title: BAL fluid, Afghanistan_particulate_matter

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
3_Chu_G5
cell-level-metadata.csv.gz
umi-count-matrix.csv.gz

data_processing:
Fastqs were processed using cellranger (v. 2.2.0) with the mm10 genome assembly to generate UMI gene count matrices per sample. Seurat (v. 2.3.4) was used to aggregate all samples into a single matrix and to perform initial quality control filtering, normalization, and clustering. Cells were removed if there were fewer than 250 genes detected, a unique molecular identifier (UMI) count less than 250 or greater than 10,000, or if the proportion of UMIs mapped to mitochondrial genes was greater than 10%. Genes were excluded if they were detectable in fewer than 5 cells.
Genome_build: mm10
Supplementary_files_format_and_content: UMI count matrix and associated cell-level metadata

source_name: mouse bronchoalveolar lavage (BAL) cells

extract_protocol:
Fresh BAL cells were obtained by lavage of lungs with PBS, with minimal damage to the tracheas to avoid red blood cell contamination.  Each mouse was lavaged 5 times. To remove mucus in the BAL preparation, cells were resuspended in PBS and passed through 70 µm and then 40 µm pore size cell strainers. Cytospin slides were used to confirm that the cells were in a single cell suspension prior to sequencing.  The viability of cells as evaluated by trypan blue staining was between 60 to 80%.
10x Genomics 3' end kit (v2).

treatment_protocol: C57BL/6 mice were obtained from Jackson Laboratories and housed under pathogen-free conditions. The Naval Medical Research Unit Dayton (NAMRU-D) at the Wright Patterson Air Force Base performed the whole body PM exposures and the allergen instillations were conducted at National Jewish Health (NJH) in Denver, CO. This study was approved by the Institutional Animal Care and Use Committee (IACUC) at NJH and by ACURO at NAMRU-D. Mice were exposed to filtered air or aerosolized APM (5 mg/m3)   for 6 hours per day for 12 consecutive days, via whole body exposure chambers (n=30/group) at the NAMRU-D facility as described previously (See reference). After the last APM exposure, mice were shipped to National Jewish Health where they were allowed to acclimatize. 9 days after the last APM exposure, the allergen sensitizations were initiated. On day 22 and day 29 of the study, mice were sensitized to either sterile PBS (control) or 10 µg of house dust mite (HDM) suspended in PBS via intranasal instillation (n=15/group). On days 36, 37, and 38, mice were challenged with either PBS or HDM. On day 39, mice from each group were anesthetized for analysis of airway physiology on the flexiVent (n=8/group) or euthanized and the lungs were lavaged and pooled for single cell RNAseq (n=7/group). For single cell RNA-seq 7 mice per condition were pooled into single samples per treatment group. (T. R. Sterner et al., Toxicity and occupational exposure assessment for hydroprocessed esters and fatty acids (HEFA) alternative jet fuels. J Toxicol Environ Health A 83, 181-202 (2020).)

tag: strain

value: Afghanistan particulate matter (APM)

value: bronchoalveolar lavage (BAL) cells


title: SPMS [S2]

status: Public on Jan 06 2022

type: SRA

city: La Jolla

first: Yasuyuki

last: Kihara

state: California

address: 10901 N Torrey Pines Rd

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: transcriptomic

data_processing:
Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger V3.0.2, 10x Genomics) for barcode correction, alignment to the GRCh38 genome, and UMI collapsing.
gene-UMI count matrices from individual samples were normalized, clustered, and integrated in Seurat V3.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: We provide the error-corrected gene-UMI count matrices that were directly ouput by Cellranger. We also provide a cell-level metadata file that contains only quality-filtered cells as well as the corresponding cell type annotations that are included in our final analysis.

molecule: total RNA

organism: Homo sapiens

source_name: Post-mortem prefrontal cortices (BA10)_SPMS

extract_protocol:
Post-mortem prefrontal cortices (BA10) from donors who suffered from RRMS or SPMS were cryo-sectioned at 300 µm. The buffers used in this procedure were made in autoclaved diethyl pyrocarbonate (DEPC; MilliporeSigma, Cat# D5758)-treated water. All the steps from here on were performed at 4 ºC with additional equilibration time at each step. The samples were initially placed in 0.5 mL of nuclear extraction buffer (NEB; 0.32 M Sucrose, 5 mM CaCl2.2H20, 3 mM (CH3COO)2Mg.4H2O, 0.1 mM EDTA, 10 mM Tris/HCl (pH 8.0), 0.1% Triton X-100 with cOmpleteTM mini protease inhibitor cocktail tablet (MilliporeSigma, Cat# 11836153001) and fresh 0.2% RNase inhibitor (Takara, Cat# 2313A)) for 15 minutes. After adding another 0.5 mL NEB, the samples were homogenized thoroughly with a Dounce homogenizer. Upon transferring this homogenate to a new tube, the Dounce homogenizer was rinsed with 1 mL of NEB. Homogenates were then passed through a CellTrics® 50 µm filer (Sysmex, Cat# 04-004-2324). After washing the filter with NEB once, the filtrates were centrifuged at 1600 x g for 5 mins. The resulting pellets were resuspended with 1 mL of PBSE (1X PBS, 2 mM EGTA and fresh 0.2% RNase inhibitor), transferred into a new tube, diluted with PBSE, and centrifuged again at 1600 x g for 5 mins. Meanwhile, density gradients of OptiPrepTM (MilliporeSigma, Cat# D1556) were made in FACS tubes with 0.4 mL 35% OptiPrepTM on bottom and 2 mL 10% OptiPrepTM on top. Solutions used for density gradients were as follows: OptiPrepTM, solution B (6X concentrations: 120 mM Tricine/NaOH pH 7.8, 150 mM KCl and 30 mM MgCl2.6H2O) and solution D (0.25 M Sucrose in 1X solution B with freshly added 0.2% RNase inhibitor). The OptiPrepTM solutions were diluted with solution D to make the final concentrations to 35% and 10%. Nuclear pellets were resuspended with 0.2 mL solution D, followed by addition of 0.2 mL of 10% OptiPrepTM solutions, which were layered onto the 10% OptiPrepTM solution, and centrifuged at 3250 x g for 10 mins. The nuclei that settled at the boundary of 35% and 10% were collected, washed twice with PBSE containing 1% fatty acid-free bovine serum albumin (BSA; Gemini Bio, Cat# 700-107P), passed through CellTrics® 50 µm filter, washed again with PBSE + BSA, and labeled with DAPI (1:100,000, 4',6-diamidino-2-phenylindole; MilliporeSigma, Cat# D9542). About 3 x 105 nuclei were sorted using a BD FACSAria™ II (BD Biosciences) into a precoated collection tube filled with 1 mL of PBSE + BSA. The nuclei were washed once and resuspended in PBSE + BSA to obtain around 1500 cells/µL, and the counts were confirmed using a CountessTM II (Thermo Fisher Scientific). Single-nucleus capture (target capture of 5,000 nuclei per sample) and library preparation was conducted using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics, Cat# PN-1000075) and Chromium Single Cell B Chip Kit (10X Genomics, Cat# PN-1000074) according to the manufacturer's instruction.
Single-nucleus libraries were prepared using standard Illumina protocols and were sequenced on the Illumina NovaSeq 6000 machine at GENEWIZ, Inc.

tag: subject status

value: suffered from SPMS

tag: post-mortem interval

tag: age at death

tag: Sex

value: M

tag: tissue

value: Post-mortem prefrontal cortices (BA10)

tag: edss

tag: rin


title: D2_MyoD_1

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
Trimmomatic v0.36 used for trimming adapter sequences and low quality reads
Kallisto v0.44 used for mapping reads and quantifying gene expression
edgeR v3.28 used for differential gene expression analysis
WebGestalt used for pathway enrichment analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited raw counts

organism: Mus musculus

source_name: Mouse embryonic fibroblasts expressing MyoD

extract_protocol:
Cultured cells were harvested using trypsin and total RNA was extracted using RNeasy mini kit (Qiagen, 74104). FACS-purified cells were directly sorted into cell lysis buffer and processed for total RNA extraction using the same kit.
The RNA quality was measured with a Fragment Analyzer (Agilent, Santa Clara, California, USA) and only those samples with a 28S/18S ratio over 1.9 were used for library construction according to the TruSeq Stranded mRNA protocol (Illumina, Inc., California, USA). Briefly, 100-1000 ng of ploy A-enriched total RNA was reverse-transcribed into double-stranded cDNA. The cDNA was fragmented, end-repaired and adenylated. Then, TruSeq adapters containing unique dual indices (UDI) were ligated to processed cDNA for multiplexing. Using PCR, fragments containing TruSeq adapters on both ends were selectively enriched and the quality and quantity of the enriched libraries were determined using a Fragment Analyzer, which showed an average fragment size of approximately 360 bp. As a final step, the libraries were diluted in a concentration of 10 nM in Tris-Cl buffer (10 mM, pH8.5) with 0.1% Tween 20 and used for sequencing. The sequencing was carried out on Novaseq 6000 (Illumina, Inc., California, USA) with 100bp single end reads according to standard protocol.

tag: cell type

value: Myotubes

tag: genotype

tag: treatment

value: Treated with Dox for 2 days


title: BAL fluid, house_dust_mite_and_Afghanistan_particulate_matter

description:
4_Chu_G6
cell-level-metadata.csv.gz
umi-count-matrix.csv.gz

molecule: polyA RNA

value: house dust mite and Afghanistan particulate matter (HDM + APM)


title: knock down [YTa22-7]

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR aligner by using the NCBI37 assembly gene
Read counts for individual genes were produced using the unstranded count feature in HTSeq program
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files of read count for each sample

source_name: RGLs Ribosomal profiling

extract_protocol:
We used Gli1CreERT2:Rpl22HAf/+:Klf9f/f or +/+ mice which enables expression of haemagglutinin (HA)-tagged ribosomal protein RPL22 (RPL22–HA) following Cre recombination in Gli1+ Klf9f/f or +/+ RGLs. RiboTag immunoprecipitation and RNA extraction were performed 4 days after last TAM injection following the original protocol with minor modifications (Sanz et al., 2009). 6 dentate gyri from 3 mice were pooled per sample and homogenized with a dounce homogenizer in 900 ul cycloheximide-supplemented homogenization buffer. Homogenates were centrifuged and the supernatant incubated on a rotator at 4°C for 4 hours with 9ul anti-HA antibody (CST Rb anti-HA #3724, 1:100) to bind the HA- tagged ribosomes. Magnetic IgG beads (Thermo Scientific Pierce #88847) were conjugated to the antibody-ribosome complex via overnight incubation on a rotator at 4°C. RNA was isolated by RNeasy Plus Micro kit (Qiagen 74034) following the manufacturer’s protocol. Eluted RNA was stored at -80°C. For enrichment analysis, 45ul of homogenate (pre- anti-HA immunoprecipitation) was set aside after centrifugation, kept at -20°C overnight, and purified via RNeasy Micro kit as an ‘input’ sample, and used to determine NSC enrichment. RNA quantity and quality were measured with a Tape Station (Agilent) and Qubit fluorimeter (Thermo Fisher Scientific). Sequencing libraries were prepared using Ultra Low Input RNA Kit (Clontech).
See above

treatment_protocol: TAM

tag: genotype/variation

value: GliCreERT2 Klf9 f/f Ribotag


title: Maxillary palp nuclei

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

data_processing:
Mosquito genomes were indexed using cellranger mkref (version 6.0.2). Fastq files were aligned to the indexed genome and the gene expression in each cell was determined by cellranger count (version 6.0.2). Intron expressions were included by adding the --include-introns parameter to the cellragner count.
Genome_build: AaegL5.0
Supplementary_files_format_and_content: Expression matrix generated by Cell Ranger

organism: Aedes aegypti

source_name: Maxillary palp

extract_protocol:
Nuclei extraction from mosquito antennae and max palp were performed as previously described (Li et al. Fly Cell Atlas) with modifications.
Prepare fresh homogenization buffer (for recipe, see Li et al. Fly Cell Atlas) and keep on ice.
Thaw samples from -80ºC on ice. Spin down samples in 100 µl Schneider’s medium using the bench top spinner, discard medium as much as possible.
Antennae or Max palp from multiple dissection sessions were combined into a single 1.5 ml EP tube using a low-retention 200 uL filter tip (Rainin 30389240) with ~1 mm from the distal end trimmed using a sterilized and RNAse away-treated (Thermo Fisher 7000TS1) razor blade (VWR 10835-965). And add 100 µl Homogenization butter.
Use a pestle motor (Kimble 6HAZ6) to grind the sample for 30s–60s on ice.
Add 900 µl homogenization buffer, and transfer 1000 µl homogenized sample into the 1ml dounce (Wheaton 357538). Dounce sets should be autoclaved at 200ºC >5h or overnight.
Release nuclei by 20 strokes of loose dounce pestle and 40 of tight dounce pestle. Keep on ice. Avoid bubbles.
Filter 1000 µl sample through 5 ml cell strainer (35 µm), and then filter sample using 40 µm Flowmi (BelArt, H13680-0040) into 1.5 ml EP tube.
Centrifuge for 10 min at 1000g at 4ºC. Discard the supernatant. Do not disturb the pellet.
Re-suspend the nuclei using 500ul 1xPBS/0.5%BSA with RNase inhibitor (9.5 ml 1x PBS, 0.5 ml 10% BSA, 50 µl RNasin Plus). Pipet more than 20 times to completely re-suspend the nuclei. Filter sample using 40 µm Flowmi into a new 5 ml FACS tube and keep the tube on ice. Now the single-nucleus suspensions are ready for FACS.
10x Genomics sequencing libraries were prepared following the standard protocol from 10x Genomics 3’ v3.1 kit with following settings. All PCR reactions were performed using the Biorad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. 13 cycles were used for cDNA amplification and 16 cycles were used for sample index PCR. As per 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on Agilent 4200 TapeStation.

value: Maxillary palp


title: RRMS [S10]

source_name: Post-mortem prefrontal cortices (BA10)_RRMS

value: suffered from RRMS


title: SPMS [S3]

value: F


title: Antenna nuclei Rep1

source_name: Antenna

value: Antenna


title: BAL fluid, control

description:
1_Chu_G1
cell-level-metadata.csv.gz
umi-count-matrix.csv.gz

value: control air


title: BAL fluid, house_dust_mite

description:
2_Chu_G2
cell-level-metadata.csv.gz
umi-count-matrix.csv.gz

value: house dust mite (HDM)


title: Antenna nuclei Rep2


title: knock down [YTa22-6]


title: wild type [YTa22-3]

value: GliCreERT2 Klf9 +/+ Ribotag


title: RRMS [S1]


title: 6W-LONP1-mKO biological rep2

status: Public on Jan 05 2022

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

description:
Gastrocnemius muscle from LONP1-mKO mouse
6W-LONP1-mKO_VS_WT_genes.fpkm_tracking
6W-LONP1-mKO_VS_WT_gene_exp.txt

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Gastrocnemius muscle from 6-week-old LONP1-mKO mouse

extract_protocol:
Gastrocnemius muscle  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gastrocnemius muscle

tag: age

value: 6 weeks


title: 6W-LONP1-mKO biological rep1


title: 6W-WT biological rep1

description:
Gastrocnemius muscle from wild-type mouse
6W-LONP1-mKO_VS_WT_genes.fpkm_tracking
6W-LONP1-mKO_VS_WT_gene_exp.txt

source_name: Gastrocnemius muscle from 6-week-old wild-type mouse

value: wild-type


title: 2W-LONP1-mKO biological rep1

description:
Gastrocnemius muscle from LONP1-mKO mouse
2W-LONP1-mKO_VS_WT_genes.fpkm_tracking
2W-LONP1-mKO_VS_WT_gene_exp.txt

source_name: Gastrocnemius muscle from 2-week-old LONP1-mKO mouse

value: 2 weeks


title: 6W-WT biological rep2


title: 2W-WT biological rep2

description:
Gastrocnemius muscle from wild-type mouse
2W-LONP1-mKO_VS_WT_genes.fpkm_tracking
2W-LONP1-mKO_VS_WT_gene_exp.txt

source_name: Gastrocnemius muscle from 2-week-old wild-type mouse


title: 2W-LONP1-mKO biological rep2


title: 2W-WT biological rep1


title: wild type [YTa22-8]


title: Raji cells - H3K27me3_rep1

city: Seattle

first: Rimas

last: Orentas

state: Washington

address: 1100 Olive Way NE

department: BTCCCR

institute: Seattle Children's Research Institute

library_source: genomic

data_processing:
Library strategy: Cut&Tag
sequenced on a HiSeq instrument (Novogene, Sacramento, CA), paired-end 150, with read depth of 17M per sample, basecallling bcl2fastq
Sequencing adaptors identified and trimmed by TrimGalore (Trim Galore (RRID:SCR_011847)).
Sequencing reads were aligned to the NCBI EBV genome using the Bowtie2 package
Alignment results were normalized by the RPKM (Reads Per Kilobase of transcript, per Million mapped reads) method by DeepTools2
Genome_build: Human gammaherpesvirus 4, NCBI Reference Sequence: NC_007605.1
Supplementary_files_format_and_content: Bigwig

molecule: genomic DNA

source_name: Burkitt's lymphoma cell line

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 2 mM l-glutamine, 10 mM HEPES (Invitrogen), and 10% heat-inactivated FBS (VWR).

extract_protocol:
Fresh cells (2x105 to 5x105 per treatment) were harvested and washed twice in 1.5 Ml wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine (Sigma S2501); 1× Protease inhibitor cocktail, Roche), and Cut&Tag libraries generated, following the protocol “Bench top CUT&Tag V.2” (Hatice S Kaya-Okur, Steven Henikoff 2019. Bench top CUT&Tag. protocols.io, dx.doi.org/10.17504/protocols.io.bcuhiwt6)
Cut&Tag libraries generated, following the protocol “Bench top CUT&Tag V.2” (Hatice S Kaya-Okur, Steven Henikoff 2019. Bench top CUT&Tag. protocols.io, dx.doi.org/10.17504/protocols.io.bcuhiwt6)

treatment_protocol: treated with 1nM Bryostatin at 37°C overnight

tag: cell line

value: Raji

value: no treatment

tag: cut&tag antibodies


title: Raji cells - H3K4me2_rep1


title: Raji cells treated w/ bryostatin - H3K4me2_rep1

value: treated with 1nM Bryostatin


title: Raji cells - H3K4me3_rep1


title: Raji cells treated w/ bryostatin - H3K4me3_rep1


title: Raji cells treated w/ bryostatin - H3K27me3_rep1


title: Epilepsy_BC41_4

city: Los Angeles

first: Mitchell

last: Krawczyk

state: CA

address: 635 Charles E Young Dr S

institute: UCLA

data_processing:
FASTQ files were mapped using STAR, then used HTSEQ to generate count files. We calculated RPKM by running EdgeR-Limma-Voom in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts files (HTSeq output) contain gene counts, one file per sample

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) under the protocols of the manufacturer
We used the Ovation RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. We then used the Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7500) to perform end repair, adaptor ligation, and 10 cycles of PCR enrichment according to manufacturer’s instructions.

value: astrocytes

tag: sequencing batch

tag: patient diagnosis

value: epilepsy


title: Peritumor_BC39_3

value: peritumor


title: Epilepsy_BC46_4


title: Epilepsy_BC27_3


title: Epilepsy_BC44_4


title: Epilepsy_BC19_4


title: Epilepsy_BC45_4


title: Epilepsy_BC32_3


title: Epilepsy_BC22_4


title: Epilepsy_BC21_4


title: Peritumor_BC15_4


title: Control_BC18_4

value: control


title: Control_BC37_3


title: Epilepsy_BC22_3


title: Epilepsy_BC14_4


title: Epilepsy_BC13_4


title: Control_BC11_4


title: Peritumor_BC10_4


title: Epilepsy_BC6_4


title: Epilepsy_BC5_1


title: Epilepsy_BC8_4


title: Control_BC4_4


title: Epilepsy_BC3_4


title: Epilepsy_BC20_4


title: Epilepsy_BC38


title: Epilepsy_BC1_4


title: Control_BC36


title: Control_BC35


title: Epilepsy_BC31


title: Control_BC34


title: Control_BC29


title: Control_BC24


title: Control_BC28


title: Epilepsy_BC18


title: Control_BC17


title: Epilepsy_BC12_4


title: Epilepsy_BC13


title: Epilepsy_BC15


title: Epilepsy_BC16


title: Epilepsy_BC12


title: Epilepsy_BC6


title: Epilepsy_BC5_4


title: Control_BC5


title: Epilepsy_BC4


title: Peritumor_BC1


title: Peritumor_BC3


title: Epilepsy_BC30


title: Cerebral cortex, EA, 4

city: Hangzhou

first: Congcong

last: Ma

address: No. 548, binwen Road

institute: Zhejiang Chinese Medical University

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 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads (1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: .Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cerebral cortex

value: Electroacupuncture


title: Cerebral cortex, EA, 5


title: Cerebral cortex, EA, 1


title: Cerebral cortex, EA, 3


title: Cerebral cortex, control, 3

value: Control


title: Cerebral cortex, control, 5


title: Epilepsy_BC2_4


title: Cerebral cortex, control, 2


title: Cerebral cortex, control, 1


title: GDF15_4

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

data_processing:
10x Genomics Cell Ranger v3.1
Genome_build: Referecne created from Ensembl Rattus_norvegicus.Rnor_6.0.101
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix

source_name: area postrema and nucleus tractus solitarius

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols

value: frozen postmortem brain

tag: strain

value: Sprague Dawley

value: male

value: GDF15 (100 μg/kg)


title: GDF15_1


title: GDF15_2


title: GDF15_3


title: hESC-derived EPCs, TGF_3

type: RNA

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

description: Gene expression after 72 hours in TGFβ1-induced cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: hESC-derived differentiated cells, 72hours,30ng/ml TGFβ1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: hESC-derived endothelial progenotors were cultured under 30ng/ml TGFβ1 with or without 50 mM NAM. The cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

value: hESC-derived endothelial progenitors


title: hESC-derived EPCs, TGF_NAM_2

description: Gene expression after 72 hours in TGFβ1-induced cells with NAM treatment

source_name: hESC-derived differentiated cells, 72hours,30ng/ml TGFβ1，50 mm NAM

value: TGFβ1, NAM


title: hESC-derived EPCs, TGF_NAM_3


title: hESC-derived EPCs, TGF_NAM_1


title: hESC-derived EPCs, TGF_2


title: XP524 24h rep1

city: Chicago

first: Rui

last: Xiong

state: IL

address: 833 S Wood St, room 335

institute: University of Illinois at Chicago

data_processing:
Illumina Casava software used for basecalling.
The RNAseq raw reads were mapped to the human GRCh38 reference genome using Burrows Wheeler Aligner- Maximum Exact Match (BWA MEM) algorithm. The raw count for each gene was quantified using the general purpose read summarization function, featureCounts against ENSEMBL genes.
Differential analysis was performed using edgeR, including a batch effect correction for batch effects.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table raw counts and normalized reads of sequencing reads

source_name: PANC1_XP524 24h

growth_protocol: Human pancreatic cancer cells (Panc1) were cultured in DMEM supplemented with 10% heat-inactivated FBS, penicillin (100U/mL), and streptomycin (100mg/mL).

extract_protocol:
After 24 hours RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) per the manufacturer’s instructions. Quality control, sequencing, and data analysis were performed by Novogene.
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beadsThe mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose.

treatment_protocol: Panc1 cells were treated with either a DMSO vehicle, 1μM of JQ-1, JQ and SGC-CBP30, or XP-524.

value: Pancreatic cancer cells

value: 24 hour treatment


title: XP524 24h rep2


title: JQ1 CBP 24h rep2

source_name: PANC1_JQ1 CBP 24h


title: XP524 24h rep3


title: JQ1 CBP 24h rep3


title: Cerebral cortex, EA, 2


title: Cerebral cortex, control, 4


title: JQ1 CBP 24h rep1


title: JQ1 24h rep1

source_name: PANC1_JQ1 24h


title: JQ1 24h rep2


title: Control 24h rep3

source_name: PANC1_Control 24h


title: JQ1 24h rep3


title: Control 24h rep1


title: Control 24h rep2


title: Peritumor_BC20


title: SW48_YAP1_Dox_Rep1

first: Miju

last: Kim

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
For RNA-sequencing, libraries were sequenced using the Illumina HiSeq 2500.
Sequenced reads were mapped to the reference human genome (hg19) using Tophat 2.0.2 (Trapnell et al., 2010) and genome annotation from the UCSC genome browser (Kent et al., 2002).
Transcripts were assembled and tested for abundance and differential expression using Cufflinks 2.0.2 module (Trapnell et al., 2010) with default setting on GenePattern (Reich et al., 2006)
For ChIP-sequencing, libraries were sequenced using Illumina NextSeq 500.
All samples were processed using the ChiLin pipeline (Qin et al., 2016) for reads mapping and peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: Diff file with differential gene expression profiles
Supplementary_files_format_and_content: Peak BigWig files

growth_protocol: HT29, SKCO1 and SW48 shYAP1 cells expressing either GFP, YAP1 or PRDM14 were maintained in McCoy’s 5A, EMEM, or RPMI 1640 supplemented with 100 units/mL of penicillin, 100 μg/mL of streptomycin and 10% FBS, respectively.

extract_protocol:
For RNA-sequencing, total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen #74134). For ChIP-sequencing, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA-sequencing libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420). ChIP-sequencing libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics #R400427).

treatment_protocol: Cells were treated with water as a control or with 1 mg/ml of doxycycline to suppress YAP1 for 2 days.

value: SW48 colon cancer cells


title: SW48_YAP1_Dox_Rep2


title: SW48_P14_Dox_Rep2


title: SW48_GFP_Dox_Rep1


title: SW48_GFP_Dox_Rep2


title: Scer csRNA-input rep1

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: scer-tsr.txt

data_processing:
For csRNA-seq, sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the appropriate genome using STAR with default parameters[PMID: 23104886]. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded. Transcription Start Regions (TSRs), representing loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findcsRNATSS.pl tool, which uses short input RNA-seq, traditional total RNA-seq, and annotated gene locations to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (Duttke et al. for more details[PMID:31649059]). Replicate experiments were first pooled to form meta-experiments for each condition prior to identifying TSRs. Annotation information, including gene assignments, promoter distal, stable transcript, and bidirectional annotations are provided by findcsRNATSS.pl.
For RNA-seq, reads from accession GSE171286 were downloaded and aligned to the C. immitis genome (ASM14933v2)  using STAR with default parameters. Reference-guided transcranscript assembly was performed using StringTie2 (Kovaka et al. 2019) with the Ensembl gene annotation (GTF file) and additional parameters “-m 100 --rf”. Assembled transcripts were compared to the existing C. immitis annotation using cuffcompare.
Genome_build: C. immitis (ASM14933v2), S. cerevisiae (R64-1-1/sacCer3), S. pombe (ASM294v2), A. bisporus (gca_000300555/Agabi_varbur_1)
Supplementary_files_format_and_content: Tab-delimited Text file describing TSR positions and annotations, GTF formated transcript definition files

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: C. immitis R.S. strain was grown as mycelia or spherules as previously described (Viriyakosol et al. 2013). To grow mycelia, 2×10^6 arthroconidia/ml were incubated in 250 ml flat-bottom Erlenmeyer flasks (Corning) in 50 ml GYE media. Flasks were cultured in a 30°C incubator without shaking for 5 days. To grow spherules, arthroconidia were washed 2 times in modified Converse media (Converse 1956). The spores were inoculated at 4×106 arthroconidia/ml into a 250 ml baffled Erlenmeyer flask containing 50 ml of modified Converse media. Flasks were set up and grown on a shaker at 160 rpm, in 14% CO2 at 42°C. Four flasks were harvested 2 days after inoculation and the remaining four flasks after 8 days. Fresh Converse media was not added.  The spherules did not rupture and release endospores within that time in this culture system. Saccharomyces cerevisiae (strain RYH2863) was grown as described previously (Neal et al. 2018). Schizosaccharomyces pombe (strain TH972) was generously provided by Tony Hunter (SALK Institute for Biological Sciences) and grown in Yeast Extract with Supplements (YES)(Leverson et al. 2002). White and brown ecotypes of Agaricus bisporus, better known as ‘Champignon’ or ‘crimini mushroom’ were kindly provided by Monterey Mushroom farms.

extract_protocol:
Trizol extraction after tissue homogenisation
For RNA-Seq, strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Yeast Ribo-Zero rRNA Removal Kit (Illumina) and then using the TruSeq Stranded total RNA-Seq kit (Illumina) according to manufacturer's instructions. Then 100 bases were sequenced from both ends using a HiSeq 4000 according to the manufacturer's instructions (Illumina).    csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen) and RNAs were 5’dephosporylation by quickCIP (NEB). Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.
csRNA-seq, sRNA-seq, total RNA-seq

treatment_protocol: untreated

tag: tagtreatment

value: untreated

tag: method

value: sRNA-seq (csRNA-seq input)


title: SW48_P14_Dox_Rep1


title: Scer csRNA-seq rep1

description: scer-tsr.txt

value: csRNA-seq


title: SKCO1_YAP1_Dox_Rep1

value: SKCO1 colon cancer cells


title: SKCO1_P14_Dox_Rep2


title: hESC-derived EPCs, TGF_1


title: SKCO1_GFP_Dox_Rep2


title: SKCO1_P14_Dox_Rep1


title: HT29_P14_Dox_Rep2

value: HT29 colon cancer cells


title: HT29_YAP1_Dox_Rep2


title: HT29_GFP_Dox_Rep2


title: HT29_P14_Dox_Rep1


title: SKCO1_GFP_Dox_Rep1


title: HT29_YAP1_Dox_Rep1


title: Spombe RNA-seq rep1

description: spombe-tsr.txt

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

value: strain TH972

value: ribo-0 total RNA-seq


title: HT29_GFP_Dox_Rep1


title: SKCO1_YAP1_Dox_Rep2


title: SAMPLE 398 [Genotype 398]

type: genomic

city: Brandon

first: James

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

hyb_protocol: not provided

scan_protocol: Illuina iScan instrument

data_processing: Illumina Genome Studio software was used for clustering

label: Cy3, Cy5

organism: Hordeum vulgare

source_name: leaf tissue

label_protocol: not provided

growth_protocol: Seeds of barley were surface sterilized with dilute bleach solution (6% per vol) then germinated on cotton balls.

extract_protocol: Qiagen, 96 well DNeasy protocol as per manufacturers instructions

treatment_protocol: leaves were cut and placed in liquid nitorgen then freeze dried.

value: leaf

value: barley genotype 398


title: SAMPLE 400 [Genotype 400]

value: barley genotype 400


title: SAMPLE 399 [Genotype 399]

value: barley genotype 399


title: SAMPLE 397 [Genotype 397]

value: barley genotype 397


title: SAMPLE 385 [Genotype 385]

value: barley genotype 385


title: SAMPLE 391 [Genotype 391]

value: barley genotype 391


title: SAMPLE 392 [Genotype 392]

value: barley genotype 392


title: SAMPLE 387 [Genotype 387]

value: barley genotype 387


title: SAMPLE 389 [Genotype 389]

value: barley genotype 389


title: SAMPLE 396 [Genotype 396]

value: barley genotype 396


title: SAMPLE 394 [Genotype 394]

value: barley genotype 394


title: SAMPLE 374 [Genotype 374]

value: barley genotype 374


title: SAMPLE 382 [Genotype 382]

value: barley genotype 382


title: SAMPLE 380 [Genotype 380]

value: barley genotype 380


title: SAMPLE 383 [Genotype 383]

value: barley genotype 383


title: SAMPLE 395 [Genotype 395]

value: barley genotype 395


title: SAMPLE 386 [Genotype 386]

value: leaf

value: barley genotype 386


title: SAMPLE 393 [Genotype 393]

value: barley genotype 393


title: SAMPLE 388 [Genotype 388]

value: barley genotype 388


title: SAMPLE 373 [Genotype 373]

value: barley genotype 373


title: SAMPLE 378 [Genotype 378]

value: barley genotype 378


title: SAMPLE 379 [Genotype 379]

value: barley genotype 379


title: SAMPLE 384 [Genotype 384]

value: barley genotype 384


title: SAMPLE 375 [Genotype 375]

value: barley genotype 375


title: SAMPLE 381 [Genotype 381]

value: barley genotype 381


title: SAMPLE 372 [Genotype 372]

value: barley genotype 372


title: manR mutant grown on M9+Glc

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using bowtie2 v.2.3.5 with '--very-sensitive' option.
For counting reads which mapped to each CDS, featureCounts in Subread package was used.
Finally, TPM (transcript per million) normalization of retrieved counts and fold change calculation between groups were performed by R.
Genome_build: Vibrio cholerae O1 biovar El Tor str. N16961 (GCA_003063785.1)
Supplementary_files_format_and_content: TPM normalized value and fold change

growth_protocol: V. cholerae WT or mutant cells cultured overnight were diluted 100-fold in 10 mL of fresh LB medium and cultured at 37°C until OD600 reached 0.5.

extract_protocol:
After fixing the cells with the same volume of 100% methanol for 1 h at -20°C, total RNA was isolated using the TaKaRa MiniBEST Universal RNA Extraction Kit (#9767A, Takara Bio) according to the manufacturer’s instructions.
Library was constructed using NEBNext® rRNA Depletion Kit (Bacteria) (#E7850) and NEBNext Ultra II RNA library Prep kit for Illumina (#E7770) following manufacturer's instructions.

treatment_protocol: The cell pellets were rinsed twice with M9 medium lacking a carbon source. Each culture was divided into several aliquots and supplemented with 0.2% indicated sugar. These samples were cultured for 30 min at 37°C.

value: VC1825 gene deletion mutant

tag: culture condition

value: M9 minimal medium + 0.2% glucose


title: SAMPLE 371 [Genotype 371]

value: barley genotype 371


title: SAMPLE 376 [Genotype 376]

value: barley genotype 376


title: manR mutant grown on M9+Fru

organism: Vibrio cholerae O1 biovar El Tor str. N16961

value: M9 minimal medium + 0.2% fructose


title: SAMPLE 390 [Genotype 390]

value: barley genotype 390


title: manR mutant grown on M9

value: M9 minimal medium


title: V. cholerae grown on M9+Man

source_name: Man

value: Wild-type

value: M9 minimal medium + 0.2% mannose


title: SAMPLE 362 [Genotype 362]

value: leaf

value: barley genotype 362


title: SAMPLE 368 [Genotype 368]

value: barley genotype 368


title: SAMPLE 360 [Genotype 360]

value: barley genotype 360


title: Liver_WT_PBS_4

city: Wien

first: Kevin

last: Eislmayr

address: Dr.-Bohr-Gasse 9/4

country: Austria

institute: University of Vienna

description: Multiplexed sample sequenced on 1 lanes -> raw files contain demultiplexed reads

data_processing:
Raw sequencing reads were demultiplexed, and after barcode, adaptor and quality trimming with cutadapt (http://dx.doi.org/10.14806/ej.17.1.200), quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The remaining reads were mapped to the GRCm38/mm10 mouse genome assembly using genomic short-read RNA-Seq aligner STAR version 2.5 {Dobin, 2013}.
Analysis was carried out using HTSeq (Anders, 2015). Differential expression analysis was performed based on read counts using DESeq2 (Love, 2014). DESeq2 (V1.26.0) (Love et al., 2014) with log2-fold-change shrinkage correction in R-project version 3.6.1 with RStudio IDE version 1.0.143 (Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/) (Team, 2017).
Genome_build: GRCm38/mm10 mouse genome assembly

source_name: Murine liver tissue

extract_protocol:
Total RNA was isolated using 1 ml TRIzol reagent (Life Technologies) according to the manufacturer’s protocol. Contaminating DNA was removed by digestion with 20 U recombinant DNase I (Roche).
RNA-Seq library was prepared using Automated library preparation and multiplexing with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: For infection, mice were anesthetized by an intraperitoneal injection (i.p.) of 100 µg/g weight ketamine (Ketamidor, Richter pharma) and 10 µg/g weight xylazine (Sedaxylan, Dechra). The fur of the upper left hind limb from anesthetized animals were shaved and 50 µL (2-3 x 108 CFU) of freshly prepared Streptococcus pyogenes suspension was injected subcutaneously (s.c.) in the region of the vastus lateralis.

value: liver

value: WT knockout

value: PBS


title: Liver_Il1b_PBS_4

value: Il1b knockout


title: SAMPLE 366 [Genotype 366]

value: barley genotype 366


title: SAMPLE 364 [Genotype 364]

value: barley genotype 364


title: Liver_WT_PBS_3


title: SAMPLE 377 [Genotype 377]

value: barley genotype 377


title: V. cholerae grown on M9


title: manR mutant grown on M9+Man

value: VC1825 gene deletion mutant


title: Liver_WT_PBS_2


title: SAMPLE 363 [Genotype 363]

value: barley genotype 363


title: SAMPLE 361 [Genotype 361]

value: barley genotype 361


title: SAMPLE 352 [Genotype 352]

value: barley genotype 352


title: SAMPLE 356 [Genotype 356]

value: barley genotype 356


title: SAMPLE 358 [Genotype 358]

value: barley genotype 358


title: SAMPLE 359 [Genotype 359]

value: leaf

value: barley genotype 359


title: SAMPLE 357 [Genotype 357]

value: barley genotype 357


title: SAMPLE 369 [Genotype 369]

value: barley genotype 369


title: SAMPLE 367 [Genotype 367]

value: barley genotype 367


title: Liver_Il1b_PBS_1

value: liver


title: SAMPLE 365 [Genotype 365]

value: barley genotype 365


title: Liver_Il1a_PBS_2

value: Il1a knockout

value: PBS


title: Liver_Il1b_PBS_3

value: Il1b knockout


title: Liver_Il1b_PBS_2


title: Liver_Il1a_PBS_4


title: SAMPLE 355 [Genotype 355]

value: barley genotype 355


title: SAMPLE 350 [Genotype 350]

value: barley genotype 350


title: Spleen_WT_GAS_2

description: Multiplexed sample sequenced on 2 lanes -> two raw files, one for demultiplexed reads from each lane

source_name: Murine spleen tissue

value: spleen

value: WT knockout

value: GAS


title: Spleen_WT_GAS_3


title: SAMPLE 351 [Genotype 351]

value: barley genotype 351


title: Spleen_WT_GAS_1


title: Liver_WT_PBS_1


title: Spleen_WT_GAS_4


title: SAMPLE 370 [Genotype 370]

value: barley genotype 370


title: SAMPLE 349 [Genotype 349]

value: leaf

value: barley genotype 349


title: V. cholerae grown on M9+Glc

source_name: Glc

value: Wild-type

value: M9 minimal medium + 0.2% glucose


title: Liver_Il1a_PBS_3


title: Spleen_Il1b_GAS_2


title: SAMPLE 343 [Genotype 343]

value: barley genotype 343


title: Spleen_Il1b_GAS_1


title: SAMPLE 354 [Genotype 354]

value: barley genotype 354


title: SAMPLE 339 [Genotype 339]

value: barley genotype 339


title: SAMPLE 348 [Genotype 348]

value: barley genotype 348


title: SAMPLE 345 [Genotype 345]

value: barley genotype 345


title: SAMPLE 344 [Genotype 344]

value: barley genotype 344


title: V. cholerae grown on M9+Fru

source_name: Fru

value: M9 minimal medium + 0.2% fructose


title: Liver_Il1a_PBS_1

value: liver

value: Il1a knockout

value: PBS


title: SAMPLE 347 [Genotype 347]

value: barley genotype 347


title: Spleen_Il1b_GAS_3

value: spleen

value: Il1b knockout

value: GAS


title: Spleen_Il1b_GAS_4


title: Spleen_Il1a_GAS_2


title: SAMPLE 342 [Genotype 342]

value: leaf

value: barley genotype 342


title: Liver_WT_GAS_4

value: WT knockout


title: Spleen_Il1a_GAS_3


title: SAMPLE 341 [Genotype 341]

value: barley genotype 341


title: SAMPLE 334 [Genotype 334]

value: barley genotype 334


title: Spleen_Il1a_GAS_4


title: Liver_WT_GAS_2


title: Liver_WT_GAS_3


title: SAMPLE 336 [Genotype 336]

value: barley genotype 336


title: SAMPLE 338 [Genotype 338]

value: barley genotype 338


title: Liver_WT_GAS_1


title: SAMPLE 340 [Genotype 340]

value: barley genotype 340


title: SAMPLE 335 [Genotype 335]

value: barley genotype 335


title: Liver_Il1b_GAS_2


title: SAMPLE 332 [Genotype 332]

value: barley genotype 332


title: SAMPLE 337 [Genotype 337]

value: barley genotype 337


title: Liver_Il1b_GAS_3

value: liver


title: Liver_Il1b_GAS_4


title: SAMPLE 346 [Genotype 346]

value: barley genotype 346


title: Liver_Il1a_GAS_4

value: Il1a knockout


title: Liver_Il1a_GAS_3


title: Liver_Il1a_GAS_2


title: SAMPLE 330 [Genotype 330]

value: barley genotype 330


title: Liver_Il1a_GAS_1


title: Liver_Il1b_GAS_1

value: Il1b knockout


title: SAMPLE 329 [Genotype 329]

value: barley genotype 329


title: Spleen_Il1a_GAS_1

value: spleen

value: GAS


title: Ubc-Cre_Rai1ACKO_A

city: Guangzhou

first: Jin

last: Xu

state: Guandong

address: No. 135 Xingang Xilu

department: School of Life Sciences

institute: Sun Yat-Sen University

data_processing:
Basecalls performed using  CASAVA v1.8.2
The adaptor sequencing were first scaned and removed for the raw reads by cutadapt (version 1.6 ).
The trimmed sequence were mapped to mouse reference genome (mm9) using Tophat2 with parameters “-I 1000000 --max-coverage-intron 1000000 --max-segment-intron 1000000  --no-coverage-search --b2-very-sensitive   --microexon-search”.
Read pairs, which aligned concordantly to the genome were counted according to the RefGene annotation from UCSC using DEGseq (v0.50.1).
The longest isoform were selected when there are multiple isoforms.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: hypothalamus

growth_protocol: Mouse brains from adult onset Rai1 conditional knockouts were used

extract_protocol:
Hotahalmus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Ubc-CreERT2 and TAM injection was used to delete Rai1 from the hypothalamus.

value: F1 of B6/FVB

value: hypothalamus

value: 30 weeks


title: SAMPLE 328 [Genotype 328]

value: leaf

value: barley genotype 328


title: SAMPLE 331 [Genotype 331]

value: barley genotype 331


title: SAMPLE 333 [Genotype 333]

value: barley genotype 333


title: SAMPLE 324 [Genotype 324]

value: barley genotype 324


title: SAMPLE 322 [Genotype 322]

value: barley genotype 322


title: SAMPLE 325 [Genotype 325]

value: barley genotype 325


title: SAMPLE 326 [Genotype 326]

value: barley genotype 326


title: WT-A

value: wild type


title: SW48_YAP1_Dox_ChIP_Rep1

value: SW48 colon cancer cells


title: SW48_PRDM14_Dox_ChIP_Rep2


title: Ubc-Cre_Rai1ACKO_B


title: SAMPLE 327 [Genotype 327]

value: barley genotype 327


title: SW48_H3K27ac_Dox_ChIP_Rep2


title: SAMPLE 319 [Genotype 319]

value: barley genotype 319


title: SW48_PRDM14_Dox_ChIP_Rep1


title: SW48_YAP1_Dox_ChIP_Rep2


title: SAMPLE 323 [Genotype 323]

value: barley genotype 323


title: WT-B


title: SW48_H3K27ac_Dox_ChIP_Rep1


title: SKCO1_YAP1_Dox_ChIP_Rep2

value: SKCO1 colon cancer cells


title: SKCO1_YAP1_Dox_ChIP_Rep1


title: SKCO1_PRDM14_Dox_ChIP_Rep2


title: SAMPLE 321 [Genotype 321]

value: barley genotype 321


title: SKCO1_H3K27ac_Dox_ChIP_Rep2


title: SKCO1_H3K27ac_Dox_ChIP_Rep1


title: HT29_YAP1_Dox_ChIP_Rep2

value: HT29 colon cancer cells


title: SAMPLE 318 [Genotype 318]

value: barley genotype 318


title: HT29_YAP1_Dox_ChIP_Rep1


title: HT29_PRDM14_Dox_ChIP_Rep2


title: SAMPLE 320 [Genotype 320]

value: leaf

value: barley genotype 320


title: SAMPLE 316 [Genotype 316]

value: barley genotype 316


title: SAMPLE 312 [Genotype 312]

value: barley genotype 312


title: SAMPLE 315 [Genotype 315]

value: barley genotype 315


title: SAMPLE 304 [Genotype 304]

value: barley genotype 304


title: SAMPLE 310 [Genotype 310]

value: barley genotype 310


title: HT29_PRDM14_Dox_ChIP_Rep1


title: SAMPLE 313 [Genotype 313]

value: barley genotype 313


title: SAMPLE 306 [Genotype 306]

value: barley genotype 306


title: SAMPLE 308 [Genotype 308]

value: barley genotype 308


title: SAMPLE 301 [Genotype 301]

value: barley genotype 301


title: SKCO1_PRDM14_Dox_ChIP_Rep1


title: SAMPLE 307 [Genotype 307]

value: barley genotype 307


title: HT29_H3K27ac_Dox_ChIP_Rep2


title: MSG21

city: Bethesda

first: Jacqueline

middle: W.

last: Mays

state: MD

address: 30 Convent Dr, Room 303

institute: NIDCR, NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v3.0.1 using default settings.
Secondary analysis was performed using Seurat v3.4
Genome_build: hg38 (10X Genomics)
Supplementary_files_format_and_content: CellRanger v3.0.1 standard output gene count matrices.

source_name: labial minor salivary gland

extract_protocol:
Labial MSG biopsies were obtained from healthy volunteers . MSG tissue biopsies from four healthy volunteers were mechanically dissociated using the m_lung_01.01 program on the gentleMACS dissociator (Miltenyi Biotec). Tissues were then enzymatically digested with 610 U/mL Collagenase type 2 (Worthington) and 0.04 mg/mL DNase I (Sigma) for 40 minutes at 37oC with agitation. Cells were further dissociated using m_lung_02.01 program on the gentleMACS dissociator. The digested tissue was filtered through a 70 μm cell strainer (Miltenyi Biotec), washed and resuspended in RPMI 1640 (supplemented with 2% FBS, 50U/mL penicillin and 50 μg /mL streptomycin).
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v3 (10X Genomics).  Libraries were then pooled and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

value: labial minor salivary gland

tag: volunteer

value: Healthy Volunteer


title: SAMPLE 305 [Genotype 305]

tag: tissue

value: barley genotype 305


title: MSG18


title: SAMPLE 353 [Genotype 353]

value: barley genotype 353


title: SAMPLE 309 [Genotype 309]

value: barley genotype 309


title: HT29_H3K27ac_Dox_ChIP_Rep1

value: HT29 colon cancer cells


title: SAMPLE 302 [Genotype 302]

value: leaf

value: barley genotype 302


title: SAMPLE 303 [Genotype 303]

value: barley genotype 303


title: MSG15


title: SAMPLE 311 [Genotype 311]

value: barley genotype 311


title: SAMPLE 300 [Genotype 300]

value: barley genotype 300


title: HCC1806_total_tRNA_2

city: New York

first: Maria

last: Passarelli

state: New York

address: Rockefeller University, 1230 York Ave

institute: Rockefeller University

description:
tRNA probe
tRNAprof_mcf_HCC_tot_deseq2_result.txt

data_processing:
Reads were aligned to tRNA space using bowtie2-2.4.1 (charged tRNA profiling) or to mm10 using STAR v2.5.2a (RNA-Seq, Ribo-Seq, polysome profiling, riboTag).
tRNA reads that were aligned to tRNA probes in tRNA space were counted using samtools.
Polysome profiling, RNA-Seq, Ribo-Seq and RiboTag reads that were aligned to coding sequences were counted using featureCounts or htseq-count (Ribo-Seq)
Differentially expressed transcripts were determined using DESeq2 or xtail (Ribo-Seq)
Genome_build: mm10
Supplementary_files_format_and_content: differential gene expression by deseq2 or xtail, .csv or .txt

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS.HCC1806 cells were maintained in RPMI supplemented with 10% FBS, sodium pyruvate, and HEPES.

extract_protocol:
RNA was extracted using 0.3M NaOAc lysis buffer and phenol chloroform extraction (charged tRNA profiling), or as previously described (polysome profiling - Gandin et al 2014, ribosome profiling: McGlincy & Ingolia 2017, RiboTag: Sanz et al 2009)
charged tRNA profiling libraries were conducted as previously described (Goodarzi et al, 2016). RNA-Seq, polysome profiling and RiboTag libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina). Ribo-Seq libraries were constructed as described previously (McGlincy and Ingolia, 2017).

value: breast cancer cell line

tag: fraction

value: total tRNA


title: HCC1806_total_tRNA_1


title: HCC1806_total_tRNA_3


title: MSG11


title: SAMPLE 298 [Genotype 298]

value: barley genotype 298


title: lc120T_3

city: Harbin city

first: mengdi

last: li

state: Heilongjiang Province, China

address: Heilongjiang University, Nangang District, Harbin city, Heilongjiang Province

institute: Heilongjiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Phaseolus vulgaris

source_name: blade

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: variety

value: true leaves of the plants

value: treated with coldstress for 3 days


title: SAMPLE 297 [Genotype 297]

value: barley genotype 297


title: SAMPLE 317 [Genotype 317]

value: barley genotype 317


title: HCC1806_charged_tRNA_3

description:
tRNA probe
tRNAprof_mcf_HCC_chg_deseq2_result.txt

value: charged tRNA


title: lc120T_2


title: HCC1806_charged_tRNA_2


title: lc120T_1


title: mcf10a_total_tRNA_3


title: lc120CK_2

value: untreated


title: lc120CK_3


title: lc120CK_1


title: HCC1806_charged_tRNA_1


title: SAMPLE 295 [Genotype 295]

value: barley genotype 295


title: SAMPLE 296 [Genotype 296]

value: barley genotype 296


title: mcf10a_total_tRNA_2


title: SAMPLE 294 [Genotype 294]

value: barley genotype 294


title: SAMPLE 293 [Genotype 293]

value: leaf

value: barley genotype 293


title: lc093T_2


title: lc093T_1


title: lc093T_3


title: mcf10a_total_tRNA_1


title: lc093CK_3


title: SAMPLE 292 [Genotype 292]

value: barley genotype 292


title: SAMPLE 291 [Genotype 291]

value: barley genotype 291


title: SAMPLE 289 [Genotype 289]

value: barley genotype 289


title: mcf10a_charged_tRNA_3

value: breast cancer cell line


title: mcf10a_charged_tRNA_2


title: SAMPLE 288 [Genotype 288]

value: barley genotype 288


title: SAMPLE 314 [Genotype 314]

value: barley genotype 314


title: mcf10a_charged_tRNA_1


title: SAMPLE 290 [Genotype 290]

value: barley genotype 290


title: control_serum2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: whole serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

tag: disease state

value: healthy control

value: whole serum

tag: description

value: age- and sex-matched controls


title: control_serum1


title: colorectal_serum7

value: colorectal cancer

value: Rectal cancer


title: SAMPLE 299 [Genotype 299]

tag: genotype

value: barley genotype 299


title: control_serum4


title: control_serum6


title: control_serum5


title: control_serum7


title: lc093CK_1

value: true leaves of the plants

tag: treatment

value: untreated


title: control_serum3


title: colorectal_serum6

value: Sigmoid colon cancer


title: colorectal_serum4


title: SAMPLE 286 [Genotype 286]

value: leaf

value: barley genotype 286


title: SAMPLE 281 [Genotype 281]

value: barley genotype 281


title: SAMPLE 282 [Genotype 282]

value: barley genotype 282


title: colorectal_serum5


title: SAMPLE 284 [Genotype 284]

value: barley genotype 284


title: KO-SUL E18.5 placenta Replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Comparisons: Genotype effect,  Prenatal treatment effect on postnatal gene expression

hyb_protocol: The biotinylated RNA was fragmented and hybridized to the Affymetrix array for 16 hr at 45 degree C in a hybridization oven rotating at 60 rpm. The array was washed and stained with streptavidin–phycoerythrin using an Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2) using the MAS5 algorithm to generate .CHP files.

label: biotin

source_name: Homogenized placenta tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from placenta homogenates of each mouse (n= 3 per group) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) and then evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol:
Time-pregnant Nrf2+/+ and Nrf2-/- mice and time-pregnant foster dams were received  9 umol (1.67 mg) of pure SFN or vehicle (PBS) by oral gavage (100 ul) on embryonic days 11.5, 13.5, 15.5, and 17.5. At E18.5, dams were euthanatized by carbon dioxide, the abdominal cavity is opened, and the uterus and ovaries are removed intact. The uterus is spread out, extraembryonic membranes (amnion, yolk sac, chorion, allantois) from each embryo are removed and placenta was separated from embryo. The placenta was snap frozen in liquid nitrogen.
Neonatal mice and their foster dams were exposed to room-air exposure. Food and water were provided ad libitum. In 24 hr after birth (P1, saccular stage of lung maturation), neonatal mice were placed in cages in a hyperoxia chamber, and were exposed to 100 percent (≥95 percent) O2 (UHP grade, Min. purity 99.994 percent O2 tanks, National Welders, Durham, NC) 23 hr/day continuously for 1, 2, or 3 d with their foster dams. Water and feed were provided ad libitum during the exposure. Neonatal mice and their foster dams assigned to room-air exposure were placed in cages placed on counter top with food and water provided ad libitum for the same exposure duration. The temperature (72±3 degree F) and humidity (50±15 percent) of the chamber were monitored, and mice were exposed to a 12-hr light-dark cycle. The hyperoxia chamber was opened once each morning for 1 hr to replace foster dams and to check animal health (morbidity and mortality) and water and feed.

tag: prenatal treatment

value: SUL

value: placenta


title: KO-SUL E18.5 placenta Replicate 3


title: SAMPLE 287 [Genotype 287]

value: barley genotype 287


title: colorectal_serum3


title: MT4_HIV-1_rep1

city: Wuhan

first: Jialu

last: Qiao

state: Hubei

address: Sanjiaohu Road No.8

institute: Jianghan University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16 – 20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: miRNA expression in MT4 cells inoculated with pseudotyped HIV-1-GFP for 48h

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Human T cells MT4 were grown in RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum at 37°C in 5% CO2. MT4 cells inoculated with or without HIV-1-GFP  for 48h and the infectivity was over 90% by analyzing with flow cytometer.

tag: cell line

tag: cell type

value: Human T cells

value: pseudotyped HIV-1-GFP for 48h


title: SAMPLE 279 [Genotype 279]

value: barley genotype 279


title: SAMPLE 283 [Genotype 283]

value: barley genotype 283


title: MT4_HIV-1_rep3


title: SAMPLE 285 [Genotype 285]

value: barley genotype 285


title: SAMPLE 280 [Genotype 280]

value: barley genotype 280


title: colorectal_serum2

value: colorectal cancer

value: whole serum

value: Rectal cancer


title: KO-SUL E18.5 placenta Replicate 1


title: MT4_HIV-1_rep2


title: colorectal_serum1


title: MT4_mock_rep1

source_name: miRNA expression in MT4 cells inoculated without pseudotyped HIV-1-GFP for 48h

value: mock


title: KO-PBS E18.5 placenta Replicate 3

value: PBS


title: KO-PBS E18.5 placenta Replicate 2


title: MT4_mock_rep3


title: MT4_mock_rep2


title: SAMPLE 277 [Genotype 277]

value: leaf

value: barley genotype 277


title: SAMPLE 278 [Genotype 278]

value: barley genotype 278


title: SAMPLE 275 [Genotype 275]

value: barley genotype 275


title: WT-SUL E18.5 placenta Replicate 3

value: SUL

value: placenta


title: macrophages_M2differentiation_Hyperglycemia_6day_donor10

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: human buffy coat, M2 differentiated macrophages, hyperglycemia, 6 days

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

growth_protocol: Monocytes were isolated from Buffy coats obtained from healthy blood donors. The isolation was carried out using CD14 positive selection (Miltenyi Biotec), resulting in 90–98% monocyte purity, controlled by flow cytometry. The cells were seeded into cell culture dishes in customized serum free medium (SFM from Gibco) supplemented with 5 mM glucose for normoglycemic conditions or 25 mM for hyperglycemic conditions at a concentration of 1x106 cells/mL. Macrophage were differentiated in the presence of M-CSF at 5 ng/mL (Peprotech; #A300-25B) and Dexamethasone 10-8 M (Sigma, #D2915). For M1 polarization IFN-gamma was used at the concentration of 100 ng/mL (Peprotech; # 300-02), for M2 polarization, IL-4 was used at the concentration of 10 ng/mL (Peprotech; #200-04). The conditions were maintained for 6 days with 7.5% CO2 at 37°C.

extract_protocol: After incubation with 0,0100% (100ppm) TiNPs for 6 days, cells were lysed in TRK lysis buffer and RNA was isolated using E.Z.N.A. Total RNA kit I (Omega Bio-tek, USA) according to the manufacturer's instructions. The concentration of isolated RNA was determined with a Tecan Infinite® 200.

treatment_protocol: Titanium nanoparticles  were added for a final concentration of 0,0100% (100ppm).

tag: blood cells

value: macrophages

value: grown 6 days in hyperglycemia conditions


title: KO-PBS E18.5 placenta Replicate 1


title: SAMPLE 276 [Genotype 276]

value: barley genotype 276


title: macrophages_M2differentiation_Hyperglycemia_6day_donor11


title: macrophages_M2differentiation_Hyperglycemia_6day_donor8


title: WT-SUL E18.5 placenta Replicate 1


title: macrophages_M2differentiation_Hyperglycemia_6day_donor7


title: macrophages_M2differentiation_Hyperglycemia_6day_donor9


title: SAMPLE 274 [Genotype 274]

value: barley genotype 274


title: SAMPLE 273 [Genotype 273]

value: barley genotype 273


title: SAMPLE 272 [Genotype 272]

value: barley genotype 272


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor7

source_name: human buffy coat, M2 differentiated macrophages, hyperglycemia, titanium nanoparticles, 6 days

value: grown 6 days in hyperglycemia conditions with titanium nanoparticles


title: WT-SUL E18.5 placenta Replicate 2


title: WT-PBS E18.5 placenta Replicate 3


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor5


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor3


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor6


title: KO-SUL/O2 3d neonate lung Replicate 3

description: Comparisons: Genotype effect,  Prenatal treatment effect, Postnatal exposure effect on postnatal gene expression

source_name: Homogenized lung tissue

extract_protocol: Total RNA was extracted from lung homogenates of each mouse (n=2 or 3 per group) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) and then evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol:
Time-pregnant Nrf2+/+ and Nrf2-/- mice and time-pregnant foster dams were received  9 umol (1.67 mg) of pure SFN or vehicle (PBS) by oral gavage (100 ul) on embryonic days 11.5, 13.5, 15.5, and 17.5. Two days before the scheduled delivery, time-pregnant Nrf2+/+ and Nrf2-/- mice were cohabitated with time-pregnant foster dams. On the birth (PND0), neonatal mice from multiple litters of the same prenatal treatment or same genotype were pooled  and reassigned to exposure groups with a foster dam per group. Neonatal mice and their foster dams were were placed in cages in a hyperoxia chamber and exposed to ≥95% O2 (hyperoxia) exposure from PND1 to PND4 for 3 days continuously. Food and water were provided ad libitum during the exposure.  Noenates with foster dams assigned to room air exposure were placed on counter top with food and water provided ad libitum for the same exposure duration. The temperature (72±3 degree F) and humidity (50±15 percent) of the chamber were monitored, and mice were exposed to a 12-hr light-dark cycle. The hyperoxia chamber was opened once each morning for approximately 1 hr to replace foster dams and to check animal health (morbidity and mortality) and water and feed.
Neonatal mice and their foster dams were exposed to room-air exposure. Food and water were provided ad libitum. In 24 hr after birth (P1, saccular stage of lung maturation), neonatal mice were placed in cages in a hyperoxia chamber, and were exposed to 100 percent (≥95 percent) O2 (UHP grade, Min. purity 99.994 percent O2 tanks, National Welders, Durham, NC) 23 hr/day continuously for 1, 2, or 3 d with their foster dams. Water and feed were provided ad libitum during the exposure. Neonatal mice and their foster dams assigned to room-air exposure were placed in cages placed on counter top with food and water provided ad libitum for the same exposure duration. The temperature (72±3 degree F) and humidity (50±15 percent) of the chamber were monitored, and mice were exposed to a 12-hr light-dark cycle. The hyperoxia chamber was opened once each morning for 1 hr to replace foster dams and to check animal health (morbidity and mortality) and water and feed.

tag: postnatal exposure

value: hyperoxia (O2)

value: lung


title: WT-PBS E18.5 placenta Replicate 1


title: SAMPLE 271 [Genotype 271]

value: barley genotype 271


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor8


title: SAMPLE 269 [Genotype 269]

value: barley genotype 269


title: lc093CK_2

value: true leaves of the plants

value: untreated


title: macrophages_M1differentiation_Hyperglycemia_6day_donor7

source_name: human buffy coat, M1 differentiated macrophages, hyperglycemia, 6 days


title: macrophages_M1differentiation_Hyperglycemia_6day_donor9


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor2


title: SAMPLE 268 [Genotype 268]

source_name: leaf tissue

value: leaf

value: barley genotype 268


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor1


title: KO-SUL/O2 3d neonate lung Replicate 2

value: SUL


title: macrophages_M1differentiation_Hyperglycemia_6day_donor6


title: KO-PBS/O2 3d neonate lung Replicate 3

value: PBS


title: macrophages_M1differentiation_Hyperglycemia_6day_donor4

value: macrophages


title: macrophages_M1differentiation_Hyperglycemia_6day_donor5

value: grown 6 days in hyperglycemia conditions


title: macrophages_M1differentiation_Hyperglycemia_6day_donor3


title: KO-SUL/O2 3d neonate lung Replicate 1


title: macrophages_M1differentiation_Hyperglycemia_6day_donor8


title: SAMPLE 267 [Genotype 267]

value: barley genotype 267


title: SAMPLE 265 [Genotype 265]

value: barley genotype 265


title: SAMPLE 266 [Genotype 266]

value: barley genotype 266


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor9

source_name: human buffy coat, M1 differentiated macrophages, hyperglycemia, titanium nanoparticles, 6 days


title: KO-PBS/O2 3d neonate lung Replicate 1


title: macrophages_M1differentiation_Hyperglycemia_6day_donor2


title: KO-SUL/Air 3d neonate lung Replicate 3

value: air


title: KO-PBS/O2 3d neonate lung Replicate 2


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor8

value: grown 6 days in hyperglycemia conditions with titanium nanoparticles


title: SAMPLE 263 [Genotype 263]

value: barley genotype 263


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor7


title: SAMPLE 264 [Genotype 264]

value: barley genotype 264


title: KO-SUL/Air 3d neonate lung Replicate 2

value: lung


title: WT-PBS E18.5 placenta Replicate 2

value: placenta


title: macrophages_M1differentiation_Hyperglycemia_6day_donor1


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor4


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor2


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor3


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor6


title: KO-SUL/Air 3d neonate lung Replicate 1


title: macrophages_M2differentiation_Normoglycemia_6day_donor4

source_name: human buffy coat, M2 differentiated macrophages, normoglycemia, 6 days

value: grown 6 days in normoglycemia conditions


title: KO-PBS/Air 3d neonate lung Replicate 2


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor1


title: macrophages_M2differentiation_Normoglycemia_6day_donor5


title: SAMPLE 261 [Genotype 261]

value: barley genotype 261


title: macrophages_M1differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor5


title: macrophages_M2differentiation_Normoglycemia_6day_donor2


title: SAMPLE 262 [Genotype 262]

value: leaf

value: barley genotype 262


title: SAMPLE 260 [Genotype 260]

value: barley genotype 260


title: macrophages_M2differentiation_Normoglycemia_6day_donor3


title: macrophages_M2differentiation_Normoglycemia_6day_donor1


title: KO-PBS/Air 3d neonate lung Replicate 3

value: PBS


title: SAMPLE 258 [Genotype 258]

value: barley genotype 258


title: KO-PBS/Air 3d neonate lung Replicate 1


title: macrophages_M2differentiation_Hyperglycemia_Titaniumnanoparticles_6day_donor4

value: macrophages


title: WT-SUL/O2 3d neonate lung Replicate 3

value: SUL

value: hyperoxia (O2)


title: SAMPLE 257 [Genotype 257]

value: barley genotype 257


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor8

source_name: human buffy coat, M2 differentiated macrophages, normoglycemia, titanium nanoparticles, 6 days

value: grown 6 days in normoglycemia conditions with titanium nanoparticles


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor5


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor6


title: WT-SUL/O2 3d neonate lung Replicate 2


title: SAMPLE 256 [Genotype 256]

value: barley genotype 256


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor4


title: SAMPLE 270 [Genotype 270]

value: barley genotype 270


title: WT-PBS/O2 3d neonate lung Replicate 2


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor7


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor2


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor1


title: WT-SUL/Air 3d neonate lung Replicate 1

value: air


title: macrophages_M1differentiation_Normoglycemia_6day_donor9

source_name: human buffy coat, M1 differentiated macrophages, normoglycemia, 6 days


title: macrophages_M1differentiation_Normoglycemia_6day_donor8


title: WT-PBS/O2 3d neonate lung Replicate 3

value: lung


title: SAMPLE 259 [Genotype 259]

value: barley genotype 259


title: SAMPLE 252 [Genotype 252]

value: barley genotype 252


title: macrophages_M1differentiation_Normoglycemia_6day_donor6

value: grown 6 days in normoglycemia conditions


title: macrophages_M1differentiation_Normoglycemia_6day_donor7


title: macrophages_M2differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor3


title: WT-SUL/Air 3d neonate lung Replicate 3


title: macrophages_M1differentiation_Normoglycemia_6day_donor5


title: SAMPLE 254 [Genotype 254]

value: leaf

value: barley genotype 254


title: SAMPLE 255 [Genotype 255]

value: barley genotype 255


title: WT-PBS/Air 3d neonate lung Replicate 2

value: PBS


title: SAMPLE 253 [Genotype 253]

value: barley genotype 253


title: B10507-T1c

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

description:
Bisulfite-treated DNA
CpG_quantification.txt

data_processing:
Read pairs were merged with PEAR. Assembled reads were mapped to the reference fasta file using Bismark with the --non_directional flag. Methylation status per CpG per read was extracted using bismark_methylation_extractor, and then summarized to a total count, methylated count, and % methylation per CpG for all reads in the sample.
Genome_build: Custom amplicon reference is a combination of HBV genomic sequence derived from subtype ayw (ACCESSION No: V01460 J02203) (sequence "virus_ref" in amplicon_reference.fa) and promoter sequences for 3 genes from mm10 (sequences "IGFBP1", "APOB", and "CYP2E1")
Supplementary_files_format_and_content: CpG Tab-delimited text (contains total read counts, methylated read counts, and % methylation for each CpG in each sample)
Supplementary_files_format_and_content: FASTA (reference genomic sequences for HBV and mouse sequences)

source_name: Liver

growth_protocol: 12-15 month old mice

extract_protocol:
Protein-free mouse genomic DNA was isolated from liver tissue as described (McFadden, V.C., Shalaby, R.E., Iram, S., Oropeza, C.E., Landolfi, J.A., Lyubimov, A.V., Maienschein-Cline, M., Green, S.J., Kaestner, K.H., and McLachlan, A. (2017). PLOS Pathogens 13, e1006239).
Genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning™ Kit (D5030; Zymo Research, Inc., Irvine, CA, USA). The CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite- treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps as described previously (McFadden et al. 2017).  Twelve HBV primer pairs targeting 94 of the 99 CpG sites were used.   The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACAATACCTAAACCTTTACCC-3’ (oligo CS1FP1; HBV nucleotide coordinates 1131-1150) and 5’-TACGGTAGCAGAGACTTGGTCTGTTTTAGTTAGTGGGGGT-3’ (oligo CS2RP1; HBV coordinates 1214-1197), (ii) 5’-ACACTGACGACATGGTTCTACACAAACTTTCACTTTCTC-3’ (oligo CS1FP1a; HBV coordinates 1086-1102) and 5’-TACGGTAGCAGAGACTTGGTCTGTTGATGGTTTATGATTAA (oligo CS2RP1a; HBV coordinates 1233-1215), (iii) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’-TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (iv) 5’-ACACTGACGACATGGTTCTACATTAAACTCTCAACAATATCA-3’ (oligo CS1FP3; HBV nucleotide coordinates 1668-1687) and 5’-TACGGTAGCAGAGACTTGGTCTAAGTTATTTAAGGTATAGTTTG-3’ (oligoCS2RP3; HBV nucleotide coordinates 1896-1875), (v) 5’-ACACTGACGACATGGTTCTACAGTGGTTTTGGGGTATGG-3’ (oligo CS1FP4; HBV nucleotide coordinates 1890-1906) and 5’-TACGGTAGCAGAGACTTGGTCTCAAATTAACACCCACCC-3’ (oligo CS2RP4; HBV nucleotide coordinates 2130-2114), (vi) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’ (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), (vii) 5’- ACACTGACGACATGGTTCTACAGATTGTAATTGATTATGTTTG -3’ (oligo CS1FP6; HBV nucleotide coordinates 2625-2645) and 5’- TACGGTAGCAGAGACTTGGTCTCCATACTATAAATCTTATTCCC-3’ (oligo CS2RP6; HBV nucleotide coordinates 2832-2853), (viii) 5’-ACACTGACGACATGGTTCTACAGGGAATAAGATTTATAGTATGG (oligo CS1FP7; HBV  nucleotide coordinates 2832-2853) and 5’-TACGGTAGCAGAGACTTGGTCTTAAACCTAAAAACTCCACC-3’ (oligo CS2RP7; HBV nucleotide coordinates 3061-3043, (ix) 5’-ACACTGACGACATGGTTCTACAAATCAAAAAAACAACCTACC-3’ (oligo CS1FP8; HBV  nucleotide coordinates 3115-3134) and 5’-TACGGTAGCAGAGACTTGGTCTGTGAGTGATTGGAGGT-3’ (oligo CS2RP8; HBV  nucleotide coordinates 340-325), (x) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV  nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712), (xi) 5’-ACACTGACGACATGGTTCTACAGGATGATGTGGTATTGG-3’ (oligo CS1FP10; HBV nucleotide coordinates 743-759) and 5’-TACGGTAGCAGAGACTTGGTCTCAAAACCCAAAAAACCCAC-3’ (oligo CS2RP10; HBV nucleotide coordinates 1020-1002), and (xii) 5’-  ACACTGACGACATGGTTCTACATTGATGTTTTTGTATGTA-3’ (oligo CS1FP11;  HBV nucleotide coordinates 1053-1070) and 5’-TACGGTAGCAGAGACTTGGTCTATAACCAAACCCCAACC-3’ (oligo CS2RP11; HBV nucleotide coordinates 1222-1206).  These primers contained linker sequences (underlined) at the 5’ ends of the oligonucleotides, termed common sequences (CS1 and CS2). These PCR reactions were performed using ZymoTaq PreMix according to the manufacturer’s instructions (Zymo Research).  PCR amplification involved 10 minutes denaturation at 95°C, followed by 40 cycles of 95°C for 30 s, 50°C for 40 s (ramp rate 95-50 was set to 0.3C/s), 72°C for 60 s.  Finally, a 7 minute incubation at 72°C was performed.  The HBV amplicons were subsequently subjected to a second stage PCR reaction (MyTaq HS Mix, 2X, Bioline USA Inc., Taunton, MA, USA), used to incorporate unique barcodes and sequencing adapters. The PCR primers used were 5’-  AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA-3’ (oligo PE1CS1) and 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNTACGGTAGCAGAGACTTGGTCT-3’ (oligo PE2BCCS2).  The 10-base sample-specific barcodes are indicated with bold Ns and represent barcode sequences from a set of 384 unique primer pairs (Fluidigm Access Array Barcode Library for Illumina Sequencers).  PCR amplification involved 5 minutes denaturation at 95°C, followed by 8 cycles of 95°C for 30 s, 60°C for 30 s, 72°C for 30 s.  Finally, a 7 minute incubation at 72°C was performed.  The resulting final PCR products (libraries) contain Illumina sequencing adapters and a sample-specific barcode. Pooled libraries were sequenced using an Illumina MiSeq instrument and data were analyzed using the Casava1.8 pipeline. Sequencing was performed using MiSeq V3 chemistry, with paired-end 2x300 base reads, employing Access Array custom sequencing primers.

value: HBV(+/-)Pten(fl/fl)Cre(+/-)

value: HCC

value: liver


title: macrophages_M1differentiation_Normoglycemia_6day_donor2

value: macrophages


title: macrophages_M1differentiation_Normoglycemia_6day_donor3


title: macrophages_M1differentiation_Normoglycemia_6day_donor4


title: SAMPLE 250 [Genotype 250]

value: barley genotype 250


title: B10507-NT3

value: Pten-null non-tumor liver


title: macrophages_M1differentiation_Normoglycemia_6day_donor1


title: WT-PBS/Air 3d neonate lung Replicate 1


title: WT-PBS/Air 3d neonate lung Replicate 3


title: B10490-NT3


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor9

source_name: human buffy coat, M1 differentiated macrophages, normoglycemia, titanium nanoparticles, 6 days

value: grown 6 days in normoglycemia conditions with titanium nanoparticles


title: SAMPLE 249 [Genotype 249]

value: barley genotype 249


title: B10490-T1c


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor7


title: B10485-T2c


title: R-6-5-2

city: Ithaca

first: Joel

middle: D

last: Baines

state: NY

address: 235 Hungerfordhill Rd

institute: Cornell University

description:
repair-infected HeP2 cells at 6 hpi with 5 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

data_processing:
Library strategy: PRO-seq
Adapter trimming and processing using Cut Adapt
Raw genome algnments usign BWA
Conversion of BAM files to strand specific BigWigs using kentsource
https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Genome_build: hg38 human genome build, Dm3 Drosophila genome build, HSV-1 (F) strain in-house genome build
Supplementary_files_format_and_content: read count data in BigWig files

organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1

source_name: HeP-2 cells, S2 Cells, HSV-16

growth_protocol: Hep-2 cells were grown and maintained with DMEM 10% fetal bovine serum and the Drosophila S2 cells were grown in Schneider's medium supplemented with 10% NBS

extract_protocol:
Nuclei were extracted as previoulsy described (Birkenheuer and Baines 2020, Journal of Virology).  Global run-on reactions were performed as described by Lopes et al 2017, GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. Methods Mol Biol 1543:45-55, and were allowed to proceed for 5 or 30 mins of run-on.  Reactions were stopped by the addition of Trizol.
Libraries were constructed similar to the construction of PRO-seq libraries with adapter ligations for the 3' end being performed first and cap removal and 5' phosphate repair and 5' adapter ligation being performed after the 3' end of the RNA was ligated to the sequencing adapter.  However, instead of using magnetic beads for this process, anti Br-dUTP conjugated agarose beads were used for this process with the blocking, washing, and elution conditions described by (Lopes et al, 2017, GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. Methods Mol Biol 1543:45-55.).
Libraries were created using Illumina Index primers for sequencing on the NextSeq550 75 base pair single end sequencing.

treatment_protocol: Hep-2 cells were infected with the mutant viruses at a MOI of 5 and allowed to progress to 3 or 6 hours post infection.

tag: cell line (human)

value: HeP-2 cells

tag: cell line (drosophila)

value: S2 cells

tag: cell type (human)

value: lung epithelial carcinoma cells

tag: viral infection

value: infected with HSV-1 US1/US1.5 deletion virus with repaired US1/US1.5 gene

tag: infection timepoint

value: 6 hours post infection

tag: run-on time

value: 5 min of run on with Br-UTP


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor8


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor5


title: R-6-5-1

description:
repair-infected HeP2 cells at 6 hpi with 5 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-15


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor2


title: SAMPLE 248 [Genotype 248]

tag: tissue

value: leaf

value: barley genotype 248


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor3


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor6


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor1


title: B10485-NT3


title: B10431-T3


title: SAMPLE 245 [Genotype 245]

value: barley genotype 245


title: B10431-NT2

value: HBV(+/-)Pten(fl/fl)Cre(+/-)


title: SAMPLE 246 [Genotype 246]

value: barley genotype 246


title: SAMPLE 244 [Genotype 244]

value: barley genotype 244


title: R-6-30-1

description:
repair-infected HeP2 cells at 6 hpi with 30 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-13

value: 30 min of run on with Br-UTP


title: R-3-5-2

description:
repair-infected HeP2 cells at 3 hpi with 5 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-12

value: 3 hours post infection


title: R-3-5-1

description:
repair-infected HeP2 cells at 3 hpi with 5 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-11


title: macrophages_M1differentiation_Normoglycemia_Titaniumnanoparticles_6day_donor4

value: macrophages


title: R-6-30-2

description:
repair-infected HeP2 cells at 6 hpi with 30 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-14


title: d22-6-5-2

description:
d22-infected HeP2 cells at 6 hpi with 5 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-8

value: infected with HSV-1 bearing full US1/US1.5 gene deletion


title: R-3-30-1

description:
repair-infected HeP2 cells at 3 hpi with 30 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-9


title: B10423-NT3

value: Pten-null non-tumor liver

value: liver


title: R-3-30-2

description:
repair-infected HeP2 cells at 3 hpi with 30 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-10

value: HeP-2 cells

value: S2 cells


title: d22-6-5-1

description:
d22-infected HeP2 cells at 6 hpi with 5 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-7

value: lung epithelial carcinoma cells


title: SAMPLE 247 [Genotype 247]

source_name: leaf tissue

value: barley genotype 247


title: SAMPLE 242 [Genotype 242]

value: barley genotype 242


title: SAMPLE 251 [Genotype 251]

value: leaf

value: barley genotype 251


title: B10406-NT3


title: d22-6-30-1

description:
d22-infected HeP2 cells at 6 hpi with 30 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-5

value: 6 hours post infection


title: d22-3-5-2

description:
d22-infected HeP2 cells at 3 hpi with 5 min of run on rep 2
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-4

value: 5 min of run on with Br-UTP


title: d22-3-5-1

description:
d22-infected HeP2 cells at 3 hpi with 5 min of run on rep 1
labeled RNA was extracted and prepared for sequencing with sequential, specific 3' and 5' RNA adapters.  Libraries were reverse transcribed and sequenced with Illumina Next Seq550 75bp single end sequencing, the spiked in drosophila s2 cells were used for normalization after BigWig creation

source_name: HeP-2 cells, S2 Cells, HSV-3