title: THP-1 conditioned with LrS for 48hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 48hr Control Rep4

source_name: THP-1 with LrS for 48hrs Rep4


title: THP-1 conditioned with LA for 72hrs Replicate 3

status: Public on Apr 12 2024

type: RNA

city: Oshawa

first: Michael

middle: P

last: Jeffrey

state: Ontario

address: 2000 Simcoe St N

department: Faculty of Science

country: Canada

institute: Ontario Tech University

description: Biological Replicate 3 of 4

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50C for 18h on the Agilent whole human gene expression microarray (GE 4x44K; GPL10332).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with ImaGene® microarray analysis software.

data_processing: Global LOWESS normalization was conducted with ImaGene® microarray analysis software.

molecule: total RNA

organism: Homo sapiens

source_name: THP-1 72hr Control Rep3

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript IV (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

growth_protocol: The THP-1 human peripheral blood monocyte cell line (ATCC #TIB-202) was maintained in an undifferentiated state using RPMI-1640 medium supplemented with 0.05 mM β-mercaptoethanol, 10% calf serum and 0.05 mg/mL gentamicin and cultured in a humidified incubator at 37oC and 5% CO2

extract_protocol: Total RNA was extracted by using TRIzol Reagent (ThermoFisher Scientific, MA, USA) following manufacturer's protocol with PhaseLock tubes (5 Prime, MD). Total extracted RNA was then purified using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany). The purity and quality of RNA was determined using both the ND100 NanoDrop and an Agilent 2000 Bioanalyzer, respectively. Only samples with an RNA Integrity Number (RIN) greater than 9.0 were used for microarray analysis.

treatment_protocol: THP-1 cells were incubated for 24-, 48-, or 72-hrs with either the Lacticaseibacillus rhamnosus R0011 secretome (LrS) (20% v/v) or a matched L-lactic acid control (LA). For some experiments, THP-1 cells were challenged with LPS (125ng/mL) alone for 6 hours or after 72-hrs of conditioning with the LrS.

tag: cell line

value: THP-1 (ATCC #TIB-202)

tag: tissue

value: Peripheral Blood Monocyte

source_name: THP-1 with LA for 72hrs Rep3


title: THP-1 conditioned with LA for 24hrs Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 24hr Control Rep3

source_name: THP-1 with LA for 24hrs Rep3


title: THP-1 conditioned with LrS for 72hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LrS for 72hrs Rep2

source_name: THP-1 72hr Control Rep2


title: THP-1 conditioned with LrS for 48hrs Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 48hr Control Rep3

source_name: THP-1 with LrS for 48hrs Rep3


title: THP-1 conditioned with LA for 24hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LA for 24hrs Rep2

source_name: THP-1 24hr Control Rep2


title: THP-1 conditioned with LrS for 72hrs Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 with LrS for 72hrs Rep3


title: THP-1 conditioned with LrS for 48hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LrS for 48hrs Rep1

source_name: THP-1 48hr Control Rep1


title: liver, ACSS1K635Q, control diet, biol rep 2

type: SRA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using HiSAT2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

organism: Mus musculus

source_name: liver

extract_protocol:
Qiagen RNEasy Kit
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: Mice in the fasted group were food denied for 48 hours, but all mice were given free access to water.

value: liver

tag: Sex

value: female

tag: strain

tag: genotype

tag: treatment

value: control diet


title: liver, ACSS1K635Q, fasted, biol rep 1

value: fasted


title: liver, ACSS1K635Q, control diet, biol rep 1


title: liver, WT, control diet, biol rep 2

value: WT


title: THP-1 with LPS only Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LPS Rep1

source_name: THP-1 Control Rep1


title: THP-1 conditioned with LrS for 48hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LrS for 48hrs Rep2

source_name: THP-1 48hr Control Rep2


title: liver, ACSS1K635Q, fasted, biol rep 2


title: liver, WT, fasted, biol rep 2


title: THP-1 conditioned with LA for 48hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 48hr Control Rep4

source_name: THP-1 with LA for 48hrs Rep4


title: MEG3 (10nM) gapmeR siRNA 3

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
MEG3_3
PE100

data_processing:
Raw fastq files were processed using the nf-core RNA-Seq pipeline release 3.12.0 (https://github.com/nf-core/rnaseq/tree/3.12.0).
Assembly: hg38
Supplementary files format and content: bigWig files

source_name: HUVEC

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) (C-12203) were purchased from Promocell, Germany, and cultured in the recommended growth media (EGM2) according to the manufacturer’s instructions under 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using Monarch kit (New England BioLabs (NEB) #T2010). RNA concentration and purity were assessed using a NanoDrop2000 Spectrophotometer (ThermoFisher).
(1) Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; (2) mRNA molecules were fragmented into small pieces; (3) The fragmented mRNA was synthesized into first strand cDNA using random primers; (4) The second strand cDNA was synthesized with dUTP instead of dTTP; (5) The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; (6) Perform PCR amplification; (7) Library quality control; (8) Library circularization; (9) The library was amplified to make DNA nanoball (DNB); (10) Sequencing on DNBSEQ (DNBSEQ Technology) platform.
(1) DNBSEQ Eukaryotic Strand-specific mRNA library; (2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence).

treatment_protocol: HUVECs were seeded onto 12-well plate, for 24 h. Next day OPTIMEM medium was added before adding transfection complexes prepared by mixing lipofectamine iMaxTM (ThermoFisher) with LNA GapmeRs against MEG3 (10nM, Qiagen). Transfected cells were incubated (6 h), then complexes and optimum replaced with medium for further 48 h.

value: HUVEC

tag: cell type

value: Human umbilical vein endothelial cells

value: MEG3 GapmeR


title: THP-1 conditioned with LrS for 72hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LrS for 72hrs Rep1

source_name: THP-1 72hr Control Rep1


title: liver, WT, fasted, biol rep 1


title: THP-1 conditioned with LrS for 24hrs Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 24hr Control Rep3

source_name: THP-1 with LrS for 24hrs Rep3


title: MEG3 (10nM) gapmeR siRNA 2

description:
MEG3_2
PE100


title: MEG3 (10nM) gapmeR siRNA 1

description:
MEG3_1
PE100


title: scramble gapmeR control siRNA 3

description:
SCR3
PE100

value: scramble control siRNA


title: scramble gapmeR control siRNA 4

description:
SCR4
PE100


title: scramble gapmeR control siRNA 2

description:
SCR2
PE100


title: Scramble gapmeR control siRNA 1

description:
SCR1
PE100


title: THP-1 with LPS only Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 Control Rep4

source_name: THP-1 with LPS Rep4


title: THP-1 conditioned with LrS for 24hrs Replicate 1

description: Biological Replicate 1 of 4

source_name: THP-1 with LrS for 24hrs Rep1

source_name: THP-1 24hr Control Rep1


title: THP-1 conditioned with LA for 48hrs Replicate 3

description: Biological Replicate 3 of 4

source_name: THP-1 48hr Control Rep3

source_name: THP-1 with LA for 48hrs Rep3


title: Lung CD4-positive cell IL6KO SuHx 7d 2

city: Suita

first: Tadakatsu

last: Inagaki

state: Osaka

address: 6-1, Kishibesinnmachi

department: Vascular Physiology

country: Japan

institute: National Cerebral and Cardiovascular Center

description:
MACS
Lung CD4-positive cell SuHx day 7.csv

data_processing:
A minimum 25M reads per library with 75 bp paired-ends reads were generated per sample.
Quality control of the resulting sequence data was performed using CLC genomics workbench
Trimmed and filtered reads were aligned to rat genome Rn6 reference and mouse genome GRCm38
Assembly: Rn6 and GRCm38
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Cells and tissues were lysed in Trizol and RNA was extracted using PureLink RNA Mini Kit (Thermo Fisher Scientific,) and PureLink DNase (Thermo Fisher Scientific,) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: cell subset

tag: time

value: day 7

value: Sugen-Hypoxia


title: THP-1 conditioned with LrS for 24hrs Replicate 4

description: Biological Replicate 4 of 4

source_name: THP-1 24hr Control Rep4

source_name: THP-1 with LrS for 24hrs Rep4


title: THP-1 conditioned with LrS for 24hrs Replicate 2

description: Biological Replicate 2 of 4

source_name: THP-1 with LrS for 24hrs Rep2

source_name: THP-1 24hr Control Rep2


title: Lung CD4-positive cell WT SuHx 7d 2

value: Wild type


title: Total Lung Tissue IL6KO SuHx 7d 3

description: Total lung SuHx day 7.csv


title: Total Lung Tissue IL6KO SuHx 7d 2

description: Total lung SuHx day 7.csv


title: liver, WT, control diet, biol rep 1

source_name: liver


title: Total Lung Tissue WT SuHx 7d 1

description: Total lung SuHx day 7.csv


title: Total Lung Tissue IL6KO SuHx 56d 2

description: Total lung SuHx day 56.csv

value: day 56


title: Total Lung Tissue IL6KO SuHx 56d 3

description: Total lung SuHx day 56.csv


title: Total Lung Tissue WT SuHx 7d 3

description: Total lung SuHx day 7.csv


title: ZsGreen1-, Ldlr KO, 0 week WD [RBM043M]

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description:
10x Genomics cell multiplexing library
RBM043_sample1_barcodes.tsv.gz
RBM043_sample1_features.tsv.gz
RBM043_sample1_matrix.mtx.gz
RBM043_sample2_barcodes.tsv.gz
RBM043_sample2_features.tsv.gz
RBM043_sample2_matrix.mtx.gz
RBM043_sample3_barcodes.tsv.gz
RBM043_sample3_features.tsv.gz
RBM043_sample3_matrix.mtx.gz

library_source: other

data_processing:
Fastq files were processed by cellranger multi pipeline from Cell Ranger 6.1.2. A custom mouse genome was used that included ZsGreen1 sequence. Annotation from TotalSeq-A Mouse Universal Cocktail was used for ADT library quantification. Duplicate gene symbols were suffixed with numbers. Cell Ranger output files were provided for each demultiplexed sample.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Aorta

extract_protocol:
RNA was extracted using 10x Genomics Chromium Single Cell 3' v3 protocol.
Library was constructed using 10x Genomics Chromium Single Cell 3' v3 protocol.

treatment_protocol: Aortic tissue from ROSA26LSL-ZsGreen1/+Myh11-CreERT2 mice was digested at various time points of western diet feeding (0, 8, 16, 26 weeks) and subjected to CITE-seq single cell profiling

value: Aorta

value: Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)

tag: diet

value: Western diet

tag: lineage

value: non-SMC lineage

tag: library type

value: HTO

tag: antibodies/tags


title: Total Lung Tissue WT SuHx 7d 2

description: Total lung SuHx day 7.csv


title: Total Lung Tissue IL6KO SuHx 56d 1

description: Total lung SuHx day 56.csv


title: Total Lung Tissue WT SuHx 56d 2

description: Total lung SuHx day 56.csv


title: ZsGreen1-, Ldlr KO, 0 week WD [RBM043F]

description:
10x Genomics feature barcode library
RBM043_sample1_barcodes.tsv.gz
RBM043_sample1_features.tsv.gz
RBM043_sample1_matrix.mtx.gz
RBM043_sample2_barcodes.tsv.gz
RBM043_sample2_features.tsv.gz
RBM043_sample2_matrix.mtx.gz
RBM043_sample3_barcodes.tsv.gz
RBM043_sample3_features.tsv.gz
RBM043_sample3_matrix.mtx.gz

value: ADT

value: TotalSeq-A Mouse Universal Cocktail, V1.0


title: ZsGreen1-, Ldlr KO, 0 week WD [RBM043]

description:
10x Genomics 3' mRNA library
RBM043_sample1_barcodes.tsv.gz
RBM043_sample1_features.tsv.gz
RBM043_sample1_matrix.mtx.gz
RBM043_sample2_barcodes.tsv.gz
RBM043_sample2_features.tsv.gz
RBM043_sample2_matrix.mtx.gz
RBM043_sample3_barcodes.tsv.gz
RBM043_sample3_features.tsv.gz
RBM043_sample3_matrix.mtx.gz

molecule: polyA RNA

value: mRNA


title: Total Lung Tissue WT SuHx 56d 1

description: Total lung SuHx day 56.csv


title: ZsGreen1+, Ldlr KO, 0 week WD [RBM042F]

description:
10x Genomics feature barcode library
RBM042_sample1_barcodes.tsv.gz
RBM042_sample1_features.tsv.gz
RBM042_sample1_matrix.mtx.gz
RBM042_sample2_barcodes.tsv.gz
RBM042_sample2_features.tsv.gz
RBM042_sample2_matrix.mtx.gz
RBM042_sample3_barcodes.tsv.gz
RBM042_sample3_features.tsv.gz
RBM042_sample3_matrix.mtx.gz

value: SMC lineage


title: ZsGreen1-, Ldlr KO, 26 weeks WD [RBM033]

description:
10x Genomics 3' mRNA library
RBM033_sample1_barcodes.tsv.gz
RBM033_sample1_features.tsv.gz
RBM033_sample1_matrix.mtx.gz
RBM033_sample2_barcodes.tsv.gz
RBM033_sample2_features.tsv.gz
RBM033_sample2_matrix.mtx.gz
RBM033_sample3_barcodes.tsv.gz
RBM033_sample3_features.tsv.gz
RBM033_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 26 weeks WD [RBM033F]

description:
10x Genomics feature barcode library
RBM033_sample1_barcodes.tsv.gz
RBM033_sample1_features.tsv.gz
RBM033_sample1_matrix.mtx.gz
RBM033_sample2_barcodes.tsv.gz
RBM033_sample2_features.tsv.gz
RBM033_sample2_matrix.mtx.gz
RBM033_sample3_barcodes.tsv.gz
RBM033_sample3_features.tsv.gz
RBM033_sample3_matrix.mtx.gz


title: Lung CD4-positive cell IL6KO SuHx 7d 1


title: ZsGreen1+, Ldlr KO, 26 weeks WD [RBM032M]

description:
10x Genomics cell multiplexing library
RBM032_sample1_barcodes.tsv.gz
RBM032_sample1_features.tsv.gz
RBM032_sample1_matrix.mtx.gz
RBM032_sample2_barcodes.tsv.gz
RBM032_sample2_features.tsv.gz
RBM032_sample2_matrix.mtx.gz
RBM032_sample3_barcodes.tsv.gz
RBM032_sample3_features.tsv.gz
RBM032_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 26 weeks WD [RBM032F]

description:
10x Genomics feature barcode library
RBM032_sample1_barcodes.tsv.gz
RBM032_sample1_features.tsv.gz
RBM032_sample1_matrix.mtx.gz
RBM032_sample2_barcodes.tsv.gz
RBM032_sample2_features.tsv.gz
RBM032_sample2_matrix.mtx.gz
RBM032_sample3_barcodes.tsv.gz
RBM032_sample3_features.tsv.gz
RBM032_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 26 weeks WD [RBM032]

description:
10x Genomics 3' mRNA library
RBM032_sample1_barcodes.tsv.gz
RBM032_sample1_features.tsv.gz
RBM032_sample1_matrix.mtx.gz
RBM032_sample2_barcodes.tsv.gz
RBM032_sample2_features.tsv.gz
RBM032_sample2_matrix.mtx.gz
RBM032_sample3_barcodes.tsv.gz
RBM032_sample3_features.tsv.gz
RBM032_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 16 weeks WD [RBM025F]

description:
10x Genomics feature barcode library
RBM025_sample1_barcodes.tsv.gz
RBM025_sample1_features.tsv.gz
RBM025_sample1_matrix.mtx.gz
RBM025_sample2_barcodes.tsv.gz
RBM025_sample2_features.tsv.gz
RBM025_sample2_matrix.mtx.gz
RBM025_sample3_barcodes.tsv.gz
RBM025_sample3_features.tsv.gz
RBM025_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 26 weeks WD [RBM033M]

description:
10x Genomics cell multiplexing library
RBM033_sample1_barcodes.tsv.gz
RBM033_sample1_features.tsv.gz
RBM033_sample1_matrix.mtx.gz
RBM033_sample2_barcodes.tsv.gz
RBM033_sample2_features.tsv.gz
RBM033_sample2_matrix.mtx.gz
RBM033_sample3_barcodes.tsv.gz
RBM033_sample3_features.tsv.gz
RBM033_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 16 weeks WD [RBM025]

description:
10x Genomics 3' mRNA library
RBM025_sample1_barcodes.tsv.gz
RBM025_sample1_features.tsv.gz
RBM025_sample1_matrix.mtx.gz
RBM025_sample2_barcodes.tsv.gz
RBM025_sample2_features.tsv.gz
RBM025_sample2_matrix.mtx.gz
RBM025_sample3_barcodes.tsv.gz
RBM025_sample3_features.tsv.gz
RBM025_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 16 weeks WD [RBM025M]

description:
10x Genomics cell multiplexing library
RBM025_sample1_barcodes.tsv.gz
RBM025_sample1_features.tsv.gz
RBM025_sample1_matrix.mtx.gz
RBM025_sample2_barcodes.tsv.gz
RBM025_sample2_features.tsv.gz
RBM025_sample2_matrix.mtx.gz
RBM025_sample3_barcodes.tsv.gz
RBM025_sample3_features.tsv.gz
RBM025_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 16 weeks WD [RBM024M]

description:
10x Genomics cell multiplexing library
RBM024_sample1_barcodes.tsv.gz
RBM024_sample1_features.tsv.gz
RBM024_sample1_matrix.mtx.gz
RBM024_sample2_barcodes.tsv.gz
RBM024_sample2_features.tsv.gz
RBM024_sample2_matrix.mtx.gz
RBM024_sample3_barcodes.tsv.gz
RBM024_sample3_features.tsv.gz
RBM024_sample3_matrix.mtx.gz


title: Total Lung Tissue WT SuHx 56d 3

description: Total lung SuHx day 56.csv


title: ZsGreen1+, Ldlr KO, 16 weeks WD [RBM024]

description:
10x Genomics 3' mRNA library
RBM024_sample1_barcodes.tsv.gz
RBM024_sample1_features.tsv.gz
RBM024_sample1_matrix.mtx.gz
RBM024_sample2_barcodes.tsv.gz
RBM024_sample2_features.tsv.gz
RBM024_sample2_matrix.mtx.gz
RBM024_sample3_barcodes.tsv.gz
RBM024_sample3_features.tsv.gz
RBM024_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 8 weeks WD [RBM023M]

description:
10x Genomics cell multiplexing library
RBM023_sample1_barcodes.tsv.gz
RBM023_sample1_features.tsv.gz
RBM023_sample1_matrix.mtx.gz
RBM023_sample2_barcodes.tsv.gz
RBM023_sample2_features.tsv.gz
RBM023_sample2_matrix.mtx.gz
RBM023_sample3_barcodes.tsv.gz
RBM023_sample3_features.tsv.gz
RBM023_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 8 weeks WD [RBM023]

description:
10x Genomics 3' mRNA library
RBM023_sample1_barcodes.tsv.gz
RBM023_sample1_features.tsv.gz
RBM023_sample1_matrix.mtx.gz
RBM023_sample2_barcodes.tsv.gz
RBM023_sample2_features.tsv.gz
RBM023_sample2_matrix.mtx.gz
RBM023_sample3_barcodes.tsv.gz
RBM023_sample3_features.tsv.gz
RBM023_sample3_matrix.mtx.gz


title: ZsGreen1-, Ldlr KO, 8 weeks WD [RBM023F]

description:
10x Genomics feature barcode library
RBM023_sample1_barcodes.tsv.gz
RBM023_sample1_features.tsv.gz
RBM023_sample1_matrix.mtx.gz
RBM023_sample2_barcodes.tsv.gz
RBM023_sample2_features.tsv.gz
RBM023_sample2_matrix.mtx.gz
RBM023_sample3_barcodes.tsv.gz
RBM023_sample3_features.tsv.gz
RBM023_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 8 weeks WD [RBM022F]

description:
10x Genomics feature barcode library
RBM022_sample1_barcodes.tsv.gz
RBM022_sample1_features.tsv.gz
RBM022_sample1_matrix.mtx.gz
RBM022_sample2_barcodes.tsv.gz
RBM022_sample2_features.tsv.gz
RBM022_sample2_matrix.mtx.gz
RBM022_sample3_barcodes.tsv.gz
RBM022_sample3_features.tsv.gz
RBM022_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 0 week WD [RBM042]

description:
10x Genomics 3' mRNA library
RBM042_sample1_barcodes.tsv.gz
RBM042_sample1_features.tsv.gz
RBM042_sample1_matrix.mtx.gz
RBM042_sample2_barcodes.tsv.gz
RBM042_sample2_features.tsv.gz
RBM042_sample2_matrix.mtx.gz
RBM042_sample3_barcodes.tsv.gz
RBM042_sample3_features.tsv.gz
RBM042_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 8 weeks WD [RBM022M]

description:
10x Genomics cell multiplexing library
RBM022_sample1_barcodes.tsv.gz
RBM022_sample1_features.tsv.gz
RBM022_sample1_matrix.mtx.gz
RBM022_sample2_barcodes.tsv.gz
RBM022_sample2_features.tsv.gz
RBM022_sample2_matrix.mtx.gz
RBM022_sample3_barcodes.tsv.gz
RBM022_sample3_features.tsv.gz
RBM022_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 0 week WD [RBM042M]

description:
10x Genomics cell multiplexing library
RBM042_sample1_barcodes.tsv.gz
RBM042_sample1_features.tsv.gz
RBM042_sample1_matrix.mtx.gz
RBM042_sample2_barcodes.tsv.gz
RBM042_sample2_features.tsv.gz
RBM042_sample2_matrix.mtx.gz
RBM042_sample3_barcodes.tsv.gz
RBM042_sample3_features.tsv.gz
RBM042_sample3_matrix.mtx.gz


title: ZsGreen1+, Ldlr KO, 8 weeks WD [RBM022]

description:
10x Genomics 3' mRNA library
RBM022_sample1_barcodes.tsv.gz
RBM022_sample1_features.tsv.gz
RBM022_sample1_matrix.mtx.gz
RBM022_sample2_barcodes.tsv.gz
RBM022_sample2_features.tsv.gz
RBM022_sample2_matrix.mtx.gz
RBM022_sample3_barcodes.tsv.gz
RBM022_sample3_features.tsv.gz
RBM022_sample3_matrix.mtx.gz


title: Subject_3_pre_NeoVax_region_3

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: We obtained multiple regions from resected brain tumor of Subject 3 prior to NeoVax administration and one biopsy of the brain tumor after NeoVax administration

hyb_protocol: 30 ng Dnase-treated RNA was used as input for CAR-T Characterization gene expression panel from NanoString Technologies. Hybridization with reporter CodeSet and capture ProbeSet was performed according to manufacturer's protocl for 16 hours at 65 degrees C. Hybridized samples were then processed on the nCounter MAX/FLEX prpe station using high sensitivity setting.

scan_protocol: Cartridges were scanned on nCounter digitial analyzer at Max setting (555 fields of view)

data_processing: Digital counts were normalized using a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane. All normalization techniques were applied in nSolver software according to manufacturer's protocol.

source_name: Glioblastoma resected tumor pre-NeoVax

extract_protocol: Tumor RNA was extracted using the High Pure isolation kit (Roche Life Science)

value: primary human glioblastoma

tag: brain tumor region

tag: neovax status

tag: age (years)

value: female

tag: overall survival (days)


title: Subject_3_post_NeoVax

source_name: Glioblastoma resected tumor post-NeoVax


title: Subject_3_pre_NeoVax_region_2


title: PtrBLH

city: Syracuse

first: Dan

last: Wang

address: 107 College Place

department: Biology

institute: Syracuse University

library_source: genomic

data_processing:
The raw reads were trimmed by Trimmomatic , and reads which have MAPQ<30 and multiple duplicates  were removed by SAMtools
ChIP-Seq reads were mapped to the Populus tremula × alba genome (https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4) by Bowtie2 with default parameters
Peaks were called by MACS V2.1.0 with the significant cutt-off q-value <=0.01
BigWig files were generated by Chipseeker R package. narrowPeak files were generated by MACS v2.1.0 with default setting.
Assembly: Populus tremula × alba genome (https://urgi.versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4)
Supplementary files format and content: BigWig and narrowPeak (except for Input)

molecule: genomic DNA

organism: Populus tremula x Populus alba

source_name: Leaf

extract_protocol:
leaf tissue was harvested and immediately cross-linked with 1 % formaldehyde under vacuum for 15 minutes at 25 °C. The cross-linking was stopped by adding glycine to the final concentration of 0.125 M for 5 minutes under vacuum. The cross-linked samples were washed three times with double distilled water. The ChIP assay based on GFP Monoclonal Antibody (Invitrogen, USA) was performed as described previously (Saleh et al., 2008; Li et al., 2014). Chromatin samples without GFP antibody immunoprecipitation were used as the control.
The library was prepared by NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, USA).

value: Leaf

tag: chip antibody


title: ZsGreen1+, Ldlr KO, 16 weeks WD [RBM024F]

description:
10x Genomics feature barcode library
RBM024_sample1_barcodes.tsv.gz
RBM024_sample1_features.tsv.gz
RBM024_sample1_matrix.mtx.gz
RBM024_sample2_barcodes.tsv.gz
RBM024_sample2_features.tsv.gz
RBM024_sample2_matrix.mtx.gz
RBM024_sample3_barcodes.tsv.gz
RBM024_sample3_features.tsv.gz
RBM024_sample3_matrix.mtx.gz

tag: tissue


title: PtrC2H2ZF2

value: GFP Monoclonal Antibody (Invitrogen, USA)


title: PtrARF5a


title: PtrC2H2ZF1


title: Subject_3_pre_NeoVax_region_1

tag: Sex


title: D23580 cotrimoxazole replicate 2 [Barseq9]

city: Palo Alto

first: Benjamin

state: CA

address: 299 Campus Drive

institute: Stanford

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq9_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq9_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq9_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq9_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B).

extract_protocol:
DNA was extracted using a Qiagen gDNA kit using standard procedures.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Each library was grown in stresses (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B) overnight for 16 hours.

value: Bacterial Tn library

value: 20 ug/mL cotrimoxazole


title: D23580 rifampicin replicate 2 [Barseq9]

value: 4 ug/mL rifampicin


title: D23580 polymyxin B replicate 2 [Barseq9]

value: 2.5 ug/mL polymyxin B


title: Input


title: D23580 gentamycin replicate 2 [Barseq9]

value: 2.5 ug/mL gentamycin


title: D23580 time 0 replicate 2 [Barseq9]

description: time0 is used as reference for other samples


title: PtrCORONA


title: PtrNAC127


title: 4/74 rifampicin replicate 2 [Barseq9]

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

value: 2 ug/mL rifampicin


title: D23580 LB replicate 2 [Barseq9]

value: LB


title: D23580 rifampicin replicate 1 [Barseq9]


title: D23580 LB replicate 1 [Barseq9]


title: 4/74 gentamycin replicate 2 [Barseq9]


title: D23580 cotrimoxazole replicate 1 [Barseq9]


title: D23580 time 0 replicate 1 [Barseq9]


title: 4/74 cotrimoxazole replicate 2 [Barseq9]

value: 0.25 ug/mL cotrimoxazole


title: D23580 gentamycin replicate 1 [Barseq9]


title: 4/74 LB replicate 2 [Barseq9]


title: D23580 time 0 replicate 3 [Barseq12]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM2702v1 for D23580.
Supplementary files format and content: Barseq12_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq12_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then used to infect THP-1 macrophages at an MOI of 10. THP-1 cells were grown in RPMI+10% FBS+2 mM glutamax.

extract_protocol:
At the end of the infection, THP-1 cells were lysed with 2% saponin for 30 minutes, and then DNA was isolated using the epicentre masterpure DNA extraction kit.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: THP-1 macrophages were infected with Salmonella for 1 hour (MOI~10), then treated with high gentamycin (100 ug/mL) for 1 hour, then the infection was allowed to proceed for 16 hours in low gentamycin (10 ug/mL).


title: 4/74 polymyxin B replicate 2 [Barseq9]


title: D23580 macrophage rep 1 [Barseq12]


title: 4/74 time 0 replicate 2 [Barseq9]


title: D23580 macrophage rep 3 [Barseq12]


title: D23580 time 0 replicate 1 [Barseq12]


title: D23580 time 0 replicate 2 [Barseq12]


title: D23580 macrophage rep 2 [Barseq12]


title: D23580 protamine [Barseq6]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq6_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq6_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq6_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq6_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either anaerobic LB, GMM, zinc overload, Nmedia, protamine- the second set of samples).

treatment_protocol: Each library was grown in stresses (anaerobic LB, GMM, zinc overload, Nmedia, protamine- the second set of samples) overnight for 16 hours.

value: 6.125 ug/mL protamine


title: 4/74 cotrimoxazole replicate 1 [Barseq9]


title: D23580 zinc  [Barseq6]

value: 500 uM zinc


title: 4/74 gentamycin replicate 1 [Barseq9]


title: 4/74 rifampicin replicate 1 [Barseq9]


title: D23580 GMM  [Barseq6]

value: GMM


title: D23580 time0, rep 2  [Barseq6]


title: D23580 time 0  [Barseq6]


title: D23580 zinc [Barseq5]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq5_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq5_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq5_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq5_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either anaerobic LB, GMM, zinc, Nmedia, protamine).

treatment_protocol: Each library was grown in stresses (anaerobic LB, GMM, zinc, Nmedia, protamine) overnight for 16 hours.


title: D23580 protamine [Barseq5]


title: D23580 polymyxin B replicate 1 [Barseq9]


title: 4/74 time 0 replicate 1 [Barseq9]


title: D23580 GMM [Barseq5]


title: 4/74 macrophage rep 3 [Barseq12]


title: D23580 Nmedia [Barseq5]

value: Nmedia


title: D23580 anaerobic LB [Barseq5]


title: D23580 time0 [Barseq5]


title: mv D23580 sodium hypochlorite replicate 2 [Barseq4]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq4_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq4_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq4_para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq4_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite).

treatment_protocol: Each library was grown in stresses (either InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite) overnight for 16 hours.

value: 12.5 ug/mL sodium hypochlorite


title: 4/74 macrophage rep 1 [Barseq12]


title: mv D23580 H2O2 replicate 2 [Barseq4]


title: 4/74 macrophage rep 2 [Barseq12]


title: mv D23580 InSPI2 replicate 2 [Barseq4]


title: 4/74 time 0 replicate 3 [Barseq12]


title: 4/74 time 0 replicate 2 [Barseq12]


title: D23580 Nmedia  [Barseq6]


title: mv D23580 sodium hypochlorite replicate 1 [Barseq4]


title: mv D23580 time 0 replicate 2 [Barseq4]


title: 4/74 LB replicate 1 [Barseq9]


title: mv D23580 Nitric oxide replicate 2 [Barseq4]

value: 1 mM spermine NONOate


title: D23580 anaerobic LB  [Barseq6]

value: anaerobic LB


title: mv D23580 H2O2 replicate 1 [Barseq4]


title: 4/74 time 0 replicate 1 [Barseq12]


title: mv D23580 time 0 replicate 1 [Barseq4]


title: mv D23580 Nitric oxide replicate 1 [Barseq4]


title: 4/74 protamine [Barseq6]

value: 3.125 ug/mL protamine


title: mv D23580 InSPI2 replicate 1 [Barseq4]


title: 4/74 Nmedia [Barseq6]


title: D23580 LB, rep 2 [Barseq3]

description:
IT028
barseq3_D23580_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150
Supplementary files format and content: Barseq3_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq3_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq3_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq3_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, ceftriaxone, ciprofloxacin, azithromycin).

treatment_protocol: Each library was grown in stresses (bLB, ceftriaxone, ciprofloxacin, azithromycin) overnight for 16 hours.


title: D23580 cipro rep2 [Barseq3]

description:
IT036
barseq3_D23580_processed.csv

value: 0.0125 ug/mL ciprofloxacin


title: D23580 cef, rep 2 [Barseq3]

description:
IT032
barseq3_D23580_processed.csv

value: Bacterial Tn library

value: 0.03 ug/mL ceftriaxone


title: 4/74 zinc  [Barseq6]


title: D23580 LB time 0, rep 2 [Barseq3]

description:
time0 is used as reference for other samples
barseq3_D23580_processed.csv


title: D23580 azithro rep 1 [Barseq3]

description:
IT020
barseq3_D23580_processed.csv

value: 5 ug/mL azithromycin


title: 4/74 time0, rep 2  [Barseq6]


title: D23580 cef, rep 1 [Barseq3]

description:
IT012
barseq3_D23580_processed.csv


title: 4/74 GMM  [Barseq6]


title: D23580 LB, rep 1 [Barseq3]

description:
IT008
barseq3_D23580_processed.csv


title: 4/74 anaerobic LB  [Barseq6]


title: D23580 naCl replicate 2

description:
IT036
barseq2_D23580_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq2_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq2_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq2_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq2_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either bile stress, iron limitation, osmotic pressure, heat shock).

treatment_protocol: Each library was grown in stresses (bile stress, iron limitation, osmotic pressure, heat shock) overnight for 16 hours.

value: 0.4 M NaCl


title: D23580 LB time 0, rep 1 [Barseq3]


title: 4/74 time 0  [Barseq6]


title: D23580 42 degrees replicate 2

description:
IT040
barseq2_D23580_processed.csv

value: 42 degrees


title: D23580 bile replicate 2

description:
IT028
barseq2_D23580_processed.csv

value: 4% bile


title: D23580 iron replicate 2

description:
IT032
barseq2_D23580_processed.csv

value: 0.2 mM 2-2' bipyridyl


title: D23580 azithro rep 2 [Barseq3]

description:
IT040
barseq3_D23580_processed.csv


title: D23580 time 0 replicate 2

description:
time0 is used as reference for other samples
barseq2_D23580_processed.csv


title: 474 Nmedia [Barseq5]


title: 474 protamine [Barseq5]


title: D23580 naCl replicate 1

description:
IT016
barseq2_D23580_processed.csv


title: D23580 42 degrees replicate 1

description:
IT020
barseq2_D23580_processed.csv


title: 474 zinc  [Barseq5]


title: D23580 bile replicate 1

description:
IT008
barseq2_D23580_processed.csv


title: D23580 iron replicate 1

description:
IT012
barseq2_D23580_processed.csv


title: 474 GMM [Barseq5]


title: 4/74 polymyxin B replicate 1 [Barseq9]

value: 2.5 ug/mL polymyxin B


title: D23580 time 0 replicate 1


title: D23580 cipro rep1 [Barseq3]

description:
IT016
barseq3_D23580_processed.csv


title: D23580 M9 glucose rep 2

description:
IT040
Barseq1_D23580_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150
Supplementary files format and content: Barseq1_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0
Supplementary files format and content: Barseq1_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0
Supplementary files format and content: Barseq1_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0
Supplementary files format and content: Barseq1_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either NonSPI2, InSPI2, inSPI2-Mg, or M9 glucose)

extract_protocol:
DNA was extracted using a Qiagen gDNA kit using standard procedures
purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Each library was grown in a different minimal media (NonSPI2, InSPI2, InSPI2-MG, M9 glucose) overnight for 16 hours

value: M9 glu


title: D23580 InSPI2, rep 2

description:
IT032
Barseq1_D23580_processed.csv


title: D23580 inSPI2Mg rep2

description:
IT036
Barseq1_D23580_processed.csv


title: 474 anaerobic LB [Barseq5]

value: LB


title: 4/74 time0 [Barseq5]


title: D23580 M9 glucose rep 1

description:
IT020
Barseq1_D23580_processed.csv


title: mv 4/74 sodium hypochlorite replicate 2 [Barseq4]


title: D23580 inSPI2Mg rep1

description:
IT016
Barseq1_D23580_processed.csv


title: D23580 NonSPI2, rep 1

description:
IT008
Barseq1_D23580_processed.csv


title: D23580 time 0, rep 1

description:
time0 is used as reference for other samples
Barseq1_D23580_processed.csv


title: mv 4/74 H2O2 replicate 2 [Barseq4]


title: mv 4/74 time 0 replicate 2 [Barseq4]


title: Ty2 cotrimoxazole replicate 2 [Barseq9]

organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

value: 0.06 ug/mL cotrimoxazole


title: Ty2 rifampicin replicate 2 [Barseq9]

value: 4 ug/mL rifampicin


title: mv 4/74 InSPI2 replicate 2 [Barseq4]


title: Ty2 polymyxin B replicate 2 [Barseq9]

value: 1 ug/mL polymyxin B


title: Ty2 LB replicate 2 [Barseq9]


title: Ty2 gentamycin replicate 2 [Barseq9]

value: 1 ug/mL gentamycin


title: Ty2 polymyxin B replicate 1 [Barseq9]


title: mv 4/74 sodium hypochlorite replicate 1 [Barseq4]

value: 12.5 ug/mL sodium hypochlorite


title: Ty2 rifampicin replicate 1 [Barseq9]


title: Ty2 cotrimoxazole replicate 1 [Barseq9]


title: D23580 NonSPI2, rep 2

description:
IT028
Barseq1_D23580_processed.csv


title: mv 4/74 Nitric oxide replicate 1 [Barseq4]

value: 1 mM spermine NONOate


title: Total Lung Tissue IL6KO SuHx 7d 1

description: Total lung SuHx day 7.csv

value: Lung

value: day 7

value: Sugen-Hypoxia


title: Ty2 time 0 replicate 2 [Barseq9]

value: Bacterial Tn library


title: Ty2 gentamycin replicate 1 [Barseq9]


title: Ty2 LB replicate 1 [Barseq9]


title: Ty2 THP-1 infection replicate 3 [Barseq13]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness. Data was analyzed using DEseq2 analysis, as has previously been done with macrophage Tn library papers and Salmonella.
Assembly: ASM754v1 for Ty2, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq13_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq13_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then used to infect THP-1 human macrophages at an MOI of 100. Infections were allowed to proceed for 1 hour, then cells were treated with media+high gentamycin (100 ug/mL) for 1 hour to kill extracellular bacteria. Media was then changed to low gentamycin (10 ug/mL) for the duration of the infection, which proceeded for 18 hours.

extract_protocol:
DNA was extracted using the epicentre masterpure dna extraction kit, which was applied to macrophages lysed with 2% saponin after the duration of the 18 hour infection.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Macrophages were infected with Ty2 and para9150 libraries for 18 hours after changing the media to high gentamycin (10 ug/mL).


title: Ty2 time 0 replicate 1 [Barseq9]


title: mv 4/74 InSPI2 replicate 1 [Barseq4]


title: mv 4/74 Nitric oxide replicate 2 [Barseq4]


title: D23580 InSPI2, rep 1

description:
IT012
Barseq1_D23580_processed.csv


title: Ty2 THP-1 infection replicate 1 [Barseq13]


title: Ty2 THP-1 infection replicate 2 [Barseq13]


title: mv 4/74 time 0 replicate 1 [Barseq4]


title: Ty2 time 0 replicate 1 [Barseq13]


title: Ty2 time 0 replicate 2 [Barseq13]


title: Lung CD4-positive cell WT SuHx 7d 1

description:
MACS
Lung CD4-positive cell SuHx day 7.csv

value: Wild type


title: Ty2 time0, rep 2  [Barseq6]


title: Ty2 protamine [Barseq6]

value: 2.3 ug/mL protamine


title: Ty2 Nmedia [Barseq6]

value: Nmedia


title: 4/74 cipro rep 2 [Barseq3]

description:
IT033
barseq3_ST474_processed.csv

value: 0.0125 ug/mL ciprofloxacin


title: Ty2 zinc  [Barseq6]

value: 500 uM zinc


title: 4/74 azithro rep 2 [Barseq3]

description:
IT037
barseq3_ST474_processed.csv

value: 5 ug/mL azithromycin


title: Ty2 GMM  [Barseq6]

value: GMM


title: 4/74, cef rep 2 [Barseq3]

description:
IT029
barseq3_ST474_processed.csv

value: 0.03 ug/mL ceftriaxone


title: 4/74 LB, rep 2 [Barseq3]

description:
IT025
barseq3_ST474_processed.csv

value: LB


title: Ty2 protamine [Barseq5]


title: Ty2 time 0  [Barseq6]


title: 4/74 LB time 0, rep 2 [Barseq3]

description:
time0 is used as reference for other samples
barseq3_ST474_processed.csv


title: Ty2 Nmedia [Barseq5]


title: Ty2 anaerobic LB [Barseq5]


title: Ty2 time0 [Barseq5]


title: Ty2 zinc [Barseq5]


title: 4/74 cipro rep 1 [Barseq3]

description:
IT013
barseq3_ST474_processed.csv


title: Ty2 GMM [Barseq5]


title: 4/74 azithro rep 1 [Barseq3]

description:
IT017
barseq3_ST474_processed.csv


title: mv Ty2 sodium hypochlorite replicate 2 [Barseq4]


title: 4/74, cef rep 1 [Barseq3]

description:
IT009
barseq3_ST474_processed.csv


title: mv Ty2 Nitric oxide replicate 2 [Barseq4]

value: 250 uM spermine NONOate


title: mv Ty2 H2O2 replicate 2 [Barseq4]


title: 4/74 LB, rep 1 [Barseq3]

description:
IT005
barseq3_ST474_processed.csv


title: mv Ty2 InSPI2 replicate 2 [Barseq4]


title: 4/74 LB time 0, rep 1 [Barseq3]


title: mv Ty2 time 0 replicate 2 [Barseq4]


title: mv Ty2 Nitric oxide replicate 1 [Barseq4]


title: Ty2 anaerobic LB  [Barseq6]

value: anaerobic LB


title: mv Ty2 sodium hypochlorite replicate 1 [Barseq4]

value: 12.5 ug/mL sodium hypochlorite


title: 4/74 42 degrees replicate 2

description:
IT037
barseq2_ST474_processed.csv

value: 42 degrees


title: mv Ty2 InSPI2 replicate 1 [Barseq4]


title: mv Ty2 H2O2 replicate 1 [Barseq4]


title: 4/74 iron replicate 2

description:
IT029
barseq2_ST474_processed.csv

value: 0.2 mM 2-2' bipyridyl


title: 4/74 naCl replicate 2

description:
IT033
barseq2_ST474_processed.csv

value: 0.4 M NaCl


title: mv Ty2 time 0 replicate 1 [Barseq4]


title: Ty2 azithro rep 2 [Barseq3]

description:
IT038
barseq3_Ty2_processed.csv

value: 2.5 ug/mL azithromycin


title: 4/74 bile replicate 2

description:
IT025
barseq2_ST474_processed.csv

value: Bacterial Tn library

value: 4% bile


title: Ty2 cef rep 1 [Barseq3]

description:
IT030
barseq3_Ty2_processed.csv


title: Ty2 cef rep 2 [Barseq3]

description:
IT041
barseq3_Ty2_processed.csv


title: Ty2 LB, rep 2 [Barseq3]

description:
IT026
barseq3_Ty2_processed.csv


title: Ty2 cipro rep 2 [Barseq3]

description:
IT034
barseq3_Ty2_processed.csv

value: 0.125 ug/mL ciprofloxacin


title: Ty2 cipro rep 1 [Barseq3]

description:
IT014
barseq3_Ty2_processed.csv


title: Ty2 azithro rep 1 [Barseq3]

description:
IT018
barseq3_Ty2_processed.csv


title: Ty2 LB time 0, rep 2 [Barseq3]

description:
time0 is used as reference for other samples
barseq3_Ty2_processed.csv


title: Ty2 LB, rep 1 [Barseq3]

description:
IT006
barseq3_Ty2_processed.csv


title: 4/74 bile replicate 1

description:
IT005
barseq2_ST474_processed.csv


title: 4/74 naCl replicate 1

description:
IT013
barseq2_ST474_processed.csv


title: 4/74 iron replicate 1

description:
IT009
barseq2_ST474_processed.csv


title: Ty2 LB time 0, rep 1 [Barseq3]


title: 4/74 M9glucose rep 2

description:
IT037
Barseq1_ST474_processed.csv

value: M9 glu


title: Ty2 naCl replicate 1

description:
IT014
barseq2_Ty2_processed.csv


title: Ty2 42 degrees replicate 1

description:
IT018
barseq2_Ty2_processed.csv


title: Ty2 naCl replicate 2

description:
IT034
barseq2_Ty2_processed.csv


title: Ty2 42 degrees replicate 2

description:
IT038
barseq2_Ty2_processed.csv


title: 4/74 time 0 replicate 1

description:
time0 is used as reference for other samples
barseq2_ST474_processed.csv


title: Ty2 time 0 replicate 2

description:
time0 is used as reference for other samples
barseq2_Ty2_processed.csv


title: Ty2 bile replicate 2

description:
IT026
barseq2_Ty2_processed.csv


title: Ty2 InSPI2 rep 2

description:
IT030
Barseq1_Ty2_processed.csv


title: Ty2 time 0 replicate 1


title: Ty2 inSPI2Mg rep 2

description:
IT034
Barseq1_Ty2_processed.csv


title: 4/74 inSPI2Mg rep 2

description:
IT033
Barseq1_ST474_processed.csv


title: 4/74 time 0 replicate 2


title: 4/74, InSPI2 rep 2

description:
IT029
Barseq1_ST474_processed.csv


title: Ty2 NonSPI2, rep 2

description:
IT026
Barseq1_Ty2_processed.csv


title: Ty2 bile replicate 1

description:
IT006
barseq2_Ty2_processed.csv


title: Ty2 LB time 0, rep 2

description:
time0 is used as reference for other samples
Barseq1_Ty2_processed.csv


title: 4/74 M9glucose rep 1

description:
IT017
Barseq1_ST474_processed.csv


title: mv 4/74 H2O2 replicate 1 [Barseq4]


title: Ty2 M9 glucose rep 1

description:
IT018
Barseq1_Ty2_processed.csv


title: 4/74 42 degrees replicate 1

description:
IT017
barseq2_ST474_processed.csv


title: Ty2 inSPI2Mg rep 1

description:
IT014
Barseq1_Ty2_processed.csv


title: 4/74 NonSPI2, rep 2

description:
IT025
Barseq1_ST474_processed.csv


title: Ty2 iron replicate 2

description:
IT030
barseq2_Ty2_processed.csv


title: Ty2 iron replicate 1

description:
IT010
barseq2_Ty2_processed.csv


title: 4/74 inSPI2Mg rep 1

description:
IT013
Barseq1_ST474_processed.csv


title: Ty2 M9 glucose rep 2

description:
IT038
Barseq1_Ty2_processed.csv


title: Ty2 InSPI2 rep 1

description:
IT010
Barseq1_Ty2_processed.csv


title: 4/74, InSPI2 rep 1

description:
IT009
Barseq1_ST474_processed.csv


title: Ty2 time 0, rep 1


title: Cytotrophoblast infected, biol rep 1

city: Pittsburgh

first: Rafaela

middle: Jose

last: da Silva

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittburgh

data_processing:
CLC Genomics Workbench v 23.0
Assembly: Read libraries were mapped to the human (hg38) transcriptomes using CLC Genomics Workbench.
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism:
Toxoplasma gondii
Homo sapiens

source_name: Trophoblast cells

growth_protocol: Trophoblast stem cells were seeded at a ratio of 1.5 x 10^5 in 6-well plates and induced to form syncytiotrophoblast cells using a differentiation medium. After 5 days of differentiation, cells were infected or mock-infected with T. gondii RH: YFP (5 parasites/cell). For comparison, cytotrophoblast cells were seeded in a 6-well plate and infected or mock-infected with T. gondii at the same MOI used for syncytiotrophoblast cells.

extract_protocol:
Qiagen Rneasy
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Trophoblast cells

tag: cell line

value: Trophoblast stem cell (clone 27)

value: Cytotrophoblast

value: Trophoblast stem cell media


title: Syncytiotrophoblast infected, biol rep 3

value: Syncytiotrophoblast


title: Cytotrophoblast infected, biol rep 3


title: Ty2 NonSPI2, rep 1

description:
IT006
Barseq1_Ty2_processed.csv

tag: genotype


title: Cytotrophoblast infected, biol rep 2

tag: treatment


title: 4/74 time 0, rep 1

description:
time0 is used as reference for other samples
Barseq1_ST474_processed.csv


title: 4/74 NonSPI2, rep 1

description:
IT005
Barseq1_ST474_processed.csv


title: Syncytiotrophoblast infected, biol rep 1

tag: cell type


title: HUVECs, PPCN-S.QK, 72h, rep 1

city: Chicago

first: Bin

last: Jiang

state: IL

address: 676 N St Clair St, Suite 650

institute: Northwestern University

data_processing:
Raw reads were trimmed with trim_galore version 0.4.4 (parameter stringency 5)
Trimmed reads were aligned with STAR version 2.7.5.
Aligned reads were counted with htseq-count version 0.9.1.
Assembly: hg38
Supplementary files format and content: gene counts

source_name: HUVEC

extract_protocol:
Extraction of RNA was carried out utilizing the Aurum™ Total RNA Mini Kit (Bio-rad), following the manufacturer's protocol. The quality of the extracted RNA was assessed using the Agilent Bioanalyzer 2100, with acceptance criteria for RNA integrity numbers (RIN) set at > 7. Quantification was performed using Qubit. To construct RNA sequencing libraries, Illumina TruSeq mRNA Sample Preparation Kits were employed, adhering to the manufacturer's instructions. The procedure involved the capture of polyadenylated mRNAs from total RNA through oligo-dT selection. Subsequently, cDNA synthesis occurred through reverse transcription, and each sample was ligated to Illumina sequencing adapters featuring unique barcode sequences. Following this, barcoded samples underwent PCR amplification, and the resulting cDNA libraries were quantified using qPCR. To achieve a comprehensive overview, equimolar concentrations of each cDNA library were pooled and sequenced on the Illumina HiSeq 4000. Subsequently, the quality of reads in FASTQ format was evaluated using FastQC. Trimming of reads, specifically removing Illumina adapters from the 3’ ends, was executed using cutadapt. Trimmed reads were aligned to the human genome (hg38) using STAR. Read counts per gene were computed utilizing htseq-count alongside a gene annotation file for hg38 obtained from Ensembl. Normalization and differential expression analyses were conducted using DESeq2 1.42.0, employing the Wald test. The criterion for identifying significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05, employing the Benjamini-Hochberg method. Genes were annotated with biomaRt 2.58.0 using GRCh38.p14 human genome. Gene set enrichment analysis was done using clusterProfiler 4.10.0 with gene sets c2.all.v2023.2.Hs.symbols, h.all.v2023.2.Hs.symbols, and c5.all.v2023.2.Hs.symbols.
To construct RNA sequencing libraries, Illumina TruSeq mRNA Sample Preparation Kits were employed, adhering to the manufacturer's instructions.

value: HUVEC

value: Endothelial cells

value: WT


title: HUVECs, PPCN-S.QK, 72h, rep 3


title: HUVECs, PPCN-S.A5G81, 72h, rep 3


title: HUVECs, PPCN-S.QK, 72h, rep 2


title: Hypsibius 1mg/mL Bleomycin biol rep 3

city: Chapel Hill

first: Courtney

middle: M

last: Clark-Hachtel

state: NC

address: 120 South Rd

institute: UNC Chapel Hill

data_processing:
Reads were adapter trimmed then mapped to the most recent genome for H. exemplaris (v3.1.5) using BBduk and BBmap (ver 39.01), and counts were assigned with featureCounts (ver 2.0.6) using the annotation file associated with this genome
Reads were aggregated at the level of genes and only genes with more than one count in at least two samples were kept for differential expression analysis.
Transcript abundance, fold changes, and FDR values were determined using EdgeR
Assembly: nHd_3.1.5
Supplementary files format and content: tab-deliminated text file including raw counts for each samples
Supplementary files format and content: tab-delimiated text files including edgeR output (logFC, CPM, FDR) for 0 mg/mL, 10 µg/mL, 100 µg/mL, and 1 mg/mL Bleomycin

organism: Hypsibius exemplaris

source_name: whole body

extract_protocol:
RNA was isolated immediately from each replicate using the PicoPure RNA isolation kit (Applied Biosystems) following slightly modified manufacturer instructions.
Libraries were constructed using the KAPA mRNA stranded library prep kit and fragmented to ~300bp

treatment_protocol: Approximately 200 adult animals were used for each replicate (3 replicates each of untreated (0 mg/mL), 10 µg/mL, 100 µg/mL, and 1 mg/mL Bleomycin). Animals were exposed to an appropriate dose of Bleomycin for 24 hours (or or spring water, untreated (0 mg/mL)).

value: whole body

value: 1mg/mL Bleomycin


title: Hypsibius 1mg/mL Bleomycin biol rep 2


title: HUVECs, PPCN-S.A5G81, 72h, rep 2


title: Hypsibius 0 mg/mL Bleomycin biol rep 1

value: 0 mg/mL Bleomycin


title: Hypsibius 0 mg/mL Bleomycin biol rep 3


title: HUVECs, PPCN-S.A5G81, 72h, rep 1


title: HUVECs, PPCN-QK, 72h, rep 2

value: PPCN-QK


title: HUVECs, PPCN-QK, 72h, rep 3


title: HUVECs, PPCN-QK, 72h, rep 1


title: HUVECs, PPCN-A5G81, 72h, rep 3


title: Hypsibius 100µg/mL Bleomycin biol rep 3

value: 100µg/mL Bleomycin


title: Syncytiotrophoblast infected, biol rep 2


title: HUVECs, PPCN-A5G81, 72h, rep 1


title: HUVECs, PPCN-RGD, 72h, rep 3

value: PPCN-RGD


title: Hypsibius 0 mg/mL Bleomycin biol rep 2


title: HUVECs, PPCN, 72h, rep 1

value: PPCN


title: Hypsibius 100µg/mL Bleomycin biol rep 1


title: HUVECs, PPCN-S.QK, 24h, rep 3


title: Hypsibius 10µg/mL Bleomycin biol rep 3

value: 10µg/mL Bleomycin


title: HUVECs, PPCN, 72h, rep 3


title: Hypsibius 10µg/mL Bleomycin biol rep 2


title: Hypsibius 100µg/mL Bleomycin biol rep 2


title: HUVECs, PPCN-S.QK, 24h, rep 2


title: HUVECs, PPCN-RGD, 72h, rep 2


title: Hypsibius 10µg/mL Bleomycin biol rep 1


title: HUVECs, PPCN, 72h, rep 2


title: HUVECs, PPCN-S.A5G81, 24h, rep 3


title: Hypsibius 0 Gy IR biol rep 3

description:
He_0_3
Hyp_IR_counts_s2.txt

data_processing:
Reads were adapter trimmed then mapped to the most recent genome for H. exemplaris (v3.1.5) using BBduk and BBmap (ver 39.01), and counts were assigned with featureCounts (ver 2.0.6) using the annotation file associated with this genome.
Reads were aggregated at the level of genes and only genes with more than one count in at least two samples were kept for differential expression analysis.
Transcript abundance, fold changes, and FDR values were determined using EdgeR
Assembly: nHd_3.1.5
Supplementary files format and content: tab-deliminated text file including raw counts for each samples
Supplementary files format and content: tab-delimiated text files including edgeR output (logFC, CPM, FDR) for 100, 500, and 2180 Gy

treatment_protocol: Approximately 200 adult animals were used for each replicate (3 replicates each of unirradiated (0 Gy), 100 Gy, 500 Gy, and 2,180 Gy). Animals were exposed to an appropriate dose of IR (or left on the lab bench for 24 hours, unirradiated (0 Gy)).

value: 0 Gy IR


title: HUVECs, PPCN-S.A5G81, 24h, rep 1


title: Hypsibius 0 Gy IR biol rep 2

description:
He_0_2
Hyp_IR_counts_s2.txt


title: HUVECs, PPCN-S.QK, 24h, rep 1


title: HUVECs, PPCN-QK, 24h, rep 3


title: HUVECs, PPCN-QK, 24h, rep 2


title: HUVECs, PPCN-QK, 24h, rep 1


title: Hypsibius 0 Gy IR biol rep 1

description:
He_0_1
Hyp_IR_counts_s2.txt


title: HUVECs, PPCN-S.A5G81, 24h, rep 2


title: HUVECs, PPCN-A5G81, 72h, rep 2


title: HUVECs, PPCN-RGD, 72h, rep 1


title: HUVECs, PPCN-A5G81, 24h, rep 3


title: Hypsibius 2180 Gy IR biol rep 3

description:
He_2180_3
Hyp_IR_2180vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt

value: 2180 Gy IR


title: HUVECs, PPCN-A5G81, 24h, rep 2


title: HUVECs, PPCN-RGD, 24h, rep 3


title: Hypsibius 2180 Gy IR biol rep 2

description:
He_2180_2
Hyp_IR_2180vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt


title: HUVECs, PPCN-RGD, 24h, rep 2


title: Hypsibius 2180 Gy IR biol rep 1

description:
He_2180_1
Hyp_IR_2180vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt


title: HUVECs, PPCN, 24h, rep 3


title: Hypsibius 500 Gy IR biol rep 3

description:
He_500_3
Hyp_IR_500vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt

value: 500 Gy IR


title: HUVECs, PPCN, 24h, rep 1


title: HUVECs, PPCN, 24h, rep 2


title: D04-1277

city: Woodbury

first: Ashraf

middle: Sameh

last: Shabaneh

address: 2768 Liberty Trail

department: Institute of Health Informatics

institute: University of Minnesota

description: Skin, forearm, left dorsal_x000D_ - Basal vacuolopathy with dyskeratosis, favor acute graft versus host disease, grade II- see _x000D_                description._x000D_

data_processing:
Unaligned reads alignment via Pathseq - microbiome analysis.
Aligned and assembled using hisat2 and Cufflinks. Single gene analysis performed and pathway analysis via Enrichr.
Assembly: GRCh38_canon
Supplementary files format and content: comma delimited FPKM counts
Supplementary files format and content: comma delimited microbiome counts

source_name: Skin

extract_protocol:
extracted RNA from the FFPE biopsies using PureLink FFPE RNA Isolation Kit. FFPE samples yielded an adequate quantity of RNA for sequencing (median = 98717524.5 reads, range = 74316820 to 229178960).
After extraction, we prepared the libraries with the SMARTer Stranded Total RNA Kit v2.
Performed sequencing on a single lane of a NovaSeq S4 2x150-bp.

value: Skin

tag: day 28_agvhd_response

value: CR


title: D05-1128

description: Skin, forearm, left_x000D_ - Focal basal vaculopathy with scattered dyskeratosis, consistent with acute graft versus_x000D_ ¬†¬†¬†¬†¬†   host disease, Grade II- see description_x000D_

value: NR


title: Hypsibius 500 Gy IR biol rep 2

description:
He_500_2
Hyp_IR_500vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt


title: D05-1139

description: Skin, wrist, right_x000D_ - Basal vaculopathy with dyskeratoses, consistent with acute graft versus host disease, grade II-¬†¬†¬†¬†¬†   see description_x000D_


title: Hypsibius 100 Gy IR biol rep 3

description:
He_100_3
Hyp_IR_100vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt

value: 100 Gy IR


title: HUVECs, PPCN-RGD, 24h, rep 1

value: HUVEC

value: Endothelial cells


title: Hypsibius 100 Gy IR biol rep 1

description:
He_100_1
Hyp_IR_100vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt

value: whole body


title: D05-2419

description: Skin, forearm, left_x000D_ - Basal vaculopathy with dyskeratoses, consistent with acute graft versus host disease,_x000D_ ¬†¬†¬†¬†¬†   Grade II- see description_x000D_

value: PR


title: D04-1914

description: Skin, forearm, left_x000D_ - Focal basal vaculopathy with dyskeratosis, consistent with acute graft versus host_x000D_ ¬†¬†¬†¬†¬†   disease, Grade II- see description_x000D_


title: D05-273

description: Skin, forearm, left_x000D_ - Consistent with acute graft vs. host disease, Grade II- see description_x000D_


title: HUVECs, PPCN-A5G81, 24h, rep 1

value: WT


title: D04-1746

description: Skin, forearm, left_x000D_ - Acute graft versus host disease, Grade II- see description_x000D_


title: D05-1965

description: Skin, forearm, right_x000D_ - Basal vaculopathy with dyskeratoses, consistent with acute graft versus host disease,_x000D_ ¬†¬†¬†¬†¬†   Grade II- see description_x000D_


title: D05-690

description: Skin, forearm, left_x000D_ - Focal basal vaculopathy with dyskeratosis, favor acute graft versus host disease, Grade II,-_x000D_ ¬†¬†¬†¬†¬†   see description_x000D_


title: Syncytiotrophoblast mock infected, biol rep 3

value: Trophoblast cells

value: Trophoblast stem cell (clone 27)

value: Syncytiotrophoblast

value: Trophoblast stem cell media


title: D06-1187

description: Skin, forearm, right_x000D_ - Consistent with graft versus host disease, Grade I1- see description_x000D_


title: D06-1359

description: Skin, forearm, right_x000D_ - Basal vaculopathy with dyskeratoses, consistent with acute graft versus host disease, _x000D_ ¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†grade II-III- see description_x000D_


title: Syncytiotrophoblast mock infected, biol rep 2


title: Syncytiotrophoblast mock infected, biol rep 1


title: D06-1509

description: Skin, forearm, right;_x000D_ - Basal vaculopathy with dyskeratoses, consistent with acute graft versus host disease,_x000D_ ¬†¬†¬†¬†¬†  Grade II- see description_x000D_


title: D06-1615


title: Hypsibius 100 Gy IR biol rep 2

description:
He_100_2
Hyp_IR_100vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt


title: D06-1559

description: Skin, forearm, left_x000D_ - Focal basal layer degeneration with scattered apoptoses, consistent with an acute_x000D_ ¬†¬†¬†¬†¬†   graft versus host disease, Grade II- see description_x000D_


title: D04-2308

description: Skin, forearm, left lateral_x000D_ -Acute graft versus host disease, grade II._x000D_ ¬†¬†¬†¬†¬†  (See microscopic description)_x000D_


title: Hypsibius 500 Gy IR biol rep 1

description:
He_500_1
Hyp_IR_500vC_EdgeR_output.txt
Hyp_IR_counts_s2.txt


title: D05-1303

description: Skin, forearm, left dorsal_x000D_ - Focal basal vaculopathy with dyskeratoses, consistent with acute graft versus host_x000D_ ¬†¬†¬†¬†¬†   disease, Grade II- see description_x000D_


title: Cytotrophoblast mock infected, biol rep 3

value: Cytotrophoblast


title: D06-552

description: Skin, forearm, left_x000D_ - Graft versus host disease, Grade II- see description_x000D_


title: Cytotrophoblast mock infected, biol rep 2


title: D05-1393


title: Cytotrophoblast mock infected, biol rep 1


title: D08-1209

description: Skin, forearm, left dorsal_x000D_ ¬†¬†¬†¬†¬†- Focal basal layer degeneration, consistent with acute graft versus host disease, grade II- _x000D_ ¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†¬†see description  _x000D_ _x000D_


title: D08-1311

description: Skin, forearm, right_x000D_ - Interface change, consistent with acute graft versus host disease, grade II- see description  _x000D_ _x000D_


title: D08-368

description: Skin, forearm, left_x000D_ - Consistent with acute graft versus host disease, Grade II- see description  _x000D_ _x000D_


title: D09-2573

description: Skin, forearm, right_x000D_ - CONSISTENT WITH GRAFT VERSUS HOST DISEASE, GRADE II- SEE DESCRIPTION_x000D_ _x000D_


title: D09-561

description: Skin, forearm, left_x000D_ - Focal basal layer degeneration, consistent with_x000D_ ¬†¬†¬†¬†¬†-acute graft versus host disease, grade II- see description_x000D_ _x000D_


title: D08-1627

description: Skin, forearm, left_x000D_ - Focal basal layer degeneration, consistent with _x000D_ ¬†¬†¬†¬†¬†- acute graft versus host disease, grade II- see description  _x000D_ _x000D_


title: TF_sgRNA_Hoxb8FL_pDC

first: Ioanna

last: Tiniakou

address: 435 E 30th St

institute: NYU Langone

description: pDC

data_processing:
library strategy: sgRNA-Seq
Sequences flanking the 20 nucleotide sgRNA sequence were trimmed using cutadapt.
The remaining 20 nucleotide sgRNA sequence reads were aligned to a library index generated by 17820 sgRNA sequences using bowtie.
Assembly: mm10
Supplementary files format and content: csv; raw counts

source_name: bone marrow-derived

growth_protocol: Hoxb8-FL cells were maintained in RPMI supplemented with 10% FCS, 10% supernatant from the Flt3L-producing B16 cell line, and 10 μM β-estradiol  in humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Cells were resuspended in 3 mL NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8), and 100 μg/mL Proteinase K to every 15 x106 cells (>500x coverage) and incubated at 55°C overnight. 50 μg/mL RNAse A was added to the lysed sample and then incubated at 37°C for 30 min. Samples were chilled on ice before the addition of 1 mL of pre-chilled 7.5 M ammonium acetate to precipitate proteins, DNA was extracted by isopropanol, washed, dried and resuspended in water.
For "progenitors_0" and "progenitors" samples, 54 μg DNA corresponding to 500x coverage of the library were amplified in 5 parallel PCR1 reactions using 10.8 μg per reaction. For the "DC" sample, 24 PCR1 reactions were similarly setup for the amplification of ~250 μg of DNA corresponding to >1000x coverage of the library. For sorted cDC and pDC samples library coverage was lower (~ 240x) due to cell numbers. Two PCR1 reactions were setup for each sorted subset for the amplification of ~24-26 μg gDNA. PCR1 and subsequent PCR2 reactions for the addition of Illumina barcodes were performed as previously described (PMID: 35294876). All samples were pooled in equimolar ratio and purified with QIAquick PCR Purification Kit (Qiagen). The purified sample was run on a 2% gel and the correct size band (250–270 bp) was extracted and purified with QIAquick Gel Extraction Kit (Qiagen).

treatment_protocol: In order to achieve a representation of ~500 cells per sgRNA in the library post-selection, 120 million undifferentiated Hoxb8-FL cells were distributed to 6-well plates with 5x105 cells per well. Cells were spinoculated with the pre-determined amount of virus and 100 ng/mL zeocin was added 48 h later. Transduced cells were maintained in zeocin throughout the screen and were split every two days to prevent overconfluence. Samples of 15 million cells were obtained 9 days post selection (progenitors_0) and 13 days post selection on the day of differentiation induction (progenitors). A bulk sample of 50 million differentiated cells (DC) was obtained at the end of differentiation and prior to sorting. Hoxb8-FL-derived DCs were sorted as follows: CD11c+ CD11b+ B220- for cDCs (6.5 million) and CD11c+ CD11b- B220+ for pDCs (7.3 million). Sample cell pellets were stored at -80oC until genomic DNA (gDNA) isolation.

value: bone marrow-derived

value: hematopoietic cell

value: 20 days post selection; sorted pDC


title: D06-1667

description: Skin, forearm, left_x000D_ - Basal vaculopathy with dyskeratoses involving follicular epithelium, consistent wtih_x000D_ ¬†¬†¬†¬†¬†   acute graft versus host disease, Grade II- see description_x000D_

value: Skin


title: TF_sgRNA_Hoxb8FL_cDC

description: cDC

value: 20 days post selection; sorted cDC


title: TF_sgRNA_Hoxb8FL_DC

description: DC

value: 20 days post selection; DC


title: D11-3028

description: Skin, left forearm_x000D_ - Interface dermatitis consistent with acute graft versus host disease, grade II/IV_x000D_ -see description_x000D_


title: D11-514

description: Skin, forearm, right  _x000D_ -Consistent with acute graft versus host disease, grade II/IV- see description_x000D_

value: CR


title: TF_sgRNA_Hoxb8FL_progenitors0

value: 9 days post selection; progenitors


title: D11-369

description: Skin, right forearm_x000D_ -Consistent with acute graft versus host disease, grade early II/IV- see description  _x000D_ _x000D_

value: NR


title: tdTomato-negative CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 3

description:
FACS
Spleen CD4 of SM22a-Cre reporter mice.csv

data_processing:
A minimum 25M reads per library with 75 bp paired-ends reads were generated per sample.
Quality control of the resulting sequence data was performed using CLC genomics workbench
Trimmed and filtered reads were aligned to rat genome Rn6 reference and mouse genome GRCm38
Assembly: Rn6 and GRCm38
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Spleen

value: Spleen

value: CD4+ T cell

tag: cell subset

value: tdTomato-negative

value: Ai14; SM22alpha-Cre


title: D13-1401

description: Skin, forearm, right_x000D_ -Consistent with acute graft versus host disease, grade II/IV- (see description)._x000D_


title: D06-791

description: Skin, forearm, left_x000D_ - Dermal inflammation with epidermal degeneration, consistent with graft versus host_x000D_ ¬†¬†¬†¬†¬†   disease, Grade II- see description_x000D_

value: PR


title: D06-354

description: Skin, forearm, right_x000D_ ¬†¬†¬†¬†¬†- Focal basal layer degeneration with dyskeratoses involving follicular epithelium, consistent with acute graft versus host disease, grade II- see description_x000D_


title: D13-2559


title: tdTomato-negative CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 2


title: D07-727

description: Skin, right forearm_x000D_ - Interface dermatitis, consistent with acute graft versus host disease, Grade II-III _x000D_ ¬†¬†¬†¬†¬†-see description_x000D_


title: D06-727

description: Skin, forearm, left_x000D_ - Interface dermatitis, consistent with acute graft versus host disease, Grade II- see description_x000D_


title: D13-4062

description: Skin, forearm, right_x000D_ -Consistent with acute graft versus host disease, grade  II/IV- (see description)._x000D_


title: D13-3389


title: D13-2643

description: Skin, forearm, right_x000D_ -Consistent with acute graft versus host disease grade II/IV- (see description)._x000D_


title: D13-794


title: tdTomato-negative CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 1


title: D11-2882

description: Skin, left forearm   - Consistent with acute graft versus host disease grade II/IV- see description


title: tdTomato-positive CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 2

value: tdTomato-positive


title: D14-1833

description: Skin, forearm, left_x000D_ -Consistent with graft versus host disease grade II- see description_x000D_


title: D14-2036

description: Skin


title: D13-640

description: Skin, forearm, right_x000D_ - Consistent with acute graft versus host disease, grade II/IV- see description_x000D_


title: tdTomato-positive CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 1


title: D14-682

description: Skin, forearm, right_x000D_ -Consistent with graft versus host disease, grade 2- (see description)._x000D_


title: TF_sgRNA_Hoxb8FL_progenitors

description: progenitors

value: WT

value: 13 days post selection; progenitors


title: ZR75, PML, input

city: Cleveland

first: Hung-Ying

last: Kao

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

description: instrument model: Illumina NovaSeq X Plus 10B

data_processing:
Basecalls were performed using fastQC v0.12.0 for fastq files from Admera
ChIP-seq reads were trimmed using TrimGalore v0.6.10 with default settings, and reads with a length less than 20bp were excluded.
ChIP-seq reads were aligned to the UCSC hg38 and mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using homer v4.11
SPIKER v1.0.0 was employed to derive scaling factors from input and spike-in control in BAM files. Subsequently, the bigWig files were scaled using these factors through deepTools 3.5.4.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig

source_name: Breast; Mammary gland

growth_protocol: MCF7 cells were cultured in DMEM with 10% FBS and 1x penicillin/streptomycin, while ZR-75-1 cells were cultured in RPMI-1640 medium with 10% FBS and 1x penicillin/streptomycin. Both cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
MCF-7/ZR-75-1 cells were fixed with 1% formaldehyde and sheared with E220 focused ultrasonicator (Covaris), respectively. Sheared chromatins were mixed with 20% of lysate from MEF cells processed identically as spike-in for normalization. Mixed chromatin were incubated at 4℃ overnight with antibodies. Protein A beads were then incubated with the chromatin and antibody mixture for 2 hours at 4℃. Beads were washed, reverse-crosslinked, and DNA were purified with Qiaquick PCR purification kit (Qiagen).
KAPA HyperPrep Kit (Roche) was used to prepare ChIP-Rx libraries.

value: Breast; Mammary gland

value: epithelial cell


title: D15-1188

description: Skin, forearm, right -Consistent with acute graft versus host disease, grade..early II/IV- see description.


title: ZR75, H3K4me3, shCtrl, rep3

description:
instrument model: Illumina NovaSeq X Plus 10B
Incorporate 10% MEF cells into the sample as a spike control.

value: shRNA-Contrl


title: ZR75, H3K4me3, shCtrl, input


title: mESC Srrm2 hKO Replicate 2

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

data_processing:
Expression levels from RNA-seq profiles were pseudo-aligned using Kallisto v0.46.1 (Bray et al., 2016, Nat. Biot. 34, p.525).
Assembly: mm10 (M24)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

growth_protocol: mESCs E14tg2a.4 were grown as previously described (Ferrai et al. 2017 Mol. Syst. Biol. 13, p. 946) on 0.1% v/v gelatin-coated flasks in GMEM medium with LIF and additional supplements. Prior to collection of material for experiments, cells were grown for 24h or 72h in serum-free ESGRO medium supplemented with LIF.

extract_protocol:
Total RNA from three replicates of WT and Srrm2 heterozygous knockout cells was isolated with TRIzol (Invitrogen) and DNA was degraded with TURBO DNase (Invitrogen), according to the manufacturer’s protocol.
RNA spike-ins (Invitrogen) were added to each purified RNA sample. Total RNA libraries were produced from 600 ng of RNA using the TruSeq Stranded total RNA library preparation kit (Illumina) according to the manufacturer’s protocol. Total RNA libraries were paired-end sequenced using the NextSeq 500/550 system at 75 bp length.

treatment_protocol: mESC E14tg2a.4 wild-type and mESC E14tg2a.4 with a derived heterozygous truncation in the Srrm2 gene (SIGTR ES cell line CG0630, RRID:MMRRC_028099-UCD) were generated by the Sanger Institute Gene Trap Resource (SIGTR), Cambridge, UK, and obtained from the Mutant Mouse Resource Center (MMRRC) at University of California at Davis, an NIH-funded strain repository.

value: mouse embryonic stem cells

value: Srrm2 gene-trap SIGTR ES cell line CG0630, RRID:MMRRC_028099-UCD

value: male


title: mESC Srrm2 hKO Replicate 3


title: ZR75, H3K4me3, shCtrl, rep2


title: mESC Srrm2 hKO Replicate 1


title: NIH3T3, control, 4hrs, replicate2, ATAC-seq

first: Terry

last: Furey

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina, Chapel Hill

description:
CTL_NIH3T3_4hrs_rep2
ATACseq.4hrs.counts.txt

data_processing:
ATAC: PEPATAC v0.9.15 with default parameters
Assembly: mm10
Supplementary files format and content: counts.txt - count of reads assigned to each gene (RNAseq) or accessible chromatin region (ATAC-seq)

source_name: embryonic fibroblast cells

extract_protocol:
DNA was prepared from 50,000 MSC cells or NIH3T3 cellsusing an ATAC-seq protocol (Omni-ATAC).
ATAC DNA was prepared from 50,000 MSC cells or NIH3T3 cells using an ATAC-seq protocol (Omni-ATAC) and primers with transposase from llumina Kit (cat# 20034197).

tag: strain

value: embryonic fibroblast cells


title: NIH3T3, control, 4hrs, replicate3, ATAC-seq

description:
CTL_NIH3T3_4hrs_rep3
ATACseq.4hrs.counts.txt


title: ZR75, H3K4me3, shCtrl, rep1


title: mESC WT Replicate 3

value: Wild-type


title: NIH3T3, control, 4hrs, replicate1, ATAC-seq

description:
CTL_NIH3T3_4hrs_rep1
ATACseq.4hrs.counts.txt


title: ZR75, H3K4me3, shPML#2, rep3


title: tdTomato-positive CD4-positive cell from splenocytes of SM22alpha-Cre reporter mouse 3

description:
FACS
Spleen CD4 of SM22a-Cre reporter mice.csv


title: ZR75, H3K4me3, shPML#2, rep2


title: MSC, control, 4hrs, replicate3, ATAC-seq

description:
CTL_MSC_4hrs_rep3
ATACseq.4hrs.counts.txt

source_name: mesynchymal stem cells

value: mesynchymal stem cells


title: mESC WT Replicate 1


title: MSC, control, 4hrs, replicate2, ATAC-seq

description:
CTL_MSC_4hrs_rep2
ATACseq.4hrs.counts.txt


title: primary BMMs, Bub1 cKO, day2, rep3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

institute: Ehime University

data_processing: Data were processed using RaNA-seq

source_name: Bone marrow-derived macrophage

growth_protocol: Primary bone marrow-derived macrophages (BMMs) were cultured in MEM-α supplemented with 10% CELLect FBS, 1% antibiotic-antimycotic solution in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted using Rneasy spin column kit (Qiagen). 25 ng of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using QuantSeq 3'mRNA-Seq Library Prep Kit.

treatment_protocol: BMMs were pre-cultured with M-CSF (20 ng/ml) for 3 days. Then, osteoclast differentiation was induced by treating M-CSF (20 ng/ml) and RANKL (50 ng/ml) for 2 days.

value: Bone marrow-derived macrophage

value: macrophage

value: cKO

value: osteoclast differentiaton


title: ZR75, H3K4me3, shPML#2, rep1


title: NIH3T3, CK666, 4hrs, replicate3, ATAC-seq

description:
CK666_NIH3T3_4hrs_rep3
ATACseq.4hrs.counts.txt


title: primary BMMs, Bub1 cKO, day2, rep2


title: ZR75, PML,rep2


title: MSC, control, 4hrs, replicate1, ATAC-seq

description:
CTL_MSC_4hrs_rep1
ATACseq.4hrs.counts.txt


title: primary BMMs, Bub1 cKO, day2, rep1


title: ZR75, H3K4me3, shPML#2, input


title: NIH3T3, CK666, 4hrs, replicate2, ATAC-seq

description:
CK666_NIH3T3_4hrs_rep2
ATACseq.4hrs.counts.txt


title: primary BMMs, Ctrl, day2, rep3

value: Ctrl


title: NIH3T3, CK666, 4hrs, replicate1, ATAC-seq

description:
CK666_NIH3T3_4hrs_rep1
ATACseq.4hrs.counts.txt


title: ZR75, PML, rep1


title: primary BMMs, Ctrl, day2, rep1


title: MSC, CK666, 4hrs, replicate3, ATAC-seq

description:
CK666_MSC_4hrs_rep3
ATACseq.4hrs.counts.txt


title: MCF7, H3K4me3, shPML#2, input


title: mESC WT Replicate 2


title: MSC, CK666, 4hrs, replicate2, ATAC-seq

description:
CK666_MSC_4hrs_rep2
ATACseq.4hrs.counts.txt


title: MCF7, H3K4me3, shPML#2, rep3


title: MCF7, H3K4me3, shPML#2, rep2


title: peri-hypothalamus, IgG CUT&RUN, IRF3-2D OE model

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

data_processing:
RNA-seq data was aligned using HISAT2.
Reads were assigned to genes using featureCounts (subread) and an mm10 genome annotation modified to minimize overlapping transcripts.
Differential expression analysis (DEA) of the data was performed with edgeR using the recommended quasi-likelihood GLM method. Significantly different genes were required to have an average expression, across group, of > 1 cpm, a fold change (FC) > 0.5, an adjusted p-value, false discovery rate (fdr), value of < 0.05.
Gene set enrichment analysis (GSEA) gene ontology (GO) for biological process was carried out with WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) 49. Genes with cpm < 1 were omitted from the GSEA analysis.
Assembly: mm10
Supplementary files format and content: tab-separated-values containing raw gene expression counts from each sample
Supplementary files format and content: tab-separated-values containing normalized gene expression counts (cpms) from each sample; filtered to only genes in the DEA analysis
Library reads were mapped to the UCSC build mm10 assembly of the mouse genome using Bowtie 2.
Chromatin accessibility regions (peaks) were valled using MACS2.
Coverage summation and additional data parsing were carried out using bedtools.
Differential binding analysis including normalization and quantification were done in EdgeR. Differential peaks were defined at log2 fold change > 0.5 and a false discovery rate of < 0.05
Assembly: mm10
Supplementary files format and content: tab-separated-values containing raw reads-per-peak (coverage) from each sample
Supplementary files format and content: tab-separated-values containing normalized peak abundance (cpms) from each sample; filtered to only regions in the diff. analysis
Library reads were mapped to the mm10 mouse assembly using Bowtie 2 operating under the `--very-sensitive-local` regimen.
IRF3 peaks were called using SEACR (using IgG control) running in “relaxed” mode. CTCF peaks were called using MACS2, then filtered for reproducible peaks (per-sample) via pseudoreplication (n = 2).
Motif analysis (de novo identification, comparison with known motifs, etc.) was performed using MEME-Suite by taking a radius of 100 bp around the summit of each peak. HOCOMOCOv11 was used as the database for known motifs.
Assembly: mm10
Supplementary files format and content: tab-separated-values containing IRF3 peak information (chrom, start, end, AUC, etc.) identified via SEACR w/ relaxed thresholds
Library strategy: Cut & Run

source_name: peri-hypothalamus

extract_protocol:
TRAP IP was performed for each sample thus: 4 frozen ARC tissue samples from NuTRAPAgRP mice between 6 and 11 weeks of age were pooled and lysed with Dounce homogenizers in low-salt IP buffer (50mM Tris [pH7.5], 12mM MgCl2, 100mM KCl, 1% NP-40; 100 µg/ml cycloheximide, 2mM DTT, 0.2units/ml RNasin, 1x Roche Complete EDTA-free protease inhibitor). After centrifugation, the supernatant was incubated with GFP ab290 antibody (Abcam) on a rotor, then incubated again with Dynabeads Protein G (Thermo Fisher). RNase-inhibitors were used throughout the protocol to mitigate potential RNA degradation. RNA was isolated with the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions, and then reverse-transcribed and analyzed by qRT-PCR as described above.
TRAP-isolated RNA (<100ng) was treated with the Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module (E6111L). cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit (Illumina FC-131). Sequencing libraries were analyzed by Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM, and sequenced on a NextSeq500.
AgRP neuronal nuclei were isolated from dissected ARCs from 6-11-week-old mice and were snap frozen and stored at -80C. Isolated ARCs were dounce homogenized in nuclear preparation buffer (NPB; 10 mM HEPES [pH 7.5], 1.5mM MgCl2, 10 mM KCl, 250 mM sucrose, 0.1% NP-40, and 0.2 mM DTT), and homogenates were filtered through a 100 μM strainer and centrifuged to pellet the nuclei. Nuclei were washed with NPB, re-suspended in nuclear sorting buffer (10 mM Tris [pH 7.5], 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.1% NP-40, 0.2 mM DTT), and filtered again through a 40 μM strainer. Isolated nuclei were sorted by flow cytometry based on AgRP neuron-specific GFP expression. With this approach we routinely obtain ~2000 AgRP neuronal nuclei per mouse. Nuclei from 4 pooled mice (per sample), were isolated, subjected to FANS, and 10,000 nuclei were collected into 500-750uL PBS (0.1% NP40) in 1.5 mL microcentrifuge tubes and stored on ice. Tubes were spun at 1000 rpm for 10 mins, at 4°C. Supernatant was removed via gentle decantation. Nuclei pellets were subjected to tagmentation after resuspension in 50ul of transposase reaction mix: 25 ul TD buffer, 2.5 ul TN5 transposase, 22.5 ul dH20. Nuclei were incubated at 37°C with shaking at 600 rpm for 30 mins, then placed on ice. DNA was purified using a Qiagen minelute PCR purification kit and eluted in 10 ul of Qiagen Elution Buffer
Library construction was conducted using an initial PCR amplification using 10 ul of transposed DNA, 11ul H2O, 2ul of 25uM Primer 1, 2ul of Primer 2, and 25 ul of NEBNext HF 2X PCR mix. The following initial amplification cycle was used: 1 cycle or 72ºC (5min), 98ºC (30s), 5 cycles of 98ºC (10s), 63C (30s), 72ºC (1 min), hold at 4ºC. A side PCR reaction was conducted to determine the optimal number of amplification cycles used during the library construction, as previously described50,  using 5 ul PCR amplified DNA, 4.41 ul H2O, 0.25ul Primer 1 Adaptor, 0.25ul Primer 2 Adaptor 2 (barcoded), 0.09 ul 100x SYBR Green (Diluted from 10,000X stock with H2O), 5 ul NEBNext HF 2X PCR mix. The following initial amplification cycle was used: 1 cycle of 98ºC (30s), 20 cycles of 98ºC (10s), 63ºC (30s), 72ºC (1 min). Amplification curves were assessed to determine the number of additional cycles needed during library construction50. The requested additional number of cycles was completed by adding the sample back to the thermocycler in its same tube and master mix. Amplified libraries were purified with a Qiagen Minlute PCR purification kit, eluted in 20ul, and the volume was brought up to 100 ul with additional EB. The eluent was subjected to a two-phase size selection using Ampure Beads, initially .55X volume of elutant (55ul) was used, followed by 1.5X volume of initial sample volume (100ul x 1.5 = 150ul) minus the existing PEG that is already in the sample (150ul – 55ul = 95 ul). Finally, the library was eluted using 50ul of EB. Libraries were sequenced on a Next-seq 500 (Illumina)
~4,000 ARC nuclei, from two mice, were isolated and subjected to FANS, and collected into 0.75 mL of C&R Wash Buffer (low salt) buffer (20 mM HEPES-KOH [pH 7.5], 75 mM NaCl, 0.5 mM Spermidine, 0.1% BSA and 1x protease inhibitor cocktail from Sigma). 180 μL BioMagPlus Concanavalin A beads slurry was washed twice and re-suspended in 180 μL Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), and added to the nuclear suspension. The mixture was thoroughly mixed on a rocker for 10 minutes to allow binding of nuclei to the beads. The nuclei were pelleted with a magnet stand and blocked with Wash Buffer (20 mM HEPES-NaOH pH 7.5, 75 mM NaCl, 0.5 mM Spermidine, 0.1% BSA and 1x protease inhibitor cocktail from Sigma) supplemented with 2 mM EDTA. After washing once with Wash Buffer, nuclei were re-suspended in 50 μL Wash Buffer containing 2 μg of anti-IRF3 antibody (Proteintech, 11312-1-AP), and incubated overnight to allow antibody binding. The next day, nuclei were washed once on a magnet stand with Wash Buffer and incubated with 1:1000 pA-MN in 200 μL Wash Buffer. After 1 hour, nuclei were washed once to remove unbound pA-MN, re-suspended in 150 μL Wash Buffer, and then chilled on a 0°C metal block in a water-ice mixture. 3 μL of 100 mM CaCl2 was added to activate pA-MN, and the mixture was incubated at 0°C for 60 min. The reaction was stopped by adding 150 μL 2XSTOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A and 40 μg/mL glycogen). The protein-DNA complexes were released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit fluorometer and bioanalyzer quality control. CTCF optimization experiments were performed using DAPI-treated nuclei isolated from whole mouse cerebellum, and a CTCF antibody from (Millipore, 07-729). Peri-hypothalamus IRF3-2D IgG (IgG C&R, Figures 6, S6E, S6F) sample was generated by stereotaxically injecting a IRF3LSL-2D mouse with a AAV2-Cre-GFP in the peri-hypothalmus and ~200K GFP+ nuclei were isolated by FANS and used for CUT&RUN on the same day the IRF3Ag C&R sample was generated. IRF3 CUT&RUN from hepatocytes was conducted using primary hepatocytes isolated from IRF3LSL-2D mice as described, and transiently transduced ex vivo with adenovirus expressing Cre recombinase (Ad-Cre). IRF3 and IgG CUT&RUN from immortalized AgRP neurons (IRF3 C&R AgRPin vitro and IgG C&R AgRPin vitro, Figures S6E, S6F) was conducted using those cells transiently transduced with Ad-CMV-IRF3-2D-hPGK-eGFP (Vector Builder).
CUT&RUN libraries were prepared using the NEB Ultra II library preparation kit with important modifications35. Briefly, less than 30 ng DNA was used as input. End prep was performed at 20°C for 30 minutes and then 50°C for 60 minutes, as reduced temperature prevents melting of short DNA fragments (Liu et al., 2018). 5 pmol adaptor was added and ligated to end prep products at 20°C for 15 minutes. USERTM enzyme was then used to cleave the uracil in the loop. 1.7x volume of AMPure beads were used to purify the ligation product, which aids in the recovery of short fragments. To amplify the library, the ligation product was mixed with 2x Ultra II Q5 mix, universal primer and index primers. PCR was carried out as follows: 98°C 30 seconds, 12 cycles of 98°C 10 seconds and 65°C 10 seconds, and final extension 65°C 5 minutes. The PCR product was subjected to double size selection with 0.8x and then 1.2x AMPure beads. The purified library was quantified with Qubit and Tapestation. Libraries were pooled at similar molar amounts and sequenced using Nextseq500 platform.

value: peri-hypothalamus

tag: condition

value: fed (ad libitum)

tag: antibody

value: IgG


title: MSC, CK666, 4hrs, replicate1, ATAC-seq

description:
CK666_MSC_4hrs_rep1
ATACseq.4hrs.counts.txt


title: MCF7, H3K4me3, shPML#2, rep1

value: Breast; Mammary gland


title: AgRP neurons, IRF-3 CUT&RUN, IRF3-2D OE model

source_name: arcuate nucleus

value: arcuate nucleus

value: AgRP neuron

value: IRF-3 (Proteintech, 11312-1-AP)


title: icKO BR IP biol rep2

city: Houston

first: Matthew

middle: Neil

last: Rasband

address: 1 Baylor Plaza

department: Neuroscience

institute: Baylor College of Medicine

description:
RAS_61491
rasband_mm10_raw_count_expressions.csv

data_processing:
Quality trimming and filtering was performed using Trimmomatic v0.39
Reads were then aligned to UCSC mm10 using STAR v2.7.10b
Gene quantification was generated using quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample

source_name: oligodendrocytes

growth_protocol: NG2CreERTM;Ank3F/F;Rpl22HA/+(AnkG icKO RiboTag) and NG2CreERTM;Rpl22HA/+ (control RiboTag) mice were kept on a 12 h/12 h light/dark cycle (lights on at 7:00 am) and had access to food and water ad libitum. All animal care and experimental procedures were conducted in compliance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the Baylor College of Medicine Institutional Animal Care and Use Committee

extract_protocol:
Mice were anesthetized with isoflurane and perfused with ice-cold PBS, and the whole brain homogenates were immediately processed for IP-enrichment of ribosomes from oligodendrocytes. Three animals were pooled together for one RNA-seq sample. 10% of the cleared homogenate was collected as input. IP was performed overnight with HA-antibody (Biolegend Cat# 901505; RRID:AB_2565023) and Pierce protein A/G Magnetic Beads (Thermo Scientific Cat# 88803). RNA was isolated from both input and IP samples using RNeasy Mini Kit (Qiagen Cat# 74104) following manufacturer's protocols.
RNAseq libraries were prepared with the Takara SMARTer® Stranded Total RNA-Seq v3 - Pico Input Mammalian kit (Takara, p/n 634485) kit following manufacturer's protocols.

treatment_protocol: Genotyping for AnkG icKO RiboTag and control RiboTag mice was carried out by standard PCR on tail clips for Cre, Ank3, and Rpl22 alleles at weaning age. Tamoxifen (20 mg/ml in corn coil) was administered intraperitoneally for 5 consecutive days (100 mg/kg of body weight per day) to 8-week-old mice, which were analyzed after one month.

value: oligodendrocytes

value: AnkG icKO


title: ZR75, PML,rep3

description: instrument model: Illumina NovaSeq X Plus 10B

value: epithelial cell


title: MCF7, H3K4me3, shPML#1, input


title: cKO BR IP biol rep1

description:
RAS_61490
rasband_mm10_raw_count_expressions.csv


title: MCF7, H3K4me3, shPML#1, rep3

description:
instrument model: Illumina NovaSeq X Plus 10B
Incorporate 10% MEF cells into the sample as a spike control.


title: icKO BR input

description:
RAS_61489
rasband_mm10_raw_count_expressions.csv


title: whole cerebellum, CTCF CUT&RUN, 100K nuclei

description: CUT-RUN.CTCF.Mm_cerebellum_200K_01-1.filt.narrowPeak

source_name: cerebellum

value: cerebellum

value: male

value: CTCF (Millipore, 07-729)


title: MCF7, H3K4me3, shPML#1, rep2


title: whole cerebellum, CTCF CUT&RUN, 50K nuclei

description: CUT-RUN.CTCF.Mm_cerebellum_050K_01-1.filt.narrowPeak


title: whole cerebellum, CTCF CUT&RUN, 10K nuclei

description: CUT-RUN.CTCF.Mm_cerebellum_010K_01-1.filt.narrowPeak


title: ctrl BR IP biol rep2

description:
RAS_61488
rasband_mm10_raw_count_expressions.csv

value: control


title: primary BMMs, Ctrl, day2, rep2

value: Bone marrow-derived macrophage

value: macrophage


title: whole cerebellum, CTCF CUT&RUN, 1K nuclei

description: CUT-RUN.CTCF.Mm_cerebellum_001K_01-1.filt.narrowPeak


title: ctrl BR input

description:
RAS_61486
rasband_mm10_raw_count_expressions.csv


title: MCF7, H3K4me3, shPML#1, rep1


title: MCF7, H3K4me3, shCtrl, input

value: shRNA-Contrl