1h_rep1
Processed data file:
NA


title: SPRET_BMDM_Input_notx_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
SPRET_BMDM_Input_notx_rep1. Used for ChIP: SPRET CEBP_notx_rep1, SPRET histone_notx_rep1, SPRET PU1_notx_rep1
Processed data file:
NA


title: SPRET_BMDM_Input_KLA_1h_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
SPRET_BMDM_Input_KLA_1h_rep2. Used for ChIP: SPRET CEBP_KLA_1h_rep2, SPRET histone_KLA_1h_rep2, SPRET PU1_KLA_1h_rep2
Processed data file:
NA


title: CB-3438_2


title: SPRET_BMDM_Input_KLA_1h_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
SPRET_BMDM_Input_KLA_1h_rep1. Used for ChIP: SPRET CEBP_KLA_1h_rep1, SPRET histone_KLA_1h_rep1, SPRET PU1_KLA_1h_rep1
Processed data file:
NA


title: SPRET_BMDM_H3K4me2_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_SPRET_me2_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called on replicates with HOMER using input files, and peaks from getDifferentialPeaks with parameter -same were used for downstream analysis
genome build: SPRETEIJ_genome.tar.gz

value: H3K4me2 (Vendor:Millipore, Cat#07-030)


title: SPRET_BMDM_H3K4me2_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_SPRET_me2_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_H3K4me2_notx_rep1


title: SPRET_BMDM_H3K4me2_KLA_1h_rep2


title: SPRET_BMDM_RNA_polyA_KLA_1h_rep2


title: SPRET_BMDM_H3K27ac_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_SPRET_27ac_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: H3K27ac (Vendor:Active Motif, Cat#39135)


title: SPRET_BMDM_H3K27ac_notx_rep1


title: SPRET_BMDM_H3K27ac_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_SPRET_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_RNA_polyA_notx_rep2


title: SPRET_BMDM_Input_notx_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
SPRET_BMDM_Input_notx_rep2. Used for ChIP: SPRET CEBP_notx_rep2, SPRET histone_notx_rep2, SPRET PU1_notx_rep2
Processed data file:
NA


title: SPRET_BMDM_GRO_notx_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: SPRETEIJ_genome.tar.gz

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
GRO-seq and 5'GRO-seq: Nascent transcription was captured by global nuclear run-on sequencing (GRO-seq) (Core et al., 2008) and nascent transcription start sites by 5’GRO-seq (Lam et al., 2013). Nuclei were isolated from BMDMs using hypotonic lysis [10 mM Tris-HCl (pH 7.5), 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL CA-630] and flash frozen in GRO-freezing buffer [50 mM Tris-HCl (pH 7.8), 5 mM MgCl2, 40% Glycerol]. 3-5 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (Duttke et al., 2015) with 3x NRO buffer [15mM Tris-Cl (pH 8.0), 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/μL of SUPERase In, 1.5% Sarkosyl, 366 μM ATP, GTP (Roche), Br-UTP (Sigma Aldrich) and 1.2 μM CTP (Roche, to limit run-on length to ~40 nt)]. Reactions were stopped after five minutes by addition of 500 μL Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer.


title: SPRET_BMDM_GRO_KLA_1h_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: SPRET_BMDM_H3K27ac_KLA_1h_rep1


title: SPRET_BMDM_cJun_notx_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_cJun_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: cJun (Vendor:Santa Cruz, Cat#sc-1694)


title: SPRET_BMDM_CEBPB_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_CEBP_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: CEBPb (Vendor:Santa Cruz, Cat#sc-150)


title: SPRET_BMDM_cJun_KLA_1h_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_cJun_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_CEBPB_notx_rep2


title: SPRET_BMDM_cJun_KLA_1h_rep2


title: SPRET_BMDM_ATAC_KLA_1h_rep2

description:
ATAC-seq
Processed data file:
peaks_SPRET_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ATAC-seq: To approximately 150k nuclei in 22.5ul GRO freezing buffer, isolated as described for GRO-seq above, 25ul DNA Tagmentation buffer was added, reaction mixed and 2.5uL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) added. Mixture was incubated at 37°C for 30 minutes and subsequently purified using the Zymogen ChIP DNA purification kit as described by the manufacturer. DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 10 cycles. PCR reactions were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, size selected using PAGE/TBE gels for 160 – 280 bp and DNA eluted as described for GRO-seq.


title: SPRET_BMDM_ATAC_notx_rep1

description:
ATAC-seq
Processed data file:
peaks_SPRET_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: SPRET_BMDM_5GRO_notx_rep1

description:
5'Gro-Seq
Processed data file:
tss_SPRET_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: SPRETEIJ_genome.tar.gz


title: PWK_BMDM_RNA_polyA_notx_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_notx_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: PWKPHJ_genome.tar.gz

value: PWK/PhJ


title: SPRET_BMDM_5GRO_KLA_1h_rep2

description:
5'Gro-Seq
Processed data file:
tss_SPRET_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar


title: SPRET_BMDM_5GRO_notx_rep2


title: PWK_BMDM_PU1_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_PU1_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: PWKPHJ_genome.tar.gz


title: PWK_BMDM_RNA_polyA_KLA_1h_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_KLA_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: PWK_BMDM_PU1_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_PU1_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_PU1_KLA_1h_rep1


title: PWK_BMDM_PU1_notx_rep1


title: PWK_BMDM_p65_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_p65_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_p65_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_CEBPB_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_CEBP_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_RNA_polyA_KLA_1h_rep2


title: PWK_BMDM_p65_notx_rep1


title: PWK_BMDM_Input_p65_notx_rep1

description:
DSG and formaldehyde-crosslinked input DNA
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: PWKPHJ_genome.tar.gz


title: PWK_BMDM_Input_KLA_1h_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
PWK_BMDM_Input_KLA_1h_rep2. Used for ChIP: PWK cJun_KLA_1h_rep2, PWK p65_KLA_1h_rep2
Processed data file:
NA


title: PWK_BMDM_Input_notx_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
PWK_BMDM_Input_notx_rep2. Used for ChIP: PWK cJun_notx_rep2, PWK p65_notx_rep2
Processed data file:
NA


title: PWK_BMDM_Input_p65_KLA_1h_rep1


title: PWK_BMDM_Input_notx_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
PWK_BMDM_Input_CEBP_notx_rep2. Used for ChIP: PWK CEBP_notx_rep2, PWK histone_notx_rep2, PWK PU1_notx_rep2
Processed data file:
NA


title: PWK_BMDM_RNA_polyA_notx_rep1


title: PWK_BMDM_Input_KLA_1h_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
PWK_BMDM_Input_KLA_1h_rep1. Used for ChIP: PWK CEBP_KLA_1h_rep1, PWK histone_KLA_1h_rep1, PWK PU1_KLA_1h_rep1
Processed data file:
NA


title: PWK_BMDM_H3K4me2_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_PWK_me2_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called on replicates with HOMER using input files, and peaks from getDifferentialPeaks with parameter -same were used for downstream analysis
genome build: PWKPHJ_genome.tar.gz


title: PWK_BMDM_Input_KLA_1h_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
PWK_BMDM_Input_KLA_1h_rep2. Used for ChIP: PWK CEBP_KLA_1h_rep2, PWK histone_KLA_1h_rep2, PWK PU1_KLA_1h_rep2
Processed data file:
NA


title: PWK_BMDM_Input_notx_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
PWK_BMDM_Input_notx_rep1. Used for ChIP: PWK CEBP_notx_rep1, PWK histone_notx_rep1, PWK PU1_notx_rep1
Processed data file:
NA


title: PWK_BMDM_Input_cJun_KLA_1h_rep1


title: PWK_BMDM_H3K4me2_notx_rep1


title: PWK_BMDM_p65_KLA_1h_rep1


title: SPRET_BMDM_CEBPB_KLA_1h_rep2


title: PWK_BMDM_H3K27ac_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_PWK_27ac_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_H3K27ac_notx_rep2


title: PWK_BMDM_H3K4me2_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_PWK_me2_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_Input_cJun_notx_rep1


title: PWK_BMDM_H3K27ac_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_PWK_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_H3K27ac_KLA_1h_rep2


title: PWK_BMDM_cJun_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_cJun_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_GRO_KLA_1h_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: PWKPHJ_genome.tar.gz


title: PWK_BMDM_cJun_notx_rep1


title: PWK_BMDM_GRO_notx_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: PWK_BMDM_GRO_KLA_1h_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.bed
Processed data file available in:
GRO-Seq_processed_data.tar


title: PWK_BMDM_cJun_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_cJun_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_cJun_KLA_1h_rep1


title: PWK_BMDM_CEBPB_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_CEBP_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_CEBPB_notx_rep1


title: PWK_BMDM_ATAC_notx_rep2

description:
ATAC-seq
Processed data file:
peaks_PWK_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: PWK_BMDM_CEBPB_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_PWK_CEBP_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: PWK_BMDM_H3K4me2_KLA_1h_rep2


title: PWK_BMDM_5GRO_KLA_1h_rep2

description:
5'Gro-Seq
Processed data file:
tss_PWK_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: PWKPHJ_genome.tar.gz


title: NOD_BMDM_RNA_polyA_notx_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_notx_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: NODSHILTJ_genome.tar.gz

value: NOD/ShiLtJ


title: NOD_BMDM_RNA_polyA_KLA_1h_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_KLA_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: NOD_BMDM_RNA_polyA_notx_rep1


title: NOD_BMDM_RNA_polyA_KLA_1h_rep2


title: PWK_BMDM_ATAC_KLA_1h_rep1

description:
ATAC-seq
Processed data file:
peaks_PWK_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: PWK_BMDM_5GRO_notx_rep1

description:
5'Gro-Seq
Processed data file:
tss_PWK_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar


title: NOD_BMDM_PU1_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_PU1_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: NODSHILTJ_genome.tar.gz


title: NOD_BMDM_p65_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_p65_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_PU1_KLA_1h_rep1


title: NOD_BMDM_p65_notx_rep1


title: NOD_BMDM_Input_KLA_1h_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
NOD_BMDM_Input_KLA_1hr_rep1. Used for ChIP: NOD cJun_KLA_1hr_rep1, NOD p65_KLA_1hr_rep1
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: NODSHILTJ_genome.tar.gz


title: NOD_BMDM_Input_KLA_1h_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
NOD_BMDM_Input_KLA_1hr_rep2. Used for ChIP: NOD cJun_KLA_1h_rep2, NOD p65_KLA_1hr_rep2
Processed data file:
NA


title: NOD_BMDM_p65_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: SPRET_BMDM_cJun_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_SPRET_cJun_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_Input_notx_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
NOD_BMDM_Input_notx_rep2. Used for ChIP: NOD cJun_notx_rep2, NOD p65_notx_rep2
Processed data file:
NA


title: NOD_BMDM_Input_KLA_1h_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
NOD_BMDM_Input_KLA_1h_rep2. Used for ChIP: NOD CEBP_KLA_1h_rep2, NOD histone_KLA_1h_rep2, NOD PU1_KLA_1hr_rep1
Processed data file:
NA


title: NOD_BMDM_Input_notx_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
NOD_BMDM_Input_notx_rep1. Used for ChIP: NOD CEBP_notx_rep1, NOD histone_notx_rep1, NOD PU1_notx_rep2
Processed data file:
NA


title: PWK_BMDM_CEBPB_KLA_1h_rep2


title: NOD_BMDM_Input_notx_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
NOD_BMDM_Input_notx_rep1. Used for ChIP: NOD cJun_notx_rep1, NOD p65_notx_rep1
Processed data file:
NA


title: NOD_BMDM_Input_notx_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
NOD_BMDM_Input_notx_rep2. Used for ChIP: NOD CEBP_notx_rep2, NOD histone_notx_rep2, NOD PU1_notx_rep1
Processed data file:
NA


title: NOD_BMDM_Input_KLA_1h_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
NOD_BMDM_Input_KLA_1h_rep1. Used for ChIP: NOD CEBP_KLA_1hr_rep1, NOD histone_KLA_1h_rep1, NOD PU1_KLA_1h_rep2
Processed data file:
NA


title: NOD_BMDM_H3K4me2_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_NOD_me2_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called on replicates with HOMER using input files, and peaks from getDifferentialPeaks with parameter -same were used for downstream analysis
genome build: NODSHILTJ_genome.tar.gz


title: PWK_BMDM_ATAC_KLA_1h_rep2


title: NOD_BMDM_H3K4me2_notx_rep1


title: NOD_BMDM_H3K4me2_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_NOD_me2_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_PU1_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_PU1_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_H3K4me2_KLA_1h_rep1


title: NOD_BMDM_H3K27ac_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_NOD_27ac_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_PU1_notx_rep1


title: NOD_BMDM_H3K27ac_notx_rep1


title: NOD_BMDM_H3K27ac_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_NOD_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_H3K27ac_KLA_1h_rep1


title: NOD_BMDM_cJun_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_cJun_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_GRO_KLA_1h_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: NODSHILTJ_genome.tar.gz


title: NOD_BMDM_GRO_notx_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: NOD_BMDM_p65_KLA_1h_rep1


title: NOD_BMDM_cJun_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_cJun_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_cJun_notx_rep1


title: NOD_BMDM_CEBPB_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_CEBP_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_5GRO_KLA_1h_rep1

description:
5'Gro-Seq
Processed data file:
tss_NOD_5GRO_KLA.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: NODSHILTJ_genome.tar.gz


title: NOD_BMDM_CEBPB_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_CEBP_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_5GRO_notx_rep1

description:
5'Gro-Seq
Processed data file:
tss_NOD_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar


title: F1_C57_SPRET_BMDM_PU1_KLA_1h

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FSC_SPRET_C57_PU1_KLA.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called with HOMER using an input and peak file was used for further downstream analysis
genome build: mm10 & SPRETEIJ_genome.tar.gz

value: C57BL/6J x SPRET/EiJ


title: NOD_BMDM_ATAC_notx_rep2

description:
ATAC-seq
Processed data file:
peaks_NOD_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: F1_C57_SPRET_BMDM_Input_notx

description:
formaldehyde-crosslinked Input DNA
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for bowtie2 and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & SPRETEIJ_genome.tar.gz


title: F1_C57_SPRET_BMDM_PU1_notx

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FSC_SPRET_C57_PU1_notx.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: F1_C57_SPRET_BMDM_H3K4me2_notx

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_F1_FSC_SPRET_C57_me2_notx.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: F1_C57_PWK_BMDM_RNA_notx_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_F1_C57_PWK_notx_rep2.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for STAR and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & PWKPHJ_genome.tar.gz

value: C57BL/6J x PWK/PhJ


title: F1_C57_SPRET_BMDM_GRO_KLA_1h

description:
GRO-Seq
Processed data file:
GRO_Seq_F1_C57_SPRET_KLA.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for bowtie2 and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & SPRETEIJ_genome.tar.gz


title: F1_C57_PWK_BMDM_RNA_notx_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_F1_C57_PWK_notx_rep1.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: F1_C57_PWK_BMDM_RNA_KLA_1h_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_F1_C57_PWK_KLA_rep2.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: F1_C57_PWK_BMDM_Input_KLA_1h

data_processing:
Fastq files from sequencing experiments were mapped to parental custom genome using default parameters for bowtie2 and shifted back to reference coordinates. MARGE was used to calculated allele-specific reads for further downstream analysis
genome build: mm10 & PWKPHJ_genome.tar.gz


title: F1_C57_PWK_BMDM_Input_notx


title: F1_C57_PWK_BMDM_PU1_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FPC_PWK_C57_PU1_KLA.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: F1_C57_PWK_BMDM_H3K4me2_notx

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_F1_FPC_PWK_C57_me2_notx.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: NOD_BMDM_cJun_KLA_1h_rep1


title: F1_C57_PWK_BMDM_PU1_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_F1_BMDM_FPC_PWK_C57_PU1_notx.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: F1_C57_PWK_BMDM_GRO_KLA_1h_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_F1_C57_PWK_KLA.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: mm10 & PWKPHJ_genome.tar.gz


title: F1_C57_PWK_BMDM_GRO_notx_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_F1_C57_PWK_notx.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: F1_C57_PWK_BMDM_H3K4me2_KLA_1h

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_F1_FPC_PWK_C57_me2_KLA_1h.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: F1_C57_SPRET_BMDM_Input_KLA_1h


title: F1_C57_PWK_BMDM_GRO_KLA_1h_rep2


title: C57_BMDM_USF2_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_USF2_notx_opt.bed
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: mm10

value: Usf2 (Vendor:Santa Cruz, Cat#sc-862X)


title: NOD_BMDM_CEBPB_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_CEBP_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_USF2_notx_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_USF2_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_USF2_KLA_1h_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_USF_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_RUNX1_notx

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_Runx1_notx.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called with HOMER using an input and peak file was used for further downstream analysis
genome build: mm10

value: Runx1 (Vendor:Santa Cruz, Cat#sc365644)


title: F1_C57_SPRET_BMDM_H3K4me2_KLA_1h

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_F1_FSC_SPRET_C57_me2_KLA_1h.txt
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_USF2_KLA_1h_rep2


title: C57_BMDM_RUNX1_KLA_1h

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_Runx1_KLA.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_RNA_polyA_notx_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_notx_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: mm10


title: C57_BMDM_RNA_polyA_notx_rep2


title: C57_BMDM_RNA_polyA_KLA_1h_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_KLA_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: F1_C57_PWK_BMDM_RNA_KLA_1h_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_F1_C57_PWK_KLA_rep1.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: C57_BMDM_PU1_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_PU1_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_PU1_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_PU1_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_PU1_notx_rep1


title: C57_BMDM_PU1_KLA_1h_rep2


title: F1_C57_PWK_BMDM_GRO_notx_rep1


title: C57_BMDM_p65_notx_rep1

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_p65_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_Input_USF2_notx_rep1

description:
DSG and formaldehyde-crosslinked input DNA
Processed data file:
NA

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: mm10


title: C57_BMDM_p65_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_Input_USF2_KLA_1h_rep1


title: C57_BMDM_Input_USF2_notx_rep2


title: C57_BMDM_Input_USF2_KLA_1h_rep2


title: C57_BMDM_Input_KLA_1h_rep2a (p65, RUNX1)

description:
DSG and formaldehyde-crosslinked input DNA
C57_BMDM_Input_KLA_1h_rep2. Used for ChIP: C57 p65_KLA_1hr_rep2, C57_RUNX1_KLA_1h
Processed data file:
NA


title: C57_BMDM_Input_notx_rep2a (p65, RUNX1)

description:
DSG and formaldehyde-crosslinked input DNA
C57_BMDM_Input_notx_rep2. Used for ChIP: C57 p65_notx_rep2, C57 RUNX1_notx
Processed data file:
NA


title: C57_BMDM_Input_KLA_1h_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
C57_BMDM_Input_KLA_1h_rep1. Used for ChIP: C57 cJUN_KLA_1h_rep1, C57 p65_KLA_1h_rep1
Processed data file:
NA


title: C57_BMDM_Input_notx_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
C57_BMDM_Input_notx_rep1. Used for ChIP: C57 cJun_notx_rep1, C57_p65_notx_rep1
Processed data file:
NA


title: C57_BMDM_Input_notx_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
C57_BMDM_Input_notx_rep2. Used for ChIP: C57 CEBP_notx_rep2,C57  histone_notx_rep2, C57 PU1_notx_rep2
Processed data file:
NA


title: NOD_BMDM_CEBPB_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_NOD_CEBP_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_Input_KLA_1h_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
C57_BMDM_Input_KLA_1h_rep2. Used for ChIP: C57 CEBP_KLA_1h_rep2, C57 histone_KLA_1h_rep2, C57 PU1_KLA_1h_rep2
Processed data file:
NA


title: C57_BMDM_Input_KLA_1h_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
C57_BMDM_Input_KLA_1h_rep1. Used for ChIP: C57 CEBP_KLA_1h_rep1, C57 histone_KLA_1h_rep1, C57 PU1_KLA_1h_rep1
Processed data file:
NA


title: C57_BMDM_H3K4me2_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_C57_me2_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called on replicates with HOMER using input files, and peaks from getDifferentialPeaks with parameter -same were used for downstream analysis
genome build: mm10


title: C57_BMDM_H3K4me2_KLA_1h_rep1


title: C57_BMDM_RNA_polyA_KLA_1h_rep1


title: C57_BMDM_H3K4me2_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_C57_me2_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_H3K27ac_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_C57_27ac_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_H3K4me2_notx_rep1


title: C57_BMDM_H3K27ac_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_C57_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_H3K27ac_notx_rep1


title: C57_BMDM_p65_notx_rep2


title: C57_BMDM_H3K27ac_KLA_1h_rep1


title: C57_BMDM_GRO_notx_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: mm10


title: C57_BMDM_GRO_notx_rep2


title: C57_BMDM_GRO_KLA_1h_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: C57_BMDM_p65_KLA_1h_rep1


title: C57_BMDM_GRO_KLA_1h_rep1


title: C57_BMDM_CEBPB_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_CEBP_notx_opt.
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: C57_BMDM_CEBPB_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_CEBP_KLA_opt.
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: hhex overexpression rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: DanCer10 (GRCz10.87)
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts per peak

organism: Danio rerio

source_name: FACS sorted endothelial cells

extract_protocol:
For isolating endothelial cells from Tg(kdrl:EGFP)s843 siblings and Tg(kdrl:EGFP)s843 hhex mutant at 48 hpf, embryos were divided based on the absence of PLs.  Then, embryos were rinsed in HBSS (Gibco) followed by dissociation in TrypLE express (Gibco) at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals (for Tg(kdrl:EGFP)s843 Tg(fli1a:tdTomato-2A-hhex)bns136). RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
6ng total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit (Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 30M reads per library with 1x75bp single end setup.

tag: genotype/variation

value: hhex overexpression

tag: age

value: 48 hpf

value: AB

value: endothelial cells


title: hhex overexpression rep1


title: C57_BMDM_Input_notx_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
C57_BMDM_Input_notx_rep1. Used for ChIP: C57 CEBP_notx_rep1, C57 histone_notx_rep1, C57 histone_notx_rep1, C57 PU1_notx_rep1
Processed data file:
NA

value: bone marrow derived macropages (BMDM)

value: 7 day cultured BMDMs

value: no treatment


title: C57_BMDM_CEBPB_KLA_1h_rep1

value: KLA 1h


title: hhex mutant rep1

value: hhex mutant


title: Sibling rep1

value: wild type


title: Sibling rep2


title: BALB_BMDM_RNA_polyA_notx_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_notx_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: BALBCJ_genome.tar.gz

value: BALB/cJ


title: BALB_BMDM_RNA_polyA_KLA_1h_rep2

description:
RNA-Seq
Processed data file:
RNA_Seq_all_strains_KLA_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar


title: BALB_BMDM_RNA_polyA_KLA_1h_rep1


title: BALB_BMDM_RNA_polyA_notx_rep1


title: BALB_BMDM_PU1_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_PU1_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. HOMER was used for peak calling. IDR was applied to both replicates and the optimal peak file was used for further downstream analysis
genome build: BALBCJ_genome.tar.gz

value: PU1 (Vendor:Santa Cruz, Cat#sc-352X)


title: BALB_BMDM_PU1_notx_rep2


title: BALB_BMDM_PU1_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_PU1_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: BALB_BMDM_p65_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
BALB_p65_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: p65 (Vendor:Santa Cruz, Cat#sc-372X)


title: BALB_BMDM_p65_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_p65_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: BALB_BMDM_PU1_KLA_1h_rep1


title: BALB_BMDM_p65_KLA_1h_rep1

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Input was used for IDR.
genome build: BALBCJ_genome.tar.gz


title: BALB_BMDM_p65_notx_rep1


title: BALB_BMDM_Input_PU1_KLA_1h_rep1

description:
formaldehyde-crosslinked Input DNA
Processed data file:
NA


title: BALB_BMDM_Input_notx_rep2a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
BALB_BDMD_input_notx_rep2. Used as input for ChIP: BALB_cJun_notx_rep2, BALB p65_notx_rep2
Processed data file:
NA


title: BALB_BMDM_Input_notx_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
BALB_BMDM_input_notx_rep1. Used as input for ChIP: BALB cJun_notx_rep1, BALB p65_notx_rep1
Processed data file:
NA


title: hhex mutant rep2


title: BALB_BMDM_Input_p65_KLA_1h_rep1

description:
DSG and formaldehyde-crosslinked input DNA
Processed data file:
NA


title: BALB_BMDM_Input_cJun_KLA_1h_rep2


title: C57_BMDM_5GRO_KLA_1h_rep1

description:
5'Gro-Seq
Processed data file:
tss_C57_5GRO_KLA.
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: mm10


title: BALB_BMDM_Input_notx_rep2 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
BALB_BMDM input_notx_rep2. Used as input for ChIP: BALB CEBP_notx_rep2, BALB histone_notx_rep1, BALB PU1_notx_rep1
Processed data file:
NA


title: BALB_BMDM_Input_notx_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
BALB_BMDM input _notx_rep1. Used as input for ChIP: BALB CEBP_notx_rep1, BALB  histone_notx_rep2, BALB PU1_notx_rep2
Processed data file:
NA


title: BALB_BMDM_Input_KLA_1h_rep2 (CEBP, histone)

description:
formaldehyde-crosslinked Input DNA
BALB_BMDM input _KLA_1hr_rep2. Used as input for ChIP: BALB CEBP_KLA_1hr_rep2, BALB histone_KLA_1hr_rep2
Processed data file:
NA


title: BALB_BMDM_input_KLA_1h_rep1 (CEBP, histone, PU1)

description:
formaldehyde-crosslinked Input DNA
BALB BMDM input_KLA_1h_rep1. Used as input for ChIP: BALB CEBP_KLA_1hr_rep1, BALB histone_KLA_1h_rep1, BALB PU1_KLA_1 hr_rep2
Processed data file:
NA


title: BALB_BMDM_H3K4me2_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_BALB_me2_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Peaks were called on replicates with HOMER using input files, and peaks from getDifferentialPeaks with parameter -same were used for downstream analysis
genome build: BALBCJ_genome.tar.gz

value: H3K4me2 (Vendor:Millipore, Cat#07-030)


title: BALB_BMDM_H3K4me2_notx_rep1


title: BALB_BMDM_H3K4me2_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_BALB_me2_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: BALB_BMDM_H3K4me2_KLA_1h_rep1


title: BALB_BMDM_Input_KLA_1h_rep1a (cJun, p65)

description:
DSG and formaldehyde-crosslinked input DNA
BALB_BMDM_input_KLA_1h_rep1. Used as input for ChIP: BALB cJun_KLA_1hr_rep1, BALB p65_KLA_1h_rep2
Processed data file:
NA


title: BALB_BMDM_H3K27ac_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_BALB_27ac_notx_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: H3K27ac (Vendor:Active Motif, Cat#39135)


title: Human_CD133_rep_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

institute: University of Basel

description: Technical replicate 2 of Biological replicate 1

hyb_protocol: Hybridization was done in a chamber (Agilent technologies, USA) for 17 hrs at 650C with gentle rotation

scan_protocol: The slide was scanned and image was analysed using feature extraction tool version 9.5.3.1 (Agilent technologies, USA) and data was analysed using GeneSpring version 10 (Agilent technologies, USA)

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction.

source_name: CD133 positive population

label_protocol: Probes with higher labelling efficiency (specific activity ≥ 8pmol Cy3 or Cy5/ng cRNA) were selected for competitive hybridization as per the manufacturer’s instructions. 825ng each of Cy5 and Cy3 labelled cRNAs from CD133 negative and positive populations were mixed and added to hybridization buffer and placed on the array

growth_protocol: Retinoblastoma Y79 cells were revived and cultured in RMPI-1640 media with 10% FBS (company), antibiotics (company) and L-Glutamine (Invitrogen). Media was changed every three days and the cells were sub-cultured following observation of cell confluency of ~70%. Enrichment and characterization of putative cancer stem cells were carried out in Y79 retinoblastoma cell line. Enrichment was done by sorting the cells using the surface marker, CD133

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Y79 Retinoblastoma

value: CD133 positive sorted population

source_name: CD133 negative population

value: CD133 negative sorted population


title: BALB_BMDM_H3K27ac_notx_rep1


title: APCko_Adenoma_2

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software AGCC (Affymetrix GeneChip Command Console) version 4.0

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: liver, adenoma, Phenobarbital, 9 months

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

growth_protocol: Mice were a gift from Dr. Sabine Colnot (Paris, France) and bred under SPF conditions in an animal facility of the University of Tuebingen, Germany.

extract_protocol: RNA was isolated from snap-frozen tissue samples using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Mice were injected with 0.75 mg of Tamoxifen (single i.p. injection) at 6 weeks of age. Starting 1 week later, mice were either kept on standard chow or on a phenobarbital-containing diet (0.05%) for 9 months.

tag: gender

value: male

value: conditional APCko

value: liver, adenoma

tag: group

value: Phenobarbital

value: 9 months


title: APCko_Adenoma_5


title: APCko_Carcinoma_5

source_name: liver, carcinoma, none, 9 months

value: liver, carcinoma


title: Human_CD133_rep_4

description: Technical replicate 2 of Biological replicate 2

tag: cell line


title: BALB_BMDM_H3K27ac_KLA_1h_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_BALB_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: bone marrow derived macropages (BMDM)

value: 7 day cultured BMDMs

value: KLA 1h


title: PB_NT_5

source_name: liver, non-tumor, Phenobarbital, 9 months

value: liver, non-tumor

tag: treatment


title: APCko_Adenoma_3


title: APCko_Adenoma_1


title: APCko_Carcinoma_3


title: APCko_Carcinoma_1


title: APCko_Adenoma_4


title: APCko_Carcinoma_2


title: APCko_Carcinoma_4


title: Human_CD133_rep_3

description: Technical replicate 1 of Biological replicate 2

tag: cell population


title: BALB_BMDM_GRO_notx_rep2

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_notx_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar

data_processing:
Library strategy: GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Read counts on the gene bodies were assessed with HOMER's analyzeRepeats with parameters rna, -count genes and -tpm
genome build: BALBCJ_genome.tar.gz

value: BALB/cJ

value: no treatment


title: Human_CD133_rep_1

description: Technical replicate 1 of Biological replicate 1


title: PB_NT_3


title: C57_BMDM_CEBPB_notx_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_C57_CEBP_notx_opt.
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: CEBPb (Vendor:Santa Cruz, Cat#sc-150)


title: BALB_BMDM_GRO_notx_rep1


title: BALB_BMDM_GRO_KLA_1h_rep1

description:
GRO-Seq
Processed data file:
GRO_Seq_all_strains_KLA_1h_TPM.txt
Processed data file available in:
GRO-Seq_processed_data.tar


title: BALB_BMDM_cJun_notx_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_cJun_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: cJun (Vendor:Santa Cruz, Cat#sc-1694)


title: BALB_BMDM_cJun_notx_rep1


title: BALB_BMDM_cJun_KLA_1h_rep2

description:
DSG and formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_cJun_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: BALB_BMDM_CEBPB_notx_rep2

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_CEBP_notx_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: BALB_BMDM_cJun_KLA_1h_rep1


title: H2O_NT_5

source_name: liver, non-tumor, none, 9 months


title: PB_NT_4


title: PB_NT_2


title: H2O_NT_4


title: PB_NT_1


title: BALB_BMDM_CEBPB_notx_rep1


title: H2O_NT_2


title: V-CON-3

city: Nanjing

first: Fang

last: Yuan

address: 101Longmian Avenue

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
QC of alignment is performed to determine if resequencing is needed.
DaTA filtering:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than5).
Bowtie2 was used to map clean reads to reference gene and use HISAT to reference genome
FPKM method is used in calculated expression level
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Induced pluripotent stem cells cell line

growth_protocol: For control group, neurons were attached from day 28 with neural induction medium with 500nM SAG added from day10 to day 25; for lgx6 overexpresssion group, dox was added at 3 μg/mL from day 10 along with the whole culture process.

extract_protocol:
Total RNA was extracted in Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For lhx6 overexpresssion group, dox was added at 3 μg/mL from day 10 along with the whole culture process.

tag: sample stage

value: 50 days differentiation from ipscs

tag: sample group

value: control


title: V-CON-2

value: Induced pluripotent stem cells cell line


title: V-CON-1


title: BALB_BMDM_ATAC_notx_rep2

description:
ATAC-seq
Processed data file:
peaks_BALB_ATAC_notx_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar

tag: strain


title: V-LHX6-GOF-3

value: LHX6 overexpression


title: BALB_BMDM_CEBPB_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
peaks_BALB_CEBP_KLA_opt.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar


title: V-LHX6-GOF-2


title: BALB_BMDM_ATAC_KLA_1h_rep2

description:
ATAC-seq
Processed data file:
peaks_BALB_ATAC_KLA_opt.bed
Processed data file available in:
ATAC-seq_processed_data_files.tar


title: 75_NLW44_B_bulkRNA-seq

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description:
Sample_104988
WA09 (H9) embryonic stem cells (WiCell) were maintained feeder-free in mTeSR1 (Stem Cell Technologies) and dissociated with Accutase (Stem Cell Technologies). Cells  were plated into wells of 24 well plates pre-coated with GelTrex in mTeSR1 supplemented with 10 µM Rho-kinase inhibitor Y27632 (StemGent).  The media was replaced with mTeSR1 + 1.5 % GelTrex at 16 hours, 12 µM CHIR99021 in Advanced RPMI + Glutamax (Life Technologies) at 60 hours, and RB (Advanced RPMI + Glutamax + B27 Supplement, from Life Technologies) at 96 hours, total volume 500 uL/well. RB was changed two days later and every two days thereafter. For experiments involving modulation of endothelial cells media was supplemented with VEGF165 (50 ng/ml). Organoids were harvested on day 21, dissociated and processed for single cell RNA sequencing.

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
RNA quality was assessed on the Bioanalyzer 2100platform (Agilent) using a the Eukaryote Total RNA Nano array (Agilent). High RNA quality was obtained for the VEGF+ and VEGF- samples with RIN values of 9.7 and 9.5, respectively. We used 10 ng RNA starting material to generate cDNA using the SMART-Seq® Low Input RNA kit for sequencing (Takara) applying 8 PCR cycles. Amplified cDNA was then purified with the Agencourt AMPure XP DNA purification kit (Beckman Coulter) and analyzed on the Bioanalyzer platform using a High Sensitivity DNA array (Agilent). Two next-generation sequencing libraries were generated and barcoded using the Nextera XT DNA Library Preparation Kit (Illumina) starting with 100 pg cDNA. The two cDNA libraries were pooled and sequenced on one lane of a HiSeq500 platform with Illumina TruSeq v4 chemistry (paired-end 2x75 cycles) at the University of Michigan Sequencing core facility.
The sequences were aligned to human genome (Ensembl GRCh38) using STAR (version 2.5.2) with default parameters. The relative read counts at gene level were estimated using HTSeq (version 2.20.2). The read counts were normalized using quantile normalization function in edgeR R statistical package.
Alignment rate: A total number of 52 and 76 million reads were sequenced from VEGF+ and VEGF- RNA samples ; the alignment rate of the reads from the samples against the human  genome were 91% and 88 % respectively.
Genome_build: GRCh38

source_name: Kidney organoids

extract_protocol:
Organoids collected from a single well were dissected in ice-cold PBS and finely minced in a petri dish on ice using razor blades. The tissue were added to 1 ml of cold active protease solution (PBS, 10 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). The tissue was incubated in a 2 ml reaction tube for 15-20 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 20 seconds every 5 minutes. Single cell dissociation was confirmed with a microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.01%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.01%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 http://mccarrolllab.com/dropseq/). Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluorooctanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on the Illumina HiSeq2500 platform. Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.

value: WA09 (H9) embryonic stem cells


title: BALB_BMDM_ATAC_KLA_1h_rep1


title: 74_NLW44_A_bulkRNA-seq

description:
Sample_104987
WA09 (H9) embryonic stem cells (WiCell) were maintained feeder-free in mTeSR1 (Stem Cell Technologies) and dissociated with Accutase (Stem Cell Technologies). Cells  were plated into wells of 24 well plates pre-coated with GelTrex in mTeSR1 supplemented with 10 µM Rho-kinase inhibitor Y27632 (StemGent).  The media was replaced with mTeSR1 + 1.5 % GelTrex at 16 hours, 12 µM CHIR99021 in Advanced RPMI + Glutamax (Life Technologies) at 60 hours, and RB (Advanced RPMI + Glutamax + B27 Supplement, from Life Technologies) at 96 hours, total volume 500 uL/well. RB was changed two days later and every two days thereafter. For experiments involving modulation of endothelial cells media was supplemented with VEGF165 (50 ng/ml). Organoids were harvested on day 21, dissociated and processed for single cell RNA sequencing.


title: BALB_BMDM_5GRO_notx_rep2

description:
5'Gro-Seq
Processed data file:
tss_BALB_5GRO_notx.bed
Processed data file available in:
5GRO_processed_data.tar

data_processing:
Library strategy: 5'GRO-Seq
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for bowtie2 and shifted back to reference coordinates. Mapped data was analyzed with HOMER's analyzeRepeapts with paramer -tss.
genome build: BALBCJ_genome.tar.gz


title: V-LHX6-GOF-1


title: BALB_BMDM_CEBPB_KLA_1h_rep2


title: 77_NLW44_D_scRNA-seq

description:
No Vegf treatment
WA09 (H9) embryonic stem cells (WiCell) were maintained feeder-free in mTeSR1 (Stem Cell Technologies) and dissociated with Accutase (Stem Cell Technologies). Cells  were plated into wells of 24 well plates pre-coated with GelTrex in mTeSR1 supplemented with 10 µM Rho-kinase inhibitor Y27632 (StemGent).  The media was replaced with mTeSR1 + 1.5 % GelTrex at 16 hours, 12 µM CHIR99021 in Advanced RPMI + Glutamax (Life Technologies) at 60 hours, and RB (Advanced RPMI + Glutamax + B27 Supplement, from Life Technologies) at 96 hours, total volume 500 uL/well. RB was changed two days later and every two days thereafter. For experiments involving modulation of endothelial cells media was supplemented with VEGF165 (50 ng/ml). Organoids were harvested on day 21, dissociated and processed for single cell RNA sequencing.

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
Sequence aligned using Star
Next, using the tools embedded in Picard tools (picard-tools-1.115) and the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/), the fastq files were processed and the data matrix table containing the gene expression of the barcoded cells was generated. Individual cells were labeled with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers) in order to determine absolute transcript abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format

extract_protocol:
Organoids collected from a single well were dissected in ice-cold PBS and finely minced in a petri dish on ice using razor blades. The tissue were added to 1 ml of cold active protease solution (PBS, 10 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). The tissue was incubated in a 2 ml reaction tube for 15-20 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 20 seconds every 5 minutes. Single cell dissociation was confirmed with a microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.01%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.01%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 http://mccarrolllab.com/dropseq/). Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluorooctanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on the Illumina HiSeq2500 platform. Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.
R1 is the barcode and R2 is the mRNA sequence

value: No Vegf treatment


title: H2O_NT_1

value: male

value: conditional APCko


title: H2O_NT_3

value: 9 months


title: BALB_BMDM_5GRO_notx_rep1

value: bone marrow derived macropages (BMDM)


title: 76_NLW44_C_scRNA-seq

description:
Vegf treated
WA09 (H9) embryonic stem cells (WiCell) were maintained feeder-free in mTeSR1 (Stem Cell Technologies) and dissociated with Accutase (Stem Cell Technologies). Cells  were plated into wells of 24 well plates pre-coated with GelTrex in mTeSR1 supplemented with 10 µM Rho-kinase inhibitor Y27632 (StemGent).  The media was replaced with mTeSR1 + 1.5 % GelTrex at 16 hours, 12 µM CHIR99021 in Advanced RPMI + Glutamax (Life Technologies) at 60 hours, and RB (Advanced RPMI + Glutamax + B27 Supplement, from Life Technologies) at 96 hours, total volume 500 uL/well. RB was changed two days later and every two days thereafter. For experiments involving modulation of endothelial cells media was supplemented with VEGF165 (50 ng/ml). Organoids were harvested on day 21, dissociated and processed for single cell RNA sequencing.

value: Vegf treated


title: BALB_BMDM_5GRO_KLA_1h_rep1

description:
5'Gro-Seq
Processed data file:
tss_BALB_5GRO_KLA_1h.bed
Processed data file available in:
5GRO_processed_data.tar

value: 7 day cultured BMDMs

value: KLA 1h


title: 75_NLW44_B_scRNA-seq


title: BALB_BMDM_H3K27ac_KLA_1h_rep1

description:
formaldehyde-crosslinked ChIP-Seq
Processed data file:
regions_BALB_27ac_KLA_same.bed
Processed data file available in:
ChIP-seq_processed_data_files.tar

value: BALB/cJ

value: H3K27ac (Vendor:Active Motif, Cat#39135)


title: 74_NLW44_A_scRNA-seq


title: SPRET_BMDM_RNA_polyA_notx_6h_rep1

description:
RNA-Seq
Processed data file:
RNA_Seq_C57_SPRET_INFg_response_TPM.txt
Processed data file available in:
RNA-seq_processed_data.tar

data_processing:
Fastq files from sequencing experiments were mapped to the custom genome using default parameters for STAR and shifted back to reference coordinates. Read counts on exons were assessed with HOMER's analyzeRepeats with parameters rna, -condenseGenes and -tpm.
genome build: SPRETEIJ_genome.tar.gz

value: SPRET/EiJ

value: no treatment