title: p38i_An_IFNg rep3 (ATAC-seq_IFNg)

description: cell nuclei

data_processing:
Data were processed using the ATAC-seq pipeline from the nf-core framework (nfcore/atacseq v1.2.1;  Ewels et al., 2020; https://zenodo.org/record/3965985#.YA8a8GRKjZk) in conjunction with Docker (version 20.10.8; Merkel, 2014).
The command used was " nextflow run nf-core/atacseq --input design.csv --genome GRCm38 -profile docker -r 1.2.1 --min_reps_consensus 2".
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Assembly: mm10
Supplementary files format and content: Normalised genome-wide bigWig coverage files generated from merged BAM files included in the mergedReplicate folder of the nfcore pipeline.

source_name: WT p38i_An_IFNg, BMDM

extract_protocol:
Cells were washed twice in 1 mL ice-cold PBS, by centrifugation at 1200 g for 5 min. Cells were resuspended in 1 mL cold nuclei isolation buffer (0.32 M sucrose; 3 mM CaCl2; 2mM Mg Acetate; 0.1 mM EDTA; 10 mM Tris.HCl pH 8.0; 0.6% NP-40; 1mM DTT fresh) and placed on ice for 5 minutes. Cells were centrifuged at 700g for 5 min at 4°C. Supernatant was removed, 500 µL cold nuclei isolation buffer was added and samples were kept on ice for 3 min to further increase the number of isolated nuclei. Cells were centrifuged at 700g for 5 min at 4°C. Supernatants were removed and pelleted nuclei were gently resuspended in 200 µL cold Nuclei Resuspension Buffer (NRB) (50 mM Tris.HCl pH 8.3; 40% Glycerol; 5 mM MgCl2; 0.1mM EDTA). 50.000 nuclei (5µl) were resuspended in 7.5µl H2O, 12.5 µl TD buffer and 5 µl Tn5 transposase (Illumina). Nuclei were incubated for 30 min at 37 °C, while mixing on a plate shaker at 600 rpm. DNA was purified with Qiagen MinElute columns according to the manufacturer's instructions and eluted in 13µl of nuclease-free H2O.
12.5 µl purified DNA from the previous step were mixed with 5 µl 2.5 µM I7 index primer, 5 µl 2.5 uM I5 index primer (dual indexing), 2.5 µl Evagreen and 25 µl, 2x Q5 PCR Master Mix, (NEB). An end point PCR was run as follows: 5 min 72 ºC, 1 min 98 ºC, 10sec 98 ºC (5-7 cycles) 30sec 65 ºC (5-7 cycles), 60sec 72 ºC (NEB). The reaction was purified by adding 15 µl of SPRI beads prepared by the NGS facility (MBSpure beads) and incubated for 5 min at RT. The supernatant was transferred to a fresh well. 50µl of MBSpure beads were added and mixed well, incubated for 5 min at RT, magnetized, and the supernatant was removed. The beads were washed twice by adding 150 µl of 80% EtOH. Beads were dried for 30sec and DNA was eluted in 20 µl of nuclease-free water. The quality of the libraries was checked on a bioanalyzer to further determine the size distribution. Libraries were sequenced on a NovaSeq SP PE50.

treatment_protocol: 3x106 BMDM were seeded in 6cm non-treated tissue culture plates.The next day cells were stimulated for 140 minutes with Anisomycin (Sigma-Aldrich) alone, or either with 10ng/mL of murine IFNγ (a kind gift  from G. Adolf, Boehringer Ingelheim, Vienna) alone for 120 minutes or with Anisomycin (20 minutes pre-treatment) followed by 120 minutes stimulation with IFNγ or with p38i inhibitor (PH-797804; Selleckchem) (60 minutes pre-treatment) and Anisomycin (20 minutes pre-treatment) followed by 120 minutes stimulation with IFNγ.

value: wildtype


title: C57BL/6 Mouse, Liver, Red, 202

status: Public on Dec 18 2022

type: SRA

city: Houston

first: Michael

middle: P.

last: Dzakovich

state: TX

address: 1100 Bates Ave.

department: Pediatrics

country: USA

institute: USDA-ARS Children's Nutrition Research Center

description: Column name of samples listed in total counts file: NM-15-202

library_source: transcriptomic

data_processing:
Checked data quality using FASTQC
Removed adapters and trimmed low quality reads using Trimmomatic (ILLUMINACLIP: TruSeq3-PE-2.fa:20:30:10; MAXINFO: 40:0.7; MINLEN: 36; AVGQUAL: 20)
Aligned reads to mouse genome (GRCm38.p6) using the default settings of Rsubread
Checked for potential lane effects using multidimensional scaling and merged counts from both lanes using BAMtools
Genes with less than 0.37 counts per million (10/library size) and present in less than 11 samples total excluded from analysis
Resulting DGElist was TMM normalized and used for differential expression analysis in edgeR
Assembly: GRCm38.p6
Supplementary files format and content: Comma delimited CSV file of raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Male C57BL/6 mice were reared according to standards set by the American Association for Accreditation of Laboratory Animal Care (protocol #2010A00000095).

extract_protocol:
10 mg (± 2 mg) of preserved tissue was extracted with QIAshredders and RNEasy kits (Qiagen) according to manufacturer's directions
One µg of RNA was used to generate cDNA libraries which were prepared using the NEXTflex Rapid Directional RNA-Seq kit (PerkinElmer)

treatment_protocol: At four weeks of age, mice were randomly assigned treatment groups (n=11-12/group) and fed either a control diet, a diet supplemented with 10% (w/w) red tomato powder, or a diet supplemented with 10% (w/w) tangerine tomato powder.

tag: tissue

value: Liver

tag: age

value: 10 weeks

tag: Sex

value: Male

tag: strain

tag: treatment

value: AIN93G diet + 10% red tomato powder


title: An_c-Jun_rep1 (ChIP-seq)

city: Vienna

first: Laura

last: Boccuni

address: Dr-Bohr-Gasse, 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna

library_source: genomic

data_processing:
Raw data were processed using the ChIP-seq pipeline from the nf-core framework (nfcore/ChIP-seq v.1.2.2; Ewels et al., 2020; https://zenodo.org/record/3529400#.YA8YGmRKjZk) in conjunction with Docker (version 20.10.8; Merkel, 2014).
The command used was " nextflow run nf-core/chipseq --input design.csv  --genome GRCm38  -profile docker --min_reps_consensus 2 -r 1.2.2 --narrow_peak" .
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Assembly: mm10
Supplementary files format and content: Normalised genome-wide bigWig coverage files generated from merged BAM files with bamCompare from deeptools version 3.4.3 (https://zenodo.org/record/3965985#.Yh-DPejMJPZ) with  --scaleFactorsMethod readCount as method to scale the samples.
Supplementary files format and content: Peak .narrowPeak file were generated from the nfcore pipeline

molecule: genomic DNA

source_name: An_cJun, BMDM

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow isolated from femurs and tibias of 8- to 12-week-old mice. Femur and tibia were separated by cutting at the knee joint. Bones were flushed with Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) using a 5-mL syringe and a 25-gauge needle. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal calf serum (FCS) (Sigma-Aldrich), recombinant M-CSF, 100 units/ml penicillin, and 100 ng/ml streptomycin (Sigma-Aldrich). Cells were kept at 37°C and 5% CO2 and differentiated for 10 days.

extract_protocol:
Cells were washed 2x with ice cold PBS and crosslinked for 10 minutes at room temperature in 1% formaldehyde PBS (ThermoFisher #28906). The cross-linked chromatin was sheared by sonication, providing fragments of 200 - 1000 base pairs in length. Protein-DNA complexes were selectively immunoprecipitated using CREB,c-Jun and igG antibodies. The immunoprecipitated complexes were washed to remove non-specifically bound chromatin, the protein-DNA cross-link was reversed and proteins were removed by proteinase K digest. At least three IPs were pooled for each sample of the three biological replicates, in order to obtain enough DNA precipitated. The DNA associated with the complex was furthermore purified and used for ChIP-seq.
The library generation was carried out by the VBCF NGS facility (https://www.viennabiocenter.org/vbcf/next-generation-sequencing/). The chromatin quality was analyzed on an Agilent 2100 Bioanalyzer and a size selection of 200-1000bp was carried out.

treatment_protocol: 1.5 x 10^7 cells were seeded with 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 140 minutes with Anisomycin, or with with 10 ng/ml murine IFN-γ (a kind gift from G. Adolf, Boehringer Ingelheim, Vienna) for 120 minutes alone or in combination with 1 µM p38 inhibitor (PH-797804; Selleckchem) and 20µM JNK inhibitor (SP600125; Sigma Aldrich) for 60min pre-treatment followed by 20 minutes Anisomycin pre-treatment or the combination of the two inhibitors alone.

value: 8-12 weeks

value: Anisomycin

tag: chip antibody

value: c-Jun

tag: cell type

value: Bone marrow derived macrophage (BMDM)


title: An_IFNg rep3 (ATAC-seq_IFNg)

description: cell nuclei

source_name: WT An_IFNg, BMDM

tag: genotype


title: sample006

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.9) and multiqc (v1.6)
Alignment to the human genome using STAR (v2.7.9a)
Read count assessments using htseq-count (v0.11.3)
Assembly: GRCh38.104
Supplementary files format and content: count files, which are text files with counts per gene for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
2.5mL of whole blood was collected into PAXgene Blood RNA tubes (BD Biosciences; San Jose, CA, USA) and total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen; Germantown, MD, USA)
Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Ipswich, USA) and cDNA libraries were prepared using the NEBNext RNA First Strand Synthesis Module, NEBNext Ultra Directional RNA Second Strand Synthesis Module, and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB; Ipswich, USA)

value: Whole Blood

tag: disease state

tag: batch

value: one

tag: sampling group

value: early

tag: predicted endotype

value: NPS

tag: additional metadata

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: C57BL/6 Mouse, Liver, Tangerine, 198

description: Column name of samples listed in total counts file: NM-15-198

value: AIN93G diet + 10% tangerine tomato powder


title: sample005

value: IFN


title: C57BL/6 Mouse, Liver, Tangerine, 197

description: Column name of samples listed in total counts file: NM-15-197


title: C57BL/6 Mouse, Liver, Tangerine, 195

description: Column name of samples listed in total counts file: NM-15-195


title: C57BL/6 Mouse, Liver, Tangerine, 192

description: Column name of samples listed in total counts file: NM-15-192


title: IFNg rep3 (ATAC-seq_IFNg)

description: cell nuclei

source_name: WT IFNg, BMDM

value: IFNg


title: sample003

value: INF


title: C57BL/6 Mouse, Liver, Control, 188

description: Column name of samples listed in total counts file: NM-15-188

value: Liver

value: AIN93G diet


title: C57BL/6 Mouse, Liver, Control, 189

description: Column name of samples listed in total counts file: NM-15-189

value: 10 weeks

value: Male


title: sample002


title: An rep3 (ATAC-seq_IFNg)

description: cell nuclei

source_name: WT An, BMDM

value: wildtype

value: 8-12 weeks


title: UT rep3 (ATAC-seq_IFNg)

description: cell nuclei

source_name: WT UT, BMDM

value: untreated


title: sample001

value: IHD


title: C57BL/6 Mouse, Liver, Control, 183

description: Column name of samples listed in total counts file: NM-15-183


title: IFNg rep2 (ATAC-seq_IFNg)

description: cell nuclei

value: Bone marrow derived macrophage (BMDM)


title: C57BL/6 Mouse, Liver, Red, 186

description: Column name of samples listed in total counts file: NM-15-186

value: AIN93G diet + 10% red tomato powder


title: C57BL/6 Mouse, Liver, Control, 182

description: Column name of samples listed in total counts file: NM-15-182


title: p38i_An_IFNg rep2 (ATAC-seq_IFNg)

description: cell nuclei


title: C57BL/6 Mouse, Liver, Red, 177

description: Column name of samples listed in total counts file: NM-15-177


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 2

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo Street, BCC 305

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description:
C9-ALS/FTD 3_PIKFYVE_rep2
S23

data_processing:
Reads were aligned to the hg38 transcriptome using aligner STAR (v.2.7.8).
A gene count table was obtained using Partek E/M with Partek® Flow® software, v10.0
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed using Ingenuity Pathway Analysis (Qiagen)
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count values for each sample

source_name: neural

growth_protocol: Glia-free induced motor neurons were cultured in NeuroDiff media (NDM).

extract_protocol:
RNA was extracted using QIAGEN RNeasy Kits according to the manufacturer's instructions.
Illumina RNA NEB library preparation kit
3' RNA-seq libraries were generated using the Illumina RNA NEB library preparation kit at Novogene Ltd, according to the manufacturers’ directions. Libraries were sequenced at the Novogene on a Illumina NovaSeq 6000 sequencer. A total of 20 million to 30 million 150-bp, paired-end reads were obtained for samples.

treatment_protocol: iPSC-derived  iPSC-derived motor neurons treated with 9 μM of negative control ASO (NC ASO) or PIKFYVE ASO for three days.

value: neural

tag: cell line

value: induced neurons

value: motor neurons

value: C9ORF72 ALS/FTD

value: PIKFYVE ASO


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 3

description:
C9-ALS/FTD 3_PIKFYVE_rep3
S24


title: sample004

value: Whole Blood

value: one

value: late

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: An rep2 (ATAC-seq_IFNg)

description: cell nuclei

value: Anisomycin


title: C57BL/6 Mouse, Liver, Red, 175

description: Column name of samples listed in total counts file: NM-15-175

value: Liver

value: 10 weeks

value: Male


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with NC ASO replicate 3

description:
C9-ALS/FTD 3_NC_rep3
S21

value: NC ASO


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with NC ASO replicate 1

description:
C9-ALS/FTD 3_NC_rep1
S19


title: UT rep2 (ATAC-seq_IFNg)

description: cell nuclei

value: wildtype

value: 8-12 weeks

value: untreated


title: p38i_An_IFNg rep1 (ATAC-seq_IFNg)

description: cell nuclei

value: Bone marrow derived macrophage (BMDM)


title: An_IFNg rep2 (ATAC-seq_IFNg)

description: cell nuclei


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with NC ASO replicate 2

description:
C9-ALS/FTD 3_NC_rep2
S20

value: neural

value: induced neurons


title: C57BL/6 Mouse, Liver, Red, 170

description: Column name of samples listed in total counts file: NM-15-170

value: AIN93G diet + 10% red tomato powder


title: An_IFNg rep1 (ATAC-seq_IFNg)

description: cell nuclei


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 3

description:
C9-ALS/FTD 2_PIKFYVE_rep3
S18

value: motor neurons

value: C9ORF72 ALS/FTD

value: PIKFYVE ASO


title: IFNg rep1 (ATAC-seq_IFNg)

description: cell nuclei

value: IFNg


title: C57BL/6 Mouse, Liver, Red, 166

description: Column name of samples listed in total counts file: NM-15-166


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 1

description:
C9-ALS/FTD 2_PIKFYVE_rep1
S16


title: C57BL/6 Mouse, Liver, Tangerine, 160

description: Column name of samples listed in total counts file: NM-15-160

value: AIN93G diet + 10% tangerine tomato powder


title: C57BL/6 Mouse, Liver, Control, 159

description: Column name of samples listed in total counts file: NM-15-159

value: AIN93G diet


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 2

description:
C9-ALS/FTD 2_PIKFYVE_rep2
S17


title: An rep1 (ATAC-seq_IFNg)

description: cell nuclei

value: Anisomycin


title: UT rep1 (ATAC-seq_IFNg)

description: cell nuclei


title: C57BL/6 Mouse, Liver, Red, 157

description: Column name of samples listed in total counts file: NM-15-157

value: Liver

value: 10 weeks


title: C9ORF72 ALS/FTD 3 iPSC-derived motor neurons treated with PIKFYVE ASO replicate 1

description:
C9-ALS/FTD 3_PIKFYVE_rep1
S22


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with NC ASO replicate 3

description:
C9-ALS/FTD 2_NC_rep3
S15

value: NC ASO


title: p38i_An_IFNb rep3 (ATAC-seq_IFNb)

description: cell nuclei

source_name: WT p38i_An_IFNb, BMDM

treatment_protocol: 3x106 BMDM were seeded in 6cm non-treated tissue culture plates.The next day cells were stimulated for 140 minutes with Anisomycin (Sigma-Aldrich) alone, or either with 250 IU/mL of murine IFNβ (PBL interferon source) alone for 120 minutes or with Anisomycin (20 minutes pre-treatment) followed by 120 minutes stimulation with IFNβ or with p38i inhibitor (PH-797804; Selleckchem)(60 minutes pre-treatment) and Anisomycin (20 minutes pre-treatment) followed by 120 minutes stimulation with IFNβ.

value: wildtype


title: C57BL/6 Mouse, Liver, Red, 156

description: Column name of samples listed in total counts file: NM-15-156

value: Male


title: An_IFNb rep3 (ATAC-seq_IFNb)

description: cell nuclei

source_name: WT An_IFNb, BMDM

value: 8-12 weeks


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with NC ASO replicate 2

description:
C9-ALS/FTD 2_NC_rep2
S14


title: C57BL/6 Mouse, Liver, Control, 137

description: Column name of samples listed in total counts file: NM-15-137


title: C9ORF72 ALS/FTD 2 iPSC-derived motor neurons treated with NC ASO replicate 1

description:
C9-ALS/FTD 2_NC_rep1
S13


title: IFNb rep3 (ATAC-seq_IFNb)

description: cell nuclei

source_name: WT IFNb, BMDM

value: IFNb

value: Bone marrow derived macrophage (BMDM)


title: C57BL/6 Mouse, Liver, Control, 136

description: Column name of samples listed in total counts file: NM-15-136


title: fibroblast transcriptome rep 3

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
bigWig files were created using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: MRC-5 cells

growth_protocol: MRC5 cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (Corning), 1,000 Units/ml Penicillin-Streptomycin (Gibco) at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
For RNA extraction, cells were lysed in Trizol and total RNA was prepared using Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer’s instructions that include an on-column DNase digestion step.
RNA quality was assessed on a Bioanalyzer, and libraries were prepared using Illumina Ribo-zero kits according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSEQ6000 (100bp paired-end reads).
RNA-seq of rRNA-depleted RNA

value: MRC-5 cells


title: fibroblast transcriptome rep 2


title: UT rep3 (ATAC-seq_IFNb)

description: cell nuclei

value: untreated


title: C57BL/6 Mouse, Liver, Tangerine, 128

description: Column name of samples listed in total counts file: NM-15-128


title: C57BL/6 Mouse, Liver, Control, 122

description: Column name of samples listed in total counts file: NM-15-122


title: fibroblast transcriptome rep 1


title: PolII_Input_Rep3

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

extract_protocol:
After fixation, cells were lysed and sonication with a Bioruptor Plus sonication device (Diagenode). Sonication was conducted for 25 cycles, with 30 sec on/off at high intensity. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958 or Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the Illumina Chip-SEQ Kit multiplexed with IDT unique dual index barcodes. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequenced on an Illumina NovaSEQ6000 (100bp paired-end reads).

value: input


title: p38i_An_IFNb rep2 (ATAC-seq_IFNb)

description: cell nuclei


title: C57BL/6 Mouse, Liver, Control, 120

description: Column name of samples listed in total counts file: NM-15-120


title: PolII_Input_Rep2


title: IFNb rep2 (ATAC-seq_IFNb)

description: cell nuclei


title: An rep2 (ATAC-seq_IFNb)

description: cell nuclei


title: ST_virus_aACE2_2

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
In brief, demultiplexing was performed with sabre (parameters (P): pe -c -u -m 1 -l 10 -n), then trimmed with trimmomatic (P: SE -phred33 CROP:101 MINLEN:10 ). Fastq files were mapped to a custom GENCODE's GRCh38.p13 and SARS-CoV2 (RefSeq - NC_045512.2; ) genome (P: --outSAMattributes All --alignIntronMax 1000000 --alignEndsType Local), followed by indexing and sorting with sambamba and deduplication by je (P: MM=0 REMOVE_DUPLICATES=true ASSUME_SORTED=true ). Finally read counts were generated with Subread's featureCount.
In brief, genes with less than 5 raw read counts across all samples were removed, and genes with at least 1 count per million (CPM) in a minimum of 2 samples were kept. Prior to library size normalisation, normalisation factors were calculated with EdgeR’s calcNormFactors function. For differential gene expression analysis, normalization and transformation were performed with Limma’s  voom function. Differential gene testing was performed with Limma’s lmFit, makeContrasts, contrasts.fit, and eBayes functions. For visualization purposes, this data was log2 CPM transformed using EdgeR’s cpm function and parameters: prior = 1, log = TRUE, normalized.lib.sizes = TRUE. Correspondence analyses were performed with MADE4.
Genome_build: hg38 and SARS-CoV2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iTSC derived syncytiotrophoblast cells

growth_protocol: Induced trophoblast stem cells (iTSCs) were maintained as previously (Liu et al., 2020, Okae et al., 2018). Briefly, iTSCs were cultured in TSC medium consisted of DMEM/F-12, GlutaMAX (ThermoFisher) supplemented with 0.3% BSA (Sigma), 0.2% FBS (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1 mM 2-mercaptoethanol (ThermoFisher), 0.5% penicillin–streptomycin (ThermoFisher), 1.5 μg/ml l-ascorbic acid (Sigma), 5 μM Y27632 (ROCK inhibitor; Selleckchem), 2 μM CHIR99021 (Miltenyi Biotec), 0.5 μM A83-01 (Sigma), 1 μM SB431542, 50 ng/ml EGF (Peprotech) and 0.8 mM VPA (Sigma) onto 5 μg/ml collagen IV (Sigma-Aldrich)-coated plates. The iTSCs were routinely passaged every 4-5 days with medium replacement performed every other day.      Differentiation of iTSCs into STs was performed and modified as previously described (Okae et al., 2018). For the differentiation of iTSCs into STs, iTSCs were seeded at a density of 3.75 × 104 cells per well onto a 24-well plate pre-coated with 2.5 μg/ml collagen IV (Sigma) and cultured in 500 μl ST differentiation medium (DMEM/F-12, GlutaMAX (ThermoFisher) supplemented with 0.3% BSA (Sigma), 4% KSR (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1 mM 2-mercaptoethanol (ThermoFisher), 0.5% penicillin–streptomycin  (ThermoFisher), 2.5 μM Y27632 (Selleckchem) and 2 μM forskolin (Selleckchem)). Medium was replaced on day 3 of differentiation, and cells were analysed on day 6.

extract_protocol:
RNA was extracted from cells using RNeasy micro kit (74004, Qiagen)  and QIAcube (Qiagen); or miRNeasy micro kit (217084, Qiagen) according to the manufacturer’s instructions. Reverse transcription was then performed using QuantiTect reverse transcription kit (Qiagen, catalogue no. 205311).
Briefly index is added during  initial pA priming and pooled samples amplified using template switching  oligo. P5 is added by PCR and P7 by Nextera transposase.

treatment_protocol: Virus: Placental cells (TSCs, terminally differentiated EVTs/STs and differentiating STs) in 24 well plates were infected in duplicate or triplicate with 104 tissue-culture infectious dose 50 (TCID50) of SARS-CoV-2; ACE2 Blockade: For ACE2 blockade, placental cells were treated with either 20 μg/ml of both WCSL141 and WCSL148 or 40 μg/ml of human IgG1 isotype control for 30 mins prior to SARS-CoV-2 infection as above. Following virus removal, cells were cultured in media containing 20 μg/ml of both ACE2-blocking antibodies or 40 μg/ml of isotype control until the end of the experiment. Infectious virus titres and genome copies were determined as above. Each experiment was repeated independently twice.  (Australia/VIC01/2020) for 1h. Virus was removed and cells cultured in cell type-specific medium for 3 days. Supernatants were collected and medium replaced daily. Median TCID50 in supernatants were determined by 10-fold serial dilution in Vero cells and calculated using the Reed and Muench method. RNA was extracted from supernatants using the QIAamp Viral RNA mini kit (Qiagen) and E-gene expression assessed using the SensiFAST Probe No-Rox One Step Kit (Bioline) and the following primers/probes: Fwd: 5’-ACAGGTACGTTAATAGTTAATAGCGT’-3, Rev: ATATTGCAGCAGTACGCACACA and Probe: FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ. Viral genomes were interpolated using a standard curve generated by a plasmid containing the E-gene. Each experiment was repeated independently at least twice. ACE2 Blockade: For ACE2 blockade, placental cells were treated with either 20 μg/ml of both WCSL141 and WCSL148 or 40 μg/ml of human IgG1 isotype control for 30 mins prior to SARS-CoV-2 infection as above. Following virus removal, cells were cultured in media containing 20 μg/ml of both ACE2-blocking antibodies or 40 μg/ml of isotype control until the end of the experiment. Infectious virus titres and genome copies were determined as above. Each experiment was repeated independently twice.

value: Infected + aACE2 Ab

value: WT


title: ST_virus_aACE2_3


title: PolII_ChIP_Rep3

value: Pol II


title: UT rep2 (ATAC-seq_IFNb)

description: cell nuclei


title: PolII_ChIP_Rep2


title: An rep3 (ATAC-seq_IFNb)

description: cell nuclei


title: C57BL/6 Mouse, Liver, Red, 133

description: Column name of samples listed in total counts file: NM-15-133

value: AIN93G diet + 10% red tomato powder


title: p38i_An_IFNb rep1 (ATAC-seq_IFNb)

description: cell nuclei


title: PolII_ChIP_Rep1


title: An_IFNb rep1 (ATAC-seq_IFNb)

description: cell nuclei


title: RNAseq_24hpi_rep_2

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
bigWig files were created using deepTools
Genome_build: hg19
Genome_build: HHV5 (HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-reference-genomes.git)
Supplementary_files_format_and_content: bigWig files

organism:
Homo sapiens
Human betaherpesvirus 5

growth_protocol: HCMV MRC5 infected with TB40/Ewt-GFP were kept in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (Corning), and 1,000 Units/ml Penicillin-Streptomycin (Gibco) at 37°C in a humidified incubator at 5% CO2.

treatment_protocol: For each infection, 5x10^6 MRC5 were seeded in 15 cm dishes the day before the infection. The following day, medium was replaced with 10ml of DMEM supplemented with 10% FBS without antibiotics. Confluent MRC5 were infected with HCMV at a multiplicity of infection (MOI) of 2 with TB40/Ewt-GFP. After 1-hour incubation at 37°C, 10 ml of media without antibiotics were added to the plate and the cells incubated at 37°C for 23 hours. Cells were collected at 24hpi.

tag: infection

value: TB40/E wtGFP strain of HCMV

value: infected, 24 hpi


title: ST_virus_aACE2_1


title: RNAseq_24hpi_rep_1


title: H3K27Ac_Input_Rep3


title: IFNb rep1 (ATAC-seq_IFNb)

description: cell nuclei


title: H3K27Ac_24hpi_ChIP_Rep2

description: ChIPseq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using deepTools
Genome_build: hg19
Genome_build: HHV5 (HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-reference-genomes.git)
Supplementary_files_format_and_content: bigWig files

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies)


title: H3K27Ac_Input_Rep2


title: H3K27Ac_24hpi_ChIP_Rep1

description: ChIPseq


title: An rep1 (ATAC-seq_IFNb)

description: cell nuclei

value: Anisomycin


title: ST_virus_1

value: Infected + isotype control Ab


title: ST_virus_2


title: An_IFNb rep2 (ATAC-seq_IFNb)

description: cell nuclei

value: wildtype


title: PolII_Input_Rep1


title: H3K27Ac_24hpi_Input_Rep2

description: input


title: UT rep1 (ATAC-seq_IFNb)

description: cell nuclei


title: ST_ctr_aACE2_2

value: Control + aACE2 Ab


title: H3K27Ac_ChIP_Rep3


title: H3K27Ac_24hpi_Input_Rep1

description: input


title: Chondrocyte scRNAseq

city: Oklahoma City

first: Timothy

middle: M

last: Griffin

state: OK

address: 825 NE 13th St

department: Aging and Metabolism

institute: OMRF

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
RNA-seq reads were aligned and counted using CellRanger version 4.0.0 with default settings
CellRanger output was demultiplexed, concatenated, and analyzed using Seurat version 4.0.3
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: FASTQs, MarketMatrix (.tsv and .mtx), and Seurat object (.Rdata)

source_name: cartilage

growth_protocol: Chondrocytes extracted from neonatal cartilage were cultured at 37ºC and 5% CO2 in 1 ml DMEM (Life Technology, 10567014) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin. Confluent cells were released by Trypsin-EDTA digestion, washed, filtered and suspended in 1X PBS with 1% BSA for single cell genomics

extract_protocol:
a single cell suspension was added to the Chromium controller
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: cultured primary chondrocytes

tag: mouse strain


title: ST_virus_3


title: ST_ctr_aACE2_1


title: H3K27Ac_ChIP_Rep2


title: PolII_24hpi_ChIP_Rep2

description: ChIPseq

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: ST_ctr_3

value: Control + isotype control Ab


title: Lumbar microglia, SNTr48h

city: San Francisco

first: Wulin

last: Tan

state: California

address: Room 345, Rock Hall, 1550 4th St

department: Anesthesia

institute: UCSF

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
fastq files were processed by CellRanger 2.1.1.
Read alignment and count summarization were performed using CellRanger v2.1.1 CellRanger count.
Counts from different samples were aggregated using CellRanger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain read counts for all cells in a matrix; genes.tsv files contain Ensembl IDs and gene symbols; barcode.tsv files contain the 10X barcodes to identify cells.

source_name: lumbar microglia

extract_protocol:
lumbar cords were dissected. microglia were sorted by cx3cr1-YFP(+).
Chromium Next GEM Automated Single Cell 3′ Library and Gel Bead Kit v3.1 (10X genomics)

treatment_protocol: sciatic nerve transection

value: lumbar cord

value: microglia

value: injury 48h


title: PolII_24hpi_ChIP_Rep1

description: ChIPseq

value: MRC-5 cells


title: H3K27Ac_ChIP_Rep1


title: Lumbar microglia, SNTr24h

value: injury 24h


title: SCLC2

city: Los Angels

first: Xuexi

last: Zhang

address: AHSP A9404, 8700 Beverly Blvd

department: Medicine

institute: Cedars Sinai Medical Center

data_processing:
We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 3.0.0 and Seurat suite version 3.0.0 for downstream analysis.
For clustering, principal-component analysis was performed for dimension reduction.
Top 10 principal components (PCs) were selected by using a permutationbased test implemented in Seurat and passed to t-SNE for clustering visualization. Seq version 3.1.0 integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters. The Benjamini-Hochberg procedure was used for correcting errors of multiple testing.

source_name: human SCLC

extract_protocol:
Resected tumor was transported in MACS Tissue Storage Solution (Miltenyi Biotec) on ice immediately after surgical procurement. A small fragment was fixed in 4% paraformaldehyde (Solarbio) at 4 °C overnight and then paraffin embedded for immunohistochemical analysis and whole-exome sequencing (WES). Remaining tumor was minced into tiny cubes (<1 mm3), and enzymatically digested with MACS tumor dissociation kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C, according to the manufacturer’s instructions. After digestion, the cells were centrifuged at 400 g at 4 °C for 5 min, and then resuspended in 100U/ml DNase I (Sigma-Aldrich Cat# D4527) and incubated at 37 °C for 15 min. After filtering and centrifuge, the pellet was suspended in red blood cell lysis buffer (Solarbio) and incubated on ice for 2 min to lyse red blood cells. And the solution diluted with HBSS then centrifuged (600 g, 5 minutes, 4°C). The supernatant was removed, and the cells resuspended in appropriate solution for further analysis.
The protoplast suspension was loaded into Chromium microfluidic chips with 30 v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina nova6000 according to the manufacturer’s instructions (Illumina).

tag: sample type

value: Sorted human lung SCLC cells

value: SCLC

tag: assay

value: scRNA-sequencing


title: Lumbar microglia, naïve

tag: tissue

value: naïve


title: PolII_24hpi_Input_Rep2

description: input

value: TB40/E wtGFP strain of HCMV

value: infected, 24 hpi


title: PolII_24hpi_Input_Rep1

description: input


title: ST_ctr_1

value: WT


title: ST_ctr_2


title: SCLC1


title: ST_ctr_aACE2_3


title: H3K27Ac_Input_Rep1

value: input


title: E24h-3 input

status: Public on Dec 17 2022

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
The adapters and low quality bases were removed by using fastp(v0.20.0)
The rRNA reads were removed by using Bowtie2(v2.2.5)
The Fastq files were aligned to the reference genome using HISAT2 (v2.1.0)
The m6A peak calling by using exomepeak2 (v1.0.0)
Sequence motifs on m6A peaks were identified by HOMER
Assembly: Spodoptera frugiperda
Supplementary files format and content: bed

organism: Spodoptera frugiperda

source_name: Embryo

growth_protocol: The S. frugiperda was maintained in our laboratory and larvae were fed on artificial diet consisting of soybean powder, wheat germ, and yeast as described previously (Pinto et al., 2019). The pests were kept under controlled conditions with the temperature 26 ± 1°C, relative humidity 70 ± 10%, photoperiod 12 h light/12 h dark. The adult pest was fed on 5% sugar water.

extract_protocol:
Embryos were collected, flash frozen on dry ice, and total RNAs were extracted using Trizol reagent, and the mRNA was enriched by Oligo(dT) beads and fragmented into 100-nucleotide-long fragments using fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl PH 7.0). The short fragments were divided into two parts: one was captured with m6A specific antibody for enrichment of mRNA with m6A modification, the other was the input data without capture using m6A antibody for the transcriptomic library construction.
The mRNA was enriched by Oligo(dT) beads and fragmented into 100-nucleotide-long fragments using fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl PH 7.0). The short fragments were divided into two parts: one was captured with m6A specific antibody for enrichment of mRNA with m6A modification, the other was the input data without capture using m6A antibody for the transcriptomic library construction. The enriched RNA was reverse transcribed into cDNA with random primers by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, New England Biolabs, Ipswich, MA, USA). Next, the cDNA fragments were end-repaired and ligated to Illumina sequencing adapters. Finally, we got qualified library for sequencing using Illumina NovaSeqTM 6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: A large number of the embryos from 2 h and 24 h after oviposition were collected.

tag: developmental stage

value: 24 h embryos after oviposition

value: Embryo

tag: antibody


title: E24h-2


title: E24h-1 input


title: E24h-3


title: E24h-2 input


title: E24h-1


title: E2h-3 input

value: 2 h embryos after oviposition


title: E2h-3


title: E2h-2 input


title: E2h-1 input


title: E2h-2


title: E2h-1


title: vein_B1: Vein, diestrus, rep 1

city: Beijing

first: Yiran

last: Zhou

address: 38 Xueyuan Rd

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, including those containing more than 5% of unknown nucleotides or more than 20% of low-quality (Q-value no larger than 10) bases.
Reads that passed the above filtration and quality control were mapped to GRCm38.p5 from NCBI, by using Bowtie2 (v2.2.5) with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Gene abundances were quantified by RSEM software (v1.2.8) with default parameters. The gene expression level was normalized by using Fragments Per Kilobase of transcript per Million mapped reads (FPKM) method, where the number of fragments mapped to the specific gene was normalized by the total number of fragments that mapped to reference genes and the number of bases on this specific gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Vein

growth_protocol: Female 10-week-old C57BL/6 mice were raised in standard cages in a temperature- and humidity-controlled environment, on a 12-h light/dark cycle, with regular feeding and free access to water. All animal care and experimental protocols complied with the Declaration of Helsinki, Animal Management Rules of the Ministry of Health of the People’s Republic of China and the guide for the Care and Use of the Laboratory Animals of Peking University. The protocol was approved by the Peking University Animal Ethics Committee.

extract_protocol:
Tissues were harvested and frozen on dry ice. Total RNA was extracted by using mRNA Enrichment Protocol according to the manufacturer's guideline.
RNA libraries were prepared for sequencing using BGISEQ-500.

treatment_protocol: The vaginal secretions collected from the same batch of mice were stained with methylene blue to identify the estrus cycle that the mice experienced. Those who were in estrus or diestrus would be divided into two groups.One group is for mice during estrus,the other is for mice during distrus.

tag: strain

tag: age

value: 10 weeks

tag: Sex

value: female

tag: period

value: diestrus

value: Vein


title: womb_A1: Womb, estrus, rep 1

source_name: Womb

value: estrus

value: Womb


title: stomach_A2: Stomach, estrus, rep 2

source_name: Stomach

value: Stomach


title: vein_A1: Vein, estrus, rep 1


title: WAT_A1: White adipose tissue, estrus, rep 1

source_name: White adipose tissue

value: White adipose tissue


title: womb_A3: Womb, estrus, rep 3


title: stomach_A3: Stomach, estrus, rep 3


title: WAT_B3: White adipose tissue, diestrus, rep 3


title: womb_A2: Womb, estrus, rep 2


title: stomach_B1: Stomach, diestrus, rep 1


title: vein_B2: Vein, diestrus, rep 2


title: womb_B3: Womb, diestrus, rep 3


title: WAT_B1: White adipose tissue, diestrus, rep 1


title: WAT_A3: White adipose tissue, estrus, rep 3


title: WAT_A2: White adipose tissue, estrus, rep 2


title: womb_B1: Womb, diestrus, rep 1


title: vein_A3: Vein, estrus, rep 3


title: stomach_A1: Stomach, estrus, rep 1


title: spleen_B3: Spleen, diestrus, rep 3

source_name: Spleen

value: Spleen


title: WAT_B2: White adipose tissue, diestrus, rep 2


title: vein_A2: Vein, estrus, rep 2


title: stomach_B3: Stomach, diestrus, rep 3


title: spleen_A3: Spleen, estrus, rep 3


title: spleen_A2: Spleen, estrus, rep 2


title: vein_B3: Vein, diestrus, rep 3


title: spleen_B2: Spleen, diestrus, rep 2


title: spleen_A1: Spleen, estrus, rep 1


title: spleen_B1: Spleen, diestrus, rep 1


title: womb_B2: Womb, diestrus, rep 2


title: stomach_B2: Stomach, diestrus, rep 2


title: ovary_B2: Ovary, diestrus, rep 2

source_name: Ovary

value: Ovary


title: ovary_B3: Ovary, diestrus, rep 3


title: muscle_B3: Muscle, diestrus, rep 3

source_name: Muscle

value: Muscle


title: liver_B2: Liver, diestrus, rep 2

source_name: Liver

value: Liver


title: ovary_A3: Ovary, estrus, rep 3


title: ovary_A1: Ovary, estrus, rep 1


title: muscle_B1: Muscle, diestrus, rep 1


title: kidney_B2: Kidney, diestrus, rep 2

source_name: Kidney

value: Kidney


title: liver_A1: Liver, estrus, rep 1


title: muscle_A1: Muscle, estrus, rep 1


title: muscle_A2: Muscle, estrus, rep 2


title: liver_A3: Liver, estrus, rep 3


title: muscle_A3: Muscle, estrus, rep 3


title: liver_B1: Liver, diestrus, rep 1


title: liver_B3: Liver, diestrus, rep 3


title: ovary_A2: Ovary, estrus, rep 2


title: muscle_B2: Muscle, diestrus, rep 2


title: kidney_A2: Kidney, estrus, rep 2


title: kidney_B1: Kidney, diestrus, rep 1


title: kidney_B3: Kidney, diestrus, rep 3


title: hypo_B3: Hypothalamus, diestrus, rep 3

source_name: Hypothalamus

value: Hypothalamus


title: hypo_B2: Hypothalamus, diestrus, rep 2


title: hypo_A1: Hypothalamus, estrus, rep 1


title: hypo_A3: Hypothalamus, estrus, rep 3


title: kidney_A1: Kidney, estrus, rep 1


title: hypo_A2: Hypothalamus, estrus, rep 2


title: liver_A2: Liver, estrus, rep 2


title: ovary_B1: Ovary, diestrus, rep 1


title: kidney_A3: Kidney, estrus, rep 3


title: heart_B3: Heart, diestrus, rep 3

source_name: Heart

value: Heart


title: duo_B3: Duodenum, diestrus, rep 3

source_name: Duodenum

value: Duodenum


title: heart_A1: Heart, estrus, rep 1


title: heart_A2: Heart, estrus, rep 2


title: duo_A1: Duodenum, estrus, rep 1


title: duo_B1: Duodenum, diestrus, rep 1


title: duo_A2: Duodenum, estrus, rep 2


title: duo_A3: Duodenum, estrus, rep 3


title: heart_B2: Heart, diestrus, rep 2


title: heart_A3: Heart, estrus, rep 3


title: cerebrum_B1: Cerebrum, diestrus, rep 1

source_name: Cerebrum

value: Cerebrum


title: cerebrum_A2: Cerebrum, estrus, rep 2

value: 10 weeks


title: BAT_B3: Brown adipose tissue, diestrus, rep 3

source_name: Brown adipose tissue

value: female

value: Brown adipose tissue


title: cerebrum_A3: Cerebrum, estrus, rep 3


title: cerebrum_B3: Cerebrum, diestrus, rep 3

value: diestrus


title: cerebrum_A1: Cerebrum, estrus, rep 1

value: estrus


title: cerebrum_B2: Cerebrum, diestrus, rep 2


title: BAT_B1: Brown adipose tissue, diestrus, rep 1


title: BAT_B2: Brown adipose tissue, diestrus, rep 2


title: BAT_A2: Brown adipose tissue, estrus, rep 2


title: aorta_B3: Aorta, diestrus, rep 3

source_name: Aorta

value: Aorta


title: BAT_A3: Brown adipose tissue, estrus, rep 3


title: aorta_B2: Aorta, diestrus, rep 2


title: aorta_A3: Aorta, estrus, rep 3


title: hypo_B1: Hypothalamus, diestrus, rep 1


title: aorta_A2: Aorta, estrus, rep 2


title: duo_B2: Duodenum, diestrus, rep 2


title: aorta_B1: Aorta, diestrus, rep 1


title: aorta_A1: Aorta, estrus, rep 1


title: heart_B1: Heart, diestrus, rep 1


title: COS: passion fruit seeding leaves, 5% amino-oligosaccharide agent-treated group,rep2

city: Guiyang

first: liqun

state: Guizhou

address: Jiaxiu South Road, Huaxi District

institute: GZ university

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.  All downstream analyses were based on clean data of high quality.
Assembly: De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Supplementary files format and content: All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of Evalue<0.00001.
Supplementary files format and content: Differentially expressed Unigene analysis:Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.

organism: Passiflora edulis

source_name: seedling leaves

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp).And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: seedling leaves

tag: treatment

value: 5% amino-oligosaccharide AS


title: BAT_A1: Brown adipose tissue, estrus, rep 1


title: P7

city: Shanghai

first: Shaocong

last: Mo

address: 12th Urumqi middle road

institute: Huashan Hospital, Fudan University

description: Colonic mucosa

data_processing:
fastqc was used for quanlity control
Trim-galore was used for filtering
Hisat2 was used for blasting to GRh38
samtools was used for sorting
featurecount was used for counting
Assembly: GRh38.release105
Supplementary files format and content: counts
Supplementary files format and content: counts

source_name: Colon

extract_protocol:
total RNA was extracted by Trizol
Poly (A) RNA from 1 mg total mRNA were used to generate the cDNA libraries, respectively, according to TruSeq RNA Sample Prep Kit protocol.

value: Colon


title: P4

description: Colonic mucosa


title: P1

description: Colonic mucosa


title: td-Hepa-YC (D28)-7

first: Meng

middle: meng

last: Jiang

address: number 3728, Jinke Road

institute: Shanghai Institute of Materia Medica

data_processing:
RNA-seq data were uniquely mapped to mm10 reference genome by TopHat v1.4.1
Expression values were assigned to gene level by Cufflinks v1.3.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene id and RPKM value

source_name: liver

extract_protocol:
Mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA library for RNA-seq was prepared as flows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: liver

tag: genotype

value: Fah-/-

value: mice transplanted with td-Hepatocytes and then treated with YC for 28 days after NTBC withdrawal


title: td-Hepa-YC (D28)-2


title: td-Hepa-YC (D28)-4


title: P2

description: Colonic mucosa


title: td-Hepa-YC (D28)-3


title: P6

description: Colonic mucosa


title: td-Hepa-YC (D28)-1


title: P5

description: Colonic mucosa


title: td-Hepa-YC (D28)-6


title: P3

description: Colonic mucosa


title: td-Hepa-YC (D28)-5


title: td-Hepa-Vehicle (D28)-7

value: mice transplanted with td-Hepatocytes and then treated with vehicle for 28 days after NTBC withdrawal


title: td-Hepa-Vehicle (D28)-8


title: td-Hepa-Vehicle (D28)-6


title: td-Hepa-Vehicle (D28)-3


title: siWTAP+H. pylori

city: Hong Kong

first: Judeng

last: ZENG

address: Room 902, Li Ka Shing Medical Science Building, Prince of Wales Hospital

institute: The Chinese University of Hong Kong

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to perform quality control.
Reads mapping to the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Hg38
Supplementary files format and content: processed data_counts.xlsx (counts values for each sample)

growth_protocol: The stored (at -80℃) H. pylori strains were spread on the horse blood agar plates (Thermo Fisher, PB0122A) and grown in an anaerobic jar with a microaerobic environment (Oxoid CampyGen 2.5L Sachet, Thermo Fisher, CN0025A) at 37℃ for 4 - 5 days. Human gastric epithelial cell line HFE145 was cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Thermo Fisher, 11995065) supplemented with 10% Fetal Bovine Serum (FBS, Gibco, Thermo Fisher, A4766801) at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted form treated cells using RNAiso reagent (Takara, 9109) according to the manufacturer’s instructions.
Library construction and sequencing services were provided by Novogene using the Illumina Novaseq 6000 system (Novogene, Tianjin, China) following a standard protocol.

treatment_protocol: HFE145 cells transfected with negative control or 20 nM WTAP siRNAs were infected with or without H. pylori (MOI 1:100) for 24 hours.

tag: cell type

value: Normal gastric epithelial cell

value: Cells transfected with 20 nM WTAP siRNAs were co-cultured with H. pylori (MOI 1:100) for 24 hours


title: td-Hepa-Vehicle (D28)-5


title: CK: passion fruit seeding leaves,CK group,rep2

value: the solvent without compound solution


title: td-Hepa-Vehicle (D28)-4


title: td-Hepa-Vehicle (D28)-2


title: siWTAP

value: Cells transfected with 20 nM WTAP siRNAs


title: Fah (D0)-7

value: Normal liver


title: Fah (D0)-2


title: siNC

value: Cells transfected with negative control


title: Fah (D0)-4


title: U2OS, 3hdex, input, rep2

city: Boulder

first: Nickolaus

middle: Charles

last: Lammer

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado, Boulder

data_processing:
Reads were tagged with UMIs using UMI-tools (v1.1.2). Reads were then trimmed using Trim Galore (v0.6.6) using the options: --2colour 20, --paired.
Trimmed reads were aligned to the hg38 genome assembly using STAR (v2.7.3a) and deduplicated using UMI-tools (v1.1.2) using the options: --paired, --unpaired-reads discard, --chimeric-pairs discard.
Deduplicated read coverage over gene bodies was counted using featureCounts (Rsubread v2.0.1, R v4.0.3) and Gencode v39 gene annotations.
Assembly: hg38
Supplementary files format and content: rip_gene_stranded_counts.csv: Matrix containing counts of deduplicated reads over gene bodies for each gene in each sample.

growth_protocol: Cells were cultured at 37°C with 5% CO2. Cells were grown to about 15 million cells in DMEM supplemented with 10% charcoal-stripped FBS and 1X Pen-strep (100 U/ml penicillin, 100 µg/ml streptomycin).

extract_protocol:
Harvested cells were lysed with a Bioruptor (Diagenode, UCD-200) and GR-HaloTag was pulled down using Magne HaloTag beads (Promega). Input samples were taken before mixing samples with beads. After denaturing and high salt washes, RNA was liberated from the beads using proteinase K (New England Biolabs). RNA was isolated and purified using TRIzol and the RNeasy MinElute cleanup kit (QIAGEN). Input samples were treated the same way excluding bead wash steps.
Libraries were prepared using the KAPA RNA HyperPrep kit with RiboErase. Adapters used were IDT xGen UDI-UMI Adapters.

treatment_protocol: Cells were treated with 100 nM dexamethasone for 1, 2, or 3 hours or equivalent volume of ethanol (0.01%) for the zero-dexamethasone cells. After dex treatment, media was replaced with 1X PBS and cells were subjected to UV crosslinking (254 nm, 400 mJ/cm2) and then scraped off, pelleted, and flash frozen.

value: osteosarcoma

value: wt GR-HaloTag

value: 100 nM dexamethasone, 3 hour


title: U2OS, 2hdex, pulldown, rep2

value: 100 nM dexamethasone, 2 hour


title: U2OS, 1hdex, pulldown, rep2

value: 100 nM dexamethasone, 1 hour


title: U2OS, 0hdex, pulldown, rep2

value: 0.01% Ethanol


title: td-Hepa-Vehicle (D28)-1


title: 2022.4.7 AMSC 6h-4

city: Hang Zhou

first: Yelei

last: Cen

address: Yuhangtang Road No.388,Zhejiang Province,P.R.China

institute: Zhejiang University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quailty sequence using CLC genomics benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomics benchwork (parameter - mismath cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomics benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: 500mg/kg APAP and AMSC treated


title: Control, HepG2, rep3

type: RNA

city: Ankara

first: Aysegul

last: Tombuloglu

address: Universiteler Mah.

department: Medical Informatics

country: Turkey

institute: Middle East Technical University

description: Gene expression data from untreated HepG2 cells

hyb_protocol: Hybridization(16 hours at 45°C) was carried out according to Affymetrix whole transcript expression array protocol.

scan_protocol: Chips were scanned using GeneChip Scanner 3000

data_processing: CEL files were imported within R environment as the raw dataset which was normalized and summarized using RMA and re-mapped to Ensembl Transcript IDs using custom Brainarray cdf.

label: biotin

source_name: Untreated HepG2 cells

label_protocol: Extracted RNA samples were used to prepare biotinylated cRNA according to Affymetrix whole transcript expression array protocol.

growth_protocol: HepG2 cells were cultured in low-glucose DMEM supplemented with L-glutamine, sodium pyruvate and 10 % FBS, 1% pen-strep solution in 25 mM HEPES.

extract_protocol: Total RNAs was isolated by Qiagen RNeasy total RNA isolation kit (Qiagen, Germany).

treatment_protocol: HepG2 cells cultured for 24 hours were treated with boric acid at half maximal inhibitory concentration (IC50= 24 mM boric acid) for 24 hours.

value: control


title: Fah (D0)-3

value: liver

value: Fah-/-


title: U2OS, 1hdex, input, rep2


title: 2022.4.7 AMSC 6h-3


title: Control, HepG2, rep2


title: U2OS, 0hdex, input, rep2


title: Boric acid treatment at IC50, HepG2, rep2

description: Gene expression data from HepG2 cells treated with  boric acid  at half maximal inhibitory concentration (IC50=24 mM) for 24 hours

value: boric acid


title: 2022.4.7 AMSC 6h-2


title: Boric acid treatment at IC50, HepG2, rep1

source_name: HepG2 cells treated with boric acid at half maximal inhibitory concentration


title: Boric acid treatment at IC50, HepG2, rep3


title: Control, HepG2, rep1


title: U2OS, 3hdex, pulldown, rep1


title: Fah (D0)-5


title: U2OS, 2hdex, pulldown, rep1


title: siNC+H. pylori

value: Normal gastric epithelial cell

value: Cells transfected with negative control were co-cultured with H. pylori (MOI 1:100) for 24 hours


title: 2022.4.7 APAP 6h-2

value: 500mg/kg APAP treated


title: 2022.4.7 APAP 6h-3


title: Fah (D0)-1


title: U2OS, 2hdex, input, rep2


title: Fah (D0)-6


title: 2022.4.7 NC-2


title: U2OS, 1hdex, pulldown, rep1


title: U2OS, 3hdex, pulldown, rep2


title: 2022.4.4 NC-1


title: U2OS, 0hdex, pulldown, rep1


title: 12w_bsh+_T_3

city: Bethesda

first: Lulu

last: Sun

state: Maryland

address: 37 Convent Drive

institute: National Cancer Institute

data_processing:
23 mRNA-Seq samples were pooled and sequenced on NextSeq2000 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing. The samples have 31 to 43 million pass filter reads with more than 94% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 95%. Unique alignment is above 73%. There are 2.89 to 6.16% unmapped reads.
The mapping statistics are calculated using Picard software. The samples have between 0.12-0.24% ribosomal bases. Percent coding bases are between 48-59%. Percent UTR bases are 34-43%, and mRNA bases are between 91-95% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 57-72% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools. The raw counts are provided as part of the data delivery.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon tumor tissue

extract_protocol:
Total RNA was isolated from mouse colon using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, #74136) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep.

treatment_protocol: 6-8 weeks old male Cdx2Apcf/wl were fed a 60% HFD for 2w or 12w, and at that time the mice were colonized with BF638R bsh- or BF638R bsh+ twice a week.

value: colon

value: BF638R bsh+ for 12w


title: 12w_bsh+_T_2


title: U2OS, 2hdex, input, rep1


title: 12w_bsh+_T_1


title: 2022.4.7 APAP 6h-1


title: 12w_bsh-_T_4

value: BF638R bsh- for 12w


title: 2022.4.7 NC-1


title: U2OS, 1hdex, input, rep1

value: osteosarcoma


title: 12w_bsh-_T_3


title: 12w_bsh-_T_2


title: bone_calcitriol_scRNA

city: Tokyo

first: Ayako

last: Hanai

address: 3-6-6, Asahi-machi, Machida-shi

country: Japan

institute: Kyowa Kirin Co., Ltd.

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads (FASTQ files) were mapped to the mouse reference genome (mm10) using Cell Ranger (v. 4.0.0; 10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
The downstream analysis was performed using the Seurat R package (version 3.2.2). The output matrices from Cell Ranger were converted into Seurat objects and barcodes with < 200 genes were excluded to eliminate low-quality cells or cell-free droplets as a primary quality control.
Following the primary quality control, each object was normalized and scaled according to the Seurat standard workflow, followed by principal component analysis based on the top 2000 highly variable genes, Uniform Manifold Approximation and Projection (UMAP) dimension reduction, and unsupervised clustering. After the clusters were obtained, the clusters with a high mitochondrial gene fraction (median of percent.mt > 10%), low gene counts (median of nFeature < 1000), and low Unique Molecular Identifier (UMI) counts (median of nCount < 2000) were excluded to eliminate dead cells as the secondary quality control.
The UMAP coordinate and the unsupervised cluster information of each cell was incorporated in the cloupe(Loupe Browser 6.0.0; 10xGenomics; https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/what-is-loupe-cell-browser ) file for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and barcodes files
Supplementary files format and content: Tab-separated values files and features files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone

extract_protocol:
The femurs were pooled for each group and treated as one sample. Epiphyses were cut off, and the marrow was flushed out by centrifugation. Mouse femurs were disrupted by Cryo-Press (Microtec Co., Ltd.) and digested with 1.6 U/mL collagenase D (Roche Diagnostics) in HBSS; pH = 7.8; FUJIFILM Wako Pure Chemical Corporation) for 30 min. The supernatant was discarded. Enzyme treatment and removal of supernatant steps were repeated twice. Residual bone pieces were treated with 20 mM ethylene glycol bis(β-aminoethylether)-N,N,N',N'-tetraacetic acid disodium salt solution (neutral) (EGTA; Nacalai Tesque, Inc.) in HBSS for 15 min and then with 1.6 U/mL collagenase D for 20 min to collect the cells. Treatment with collagenase D was repeated twice. All digestion steps were carried out in a 3.5 mL solution in a six-well petri dish, on a rotating shaker at 120 rpm in a 37°C incubator. After centrifugation and removal of supernatant, cell pellets were suspended in 1% (w/v) BSA-PBS(-); pH = 7.0 (Nacalai Tesque, Inc.). To remove CD45-positive cells, cell suspensions were mixed with CD45 microbeads (Miltenyi Biotec) and incubated at 4°C for 15 min in PEB buffer and rinsed. PEB buffer contains MACS® BSA stock solution (Miltenyi Biotec) and autoMACS rinsing solution (Miltenyi Biotec) in a 1:20 ratio. Cell suspensions were passed through the LD column (Miltenyi Biotec). The flow-through was collected, centrifuged, and resuspended in 1% BSA-PBS. Cells were passed through a 40 μm nylon strainer and used for scRNA-seq.
Library was constructed according to the manufacter’s instructions (Chromium Next GEM Automated Single Cell 3’ Reagent Kits v3.1, 10x Genomics). Briefly, mouse bone cells were resuspended in the 1% BSA-PBS and set together with the other reagents on the Chromium Connect to generate the sequence library.

value: Femoral cell

value: Bone

value: 7 week old

value: calcitriol-injected


title: bone_untreated_scRNA

description: 10x Genomics

value: untreated


title: U2OS, 0hdex, input, rep1

description: 1I0. De-duplicated BAM file is provided due to lost UMI read file.

value: wt GR-HaloTag

value: 0.01% Ethanol


title: U2OS, 3hdex, input, rep1

value: 100 nM dexamethasone, 3 hour


title: splenic-CD8-memory-PMSS1-28d-2

city: München

first: Maximilian

middle: Richard

last: Koch

address: Trogerstr. 30

department: Inst. for med. Micobiology

country: Germany

institute: TUM

description: bulkRNA-Seq of 10000 cells

data_processing:
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (Version 2.5.4). Read counts per gene locus were obtained using htseq-count (Version 0.11.4).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization and differential expression analysis. Batch effects were identified using sva (Version 3.34.0) and subsequently modelled in the design formula of DESeq2.
Assembly: mm10
Supplementary files format and content: Matrix table, in txt format, with raw read counts per gene locus from htseq-count.

source_name: splenic CD8+ T cells

growth_protocol: not applicable

extract_protocol:
10000 cells were sorted of each population. Rneasy Plus Mini Kit (Quiagen) was used for RNA isolation according to the manufacturer's protocol.
SMART-Seq V4 Ultra Low Input RNA Kit (Takara) was used according to the manufacturer's protocol for library contruction.

treatment_protocol: not applicable

value: spleen

value: CD8+ T cells

value: H. pylori strain PMSS1


title: splenic-CD8-memory-PMSS1-28d-3

description: bulkRNA-Seq of 10000 cells


title: 12w_bsh+_NT_3

source_name: Colon non-tumor tissue


title: 12w_bsh+_NT_2


title: 12w_bsh+_NT_4


title: 12w_bsh+_NT_1


title: splenic-CD8-memory-PMSS1-28d-1

description: bulkRNA-Seq of 10000 cells


title: 12w_bsh-_NT_4


title: 12w_bsh-_NT_3


title: U2OS, Ctrl R470A GR-HaloTag, 3hdex, rep2

data_processing:
Reads were tagged with UMIs using UMI-tools (v1.1.2). Reads were then trimmed using Trim Galore (v0.6.6) using the options: --2colour 20, --paired.
Trimmed reads were aligned to the hg38 genome assembly using STAR (v2.7.3a) and deduplicated using UMI-tools (v1.1.2) using the options: --paired, --unpaired-reads discard, --chimeric-pairs discard.
Deduplicated read coverage over exons was counted using featureCounts (Rsubread v2.0.1) and Gencode v39 gene annotations.
Assembly: hg38
Supplementary files format and content: 4su_exon_stranded_counts.csv: Matrix containing counts of deduplicated reads over exons for each gene in each sample.
Library strategy: 4sU-seq

growth_protocol: Cells were cultured at 37°C with 5% CO2. Cells were plated to be 80% confluent by the time of treatment, about 48 hours after plating, with DMEM supplemented with 10% charcoal-stripped FBS and 1X Pen-strep (100 U/ml penicillin, 100 µg/ml streptomycin).

extract_protocol:
RNAs labeled with 4-thiouridine (4sU) were isolated as described previously (Methods Mol Biol. 2017;1648:169-176. doi: 10.1007/978-1-4939-7204-3_13).
Briefly, TRIzol was applied to cell dishes to lyse and extract RNA. Total RNA was subjected to biotinylation to modify 4sU-labeled RNAs. The biotinylation reagent used was biotin-MTSEA-XX at 0.1 mg/mL (Biotium). Biotinylated RNAs were isolated using magnetic streptavidin beads.
Libraries were prepared using the KAPA RNA HyperPrep kit with RiboErase. Adapters used were IDT xGen UDI-UMI Adapters.

treatment_protocol: Cells were treated with 100 nM dexamethasone for 1, 2, or 3 hours or equivalent volume of ethanol (0.01%) for the control cells. Cells were also treated with 200 μM 4-thiouridine for the last hour of treatment, 1 hour for control cells.

value: R470A GR-HaloTag

value: 100 nM dexamethasone, 3 hours


title: U2OS, Ctrl R470A GR-HaloTag, 2hdex, rep2

value: 100 nM dexamethasone, 2 hours


title: gastric-CD8-TRM-PMSS1-28d-2

description: bulkRNA-Seq of 10000 cells

source_name: gastric CD8+ T cells

value: stomach


title: U2OS, Ctrl R470A GR-HaloTag, 3hdex, rep1


title: U2OS, Ctrl R470A GR-HaloTag, 2hdex, rep1


title: gastric-CD8-TRM-PMSS1-28d-1

description: bulkRNA-Seq of 10000 cells


title: 12w_bsh-_NT_1

value: colon

value: BF638R bsh- for 12w


title: NAIO3+IL4_4

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description: NAIO3+IL-4 treated replicate 4

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150bp paired-end reads were generated.
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.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. 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: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: RPE-sclera complex

extract_protocol:
RNA from RPE-sclera was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NAIO3+IL4 treatment for 7 days

value: RPE-sclera complex


title: KO_3

city: Hefei

first: Yujie

last: Li

state: Anhui

address: 1129 Huizhou Ave

institute: University of Science and Technology of China

data_processing:
All of the analyses were performed using the free online platform of Majorbio Cloud Platform
High-quality reads in each sample were mapped to the reference genome using Bowtie2.
In this step, randomly selected 10000 raw reads in each sample are aligned to Rfam database. Based on the annotation results, percentage of rRNA in each sample is calculated, which is estimated as rRNA contamination.
Quantify gene and isoform abundances from single-end or paired-end RNA-Seq data using RSEM, Kallisto, and Salmon.
Goatools is used to identify statistically significantly enriched GO term using Fisher’s exact test.
KOBAS 2.0 is used to identify statistically significantly enriched pathway using Fisher’s exact test.
Assembly: Staphylococcus aureus NCBI genome JAFFHX000000000.1
Supplementary files format and content: DEG-WT_vs_KO_20221213.txt

organism: Staphylococcus aureus

source_name: USA300 LAC

growth_protocol: Overnight cultures of narG knockout mutant and S. aureus wild-type strains were diluted in TSB medium (OD600 = 0.05)

extract_protocol:
TTotal RNA was extracted from S. aureus strains by CTAB method and the RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA.

treatment_protocol: All the strains were  grown to the stationary-phase (OD600 = 0.5).

value: USA300 LAC

value: narG knockout

value: growth phase


title: U2OS, Ctrl R470A GR-HaloTag, 1hdex, rep2

value: osteosarcoma

value: 100 nM dexamethasone, 1 hour


title: NAIO3+IL4_3

description: NAIO3+IL-4 treated replicate 3


title: KO_2


title: U2OS, Ctrl R470A GR-HaloTag, 1hdex, rep1


title: 2w_bsh+_4

source_name: Normal Colon

value: BF638R bsh+ for 2w


title: 12w_bsh-_T_1


title: NAIO3+IL4_2

description: NAIO3+IL-4 treated replicate 2


title: 2w_bsh+_3


title: KO_1


title: W3

value: WT


title: 2w_bsh+_2


title: 2w_bsh+_1


title: 12w_bsh-_NT_2


title: W2


title: U2OS, Ctrl R470A GR-HaloTag, 0hdex, rep1

value: 0.01% Ethanol


title: NAIO3+IL4_1

description: NAIO3+IL-4 treated replicate 1


title: U2OS, Ctrl R470A GR-HaloTag, 0hdex, rep2


title: U2OS, SoF K492A GR-HaloTag, 3hdex, rep2

value: K492A GR-HaloTag


title: NAIO3_3

description: NAIO3 treated replicate 3

value: NAIO3 treatment for 7 days


title: 2w_bsh-_3

value: BF638R bsh- for 2w


title: W1


title: NAIO3_2

description: NAIO3 treated replicate 2


title: NAIO3_4

description: NAIO3 treated replicate 4


title: U2OS, SoF K492A GR-HaloTag, 3hdex, rep1

value: 100 nM dexamethasone, 3 hours


title: 2w_bsh-_4


title: Fst cKO apex rep3

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

data_processing:
HiSeq Control Software v3.3 for system control and base calling through Real Time Analysis v2.5.2 (Illumina)
Sequencing reads in Fastq files with three replicates of each sample group were aligned to Mus musculus genome (assembly GRCm38) with STAR aligner (version 2.5.2b).
Read counts and fragments per kilobase of transcript per million mapped reads (FPKM) were calculated based on the mouse GRCm38 Ensembl Release 82 gene annotation. Cuffdiff (version 2.2.1) was used for searching differentially expressed genes (DEGs) setting pairwise comparison for all sample groups at once.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts, FPKMs, averaged FPKMs for each sample group

source_name: cochlea

extract_protocol:
cochleae were dissected from 4-week-old control and Fst cKO mutant mice and divided into three regions along the tonotopic axis, base, middle, and apex. Each cochlear region from each genotype was pooled together and RNAs were extracted.
The RNAs were divided into three technical replicates and were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 with Ribo-Zero (Illumina)

value: cochlea

value: Fst cKO

value: Fst conditional knock-out

tag: region

value: apex


title: NAIO3_1

description: NAIO3 treated replicate 1

value: RPE-sclera complex


title: 2w_bsh-_2

value: colon


title: U2OS, SoF K492A GR-HaloTag, 2hdex, rep2

value: 100 nM dexamethasone, 2 hours


title: U2OS, SoF K492A GR-HaloTag, 2hdex, rep1


title: Fst cKO apex rep2


title: PBS_4

description: PBS treated replicate 4

value: PBS treatment for 7 days


title: 2w_bsh-_1


title: Fst cKO apex rep1


title: U2OS, SoF K492A GR-HaloTag, 1hdex, rep1

value: osteosarcoma


title: U2OS, SoF K492A GR-HaloTag, 1hdex, rep2

value: 100 nM dexamethasone, 1 hour


title: Fst cKO middle rep3

value: middle


title: PBS_2

description: PBS treated replicate 2


title: PBS_3

description: PBS treated replicate 3


title: Fst cKO middle rep2


title: PAO1161 ParA L84K, replicate 2

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
CP032126.fa
CP032126.bed
CP032126_PA_names.bed

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO1161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
Obtained *.sam files were sorted (samtools sort -n), run through samtools fixmate with the -m option, again sorted (samtools sort) and duplicates were marked with samtools markdup. Samtools ver. 1.9 was used.
The files were indexed and used to generate coverage *.bigwig files, normalized to 1× sequencing depth (RPGC), without binning and smoothing using the bamCoverage tool ver 3.3.0 included in deepTools.
Assembly: CP032126
Supplementary files format and content: Processed files in bigwig format represent normalized coverages of individual base pairs in the P. aeruginosa PAO1161 genome. Reference genome is enclosed in fasta format (CP032126.fa) and the annotation used is enclosed as a .bed (CP032126.bed). A modified .bed file with PAO1161 feature names changed to the names of corresponding PAO1 genes (PA… format) is included for convenience of data browsing e.g. using IGV (CP032126_PA_names.bed).

organism: Pseudomonas aeruginosa

source_name: bacterial cell

growth_protocol: P. aeruginosa PAO1161 strains were freshly  streaked from glycerol stocks kept at -80oC. Two independent overnight cultures from each strain were inoculated from single colonies and grown overnight with shaking at 37oC. After that they were diluted 1:100 in L broth (DifcoTM L Broth, Lennox, BD) and grown with shaking at 37oC until reaching exponential phase with optical density about 0.5 (OD600).

extract_protocol:
Chromatin immunoprecipitation (ChIP) protocol was based on the method described earlier (Kawalek et al, 2018; Nucleic Acids Res. 46:9, 4592-4606; Modrzejewska et al, 2021; mSystems 6:4, e0001521). Two cultures of each strain with similar OD600 were combined, formaldehyde was added from a 37% stock to a final concentration of 1%, and the cultures were kept for 10 min at room temperature with gentle inverting. Glycine was added to a final concentration of 0.5 M and the cultures were incubated for 5 min at room temperature with gentle rotation. Cells were then harvested by centrifugation (20 min, 3000 x g, 25 mL of culture in 50 mL conical tubes, 4 tubes per strain), washed twice with ice-cold Tris-buffered saline (25 mM Tris-HCl, 150 mM NaCl, pH=7.6), resuspended in 1 mL of TBS, transferred to a fresh 1.5 mL tube and centrifuged (2 min, 6000 x g). The cell pellets were frozen at -70oC. The pellets were thawed on ice, suspended in 0.5 mL of lysis buffer [10 mM Tris-HCl, 20% (w/v) sucrose, 50 mM NaCl, 10 mM ethylenediaminetetraacetic acid (EDTA), pH=8.0] supplemented with 10 µl of Protease Inhibitor Cocktail (Sigma, PA8849) and 125 µL of lysozyme (20 mg/mL) and incubated for 30 min at 37oC. Four samples for each strain were combined in 15 mL. Subsequently, 1.5 mL of IP-buffer [50 mM Tris-HCl, pH=7.5, 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (m/v) sodium deoxycholate], 30 µL protease inhibitor cocktail, PMSF (phenylmethanesulfonyl fluoride) to a final concentration of 2 mM, SDS (sodium dodecyl sulphate) to a final concentration of 0.1% were added to each sample. The samples were sonicated 20 times for 20 s each with 1 min break on ice using a Microson ultrasonic cell disruptor Xl2000 (Misonix) with 5-mm tip and 90% of output power to obtain DNA fragments of an average length of 250-350 bp. DNA fragmentation was checked by agarose gel electrophoresis. After sonication, samples were aliquoted (1 mL in 1.5 mL tubes) and stored at -70oC. Sonicated lysate was thawed on ice and 150 μL of each strain variant was incubated with 20 μL of magnetic beads coupled with protein A (Dynabeads Protein A, Invitrogen, 10001D) previously separated from original suspension using Magnetic Separation Stand. Such pre-clearing step was performed for minimum 1 hour at 4oC with rotation of the mixtures. In the meantime 50 μL of magnetic beads were prepared for each reaction by separating from the suspension as above. It was then mixed with anti-ParB antibodies (3 μg,  diluted in 200 μL of PBS with 0.05% Tween-20. Mixtures of magnetic beads and antibodies were incubated for 10 minutes at 4oC with gentle rotation. Beads with bound antibodies were then separated from the supernatant, washed once with 200 μL of the PBS with 0.05% Tween-20 solution and stored on ice. Pre-cleared lysate was separated from the beads used for pre-incubation and added to the beads coated with antibodies. Mixture containing lysate and magnetic beads with antibodies was incubated at 4oC for 20 minutes with mixing on rotator. Beads were then collected and washed. Elution was performed twice for 15 minutes in 50 μL at 65oC in thermoblock with shaking (1400 rpm). All 100 μL of obtained eluates were incubated with 1 μL of RNase A (100 mg/mL, Qiagen, 19101) for 30 min at 65oC. Then, 5 μL of Proteinase K (20 mg/mL, Qiagen, 19133) was added and the samples were incubated for 1 h at 50oC followed by overnight incubation at 65oC. Such prepared probes were stored on ice and 3 μL of 3 M sodium acetate (pH=5) was added. DNA purification was performed using Qiaquick Qiagen PCR purification Kit according to manufacturer’s instructions. The DNA was stored at -20oC.
NGS library was constructed using QiaSeq Ultralow Input Library kit. Sample was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

value: PAO1161 leu-

value: parA (L84K)

value: bacterial cell

tag: growth phase

value: logarithmic phase of liquid culture

tag: chip antibody

value: Anti-ParB (rabbit, polyclonal)


title: PBS_1

description: PBS treated replicate 1


title: U2OS, SoF K492A GR-HaloTag, 0hdex, rep2

tag: cell line

value: K492A GR-HaloTag

value: 0.01% Ethanol


title: U2OS, SoF K492A GR-HaloTag, 0hdex, rep1


title: Fst cKO middle rep1

value: cochlea

value: Fst cKO


title: PAO1161 ParA L84K, replicate 1


title: NRMTF3

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRMTF3

data_processing:
Illumina Casava 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 STAR (ver2.5) software.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (2_1.6.3).  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, pvalue and adjusted pvalue for each group.

source_name: Retina

extract_protocol:
Retinas were extracted, stored in RNAlater solution(QIAGEN). RNA was harvested using RNAeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: 4 weeks

value: female


title: Fst cKO base rep2

value: Fst conditional knock-out

value: base


title: U2OS, wt GR-HaloTag, 3hdex, rep2

value: osteosarcoma

value: wt GR-HaloTag

value: 100 nM dexamethasone, 3 hours


title: NRMTF2

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRMTF2


title: U2OS, wt GR-HaloTag, 3hdex, rep1


title: PAO1161 ParB G11A, replicate 2

value: PAO1161 leu-

value: parB (G11A)


title: Fst cKO base rep1


title: PAO1161 ParB G11A, replicate 1

value: bacterial cell


title: PAO1161 ΔparB, replicate 1

value: {delta}parB

value: logarithmic phase of liquid culture


title: NRMTF1

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRMTF1


title: Control apex rep3

value: WT

value: untreated

value: apex


title: U2OS, wt GR-HaloTag, 2hdex, rep2

value: 100 nM dexamethasone, 2 hours


title: PAO1161 parAstop Δsmc, replicate 2

value: {delta}smc parAstop

value: Anti-ParB (rabbit, polyclonal)


title: Control apex rep2

value: cochlea


title: NRCTF2

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRCTF2

value: retina

value: 4 weeks

value: wild type

value: female


title: U2OS, wt GR-HaloTag, 2hdex, rep1

value: osteosarcoma

value: wt GR-HaloTag


title: PAO1161 parAstop Δsmc, replicate 1

value: PAO1161 leu-


title: Control apex rep1


title: Fst cKO base rep3

value: Fst cKO

value: Fst conditional knock-out

value: base


title: NRCTF1

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRCTF1


title: PAO1161 Δsmc, replicate 2

value: {delta}smc

value: bacterial cell

value: logarithmic phase of liquid culture


title: U2OS, wt GR-HaloTag, 1hdex, rep2

value: 100 nM dexamethasone, 1 hour


title: U2OS, wt GR-HaloTag, 1hdex, rep1


title: Control middle rep3

value: WT

value: untreated

value: middle


title: Control middle rep2

value: cochlea


title: PAO1161 Δsmc, replicate 1

value: Anti-ParB (rabbit, polyclonal)


title: PAO1161 reference (wild-type), replicate 2

value: wild-type


title: Control middle rep1


title: NRMTM3

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRMTM3

value: retina

value: 4 weeks

value: male


title: U2OS, wt GR-HaloTag, 0hdex, rep1

value: osteosarcoma

value: wt GR-HaloTag

value: 0.01% Ethanol


title: PAO1161 reference (wild-type), replicate 1

value: PAO1161 leu-


title: NRMTM2

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRMTM2


title: Control base rep3

value: base


title: NRMTM1

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRMTM1


title: NRCTM3

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRCTM3

value: wild type


title: 293FT-RocA03-2

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

description: Disome profiling

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality control and the adaptor sequences were trimmed using the cutadapt program.
Reads with length between 30-70 nt were kept for following data analyses. Low-quality reads with Phred quality scores lower than 25 (>75% of bases) were removed using the fastx quality filter (http://hannonlab.cshl.edu/fastx_toolkit/).
Then sequence reads originating from rRNAs were identified and discarded by aligning the reads to human rRNA reference sequences using Bowtie 1.1.2 with no mismatch allowed.
The remaining reads were mapped to the genome and transcriptome using STAR (2.7.7a) with the following parameters: --runThreadN 8 --outFilterType Normal --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --alignEndsType EndToEnd --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMattributes.
The metagene analysis of Disome-seq data was performed with RiboMiner (https://github.com/xryanglab/RiboMiner). Disome density around polypurine motifs, the length distribution versus disome density at each position, and coverage of a single transcript were all computed by custom python scripts.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files include average read density normalized with RPM  at each codon for 374 RUG genes aligned to translation start codon
Supplementary files format and content: tab-delimited text files include average read density normalized with RPM  at each codon for 643 RDG genes aligned to translation start codon
Library strategy: Disome profiling

growth_protocol: HEK293FT cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  with 5% CO2 at 37C.

extract_protocol:
Cells treated with 100μg/mL cycloheximide for 5min and rinsed with cold PBS contained 100μg/mL cycloheximide then harvest cells use scraper and cells lysed with lysis buffer(20mM Tris, 150mM NaCl, 5mM MgC12, 1mM DTT, 25U/mL DNaseI, 100ug/mL cycloheximide, 1%(V/V) TritonX-100, 0.1%(V/V) NP-40) for 10 minutes on ice and mix cells by flicked the bottom of the tube avoided votexed, then 13,000 g centrifuge for 10 minutes at 4℃ to collect the cell lysate. After clarification, 5 OD260 units of cell lysate were treated with 450 units of RNaseI ( Ambion:AM2295) for 45 minutes at room temperate and the reaction was stopped with SUPERase•In(Ambion: AM2694).The disome fractions were purified with Sephacryl S400 columns (GE Healthcare) and the RNAs were extracted with trizol followed the instructions (Invitrogen: 15596018 ).
Libraries were prepared as described in previous reports (Ingolia Nicholas, Ghaemmaghami et al. 2009)

treatment_protocol: Cells were treated with 0.3μM RocA for 30min，add the same volume of DMSO as control condition.

value: human embryonal kidney cells

value: 0.3 µM RocA treatment


title: NRCTF3

description:
2 female retinas
NRMTFvsNRCTF_DEG.txt
NRCTF3

value: female


title: 293FT-RocA03-1

description: Disome profiling


title: neurospheres, p300f/f

city: San Juan de Alicante

first: Ángel

last: Márquez Galera

address: Av. Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

data_processing:
Libraries were sequenced together in a unique cell flow on an Illumina HiSeq2500 sequencer to obtain 75 bp paired-end reads following sequencer manufacturer’s instructions sequencer, with an average sequencing depth of an average of 290 million reads per sample. Quality control was performed using FastQC v0.11.9. Sequenced samples were processed using the Cell Ranger v3.1 pipeline (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome customized to count reads in exons and introns (pre-mRNA) (gene annotation version 94).
Bioinformatic analysis were performed as described previously in (Lipinski et al., 2020). Single-nucleus RNA-seq data were pre-processed and further analyzed in R using Seurat v2.3.4 (Butler et al., 2018; Stuart et al., 2019) using the following filter parameters: genes, nCell < 5; cells, nGene < 200. Barcodes with total unique molecular identifier (UMI) count > 10% of the 99th percentile of the expected recovered cells were selected for further analysis. We retrieved 4,884 (control), 3,017 (Crebbpf/f+Cre) and 4,648 (Ep300f/f+Cre) high nuclei per sample. Mean reads per nucleus were 62,810 (control), 99,066 (Crebbpf/f+Cre) and 65,928 (Ep300f/f+Cre). Data were then normalized using global-scaling normalization (method: LogNormalize, scale.factor = 10,000). To identify major cell populations in the differentiated cultures, datasets were analyzed separately.
Highly variable genes (HVGs) were detected using FindVariableGenes function with default parameters. Then, normalized counts on HVGs were scaled and centered using ScaleData function with default parameters. Principal component analysis (PCA) was performed over the first ranked 1000 HVGs. Plots of the two principal components of the PCA, where cells were colored by dataset, excluded the presence of batch effects. Cluster detection was carried out with Louvain algorithm using 20 first PCA dimensions at resolution = 0.6 (the default and the optimal according to cell number, data dispersion, and co-expression of previously reported cell markers). Visualization and embedding were performed using t t-Distributed Stochastic Neighbor Embedding (tSNE)  (Laurens van der Maaten, 2008) and Uniform Manifold Approximation and Projection (UMAP) (McInnes et al., 2018) over PCA using the 20 first PCA dimensions.
After characterizing the cell heterogeneity of each condition separately, data from the control, CBP-ablated, and p300-ablated conditions were merged into a single data set. Using the first 1,000 HVGs from each sample, a total of 1,421 unique HVGs detected in the 3 conditions were obtained. Normalized counts on merged HVGs were scaled and centered using ScaleData function with default parameters and PCA was performed over them. Plots of the two principal components of the PCA, where cells were colored by dataset, excluded the presence of batch effects. Subsequent analyses repeated the same strategy and the same clustering and visualization parameters as in the individual analyses.  FindAllMarkers function with default parameters was used to identify gene markers for each cluster and to assign the cell-type identity. Populations were identified combining the clustering results over the merged dataset with clustering information obtained from the datasets separately, together with co-expression of population markers and information from external scRNA-seq datasets from the Allen Brain Map portal (Yao et al., 2021) and the Atlas of the Developing Mouse Brain (La Manno et al., 2021). Twelve clusters were unbiasedly identified but three of them were closely distributed and manually fused since they presented minor expression differences. UMAP plots of gene expression show normalized count (UMIs) per nucleus. Clustering was performed on merged dataset from control, CBP-ablated and p300-ablated conditions and populations were identified combining these results with clustering information obtained in the datasets separately, together with co-expression of population markers. FindAllMarkers function with default parameters was used to identify gene markers for each cluster and to assign cell-type identity to clusters based on scRNA-seq dataset of the Allen Brain Map portal (Mouse Whole Cortex and Hippocampus SMART-seq (2019) with 10x-SMART-seq taxonomy (2020).
Differential expression analysis (DEA) was used to identify population gene effects between the different conditions. For DEA, the nuclei of each population were compared against all the other nuclei in the merged dataset using Wilcoxon Rank Sum test on normalized counts with the following parameters (logfc.threshold = 0.25; min.pct = 0.25). Gene Ontology (GO) functional enrichment analyses for Biological Process (BP) were performed using clusterProfiler (v3.15.2). All enriched terms were considered significant at adjusted P values by BH cutoff < 0.05. The reference gene set used to perform the analysis was C5 (GO Biological Process) collection from the Molecular Signatures Database (MSigDB) (v6.2).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: nuclear RNA

source_name: Brain

extract_protocol:
For the single nucleus RNA-Seq experiment, a pool of ~15 differentiated neurosphere cultures from control, CBPf/f+Cre and p300f/f+Cre at 15DIV were used. Differentiation medium II was removed and wells were washed with cold HBSS. Cold Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 Substitute in Nuclease-Free Water) was added (500 µl) immediately to every well, gently pipetted until cells were completely suspended and kept on ice for 5 min to lyse cells. The nuclei suspension from the different samples (control, CBPf/f+Cre and P300f/f+Cre) was transferred to a 15ml tube and centrifuged at 500 rcf for 5 min at 4°C. Supernatant were removed and nuclei pellet was resuspended in 1 ml of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2 U/μl RNase Inhibitor). Centrifugation and nuclei wash steps were repeated twice.
Nuclei suspension was sorted on FACS Aria III (BD Biosciences) at 4°C and immediately proceed to 10x Genomics single cell protocol. 16,000 nuclei per sample (pool of ~15 differentiated neurosphere cultures) were loaded into single cell Chromium Chip B and Chromium Controller was run to generate partitioning thousands of nuclei into nanoliter-scale Gel Beads-in-emulsion (GEMs) and immediately reversed transcribed, where all generated full-length cDNA (from poly-adenylated mRNA) share a common 10x Barcode. Post-GEM-RT cleanup, cDNA amplification and 3ʹ Gene Expression Library Construction were performed with Chromium Single Cell 3’ Library & Gel Bead Kit v3. Quality control of cDNA and libraries were performed with Agilent Bioanalyzer in a High Sensitivity chip.

value: Brain

value: tamoxifen


title: NRCTM2

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRCTM2


title: neurospheres, control

value: control


title: Control base rep1

value: cochlea

value: WT

value: untreated


title: 293FT-DMSO-1

description: Disome profiling

value: DMSO treatment


title: NRCTM1

description:
2 male retinas
NRNTMvsNRCTM_DEG.txt
NRCTM1

value: retina

value: 4 weeks

value: male


title: U2OS, wt GR-HaloTag, 0hdex, rep2

value: osteosarcoma

value: wt GR-HaloTag

value: 0.01% Ethanol


title: Mouse_Liver_10x_SingleCell_KO3

status: Public on Dec 16 2022

city: Berkeley

first: Danica

last: Chen

address: 335 Morgan Hall

institute: University of California, Berkeley

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma-separated values file

source_name: Liver

extract_protocol:
Hepatocytes and non-parenchymal cells (NPCs) were isolated by a two-step collagenase perfusion method (Tabula Muris et al., 2018). Cell viability was confirmed by trypan blue exclusion.
3000 hepatocytes and 3000 NPCs were mixed and used directly for scRNA-seq analysis using 10X Genomics Chromium Single-Cell 3’ according to the manufacturer’s instructions.

value: Liver

value: SIRT7 KO


title: Mouse_Liver_10x_SingleCell_WT3

description: 10x Genomics


title: Mouse_Liver_10x_SingleCell_WT2

description: 10x Genomics


title: Mouse_Liver_10x_SingleCell_KO2

description: 10x Genomics


title: Mouse_Liver_10x_SingleCell_KO1

description: 10x Genomics


title: Mouse_Liver_10x_SingleCell_WT1

description: 10x Genomics