title: XIAK15.1a_KiC_24wk

city: Boston

first: Elliot

last: Akama-Garren

address: 200 Longwood Ave

institute: Harvard Medical School

data_processing:
FASTQ files were aligned using BWA-mem to the GRCm38.ERCC genome
Counts were generated using featureCounts
Assembly: mm10
Supplementary files format and content: comma seperated value file contains raw counts for each Sample

source_name: Pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-seq Library Kit (Lexogen) following manufacturer's protocols.

value: Pancreas

value: KiC


title: C60_F6_L1_0w_RepC_Replicate1

status: Public on Feb 02 2023

type: SRA

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

library_source: transcriptomic

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.

molecule: total RNA

organism: Mus musculus

source_name: Murine Epidermal cells

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

treatment_protocol: Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior wounding.

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes

tag: time

tag: plate

tag: population

tag: replicate


title: human pericyte cells, MC, scr_4

city: Auckland

first: Maize

last: Cao

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

data_processing:
Raw data quality control was applied using FastQC software and then trimmed with Trimmomatic.
Reads were aligned to the GRCh38 reference genome with HISAT2 and quantified with StringTie.
Count data was imported into the R software environment  with the tximport package to perform differential expression analysis using DESeq2 and differential exon usage analysis using DEXSeq.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files include DEG analysis results and DEU analysis results

organism: Homo sapiens

source_name: brain

extract_protocol:
RNA was isolated and purified using the RNAqueous®-Micro Total RNA Isolation Kit following manufacturer's recommendations
0.5-1μg RNA per sample was used as input material. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations
150 bp paired-end reads

tag: tissue

value: brain

tag: brain region

value: motor cortex

value: brain pericytes

tag: treatment

value: scr


title: human pericyte cells, MC, siTDP_4

value: siTDP


title: AGH146_5

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 Center Drive, 6/230

country: USA

institute: NIH, NICHD

description: Biological replicate 2

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Histone H3, Rpb3, Rpb1, Gcn4, TBP and myc-tagged Spt7, Srb6 and Eaf1 were created using custom R programs.
The processed data were converted to the bigwig files supplied here. Bigwig files for each sample have a  DNA length exclusion limit is: 50 - 300 bp.
Bigwig files for the merged replicates of the H3 ChIP samples were made with DNA length exclusion of 50-200 bp. These files were used for the IGV view figure in our manuscript. These merged files are available on the series record.
Assembly: SacCer3
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: myc ChIP-seq (+SM) Repl. 2

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM). For anchor away strains, cells were treated with rapamycin for 90 min before adding SM or no SM.

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-histone H3, anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001), anti-Rpb1 (Biolegend, Cat#664906) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

tag: genotype

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 EAF1-myc13::HIS3MX6 gcn5delta::kanMX4

tag: chip antibody

value: myc

value: Formaldehyde-fixed and sonicated


title: AGH146_4

description: Biological replicate 1

source_name: myc ChIP-seq (+SM) Repl. 1


title: C60_F7_L1_0w_RepC_Replicate1


title: human pericyte cells, MC, siTDP_3


title: C60_F5_L1_0w_RepC_Replicate1


title: AGH145_24

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: 187273 - Liver metastasis

type: RNA

city: Glasgow

first: Colin

last: Wood

state: Scotland

address: 84 Castle Street

department: Academic Unit of Surgery

country: United Kingdom

institute: University of Glasgow

hyb_protocol: RNA samples were incubated for 16 hours at 65°C in hybridisation buffer containing IO360 CodeSet, including reporter and capture probes in addition to target RNA forming a tripartite hybridisation complex.  Hybridized samples were processed using the nCounter Prep Station (High Sensitivity Protocol), in accordance with IO360 panel guidelines by Nanostring.

data_processing: Raw gene expression count data were normalized using NanoString nSolver 4.0 software using 6 positive controls and 8 negative controls to account for background noise and sample variation across runs (GeNorm Algorithm).

source_name: Liver metastasis

label_protocol: Total RNA (Average concentration = 35ng/µl) was used for gene expression analysis using the commercially available IO360 panel (nCounter, NanoString) (770 genes). Each 5µl RNA sample was analysed in sets of 11. Panel standards were used in each assay to allow for differences in technical assay performance across runs. Samples and panel standards were spiked with positive control probes ranging from 128fM to 0.125fM in a four-fold dilution series. Positive controls were used to assess the linearity of the assays and used for normalisation. Additionally, eight negative control probes were used for which no RNA target was present. RNA samples were incubated for 16 hours at 65C in hybridisation buffer containing IO360 CodeSet, including reporter and capture probes in addition to target RNA forming a tripartite hybridisation complex. Hybridized samples were processed using the nCounter Prep Station (High Sensitivity Protocol), in accordance with IO360 panel guidelines by Nanostring. Data acquisition was performed by using the Nanostring’s Digital Analyser (FOV, 555)

extract_protocol: RNA was extracted from the samples using AllPrep DNA/RNA FFPE Kit (Qiagen) according to manufacturer’s protocol, using xylene for deparaffinisation.  All RNA samples were treated on-column with DNAse I and were eluted in 20ul RNAse-free H2O.  RNA quantity was assessed using RNA BR assay and the Qubit® 2.0 fluorometer (Invitrogen, Life Technologies).  RNA integrity (RIN) values were determined using Agilent 2100 Bioanalyzer (Agilent Technologies) (maximum RIN = 2.1).

tag: gms

tag: cms

tag: msi

tag: apc

tag: kras

tag: braf

tag: alive 5yr

value: cancer death

tag: time death (mths)

tag: age

tag: Sex

tag: t

tag: n

tag: side

value: right

tag: mgps

tag: neo adj

value: n


title: C60_F4_L1_0w_RepC_Replicate1

tag: strain

tag: cell type

tag: time

tag: plate

tag: population

tag: replicate


title: C60_F3_L1_0w_RepC_Replicate1


title: human pericyte cells, MC, scr_3

tag: tissue

tag: brain region

tag: treatment


title: human pericyte cells, MC, siTDP_5


title: C60_F2_L1_0w_RepC_Replicate1


title: AGH145_21

description: Biological replicate 3

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4

tag: chip antibody


title: human pericyte cells, MC, scr_2


title: AGH145_23

description: Biological replicate 2


title: AGH145_22

description: Biological replicate 1


title: C60_F12_L1_0w_RepC_Replicate1


title: human pericyte cells, MC, siTDP_2


title: human pericyte cells, MC, siTDP_1


title: C60_F11_L1_0w_RepC_Replicate1


title: AGH145_20

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta


title: human pericyte cells, MC, scr_1


title: AGH145_19

description: Biological replicate 1


title: C60_E7_L1_0w_RepC_Replicate1


title: C60_F1_L1_0w_RepC_Replicate1


title: 187256 - Liver metastasis

tag: gms

tag: cms

tag: number of mutations

tag: msi

value: no

tag: apc

value: wt

tag: kras

value: mt

tag: braf

tag: alive 5yr

value: alive

tag: age

tag: Sex

value: rectal


title: 187269 - Liver metastasis

tag: time death (mths)

tag: t

tag: n

tag: side

tag: mgps

tag: neo adj


title: 187265 - Colorectal primary

source_name: Colorectal primary

value: left

value: y


title: 187256 - Colorectal primary


title: 187284 - Colorectal primary

value: yes


title: 187284 - Liver metastasis


title: 187254 - Colorectal primary


title: 187286 - Liver metastasis


title: 187254 - Liver metastasis


title: 187286 - Colorectal primary


title: 187273 - Colorectal primary


title: C60_E6_L1_0w_RepC_Replicate1

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes

tag: time

tag: plate

tag: population

tag: replicate


title: AGH145_16

description: Biological replicate 3

source_name: myc ChIP-seq (+SM) Repl. 3

tag: genotype

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SPT7-myc13::HIS3MX6

tag: chip antibody

value: myc

tag: treatment

value: Formaldehyde-fixed and sonicated


title: AGH145_15

description: Biological replicate 2


title: AGH145_13

description: Biological replicate 3

source_name: myc ChIP-seq (no SM) Repl. 3


title: AGH145_18

description: Biological replicate 3

source_name: myc ChIP-seq (no SM) Repl. 2


title: C60_F10_L1_0w_RepC_Replicate1


title: AGH145_14

description: Biological replicate 1


title: C60_E9_L1_0w_RepC_Replicate1


title: 187269 - Colorectal primary

tag: gms

tag: cms

tag: number of mutations

tag: msi

tag: apc

tag: kras

tag: braf

tag: alive 5yr

value: cancer death

tag: age


title: 187252 - Liver metastasis

tag: Sex

tag: t

tag: n

tag: side

tag: mgps

tag: neo adj

value: n


title: C60_E4_L1_0w_RepC_Replicate1

tag: strain

tag: cell type

tag: time

tag: plate

tag: population

tag: replicate


title: AGH145_12

description: Biological replicate 2

tag: genotype

tag: chip antibody

tag: treatment


title: C60_E5_L1_0w_RepC_Replicate1


title: AGH145_17

description: Biological replicate 2

source_name: myc ChIP-seq (no SM) Repl. 1


title: C60_E3_L1_0w_RepC_Replicate1


title: AGH145_11

description: Biological replicate 1


title: C60_E2_L1_0w_RepC_Replicate1


title: C60_E12_L1_0w_RepC_Replicate1


title: 187278 - Liver metastasis

tag: gms

tag: cms

tag: number of mutations

tag: msi

tag: apc

tag: kras

tag: braf

tag: alive 5yr


title: C60_E11_L1_0w_RepC_Replicate1

tag: strain


title: AGH145_9

description: Biological replicate 2

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SPT7-myc13::HIS3MX6 eaf1delta::kanMX4


title: C60_E10_L1_0w_RepC_Replicate1

tag: cell type


title: AGH145_5

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SPT7-myc13::HIS3MX6 gcn5delta::kanMX4


title: AGH145_8

description: Biological replicate 1


title: Liver of C57BL/6 mice, LPS Treatment, Repeat experiment 3

city: Chongqing

first: Qihuan

last: Fu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Chongqing University Cancer Hospital

country: China

institute: Chongqing University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: Liver

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
RNA sequencing was performed by Microwave Biotechnology Ltd. using the EASY-RNAseq method.

treatment_protocol: The day before the experiment, animals were fasted overnight (16 hours) and intraperitoneally injected with 200 ul of HBSS (Control) or 6 mg/kg LPS (final dose).

tag: tissue

value: Liver

tag: Sex

value: Male

tag: age

value: 6-8 weeks old

value: WT

value: LPS treatment


title: Liver of C57BL/6 mice, LPS Treatment, Repeat experiment 1


title: Liver of C57BL/6 mice, Control, Repeat experiment 2

value: No treatment


title: AGH145_4

description: Biological replicate 2


title: AGH145_3

description: Biological replicate 1


title: C60_D9_L1_0w_RepC_Replicate1

tag: time

tag: plate

tag: population

tag: replicate


title: Liver of C57BL/6 mice, Control, Repeat experiment 1

tag: genotype

tag: treatment


title: AGH140_22

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta

tag: chip antibody


title: C60_D8_L1_0w_RepC_Replicate1


title: AGH140_21

description: Biological replicate 1


title: C60_D7_L1_0w_RepC_Replicate1


title: GZ21T 2, lesional

city: Baltimore

first: Zachary

last: Bordeaux

address: 206 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins

data_processing:
Data were processed using the TrimGalore toolkit.
Rsem-1.3.0 was used for alignments and generating gene and isoform expression levels.
Reads were mapped to the GRCm38.mm10 version of the mouse genome and transcriptome. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Normalization and differential expression were carried out using the DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts values for each Sample and DESeq2 files for all comparisons

source_name: Skin

growth_protocol: Female SKH1 mice between 6-8 weeks of age were irradiated with 500 J/m2 (the minimum erythemal dose (Pillon et al., 2017)) ultraviolet B five days per week for ten weeks to induce actinic keratoses lesions

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries were prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturers instructions

treatment_protocol: Mice in the control group were treated with 0.25 g topical placebo cream five days per week, while mice in the treatment group received 0.25 g topical GZ21T five days per week

value: Skin

value: Female

tag: disease

value: Actinic keratoses


title: GZ21T 3, lesional


title: AGH145_10

description: Biological replicate 3


title: C60_D6_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed

value: Keratinocytes


title: C60_E1_L1_0w_RepC_Replicate1


title: AGH139_22

description: Biological replicate 1

value: myc

value: Formaldehyde-fixed and sonicated


title: GZ21T 1, lesional


title: Liver of C57BL/6 mice, Control, Repeat experiment 3


title: SET-E2-90min-rep1

city: Nanjing

first: Changying

last: Guo

state: Jiangsu

address: Longmian Avenue, No. 639

department: School of Life Science and Technology

institute: China Pharmaceutical university

data_processing:
Rawdata were filter by Fastp (v0.12.4) to remove low quality reads and adaptor sequence. The parameters for fastp are listed as follows: "-g -q 5 -u 50 -n 15 -l 150"
High quality and adaptor-removed clean data were submitted to Bowtie2 (v2.25) for alignment using hg19 assembly. The parameters for bowtie2 are: "  --reorder   --very-sensitive-local -x mm10 --local --no-mixed --no-discordant  --phred33 -I 10 -X 700"
Mapped reads contain abundant redundant duplicates were tagged by Picard tools (v2.27.1) .
To obtain enriched peaks over the local background, MACS2 software (v2.2.6) was used with arguments “-f BEMPE -q 0.01” for narrow peak and “-f BEMPE --broad --broad-cutoff 0.01” for broad peak. In addition, “--min-length” parameter also configurated depend on average length of peaks.
To obtain portable coverage plots, MACS2-derived bedgraphs were converted to bigwig file using UCSC tools "bedGraphToBigWig" .
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Breast

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were treated with Con-A beads, antibodies and reagents following the instrunction of Hyperactive In-Situ ChIP Library Prep Kit.
Libraries were prepared using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina from Vazyme biotech co.. Two hundred thousand cells were used as starting material for samples. Library were amplified using appropriate cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using VAHTS DNA Clean Beads from Vazyme biotech co.. Libraries were validated using Qubit, AATI and QPCR.

value: Breast

tag: cell line

value: Human ER+ breast cancer cell

tag: antibody

value: 17β-estradiol (E2), 100nM, 90min


title: AGH139_21

description: Biological replicate 1


title: C60_D4_L1_0w_RepC_Replicate1


title: SET-E2-0min-rep2

value: Vehicle (EtOH)


title: AGH138_14

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6 eaf1delta::kanMX4


title: C60_D3_L1_0w_RepC_Replicate1


title: Liver of C57BL/6 mice, LPS Treatment, Repeat experiment 2

value: Liver

value: Male

value: 6-8 weeks old


title: SET-E2-0min-rep1


title: Control 3, Peri-lesional

value: Control


title: Control 3, non-lesional


title: SET-E2-90min-rep2


title: AGH140_8

description: Biological replicate 2


title: C60_D5_L1_0w_RepC_Replicate1


title: C60_D2_L1_0w_RepC_Replicate1


title: ERa-E2-90min-rep2


title: C60_D12_L1_0w_RepC_Replicate1


title: Control 3, lesional


title: 187278 - Colorectal primary

tag: gms

tag: cms

tag: number of mutations

tag: msi

value: no

tag: apc

value: mt

tag: kras

value: wt

tag: braf

value: alive

tag: t

tag: n

tag: side

value: left

tag: mgps

tag: neo adj

value: n


title: Control 2, non-UV exposed

tag: tissue

value: Skin

tag: genotype

tag: treatment

tag: Sex

value: Female

value: Actinic keratoses


title: C60_D11_L1_0w_RepC_Replicate1

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes

tag: time

tag: plate

tag: population

tag: replicate


title: ERa-E2-90min-rep1

value: Breast

tag: cell line

value: Human ER+ breast cancer cell

tag: antibody

value: 17β-estradiol (E2), 100nM, 90min


title: ERa-E2-0min-rep2

value: Vehicle (EtOH)


title: Control 3, non-UV exposed

tag: disease


title: AGH141-20

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6 gcn5delta::kanMX4

tag: chip antibody

value: myc

value: Formaldehyde-fixed and sonicated


title: C60_D10_L1_0w_RepC_Replicate1


title: AGH140_14

description: Biological replicate 2


title: Control 2, Peri-lesional

value: Control


title: C60_D1_L1_0w_RepC_Replicate1


title: AGH138_16

description: Biological replicate 4

source_name: myc ChIP-seq (+SM) Repl. 4

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6


title: AGH139_14

description: Biological replicate 1


title: C60_C9_L1_0w_RepC_Replicate1


title: Control 1, non-UV exposed


title: C60_C8_L1_0w_RepC_Replicate1


title: Control 2, lesional


title: AGH139_8

description: Biological replicate 1

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6 eaf1delta::kanMX4


title: Control 1, non-lesional


title: ERa-E2-0min-rep1


title: S_day46_1

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

description: biological replicate 1

data_processing:
The raw RNA-seq raw data were trimmed to remove the adapter sequences (including GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTCTACTATCTCGTATGCCGTCTTCTGCTTG and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGG -TGGTCGCCGTATCATT) with command-line tool cutadapt (1.8.1). Then the trimmed files were aligned with Tophat (version 2.0.9) to GRCh37/hg19 Homo sapiens reference genome.
The human gene symbols and their raw counts were calculated using the HTSeq (version 0.6.1p1) package in Python with the hg19 Homo sapiens gtf file. Differential gene-expression analysis was performed using the edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM) method across all samples.

source_name: iPS-derived cardiomyocytes

growth_protocol: All pluripotent cell lines were grown in Matrigel-coated 12-well plates in Essential 8™ Medium (Thermo Fisher Scientific, MA) at 37 °C in 5% CO2 in compressed air and high humidity

extract_protocol:
Total RNA was extracted from the same number of cells among each group using QIAzol lysis reagent (Qiagen), and RNA was then subjected to DNase I digestion and purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was checked with a NanoDrop, and only samples with a ratio of 260/280 between 2.0 - 2.1 were subsequently used for ribosome depletion.
The library preparation and RNA-sequencing were done by Novogene Corporation Inc (Sacramento, CA). The RNA-seq libraries were constructed using NEBNext UltraTM II RNA Library Prep Kit for Illumina and were sequenced by Novaseq 6000 PE150 system. Raw reads of FASTQ format were firstly processed through fastp, and 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

treatment_protocol: The DNA sequences of SARS-CoV-2 (Wuhan-Hu-1 strain, GenBank: NC_045512.2) was used for DNA synthesis of each gene (General Bio, China). The viral genes were firstly cloned into pcDNA6B-Flag vector as described in our previous publication (PMID: 33203855). The constructs were further subcloned into a lentivirus transfer plasmid pCDH-CMV-MCS-EF1α-copGFP (System Biosciences, #CD511B-1, Palo Alto, CA, USA) with standard molecular cloning methods. C113-hiPSCs obtained them from the Stanford Cardiovascular Institute (SCVI) Biobank was used for this study. C113-hiPSCs were differentiated into cardiomyocytes, and then were transfected with plasmids carrying SARS-CoV-2 subunits with a lentivirial transfection method.  After 4 days of treatment, the GFP expression was examined in the transfected cardiomyocytes. Cells after transfection with 9B, S, and control groups at day 32 and day 46 were harvested for RNA isolation and RNA-seq.

value: iPS-derived cardiomyocytes

value: S

tag: differentiation time (days)


title: 187252 - Colorectal primary

tag: gms

tag: cms

tag: number of mutations

tag: msi

value: no

tag: apc

value: mt

tag: kras

tag: braf

value: wt

tag: alive 5yr

value: alive

tag: age

tag: t

tag: n

tag: side

value: left

tag: mgps

value: n


title: S_day46_2

description: biological replicate 2

tag: cell line

tag: cell type

tag: treatment


title: 9B_day46_2

description: biological replicate 2

tag: differentiation time (days)


title: AGH141_17

description: Biological replicate 2

tag: strain

tag: genotype

tag: chip antibody


title: AGH141_18

description: Biological replicate 3


title: C60_C7_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed

value: Keratinocytes

tag: time

tag: plate

tag: population

tag: replicate


title: Control 1, Peri-lesional

tag: tissue

value: Skin

tag: Sex

value: Female

tag: disease

value: Actinic keratoses


title: AGH139_12

description: Biological replicate 1

value: myc

value: Formaldehyde-fixed and sonicated


title: C60_C5_L1_0w_RepC_Replicate1


title: AGH141_19

description: Biological replicate 4

source_name: myc ChIP-seq (no SM) Repl. 4

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6


title: 9B_day46_1

description: biological replicate 1


title: Control_day46_2

description: biological replicate 2


title: Control 1, lesional

value: Control


title: Control_day46_1

description: biological replicate 1

value: iPS-derived cardiomyocytes


title: C60_C3_L1_0w_RepC_Replicate1


title: AGH140_11

description: Biological replicate 2


title: C60_C2_L1_0w_RepC_Replicate1


title: AGH139_11

description: Biological replicate 1


title: S_day32_2

description: biological replicate 2

value: S


title: C60_C12_L1_0w_RepC_Replicate1


title: C60_C11_L1_0w_RepC_Replicate1


title: AGH127_8

description: Biological replicate 2

source_name: Gcn4 ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: C60_C10_L1_0w_RepC_Replicate1

source_name: Murine Epidermal cells


title: 9B_day32_2

description: biological replicate 2


title: 9B_day32_1

description: biological replicate 1


title: WT,scRNAseq

city: Beijing

first: Ziyu

last: Li

address: 5 Summer Palace Road, Haidian District, Beijing, China

department: Biomedical Pioneering Innovation Center

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

molecule: polyA RNA

source_name: TME

extract_protocol:
To obtain MC38 tumor-infiltrating bystander P14 and SM cells, tumors were mechanically minced, digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, tumor-infiltrating lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. Meanwhile, to obtain memory SM cells, lymphocytes of the spleens of LCMV Armstrong-infected mice were harvested by mashing the spleens through cell strainer (BD Falcon). Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD8, CD4, Va2, CD45.1, and CD45.2 and P14/SM cells were FACS-sorted.
The scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3' reagent Kits (10x Genomics) according to the manufacturer's instructions. Briefly, FACS-sorted P14 or SM cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, folloed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.

value: TME

value: P14 and SM bystander cells

value: NDV-WT


title: PBS,scRNAseq

description: 10x Genomics

value: PBS


title: C60_C1_L1_0w_RepC_Replicate1


title: AGH127_6

description: Biological replicate 3

source_name: Gcn4 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: Control_day32_1

description: biological replicate 1


title: C60_B9_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed


title: Control_day32_2

description: biological replicate 2


title: Y1cKO_Ribo rep2

city: Hangzhou

first: Sujun

last: Yan

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Hisat2 v2.2.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
DEseq2

source_name: inguinal white adipose tissue

extract_protocol:
Inguinal adipose tissue was removed and lysis, 1/5 for RNA-seq, 4/5 for Ribosome profiling and further Ribo-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: inguinal white adipose tissue

tag: age

value: 9-week old


title: AGH127_7

description: Biological replicate 1

source_name: Gcn4 ChIP-seq (+SM) Repl. 1


title: D60,scRNAseq

description: 10x Genomics

source_name: Spleen

value: Spleen

value: SM conventional memory cells


title: GP,scRNAseq

description: 10x Genomics

value: NDV-GP


title: Severe patient 4

city: Boadilla del Monte

first: CARMELA

last: PABLO-TORRES JIMÉNEZ

state: Urbanización Montepríncipe

address: Urbanización Montepríncipe

country: Spain

institute: SAN PABLO CEU UNIVERSITY

description: Gene expression data from CD3+ cells

hyb_protocol: The fragmented and labeled cDNA of all the samples was hybridized (4 samples for each strip) for 20 hours at 48ºC

scan_protocol: Gene chips were stained and imaged using GeneAtlas System

data_processing: CEL raw files were normalized and transformed into expression measures using Expression Console Software (Affymetrix). The Robust Multi‐array Average (RMA) algorithm was used for background correction, normalization, and summarization of the probe‐set level expression of the samples.

label: biotin

source_name: CD3+ cells from a severe allergic subject

label_protocol: Single-stranded cDNA was fragmented by UDG and APE1 and labeled by TdT using DNA labeling reagent that was covalently linked to biotin

extract_protocol: RNA was extracted from Ficoll®‐isolated CD3+ using RNeasy® Mini Kit (Qiagen, Hilden, Germany) with DNase treatment following manufacturer procedure. RNA concentration was determined using a NanoDrop™ 2000/2000c Spectrophotometer

value: CD3+ cells

value: Severe

value: Older than 18


title: S_day32_1

description: biological replicate 1

value: iPS-derived cardiomyocytes


title: AGH127_5

description: Biological replicate 2

value: Formaldehyde-fixed and sonicated


title: AGH127_9

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: C60_B7_L1_0w_RepC_Replicate1

value: Keratinocytes


title: Y1CTL_RIbo rep2


title: Y1cKO_Ribo rep1


title: AGH127_2

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta


title: AGH127_4

description: Biological replicate 1


title: Aged, replicate 2, scATAC-seq

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ files using the ‘bcl-convert’ command (Illumina, v3.9.3) and aligned to the mm10 reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0) using cellranger-atac count (v2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated ATAC fragment files and corresponding tabix indexes generated by CellRanger.

source_name: Hindlimb skeletal muscle

extract_protocol:
Young (3 months old) and aged (28-29 months old) Pax7CreER/+;Rosa26TdTomato/+  female mice were obtained from a breeding colony at UM. All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and the Institutional Animal Care and Committee and were in accordance with the U.S. National Institute of Health (NIH).
Mouse hindlimb muscles were extracted and placed into separate petri dishes containing ice-cold PBS. Using surgical scissors, muscle tissues were minced and placed into 20mL of digestion buffer (DMEM with Collagenase type II (0.2%) and Dispase II (2.5U/mL)) per mouse. Samples were placed on a shaker in a 37˚C incubator for 1.5 hours and mixed by pipette every 30 minutes. The enzymes were then inactivated by addition of 20mL 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media. The solution was passed through a 70um cell strainers, centrifuged, washed in PBS containing 3% BSA, and nuclei isolation was performed according to 10x Demonstrated Protocol CG000375 Revision B starting at step 1.1c. Nuclei from two age-matched mice were pooled prior to sorting, at step 1.1n, and 7-AAD+ nuclei were sorted on a Sony MA900 or MoFlo Astrios 3. Sorted nuclei were then permeabilized according to the same protocol.
ATAC-Seq Next GEM (10x Genomics, v1.1); 10,000 permeabilized nuclei were loaded onto the 10x Genomics Chromium single cell controller and single nuclei were captured into nanoliter-scale gel bead-in-emulsions (GEMs). Single nuclei ATAC library constructions were performed using the ATAC-seq Next GEM kit (10x Genomics). All libraries were submitted for 51x51bp paired-end sequencing on a NovaSeq 6000 with 50,000 targeted reads per cell.

value: Single nuclei

value: Hindlimb skeletal muscle

value: 28-29 months


title: C60_B5_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed


title: Y1cKO_RNA rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Hisat2 v2.2.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
DEseq2

value: inguinal white adipose tissue


title: C60_B4_L1_0w_RepC_Replicate1


title: AGH129_21

description: Biological replicate 2

source_name: Gcn4 ChIP-seq (no SM) Repl. 2


title: AGH127_1

description: Biological replicate 1


title: C60_B3_L1_0w_RepC_Replicate1


title: AGH129_20

description: Biological replicate 1

source_name: Gcn4 ChIP-seq (no SM) Repl. 1


title: C60_B2_L1_0w_RepC_Replicate1


title: Y1cKO_RNA rep1

value: 9-week old


title: AGH125_12

description: Biological replicate 3

source_name: TBP ChIP-seq (+SM,+dox) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4

value: TBP


title: Y1CTL_RNA rep2


title: C60_B8_L1_0w_RepC_Replicate1


title: Y1CTL_RNA rep1


title: C60_B12_L1_0w_RepC_Replicate1


title: AGH125_11

description: Biological replicate 2

source_name: TBP ChIP-seq (+SM,+dox) Repl. 2


title: Runx1+23GFP- EC cells [GFP-depleted_EC]

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

data_processing:
Genome_build: mm9
Supplementary_files_format_and_content: The file "processed_RNAseq_Runx1-HE.xlsx" contains gene information and RPKM values for each samples
Illumina RTA 1.12.4.2 software used for basecalling.
RNA-Seq reads were aligned to the mm9 genome assembly using bwa-aln version 0.5.7
Whole transcriptomes were assembled for the libraries, and differential expression data was generated using CuffDiff

source_name: E10.5 AGM

extract_protocol: AGM were dissected from E10.5 Runx1+23GFP transgenic embryos and CD31+CD117-CD45-Runx1+23GFP- cells were isolated by FACS along with CD31+CD117-CD45- cells from WT littermates. Cells were lyzed in Trizol and RNA was extracted following manufacturer's protocol.

tag: developmental stage

value: GFP+


title: AGH125_10

description: Biological replicate 1

source_name: TBP ChIP-seq (+SM,+dox) Repl. 1


title: bulk EC

value: WT


title: C60_B11_L1_0w_RepC_Replicate1


title: C60_B6_L1_0w_RepC_Replicate1


title: AGH125_9

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1delta::hphMX4


title: Y1CTL_Ribo rep1


title: AGH125_8

description: Biological replicate 2


title: Control 2, non-lesional

source_name: Skin

value: Skin

value: Control

value: Female

value: Actinic keratoses


title: C60_B10_L1_0w_RepC_Replicate1

value: Keratinocytes


title: midbrain WT 8

city: Goettingen

first: Tiago

middle: Fleming

last: Outeiro

address: Waldweg 33

department: Experimental Neurodegeneration

country: Germany

institute: University Medical Center Goettingen

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned to MiRBase v19 using miRDeep2
Genome_build: mm9
Supplementary_files_format_and_content: table with DESeq data

source_name: midbrain

extract_protocol:
Midbrains were dissected on ice, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.Small RNA libraries were prepared from 1 µg total RNA using the Illumina TruSeq Small RNA Sample Preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: midbrain

value: 6 months old

value: wild type


title: C60_B1_L1_0w_RepC_Replicate1


title: AGH125_7

description: Biological replicate 1

value: Formaldehyde-fixed and sonicated


title: midbrain WT 6


title: midbrain WT 7


title: C60_C6_L1_0w_RepC_Replicate1

value: CBA C57BL/6 mixed


title: midbrain WT 5


title: C60_A8_L1_0w_RepC_Replicate1


title: C60_A7_L1_0w_RepC_Replicate1


title: midbrain WT 4


title: midbrain WT 3


title: C60_A5_L1_0w_RepC_Replicate1


title: AGH125_4

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: AGH125_3

description: Biological replicate 3

source_name: TBP ChIP-seq (no SM,+dox) Repl. 3


title: C60_A4_L1_0w_RepC_Replicate1

source_name: Murine Epidermal cells


title: AGH125_5

description: Biological replicate 2


title: AGH125_2

description: Biological replicate 2

source_name: TBP ChIP-seq (no SM,+dox) Repl. 2


title: midbrain WT 2


title: C60_A12_L1_0w_RepC_Replicate1


title: AGH132_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: C60_A2_L1_0w_RepC_Replicate1


title: C60_A9_L1_0w_RepC_Replicate1


title: AGH125_1

description: Biological replicate 1

source_name: TBP ChIP-seq (no SM,+dox) Repl. 1


title: C60_A10_L1_0w_RepC_Replicate1


title: AGH132_11

description: Biological replicate 2


title: C56_H9_L1_8w_RepB_Replicate2


title: AGH132_10

description: Biological replicate 1


title: midbrain A30P 8

value: A30P alpha-synuclein +/+


title: midbrain A30P 7


title: AGH132_8

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4

value: TBP


title: C56_H8_L1_8w_RepB_Replicate2


title: midbrain A30P 4


title: midbrain A30P 2


title: AGH132_7

description: Biological replicate 1


title: C56_H7_L1_8w_RepB_Replicate2


title: AGH132_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta


title: C56_H6_L1_8w_RepB_Replicate2


title: midbrain A30P 1


title: AP2R-2_INPUT_2

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: Peak-calling, text.

organism: Plasmodium berghei

growth_protocol: Balb/c mice were infected with PbAP2-FG2::GFP or AP2R-2::GFP.

extract_protocol:
Whole blood was withdrawn from infected mice, diluted in medium, and filtered with Plasmodipur to remove lymphocytes. The samples were then fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were lysed in SDS lysis buffer. The lysates were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power. After centrifugation of the sonicated lysates, the supernatants were subjected to immunoprecipitation with anti-GFP antibodies conjugated on Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Infected mice were treated with sulfadiazine for 2 days.

tag: Stage

value: Gametocyte

value: ANKA

tag: antibody


title: AGH132_5

description: Biological replicate 2


title: AP2R-2_IP(anti-GFP)_2

value: anti-GFP


title: AP2R-2_INPUT_1


title: AGH132_4

description: Biological replicate 1


title: C60_A11_L1_0w_RepC_Replicate1

tag: cell type


title: midbrain A30P 6


title: AGH132_9

description: Biological replicate 3

tag: treatment


title: AGH132_3

description: Biological replicate 3


title: C56_H2_L1_8w_RepB_Replicate2


title: midbrain A30P 3


title: AP2R-2_IP(anti-GFP)_1


title: C56_H1_L1_8w_RepB_Replicate2


title: PbAP2-FG2_INPUT_2


title: AGH132_1

description: Biological replicate 1


title: C56_H4_L1_8w_RepB_Replicate2


title: C56_H10_L1_8w_RepB_Replicate2


title: C56_G9_L1_8w_RepB_Replicate2


title: PbAP2-FG2_IP(anti-GFP)_2


title: C56_G8_L1_8w_RepB_Replicate2


title: PbAP2-FG2_INPUT_1


title: C56_H5_L1_8w_RepB_Replicate2


title: AGH130_18

description: Biological replicate 3

source_name: Rpb1 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4 EAF1-FRB::natMX4


title: C56_G6_L1_8w_RepB_Replicate2


title: AGH130_16

description: Biological replicate 1

source_name: Rpb1 ChIP-seq (+SM) Repl. 1


title: AGH130_17

description: Biological replicate 2

source_name: Rpb1 ChIP-seq (+SM) Repl. 2


title: AGH130_14

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4


title: AGH130_15

description: Biological replicate 3


title: C56_G5_L1_8w_RepB_Replicate2

value: Keratinocytes


title: ap2r-2(-) 3

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: txt, raw read count

source_name: Gametocyte

growth_protocol: Parasites were inoculated in Balb/c mice.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s instructions.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Infected mice were treated with sulfadiazine in their drinking water for 2 days in order to deplete asexual blood-stage parasites.

value: gametocyte


title: C56_G4_L1_8w_RepB_Replicate2

data_processing:
Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.


title: PbAP2-FG2_IP(anti-GFP)_1


title: ap2r-2(-) 2


title: ap2r-2(-) 1


title: C56_G2_L1_8w_RepB_Replicate2


title: AGH132_2

description: Biological replicate 2


title: pbap2-fg2(-) 3


title: C56_G11_L1_8w_RepB_Replicate2


title: pbap2-fg2(-) 2


title: C56_G10_L1_8w_RepB_Replicate2


title: AGH130_11

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 EAF1-FRB::natMX4


title: AGH130_10

description: Biological replicate 1


title: C56_G1_L1_8w_RepB_Replicate2


title: AGH130_13

description: Biological replicate 1


title: C56_F8_L1_8w_RepB_Replicate2


title: pbap2-fg2(-) 1


title: AGH130_8

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1delta::hphMX4


title: C56_F9_L1_8w_RepB_Replicate2


title: AGH130_7

description: Biological replicate 1

value: Formaldehyde-fixed and sonicated


title: AGH130_6

description: Biological replicate 3


title: C56_F6_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed


title: C56_F7_L1_8w_RepB_Replicate2


title: AGH130_9

description: Biological replicate 3


title: C56_F5_L1_8w_RepB_Replicate2


title: AGH130_12

description: Biological replicate 3


title: AGH130_4

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: bat_ab08_tsts_nv_3

city: Oakland

first: Ravi

last: Sachidanandam

address: 2945 Webster St

institute: Girihlet Inc.

description: From euthanized bat infected with Marburg

data_processing:
Kallisto was used to determine transcript expression levels from reads. Kallisto uses pseudo-alignments and is relatively more accepting of errors/variants in reads31
kallisto version 0.44.0 was used to generate the processed files.
A custom reference database of RNA sequences was used, it is attached to this dataset (bat_master_rna.fa)
The reference rna database was indexed using the command: kallisto index -i bat_23 -k 23  bat_master_rna.fa
The processed files were generated using the following commands,
For Single end reads:
kallisto quant -i ref/bat_23 --single -t 30 -l 250 -s 60 -o outfile infile
For Paired-end reads;
kallisto quant -i ref/bat_23  -t 30  -o outfile infileR1 infileR2"
Genome_build: bat_master_rna.fa; a database of bat transcripts were assembled from a variety of sources, and the genes were names on the basis of mouse and/or human homologues
Supplementary_files_format_and_content: Expression values from Kallisto

organism: Chiroptera

source_name: Testes_from euthanized bat infected with Marburg

growth_protocol:
Two immortalized cell lines, derived from R. aegyptiacus bats, were used in the study, including R06EJ (fetus body) and RoNi/7 (adult bat kidney). The R06EJ cells were maintained in Dulbecco's modified Eagle's medium (DMEM)?F-12 GlutaMAX medium, and RoNi/7 cells were maintained in DMEM (Life Technologies, Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (HyClone, Thermo Fisher Scientific, Waltham, MA) and antibiotic-antimycotic (Life Technologies, Thermo Fisher Scientific, Waltham, MA) as previously described. Cells were seeded in 6-well plates (Corning) in the density assuring formation of 80-100% confluent monolayer in 24 hours. Cells either transfected by PolyI:C (using Trans-IT mRNA reagent [Mirrus Bio] per manufacturer?s recommendation), or infected with filoviruses at multiplicity of infection (MOI) of 2 plaque forming units (PFU) per cell as determined previously in Vero E6 cells. After one hour of adsorption, the inoculum was removed, cell monolayers washed three times with phosphate buffered saline (PBS), and two ml of fresh culture medium was added into each well. Cells transfected with PolyI:C were harvested after 6, 12 and 24 hours whereas cells infected with filoviruses were harvested after 8, 12 and 24 hours. Prior to harvesting, cell medium was removed, the monolayer washed twice with PBS, and lysed in 1 ml of TRIzol reagent. Productive filovirus infections in cell culture were confirmed by the presence of eGFP expression [15]. Active replication in the cells was also evidenced by expression of all viral genes (from sequencing data), including MARV, which could not be visualized and did not produce cytopathic effect at harvesting (Table 1)
Viruses:  Recombinant wild-type EBOV, strain Mayinga, was recovered from the full-length clone and support plasmids in HEK 293T cells and passaged twice in Vero E6 cells for amplification, as described previously29. Recombinant wild-type MARV, strain Uganda, was recovered similarly in BHK-21 cells as described previously30 and was also passaged twice in Vero E6 cells for amplification.
Bat experimental protocol: Adult Egyptian rousettes were obtained from a commercial source and quarantined for 30 days under ABSL-2 conditions. Animals were implanted with microchip transponders for animal ID and temperature data collection. For studies with EBOV and MARV, animals were transferred to the Galveston National Laboratory ABSL-4 facility. Animals were segregated into groups of three. Except for one MARV-infected male, all bats were female. Each group was housed in a separate cage for inoculation with the same virus. After acclimation to the facility, animals were anesthetized with isoflurane and infected subcutaneously in the scapular region with 105 focus forming units (FFU; titrated on Vero E6 cells) of EBOV or MARV. Every other day, animals were anesthetized by isoflurane, weighed, temperature was determined via transponder, and 100-150 µL of blood was collected from the propatagial vein. Nucleases in blood were inactivated in 1 mL of TRIzol reagent (Thermo-Fisher Scientific). Samples were then removed from ABSL-4 containment, and RNA was extracted. Droplet-digital RT-PCR (ddRT-PCR) with primers specific to the nucleoprotein (NP) gene was used to detect viremia. If fewer than 106 MARV RNA copies/mL viremia were detected in a MARV-inoculated bat, the animal was observed for additional 2 days to allow the animal to reach a higher viral RNA load. In 48-96 hours after first observation of viremia, the animal was euthanized under deep isoflurane sedation via cardiac exsanguination confirmed by bilateral open chest. All EBOV-inoculated bats were euthanized 48 hours after the first detection of viremia, independent of viral RNA load. Tissues were collected (listed in Table S1) and immediately homogenized in an appropriate volume of TRIzol reagent and stored at -80°C. Tissue sections were also homogenized in minimal essential media (MEM) supplemented with 10% fetal bovine serum and stored at -80°C. Additional tissue sections were fixed in 10% neutral buffered formalin for histopathology.
All animal procedures were performed in compliance with protocols approved by the Institutional Animal Care and Use Committee at the University of Texas Medical Branch at Galveston.

extract_protocol:
Tissues and PBMCs were also collected from three uninfected control animals. Given that the course of infection appears to be relatively short in these animals21, we sacrificed them shortly after onset of viremia in the infected animals to ensure adequate capture of changes in transcriptional dynamics. As such, animals were bled every other day, and viral loads were assessed via ddRT-PCR. In addition, animals were weighed, and temperature was determined with each bleed.
Total RNA was isolated from samples using Ambion's RNA isolation and purification kit. PolyA-tailed mRNA was selected using beads with oligo-deoxythymidine and then fragmented. cDNA was synthesized using random hexamers and ligated with bar-coded adaptors compatible with Illumina's NextSeq 500. A total of 88 samples, as 75 nucleotide-long single-end reads, were sequenced on the NextSeq

treatment_protocol: Myotis lucifugus bats infected with RV. For a separate rabies study, bats were inoculated at 104 , 50% tissue culture infectious dose (TCID50) with a Myotis lucgus RV variant in their deltoid muscle.  Bats were inoculated, maintained, and euthanized as described earlier [28].  Brain, lung, and spleen tissue were aseptically collected from control and RV-inoculated bats following euthanasia due to clinical RV infection or at the end of the study (Table 2). Tissues were placed in 800 µl Trizol (Ambion) and stored at -80 oC until further processing could occur.

tag: tissue/cell line

value: Testes

value: infected with Marburg


title: bat_ab08_smlint_nv_1

source_name: Small Intestine_from euthanized bat infected with Marburg

value: Small Intestine


title: bat_ab08_slvglnd_nv_2

source_name: Salivary gland_from euthanized bat infected with Marburg

value: Salivary gland


title: bat_ab08_tsts_nv_2


title: bat_ab08_spln_nv_1

source_name: Spleen_from euthanized bat infected with Marburg

value: Spleen


title: bat_ab08_tsts_nv_1


title: C56_F4_L1_8w_RepB_Replicate2

extract_protocol:
Flow citometry was used to sort tomato positive epidermal cells.
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

tag: strain


title: AGH130_3

description: Biological replicate 3

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Histone H3, Rpb3, Rpb1, Gcn4, TBP and myc-tagged Spt7, Srb6 and Eaf1 were created using custom R programs.
The processed data were converted to the bigwig files supplied here. Bigwig files for each sample have a  DNA length exclusion limit is: 50 - 300 bp.
Bigwig files for the merged replicates of the H3 ChIP samples were made with DNA length exclusion of 50-200 bp. These files were used for the IGV view figure in our manuscript. These merged files are available on the series record.
Assembly: SacCer3
Supplementary files format and content: bigWig

source_name: Rpb1 ChIP-seq (no SM) Repl. 3

tag: genotype


title: C56_F3_L1_8w_RepB_Replicate2


title: bat_ab08_slvglnd_nv_1


title: bat_ab08_pbmc_nv_1

source_name: PBMC_from euthanized bat infected with Marburg

value: PBMC


title: C56_F2_L1_8w_RepB_Replicate2


title: AGH130_2

description: Biological replicate 2

source_name: Rpb1 ChIP-seq (no SM) Repl. 2

tag: chip antibody


title: bat_ab08_lvr_nv_1

source_name: Liver_from euthanized bat infected with Marburg

value: Liver


title: AGH130_5

description: Biological replicate 2


title: C56_F12_L1_8w_RepB_Replicate2

tag: time


title: AGH130_1

description: Biological replicate 1

source_name: Rpb1 ChIP-seq (no SM) Repl. 1


title: AGH138_15

description: Biological replicate 3

source_name: myc ChIP-seq (no SM) Repl. 3

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0 SRB6-myc13::HIS3MX6

value: myc


title: bat_ab08_lng_nv_1

source_name: Lung_from euthanized bat infected with Marburg

value: Lung


title: C56_F11_L1_8w_RepB_Replicate2

source_name: Murine Epidermal cells

value: Keratinocytes

tag: plate


title: bat_ab08_lrgint_nv_1

source_name: Large Intestine_from euthanized bat infected with Marburg

value: Large Intestine


title: AGH122_18

description: Biological replicate 3

source_name: Rpb3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4 EAF1-FRB::natMX4


title: AGH122_17

description: Biological replicate 2

source_name: Rpb3 ChIP-seq (+SM) Repl. 2


title: bat_ab08_kdny_nv_1

source_name: Kidney_from euthanized bat infected with Marburg

value: Kidney


title: AGH122_16

description: Biological replicate 1

source_name: Rpb3 ChIP-seq (+SM) Repl. 1

value: Formaldehyde-fixed and sonicated


title: C56_F10_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed

tag: population


title: C56_E9_L1_8w_RepB_Replicate2

tag: replicate


title: C56_E7_L1_8w_RepB_Replicate2


title: AGH122_14

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4


title: AGH122_13

description: Biological replicate 1


title: bat_ab07_spln_nv_2


title: AGH122_15

description: Biological replicate 3


title: C56_E8_L1_8w_RepB_Replicate2


title: C56_E6_L1_8w_RepB_Replicate2


title: AGH122_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 EAF1-FRB::natMX4


title: bat_ab07_slvglnd_nv_2

value: infected with Marburg


title: bat_ab07_smlint_nv_1

value: Small Intestine


title: bat_ab07_spln_nv_1


title: C56_E4_L1_8w_RepB_Replicate2


title: C56_E3_L1_8w_RepB_Replicate2


title: AGH122_11

description: Biological replicate 2


title: bat_ab07_pbmc_nv_2


title: AGH122_8

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1delta::hphMX4


title: AGH122_9

description: Biological replicate 3


title: C56_E12_L1_8w_RepB_Replicate2


title: C56_E11_L1_8w_RepB_Replicate2


title: AGH122_7

description: Biological replicate 1


title: bat_ab07_lvr_nv_1


title: bat_ab07_pbmc_nv_1


title: bat_ab07_lrgint_nv_1


title: C56_E1_L1_8w_RepB_Replicate2


title: AGH122_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: bat_ab07_slvglnd_nv_1

value: Salivary gland


title: C56_D9_L1_8w_RepB_Replicate2


title: C56_E5_L1_8w_RepB_Replicate2


title: bat_ab07_kdny_nv_1


title: bat_ab07_lng_nv_1


title: C56_D8_L1_8w_RepB_Replicate2


title: AGH125_6

description: Biological replicate 3

source_name: TBP ChIP-seq (+SM,+dox) Repl. 3

value: TBP


title: bat_ab06_spln_nv_1

value: Spleen


title: AGH122_4

description: Biological replicate 1


title: AGH122_3

description: Biological replicate 3

source_name: Rpb3 ChIP-seq (no SM) Repl. 3


title: AGH122_5

description: Biological replicate 2


title: AGH122_2

description: Biological replicate 2

source_name: Rpb3 ChIP-seq (no SM) Repl. 2


title: C56_D7_L1_8w_RepB_Replicate2


title: C56_D6_L1_8w_RepB_Replicate2


title: AGH122_10

description: Biological replicate 1


title: bat_ab06_slvglnd_nv_1

source_name: Salivary gland_from euthanized bat infected with Marburg


title: bat_ab06_smlint_nv_1

source_name: Small Intestine_from euthanized bat infected with Marburg


title: C56_E10_L1_8w_RepB_Replicate2


title: bat_ab06_pbmc_nv_1

source_name: PBMC_from euthanized bat infected with Marburg

value: PBMC


title: AGH122_1

description: Biological replicate 1

source_name: Rpb3 ChIP-seq (no SM) Repl. 1


title: bat_ab06_lrgint_nv_1


title: bat_ab06_lvr_nv_1

source_name: Liver_from euthanized bat infected with Marburg

value: Liver


title: AGH124_22

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0 yng2delta::kanMX4


title: AGH124_21

description: Biological replicate 2


title: C56_D5_L1_8w_RepB_Replicate2

value: Keratinocytes


title: bat_ab06_lng_nv_1

value: Lung


title: C56_D2_L1_8w_RepB_Replicate2


title: AGH124_20

description: Biological replicate 1


title: C56_D12_L1_8w_RepB_Replicate2


title: C56_D11_L1_8w_RepB_Replicate2


title: bat_ab05_spln_nv_1

description: From euthanized bat infected with Ebola with Marburg GP

source_name: Spleen_from euthanized bat infected with Ebola with Marburg GP

value: infected with Ebola with Marburg GP


title: AGH123_14

description: Biological replicate 2

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0

value: Formaldehyde-fixed and sonicated


title: bat_ab06_kdny_nv_1

value: Kidney


title: C56_D10_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed


title: bat_ab05_smlint_nv_1

source_name: Small Intestine_from euthanized bat infected with Ebola with Marburg GP


title: AGH123_13

description: Biological replicate 1


title: bat_ab05_slvglnd_nv_1

source_name: Salivary gland_from euthanized bat infected with Ebola with Marburg GP


title: C56_D1_L1_8w_RepB_Replicate2

source_name: Murine Epidermal cells


title: C56_D4_L1_8w_RepB_Replicate2


title: AGH123_18

description: Biological replicate 3


title: AGH123_17

description: Biological replicate 2


title: C56_C9_L1_8w_RepB_Replicate2


title: C60_A3_L1_0w_RepC_Replicate1


title: C56_D3_L1_8w_RepB_Replicate2


title: AGH123_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: midbrain WT 1

source_name: midbrain

tag: tissue

value: midbrain

value: 6 months old

value: wild type


title: bat_ab05_pbmc_nv_1

source_name: PBMC_from euthanized bat infected with Ebola with Marburg GP


title: AGH123_11

description: Biological replicate 2

source_name: Rpb3 ChIP-seq (+SM) Repl. 2


title: AGH123_16

description: Biological replicate 1


title: C56_C7_L1_8w_RepB_Replicate2


title: C56_C8_L1_8w_RepB_Replicate2


title: AGH123_10

description: Biological replicate 1


title: C56_C6_L1_8w_RepB_Replicate2


title: bat_ab05_tsts_nv_1

source_name: Testes_from euthanized bat infected with Ebola with Marburg GP

value: Testes


title: C56_C5_L1_8w_RepB_Replicate2


title: AGH123_15

description: Biological replicate 3

source_name: Rpb3 ChIP-seq (+SM) Repl. 3


title: bat_ab05_lvr_nv_2

source_name: Liver_from euthanized bat infected with Ebola with Marburg GP


title: bat_ab05_lvr_nv_1


title: C56_C4_L1_8w_RepB_Replicate2


title: bat_ab05_lng_nv_2

source_name: Lung_from euthanized bat infected with Ebola with Marburg GP


title: AGH123_8

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: AGH123_9

description: Biological replicate 3


title: bat_ab05_lrgint_nv_1

source_name: Large Intestine_from euthanized bat infected with Ebola with Marburg GP

value: Large Intestine


title: AGH123_7

description: Biological replicate 1

source_name: Rpb3 ChIP-seq (+SM) Repl. 1


title: C56_C2_L1_8w_RepB_Replicate2


title: AGH123_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta


title: bat_ab05_kdny_nv_1

source_name: Kidney_from euthanized bat infected with Ebola with Marburg GP


title: bat_ab05_mslnode_nv_1

source_name: Mesenchymal lymph node_from euthanized bat infected with Ebola with Marburg GP

value: Mesenchymal lymph node


title: bat_ab05_lng_nv_1


title: C56_C3_L1_8w_RepB_Replicate2


title: C56_C12_L1_8w_RepB_Replicate2


title: bat_ab05_axlnode_nv_1

source_name: Axial lymph node_from euthanized bat infected with Ebola with Marburg GP

value: Axial lymph node


title: bat_ab04_spln_nv_1

value: Spleen


title: C56_C10_L1_8w_RepB_Replicate2

value: Keratinocytes


title: bat_ab04_smlint_nv_1

value: Small Intestine

value: infected with Ebola with Marburg GP


title: C56_C11_L1_8w_RepB_Replicate2


title: AGH123_4

description: Biological replicate 1

value: Formaldehyde-fixed and sonicated


title: AGH123_3

description: Biological replicate 3

source_name: Rpb3 ChIP-seq (no SM) Repl. 3


title: AGH123_5

description: Biological replicate 2


title: C56_C1_L1_8w_RepB_Replicate2


title: C56_B9_L1_8w_RepB_Replicate2


title: bat_ab04_slvglnd_nv_2

value: Salivary gland


title: C56_B8_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed


title: AGH123_1

description: Biological replicate 1

source_name: Rpb3 ChIP-seq (no SM) Repl. 1


title: AGH123_2

description: Biological replicate 2

source_name: Rpb3 ChIP-seq (no SM) Repl. 2


title: C56_B7_L1_8w_RepB_Replicate2


title: AGH117_17

description: Biological replicate 1

source_name: MNase H3 ChIP-seq (+SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4

value: MNase


title: bat_ab04_slvglnd_nv_1

source_name: Salivary gland_from euthanized bat infected with Ebola with Marburg GP


title: C56_B6_L1_8w_RepB_Replicate2

source_name: Murine Epidermal cells


title: bat_ab04_pbmc_nv_2

source_name: PBMC_from euthanized bat infected with Ebola with Marburg GP

value: PBMC


title: AGH117_18

description: Biological replicate 2

source_name: MNase H3 ChIP-seq (+SM) Repl. 2


title: AGH117_15

description: Biological replicate 1

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0 yng2delta::kanMX4


title: bat_ab04_mslnode_nv_1


title: C56_B4_L1_8w_RepB_Replicate2


title: bat_ab04_pbmc_nv_1


title: AGH117_16

description: Biological replicate 2


title: bat_ab04_lvr_nv_1

value: Liver


title: bat_ab04_lrgint_nv_1


title: bat_ab04_lrgint_nv_2


title: AGH117_13

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta rtt109delta::kanMX4


title: C56_B2_L1_8w_RepB_Replicate2


title: C56_B3_L1_8w_RepB_Replicate2


title: C56_B12_L1_8w_RepB_Replicate2


title: AGH112_6

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4


title: AGH112_5

description: Biological replicate 1


title: bat_ab04_lng_nv_1

value: Lung


title: C56_B11_L1_8w_RepB_Replicate2


title: bat_ab04_kdny_nv_1

value: Kidney


title: bat_ab04_axlnode_nv_1

value: Axial lymph node


title: C56_B10_L1_8w_RepB_Replicate2


title: AGH117_10

description: Biological replicate 2

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0


title: C56_B1_L1_8w_RepB_Replicate2

value: Keratinocytes


title: bat_ab03_spln_nv_1

description: From euthanized bat infected with Ebola

source_name: Spleen_from euthanized bat infected with Ebola

value: Spleen

value: infected with Ebola


title: C56_B5_L1_8w_RepB_Replicate2


title: bat_ab03_smlint_nv_1

description: From euthanized bat infected with Ebola

source_name: Small Intestine_from euthanized bat infected with Ebola

value: Small Intestine


title: AGH117_8

description: Biological replicate 2

source_name: MNase H3 ChIP-seq (no SM) Repl. 2

value: Formaldehyde-fixed and sonicated


title: bat_ab03_slvglnd_nv_1

description: From euthanized bat infected with Ebola

source_name: Salivary gland_from euthanized bat infected with Ebola

value: Salivary gland


title: AGH117_9

description: Biological replicate 1


title: AGH117_14

description: Biological replicate 2


title: C56_A8_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed


title: bat_ab03_pbmc_nv_1

description: From euthanized bat infected with Ebola

source_name: PBMC_from euthanized bat infected with Ebola


title: C56_A7_L1_8w_RepB_Replicate2


title: AGH117_7

description: Biological replicate 1

source_name: MNase H3 ChIP-seq (no SM) Repl. 1

value: MNase


title: AGH117_6

description: Biological replicate 3

source_name: MNase H3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta


title: AGH117_5

description: Biological replicate 2


title: C56_A6_L1_8w_RepB_Replicate2


title: bat_ab03_mslnode_nv_1

description: From euthanized bat infected with Ebola

source_name: Mesenchymal lymph node_from euthanized bat infected with Ebola

value: Mesenchymal lymph node


title: AGH117_4

description: Biological replicate 1


title: C56_A5_L1_8w_RepB_Replicate2


title: C56_A3_L1_8w_RepB_Replicate2


title: C56_A4_L1_8w_RepB_Replicate2


title: bat_ab03_lng_nv_1

description: From euthanized bat infected with Ebola

source_name: Lung_from euthanized bat infected with Ebola


title: AGH117_3

description: Biological replicate 3

source_name: MNase H3 ChIP-seq (no SM) Repl. 3


title: C56_A9_L1_8w_RepB_Replicate2


title: C56_A2_L1_8w_RepB_Replicate2


title: bat_ab03_axlnode_nv_1

description: From euthanized bat infected with Ebola

source_name: Axial lymph node_from euthanized bat infected with Ebola


title: OptoFrequenciesTranscriptomics_5Hz_Male_Rep_3

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

data_processing:
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: .tar.gz zipped directories with kallisto output (pseudoaligned read counts and tpm measures of trancripts) containing .h5 and .tsv files

source_name: brain

extract_protocol:
Trizol
illumina TrueSeq

value: brain

tag: brain region

value: hippocampus

tag: sub region

value: vHC

tag: animalid

tag: group

value: OptoFrequenciesTranscriptomics

tag: virus

value: Stimulation

tag: timepoint

tag: stimulation frequency

tag: Sex

value: Male


title: AGH124_18

description: Biological replicate 3

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-histone H3, anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001), anti-Rpb1 (Biolegend, Cat#664906) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4 EAF1-FRB::natMX4

tag: treatment


title: bat_ab02_spln_nv_1

description: From euthanized bat infected with Ebola

tag: tissue/cell line


title: OptoFrequenciesTranscriptomics_5Hz_Male_Rep_4

tag: genotype


title: OptoFrequenciesTranscriptomics_3Hz_Male_Rep_3


title: AGH124_17

description: Biological replicate 2

tag: strain

tag: chip antibody


title: C56_A11_L1_8w_RepB_Replicate2

city: Turin

first: Andrea

last: Lauria

institute: University of Turin

tag: cell type

value: Keratinocytes

tag: time

tag: plate


title: bat_ab03_lvr_nv_1

description: From euthanized bat infected with Ebola

source_name: Liver_from euthanized bat infected with Ebola

value: Liver


title: AGH124_16

description: Biological replicate 1

source_name: MNase H3 ChIP-seq (+SM) Repl. 1


title: bat_ab03_lrgint_nv_1

description: From euthanized bat infected with Ebola

source_name: Large Intestine_from euthanized bat infected with Ebola

value: Large Intestine

value: infected with Ebola


title: bat_ab02_slvglnd_nv_2

description: From euthanized bat infected with Ebola


title: bat_ab02_smlint_nv_1

description: From euthanized bat infected with Ebola

value: Small Intestine


title: C56_A10_L1_8w_RepB_Replicate2

source_name: Murine Epidermal cells

tag: population

tag: replicate


title: AGH117_2

description: Biological replicate 2

value: Formaldehyde-fixed and sonicated


title: C56_A12_L1_8w_RepB_Replicate2

value: CBA C57BL/6 mixed


title: OptoFrequenciesTranscriptomics_Sham_Male_Rep_3

tag: tissue

tag: brain region

tag: sub region

value: Sham


title: bat_ab03_kdny_nv_1

description: From euthanized bat infected with Ebola

source_name: Kidney_from euthanized bat infected with Ebola

value: Kidney


title: AGH124_15

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4

value: MNase


title: C55_H9_L1_8w_RepB_Replicate1


title: bat_ab02_slvglnd_nv_1

description: From euthanized bat infected with Ebola

value: Salivary gland


title: AGH117_1

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta


title: C55_H8_L1_8w_RepB_Replicate1


title: bat_ab02_pbmc_nv_1

description: From euthanized bat infected with Ebola

value: PBMC


title: OptoFrequenciesTranscriptomics_Sham_Male_Rep_2

value: brain

value: hippocampus

value: vHC

tag: animalid

tag: group

value: OptoFrequenciesTranscriptomics

tag: virus

value: Stimulation


title: AGH124_14

description: Biological replicate 2

source_name: MNase H3 ChIP-seq (+SM) Repl. 2


title: OptoFrequenciesTranscriptomics_5Hz_Male_Rep_2

tag: timepoint

tag: stimulation frequency

tag: Sex

value: Male


title: AGH124_13

description: Biological replicate 1

tag: genotype

tag: treatment


title: C55_H6_L1_8w_RepB_Replicate1

tag: strain

value: Keratinocytes


title: bat_ab02_mslnode_nv_1

description: From euthanized bat infected with Ebola

tag: tissue/cell line

value: Mesenchymal lymph node

value: infected with Ebola


title: C55_H5_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

tag: cell type

tag: time


title: C55_H3_L1_8w_RepB_Replicate1

tag: plate

tag: population


title: bat_ab02_lvr_nv_2

description: From euthanized bat infected with Ebola

value: Liver


title: OptoFrequenciesTranscriptomics_15Hz_Male_Rep_2

tag: tissue

tag: replicate


title: AGH124_11

description: Biological replicate 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 EAF1-FRB::natMX4

tag: chip antibody

value: Formaldehyde-fixed and sonicated


title: OptoFrequenciesTranscriptomics_3Hz_Male_Rep_2

tag: brain region

tag: sub region

tag: animalid


title: AGH124_12

description: Biological replicate 3

value: MNase


title: OptoFrequenciesTranscriptomics_15Hz_Male_Rep_3

tag: group

tag: virus

tag: timepoint


title: C55_H2_L1_8w_RepB_Replicate1


title: bat_ab02_lrgint_nv_1

description: From euthanized bat infected with Ebola

value: Large Intestine


title: bat_ab02_lvr_nv_12h_1

description: From euthanized bat infected with Ebola


title: OptoFrequenciesTranscriptomics_15Hz_Male_Rep_1

tag: genotype

tag: stimulation frequency

tag: Sex


title: AGH124_9

description: Biological replicate 3

tag: strain

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1delta::hphMX4

tag: treatment


title: OptoFrequenciesTranscriptomics_3Hz_Male_Rep_1


title: OptoFrequenciesTranscriptomics_Sham_Male_Rep_1

value: Sham


title: AGH124_8

description: Biological replicate 2


title: C55_H1_L1_8w_RepB_Replicate1

tag: cell type

tag: time


title: bat_ab02_lng_nv_1

description: From euthanized bat infected with Ebola

tag: tissue/cell line

value: Lung


title: C55_G9_L1_8w_RepB_Replicate1

tag: plate

tag: population


title: AGH124_7

description: Biological replicate 1

tag: chip antibody


title: OptoFrequenciesTranscriptomics_5Hz_Male_Rep_1

tag: tissue

value: brain

tag: brain region

value: hippocampus

tag: replicate


title: C55_G8_L1_8w_RepB_Replicate1


title: AGH124_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: OptoFrequenciesTranscriptomics_3Hz_Female_Rep_3

tag: sub region

value: vHC

tag: animalid

tag: group

value: OptoFrequenciesTranscriptomics

value: Stimulation

value: Female


title: bat_ab02_axlnode_nv_1

description: From euthanized bat infected with Ebola

value: Axial lymph node

value: infected with Ebola


title: C55_G7_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

value: Keratinocytes


title: AGH124_5

description: Biological replicate 2

tag: genotype

value: Formaldehyde-fixed and sonicated


title: AGH124_10

description: Biological replicate 1

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 EAF1-FRB::natMX4

value: MNase


title: OptoFrequenciesTranscriptomics_5Hz_Female_Rep_3

tag: virus

tag: timepoint

tag: stimulation frequency


title: bat_ab01_smlint_nv_1

description: From euthanized bat infected with Ebola

source_name: Small Intestine_from euthanized bat infected with Ebola

value: Small Intestine

tag: treatment


title: AGH124_4

description: Biological replicate 1

tag: strain


title: C55_G6_L1_8w_RepB_Replicate1

tag: cell type

tag: time


title: bat_ab01_slvglnd_nv_1

description: From euthanized bat infected with Ebola

tag: tissue/cell line

value: Salivary gland


title: OptoFrequenciesTranscriptomics_15Hz_Female_Rep_3

tag: Sex


title: C55_G4_L1_8w_RepB_Replicate1

tag: plate

tag: population


title: C55_G3_L1_8w_RepB_Replicate1


title: AGH124_3

description: Biological replicate 3

tag: chip antibody


title: bat_ab02_kdny_nv_1

description: From euthanized bat infected with Ebola

value: Kidney


title: AGH124_2

description: Biological replicate 2

source_name: MNase H3 ChIP-seq (no SM) Repl. 2


title: OptoFrequenciesTranscriptomics_Sham_Female_Rep_3

tag: tissue

value: brain

tag: brain region

tag: replicate

value: Sham


title: bat_ab01_mslnode_nv_2

description: From euthanized bat infected with Ebola

value: Mesenchymal lymph node


title: bat_ab01_pbmc_nv_1

description: From euthanized bat infected with Ebola

value: PBMC


title: OptoFrequenciesTranscriptomics_3Hz_Female_Rep_2

value: hippocampus

tag: sub region

value: vHC

tag: animalid

tag: group

value: OptoFrequenciesTranscriptomics


title: C55_G2_L1_8w_RepB_Replicate1


title: AGH124_1

description: Biological replicate 1

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: bat_ab01_mslnode_nv_1

description: From euthanized bat infected with Ebola

value: infected with Ebola


title: OptoFrequenciesTranscriptomics_5Hz_Female_Rep_2

tag: virus

value: Stimulation

tag: timepoint

tag: stimulation frequency

value: Female


title: C55_G12_L1_8w_RepB_Replicate1

tag: strain

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes


title: AGH118_18

description: Biological replicate 3

source_name: H3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4 EAF1-FRB::natMX4

tag: treatment

value: Formaldehyde-fixed and sonicated


title: bat_ab01_spln_nv_1

description: From euthanized bat infected with Ebola

source_name: Spleen_from euthanized bat infected with Ebola

tag: tissue/cell line

value: Spleen


title: bat_ab01_lvr_nv_1

description: From euthanized bat infected with Ebola

value: Liver


title: AGH118_17

description: Biological replicate 2

source_name: H3 ChIP-seq (+SM) Repl. 2


title: C55_G11_L1_8w_RepB_Replicate1

tag: time

tag: plate


title: C55_G5_L1_8w_RepB_Replicate1

tag: population


title: AGH118_16

description: Biological replicate 1

source_name: H3 ChIP-seq (+SM) Repl. 1

tag: chip antibody


title: OptoFrequenciesTranscriptomics_15Hz_Female_Rep_1

tag: tissue

value: brain

tag: brain region

tag: Sex


title: AGH118_15

description:
Biological replicate 3
Normalized_Occ.AGH118_13-15C.rmdup.50-200.bw

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 gcn5delta::hphMX4


title: C55_G10_L1_8w_RepB_Replicate1

tag: replicate


title: OptoFrequenciesTranscriptomics_5Hz_Female_Rep_1

tag: sub region

tag: animalid

tag: group


title: C55_G1_L1_8w_RepB_Replicate1


title: bat_ab01_lng_nv_2

description: From euthanized bat infected with Ebola

value: Lung


title: OptoFrequenciesTranscriptomics_15Hz_Female_Rep_2

tag: genotype

tag: virus

tag: timepoint


title: bat_ab01_lng_nv_1

description: From euthanized bat infected with Ebola


title: AGH118_14

description:
Biological replicate 2
Normalized_Occ.AGH118_13-15C.rmdup.50-200.bw

tag: strain


title: C55_F9_L1_8w_RepB_Replicate1

tag: cell type


title: OptoFrequenciesTranscriptomics_Sham_Female_Rep_1

tag: treatment

tag: stimulation frequency

value: Sham


title: AGH118_13

description:
Biological replicate 1
Normalized_Occ.AGH118_13-15C.rmdup.50-200.bw


title: bat_ab01_kdny_nv_2

description: From euthanized bat infected with Ebola

tag: tissue/cell line

value: Kidney


title: OptoFrequenciesTranscriptomics_3Hz_Female_Rep_1

value: hippocampus

value: vHC


title: C55_F8_L1_8w_RepB_Replicate1

tag: time

tag: plate

tag: population


title: AGH118_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 EAF1-FRB::natMX4

tag: chip antibody


title: OptoFrequenciesTranscriptomics_Sham_Female_Rep_2

tag: tissue

tag: brain region

value: OptoFrequenciesTranscriptomics

tag: Sex


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_12

tag: sub region

tag: animalid

tag: replicate

value: RetroOptoTranscriptomics

value: Stimulation

value: Male


title: C55_F7_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

value: Keratinocytes


title: AGH118_11

description: Biological replicate 2

tag: genotype

value: Formaldehyde-fixed and sonicated


title: C55_F6_L1_8w_RepB_Replicate1


title: RetroOptoTranscriptomics_Homecage_NA_Rep_10

tag: group

tag: virus

value: Homecage

tag: timepoint


title: bat_ab01_axlnode_nv_1

description: From euthanized bat infected with Ebola

value: Axial lymph node

tag: treatment

value: infected with Ebola


title: AGH118_10

description: Biological replicate 1

tag: strain


title: C55_F5_L1_8w_RepB_Replicate1

tag: cell type


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_11

value: brain

value: Control

tag: stimulation frequency


title: bat_ab01_lrgint_nv_1

description: From euthanized bat infected with Ebola

tag: tissue/cell line

value: Large Intestine


title: ro6_wt_1

description: From cell line  infected with NAIVE

source_name: R06 bat cell culture_infected with NAIVE

value: R06 bat cell culture

value: infected with NAIVE


title: AGH118_9

description:
Biological replicate 3
Normalized_Occ.AGH118_7-9C.rmdup.50-200.bw

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 eaf1delta::hphMX4


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_11

value: hippocampus

value: vHC


title: C55_F4_L1_8w_RepB_Replicate1

tag: time

tag: plate

tag: population


title: ro6_nv_24h_2

description: From cell line  infected with NAIVE


title: ro6_nv_24h_1

description: From cell line  infected with NAIVE


title: AGH118_8

description:
Biological replicate 2
Normalized_Occ.AGH118_7-9C.rmdup.50-200.bw

tag: chip antibody


title: C55_F3_L1_8w_RepB_Replicate1


title: AGH118_7

description:
Biological replicate 1
Normalized_Occ.AGH118_7-9C.rmdup.50-200.bw


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_10

tag: tissue

tag: brain region

value: RetroOptoTranscriptomics

tag: Sex


title: C55_F2_L1_8w_RepB_Replicate1

tag: replicate


title: ro6_nv_12h_4

description: From cell line  infected with NAIVE


title: ro6_nv_12h_3

description: From cell line  infected with NAIVE


title: bat_ab01_kdny_nv_12h_1

description: From euthanized bat infected with Ebola

value: Kidney


title: AGH118_6

description:
Biological replicate 3
Normalized_Occ.AGH118_4-6C.rmdup.50-200.bw

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: ro6_nv_12h_1_R1

description: From cell line  infected with NAIVE


title: AGH118_5

description:
Biological replicate 2
Normalized_Occ.AGH118_4-6C.rmdup.50-200.bw


title: C55_F11_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed


title: RetroOptoTranscriptomics_Homecage_NA_Rep_8

tag: sub region

tag: animalid

tag: group

value: Male


title: C55_F12_L1_8w_RepB_Replicate1

value: Keratinocytes


title: ro6_eb_vp35_24h_2

description: From cell line  infected with Ebola

source_name: R06 bat cell culture_infected with Ebola

tag: treatment


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_10

tag: virus

value: Stimulation

tag: timepoint


title: AGH118_4

description:
Biological replicate 1
Normalized_Occ.AGH118_4-6C.rmdup.50-200.bw

tag: strain

value: Formaldehyde-fixed and sonicated


title: AGH118_3

description:
Biological replicate 3
Normalized_Occ.AGH118_1-3C.rmdup.50-200.bw

source_name: H3 ChIP-seq (no SM) Repl. 3


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_9

tag: stimulation frequency


title: C55_F1_L1_8w_RepB_Replicate1

tag: cell type

tag: time


title: RetroOptoTranscriptomics_Homecage_NA_Rep_9

value: Homecage


title: C55_F10_L1_8w_RepB_Replicate1

tag: plate

tag: population


title: AGH118_2

description:
Biological replicate 2
Normalized_Occ.AGH118_1-3C.rmdup.50-200.bw

source_name: H3 ChIP-seq (no SM) Repl. 2

tag: chip antibody


title: ro6_eb_vp35_24h_1

description: From cell line  infected with Ebola

tag: tissue/cell line

value: infected with Ebola


title: C55_E9_L1_8w_RepB_Replicate1


title: RetroOptoTranscriptomics_Homecage_NA_Rep_7

source_name: brain

tag: tissue

value: brain

tag: brain region

tag: Sex


title: ro6_eb_vp35_12h_2

description: From cell line  infected with Ebola


title: AGH118_1

description:
Biological replicate 1
Normalized_Occ.AGH118_1-3C.rmdup.50-200.bw

source_name: H3 ChIP-seq (no SM) Repl. 1

tag: genotype


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_8

tag: sub region

tag: animalid

tag: replicate

value: Control


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_9

tag: group

tag: virus

tag: treatment


title: ro6_eb_vp35_12h_1

description: From cell line  infected with Ebola

value: R06 bat cell culture


title: C55_E8_L1_8w_RepB_Replicate1

tag: strain


title: AGH111_15

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0 yng2delta::kanMX4


title: C55_E7_L1_8w_RepB_Replicate1

tag: cell type


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_8

tag: timepoint

tag: stimulation frequency


title: ro6_eb_vp24_24h_2

description: From cell line  infected with Ebola


title: RetroOptoTranscriptomics_Homecage_NA_Rep_6


title: C55_E6_L1_8w_RepB_Replicate1

tag: time

tag: plate

tag: population


title: ro6_eb_vp24_24h_1

description: From cell line  infected with Ebola

tag: tissue/cell line


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_7

tag: tissue

tag: brain region


title: AGH111_14

description: Biological replicate 2

tag: genotype

tag: chip antibody


title: AGH111_13

description: Biological replicate 1


title: C55_E5_L1_8w_RepB_Replicate1


title: ro6_eb_vp24_12h_2

description: From cell line  infected with Ebola


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_7

tag: sub region

tag: animalid

tag: Sex


title: AGH134_22

description: Biological replicate 3


title: C55_E4_L1_8w_RepB_Replicate1

tag: replicate


title: AGH133_18

description: Biological replicate 2

tag: treatment


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_6

tag: group

tag: virus


title: C55_E3_L1_8w_RepB_Replicate1

tag: strain

tag: cell type


title: AGH133_17

description: Biological replicate 1


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_6

tag: timepoint

tag: stimulation frequency


title: C55_E2_L1_8w_RepB_Replicate1

tag: time

tag: plate

tag: population


title: AGH111_6

description: Biological replicate 3

value: MATa his3delta1 leu2delta0 lys2delta0 ura3delta0


title: ro6_eb_dbl_12h_2

description: From cell line  infected with Ebola

tag: tissue/cell line


title: ro6_eb_dbl_24h_1

description: From cell line  infected with Ebola


title: RetroOptoTranscriptomics_Homecage_NA_Rep_5

tag: tissue

tag: brain region

value: hippocampus

tag: genotype


title: C55_E12_L1_8w_RepB_Replicate1


title: C55_E11_L1_8w_RepB_Replicate1


title: AGH111_4

description: Biological replicate 1

tag: chip antibody


title: ro6_eb_dbl_12h_1

description: From cell line  infected with Ebola


title: AGH111_5

description: Biological replicate 2


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_4

tag: sub region

value: vHC

tag: animalid

tag: Sex


title: ro6_eb_8h_2

description: From cell line  infected with Ebola

tag: treatment


title: ro6_eb_vp24_12h_1

description: From cell line  infected with Ebola


title: AGH111_3

description: Biological replicate 3


title: ro6_eb_24h_1

description: From cell line  infected with Ebola


title: RetroOptoTranscriptomics_Homecage_NA_Rep_4

tag: replicate

tag: group

value: RetroOptoTranscriptomics

tag: virus


title: C55_D9_L1_8w_RepB_Replicate1

tag: strain

tag: cell type


title: ro6_eb_dbl_24h_2

description: From cell line  infected with Ebola


title: ro6_eb_8h_1

description: From cell line  infected with Ebola


title: rn7_nv_24h_3

description: From cell line  infected with NAIVE

source_name: RoNi/7 bat cell culture_infected with NAIVE

value: RoNi/7 bat cell culture

value: infected with NAIVE


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_5

tag: timepoint

tag: stimulation frequency


title: AGH111_2

description: Biological replicate 2


title: AGH111_1

description: Biological replicate 1


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_4


title: C55_D8_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

tag: time

tag: plate

tag: population


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_5

tag: tissue

tag: brain region

value: Male


title: AGH111_18

description: Biological replicate 3

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta sas3delta::kanMX4

tag: chip antibody


title: C55_D6_L1_8w_RepB_Replicate1

value: Keratinocytes


title: RetroOptoTranscriptomics_Homecage_NA_Rep_3

tag: sub region

tag: animalid


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_3

tag: treatment

value: Stimulation

tag: Sex


title: C55_E1_L1_8w_RepB_Replicate1

tag: replicate


title: C55_D5_L1_8w_RepB_Replicate1


title: rn7_nv_24h_2

description: From cell line  infected with NAIVE

tag: tissue/cell line


title: AGH111_17

description: Biological replicate 2

tag: strain

value: Formaldehyde-fixed and sonicated


title: AGH111_16

description: Biological replicate 1


title: C55_D4_L1_8w_RepB_Replicate1

tag: cell type


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_2

tag: group

tag: virus

tag: timepoint


title: AGH128_21

description: Biological replicate 3


title: RetroOptoTranscriptomics_Homecage_NA_Rep_2

value: Homecage

tag: stimulation frequency


title: C55_D3_L1_8w_RepB_Replicate1

tag: time

tag: plate

tag: population


title: rn7_nv_12h_4

description: From cell line  infected with NAIVE


title: RetroOptoTranscriptomics_Stimulation_Control_Rep_1

tag: tissue

value: brain

tag: brain region

tag: genotype


title: C55_D2_L1_8w_RepB_Replicate1


title: rn7_nv_12h_3

description: From cell line  infected with NAIVE


title: AGH128_19

description: Biological replicate 1

tag: chip antibody


title: AGH128_20

description: Biological replicate 2

tag: treatment


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_3

tag: sub region

tag: animalid

tag: Sex


title: C55_D12_L1_8w_RepB_Replicate1

tag: strain

tag: replicate


title: rn7_nv_12h_1_R1

description: From cell line  infected with NAIVE

tag: tissue/cell line


title: C55_D11_L1_8w_RepB_Replicate1

tag: cell type


title: rn7_nv_24h_1

description: From cell line  infected with NAIVE


title: rn7_mb_8h_2

description: From cell line  infected with Marburg

source_name: RoNi/7 bat cell culture_infected with Marburg

value: infected with Marburg


title: AGH111_12

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta rtt109delta::kanMX4


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_2

tag: group

tag: virus

tag: timepoint


title: rn7_nv_12h_5

description: From cell line  infected with NAIVE


title: C55_D10_L1_8w_RepB_Replicate1

source_name: Murine Epidermal cells

tag: time

tag: plate


title: AGH111_10

description: Biological replicate 1


title: RetroOptoTranscriptomics_Stimulation_ChR2_Rep_1

tag: tissue

tag: stimulation frequency


title: AGH111_11

description: Biological replicate 2

tag: genotype


title: rn7_ivp_24h_1

description: From cell line  infected with InVitroCulture

source_name: RoNi/7 bat cell culture_infected with InVitroCulture

value: infected with InVitroCulture


title: rn7_ivp_12h_1


title: AGH128_24

description: Biological replicate 3

tag: chip antibody


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_8

tag: brain region

value: DREADDTranscriptomics

tag: treatment

value: Clozapine


title: rn7_eb_vp35_24h_1

description: From cell line  infected with Ebola

source_name: RoNi/7 bat cell culture_infected with Ebola

value: infected with Ebola


title: C55_C9_L1_8w_RepB_Replicate1

tag: population


title: AGH128_23

description: Biological replicate 2


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_8

value: hippocampus

tag: sub region

value: dHC

tag: animalid

tag: Sex


title: C55_C8_L1_8w_RepB_Replicate1

tag: strain

tag: replicate


title: AGH128_22

description: Biological replicate 1


title: DREADDTranscriptomics_Control_45min_vHC_Rep_7

value: vHC

tag: group

value: Control


title: rn7_eb_vp24_24h_2_R1

description: From cell line  infected with Ebola

tag: tissue/cell line

value: RoNi/7 bat cell culture


title: AGH111_9

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta eaf1delta::kanMX4


title: rn7_eb_vp35_12h_1

description: From cell line  infected with Ebola


title: C55_C7_L1_8w_RepB_Replicate1

value: CBA C57BL/6 mixed

tag: cell type

value: Keratinocytes


title: RetroOptoTranscriptomics_Homecage_NA_Rep_1

value: RetroOptoTranscriptomics

tag: virus

tag: timepoint

value: Male


title: C55_C6_L1_8w_RepB_Replicate1

tag: time

tag: plate


title: rn7_mb_8h_1

description: From cell line  infected with Marburg


title: C55_E10_L1_8w_RepB_Replicate1


title: rn7_eb_vp24_24h_1_R1

description: From cell line  infected with Ebola


title: C55_C5_L1_8w_RepB_Replicate1


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_7

tag: tissue

value: brain

tag: genotype

tag: stimulation frequency


title: rn7_eb_vp24_12h_2_R1

description: From cell line  infected with Ebola

tag: treatment


title: AGH111_8

description: Biological replicate 2

tag: chip antibody

value: Formaldehyde-fixed and sonicated


title: C55_D1_L1_8w_RepB_Replicate1

tag: population


title: AGH111_7

description: Biological replicate 1


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_7

tag: brain region

tag: sub region

tag: animalid


title: C55_C4_L1_8w_RepB_Replicate1

tag: strain

tag: replicate


title: AGH129_3

description: Biological replicate 3


title: rn7_eb_vp24_12h_1_R1

description: From cell line  infected with Ebola

tag: tissue/cell line


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_6

tag: group

tag: Sex


title: AGH129_2

description: Biological replicate 2


title: C55_C3_L1_8w_RepB_Replicate1

tag: cell type


title: rn7_eb_dbl_24h_2_R1

description: From cell line  infected with Ebola


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_6

tag: virus

tag: timepoint


title: C55_C2_L1_8w_RepB_Replicate1

tag: time

tag: plate


title: rn7_eb_dbl_24h_1_R1

description: From cell line  infected with Ebola


title: DREADDTranscriptomics_Control_45min_dHC_Rep_7

tag: tissue

tag: genotype

tag: stimulation frequency


title: AGH110_15

description: Biological replicate 3

value: MATa his3delta1 leu2delta met15delta ura3delta gcn5delta::kanMX4

tag: chip antibody

tag: treatment


title: C55_C11_L1_8w_RepB_Replicate1

tag: population


title: DREADDTranscriptomics_Control_45min_dHC_Rep_6

tag: brain region

tag: sub region

tag: animalid


title: AGH129_1

description: Biological replicate 1

tag: strain


title: C55_C10_L1_8w_RepB_Replicate1

tag: replicate


title: C55_C12_L1_8w_RepB_Replicate1


title: DREADDTranscriptomics_hM3Dq_45min_vHC_Rep_5

tag: group

tag: Sex


title: rn7_eb_dbl_12h_2_R1

description: From cell line  infected with Ebola

tag: tissue/cell line


title: DREADDTranscriptomics_hM3Dq_45min_dHC_Rep_5

tag: virus

tag: timepoint


title: rn7_eb_dbl_12h_1_R1

description: From cell line  infected with Ebola


title: C55_C1_L1_8w_RepB_Replicate1

tag: cell type

tag: time

tag: plate


title: rn7_eb_8h_2

description: From cell line  infected with Ebola


title: DREADDTranscriptomics_Control_45min_vHC_Rep_5

tag: tissue

tag: genotype

tag: stimulation frequency


title: AGH129_7

description: Biological replicate 4

source_name: H3 ChIP-seq (no SM) Repl. 4

tag: chip antibody

tag: treatment


title: rn7_eb_8h_1

description: From cell line  infected with Ebola


title: rn7_eb_24h_1

description: From cell line  infected with Ebola


title: AGH110_14

description: Biological replicate 2


title: AGH129_6

description: Biological replicate 3


title: DREADDTranscriptomics_Control_45min_vHC_Rep_6

tag: brain region

tag: sub region


title: C55_B8_L1_8w_RepB_Replicate1

tag: strain

tag: population


title: C55_B9_L1_8w_RepB_Replicate1

tag: replicate


title: AGH129_5

description: Biological replicate 2


title: DREADDTranscriptomics_Control_45min_vHC_Rep_4

tag: animalid

tag: group

tag: Sex


title: C55_B7_L1_8w_RepB_Replicate1


title: AGH129_4

description: Biological replicate 1


title: bat_rbs_4

description: From euthanized bat infected with Rabies

source_name: Brain_from euthanized bat infected with Rabies

tag: tissue/cell line

value: Brain

value: infected with Rabies


title: bat_rbs_3


title: DREADDTranscriptomics_Control_45min_dHC_Rep_4

value: DREADDTranscriptomics

tag: virus

value: Clozapine

tag: timepoint


title: AGH110_13

description: Biological replicate 1


title: C55_B6_L1_8w_RepB_Replicate1

tag: cell type

tag: time

tag: plate


title: bat_cb3_spln

description: From euthanized bat

source_name: Spleen_from euthanized bat

value: Spleen

value: From euthanized bat


title: C55_B5_L1_8w_RepB_Replicate1


title: bat_cb3_lvr

description: From euthanized bat

source_name: Liver_from euthanized bat

value: Liver


title: bat_cb3_kdny

description: From euthanized bat

source_name: Kidney_from euthanized bat

value: Kidney