title: mPFC-Ctrl-8.4

city: Jouy-en-Josas

first: Anne

last: GABORY

address: Domaine de Vilvert

country: France

institute: INRAE

description: Gene expression in medial prefrontal cortex of male C3H/Hen mouse from the control condition group

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 36896 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 3413 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: medial prefrontal cortex, control condition, male individual number_8.4

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All animals were weaned on PND21 and grouped in 4-6 mice per cage by same strain, same sex, and same experimental condition under standard laboratory conditions.

extract_protocol: Total mRNA was extracted from mPFC, NAc, and hypothalamus using a TRIzol extraction kit (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Maternal separation combined with chronic unpredictable maternal stress from postnatal day 2 to 14 (Stress) vs control (Ctrl) condition.

tag: strain

tag: condition

value: Ctrl

value: medial prefrontal cortex


title: mPFC-Stress-7.6

status: Public on Jul 24 2023

type: RNA

description: Gene expression in medial prefrontal cortex of male C3H/Hen mouse from the maternal separation group

molecule: total RNA

organism: Mus musculus

source_name: medial prefrontal cortex, maternal separation, male individual number_7.6

value: Stress

tag: tissue


title: Brain_sham_WT_rep1

city: Bunkyo-ku

first: Akari

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression of WT mice in the sham-operated brain tissue

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

source_name: Brain, sham, WT, replicate 1

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from brain tissue was purified using RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min.

tag: genetic background

tag: genotype

value: Wild type

value: Brain

tag: gender

value: male


title: Brain_day3_WT_rep1

description: Gene expression of WT mice on the day 3 post-ischemic brains

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Brain, day 3, WT, replicate 1

label_protocol: 100 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.


title: Brain_sham_WT_rep_1

description: Gene expression of WT mice on the sham-operated brain tissue

source_name: Brain, sham, WT, replicare 1


title: V3 T48

type: SRA

city: London

first: Aris

last: Aristodemou

state: London

address: St Mary's Campus, Norfolk Place, Rear Lodge Immunology

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description:
150 bp PE
deseq2_norm_counts.tsv

library_source: transcriptomic

data_processing:
Transcript counts obtained using Kallisto v0.46.2 (non-default parameters: --threads=30 --bias)
Differential expression analysis performed using DESeq2 v1.32.0
Assembly: Human genome GRCh38 / HTLV-1 genome AB153134
Supplementary files format and content: Kallisto transcript abundances (tab-separated values files)
Supplementary files format and content: DESeq2-normalised transcript counts for all samples excluding V4 T24 (tab-separated values file)

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNeasy Plus Micro (Qiagen, Cat. No. 74034)
Polyadenylated transcript enrichment and strand specific library preparation was completed using the NEBNext Ultra II kit (NEB)

value: Blood

tag: cell type

value: CD4+ T cell

value: Uninfected


title: V3 T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: mPFC-Stress-7.2

source_name: medial prefrontal cortex, maternal separation, male individual number_7.2


title: V3 T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: mPFC-Ctrl-8.5

source_name: medial prefrontal cortex, control condition, male individual number_8.5


title: V1 T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: V1 T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: V1 T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: V1 T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: mPFC-Stress-7.1

source_name: medial prefrontal cortex, maternal separation, male individual number_7.1


title: mPFC-Ctrl-8.2

source_name: medial prefrontal cortex, control condition, male individual number_8.2


title: mPFC-Ctrl-6.2

source_name: medial prefrontal cortex, control condition, male individual number_6.2


title: V1 T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDK T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: mPFC-Stress-5.3

source_name: medial prefrontal cortex, maternal separation, male individual number_5.3


title: TDK T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDK T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: V1 T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDK T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDK T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: NAC-Ctrl-8.5

description: Gene expression in nucleus accumbens of male C3H/Hen mouse from the control condition group

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 33902 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31261 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: nucleus accumbens, control condition, male individual number_8.5

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 40 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Total mRNA was extracted from mPFC, NAc, and HT using a TRIzol extraction kit (Invitrogen) according to the manufacturer’s instructions.

value: Nucleus accumbens


title: TDK T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: PC3M_Luc_C6_pwt_1

city: Villeneuve d'Ascq

first: clement

last: cordier

address: Batiment SN3, cité Scientifique

institute: PhyCell

data_processing:
Poor quality sequences and adapters were trimmed or removed with Dragen, with default parameters, to retain only good quality paired reads. Illumina DRAGEN bio-IT Plateform (v3.10.4) was used for mapping on hg38 reference genome and quantification with gencode v37 annotationgtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Following analysis were conducted with R software.
Data were normalized with DESeq2bioconductor packages,and DESeq2 workflow.
Assembly: version hg38 of human reference genome
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: Metastatic Prostate Cancer Cell

growth_protocol: PC-3M cell line was purchased from ATCC (Manassas, VA, USA). PC3M-Luc-C6 cells were obtained from Caliper Life Sciences (Waltham, MA, USA).

extract_protocol:
Cells were plated in 25 cm2 dishes at 75% confluence and total RNA was extracted and purified from cells using the NucleoSpin® RNA Plus kit (Machery-Nagel, Strasbourg, France) according to manufacturer’s recommendations. Each RNA sample (three replicates per group) was validated for RNA integrity using a 18S/28S ratio.
1µg of total RNA from each sample (n=10) were used for library preparation. Library preparation were realized following manufacturer’s recommendations (Illumina Stranded mRNA Prep).
RNFinal samples pooled libraries prep were sequenced on ILLUMINA Novaseq 6000 with SP-200 cartridge (2x800Millions of 100 bases reads), corresponding to 2x26Millions of reads per sample after demultiplexing. A-seq

treatment_protocol: no treatments

tag: background strain

value: Mice metastasis from PC3

value: trpv6 overexpression

tag: treatment

value: untreated


title: PC3M_Luc_C6_2

value: wild-type


title: NAC-Stress-7.2

description: Gene expression in nucleus accumbens of male C3H/Hen mouse from the maternal separation group

source_name: nucleus accumbens, maternal separation, male individual number_7.2


title: NAC-Stress-7.4

source_name: nucleus accumbens, maternal separation, male individual number_7.4


title: PC3M_Luc_C6_1


title: NAC-Ctrl-8.2

source_name: nucleus accumbens, control condition, male individual number_8.2


title: NAC-Stress-7.6

source_name: nucleus accumbens, maternal separation, male individual number_7.6


title: PC3M_KO_3


title: PC3M_wt_3


title: PC3M_Luc_C6_pwt_2


title: NAC-Stress-5.3

source_name: nucleus accumbens, maternal separation, male individual number_5.3


title: NAC-Ctrl-8.4

source_name: nucleus accumbens, control condition, male individual number_8.4


title: PC3M_KO_2


title: PC3M_KO_1


title: PC3M_wt_2


title: HT-Ctrl-8.5

description: Gene expression in hypothalamus of male C3H/Hen mouse from the control condition group

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 7 out of 8 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 37765 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 34970 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: hypothalamus, control condition, male individual number_8.5

value: hypothalamus


title: NAC-Ctrl-6.2

source_name: nucleus accumbens, control condition, male individual number_6.2


title: Gar15-13 Decitabine 3 H3K27ac

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

library_source: genomic

data_processing:
CUT&RUN reads were aligned against human genome (hg38/GRCh38) using bowtie2 with --dovtail parameters, sorted with samtools and duplicates were marked with picard.
Peak calling of individual CUT&RUN experiments was performed with MACS2.
Assembly: hg38
Supplementary files format and content: narrowpeak and broadpeak files contain peaks generated using Macs2 (FDR < 0.05).
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Gar15-13 Decitabine tumour

growth_protocol: A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice.

extract_protocol:
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for CUT&RUN experiments using Epicypher CUTANA ChIC/CUT&RUN Kit (Cat#14-1048) and CUTANA CUT&RUN Library Prep Kit (Primer Set 1) (Cat#14-1001).
Library preparation for CUT&RUN was performed using the Epicypher CUTANA CUT&RUN Library Prep Kit (Primer Set 1) (Cat#14-1001).

treatment_protocol: Mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC).

value: Breast cancer PDX model Gar15-13

value: Decitabine

tag: replicate

tag: chip antibody

value: H3K27ac (Epicypher 13-0045)


title: Gar15-13 IgG

source_name: Gar15-13 tumour

value: IgG (Epicypher)


title: Gar15-13 Vehicle 3 H3K27ac

source_name: Gar15-13 Vehicle tumour

value: Breast cancer PDX model Gar15-16

value: Vehicle


title: Gar15-13 Decitabine 2 H3K27ac


title: HT-Stress-7.6

description: Gene expression in hypothalamus of male C3H/Hen mouse from the maternal separation group

source_name: hypothalamus, maternal separation, male individual number_7.6

value: Stress


title: HT-Stress-7.1

source_name: hypothalamus, maternal separation, male individual number_7.1


title: PC3M_wt_1


title: HT-Ctrl-6.2

source_name: hypothalamus, control condition, male individual number_6.2

value: Ctrl


title: Gar15-13 Decitabine 1 H3K27ac


title: HT-Ctrl-8.4

source_name: hypothalamus, control condition, male individual number_8.4


title: HT-Stress-5.3

source_name: hypothalamus, maternal separation, male individual number_5.3


title: HT-Stress-7.2

source_name: hypothalamus, maternal separation, male individual number_7.2


title: HT-Ctrl-8.2

source_name: hypothalamus, control condition, male individual number_8.2


title: Gar15-13 Vehicle 2 H3K27ac

value: Breast cancer PDX model Gar15-15


title: Gar15-13 Vehicle 1 H3K27ac

value: Breast cancer PDX model Gar15-14


title: Gar15-13 Decitabine 2 CTCF

value: CTCF (Millipore-Merck 07-729)


title: Gar15-13 Decitabine 3 CTCF


title: 71 MPO none 24h donor A

first: Michael

last: Robson

address: Great Maze Pond

institute: King's College London

description:
donor A
genes.readcount.annot.xls
genes.FPKM.annot.xls

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.  HTSeq was used to count the read numbers mapped of each gene.
RPKM of each gene was then calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time.
Supplementary files format and content: 2 excel files contain the read counts for all the samples and 2 excel files contain the FPKM data for all the samples.

source_name: monocytes isolated from blood

growth_protocol: Peripheral blood mononuclear cells from healthy controls were isolated from blood anticoagulated with EDTA using Ficoll-Paque (GE Healthcare) density gradient centrifugation.  For experiments including TLR agonists, monocytes were then isolated by depletion of CD16+ cells followed by positive section for CD14+ cells with magnetic microbeads (Miltenyi Biotec). For experiments performed not including TLR agonists, cells were positively selected for CD14+, but not CD16 depleted. Cells were resuspended in RPMI (Sigma) with 10% AB serum* or FCS ** (Sigma) and 1% Pen-Strep (Sigma) and plated as 500ml at 1x106 cells/ml in 48 well plates. *Without TLR agonists. ** With TLR agonists.

extract_protocol:
At 6 hours (experiments with TLR agonists) or 24 hours (experiments without TLR agonists) RNA was purified using Monarch total RNA miniprep kit (New England BioLabs Inc.) according to manufacturer’s instructions.
Library preparation and sequencing was performed by Novogene Bioinformatics Technology (Beijing, PR China). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. The read depth was 30 million reads per sample.

treatment_protocol: Where indicated, LPS (25ng/ml, Escherichia coli R515; Enzo Life Sciences, UK – catalogue number ALX-581-007-L002) or R848 (5mg/ml, Invivogen) was added.  250 mg/ml of human control, anti-PR3 or anti-MPO IgG was added and plates incubated at 37°C for the time indicated.

value: monocytes

tag: group (control, mpo, pr3)

value: MPO

tag: treatment (none, lps, r848)

tag: time (6h, 24h)


title: 72 MPO none 24h donor A


title: 69 MPO none 24h donor A


title: Gar15-13 Vehicle 3 CTCF


title: 67 MPO none 24h donor A


title: 66 MPO none 24h donor A


title: Gar15-13 Vehicle 2 CTCF


title: Gar15-13 Vehicle 1 CTCF


title: 64 PR3 none 24h donor A


title: Primary tumor of patient HN77

city: Boston

first: Sara

middle: Isabel

last: Pai

state: Massachusetts

address: 55 Fruit Street

department: Department of Surgery

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic single cell

data_processing:
scRNA alignment and quantification were done using CellRanger (version 3.1.0). QC and cell filtering were done using R package Seurat (6), based on multiple summaries (total read counts and expressed genes, mitochondrial fraction) as well as custom rules based on marker genes to identify doublets and to rescue neutrophils. The following criteria were used to filter out unwanted cells: (1) number of detected genes <500 (low quality) or >5000 (doublets), (2) >20% mitochondrial genes, (3) cells expressing tumor and immune markers (doublets). From the discarded subset, neutrophils were rescued by identifying those expressing any one of the neutrophil markers: FCGR3B, CXCR1, CXCR2, PI3, G052, or CSF3R. InferCNV was used to distinguish tumor versus non-tumor epithelial cells. The cell annotation pipeline combined the FindCluster method in Seurat’s package with visualization of UMAP coordinates using Spring viewer (7) to facilitate manual examination and cell type assignment. The process was iterative done at multiple levels: total cells to detect major compartment and lineages, followed by subclustering for more refined subdivisions into “minor states”. T cells subclustering was also using projecTILs (8). Some minor state clusters were discarded when clear biological meaning could not be attributed (for example, clustering driven by cell cycle genes). Biologically related minor states were combined into larger group as required by the context of the analysis.
Assembly: GRCh38 (Ensemble 93)
Supplementary files format and content: The unfiltered gene expression raw counts from CellRanger output (raw_feature_bc_matrix) were reformatted as sparse matrix in R data format, called "HNxxx_gex_raw_counts.rds" in the supplementary files. All genes and all detected cell barcodes are included to facilitate future re-analysis. The set of selected cells and their cell type classifications can be found the cell annotation table included as a supplementary file.

source_name: tumor

extract_protocol:
All fresh tissue samples in this study were rapidly dissociated after the surgical procedure using the Human Tumor Dissociation kit from Miltenyi Biotec (Cat#130-095-929), with minor modifications to the protocol. First, the tissue was placed into 1.5 ml tubes containing 420 µl DMEM, and minced into small fragments (1-2 mm) using surgical scissors, followed by the addition of 42µl of enzyme H, 21µl of enzyme R, 5µl of enzyme A (all provided in the kit), and 512 µl of DMEM (reaching a total volume of 1ml). Second, the minced tissue was vortexed for 2 seconds and then immediately placed into a thermomixer (Eppendorf, F1.5) for 15 minutes at 37°C, 350 rpm. Next, tissues were placed on a 50 µm filter (Cat# 04-004-2327, Sysmex), minced with a 1 ml syringe plunger, and washed with 10 ml of DMEM containing 10% heat-inactivated FCS. After spinning the tube at 1500 rpm at 4°C for 5 minutes, the supernatant was removed, and ACK buffer (Cat# A1049201, Gibco) was added to ensure the removal of red blood cells (RBCs). Following RBC lysis, the dissociated sample was resuspended in DMEM with 10% FCS and the number and viability of the cells was determined using a manual hemocytometer (Cat# 1492, Bright-line). If the sample's viability was below 70%, the EasySep Dead Cell Removal (Annexin V) kit (Cat# 17899, STEMCELL) was used, with minor modifications to the protocol, allowing cell viability enrichment with a low input of cells. Briefly, cells were washed with 1 ml of RT isolation media (PBSx1 + 2% FCS + 1 mM CaCl2), resuspended in 100 µl, and moved into a PCR 8-strip well. Next, 10 µl dead cell removal (Annexin V) and 10 µl of biotin selection cocktails (provided with the kit) were added, gently mixed with the cell suspension, and incubated for 4 minutes at RT. After the first incubation, 20 µl of vortexed RapidSpheres and 60 µl of isolation media were added, mixed, and incubated for 3 minutes at RT. Lastly, the PCR 8-strip tube containing the cells was placed on a 10x Genomics magnetic separator (Cat# 120250). After a 5-minute incubation at RT, the supernatant containing the viable cells was moved into a new 1.5 ml collection tube, span for 5 minutes at 1500 rpm, 4°C; resuspended in DMEM with 10% FCS (for 10x Genomics GEM generation and barcoding) and counted using a manual hemocytometer.
Generation of single-cell whole transcriptome libraries was done using the 10x Genomics Chromium Single Cell 5’ Library and Gel Bead Kit v1 chemistry (Cat# 1000006, 10x Genomics;) with Chromium Single Cell 5’ Feature Barcode Library kit (Cat# 1000080, 10x Genomics) according to the manufacturer instructions.
Quality control (QC) was performed for each sample after generating cDNA, using the Qubit dsDNA High Sensitivity kit (Cat# Q32854, Invitrogen) and the Agilent High Sensitivity BioA DNA kit (Cat# 5067-4626, Agilent), for concentration and size distribution evaluation respectively. Only samples that have passed QC were used for library generation and were sequenced on a NextSeq 500 sequencer (Illumina) using pair-end reads, with 26 reads for read 1 and 55 reads for read 2.

tag: subject

value: patient HN77

value: tumor

tag: Sex

value: Male

tag: age

tag: hpv-status

value: Positive

tag: smoking history

value: No

tag: original anatomic_site

value: Nasopharynx

tag: anatomic location_of_scrna-seq_specimen

value: Primary


title: 63 PR3 none 24h donor A


title: Primary tumor of patient HN76

value: patient HN76

tag: tissue

value: Oropharynx


title: Primary tumor of patient HN72

value: patient HN72

value: Negative

value: Yes

value: Oral cavity


title: Primary tumor of patient HN75

value: patient HN75


title: 60 PR3 none 24h donor A


title: Recurrence of patient HN73

value: patient HN73

value: Female

value: Locoregional recurrence


title: 65 MPO none 24h donor A

value: monocytes

value: MPO


title: 62 PR3 none 24h donor A


title: 58 PR3 none 24h donor A


title: Primary tumor of patient HN74

value: patient HN74

value: tumor


title: 70 MPO none 24h donor A


title: 61 PR3 none 24h donor A


title: Primary tumor of patient HN70

value: patient HN70

value: Male

value: Larynx/Hypopharynx


title: 59 PR3 none 24h donor A


title: Primary tumor of patient HN68

value: patient HN68

value: Positive

value: No

value: Primary


title: 57 PR3 none 24h donor A


title: Gar15-13 Decitabine 1 CTCF

value: Breast cancer PDX model Gar15-13

value: Decitabine

value: CTCF (Millipore-Merck 07-729)


title: Primary tumor of patient HN67

value: patient HN67

value: Negative

value: Yes

value: Oral cavity


title: 68 MPO none 24h donor A

value: monocytes

value: MPO


title: Recurrence of patient HN66

value: patient HN66

value: tumor

value: Oropharynx

value: Locoregional recurrence


title: Primary tumor of patient HN63

value: patient HN63

value: Male


title: Liver metastasis of patient HN71

value: patient HN71

value: Distant metastasis (Liver)


title: Primary tumor of patient HN64

value: patient HN64

value: Larynx/Hypopharynx

value: Primary


title: 54 control none 24h donor A

value: control


title: Liver metastasis of patient HN61

value: patient HN61

value: Negative

value: Nasopharynx


title: 53 control none 24h donor A

value: monocytes


title: Primary tumor of patient HN59

value: patient HN59

value: Positive

value: No


title: Primary tumor of patient HN60

value: patient HN60

value: tumor

value: Female

value: Yes

value: Oral cavity


title: 52 control none 24h donor A


title: Primary tumor of patient HN58

value: patient HN58

value: Male

value: Oropharynx


title: 51 control none 24h donor A


title: Recurrence of patient HN55

value: patient HN55

value: Larynx/Hypopharynx

value: Locoregional recurrence


title: 48 MPO none 24h donor G

description:
donor G
genes.readcount.annot.xls
genes.FPKM.annot.xls

value: MPO


title: Recurrence of patient HN57

value: patient HN57

value: Negative


title: 44 MPO none 24h donor G

value: monocytes


title: 45 MPO none 24h donor G


title: 47 MPO none 24h donor G


title: 46 MPO none 24h donor G


title: Primary tumor of patient HN52

value: patient HN52

value: Positive

value: Primary


title: 50 control none 24h donor A

value: control


title: Primary tumor of patient HN49

value: patient HN49

value: tumor

value: No


title: Primary tumor of patient HN50

value: patient HN50

value: Yes


title: Recurrence of patient HN45

value: patient HN45

value: Male


title: 55 control none 24h donor A


title: Primary tumor of patient HN46

value: patient HN46

value: Female

value: Larynx/Hypopharynx


title: 42 MPO none 24h donor G

value: MPO


title: 43 MPO none 24h donor G


title: 56 control none 24h donor A


title: 41 MPO none 24h donor G


title: Recurrence of patient HN43

value: patient HN43

value: Negative

value: Locoregional recurrence


title: Lung metastasis of patient HN42

value: patient HN42

value: Positive

value: Oropharynx

value: Distant metastasis (Lung)


title: 49 control none 24h donor A

value: monocytes

value: control


title: 40 PR3 none 24h donor G


title: Primary tumor of patient HN40

value: patient HN40

value: tumor

value: No

value: Oral cavity

value: Primary


title: 39 PR3 none 24h donor G


title: 38 PR3 none 24h donor G


title: Recurrence of patient HN38

value: patient HN38

value: Male


title: Primary tumor of patient HN39

value: patient HN39

value: Yes


title: Recurrence of patient HN35

value: patient HN35

value: Female

value: Negative


title: 36 PR3 none 24h donor G


title: Lung metastasis of patient HN33

value: patient HN33

value: Positive


title: 34 PR3 none 24h donor G


title: Recurrence of patient HN32

value: patient HN32

value: Locoregional recurrence


title: Recurrence of patient HN37

value: patient HN37

value: Larynx/Hypopharynx


title: Lung metastasis of patient HN34

value: patient HN34

value: tumor

value: Nasopharynx

value: Distant metastasis (Lung)


title: 37 PR3 none 24h donor G

value: monocytes


title: Recurrence of patient HN29

value: patient HN29

value: Male


title: Primary tumor of patient HN30

value: patient HN30

value: No

value: Oral cavity

value: Primary


title: Primary tumor of patient HN31

value: patient HN31

value: Negative

value: Yes


title: 29 control none 24h donor G

value: control


title: 30 control none 24h donor G


title: 33 PR3 none 24h donor G


title: 31 control none 24h donor G


title: 35 PR3 none 24h donor G


title: 28 control none 24h donor G


title: 27 control none 24h donor G


title: Lung metastasis of patient HN27

value: patient HN27

value: Positive

value: Oropharynx


title: 32 control none 24h donor G


title: Recurrence of patient HN26

value: patient HN26

value: tumor

value: Female

value: Locoregional recurrence


title: Lung metastasis of patient HN25

value: patient HN25

value: Distant metastasis (Lung)


title: Recurrence of patient HN28

value: patient HN28


title: 25 control none 24h donor G

value: monocytes


title: 24 MPO none 24h donor B

description:
donor B
genes.readcount.annot.xls
genes.FPKM.annot.xls

value: MPO


title: Recurrence of patient HN23

value: patient HN23

value: Male

value: Larynx/Hypopharynx


title: 22 MPO none 24h donor B


title: 23 MPO none 24h donor B


title: Liver metastasis of patient HN21

value: patient HN21

value: No

value: Distant metastasis (Liver)


title: Primary tumor of patient HN17

value: patient HN17

value: Negative

value: Unknown

value: Unknown primary of the head and neck


title: 20 MPO none 24h donor B


title: 19 MPO none 24h donor B


title: Skin metastasis of patient HN13

value: patient HN13

value: tumor

value: Female

value: Yes

value: Distant metastasis (skin)


title: Pleura metastasis of patient HN14

value: patient HN14

value: Oropharynx

value: Distant metastasis (pleura)


title: Sternum metastasis of patient HN8

value: patient HN8

value: Male

value: Distant metastasis (sternum)


title: Primary tumor of patient HN7

value: patient HN7

value: No

value: Oral cavity

value: Primary


title: 17 MPO none 24h donor B

value: monocytes

value: MPO


title: Lung metastasis of patient HN2

value: patient HN2

value: Negative

value: Distant metastasis (Lung)


title: 26 control none 24h donor G

value: control


title: 16 PR3 none 24h donor B


title: 18 MPO none 24h donor B


title: 14 PR3 none 24h donor B


title: 15 PR3 none 24h donor B


title: Recurrence of patient HN22

value: patient HN22

value: tumor

value: Locoregional recurrence


title: GOKM_D24_A

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the human genome (hg38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 99, using htseq-count (version 0.6.1p1) with stranded="reverse" option.
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Assembly: hg38
Supplementary files format and content: Processed file include raw counts.

source_name: GOKM reprogramming day 24

growth_protocol: hbdTSC cells were grown in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF. Infected-HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin supplamentd with 2ug/ml doxycycline for 14 days, 1:1 with human TSC medium for 7 days and  human TSC medium for 3 days.

extract_protocol:
Total RNA was isolated using the Macherey-Nagel RNA NucleoSpin kit (Ornat)
mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen)

value: GOKM-infected Foreskin fibroblasts


title: 13 PR3 none 24h donor B


title: GSKM_D24_B

source_name: GSKM reprogramming day 24

value: GSKM-infected Foreskin fibroblasts


title: 12 PR3 none 24h donor B


title: GSKM_D24_A


title: C_36_2

city: Kunming

first: wenjie

last: wang

address: Kunming

country: China

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae cells

growth_protocol: The WT and mutant strains were cultured in PDA at 28 °C, 180 rpm for 7 days.

extract_protocol:
The mycelium was divided and induced with about 400 nematodes for 0 and 36 h, respectively.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit foilowing manufacturer's protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

value: hyphae cells

tag: genotype

value: {delta}Aoso

value: induced with about 400 nematodes for 36 h


title: C_36_3

tag: cell type


title: Recurrence of patient HN20

value: patient HN20

value: Male

value: No

value: Oral cavity


title: C_36_1


title: 21 MPO none 24h donor B

value: monocytes

value: MPO


title: OSKM_D24_A

source_name: OSKM reprogramming day 24

value: OSKM-infected Foreskin fibroblasts


title: 11 PR3 none 24h donor B


title: OSKM_D24_B


title: B_36_3


title: 10 PR3 none 24h donor B


title: GOKM_D18_B

source_name: GOKM reprogramming day 18


title: Primary tumor of patient HN1

value: patient HN1

value: Negative

value: Yes

value: Primary


title: GSKM_D18_B

source_name: GSKM reprogramming day 18


title: 9 PR3 none 24h donor B


title: GSKM_D18_A


title: B_36_1


title: OSKM_D18_B

source_name: OSKM reprogramming day 18


title: OSKM_D18_A


title: GOKM_D18_A

value: GOKM-infected Foreskin fibroblasts


title: A_36_3

value: WT


title: GOKM_D12_B

source_name: GOKM reprogramming day 12


title: GOKM_D24_B


title: 8 control none 24h donor B

value: control


title: 7 control none 24h donor B


title: GOKM_D12_A


title: GSKM_D12_B

source_name: GSKM reprogramming day 12

value: GSKM-infected Foreskin fibroblasts


title: A_36_2

value: Fungal hyphae

value: hyphae cells


title: 6 control none 24h donor B


title: A_36_1

value: induced with about 400 nematodes for 36 h


title: GSKM_D12_A


title: OSKM_D12_B

source_name: OSKM reprogramming day 12


title: OSKM_D12_A


title: C_0_3

value: {delta}Aoso

value: induced with about 400 nematodes for 0h


title: 5 control none 24h donor B


title: B_36_2


title: GOKM_D6_B

source_name: GOKM reprogramming day 6


title: 4 control none 24h donor B


title: C_0_2


title: B_0_3


title: 2 control none 24h donor B


title: C_0_1


title: GSKM_D3_B

source_name: GSKM reprogramming day 3


title: GOKM_D3_B

source_name: GOKM reprogramming day 3


title: GSKM_D6_A

source_name: GSKM reprogramming day 6


title: OSKM_D6_A

source_name: OSKM reprogramming day 6


title: OSKM_D6_B


title: 3 control none 24h donor B

source_name: monocytes isolated from blood


title: 1 control none 24h donor B

description:
donor B
genes.readcount2.annot.xls
genes.FPKM.annot2.xls


title: GSKM_D3_A


title: B_0_2


title: GOKM_D3_A


title: 724 PR3 R848 6h donor E

description:
donor E
genes.readcount2.annot.xls
genes.FPKM.annot2.xls


title: B_0_1


title: OSKM_D3_B

source_name: OSKM reprogramming day 3


title: OSKM_D3_A


title: A_0_3


title: hiPSCs_B

source_name: Human induced pluripotent stem cells

value: Induced pluripotent stem cells


title: 722 PR3 R848 6h donor E

value: monocytes


title: GOKM_D6_A


title: GSKM_D6_B


title: 723 PR3 R848 6h donor E


title: hiPSCs_A


title: hbdTSCs_B

value: Blastocyst-derived trophoblast stem cells, line #2


title: A_0_1


title: 721 PR3 R848 6h donor E


title: Fibroblasts_KEN_B

source_name: Human foreskin fibroblasts

value: Foreskin fibroblasts


title: A_0_2

source_name: Fungal hyphae cells


title: Fibroblasts_KEN_A


title: 720 PR3 R848 6h donor E


title: 719 PR3 R848 6h donor E


title: IPDC, biol rep 2

city: Granada

first: Míriam

last: Rico Jiménez

state: Granada

address: Profesor albareda, 1

department: Biotechnology and environmental protection

country: Spain

institute: CSIC

data_processing:
Data were analyzed using Novosmart software (Novogene, Cambridge, UK).
Original image data file from Illumina sequencing is transformed into sequenced reads by CASAVA base recognition (base calling).
Trimmed sequence reads were mapped to LRQU00000000 using Bowtie2 (the mismatch parameter is set to two and other parameters are set to default)
Read count extraction and normalization were performed using FeatureCounts software and estimation of the number of Fragments Per Kilobase of transcript sequence per Millions base pair-sequenced (FPKM), respectively.
Assembly: LRQU00000000
Supplementary files format and content: Tab-delimited xls file include FPKM values for all the samples.

organism: Serratia plymuthica

growth_protocol: The parental strain Serratia plymuthica A153 and the ipdc mutant were grown to mid-logarithmic phase in lysogeny broth medium supplemented with 1mg/ml L-tryptophan at 30 ºC.

extract_protocol:
RNA was extracted f by the hot phenol method using the TRI® Reagent protocol (Ambion) according to the manufacturer's instructions. RNA concentration was determined spectrophotometrically using a NanoDrop spectrophotometer (Thermo Scientific) and RNA integrity was assessed by agarose gel electrophoresis. Genomic DNA contamination was eliminated by treating total RNA with Turbo DNA‐free (Ambion), followed by a purification with RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit following manufacturer's protocols.

tag: strain

value: ipdc knockdown


title: IPDC, biol rep 3


title: 717 PR3 R848 6h donor E


title: IPDC, biol rep 1


title: A153 WT,  biol rep 3


title: 718 PR3 R848 6h donor E


title: 716 MPO R848 6h donor E

value: MPO


title: T4

city: Xi'an

first: Guanzhi

last: Liu

state: China

address: No.157 Xiwu road Xi'an Shanxi

institute: Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Trimmed reads were identified after raw sequencing data quality control and filtering process by Solexa CHASTITY program and Cutadapt software. Adapter sequences and sequences length < 15 were removed. Subsequently, we obtained human reference genome indexing (hg38) and miRNA reference data (version 22) via  bowtie software (http://bowtie-bio.sourceforge.net/index.shtml) and miRBase database (http://www.mirbase.org/). Then, sequencing alignment and microRNA identification were achieved by miRdeep2 program.
Genome_build: we obtained human reference genome indexing (hg38) and miRNA reference data (version 22) via  bowtie software (http://bowtie-bio.sourceforge.net/index.shtml) and miRBase database (http://www.mirbase.org/)
Supplementary_files_format_and_content: txt,normalized microRNA expression data

source_name: Blood Plasma

extract_protocol:
Total RNA from plasma samples were extracted using TRIzol LS Reagent (Invitrogen) according to the manufacturer’s instructions. Then, sequencing libraries were generated by NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following the standardized protocols. Agilent Bioanalyzer 2100 system (Agilent) was used to qualified the sequencing libraries. Finally, the high-throughput next-generation sequencing was carried out using TruSeq Rapid SR Cluster Kit (Illumina) based on the Illumina NextSeq 500 sequencing platform (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: metabolic syndrome

value: plasma


title: BLaER cells, 24h CEBPA induced,rep1

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

institute: CRG

data_processing:
Hi-C data were processed using an in-house pipeline based on TADbit (Serra et al., 2017). First, quality of the reads was checked using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/) to discard problematic samples and detect systematic artefacts. Trimmomatic (Bolger et al., 2014) with the recommended parameters for paired end reads was used to remove adapter sequences and poor quality reads (ILLUMINACLIP:TruSeq3-PE.fa:2:30:12:1:true; LEADING:3; TRAILING:3; MAXINFO:targetLength:0.999; and MINLEN:36). For mapping, a fragment-based strategy as implemented in TADbit was used, which is similar to previously published protocols (Ay et al., 2015). Briefly, each side of the sequenced read was mapped in full length to the reference genome (hg38, Dec 2017 GRCh38). After this step, if a read was not uniquely mapped, we assumed the read was chimeric due to ligation of several DNA fragments.
We next searched for ligation sites, discarding those reads in which no ligation site was found. Remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. These steps were repeated for each read in the input FASTQ files. Multiple fragments from a single uniquely mapped read will result in as many contacts as possible pairs can be made between the fragments. For example, if a single read was mapped through three fragments, a total of three contacts (all-versus-all) was represented in the final contact matrix. We used the TADbit filtering module to remove non-informative contacts and to create contact matrices. The different categories of filtered reads applied are:  • self-circle: reads coming from a single restriction enzyme (RE) fragment and point to the outside.  • dangling-end: reads coming from a single RE fragment and point to the inside.  • error: reads coming from a single RE fragment and point in the same direction.  • extra dangling-end: reads coming from different RE fragments but are close enough and point to the inside. The distance threshold used was left to 500 bp (default), which is between percentile 95 and 99 of average fragment lengths.  • duplicated: the combination of the start positions and directions of the reads was repeated, pointing at a PCR artefact. This filter only removed extra copies of the original pair.  • random breaks: start position of one of the reads was too far from RE cutting site, possibly due to non-canonical enzymatic activity or random physical breaks. Threshold was set to 750 bp (default), > percentile 99.9. From the resulting contact matrices, low quality bins (those presenting low contacts numbers) were removed as implemented in TADbit’s “filter_columns” routine.
Bam files generated by TADbit were then converted to HiCsummary imput files which is a simple text file format that contains the mapping positions for a read-pair on each line.  that can be used by HOMER (samtools view /users/project/4DGenome/data/hic/samples/${id}/results/hg38_mmtv/processed_reads/${id}_both_map.bam > ${describer}_pseudobam.txt  python /software/tgraf/sam2tsv.py < ${describer}_pseudobam.txt > ${describer}_pseudobam_converted.txt  awk '{print $1, $2, $3, $4, $8, $9, $10}' ${describer}_pseudobam_converted.txt | awk '{if ($3 <= $6) {print $0}}' | sed -e 's/\ 0\ /\ -\ /g' -e 's/\ 1\ /\ +\ /g' -e 's/\ 0$/\ -$/g' -e 's/\ 1$/\ +$/g' | sed -e 's/\ /\t/g' -e 's/\$//g' > ${describer}_input_homer.txt)
Homer Tag directory were then generted using the HOMER command line: /software/tgraf/HOMER/bin/makeTagDirectory homer_${describer} -format HiCsummary ${describer}_input_homer.txt
To segment the genome into high resolution A/B compartments, we used CscoreTool (Zheng and Zheng 2018) to allow for rapid compartment analysis at 10 kb resolution, with computed C scores reflecting quantitative association with A (0 to 1) or B (-1 to 0) compartments for each bin.
Assembly: hg38
Supplementary files format and content: bigwig files chromatin compartmentalization data segmented ast 10kb resolution

source_name: BLaER KO

extract_protocol:
Cells were collected by centrifugation and wahed twice with fresh medium
Cells were collected and crosslinked with 1% formaldehyde. Nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction. DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs). Libraries were amplified for 8-12 cycles using Illumina TruSeq primers. Amplified libraries were purified and size-selected (>250bp) using Ampure XP beads.

treatment_protocol: BlaER cells were cultured for 24h  in RPMI 1640 medium supplemented with glutamine, penicillin-streptomycin and 10% FCS and b-estradiol (100nM).

tag: cell line

value: BLaER KO

value: B cells

tag: treatment

value: b-estradiol


title: BLaER cells, 24h CEBPA induced,rep2


title: BLaER cells non-induced, rep1


title: T3

description: Total RNA from plasma samples were extracted using TRIzol LS Reagent (Invitrogen) according to the manufacturer’s instructions. Then, sequencing libraries were generated by NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following the standardized protocols. Agilent Bioanalyzer 2100 system (Agilent) was used to qualified the sequencing libraries. Finally, the high-throughput next-generation sequencing was carried out using TruSeq Rapid SR Cluster Kit (Illumina) based on the Illumina NextSeq 500 sequencing platform (Illumina).


title: T2


title: C5

value: healthy control


title: hbdTSCs_A

source_name: Blastocyst-derived trophoblast stem cells


title: A153 WT,  biol rep 1

value: WT


title: C3


title: T1


title: 715 MPO R848 6h donor E

tag: group (control, mpo, pr3)


title: 714 MPO R848 6h donor E

tag: treatment (none, lps, r848)


title: 5xFAD microglia, microglial repopulation [FAD_Rep3]

city: Xiamen

first: wanbing

last: Wang

state: Fujian Province

address: 4221 Xiang'an South Road, Xindian Town

department: Medical Department

institute: Xiamen University

data_processing:
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
Used HISAT to align the clean reads to the reference genome.
Used Bowtie2 to align the clean reads to the reference genes.
Assembly: GRCm38.p6
Supplementary files format and content: processed_data.txt: Tab-delimited text file includes counts, TPM values, and FPKM values for each Sample.

source_name: Hippocampus

extract_protocol:
Total RNA was purified from the isolated microglia using TRIzol reagent (Thermo Fisher Scientiﬁc, 15596018).
RNA was used to produce the cDNA library with Smart-Seq protocol. 1 ng of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Four-month-old 5×FAD mice were fed with PLX3397 (Selleck, S7818, 290 mg/kg formulated in standard chow) for one month, then discontinued from PLX3377 feed and treated with a normal mouse diet for an additional one month, resulting in microglial repopulation.

value: Hippocampus

value: Microglia


title: 713 MPO R848 6h donor E

tag: time (6h, 24h)


title: BLaER cells non-induced, rep2


title: T5


title: C1


title: C2


title: A153 WT,  biol rep 2


title: 5xFAD microglia, microglial repopulation [FAD_Rep2]


title: CUT&TAG_day 4, control, replicate 1

data_processing:
Sequence reads were trimmed for adaptor sequence sequence using trimmomatic (parameter-  ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 TRAILING:30 MINLEN:30).
Trimmed sequence reads were mapped to mm10 using Bowtie2 (default parameter). Only uniquely mapping reads were retained.
The bigWig file was generated using bamCoverage tool in deepTools (--normalizeUsing RPGC --ignoreDuplicates).
Library strategy: CUT&Tag

source_name: Cerebral cortex

extract_protocol:
Four days after stroke onset, brains were removed and sliced in ice-cold artificial cerebrospinal fluid. Peri-infarct area was trimmed and treated with pronase (Sigma-Aldrich) for 75 minutes at room temperature. Enzyme-treated tissue was dissociated by gentle pipetting with a Pasteur pipette. Neuron enriched cell populations (Thy1+/ACSA2-/CD31-/CD45-) were collected by fluorescence-activated cell sorting (BD FACS Aria III).
The CUT&Tag library was prepared using a slightly modified Bench top CUT&Tag V.2 protocol described elsewhere (https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v2).
Isolated neurons were bound with activated concanavalin A-coated magnetic beads and primary antibody (1:50 dilution, anti-histone H3 (citrulline R2+R8+R17) antibody: ab5103, Abcam)
After removing primary antibody by wash buffer, the samples were bound with secondary antibody (1:100 dilution, guinea pig anti-rabbit IgG antibody: ABIN101961, antibodies-online.com).
After two washes with wash buffer, a 1:200 dilution of the pA-Tn5 adapter complex, which was prepared in Dig-325 buffer (0.025% digitonin, 20 mM HEPES, pH 7.5, 325 mM NaCl, 0.5 mM spermidine, 1:100 protease inhibitor cocktail), was added to the sample and then incubated with pA-Tn5 for 1 hour at room temperature. The samples were placed on a magnet stand to clear and washed three times with Dig-325 buffer.
Tagmentation buffer (10 mM MgCl2 in Dig-325 Buffer) was added and incubated at 37°C for 1 hour. To stop tagmentation and solubilize DNA fragments, 2.25 mL of 0.5 M EDTA, 2.75 mL of 10% SDS, and 0.5 mL of 20 mg/mL proteinase K were added to each sample, mixed at full-speed vortex for 2 seconds, and incubated at 50°C for 1 hour. For DNA purification, 122 mL of SPRI select beads was added to each sample, spun quickly, and held for 5 minutes. The tubes were placed on a magnetic stand to clear, the supernatant was discarded, the pellet was washed twice with 200 mL of 80% ethanol, and dried for 2 minutes.
Then, 11 uL of TE (1 mM Tris-HCl pH 8.0, 0.1 mM EDTA) was added and allowed to stand for 5 minutes. The tube was placed on a magnetic stand, and the liquid was withdrawn to a fresh tube. For library amplification, 10.5 uL of DNA solution was mixed with 1 uL of i5 and i7 primers (10 mM) each with unique barcodes for each sample, followed by the addition of 12.5 uL of NEBNext HiFi 2× PCR Master Mix (New England BioLabs).
Samples were placed in a thermocycler with a heated lid using the following cycling conditions: 72°C for 5 min, 98°C for 30 s; 18 cycles of [98°C 10 s, 63°C 30 s]; 72°C 1 min final extension, held at 4°C. Finally, 25 uL of Low-TE was added to the Post-PCR sample and 25 uL of SPRI select beads was added and incubated for 10 minutes.
The supernatant was transferred to a new tube, and 15 uL of SPRI select beads was added. Samples were incubated for 10 min, washed twice with 80% ethanol, and eluted with 12 uL of 10 mM Tris pH 8.0.

value: Cerebral cortex

value: male

value: Neurons

value: Padi4 flox/flox

value: transient brain ischemia (middle cerebral artery occlusion:MCAO)


title: CUT&TAG_sham, control, replicate 1

value: sham operation


title: 712 MPO R848 6h donor E

value: monocytes


title: 5xFAD microglia, microglial repopulation [FAD_Rep1]


title: C4


title: 710 MPO R848 6h donor E

value: MPO


title: 5xFAD microglia, normal diet [FAD_Ctrl3]

value: normal diet


title: 5xFAD microglia, normal diet [FAD_Ctrl2]


title: 5xFAD microglia, normal diet [FAD_Ctrl1]


title: day 4, cKO, replicate 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (parameter- HEADCROP:5 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:30 TRAILING:30 MINLEN:30).
Trimmed sequence reads were mapped to mm10 using hisat2 (default parameter).
Mapped reads were counted for each gene by featureCounts (default parameter) .
Read counts were TMM normalized using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TMM normalized CPM values for each Sample

extract_protocol:
RNA was purified using RNeasy Mini Kit (QIAGEN).
RNA libraries for RNA-seq were prepared using Ovation SoLo RNA-Seq Library Preparation Kit (Tecan) according to the manufacturer’s protocol.

treatment_protocol:
Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min.
Four days after stroke onset, brains were removed and sliced in ice-cold artificial cerebrospinal fluid. Peri-infarct area was trimmed and treated with pronase (Sigma-Aldrich) for 75 minutes at room temperature. Enzyme-treated tissue was dissociated by gentle pipetting with a Pasteur pipette.
Neuron-enriched cell populations (Thy1+/ACSA2-/CD31-/CD45-/O4-) were collected by fluorescence-activated cell sorting (BD FACS Aria III).


title: day 4, cKO, replicate 2


title: day 4, control, replicate 3


title: 709 MPO R848 6h donor E


title: day 4, control, replicate 2


title: day 4, control, replicate 1


title: WT microglia, normal diet [WT4]


title: 707 control R848 6h donor E

value: control


title: day 4, 15-H, replicate 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (parameter- HEADCROP:5 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:30 TRAILING:30 MINLEN:30).
Trimmed sequence reads were mapped to mm10 using hisat2 (default parameter).
Mapped reads were counted for each gene by featureCounts (default parameter) .
Read counts were TMM normalized using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TMM normalized CPM values for each sample

treatment_protocol:
Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min.
A total of 600 ng of 15-HETrE or vehicle was dissolved in 150 uL of PBS, and was then administered intravenously to MCAO mice every 24 h (24, 48, and 72 h) after stroke onset.
Four days after stroke onset, brains were removed and sliced in ice-cold artificial cerebrospinal fluid. Peri-infarct area was trimmed and treated with pronase (Sigma-Aldrich) for 75 minutes at room temperature. Enzyme-treated tissue was dissociated by gentle pipetting with a Pasteur pipette.
Neuron enriched cell populations (Thy1+/ACSA2-/CD31-/CD45-/O4-) were collected by fluorescence-activated cell sorting (BD FACS Aria III).

value: Wild type (C57BL/6N)

value: administration of 15-HETrE


title: CUT&TAG_day 4, cKO, replicate 1

value: Slc17a7-Cre; Slc32a1-Cre; Padi4 flox/flox


title: 711 MPO R848 6h donor E


title: WT microglia, normal diet [WT3]


title: day 4, 15-H, replicate 1


title: day 4, Padi4-flox, replicate 1

data_processing:
Sequence reads were trimmed for adaptor sequence sequence using trimmomatic (parameter-  ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 TRAILING:30 MINLEN:30).
Trimmed sequence reads were mapped to mm10 using Bowtie2 (default parameter). Only uniquely mapping reads were retained.
The bigWig file was generated using bamCoverage tool in deepTools (--binsize 1, --normalizeUsing RPGC ).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were extracted by treating the isolated neurons with lysis buffer (IGEPAL CA-630 0.1 %, Tris-HCl 10 mM, NaCl 10 mM and MgCl2 3 mM) and treated with Tn5 transposase (Illumina, Nextera DNA Library Preparation Kit) for fragmentation and tagmentation of genome DNA.
The DNA fragments were PCR amplified with KAPA HiFi HS ReadyMix (KAPA BIOSYSTEMS). Post-amplification libraries were size-selected at 200-1000 bp in length using AMPure XP beads (BECKMAN).

treatment_protocol:
Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min.
Four days after stroke onset, brains were removed and sliced in ice-cold artificial cerebrospinal fluid. Peri-infarct area was trimmed and treated with pronase (Sigma-Aldrich) for 75 minutes at room temperature. Enzyme-treated tissue was dissociated by gentle pipetting with a Pasteur pipette.
Neuron enriched cell populations (Thy1+/ACSA2-/CD31-/CD45-) were collected by fluorescence-activated cell sorting (BD FACS Aria III).


title: 706 control R848 6h donor E


title: WT microglia, normal diet [WT2]


title: day 4, Vehicle, replicate 3

value: administration of vehicle


title: WT microglia, normal diet [WT1]

value: WT


title: day 4, Vehicle, replicate 2


title: day 4, cKO, replicate 1


title: 705 control R848 6h donor E


title: 704 control R848 6h donor E


title: Acinar_1274_3

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
Raw reads (fastq files) were aligned to mouse reference (mm10) using STAR aligner (version 2.6) with default settings,  FPKM matrix was generated by cufflink.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text for gene FPKM, sample information, and gene annotation

source_name: pancreatic tumor

extract_protocol:
RNA isolated from murine pancreatic tumors or cultured pancreatic ducts using RNeasy extraction kit
RNA libraries were prepared for sequencing using the standard Illumina protocols

treatment_protocol: Eight week old transgenic mice were given tamoxifen and either euthanized at evidence of late stage disease or at day 4 for ex vivo culture analysis.

value: Ptf1a:CreERT2; LSL-KrasG12D; LSL-Trp5

value: pancreatic tumor

value: acinar cells


title: 708 control R848 6h donor E


title: Acinar_1247_2


title: Shoot, Warm, 30minutes, replicate 3 [Sh_030_Warm_3]

city: West Lafayette

first: Kranthi

last: Varala

state: IN

address: 625 Agriculture Mall Dr.

department: Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
Reads aligned to ITAG 3.2 with BBMap (v37.93) with default parameters
Reads assigned to features using the featureCounts program in the subread package.
Read counts were filtered to remove features with less than 0.5 RPM in at least 3 libraries and then normalized using the TMM function in edgeR
Assembly: ITAG3.2
Supplementary files format and content: Root_wO_TMM.txt contains the filtered, normalized read counts from root samples, that was used for statistical analysis
Supplementary files format and content: Shoot_wO_TMM.txt contains the filtered, normalized read counts from shoot samples, that was used for statistical analysis

organism: Solanum lycopersicum

source_name: Shoot

growth_protocol: Tomato seeds (L. M82 cultivar, TGRC accession: LA3475) were sterilized with 20% bleach solution for 20 minutes, rinsed thoroughly with deionized water, germinated on 1/2MS-media in Petri dishes in a growth chamber set at 24°C/20°C (day/night) with a photoperiod of 16h/8h (day/night) and a PAR of 100mol m-2s-1 for 7-days. Seedlings were then transferred to a hydroponics system containing Hoagland solution. The solution was renewed every 3 or 4 days and the pots were aerated for 2h/d, for 11-days.

extract_protocol: Total RNA was extracted from 15 shoot samples (two treatments + two timepoints +  three biological replicates + three time zero samples) and 9 root samples (two treatments + three biological replicates + three time zero samples) with RNeasy Plant Mini Kit (Qiagen, USA) following the manufacturer’s protocol. The quality and quantity of RNA were checked using the Nanodrop 1000 spectrophotometer (ThermoScientific, USA). RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies). All samples had RIN values >8. The RNA samples were processed, and sequencing libraries were generated using the Illumina TruSeq RNA Sample preparation kit for cDNA library preparation and sequenced on the Illumina HiSeq or NovaSeq platforms (150 cycles, paired end)

treatment_protocol: On the 18th day, tomato plants of nearly identical size were chosen and divided into two, equal groups and moved to fresh hydroponic containers 2.5 hours after the start of light cycle (i.e., Zeitgeber time (ZT) 2.5). One group remained at 24°C and the other group was transferred to 4°C in a cold-room. Both groups were exposed to light with a PAR of 100mmol m-2s-1.

value: Shoot

value: Ambient


title: Shoot, Warm, 30minutes, replicate 2 [Sh_030_Warm_2]


title: Ductal_1661_3

value: ductal cells


title: 702 control R848 6h donor E


title: 701 control R848 6h donor E


title: 703 control R848 6h donor E


title: Shoot, Cold, 30minutes, replicate 3 [Sh_030_Cold_3]

value: Cold


title: Acinar_1247_1


title: Ductal_1661_1


title: Ductal_1661_2


title: No-Sec, 10uM IPTG, rep1

first: Neel

last: Joshi

state: MA

address: 10 Gainsborough St

department: Chemistry and Chemical Biology

institute: Northeastern University

data_processing:
2x150 paired-end sequence reads
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Illumina HiSeq 4000 reads were trimmed and mapped to the reference genome {Ecoli_Nissle1917(GCF_003546975.1_ASM354697v1_genomic), sequence for plasmid pSecGFP1h and sequences for ERCC} using the STAR aligner v.2.5.2b.
Gene hit counts were calculated using featureCounts from Subread package v.1.5.2.
Assembly: Ecoli_Nissle1917(GCF_003546975.1_ASM354697v1_genomic) and the sequence for plasmid pSecGFP1h
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Escherichia coli

source_name: Escherichia coli Nissle 1917 (EcN)

growth_protocol: PBP8 cells were transformed with plasmid construct variants. Strains were grown in LB media with antibiotics (Kanamycin 50 μg/mL). 10uM IPTG was added to the media of some of the groups to induce GFP expression (for details, see treatment protocol below). The strains were grown in triplicate at 37°C and 225 RPM for 5.5 hours. Cells were then pelleted and frozen down for RNA extraction.

extract_protocol:
Total RNA was extracted by Genewiz (from Azenta Life Sciences). The extraction started with fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA following manufacturer’s protocol.
RNA samples were next quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion sequencing library was prepared by using QIAGEN Fastselect rRNA 5S/16S/23S Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).

treatment_protocol: The presence of a plasmid construct and IPTG inducer supplemented into the growth media dictate treatment groups. All-Tags 0 μM IPTG group (Samples 1-3): PBP8 transformed with pSecGFP1h plasmid DNA without induction of GFP expression or secretion, as no IPTG was provided. All-Tags 10 μM IPTG group (Samples 4-6): PBP8 transformed with pSecGFP1h plasmid DNA and provided 10 μM IPTG supplemented into LB media to induce the expression and secretion of GFP. No-Sec 10 μM IPTG group (Samples 7-9): PBP8 transformed with pSecGFP-N22 plasmid DNA and provided 10 μM IPTG supplemented into LB media to induce the expression of GFP within the cytosol. IPTG was added to media used by the All-Tags 10 μM IPTG and No-Sec 10 μM IPTG groups at the start of growth to allow cells to produce GFP for the duration of the growth period (5.5 hours).

value: Escherichia coli Nissle 1917 (EcN)

value: Prokaryote

value: PBP8 (EcN delta-csgBACDEFG::CmR); pSecGFP-N22 (plasmid DNA)

value: 10 uM IPTG


title: day 4, Vehicle, replicate 1

value: Cerebral cortex

value: male

value: Neurons

value: transient brain ischemia (middle cerebral artery occlusion:MCAO)


title: 624 PR3 R848 6h donor D

description:
donor D
genes.readcount2.annot.xls
genes.FPKM.annot2.xls

value: monocytes


title: Shoot, Cold, 30minutes, replicate 2 [Sh_030_Cold_2]


title: 623 PR3 R848 6h donor D


title: Shoot, Cold, 30minutes, replicate 1 [Sh_030_Cold_1]


title: All-Tags, 10uM IPTG, rep3

value: PBP8 (EcN delta-csgBACDEFG::CmR); pSecGFP1h (plasmid DNA)


title: All-Tags, 10uM IPTG, rep1


title: No-Sec, 10uM IPTG, rep2


title: No-Sec, 10uM IPTG, rep3


title: day 4, 15-H, replicate 2

value: Wild type (C57BL/6N)

value: administration of 15-HETrE


title: All-Tags, 10uM IPTG, rep2


title: All-Tags, 0uM IPTG, rep3

value: 0 uM IPTG


title: Shoot, pretreatment, replicate 6 [Sh_000_6]

value: Shoot


title: Shoot, Warm, 30minutes, replicate 1 [Sh_030_Warm_1]

value: Ambient


title: 621 PR3 R848 6h donor D


title: All-Tags, 0uM IPTG, rep1


title: 620 PR3 R848 6h donor D


title: Shoot, pretreatment, replicate 4 [Sh_000_4]


title: Shoot, pretreatment, replicate 5 [Sh_000_5]


title: 619 PR3 R848 6h donor D


title: 618 PR3 R848 6h donor D


title: 622 PR3 R848 6h donor D


title: 617 PR3 R848 6h donor D


title: 616 MPO R848 6h donor D

value: MPO


title: 615 MPO R848 6h donor D


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 15, tech rep 2

city: Galveston

first: Thomas

last: Geisbert

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Processed data file col_name: nhp1502316_28_419

data_processing:
Sequencing quality of each sequenced sample was analyzed with fastQC (version 0.11.7).
Raw fastq files were trimmed with trimmomatic (version 0.36) with “LEADING” and “TRAILING” set to cut sequences below quality Phred score of 3 from the beginning or end of the read, respectively. Sequences below 15bp were automatically rejected.
STAR RNA-seq aligner (Dobin & Gingeras, 2015) version 2.5.3a was then used to create an index containing the cynomolgus macaque (Version 5.0), BDBV, and VSV genomes. Trimmed reads were aligned to these genomes using STAR.
The number of reads associated with each transcript was then counted with featureCounts (subread package version 1.6.2).
Genes with multiple possible transcripts were combined to get the number of reads per gene using DESeq2 (version 1.32.0). DESeq2 was used to normalize library sizes and measure differential expression between pre-infection and post infection samples.
Assembly: Macaca_fascicularis_5.0 (GCA_000364345.1)
Supplementary files format and content: bdbv_2019_30min_raw_counts.xlsx: total gene counts, pre-normalization by DESeg2

organism: Macaca fascicularis

source_name: Blood

growth_protocol: The BDBV used in this study, strain 200706291 (GenBank accession no. MK028856.1), was isolated from a fatal human case in western Uganda during the outbreak in 2007. The challenge stock of BDBV was propagated on Vero E6 cells twice.

extract_protocol:
At least three million PBMC were inactivated with Trizol LS buffer (Thermo Fisher Scientific) for isolation of RNA. RNA was isolated using Direct-zol RNA Miniprep purification kits (Zymo Research) following the directions of the manufacturer with the optional DNAse I treatment and subsequent wash steps. RNA was eluted in 30ul of DNase/RNase-free water.
An Illumina Ribo-Zero Stranded kit was used to deplete ribosomal RNA (rRNA) and construct cDNA libraries according to the protocol provided by the manufacturer. RNA was fragmented, converted to double-stranded cDNA, and adapters ligated to each strand. The resulting base-pair cDNA fragments were then amplified by PCR. Each library was prepared with a unique indexed adapter for multiplexing. Multiplexed libraries were subjected to paired-end 75 base pair sequencing using the Illumina NextSeq550 PE platform.

value: Blood

value: PBMC

value: WT

tag: animal id

tag: animal id supp

value: Survivor 3

value: female

tag: outcome

value: survived

tag: challenge

value: BDBV

tag: time (days post infection)

tag: treatment time

value: VSV-BDBV-GP

tag: tech rep


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 28, tech rep 1

description: Processed data file col_name: nhp1502316_09_418

tag: tissue

tag: Sex


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 9, tech rep 2

description: Processed data file col_name: nhp1502316_15_417

tag: cell type

tag: genotype


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 21, tech rep 2

description: Processed data file col_name: nhp1502316_09_417


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 12, tech rep 2

description: Processed data file col_name: nhp1502316_21_415


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 5, tech rep 1

description: Processed data file col_name: nhp1502316_01_417


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 21, tech rep 1

description: Processed data file col_name: nhp1502316_07_419


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 9, tech rep 1

description: Processed data file col_name: nhp1502316_12_416


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 12, tech rep 1

description: Processed data file col_name: nhp1502316_15_418


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 5, tech rep 2

description: Processed data file col_name: nhp1502316_01_418


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 15, tech rep 1

description: Processed data file col_name: nhp1502316_21_416


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 7, tech rep 1

description: Processed data file col_name: nhp1502316_12_415


title: All-Tags, 0uM IPTG, rep2

value: Escherichia coli Nissle 1917 (EcN)

value: Prokaryote


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 1, tech rep 2

description: Processed data file col_name: nhp1502316_00_419


title: DC treated with SF and CC, rep2

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data from Dendritic cells treated with sulforaphane and cytokine cocktail

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were imported with the expression console  Build 1.4.1.46.  Gene expression profiling was performed using  Multispecies miRNA-4 Array-type from Affymetrix. The original  CDF file from Affymetrix [ProbeSet ID version] was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary. The differential expression analysis was performed with a commercial software called JMP Genomics, version 6, from SAS.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The  beads-isolated CD14+ monocytes were incubated in  medium supplemented with 1.5% autologous plasma,GM-CSF and l IL-4,  at 5% CO2 and 37°C, and were collected on day 5 or 6 as MoDC

extract_protocol: The miRNeasy® Mini Kit (Qiagen, Hilden, Germany) was used for the extraction of DC-derived miRNA according to the manufacturer's instructions

treatment_protocol: MoDCs were pretreated with sulforaphane (SF) or vehicle control (DMSO) for 30 min, followed by treatment with a cytokine cocktail (CC)

value: Dendritic cells


title: DC treated with SF and CC, rep1

source_name: Dendritic cells treated with sulforaphane and cytokine cocktail


title: DC treated with SF and CC, rep3


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 9, tech rep 3

description: Processed data file col_name: nhp1411253_09_417

value: Control

value: male

value: succumbed

value: VSV-LASV-GP


title: DC treated with DMSO and CC, rep3

description: Gene expression data from Dendritic cells treated with cytokine cocktail and vehicle control


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 0, tech rep 1

description: Processed data file col_name: nhp1502316_05_415


title: 614 MPO R848 6h donor D

description:
donor D
genes.readcount2.annot.xls
genes.FPKM.annot2.xls

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.  HTSeq was used to count the read numbers mapped of each gene.
RPKM of each gene was then calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time.
Supplementary files format and content: 2 excel files contain the read counts for all the samples and 2 excel files contain the FPKM data for all the samples.

value: monocytes


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 3, DPI 1, tech rep 1

description: Processed data file col_name: nhp1502316_05_416


title: 613 MPO R848 6h donor D

value: MPO


title: DC treated with DMSO and CC, rep2

source_name: Dendritic cells treated with cytokine cocktail and vehicle control


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 9, tech rep 4

description: Processed data file col_name: nhp1411253_09_418

value: Blood


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 9, tech rep 2

description: Processed data file col_name: nhp1411253_09_416

value: PBMC


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 9, tech rep 1

description: Processed data file col_name: nhp1411253_09_415

value: WT


title: 611 MPO R848 6h donor D


title: 609 MPO R848 6h donor D


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 5, tech rep 1

description: Processed data file col_name: nhp1411253_05_419


title: DC treated with DMSO and CC, rep1


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 7, tech rep 2

description: Processed data file col_name: nhp1411253_07_416


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 1, tech rep 2

description: Processed data file col_name: nhp1411253_01_414


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 0, tech rep 2

description: Processed data file col_name: nhp1411253_00_416


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 1, tech rep 1

description: Processed data file col_name: nhp1411253_01_413


title: 608 control R848 6h donor D

value: control


title: 610 MPO R848 6h donor D


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 7, tech rep 1

description: Processed data file col_name: nhp1411253_07_415


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 8, tech rep 1

description: Processed data file col_name: nhp1408603_08_419

value: Fatal Treated


title: PBMC, BDBV challenged, VSV-LASV-GP treated, Control, DPI 0, tech rep 1

description: Processed data file col_name: nhp1411253_00_415


title: 612 MPO R848 6h donor D


title: 607 control R848 6h donor D


title: DC treated with DMSO, rep3

description: Gene expression data from Dendritic cells treated with vehicle control

value: DMSO


title: islets and lymphocytes, Ctl-CAR-Treg treated mice, day8, mouse #2

city: Indianapolis

first: Joshua

last: Kulas

address: 1210 Waterway Blvd Ste. 2000

institute: IBRI

data_processing:
Reads which contained adapter sequences, polyN reads > 10%, and Qscore <5 in 50% of bases were removed.
High-quality reads were aligned to mm10 using hisat2 (v2.0.5).
Read count quantification was performed using featureCounts (v1.5.0-p3).
Supplementary files format and content: excel file containing raw counts for each sample
Supplementary files format and content: excel file containing FPKM values for each sample

source_name: islets with inflammation

extract_protocol:
Fresh islets from each group were pooled, and RNAs were extracted using an RNA Miniprep kit (Zymo Research, R1054).
RNAs that passed quality control were sequenced using Illumina.

value: islets with inflammation

value: primary cells

value: Ctl-CAR-Tregs


title: islets and lymphocytes, Ctl-CAR-Treg treated mice, day8, mouse #3


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 7, tech rep 2

description: Processed data file col_name: nhp1408603_07_416

value: BDBV

value: VSV-BDBV-GP


title: DC treated with DMSO, rep1

source_name: Dendritic cells treated with vehicle control

value: Dendritic cells


title: DC treated with SF, rep1

description: Gene expression data from Dendritic cells treated with sulforaphane


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 7, tech rep 1

description: Processed data file col_name: nhp1408603_07_415

value: male


title: 606 control R848 6h donor D

description:
donor D
genes.readcount2.annot.xls
genes.FPKM.annot2.xls

source_name: monocytes isolated from blood

extract_protocol:
At 6 hours (experiments with TLR agonists) or 24 hours (experiments without TLR agonists) RNA was purified using Monarch total RNA miniprep kit (New England BioLabs Inc.) according to manufacturer’s instructions.
Library preparation and sequencing was performed by Novogene Bioinformatics Technology (Beijing, PR China). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. The read depth was 30 million reads per sample.


title: DC treated with DMSO, rep2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 5, tech rep 2

description: Processed data file col_name: nhp1408603_01_419

value: succumbed


title: islets and lymphocytes, Ctl-CAR-Treg treated mice, day8, mouse #1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 1, tech rep 1

description: Processed data file col_name: nhp1408603_00_413


title: DC treated with SF, rep2

source_name: Dendritic cells treated with sulforaphane


title: 605 control R848 6h donor D


title: islets and lymphocytes, InsB:R3-Treg treated mice, day8, mouse #3


title: 604 control R848 6h donor D


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 0, tech rep 1

description: Processed data file col_name: nhp1408603_05_417


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 21, tech rep 2

description: Processed data file col_name: nhp1407844_07_414

value: Survivor 1

value: female

value: survived


title: 603 control R848 6h donor D

value: monocytes


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 0, tech rep 2

description: Processed data file col_name: nhp1408603_05_418

value: Blood

value: PBMC


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 28, tech rep 1

description: Processed data file col_name: nhp1407844_09_415

value: WT


title: islets and lymphocytes, InsB:R3-Treg treated mice, day8, mouse #1


title: 602 control R848 6h donor D

value: control


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 21, tech rep 1

description: Processed data file col_name: nhp1407844_07_413


title: islets and lymphocytes, InsB:R3-Treg treated mice, day8, mouse #2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Fatal Treated, DPI 5, tech rep 1

description: Processed data file col_name: nhp1408603_00_414

value: Fatal Treated


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 15, tech rep 2

description: Processed data file col_name: nhp1407844_05_418


title: DC treated with SF, rep3


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 28, tech rep 2

description: Processed data file col_name: nhp1407844_09_416


title: 524 PR3 R848 6h donor F

description:
donor F
genes.readcount2.annot.xls
genes.FPKM.annot2.xls


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 12, tech rep 2

description: Processed data file col_name: nhp1407844_28_414


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 12, tech rep 1

description: Processed data file col_name: nhp1407844_28_413


title: 601 control R848 6h donor D


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 15, tech rep 1

description: Processed data file col_name: nhp1407844_05_417


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 9, tech rep 2

description: Processed data file col_name: nhp1407844_21_418


title: islets and lymphocytes, non-treated non-diabetic mice, day8, mouse#2

value: islets with inflammation

value: saline buffer


title: 523 PR3 R848 6h donor F


title: islets and lymphocytes, non-treated non-diabetic mice, day8, mouse #3

value: primary cells


title: 522 PR3 R848 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 9, tech rep 1

description: Processed data file col_name: nhp1407844_21_417

value: BDBV


title: Timeseries_ChIPseq_OCT4-FKBP_NT_input

city: Amsterdam

first: Elzo

last: de Wit

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Fastq files were aligned to the mm10 reference genome using the bwa mem software version 0.7.17-r1188 with the `-M` argument.
Alignments were filtered to exclude low quality alignments with samtools version 1.10 using the command `samtools view -h -b -q 10`.
Duplicated alignments were removed using the `MarkDuplicates` command from Picard tools version 2.12.0 with the argument `REMOVE_DUPLICATES=true`.
Bigwig files were build from the fragments files, by scaling coverage to the sum of length of the standard chromosomes using a custom R script.
Peaks were called using MACS2 version 2.2.7.1 with the argument `-g mm -f BEDPE –keep-dup-all` using an input sample as the ‘control’ argument.
Assembly: mm10
Supplementary files format and content: bigWig files
Supplementary files format and content: narrowPeak files

source_name: Embryo

growth_protocol: Mouse Embryonic Stem Cells (ESCs) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10*4U of Leukemia Inhibitory Factor/LIF (Millipore), MEK inhibitor PD0325901 (1 µM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 µM, Cayman Chemical) and 1-Thioglycerol (1.5x10-4 M, SigmaAldrich). The cell lines were passaged every 2 days in daily culture.

extract_protocol:
Cells were expanded and harvested at the end of the time-point for chromatin isolation. Chromatin was fixed using double cross-linked protocol. DSG (disuccinimidyl glutarate) (2 mM final concentration) was added to cell suspension for 45 min at RT. Formaldehyde was then added (to a concentration of 1%) for an additional 15 min. Reaction was quenched with Glycine (2M).  5 million cells were harvested for each IP. Cells were lysed lysis buffer 1 (50 mM Hepes, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% N40, 0.25% Tx100), followed by buffer 2 (10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and then kept in buffer 3 (10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-DOC, 0.5% lauroylsarcosine).
Chromatin was sheared on Bioruptor Pico (Diagenode) for 5-7 cycles. Shearing of chromatin was controlled on agarose gel and shearing was stopped when reaching an average size of chromatin from 200 to 1000 base pairs. Protein beads (DyanaBeads) were prepared and coupled for 6h to the antibody of interest. Before adding chromatin beads/antibodies were washed in PBS-BSA 0.5% and then washed 3 times. Chromatin was added to beads-antibodies overnight.  Samples were washed in RIPA buffer cold RIPA 50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP40, 0.7% Na-DOC) 10 times. Followed by one extra wash in TBS buffer (20 mM Tris, 150 mM NaCl) and chromatin was eluted (50 mM Tris, 10 mM EDTA, 1% SDS). DNA was decrosslinked overnight at 65C and treated with RNaseA for 1h at 37°C. Followed by Proteinase K treatment (0.1mg/ml) AT 55°C for 1h. DNA was finally eluted and purified using miniElute PCR purification kit (Qiagen). DNA fragments were used for library preparation following KAPA HTP Library preparation Kit (Roche).

treatment_protocol: For depletion treatment, the OCT4- and SOX2--FKBP cell lines were treated with a final concentration of 500 nM dTAG-13 or DMSO (NT, Not treated). For time course experiments, cells were seeded overnight and treated the next day, by inducing protein depletion at different time points and harvesting at the end of the time course.

tag: antibody

value: Embryo

value: Embryonic Stem Cell

value: DMSO

tag: time


title: Timeseries_ChIPseq_OCT4-FKBP_2H_anti-SOX2

tag: cell line

tag: treatment


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 7, tech rep 2

description: Processed data file col_name: nhp1407844_15_416

value: VSV-BDBV-GP


title: islets and lymphocytes, diabetic mice, day8, mouse #3

value: no treatment


title: 521 PR3 R848 6h donor F

tag: group (control, mpo, pr3)

tag: treatment (none, lps, r848)


title: islets and lymphocytes, diabetic mice, day8, mouse #2


title: 520 PR3 R848 6h donor F

tag: time (6h, 24h)


title: islets and lymphocytes, diabetic mice, day8, mouse #1


title: Timeseries_ChIPseq_OCT4-FKBP_NT_anti-HA


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 5, tech rep 2

description: Processed data file col_name: nhp1407844_12_418

tag: animal id

tag: animal id supp

value: Survivor 1

value: female


title: 519 PR3 R848 6h donor F

value: monocytes


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 7, tech rep 1

description: Processed data file col_name: nhp1407844_15_415

value: Blood

tag: outcome

value: survived

tag: challenge


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 5, tech rep 1

description: Processed data file col_name: nhp1407844_12_417

value: PBMC

value: WT

tag: time (days post infection)

tag: treatment time


title: islets and lymphocytes, non-treated non-diabetic mice, day8, mouse #1

tag: tissue


title: Timeseries_ChIPseq_SOX2-FKBP_NT_input


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 1, tech rep 1

description: Processed data file col_name: nhp1407844_00_414

tag: Sex

tag: tech rep


title: 517 PR3 R848 6h donor F

tag: cell type


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 0, tech rep 2

description: Processed data file col_name: nhp1407844_00_413

tag: genotype


title: Timeseries_ChIPseq_SOX2-FKBP_2H_anti-OCT4

tag: antibody

tag: time


title: 516 MPO R848 6h donor F

value: MPO


title: Timeseries_ChIPseq_SOX2-FKBP_NT_anti-OCT4

tag: cell line

tag: treatment


title: Timeseries_ChIPseq_OCT4-FKBP_NT_anti-SOX2


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 1, DPI 0, tech rep 1

description: Processed data file col_name: nhp1407844_01_419


title: Timeseries_ChIPseq_SOX2-FKBP_6h_anti-HA


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 28, tech rep 2

description: Processed data file col_name: nhp1407408_07_418

value: Survivor 5


title: Timeseries_ChIPseq_OCT4-FKBP_2H_anti-HA


title: HMGB2_Cl13_d20_3

city: Irvine

first: Roberto

last: Tinoco

state: CA

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

data_processing:
Post-processing of the run to generate FASTQ files was performed at the Institute for Genomics and Bioinformatics (UCI IGB).
PcaHubert was used to identify any outlier samples, which were removed from further analysis.
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9). Raw reads were then quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were analyzed with the mouse Grcm38 reference genome using pseudo aligner Salmon (v1.2.1) and resulting quantification files were imported using R package tximport to get TPM values for all annotated mouse genes.
Differential analysis was done using R package DESeq2 (v1.22.2) with an FDR cut off of 0.05.

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was monitored for quality control using the Agilent Bioanalyzer Nano RNA chip and Nanodrop absorbance ratios for 260/280nm and 260/230nm.
Library construction was performed according to the Illumina TruSeq mRNA stranded protocol.
The input quantity for total RNA within the recommended range and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The concentrations for the libraries were normalized and then multiplexed together. The multiplexed libraries were sequenced using paired end 100 cycles chemistry on the NovaSeq 6000.

value: Spleen

value: HMGB2 KO P14


title: HMGB2_Cl13_d20_2


title: WT_Cl13_d20_3

value: WT P14


title: HMGB2_Cl13_d20_1


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 28, tech rep 1

description: Processed data file col_name: nhp1407408_07_417

value: BDBV


title: Timeseries_ChIPseq_SOX2-FKBP_2H_anti-HA

value: Embryo

value: Embryonic Stem Cell


title: 515 MPO R848 6h donor F

city: London

tag: group (control, mpo, pr3)

tag: treatment (none, lps, r848)


title: 518 PR3 R848 6h donor F

tag: time (6h, 24h)


title: WT_Cl13_d20_1


title: WT_Cl13_d20_2


title: 512 MPO R848 6h donor F


title: PBMC, BDBV challenged, VSV-BDBV-GP treated, Survivor 5, DPI 21, tech rep 2

description: Processed data file col_name: nhp1407408_05_419

tag: animal id

tag: animal id supp

value: VSV-BDBV-GP


title: 511 MPO R848 6h donor F


title: Timeseries_ChIPseq_SOX2-FKBP_NT_anti-HA

value: DMSO


title: HMGB2_Cl13_d8_3