title: PS19-fE4_Syn1-Cre287

city: San Francisco

first: Ayushi

last: Agrawal

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description: 10x Genomics single nucleus RNA sequencing

data_processing:
Demultiplexed fastq files were aligned to a custom reference genome built from mm10 2020-A that includes introns, using the Cellranger v6.1.1 counts function with default parameters, as described in the Cellranger documentation. UMI counts were also determined using the Cellranger counts function.
Assembly: The Homo sapiens microtubule associated protein tau (MAPT) (NCBI Reference Sequence: NM_001123066.4) and the Homo sapiens APOE are genes of interest for this study. Custom mouse reference genome was made using these genes of interest , the reference mouse genome sequence (GRCm38) from Ensembl (release 98) and the mouse gene annotation file from GENCODE (release M23), similar to those used in 10x Genomics Cell Ranger mouse reference package mm10 2020-A.
Supplementary files format and content: feature-barcode matrix in the Hierarchical Data Format (HDF5 or H5) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

molecule: nuclear RNA

source_name: hippocampus

growth_protocol: Human LoxP-floxed APOE knock-in (fE) mice with conditional deletion of the human APOE gene were generated as previously described. Briefly, homozygous fE3 and fE4 mice were crossbred with Synapsin 1-Cre transgenic mice [B6.Cg-Tg(Syn1-Cre)671Jxm/J] (The Jackson Laboratory #003966). The fE/Cre mice were crossbred with Tau-P301S (PS19) transgenic mice [B6;C3-Tg(Prnp-MAPT*P301S)PS19Vle/J] (The Jackson Laboratory #008169) that express human P301S 1N4R Tau driven by the PrP promoter to generate PS19-fE4 and PS19-fE3 mice with no Cre or Syn1-Cre. Littermates that were negative for Syn1-Cre were used as PS19-fE controls. For generation of the PS19-fE/Syn1-Cre line, only female Syn1-Cre mice were used for breeding purposes because germline recombination has been reported to occur in the progeny of male Syn1-Cre mice. All mice were on a pure C57BL/6 genetic background and were housed in a pathogen-free barrier facility on a 12 h light cycle at 19-23ºC and 30-70% humidity. Animals were identified by ear punch under brief isoflurane anesthesia and genotyped by polymerase chain reaction (PCR) of a tail clipping. All animals otherwise received no procedures except those reported in this study. For all studies, both male and female mice were used. All animal experiments were conducted in accordance with the guidelines and regulation of the National Institutes of Health, the University of California, and the Gladstone Institutes under the protocol AN176773.

extract_protocol:
The mouse hippocampus was dissected on ice and placed into a pre-chilled 2 mL Dounce with 1 mL of cold 1X Homogenization Buffer (1X HB) (250 mM Sucrose, 25 mM KCL, 5 mM MgCl2, 20 mM Tricine-KOH pH7.8, 1 mM DTT, 0.5 mM Sermidine, 0.15 mM Sermine, 0.3% NP40, 0.2 units/µL RNase inhibitor, ~0.07 tablets/sample Protease inhibitor). Dounce with “A” loose pestle (~10 strokes) and then with “B” tight pestle (~15 strokes). The homogenate was filtered using a 70 µM Flowmi strainer (Eppendorf) and transferred to a pre-chilled 2 mL LoBind tube (Fischer Scientific). Nuclei were pelleted by spinning for 5 min at 4°C at 350 RCF. The supernatant was removed and the nuclei were resuspended in 400 µL 1X HB. Next, 400 µL of 50% Iodixanol solution was added to the nuclei and then slowly layered with 600 µL of 30% Iodixanol solution under the 25% mixture, then layered with 600 µL of 40% Iodixanol solution under the 30% mixture. The nuclei were then spun for 20 min at 4°C at 3,000g in a pre-chilled swinging bucket centrifuge. 200 µL of the nuclei band at the 30%-40% interface was collected and transferred to a fresh tube. Then, 800 µL of 2.5% BSA in PBS plus 0.2 units/µL of RNase inhibitor was added to the nuclei and then were spun for 10 min at 500 RCF at 4C. The nuclei were resuspended with 2% BSA in PBS plus 0.2 units/µL RNase inhibitor to reach ~500 nuclei/µL. The nuclei were then filtered with a 40 µM Flowmi stainer. The nuclei were counted and then ~13,000 nuclei per sample were loaded onto 10x Genomics Next GEM chip G. The snRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.
The snRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.
10X Single-nucleus RNAseq

value: hippocampus


title: PS19-fE4_Syn1-Cre305

status: Public on Jan 06 2023

type: SRA

country: USA

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue

tag: genotype


title: exp7_miRNA

city: Shanghai

first: Liying

last: Jiang

address: 279 zhouzhugong road

country: China

institute: Shanghai University of Medicine and Health Sciences

library_source: transcriptomic

data_processing:
Analysis of count data was performed using the DESeq2 (differential gene expression analysis based on the negative binomial distribution) pipeline (version 1.0.19) (Anders and Huber, 2010).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: pregnant female

extract_protocol:
Total RNA  was extracted  using the RNeasy micro kit (Qiagen) according to manufacturer’s protocol  and determined by Bioanalyzer 2100 (Agilent, santa Clara, CA, USA).
miRNA-Seq libraries  were performed using the Small RNA Library Prep（NEB E7300L/E7580L）.

tag: Sex

value: female

value: peripheral blood

tag: cell type

value: lymphocyte

tag: disease state

value: gestational diabetes (GDM)


title: Post_Vaccination YF-VAX D7 CO226_D7

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

country: France

institute: Sanofi

description:
Post_Vaccination YF-VAX D7
post vaccination

data_processing:
OmicSoft Array Studio software (v9.0 -v10.0).
The reads were aligned with OmicsSoft Aligner (OSA4) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations
Multiple mappings reads and first-read-forward-strand reads were discarded from the analysis
Read counts were then subsequently analyzed using R scripts (R version 3.3.3).
All samples were scale-normalized according to their library size by the TMM method of edgeR package (v3.16.5) and transformed with voom (Limma R package v3.30.13).
For the linear modeling of differential gene expression, a model was built with Limma using the treatment condition (vaccination group and sampling time point) as a factor (relatively to the vaccination day defined as a baseline). Contrasts were set up in order to compare for every vaccination group each time point post-vaccination with baseline (Day –29)). Contrasts were also set up to compare directly vaccination groups for each time point post-vaccination relatively to their own group baseline
The tmod R package (v0.31) was used to detect functional enrichment directly on the Limma object (i.e. inference test result from the Limma R package) on the full genes list (ordered using default "minimal significant difference" ranking) coming from each contrast
Assembly: Cyno.WashU2013
Supplementary files format and content: Raw read counts from Array Studio software

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Whole Blood

extract_protocol:
Whole blood from NHPs was collected in PAXgene tubes (BD762165 –Ozyme) and stored according to the manufacturer's protocol. Total RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation
Extracted RNA samples were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300 ng of total globin-depleted RNA according to manufacturer’s instructions.

treatment_protocol: 36 male NHPs were randomized into groups of nine to receive subcutaneous injection in the deltoid muscle region of the upper arm with a single commercial dose of Stamaril (4 LogCCID50) or YF-VAX (6 LogCCID50), or 4 or 5 LogCCID50 vYF at WSL stage. Nine months after vaccination, NHPs along with six additional unvaccinated controls were challenged by a single sub-cutaneous injection of 3.0 LogCCID50 wild-type YFV Asibi strain in the scapula region.

value: Whole Blood

value: male

tag: treatment

value: YF-VAX

tag: time


title: Post_Vaccination YF-VAX D27 CO225_D27

description:
Post_Vaccination YF-VAX D27
post vaccination


title: PS19-fE4_Syn1-Cre267


title: PS19-fE4_Syn1-Cre504


title: Post_Vaccination YF-VAX D-29 CO226_D-29

description:
Post_Vaccination YF-VAX D-29
post vaccination


title: exp3_miRNA


title: exp4_miRNA


title: PS19-fE4-413


title: Post_Vaccination YF-VAX D7 CO225_D7


title: exp1_miRNA


title: UPCI-SCC-090_WT_H3K4me3_replication1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.4.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.21.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command. The data was corrected for input during bedgraph creation.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: HPV(+) head and neck cancer cell line

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated. The sonicated nuclear fraction was used as input.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: HPV(+) head and neck cancer cell line

tag: chip antibody

value: H3K4me3_ChIP (Active Motif, 39159, lot 31420006)


title: PS19-fE4-156


title: Post_Vaccination YF-VAX D3 CO464_D3

description:
Post_Vaccination YF-VAX D3
post vaccination


title: UM-SCC-47_replication2

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-47, UM-SCC-104 and FaDu were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO).  NP69SV40T was maintained in keratinocyte serum-free medium (Gibco , Carlsbad, CA). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃. Clinical samples were immediately frozen in liquid nitrogen and stored at −80℃.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: UPCI-SCC-090 was treated with 2.5nM siRNAs (siControl, siITPR3), using Lipofectamine RNAiMAX Transfection Reagent, according to the manufacturer’s instructions. RNA was extracted 48 hours after RNAi treatment.

value: WT


title: PS19-fE4-154


title: con6_miRNA

value: Control


title: Post_Vaccination YF-VAX D-29 CO225_D-29


title: PS19-fE4-129


title: PS19-fE3-478


title: con4_miRNA


title: PS19-fE3-60


title: Post_Vaccination YF-VAX D27 CO104_D27


title: con2_miRNA


title: SAS shcon

city: Taipei

first: LIYIN

last: YEH

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

country: Taiwan

institute: National Yang-ming university

data_processing:
Total RNA was subjected to mRNA enrichment, fragmentation, reverse transcription, library construction and sequencing (Genomics Co., Taipei, Taiwan). The transcriptome was then aligned according to the various genes' FPKM (Fragments Per Kb of transcript per Million mapped reads) values in order to detect discrepancies in the transcript levels within the various cells.
Genome_build: HG19
Supplementary_files_format_and_content: fpkm

source_name: SAS HNSCC cell line infected with sh.con

growth_protocol: SAS were matained with DMEM with 10% FBS, 1% L-Glutamin and 1%P/S

extract_protocol:
Total RNA were extract with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: SAS HNSCC


title: SAS sh7332

source_name: SAS HNSCC cell line infected with sh.7332


title: LP-1_DMSO_4h_Input_ChIP-seq_rep1

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

description: ChIP antibody: none (input)

data_processing:
Reads from ChIP-seq were mapped to the hg19 version of the human genome using BWA version 0.7.10. Duplicate reads were removed using samtools’ sort and rmdup functions.
IGVTools count was run with an extension of 100 and a window size of 25 bp to generate coverage signal in WIG format. The WIG files were scaled to a mean of 1.0 assuming an effective genome size of 2,700,000,000 bases.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with enhancers, tab-delimited text file including BRD4 ChIP-seq signal in enhancers and promoters and wig files

growth_protocol: LP-1 cells were cultured at 37 ˚C under 5% CO2 in IMDM medium supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Cells were incubated in lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.2 % NP-40) for 1 hour at 4 ˚C.  Chromatin was digested at a concentration of 25 x106 cells/mL with 350 U/mL MNase (Roche,10107921001) for 20 minutes at RT in MNase reaction buffer (55 mM Tris-HCl pH 7.5, 0.05 mM EDTA, 2.5 mM MgAc2, 12.5 % glycerol, 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2).  The digestion was stopped with 10 mM EDTA.  The chromatin was then sonicated with a 550 Sonic Dismembrator (Fisher Scientific) on power 4, using cycles of 0.7 seconds on and 1.4 seconds off for a total processing time of 3 minutes.  Lysates were centrifuged at 21,000 x g for 10 min at 4 ˚C.  5 x106 cell equivalents were used for each ChIP assay, diluted to 1 mL with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 1.1% Triton-X 100, 167 mM NaCl, 0.01 % SDS).  Chromatin was pre-cleared for 2 hours at 4 ˚C with Protein A Dynabeads (Life Technologies,10001D) in blocking buffer (1x PBS, 0.5 % BSA, 0.1% Tween-20).  Beads were captured and pre-cleared chromatin was incubated with antibodies overnight at 4 ˚C.  Samples were then incubated with Protein A Dynabeads in blocking buffer for 2 hours at 4 ˚C.  Beads were washed 3x with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS) and 1x with RIPA high salt buffer (10 mM Tris-HCl pH 8.0, 360 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS).  Bound chromatin was eluted with elution buffer (10 mM Tris-HCl, 1 % SDS, 300 mM NaCl, 10 mM EDTA pH 8.0).  Crosslinks were reversed by incubation at 65 ˚C for 6 hours.  Eluted chromatin was treated with 150 U/mL RNase A for 30 minutes at 37 ˚C and digested with 75 µg/mL proteinase K for 1 hour at 55 ˚C. ChIP DNA was purified with using a MinElute PCR Purification Kit (QIAGEN) and quantified with a Qubit fluorimeter (Life Technologies).
Library DNA fragments for BRD4, RNAPII, RNAPIISer2P ChIP and input DNA were ligated to Illumina adapters and size selected (200-250 bp) on a 2% agarose gel and PCR amplified for 18 cycles.  Libraries of H3K27ac ChIP and input DNA were constructed using an Ovation Ultralow DR Multiplex System Kit (NuGEN) using 15 cycles of amplification. Libraries were size selected (250-300 bp) on a 2% agarose gel.

treatment_protocol: LP-1 cells were treated with DMSO or 0.5 μM JQ1 for 4 hours.  Cells were fixed with 1% formaldehyde by the addition of 37% formaldehyde directly to the culture medium.  Cells were fixed for 10 minutes at room temperature (RT) and quenched with 0.125 M glycine, pH 7.9.

value: multiple myeloma


title: con7_miRNA


title: Post_Vaccination YF-VAX D-29 CO104_D-29


title: Post_Vaccination YF-VAX D3 CO225_D3


title: FaDu_WT_input_replication2

description:
FaDu_WT_H3K4me1_replication2.bedgraph.gz
FaDu_WT_H3K4me3_replication2.bedgraph.gz
FaDu_WT_H3K27ac_replication2.bedgraph.gz

source_name: HPV(-) head and neck cancer cell line

value: HPV(-) head and neck cancer cell line


title: con1_miRNA


title: PS19-fE3-464


title: striatum, methylphenidate 2

city: Shinagawa-ku

first: Ryota

last: Nakano

state: Tokyo

address: Hatanodai 1-5-8

department: Showa University Graduate School of Pharmacy

institute: Showa university

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Transcripts Per Million(TPM) were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: striatum

growth_protocol: Mice were housed in plastic cages in a temperature-controlled room (22±1 ℃) and maintained at a 12-h light-dark cycle, with free access to food and water.

extract_protocol:
striatum collected from 6-week-old offspring (F1) were flash-frozen in liquid nitrogen and stored at -80℃ until total RNA was extracted. Total RNA was isolated from the tissue using RNeasy Mini Kit (QIAGEN Inc., CA USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six-week-old male ICR mice (F0) were administered MPH (15 mg/kg) or saline (10 mL/kg) subcutaneously for 21 consecutive days and mated with drug-untreated female mice during their estrous cycle

value: striatum

tag: strain

value: ICR

value: methylphenidate (15 mg/kg)


title: LP-1_500nM_JQ1_4h_RNAPIISer2P_ChIP-seq

description: ChIP antibody: RNAPIISer2P (Abcam, ab5905)


title: LP-1_500nM_JQ1_4h_RNAPII_ChIP-seq

description: ChIP antibody: RNAPII (Santa Cruz Biotechnology, sc-9001)


title: FaDu_WT_H3K27ac_replication2

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: striatum, methylphenidate 1

value: female


title: Post_Vaccination YF-VAX D27 CN700_D27


title: LP-1_DMSO_4h_RNAPIISer2P_ChIP-seq


title: con5_miRNA

value: peripheral blood

value: lymphocyte


title: FaDu_WT_H3K4me3_replication2


title: Post_Vaccination YF-VAX D7 CO104_D7

value: Whole Blood


title: Post_Vaccination YF-VAX D3 CN700_D3

value: male


title: striatum, control 3

value: saline (10 ml/kg)


title: striatum, methylphenidate 3


title: Post_Vaccination YF-VAX D-29 CN700_D-29

value: YF-VAX


title: LP-1_500nM_JQ1_4h_BRD4_ChIP-seq

description: ChIP antibody: BRD4 (Bethyl Laboratories, A301-985A)


title: striatum, control 1


title: UM-SCC-104_WT_H3K27ac_replication2

value: HPV(+) head and neck cancer cell line


title: Post_Vaccination YF-VAX D3 CO104_D3


title: FaDu_WT_H3K4me1_replication2

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: LP-1_DMSO_4h_RNAPII_ChIP-seq


title: Post_Vaccination YF-VAX D7 CN685_D7


title: striatum, control 2


title: UM-SCC-104_WT_input_replication2

description:
UM-SCC-104_WT_H3K4me1_replication2.bedgraph.gz
UM-SCC-104_WT_H3K4me3_replication2.bedgraph.gz
UM-SCC-104_WT_H3K27ac_replication2.bedgraph.gz


title: Retina, 20hr, replicate 3

city: Davis

first: Marie

last: Burns

address: 1 Shields Ave

institute: University of California Davis

description: 10X Genomics

data_processing:
Processing including barcode processing, transcript alignment, and generation of gene-barcode matrices was performed using Cell Ranger (Chromium) at the UC Davis Bioinformatics Core.
Assembly: mm10
Supplementary files format and content: tsv (tab separated values) files contain gene and barcode IDs, mtx (matrix) files contain counts

source_name: Retina

growth_protocol: All Arr1-/- mice were bred and maintained in constant darkness before experimentation.

extract_protocol:
Isolated retinas were placed in 1-2 mL each of digestion buffer, consisting of Hibernate medium (HBSS; 10-547F, Lonza) supplemented with 5% fetal bovine serum (FBS), 10 mM HEPES, 0.7 mg/mL calcium chloride, 1.5 mg/mL collagenase A (Roche), and 0.1 mg/mL DNase I (Roche). Tissue was incubated at 37 °C for 15-20 minutes, with mild tricheration with a pipette. After digestion, the cell suspension was filtered through a 70 mm cell strainer (Genesee Scientific), and resuspended in PBS. Cells were then stained for viability (Zombie NIR Fixable Viability Kit, 423106, BioLegend), blocked for 5 minutes with Fc block 1 ul/sample (eBioscience) supplemented with 5% each normal rat and mouse sera, and then incubated with Biolegend antibodies raised against CD45 and CD11b diluted in Brilliant Stain Buffer (BD Biosciences) for 15-30 minutes at room temperature. After staining, cell suspensions were washed in 0.5% bovine serum albumin (BSA) with 1:50 EDTA, and ultimately resuspended in the same buffer. Cell sorting was performed at the UC Davis Flow Cytometry Shared Resource Laboratory on an Astrios EQ Cell Sorter (Beckman Coulter). Retinal immune cells were enriched by sorting for alive, CD45+ CD11b+ cells. Cells were sorted into a solution of Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fischer) supplemented with 10% FBS, and then immediately used to create the expression libraries.
Library preparation was performed following manufacturer instructions. 10X Genomics (Chromium) single-cell expression 3' v2 chemistry was used. Library preparation was primarily performed at the UC Davis DNA Technologies and Expression Core facility.

treatment_protocol: Mice were maintained in constant darkness,  or exposed to constant room lighting (approximately 200 lux) for 7 or 20 days before sample collection.

value: Retina

value: Female

value: 20 days light exposure

value: long after retinal degeneration


title: Retina, 7hr, replicate 3

description: 10X Genomics

value: 7 days light exposure

value: immediately after retinal degeneration


title: Post_Vaccination YF-VAX D27 CN685_D27


title: Post_Vaccination YF-VAX D-29 CN685_D-29


title: Post_Vaccination YF-VAX D7 CN700_D7


title: Retina, 0hr, replicate 3

description: 10X Genomics

value: 0 days light exposure

value: healthy retina


title: LP-1_DMSO_4h_BRD4_ChIP-seq

value: multiple myeloma


title: Post_Vaccination Stamaril D27 CO433_D27

description:
Post_Vaccination Stamaril D27
post vaccination

value: Stamaril


title: UM-SCC-104_WT_H3K4me1_replication2


title: UM-SCC-104_WT_H3K4me3_replication2

value: H3K4me3_ChIP (Active Motif, 39159, lot 31420006)


title: Retina, 7hr, replicate 2

description: 10X Genomics


title: UPCI-SCC-090_WT_H3K27ac_replication2

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: UPCI-SCC-090_WT_input_replication2

description:
UPCI-SCC-090_WT_H3K4me1_replication2.bedgraph.gz
UPCI-SCC-090_WT_H3K4me3_replication2.bedgraph.gz
UPCI-SCC-090_WT_H3K27ac_replication2.bedgraph.gz


title: UPCI-SCC-090_WT_H3K4me3_replication2


title: Retina, 20hr, replicate 1

description: 10X Genomics


title: Retina, 20hr, replicate 2

description: 10X Genomics


title: Post_Vaccination Stamaril D-29 CO433_D-29

description:
Post_Vaccination Stamaril D-29
post vaccination

value: Whole Blood

value: male


title: Post_Vaccination Stamaril D3 CO433_D3

description:
Post_Vaccination Stamaril D3
post vaccination


title: Retina, 0hr, replicate 2

description: 10X Genomics


title: Post_Vaccination YF-VAX D3 CN685_D3

value: YF-VAX


title: Post_Vaccination Stamaril D27 CO401_D27


title: UM-SCC-104_WT_H3K27ac_replication1

value: HPV(+) head and neck cancer cell line


title: Retina, 7hr, replicate 1

description: 10X Genomics


title: UPCI-SCC-090_WT_H3K27ac_replication1


title: UPCI-SCC-090_WT_H3K4me1_replication2

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: Post_Vaccination Stamaril D7 CO401_D7

description:
Post_Vaccination Stamaril D7
post vaccination


title: Retina, 0hr, replicate 1

description: 10X Genomics

value: Retina


title: UPCI-SCC-090_WT_H3K4me1_replication1


title: outputD

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
the MEA-seq sequences were aligned to mm9/hg19 by using bwa -aln (version 0.7.5a-r405) with default parameters
The uniq mapped fragment counts were normalized
The poisson test was used to calculate the significant difference between input and output data, then, the Benjaminiand Hochberg test was used to select the loci with q value which were lower than 0.01 as effective signals
Genome_build: mm9,hg19
Supplementary_files_format_and_content: MAE-seq enhancers text file

source_name: Mouse embryonic stem cell

growth_protocol: Both mESCs and HEK293T were purchased from ATCC and cultured in accordance with ATCC's protocol.

extract_protocol:
The cells were transfected with lipo3000, and the cells were collected for flow screening after 48 hours.
DNA was extracted from the collected fluorescent cells. Components were added according to the TruePrep DNA Library Prep kit (Vazyme; Cat.TD202) and followed by one-step PCR (72℃ for 3min, 98℃ for 30s; followed by 5-15 cycles of 98℃ for 15s, 60℃ for 30s, 72℃ for 3min; 72℃ for 5mins). The product was recovered by 2% agarose gel electrophoresis for 35 min (120v, 130mA) and sent for high-throughput sequencing. Sequence after one-step PCR amplification is 5’-AATGATACGGCGACCACCGAGATCTACACIIIIIIIITCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-NNNNNN-CTGTCTCTTATACACATCTCCGAGCCCACGAGACIIIIIIIIATCTCGTATGCCGTCTTCTGCTTG-3’, IIIIIIII: Index 2 (i5), IIIIIIII: Index 1 (i7), -NNNNNN-: random sequence.
MAE-seq

value: E14 cell


title: 3W Control (Cy5) x 3W MXD (Cy3)

type: RNA

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy3/Cy5) of Cont vs MXD 3W mouse back skin

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: 3W 3% Minoxidil-treated back skin Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Experimental protocols were reviewed and approved by the Animal Care Committee of Hoshi University School of Pharmacy and Pharmaceutical Sciences. Male C57BL/6 mice (8 weeks-old) purchased from Tokyo Laboratory Animals Science Co., Ltd. (Tokyo, Japan). The animals were housed at the Animal Institution in Hoshi University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light : 12 h dark cycle with free access to water and rodent chow.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Preliminary experiments were conducted with N-CE at 1, 10, and 20% concentrations. C57BL/6 mice were divided into 3 groups (6 mice per group): N-CE 10%, MXD 3%, and VC (propylene glycol: ethanol: water (5:3:2) was used as the vehicle control group). Briefly, starting the day after shaving, 200 μL of the adjusted sample was applied daily to the backs of the mice for observation and photography, and sampling for OMICS.

value: back skin

value: 3W 3% Minoxidil-treated

source_name: 3W Vehicle-treated back skin Cy5

value: 3W Vehicle-treated


title: Post_Vaccination Stamaril D3 CO401_D3


title: Post_Vaccination Stamaril D7 CO433_D7


title: 3W Control (Cy3) x 3W N-CE (Cy5)

description: Dye-swap (Cy3/Cy5) of Cont vs N-CE 3W mouse back skin

source_name: 3W Vehicle-treated back skin Cy3

source_name: 3W 10% Notocactus ottonis Cell extract-treated back skin Cy5


title: 3W Control (Cy3) x 3W MXD (Cy5)

source_name: 3W 3% Minoxidil-treated back skin Cy5


title: Post_Vaccination Stamaril D-29 CO401_D-29


title: outputC


title: outputB


title: NP69SV40T_WT

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Hi-C reads were processed using HiC-Pro.
Assembly: hg19
Supplementary files format and content: hic

source_name: nasopharyngeal epithelial cell line

extract_protocol:
Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).
Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in

value: nasopharyngeal epithelial cell line

tag: restricion enzyme

value: MboI


title: FaDu_WT

value: FaDu

value: HPV(-) head and neck cancer cell line


title: UM-SCC-104_WT


title: 2W Control (Cy3) x 2W N-CE (Cy5)

description: Dye-swap (Cy3/Cy5) of Cont vs N-CE 2W mouse back skin

source_name: 2W Vehicle-treated back skin Cy3

value: 2W Vehicle-treated

source_name: 2W 10% Notocactus ottonis Cell extract-treated back skin Cy5


title: GR H300 rep 1 ARID1a SiRNA + Dex

city: Bristol

first: Felicity

last: Stubbs

address: Whitson St

country: United Kingdom

institute: University of Bristol

data_processing:
Quality of sequencing was assessed using FastQC (usegalaxy.org) and sequences were trimmed to 36 bases. Single end reads were uniquely aligned to the human genome assembly (hg19) using Bowtie2 and PCR duplicates removed (SAMtools v1.3.1).
Counts were normalized to 10 million tags to allow for cross sample comparisons and visualized using the UCSC genome browser (https://genome.ucsc.edu/).
Enrichment of GR ChIP-Seq to 1% input control, were identified using findPeaks (HOMER v4.9.1) at relaxed settings (-F1 -L1 -P.1 -LP.01 -poisson .1 -style factor).
Of these, only concordant replicate enrichments that passed an estimated irreproducible discovery rate threshold were kept for downstream analysis (IDR v2.0.3 – set to 0.01). Any concordant enrichments that overlapped were merged into a single region using mergePeaks (HOMER v4.9.1) and raw input ChIP-Seq tag counts were subtracted from corresponding GR tag counts using annotatePeaks.pl. Differential fold change between all conditions was assessed using getDiffExpression.pl (HOMER v4.9.1) and DESeq284
For DESeq2 analysis, tags were normalized to total tags within enriched regions and considered significantly changed to no Dex control (as well as between treatments) if FDR <0.05, fold change > 0.585 (Log2) and p-value <0.05 adjusted for multiple comparisons. All other comparisons were given the value 0. All enrichment regions were annotated with annotatePeaks.pl (HOMER v4.9.1) to closest transcriptional start site (TSS) (UCSC RefSeq GCD_000001405.25_GCCh37.p13 (2017-04-19)). Fold change (Log2) between treatments was visualized using heatmap.2 (RStudio 1.0.153, RStudio Team (2016).
Assembly: Hg19
Supplementary files format and content: Approximate ChIP-fragment densities are compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate (all bedGraph.gz files).
Supplementary files format and content: Final matrix (FINAL_MATRIX-GR-CHIP) includes peak ID (column A), GR enrichment locations and gene name (columns B-L), Conditions compared with Log2 fold change, p value and adjusted P value (Column M-AD)

source_name: HeLa

growth_protocol: DMEM, 10% FCS.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed as previously described. Soluble chromatin was prepared using MNase digestion [50mM Tris-HCl, pH 7.5, 4mM MgCl2, 1mM CaCl2, 0.32mM sucrose, 2mM NaF, 0.2mM NaVan] with 2 units of MNase (Sigma, UK) /180μg chromatin, then immunoprecipitated with H300 GR antibody (Santa Cruz; sc-8992), RNA Polymerase II (phosphoserine-5) antibody (ACTIVE MOTIF; 39233) or rabbit non-immune serum (Santa Cruz; sc-2027). For sequencing, libraries were prepared from two replicates/condition.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested with Mnase

value: HeLa

value: Cervical cancer

value: H300 GR Santa Cruz


title: outputA


title: 2W Control (Cy5) x 2W MXD (Cy3)

description: Dye-swap (Cy3/Cy5) of Cont vs MXD 2W mouse back skin

source_name: 2W 3% Minoxidil-treated back skin Cy3

value: 2W 3% Minoxidil-treated

source_name: 2W Vehicle-treated back skin Cy5


title: Post_Vaccination Stamaril D3 CO382_D3

source_name: Whole Blood

value: Whole Blood

value: male

value: Stamaril


title: Post_Vaccination Stamaril D7 CO382_D7


title: 1W Control (Cy5) x 1W N-CE (Cy3)

description: Dye-swap (Cy3/Cy5) of Cont vs N-CE 1W mouse back skin

source_name: 1W 10% Notocactus ottonis Cell extract-treated back skin Cy3

source_name: 1W Vehicle-treated back skin Cy5

value: 1W Vehicle-treated


title: 1W Control (Cy5) x 1W MXD (Cy3)

description: Dye-swap (Cy3/Cy5) of Cont vs MXD 1W mouse back skin

source_name: 1W 3% Minoxidil-treated back skin Cy3

value: 1W 3% Minoxidil-treated


title: 3W Control (Cy5) x 3W N-CE (Cy3)

source_name: 3W 10% Notocactus ottonis Cell extract-treated back skin Cy3

value: back skin


title: 2W Control (Cy5) x 2W N-CE (Cy3)

source_name: 2W 10% Notocactus ottonis Cell extract-treated back skin Cy3


title: 1W Control (Cy3) x 1W N-CE (Cy5)

source_name: 1W Vehicle-treated back skin Cy3

source_name: 1W 10% Notocactus ottonis Cell extract-treated back skin Cy5


title: bulk-RNA-seq-Chronic 2

city: sichuan

first: Xue

middle: li

last: Hu

address: Section 3 renmin South Road

institute: sichuan university

data_processing:
scRNA seq: Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells. bulk-RNA seq:  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: scRNA seq: Matrix table with raw gene counts for every gene and every cell; bulk-RNA seq: Matrix table with raw gene counts for every gene and every sample

source_name: lung

extract_protocol:
Freshly harvested control, acute infected and chronic infected mouse lungs were digested by Lung Dissociation Kit (MACs# 130-095-927) and generate single-cell suspension according to its protocol.Single cells were suspended in 1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/ml). A part of single-cell suspensions were used to conduct scRNA seq, other part of them were used to perform bulk-RNA seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: chronic infected 2


title: 1 % INPUT Control (transfected with scrambled siRNA) +Dex


title: UPCI-SCC-090_baitE6E7_replication2

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
4C-seq reads were aligned to hg19 reference human genome, using w4Cseq.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: 4C-seq

source_name: HPV(+) head and neck cancer cell line

growth_protocol: UPCI-SCC-090 was cultured in Minimum Essential Medium with Earle's salts and L-glutamine (Gibco , Carlsbad, CA) containing 2 mM L-glutamine (Gibco , Carlsbad, CA), 1% nonessential amino acids (Gibco , Carlsbad, CA), 50 μg/mL gentamicin (Gibco , Carlsbad, CA), and 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL). UM-SCC-104 was cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). Cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
Cells were lysed and cross-linked DNA was digested with the primary restriction enzyme. Next, digested DNA was subjected to proximity ligation using T4 DNA ligase (EL0013, Thermo Scientific), followed by cross-link removal using Proteinase K (P8107S, New England Biolabs), which resulted in 3C libraries. The 3C libraries were then subjected to a second restriction enzyme digestion, followed by a circularization reaction using T4 DNA ligase.
The 4C template was used to perform a scaled-up inverse nested PCR. Inverse primers were designed and appropriate adaptors and index sequences were then added to the inverse primer pair.

value: HPV(+) head and neck cancer cell line

tag: restricion enzymes

value: Csp6I, NlaIII


title: 2W Control (Cy3) x 2W MXD (Cy5)

source_name: 2W 3% Minoxidil-treated back skin Cy5


title: Post_Vaccination Stamaril D-29 CO382_D-29


title: bulk-RNA-seq-Chronic 1

value: chronic infected 1


title: Huh-7-WT-3

city: wuhan

first: xia

last: peng

state: hubei

address: zhongnan hospital

institute: wuhan university

data_processing:
llumina Novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Transcripts Per Million (TPM) 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.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver cancer

extract_protocol:
Total RNA was extracted from HCC cell lines using TRIzol reagent (Invitrogen).
Illumina NovaSeq 6000 System (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: liver cancer

value: Huh-7 cells

value: Human liver cancer cells

value: WT

value: No treatment


title: 1 % INPUT ARID1a knockdown (transfected with ARID1a siRNA) +Dex

value: HeLa

value: Cervical cancer

value: H300 GR Santa Cruz


title: Post_Vaccination Stamaril D27 CO369_D27

value: Whole Blood

value: male

value: Stamaril


title: Post_Vaccination Stamaril D27 CO382_D27


title: GR H300 rep 1 Control -Dex


title: 1W Control (Cy3) x 1W MXD (Cy5)

value: back skin

value: 1W Vehicle-treated

source_name: 1W 3% Minoxidil-treated back skin Cy5

value: 1W 3% Minoxidil-treated


title: Huh-7-WT-2


title: Post_Vaccination Stamaril D7 CO369_D7


title: bulk-RNA-seq-Acute 2

value: lung

value: acute infected 2


title: GR H300 rep 2 ARID1a SiRNA +Dex


title: Huh-7-WT-1


title: UPCI-SCC-090_WT

value: HPV(+) head and neck cancer cell line

value: MboI


title: bulk-RNA-seq-Ctrl2

value: wild type 2


title: bulk-RNA-seq-Ctrl1

value: wild type 1


title: GR H300 rep 1 ARID1a SiRNA -Dex


title: Post_Vaccination Stamaril D-29 CO369_D-29


title: Post_Vaccination Stamaril D3 CO369_D3


title: Huh-7-KO-1

value: liver cancer

value: METTL5 sgRNA infection in Huh-7 cells

value: Human liver cancer cells

value: METTL5 sgRNA infection


title: 1 % INPUT ARID1a knockdown (transfected with ARID1a siRNA) -Dex

value: HeLa

value: Cervical cancer

value: H300 GR Santa Cruz


title: Huh-7-KO-2


title: GR H300 rep 2  Control -Dex


title: Post_Vaccination Stamaril D7 CN777_D7

value: Whole Blood

value: male

value: Stamaril


title: scRNA-seq-Chronic 2

value: chronic infected 2


title: Post_Vaccination Stamaril D27 CN777_D27


title: scRNA-seq-Chronic 1

value: lung

value: chronic infected 1


title: HCC-LM3-KO-3

value: METTL5 sgRNA infection in HCC-LM3 cells


title: scRNA-seq-Acute 2

value: acute infected 2


title: GR H300 rep 1 Control + Dex


title: Post_Vaccination Stamaril D3 CN777_D3


title: Post_Vaccination Stamaril D-29 CN777_D-29


title: bulk-RNA-seq-Acute1

value: acute infected 1


title: HCC-LM3-KO-2


title: 1 % INPUT Control (transfected with scrambled siRNA) -Dex


title: GR H300 rep 2  ARID1a SiRNA -Dex


title: scRNA-seq-Ctrl2

value: wild type 2


title: scRNA-seq-Acute1


title: Huh-7-KO-3

value: liver cancer


title: HCC-LM3-KO-1


title: GR H300 rep 2 Control +Dex


title: Post_Vaccination Stamaril D7 CN657_D7


title: HCC-LM3-WT-2

value: HCC-LM3 cells

value: WT

value: untreated


title: HCC-LM3-WT-3

value: Human liver cancer cells


title: HCC-LM3-WT-1


title: Post_Vaccination Stamaril D3 CN657_D3


title: EOS02_19: ABT263 post R-UUO

city: Edinburgh

first: Eoin

middle: D

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
Prior to RNA sequencing, RNA integrity was checked using Genechip, with only samples with RIN >7 when rechecked by the sequencing facility used to generate libraries utilized in subsequent analysis.  A PolyA library was constructed and run on an Illumina Novaseq using 5x150bp paired-end sequencing at a depth of 50M reads per library by Genewiz
RNA-Seq Analysis Snakemake Workflow (RASflow) which is a workflow based in Snakemake and Conda to run QC, alignment and quantification steps locally in Linux for windows subsystem
FastQC was used for initial quality control assessment before trimming was performed with Cutadapt. This followed the standard procedure of first trimming low quality base calls from the 3’ end of the read, before adapter trimming using the default settings- using the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC')). The “- -paired” argument was used which runs a paired-end validation on both trimmed _1 and _2 FastQ files once the trimming has completed. This step removes entire read pairs if at least one of the two sequences became shorter than a certain threshold. The final QC report was prepared in MultiQC26
Genome_build: Reads were then mapped to GRCm38.68 mouse reference transcriptome, mm10 (Ensembl 93) was used using pseudo-aligner with Salmon

source_name: kidney

extract_protocol:
kidneys were removed , digested on ice and FACS sorted using DAPI as a live/dead gate. Rin >7 only. Standard
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: age

value: 8 week


title: scRNA-seq-Ctrl1

value: wild type 1


title: EOS02_17: ABT263 post R-UUO


title: U9  C57BL/6 mice, unilateral ureteral obstruction, Day7

city: Wuhan

first: xi

last: xiong

state: Hubei Province

address: No.241, Pengliuyang Road

department: Department of Urology

institute: Wuhan Third Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni

source_name: ureter

growth_protocol: Male mice (C57BL/6, wild-type, four weeks old) with a body weight of approximately 18 g were purchased from China Three Gorges University.

treatment_protocol: Ophthalmic forceps were used to separate the ureter along the lower pole of the kidney, ligate the ureter twice at the middle and upper 1/3 of the ureter, and cut it between the two ligatures. The abdominal walls of fascia, muscle and skin were sutured in a layerwise pattern. The ureter was freed and the abdomen was closed with no ligation or disconnection of the ureter in the sham operation group.

value: ureter

value: unilateral ureteral obstruction


title: SUDHL5_Treated_BRD4_2

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files (gzipped) and corresponding TDF files suitable for visualization using the Integrative Genomics Viewer (IGV) available from the Broad Institute.

source_name: SU-DHL-5 cultured cells_ChIP_BRD4

growth_protocol: SUDHL-5 cells were cultured at 37 ˚C under 5% CO2 in RPMI medium supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Fixed cells were incubated in lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.2 % NP-40) for 1 hour at 4 ˚C.  Chromatin was digested at a concentration of 25 x106 cells/mL with 250 U/mL MNase (Roche,10107921001) for 20 minutes at RT in MNase reaction buffer (55 mM Tris-HCl pH 7.5, 0.05 mM EDTA, 2.5 mM MgAc2, 12.5 % glycerol, 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2).  The digestion was stopped with 10 mM EDTA.  The chromatin was then sonicated with a 550 Sonic Dismembrator (Fisher Scientific) on power 4, using cycles of 0.7 seconds on and 1.4 seconds off for a total processing time of 3 minutes.  Lysates were centrifuged at 21,000 x g for 10 min at 4 ˚C.  5 x106 cell equivalents were used for each ChIP assay, diluted to 1 mL with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 1.1% Triton-X 100, 167 mM NaCl, 0.01 % SDS).  Chromatin was pre-cleared for 2 hours at 4 ˚C with Protein A Dynabeads (Life Technologies,10001D) in blocking buffer (1x PBS, 0.5 % BSA, 0.1% Tween-20).  Beads were captured and pre-cleared chromatin was incubated with antibodies overnight at 4 ˚C.  Samples were then incubated with Protein A Dynabeads in blocking buffer for 2 hours at 4 ˚C.  Beads were washed 3x with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS) and 1x with RIPA high salt buffer (10 mM Tris-HCl pH 8.0, 360 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS).  Bound chromatin was eluted with elution buffer (10 mM Tris-HCl, 1 % SDS, 300 mM NaCl, 10 mM EDTA pH 8.0).  Crosslinks were reversed by incubation at 65 ˚C for 6 hours.  Eluted chromatin was treated with 150 U/mL RNase A for 30 minutes at 37 ˚C and digested with 75 µg/mL proteinase K for 1 hour at 55 ˚C. ChIP DNA was purified with using a MinElute PCR Purification Kit (QIAGEN) and quantified with a Qubit fluorimeter (Life Technologies).
NuGEN Ovation Ultralow DR multiplex system used to generate the libraries.  16 cycles of amplification was performed.  The libraries were size selected by agarose gel.  250-350bp fragments were taken.

treatment_protocol: SUDHL-5 cells were treated with DMSO or 2.5 μM CPI203 for 4 hours.  Cells were fixed with 1% formaldehyde by the addition of 37% formaldehyde directly to the culture medium.  Cells were fixed for 10 minutes at room temperature (RT) and quenched with 0.125 M glycine, pH 7.9.

tag: chip antibody vendor

value: Bethyl

tag: chip antibody vendor id


title: Post_Vaccination Stamaril D-29 CN657_D-29

data_processing:
OmicSoft Array Studio software (v9.0 -v10.0).
The reads were aligned with OmicsSoft Aligner (OSA4) in Array Studio against the Cyno.WashU2013 reference genome using WashUGene20140620 gene annotations
Naïve read count quantification was performed with the Array Studio software using WashUGene20140620 gene annotations
Multiple mappings reads and first-read-forward-strand reads were discarded from the analysis
Read counts were then subsequently analyzed using R scripts (R version 3.3.3).
All samples were scale-normalized according to their library size by the TMM method of edgeR package (v3.16.5) and transformed with voom (Limma R package v3.30.13).
For the linear modeling of differential gene expression, a model was built with Limma using the treatment condition (vaccination group and sampling time point) as a factor (relatively to the vaccination day defined as a baseline). Contrasts were set up in order to compare for every vaccination group each time point post-vaccination with baseline (Day –29)). Contrasts were also set up to compare directly vaccination groups for each time point post-vaccination relatively to their own group baseline
The tmod R package (v0.31) was used to detect functional enrichment directly on the Limma object (i.e. inference test result from the Limma R package) on the full genes list (ordered using default "minimal significant difference" ranking) coming from each contrast
Assembly: Cyno.WashU2013
Supplementary files format and content: Raw read counts from Array Studio software

value: Whole Blood

value: male

value: Stamaril


title: SUDHL5_Control_BRD4_1


title: EOS02_15: ABT263 post R-UUO


title: SUDHL5_Treated_Input_2

source_name: SU-DHL-5 cultured cells_input

value: none (input)


title: output3

source_name: Human kidney epithelial cell line


title: U8  C57BL/6 mice, unilateral ureteral obstruction, Day7

extract_protocol: The ureter was freed and the abdomen was closed with no ligation or disconnection of the ureter in the sham operation group.


title: SUDHL5_Control_Input_1


title: Post_Vaccination Stamaril D27 CN657_D27

source_name: Whole Blood

extract_protocol:
Whole blood from NHPs was collected in PAXgene tubes (BD762165 –Ozyme) and stored according to the manufacturer's protocol. Total RNA was extracted with the PAXgene 96 Blood RNA kit (Qiagen-762331) according to manufacturer’s instructions on Tecan Evo150 workstation
Extracted RNA samples were processed using the GLOBINclear™-Human kit (ThermoFisher - AM1980) for the depletion of the alpha and beta globin mRNA according to manufacturer’s instructions. Sequencing libraries were prepared with the TruSeq mRNA stranded kit (Illumina - 20162122/20146602) using 300 ng of total globin-depleted RNA according to manufacturer’s instructions.


title: EOS02_13: Vehicle post R-UUO


title: output1


title: EOS02_14: Vehicle post R-UUO


title: output2


title: RL_DMSO_Input_201412

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files and corresponding TDF files suitable for visualization using the Integrative Genomics Viewer (IGV) available from the Broad Institute.

source_name: RL

growth_protocol: Cells were grown in RPMI1640 plus 10% FBS.

extract_protocol:
Cells were fixed with formaldehyde and nuclei were isolated after cell lysis. Chromatin was digested with MNase to mono-, di, and tri-nucleosomes. Samples were then sonicated briefly to break open nuclei to harvest digested chromatin.
DNA libraries for ChIP-seq were prepared using Ovation Ultralow DR Multiplex System kits (0330-32, NuGEN) followed by Illumina sequencing at the MIT BioMicro Center.

treatment_protocol: The 2014-10 samples were treated with 0.2% DMSO for 10 days, the 2014-12 samples were treated with 0.05% DMSO for 10 days

value: RL

value: 0.05% DMSO for 10 days


title: RL_DMSO_H3K27me3_201410

value: 0.2% DMSO for 10 days

value: anti-H3K27me3 (Cell Signalling, catalog# 9733, lot# 6)


title: ABMI3

city: Zhengzhou

first: liang

middle: nian

last: nian

address: 100 Science Avenue

institute: Zhengzhou University

description: Brassica juncea(B. rapa ♀×B. nigra ♂, haploid)

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from Brassicadb database (http://brassicadb.org). Bowtie v1.0.1 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Brassica_juncea_v1.5(http://brassicadb.org)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica rapa x Brassica nigra

source_name: anther

growth_protocol: B. rapa ♀×B. nigra ♂, haploid

extract_protocol:
Flower buds from meiosis and tetrad to maturity were collected and RNA was collected with Trizol reagent. Rna-seq library was constructed with 5 ~ 10 μg total RNA as template
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anther(pollen)

tag: Stage

value: MI(mitosis(gametogenesis))

tag: genomes

value: AB


title: RL_DMSO_H3K27me3_201412


title: EOS02_12: Vehicle post R-UUO

tag: tissue

value: kidney


title: U6  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: ABMI2


title: N4  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: EOS02_11: Vehicle post R-UUO

value: 8 week


title: N3  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: ABMI1


title: EOS02_10: Vehicle post R-UUO


title: ABME2

value: young anther(pollen)

value: ME(meiosis(sporogenesis))


title: EOS02_8: ruuo7


title: N1  C57BL/6 mice, unilateral ureteral obstruction, Day0

value: ureter

value: unilateral ureteral obstruction


title: U7  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: N2  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: ABME3


title: RL_DMSO_TIC_201410


title: ABME1


title: EOS02_9: Vehicle post R-UUO


title: EOS02_7: ruuo7


title: WTU4  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: WTU6  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: Pfeiffer_GSK343_96h_R1

data_processing:
Sequencing was performed on an Illumina HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files with sample annotations, Ensembl gene annotations and log2 FPKM expression values for each library / gene.

source_name: Pfeiffer

growth_protocol: KARPAS-422, Pfeiffer, and RL cells were grown in RPMI-1640 medium containing 10% FBS and antibiotic (Life Technologies).  Cells were seeded at optimal growth density for 4 days of exponential growth (500,000 cells per ml for KARPAS-422 and Pfeiffer, and 200,000 cells per ml for RL).

extract_protocol: RNA was isolated following Trizol lysis as per the manufacturer's protocol (Life Technologies) or using Qiagen RNeasy Plus mini kits and sequenced at Ocean Ridge Biosciences.

treatment_protocol: At the time of cell seeding (day 0), cells were treated with 1.5 µM CPI-169 (KARPAS-422), GSK343 (Pfeiffer), or 0.1% DMSO (all cell lines).  4 days later, cells were harvested via centrifugation, and cell pellets immediately lysed in either Trizol (Life Technologies) or buffer RLT (Qiagen).

value: Pfeiffer

tag: concentration


title: RL_DMSO_1

value: DMSO


title: RL_DMSO_2


title: Pfeiffer_GSK343_96h_R2


title: Group C3

city: Gainesville

first: Xiang

last: Li

state: FL

department: Horticultural Sciences

institute: UNIVERSITY OF FLORIDA

description: harvested on day 8 (8 d after fruits of the first two groups), rep3

data_processing:
Cutadapt (v1.15) software
Cutadapt (v1.15) software was used to filter the sequencing data to get high quality sequence（Clean Data）for further analysis.
The reference genome and gene annotation files were downloaded from genome website (CM3.6.1_pseudomol.fa, http://cucurbitgenomics.org/organism/18, v3.6.1).
The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Assembly: CM3.6.1_pseudomol.fa, http://cucurbitgenomics.org/organism/18, v3.6.1
Supplementary files format and content: Excel files include RPKM values for each Sample

organism: Cucumis melo

source_name: ripe melon fruits

growth_protocol: All fruits were grown in the greenhouse before treatments.

extract_protocol:
Total RNA from different treatments was extracted using TRIzol reagent (Invitrogen Life Technologies).
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

treatment_protocol: (A) stored at 4°C for 7 d (without chilling injury), and then transferred to room temperature (~22°C) for 1 d; (B) held at 4°C for 8 d until use (without chilling injury); (C) harvested on day 8 (8 d after the fruits of first two groups).

value: ripe melon fruits


title: Pfeiffer_DMSO_96h_R1


title: WTU3  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: EOS02_6: ruuo7


title: EOS02_5: ruuo7


title: Group C2

description: harvested on day 8 (8 d after fruits of the first two groups), rep2


title: Group C1

description: harvested on day 8 (8 d after fruits of the first two groups), rep1


title: Karpas422_1.5uM_CPI169_R3


title: EOS02_4: uninjured


title: Group B3

description: held at 4°C for 8d, rep3

value: held at 4°C for 8d


title: WTU1  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: EOS02_3: uninjured


title: Karpas422_1.5uM_CPI169_R2


title: Group B2

description: held at 4°C for 8d, rep2


title: EOS02_2: uninjured


title: WTN4  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: Karpas422_1.5uM_CPI169_R1


title: EOS02_1: uninjured


title: Group B1

description: held at 4°C for 8d, rep1


title: WTN5  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: Pfeiffer_DMSO_96h_R2


title: Group A3

description: stored at 4°C for 7d, and then transfer to 22°C for 1d, rep3


title: Karpas422_DMSO_R3


title: WTN3  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: Karpas422_DMSO_R2


title: WTU2  C57BL/6 mice, unilateral ureteral obstruction, Day7


title: WTN1  C57BL/6 mice, unilateral ureteral obstruction, Day0


title: Karpas422_DMSO_R1


title: Group A1

description: stored at 4°C for 7d, and then transfer to 22°C for 1d, rep1


title: 5L

city: Toyoake

first: Juzoh

last: Umemori

address: 1-98 Kutsukakecho, Dengakugakubo

institute: Fujita Health University

description:
RNA from nuclei
5L_1-4

data_processing:
Cell Ranger v3.0.1 mkfastq pipeline was used to demultiplex and convert Chromium single cell 3’ RNA-sequencing barcode and read data to FASTQ files
Cell Ranger v3.0.1 count pipeline was used to generate align reads and gene-cell matrix
Cell Ranger aggr pipeline was used to combine data from multiple samples into an experiment-wide gene-barcode matrix and normalize data tothe same sequencing depth
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0) with a custum sequence (TDTOMATO_IRES_oPHR_flexi) derived from DIO-TdT-optoTrkB, a lentiviral vector
Supplementary_files_format_and_content: 10x genomics Cell Ranger output file (.h5)

source_name: Visual cortex

extract_protocol:
Nuclei extraction by Dounce homogenizer combined with filtration (35µm strainer) from visual cortex
10X Genomics Chromium Single Cell 3ʹ Gene Expression v3
3' sequencing of poly-adenylated mRNA

treatment_protocol: optpTrkB stimulatin (370nm blue LED exposure)

value: Neuron

tag: genetic modification

value: Infected with DIO-optoTrkB onto visual cortex of PV-cre mouse

tag: light stimulation

value: Light stimulated


title: dsRdRp [D3]

status: Public on Jan 05 2023

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description: Group D

data_processing:
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Rmats v3.2.5 with parameters -analysis U -t paired -a 8.
Gene expression level were calculated by RNA-Seq by Expectation Maximization (RSEM) using a protocol from Li, B. & Dewey, C. N., BMC Bioinformatics 12, 323 (2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include gene expression level for each Sample.

source_name: IEC4.1, dsRdRp

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extracted using RNeasy Mini Kit (QIAGEN Cat. No. 74104). Agilent 2100 or Fragment Analyzer was used to detect the quality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 platform.

tag: cell type

value: Intestinal epithelial

value: dsRdRp


title: dsRdRp [D1]

description: Group D

tag: treatment


title: dsCA [C1]

description: Group C

source_name: IEC4.1, dsCA

value: dsCA


title: dsCA [C3]

description: Group C


title: dsCA [C2]

description: Group C


title: dsCA+dsRdRp [F2]

description: Group F

source_name: IEC4.1, dsCA+dsRdRp

value: dsCA+dsRdRp


title: dsCA+dsRdRp [F3]

description: Group F


title: dsRdRp [D2]

description: Group D


title: CtrlsiRNA [B3]

description: Group B

source_name: IEC4.1, CtrlsiRNA

value: CtrlsiRNA


title: dsCA+dsRdRp [F1]

description: Group F


title: CtrlsiRNA [B2]

description: Group B


title: 190712_media_Plasmid

first: Julia

last: Joung

address: 75 Ames St

institute: Broad Institute

description: Other (plasmid DNA)

library_source: other

data_processing:
bcl2fastq 2.20.0
custom Python script to determine barcode distribution (see Methods)
Assembly: TF barcode sequences
Supplementary files format and content: Aggregated TF barcode counts determined using custom Python script for each condition
Library strategy: amplicon

molecule: other

organism: Escherichia coli

source_name: Plasmid library

extract_protocol:
Lentivirus RNA was extracted using the QIAmp Viral RNA Mini Kit (Qiagen 52906). Genomic DNA was extracted using the Quick-DNA Midiprep Plus Kit (Zymo D4075)
Lentivirus RNA was reverse transcribed using the qScript Flex cDNA Kit (VWR 95049-100) with a custom primer (see Methods). Libraries were prepared by PCR amplification of TF barcodes using custom primers (see Methods)

tag: differentiation protocol

tag: time point

tag: screen condition

value: Plasmid library


title: 6C

description:
RNA from nuclei
6C_1-4

tag: strain

value: Non-light stimulated


title: CtrlsiRNA [B1]

description: Group B

tag: cell line


title: PL, rep1

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

data_processing:
Primary data processing was performed by I2BC platform and consisted of: demultiplexing (with bcl2fastq2-2.18.12), adapter trimming (Cutadapt 1.15), quality control (FastQC v0.11.5), mapping (BWA v0.6.2-r126) against NDmed genome sequence (NCBI WGS project accession JPVW01000000); and aggregation as read counts for 4028 (featureCounts).
Fragment counts normalised per kilobase of feature length per million mapped fragments (fpkm) were computed with DESeq2 v1.30.1 based on robust estimation of library size.
Assembly: NCBI JPVW00000000.1
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: First 3 columns : locus tag in B. subtitilis NDmed genome (GenBank: JPVW00000000.1) ; corresponding locus tag in B. subtilis 168 reference genome (Genbank: AL009126.3) ; genes names in B. subtilis 168 as in Subtiwiki database (https://doi.org/10.1093/nar/gkab943).
Supplementary files format and content: Next 27 columns (9 cell types x 3 replicates) labelled from EX1.rawcounts to PL3.rawcounts : raw count of the number of reads mapped in each gene.
Supplementary files format and content: Last 27 columns (9 cell types x 3 replicates) labelled from EX1.log2fpkm to PL3.log2fpkm : log2(fpkm+5) for each gene.

organism: Bacillus subtilis

source_name: air-liquid pellicle

growth_protocol: Static liquid culture of 3mL of synthetic B-medium in 12-well microplates incubated at 30°C for 24 hours; 6 wells were used to collect one sample.

extract_protocol:
Cells were collected in Eppendorf tubes containing 500µl TRIzol reagent.
After centrifugation (8,000 g at 4°C for 30 seconds), the supernatant was drowned off and the pellet was snap-frozen in liquid nitrogen and stored at -80°C for later use.
Pellets were washed with 1ml TE + 60µl EDTA (10mM Tris, 1mM EDTA, pH=8) followed by centrifugation (8,000 g at 4°C for 30 seconds).
Pellets were then suspended in 1ml TRIzol reagent before transfer to a Fastprep screw cap tube containing 0.4g of glass beads (0.1mm).
Cells were disrupted by bead beating for 40 seconds 6.5m/s with FastPrep-24 instrument (MP Biomedicals, United states).
The supernatant was transferred to an Eppendorf tube and chloroform (Sigma-Aldrich, France) was added in a ratio of 1:5, followed by centrifugation (8,000 g at 4°C for 15 minutes).
The chloroform step was repeated twice before transfer of the aqueous phase was transferred to new Eppendorf, where sodium acetate (pH=5.8) was added to a final volume of 10% and 500µl of isopropanol (Sigma-Aldrich, France). Samples were left overnight at -20°C.
After centrifugation (8,000 g at 4°C for 20 minutes), pellets were washed twice by ethanol 75% and centrifugation  (8,000 g at 4°C for 15 minutes).
Then pellets were dried for 5 minutes under the hood. A RNA cleanup kit (Monarch RNA Cleanup Kit T2050, New England Biolabs, France) was used to further clean the RNA samples.
Nanodrop and Bioanalyzer instruments were used for quantity and quality controls.
Library construction and sequencing was performed by the I2BC platform (Gif-sur-Yvette, France).
Library construction was done using TruSeq Total RNA Stranded and Ribo-Zero Bacteria Illumina kits.
Sequencing was performed on an Illumina NextSeq 550 system using NextSeq 500/550 High Output Kit v2 to generate stranded single end reads (1 x 75bp).

value: air-liquid pellicle

tag: genotype

value: strain NDmed, wild-type

tag: growth medium

value: B-medium


title: WTN2  C57BL/6 mice, unilateral ureteral obstruction, Day0

value: ureter

value: unilateral ureteral obstruction


title: PL, rep3


title: DC, rep3

source_name: detached cells

value: detached cells


title: DC, rep1


title: SB, rep3

source_name: submerged biofilm

value: submerged biofilm


title: Group A2

description: stored at 4°C for 7d, and then transfer to 22°C for 1d, rep2

value: ripe melon fruits


title: PL, rep2


title: SB, rep1


title: TP, rep2

source_name: tips of dendrites on agar

growth_protocol: Plates (9cm diameter, Greiner bio-one, Austria) containing 25mL agar medium (0.7% agar) incubated at 30°C for 24 hours for cultures on semi-solid agar; 16 plates were used to collect one sample.

value: tips of dendrites on agar


title: DT, rep3

source_name: dendrites on agar

value: dendrites on agar


title: SB, rep2


title: TP, rep1


title: DT, rep2


title: BS, rep3

source_name: base of the dendrites on agar

value: base of the dendrites on agar


title: DT, rep1


title: MC, rep2

source_name: mother colony on agar

value: mother colony on agar


title: ST, rep3

source_name: planktonic stationary phase

growth_protocol: Shaken liquid culture of 10 mL of B-medium at 37 °C  sampled at OD600nm ~2.8

value: planktonic stationary phase


title: MC, rep3


title: BS, rep2


title: ST, rep2


title: MC, rep1


title: TP, rep3


title: ST, rep1


title: EX, rep3

source_name: planktonic exponential phase

growth_protocol: Shaken liquid culture of 10 mL of B-medium at 37 °C sampled at OD600nm ~0.6

value: planktonic exponential phase


title: EX, rep1


title: EX, rep2


title: Cell,SVA-infected virus,72h,rep2

city: 北碚区

first: 王

last: 晨

state: 重庆市

address: 天生路2号

department: 动物医学院

institute: 西南大学

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according   to the manufacturer’s instructions. After cluster generation, the library   preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp  Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according   to the manufacturer’s instructions. After cluster generation, the library   preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated
Raw data (raw reads) of fastq format were firstly processed through custom perl   and python scripts. In this step, clean datas(clean reads) were obtained by   removing reads containing ploy-N, with 5’ adapter contaminants, without 3’  adapter or the insert tag, containing ploy A or T or G or C and low quality reads   from raw data. At the same time, Q20, Q30, and GC-content of the raw datas  were calculated. Then, chose a certain range of length from clean reads to do all   the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et   al., 2009) without mismatch to analyze their expression and distribution on the   reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0  was used as reference, modified software mirdeep2(Friedlander et al., 2011) and   srna-tools-cli were used to obtain the potential miRNA and draw the secondary   structures. Custom scripts were used to obtain the miRNA counts as well as base   bias on the first position of identified miRNA with certain length and on each   position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA,   tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker,   Rfam database or those types of datas from the specified species itself.
Supplementary files format and content: Group3vsGroup1.Differential_analysis_results.xls

organism: Sus scrofa

extract_protocol:
SVA southwest strain was used to infect PK-15 cells (preserved in this laboratory). Cell culture in DMEM nutrient solution (Invitrogen, CA, USA) containing 10% FBS, which also contains 50 mg/mL penicillin/streptomycin antibiotic solution (Invitrogen, CA, USA), cultured under standard conditions of 5% CO2 and 37°C. PK-15 cells were infected by SVA (1.26×108 TCID50/mL), and cells were collected for high-throughput sequencing and stem ring PCR validation after 72 h infection.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA). Briefly, the piRNAs were ligated with 3′ and 5′ small RNA adapters and then converted to cDNA by reverse transcription using Illumina’s proprietary RT primers and amplification primers. PCR products were purified on an 8% polyacrylamide gel and bands corresponding to 140–160 bp were excised. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips according to the manufacturer’s instructions. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), following the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 2500/2000 platform.

value: Pig kidney cells

value: SVA-infected


title: Cell,SVA-infected virus,72h,rep1


title: Cell,non-infected virus,rep1

value: non-infected


title: Cell,non-infected virus,rep2


title: BS, rep1


title: Control group

city: Seoul

first: YONG JUN

last: CHOI

state: Seoul

address: Gangnam Severance Hospital 211 Eonjuro, Gangnam-gu Korea

department: Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Control

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Whole lung

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: Whole lung

tag: Sex

value: female

value: WT

value: BALB/c


title: Lung, MuHV-4, 8 d.p.i.

city: Liège

first: Bénédicte

last: Machiels

state: Liège

address: Avenue de Cureghem 7b, B43b

department: DMI

country: Belgium

institute: Université de Liège

description: 10x Genomics

data_processing:
Cell Ranger software (v.3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq), to perform alignment to mouse GRCm38/mm10 genome, filtering, UMI counting and to produce gene–barcode matrices (cellranger count).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
To harvest lung cells, mice were perfused with ice-cold PBS through the right ventricle. Then, lung lobes were collected into a C-Tube (Miltenyi) containing complete RPMI medium, 50 μg/mL liberase TM (Roche) and 100 µg/mL DNase I (Roche), before being processed with a gentleMACS dissociator (Miltenyi) and, finally incubated for 30 min at 37 °C.
Libraries preparations for single-cell immune profiling, sequencing, and post-processing of the raw data were performed at the GIGA-Genomics Core Facility (Belgium). Sorted cells were washed with 1X PBS (calcium and magnesium free) containing 0,04% weight/volume BSA (400 μg/mL). Cell concentration was adjusted to 1.000 total cells/μL and 12.800 cells were loaded on Chromium Controller (10x Genomics). Samples were further processed for droplet-based RNA sequencing and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10x Genomics). Amplified cDNA quality controls were performed with an Agilent bioanalyzer (Agilent) and final library profile were checked on Qiaxcel (Qiagen). Sequencing libraries were loaded in Illumina Novaseq sequencer with NovaSeq SP 100 v1 kit (Illumina, CA, USA) using the following read lengths: 28 bp for Read1 (18 bp Barcode + 10 bp Randomer), 8 bp for Sample Index and 88 bp for Read2. Library quantification was processed with KAPA Library quantification kit (KAPA Biosystems).

tag: age

value: 8 weeks old

value: Lung

value: All cells

tag: time

value: Day 8


title: PM/OVA group

description: Exposured to PM10 and ovalbumin

value: Particulate matter10 with ovalbumin


title: PM/OVA/Dex group

description: Exposured to PM10 and ovalbumin, treated with dexamethasone

value: Particulate matter10 with ovalbumin and dexamethasone


title: PM group

description: Exposured to PM10

value: Particulate matter10


title: PM/OVA/CPX group

description: Exposured to PM10 and ovalbumin, treated with Chitinase-1 inhibitor

value: Particulate matter10 with ovalbumin and Chitinase-1 inhibitor


title: Cell,SVA-infected virus,72h,rep3


title: Lung, MuHV-4, 28 d.p.i.

description: 10x Genomics

value: Day 28


title: Lung, MuHV-4, 5 d.p.i.

description: 10x Genomics

value: Day 5


title: Lung, untreated

description: 10x Genomics

value: Untreated


title: Lung, not infected, 1 dose of HDM

description: 10x Genomics

data_processing:
Cell Ranger software (v.3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq), to perform alignment to mouse GRCm38/mm10 genome, filtering, UMI counting and to produce gene–barcode matrices (cellranger count).
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: Not infected, 1 dose of hHDM


title: Lung, MuHV-4, no HDM

description: 10x Genomics

value: MuHV-4, no HDM


title: Macrophages, ILC2, infected mice, replicate 2

description: 10x Genomics

data_processing:
The nf-core/rnaseq pipeline (v.3.0) was used to generate the QC of the raw data and the count matrix.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

growth_protocol: All cells were high-speed sorted using a FACSAria Illu (BD Biosciences). 5.000 lung epithelial cells from C57BL/6 naïve mice were sorted (CD45-CD31-Epcam+ live cells) after depletion of CD45+ cells using using MojoSort™ Mouse anti-CD45 Nanobeads (Biolegend) according to the manufacturer’s protocol. 50.000 BM monocytes from C57BL/6 naïve mice were sorted (CD19-CD3-CD11b+Ly6C+ living cells), after depletion of Ly6G+ and B220+ cells using MojoSort™ Mouse anti-APC Nanobeads (Biolegend) and magnetic separation using LD columns (Miltenyi) according to the manufacturer’s protocol. Bone marrow monocytes and lung epithelial cells were co-cultured in 200 μL of RPMI 1640 medium containing Glutamax-I with 10% FCS, 1% MEM, 50 µM 2-mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin with or without 10 ng/ml recombinant murine GM-CSF (Peprotech). 3 days or not after the start of the co-culture, 2.500 ILC2s from mock- or MuHV-4 infected C57BL/6 mice (Lin-CD45+CD127+CD90.2+ST2+CD25+ living cells) were added with IL-2 (final concentration 10 ng/mL) and 15µg/mL InVivoMAb anti-mouse GM-CSF (BE0259, BioXcell) when specified.  Cells were analyzed 3 days after the addition of ILC2s and supernatant was used for analyzing cytokine levels.

extract_protocol:
From ex vivo co-culture, cells were harvested using Cell Dissociation Buffer (ThermoFisher) for 15 min in 37°C and then macrophages (FSC-Ahigh, CD11c+ living cells) were sorted using FACS and kept in TRIzol at -80°C. RNA from macrophages was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions, and quality was assessed on Agilent RNA 6000 Pico. cDNA was prepared using SmartSeq HT (1ng).
RNA-Seq libraries were prepared from 150ng (5μl at 30pg/μl), using the Illumina Nextera XT DNA Library Preparation Kit. Libraries were quantified and normalized by qPCR. Libraries were finally sequenced using Illumina NovaSeq6000 and bioinformatics analysis was performed. Approximately 25 × 106 75-base single-end reads were generated per sample.

value: Bone marrow

value: Monocytes

value: ILC2 from infected mice


title: Lung, MuHV-4, 1 dose of HDM

description: 10x Genomics

value: BALB/c

value: female

value: MuHV-4, 1 dose of HDM


title: DC, rep2

value: detached cells

value: strain NDmed, wild-type

value: B-medium


title: Cell,non-infected virus,rep3

value: Pig kidney cells

value: non-infected


title: Macrophages, ILC2, Mock mice, replicate 2

description: 10x Genomics

value: 8 weeks old

value: ILC2 from Mock mice


title: Macrophages, ILC2, Mock mice, replicate 3

description: 10x Genomics


title: Macrophages, ILC2, Mock mice, replicate 1

description: 10x Genomics


title: Lung, MuHV-4, 14 d.p.i.

description: 10x Genomics

value: Lung

value: All cells

value: Day 14


title: Macrophages, replicate 2

description: 10x Genomics

value: untreated


title: Macrophages, replicate 3

description: 10x Genomics

value: Bone marrow


title: Macrophages, replicate 1

description: 10x Genomics

value: Monocytes


title: Day 6 DMSO

city: montreal

first: Stephane

last: Richard

address: 3999 chemin de la cote sainte catherine

country: Canada

institute: McGill University

description:
musc4
d6
MuSCs cultured 4 days with DMSO then 2 days with DMSO removed.
scRNA-seq

data_processing:
Cell barcodes and UMI (unique molecular identifiers) barcodes were demultiplexed and paired-end reads were first aligned to the mouse genome (mm10) using the Cell Ranger software v3.1.0.
Pre-processing was then carried out with the Seurat v3.2.0 R package (Butler et al., 2018). Genes detected in less than 3 cells as well as cells containing less than 200 genes detected were removed.
Cells were further filtered out for each sample based on the distribution of genes detected as well as the percentage of mitochondrial counts to balance the number of cells per sample to ~4000, and the raw count matrices of all samples were merged. Read counts for each cell were then normalized by the cell total, multiplied by 10000 and natural-log transformed.
The expression of the 2000 genes with highest cell-to-cell variation was standardized and the heterogeneity associated with mitochondrial contamination was regressed out. Principal component analysis was performed on the scaled data and the top 10 principal components were used to construct a K-nearest neighbor cell graph. Clustering of cells was carried out through the Louvain algorithm with the granularity parameter set to 0.4 and visualized with the Uniform Manifold Approximation and Projection (UMAP) (Becht et al., 2019) dimensional reduction technique using the Scanpy v1.5.2 python module (Wolf et al., 2018).
Cluster biomarkers were identified using the Wilcoxon Rank Sum test. Cell trajectories across pseudotime were analyzed by the Monocle v2.16.0 R package (Trapnell et al., 2014). Cell progress was defined by differentially expressed genes based on the clusters identified by Seurat. The dimensionality of the data was reduced through the Discriminative Dimensionality Reduction with Trees (DDRTree) algorithm to two dimensions and the cells were ordered along the trajectory according to pseudotime. Genes with branch-dependent expression were identified through the branched expression analysis modeling (BEAM) test. RNA velocity analysis was performed by the scVelo v0.2.2 python module (Bergen et al., 2020). Spliced and unspliced mRNAs were first distinguished through the velocyto v0.17.17 python module (La Manno et al., 2018). Velocities representing the direction and speed of cell motion were then computed and projected onto the UMAP embedding.
Assembly: mm10 (GRCm38)
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

source_name: muscle stem cell

growth_protocol: Purified MuSCs were cultured in Ham's F10 (Gibco) with 20% FBS (HyClone), 2.5 ng/mL human recombinant bFGF (Gibco), 1% Penicillin/Streptomycin (Wisent Inc.).

extract_protocol: scRNA libraries were generated using the GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) and Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (P/N 120236 P/N 120237 10x Genomics). The sequencing ready libraries were purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin Elmer), and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824) as previously described (Couturier et al., 2020). Libraries were subsequently shipped and sequenced using Illumina NovaSeq6000 at IGM Genomics Center, UCSD, San Diego, CA.

treatment_protocol: Treated with 0.033% DMSO or 1 mM MS023 in 0.033% DMSO. The medium was changed on day 2 and day 4 of culturing.

value: WT

value: muscle stem cells

value: 4 days DMSO, then 2 days without DMSO


title: Day 0

description:
musc1
0h
FACS-sorted quiescent muscle stem cells.
scRNA-seq


title: Day 4 MS023

description:
musc3
d4MS023
MuSCs cultured 4 days with MS023.
scRNA-seq

value: 4 days MS023


title: Lung, not infected, 3 doses of HDM

description: 10x Genomics

value: BALB/c

value: female

value: Not infected, 3 doses of HDM


title: Lung, not infected, no HDM

description: 10x Genomics

value: Not infected, no HDM


title: Macrophages, ILC2, infected mice, replicate 3

description: 10x Genomics

value: ILC2 from infected mice


title: Day 4 DMSO

description:
musc2
d4
MuSCs cultured 4 days with DMSO.
scRNA-seq

value: 4 days DMSO


title: Macrophages, ILC2, infected mice, replicate 1

description: 10x Genomics

value: 8 weeks old


title: Day 6 MS023 removed at day 4

description:
musc5
d6MS023rd4
MuSCs cultured 4 days with MS023 then 2 days with MS023 removed.
scRNA-seq

value: 4 days MS023, then 2 days without MS023


title: Old LNSC Recomb 022

city: Chicago

first: Allison

last: Bennett

state: IL

address: 835 S WOLCOTT AVE

institute: University of Illinois at Chicago

data_processing:
Raw RNA-seq reads were assessed using FastQC.
Filtered reads were aligned to the mouse reference genome mm10 from Ensembl using STAR.
Genomic features were quantified against Ensembl annotations for mm10 using featureCounts.
Gene expression was normalized to counts per million units and averaged across sample groups.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing the raw gene counts for every gene in each sample.
Supplementary files format and content: Tab-delimited text file containing the normalized expression (abundance measurements) of every gene in all samples. Units are CPM (counts per million) and values in this table are in log2-scale, with a pseudo-count added to prevent taking the log of 0. Negative numbers simply indicate lower expression.

source_name: lymph node stromal cells

growth_protocol: Skin draining lymph nodes of C57BL/6 mice were digested using Dnase I, Dispase, and Collagenase IV into a single cell suspension. Cells were resuspended in endothelial cell media (Cell Biologics) and added to a 0.2% gelatin-coated 10cm dish in a 37C incubator. Media was changed every 3 days and after 7 days, lymph node cells were harvested. A CD45 magnetic bead depletion was then performed with the lymph node cell suspension to enrich for the presence of  lymph node stromal cells (LNSCs). LNSCs in endothelial cell media were then plated onto gelatin-coated 96-well plates.

extract_protocol:
LNSC wells were lysed with RLT buffer (QIAGEN) and RNA was extracted from lysates using the RNeasy Mini Kit (QIAGEN). RNA samples were DNAse treated prior to library construction. Each sample was derived from a single mouse and 8 samples per stimuli treatment (N=4 adult LNSCs and N=4 old LNSCs).
All RNA samples had a RIN score above 8. RNA samples were normalized to 50 ng and mRNA libraries were constructed using the Universal Plus mRNA-Seq kit (Tecan).

treatment_protocol: LNSCs in 96-well plates were stimulated for 20 hours at 37C with either 2ng/mL recombinant interferon alpha or supernantant from WNV-Kunjin infected bone-marrow derived dendritic cells. Untreated controls received only fresh endothelial cell media.

value: Old 18 months

value: Lymph Node Stromal Cell (LNSC)

value: 2 ng/mL recombinant IFNa


title: Old LNSC Recomb 024


title: Lung, MuHV-4, 3 doses of HDM

description: 10x Genomics

value: Lung

value: All cells

value: MuHV-4, 3 doses of HDM


title: Old LNSC Recomb 023


title: Adult LNSC BMDC 012

value: Adult 8-10 weeks

value: WNV-Kunjin infected BMDC supernatant


title: Old LNSC Control 006

value: Untreated (Cell media)


title: Old LNSC Recomb 021


title: Adult LNSC Recomb 019


title: Old LNSC BMDC 013


title: Old LNSC Control 008


title: Old LNSC BMDC 014


title: Adult LNSC BMDC 011


title: Adult LNSC BMDC 009


title: Old LNSC BMDC 015


title: Adult LNSC BMDC 010


title: Old LNSC BMDC 016


title: Adult LNSC Recomb 018


title: Old LNSC Control 005


title: Old LNSC Control 007


title: Adult LNSC Recomb 020


title: Adult LNSC Recomb 017


title: Adult LNSC Control 004


title: Adult LNSC Control 002


title: Adult LNSC Control 003


title: Adult LNSC Control 001


title: twi_MTD-Gal4_2-4_BS1

city: Berkeley

first: Benjamin

middle: Wendell

last: Booth

address: 1 Cyclotron Road

department: BioSciences

institute: Lawrence Berkeley National Laboratory

description: Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 1, 2-4 hours

data_processing:
Raw FASTQ files were aligned to the Drosophila melanogaster reference genome (Release 6)  using STAR aligner 2.7.3a  with default settings and up to 20 multiple alignments to produce BAM files.
HTSeq htseq-count v0.12.4 was used to determine read counts overlapping genes.
Differential gene expression in the RNAi experimental samples compared to the mCherry controls was determined using DESeq2 1.24.0.
bigWig files were created using a custom tool called bam2bedgraph to convert bam files into bedgraph files, then UCSC's bedGraphToBigWig to convert the bedgraph files to bigWig format.
Assembly: dm6
Supplementary files format and content: BAM alignment files aligning FASTQ read files to dm6 assembly using STAR 2.7.3a.
Supplementary files format and content: HTSeq htseq-count files produced with HTSeq v0.12.4
Supplementary files format and content: DESeq csv files produced using DESeq2 v1.24.0
Supplementary files format and content: bigWig files produced using custom bam2bedgraph script and UCSC bedGraphToBigWig tool

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Frozen embryos were homogenized using the Pellet Pestle Cordless Motor (Kimble Cat. No. 749540-0000; Pellet Pestles Sigma Cat. No. Z359947). RNA was extracted from the homogenate using TRIzol Reagent (Thermo Fisher, Cat. No. 15596026), chloroform extraction and isopropanol precipitation.  RNA was resuspended in Nuclease Free Water (Ambion AM9930) and incubated over night before purification using the RNeasy Mini Kit (QIAGEN Cat. No. 74106).  After Qiagen clean up, RNA was quantified using NanoDrop ND1000v 3.5.2.
Libraries for sequencing were made using TruSeq Stranded mRNA Library Prep (llumina 20020594).

value: embryos

value: shMTD-Gal4 (Control for twi)

tag: timepoint

value: 2-4 hours


title: twi_2-4_BS1

description:
Drosophila embryos RNAi, shtwi, replicate 1, 2-4 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000

tag: tissue

value: shtwi


title: twi_MTD-Gal4_16-18_BS1

description:
Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 1, 16-18 hours
Sequencing Instruments: Illumina NextSeq 500; Illumina HiSeq 4000

value: 16-18 hours


title: twi_MTD-Gal4_2-4_BS2

description: Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 2, 2-4 hours


title: twi_16-18_BS2

description: Drosophila embryos RNAi, shtwi, replicate 2, 16-18 hours


title: twi_MTD-Gal4_16-18_BS2

description: Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 2, 16-18 hours


title: twi_MTD-Gal4_0-1.5_BS1

description: Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 1, 0-1.5 hours

value: 0-1.5 hours


title: twi_MTD-Gal4_0-1.5_BS2

description: Drosophila embryos RNAi, shMTD-Gal4 (Control for twi), replicate 2, 0-1.5 hours


title: twi_2-4_BS2

description: Drosophila embryos RNAi, shtwi, replicate 2, 2-4 hours


title: zfh2_Sox102F_Hr3_mCherry_16-18_BS1

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 1, 16-18 hours


title: zfh2_Sox102F_Hr3_mCherry_0-1.5_BS2

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 2, 0-1.5 hours


title: zfh2_Sox102F_Hr3_mCherry_16-18_BS2

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 2, 16-18 hours


title: zfh2_0-1.5_BS2

description: Drosophila embryos RNAi, shzfh2, replicate 2, 0-1.5 hours


title: zfh2_12-14_BS1

description: Drosophila embryos RNAi, shzfh2, replicate 1, 12-14 hours

value: 12-14 hours


title: trh_6-8_BS2

description: Drosophila embryos RNAi, shtrh, replicate 2, 6-8 hours

value: shtrh

value: 6-8 hours


title: twi_0-1.5_BS1

description: Drosophila embryos RNAi, shtwi, replicate 1, 0-1.5 hours


title: zfh2_Sox102F_Hr3_mCherry_12-14_BS1

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 1, 12-14 hours


title: zfh2_0-1.5_BS1

description: Drosophila embryos RNAi, shzfh2, replicate 1, 0-1.5 hours


title: zfh2_Sox102F_Hr3_mCherry_12-14_BS2

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 2, 12-14 hours


title: twi_16-18_BS1

description: Drosophila embryos RNAi, shtwi, replicate 1, 16-18 hours


title: zfh2_16-18_BS2

description: Drosophila embryos RNAi, shzfh2, replicate 2, 16-18 hours


title: zfh2_12-14_BS2

description: Drosophila embryos RNAi, shzfh2, replicate 2, 12-14 hours


title: zfh2_Sox102F_Hr3_mCherry_0-1.5_BS1

description: Drosophila embryos RNAi, shmCherry (Control for zfh2, Sox102F, Hr3), replicate 1, 0-1.5 hours


title: trh_0-1.5_BS2

description: Drosophila embryos RNAi, shtrh, replicate 2, 0-1.5 hours


title: trh_0-1.5_BS1

description: Drosophila embryos RNAi, shtrh, replicate 1, 0-1.5 hours


title: trh_6-8_BS1

description: Drosophila embryos RNAi, shtrh, replicate 1, 6-8 hours


title: twi_0-1.5_BS2

description: Drosophila embryos RNAi, shtwi, replicate 2, 0-1.5 hours


title: trh_16-18_BS2

description: Drosophila embryos RNAi, shtrh, replicate 2, 16-18 hours


title: zfh2_16-18_BS1

description: Drosophila embryos RNAi, shzfh2, replicate 1, 16-18 hours


title: toe_0-1.5_BS2

description: Drosophila embryos RNAi, shtoe, replicate 2, 0-1.5 hours

value: shtoe


title: toe_16-18_BS1

description: Drosophila embryos RNAi, shtoe, replicate 1, 16-18 hours


title: toe_16-18_BS2

description: Drosophila embryos RNAi, shtoe, replicate 2, 16-18 hours


title: toe_6-8_BS1

description: Drosophila embryos RNAi, shtoe, replicate 1, 6-8 hours


title: toe_0-1.5_BS1

description: Drosophila embryos RNAi, shtoe, replicate 1, 0-1.5 hours


title: su(Hw)_16-18_BS2

description: Drosophila embryos RNAi, shsu(Hw), replicate 2, 16-18 hours

value: shsu(Hw)


title: trh_16-18_BS1

description: Drosophila embryos RNAi, shtrh, replicate 1, 16-18 hours


title: su(Hw)_2-4_BS2

description: Drosophila embryos RNAi, shsu(Hw), replicate 2, 2-4 hours


title: su(Hw)_0-1.5_BS2

description: Drosophila embryos RNAi, shsu(Hw), replicate 2, 0-1.5 hours


title: su(Hw)_0-1.5_BS1

description: Drosophila embryos RNAi, shsu(Hw), replicate 1, 0-1.5 hours


title: su(Hw)_16-18_BS1

description: Drosophila embryos RNAi, shsu(Hw), replicate 1, 16-18 hours


title: toe_6-8_BS2

description: Drosophila embryos RNAi, shtoe, replicate 2, 6-8 hours