title: ChIP_Z4_REP2

description:
single nucleotide bigwig coverage files were generated for total reads.
ChIP_log2_Z4.bigwig
High_confidence_Z4.bed

extract_protocol: Sequencing libraries were generated with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB #E7645).

treatment_protocol: Untreated

value: ZC3H4 associated DNA ChIP

value: ZC3H4 associated DNA


title: siZ4_rep2_r1

status: Public on Aug 06 2021

type: SRA

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
single nucleotide bigwig coverage files were generated for total reads and separate stranded reads
siZ4_POOL_antisense.bigwig
siZ4_POOL_sense.bigwig
RNAseq_Log2_siZ4_Vs_siCONT.bigwig

library_source: transcriptomic

data_processing:
RNA-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v1.15).
RNA-seq: Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
RNA-seq: Properly mapped single-end reads were extracted and indexed using samtools v1.4.1.
RNA-seq: For stranded coverage analysis, sense and antisense reads were seperated from merged BAMs using samtools v1.4.1
RNA-seq: Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.0.2
RNA-seq: Log2 files were created using BigWig compare (deepTools v3.5)
Supplementary_files_format_and_content: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) at a single nucleotide resolution across the genome.
ChIP-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! V.0.6.5 (wrapper tool for Cutadapt v2.9).
ChIP-seq: Alignment of ChIP-Seq reads using BWA to ensembl GRCh38.
ChIP-seq: PCR duplicates were removed
ChIP-seq: Replicates were merged using bamtools v2.4.0.
ChIP-seq: Bigwig files of ChIP-Seq reads were generated from BAM files using the bamCoverage of Deeptools v3.4.2
ChIP-seq: Log2 files were created using Bam compare (deepTools v3.5)
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files of ChIP-Seq reads represent normalised read coverage (CPM) at a single nucleotide nucleotide across the genome.

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: HCT116 cell lines were maintianed in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol: Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero Gold (Illumina #MRZE706). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020596)

treatment_protocol: The sample was transfected with a silencer select ZC3H4 siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies)

tag: cell line

tag: genotype/variation

value: No variation

tag: treatment

value: siZ4 treatment, nuclear RNA

tag: molecule subtype

value: Nuclear RNA


title: DZ_12128_early [DJ-53]

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

country: USA

institute: Atrium Health Wake Forest

library_source: genomic

data_processing:
library strategy: hMe-Seal
Processed leucocyte composition of MZ twin samples was obtained from HudsonAlpha Institue for Biotechnology (Illumina HumanMethylation 450K BeadChip)
hydroxymethylation reads were aligned to the hg19 using Bowtie2
Differentially hydroxymethylated regions of the monozygotic twin hydroxymethylation samples were identified, quantified, and compared using Methylaction (Bhasin et. Al. Nucleic Acids Res. 2016). Three comparisons using different combinations of covariates were made: 1. no covariates 2. All blood leucocytes excluding granulocytes 3. All blood leucocytes excluding granulocytes and age
A subset of the regions identified in the previous step was used by Methylaction to quantify the dizygotic twin hydroxymethylation samples.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized hydroxymethylation levels of each region and differential significance when comparing discordant deaths.
Supplementary_files_format_and_content: Estimated relative proportion of leukocyte cell types within a sample.

molecule: genomic DNA

source_name: dizygotic_twin_early death

growth_protocol: Whole blood was drawn from the antecubital vein into EDTA tubes after an overnight fast and immediately placed on ice. Buffy coats were obtained and used to extract DNA

extract_protocol:
Genomic DNA was isolated in digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo Fisher cat# EO0491) treatment at 55 °C for overnight. The second day, phenol:chloroform:isoamyl alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (Sigma-Aldrich, cat# P-3803) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppen- dorf tube and precipitated with 600 mL isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion).
hMe-Seal assay (NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina + single end 50bp Hiseq 2000 Illumina sequencing)

tag: twin type

tag: twin pair

tag: discordant death (when compared their corresponding twin)

value: early death

tag: tissue/molecule

value: Buffy coat DNA samples extracted from whole blood

value: DNA hydroxymethylation


title: CPSF30_R1_r1

description: single nucleotide bigwig coverage files were generated for total reads and separate stranded reads

treatment_protocol: Control: Treated for 3 h with ethanol (absolute 1ul/ml media).

value: CPSF30-mAID_P2A_[HygromycinR/NeomycinR]_SV40-pA; sleeping_beauty(TIR1; blasticidn).  Note that mAID-tagging CPSF30 is not expected to alter the behaviour of the cell line unless auxin treated

value: Control - mock treated (ethanol), nuclear RNA


title: DZ_12072_early [DJ-43]


title: ChIP_Pol II_REP2

description:
single nucleotide bigwig coverage files were generated for total reads.
ChIP_log2_Pol_II.bigwig
High_confidence_POL_II.bed

source_name: ChIP_Pol II_REP2.fq.gz

value: Pol II associated DNA ChIP

value: Polymerase associated DNA


title: DZ_12072_late [DJ-44]

source_name: dizygotic_twin_late death

value: late death


title: ChIP INPUT

description: single nucleotide bigwig coverage files were generated for total reads.

source_name: ChIP INPUT.fq.gz

value: Control ChIP

value: IgG associated DNA


title: MZ_12057_late [DJ-39]

source_name: monozygotic_twin_late death


title: MZ_11636_late [DJ-38]


title: MZ_12057_early [DJ-40]

source_name: monozygotic_twin_early death


title: ERF_FA_RRBS_rep2

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

data_processing:
Basecalls performed using bcl2fastq version 2.20.0
Single-end RRBS reads were adapter and quality trimmed (phred33 score>=20) using trimgalore v0.6.5 with the RRBS option invoked.
Bismark v0.22.1 was used to align reads to UCSC version mm10 of the mouse genome.  CpG methylation was extracted using bismark methylation extractor,  ignoring the first 4 bases of the read after inspection of m-bias plots.
Genome_build: mm10
Supplementary_files_format_and_content: The bismark CpG coverage report file contains 1-based genomic coordinates for every covered cytosine position in the experiment, and has the following fields separated by tabs: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

organism: Mus musculus

source_name: mouse ES cells_ERF-FA

growth_protocol: N-Ras−/−; H-Ras−/−; K-Rasf/f; Ubiq-CreERT2 (Raslox/lox ; Drosten et al. 2010) ESC were grown in N2B27 media supplemented with 2i/LIF (1 mM PD0325901, 3 mM CHIR99021, 1:500 LIF, made in house). N2B27 media consisted of a 1:1 mix of DMEM/F12 and Neurobasal Medium, 1X N2 supplement, 1X B27 supplement, 0.1 mM nonessential amino acids, 55 μM β-mercaptoethanol and 1% penicillin/streptomycin (all from Life Technologies). Cells were routinely cultured in 0.1% gelatinized plates and passaged with Accutase (Gibco) unless otherwise indicated.  To induce EpiLSC differentiation, cells were grown for few passages in plates pretreated with 10 mg/ml polyL-ornithine and 5 mg/ml laminin (Corning). A total of 200,000–300,000 cells per 10 cm2 were plated on plates pretreated with 5 mg/ml Fibronectin (Millipore) in N2B27 media supplemented with 1% KOSR, 12 ng/ml FGF2 (R&D systems) and 20 ng/ml Activin A (PeproTech) for 48 hours including daily media changes.

extract_protocol:
Trypsinized ESC were lysed for 2-3 hours at 55°C with lysis buffer (100 mM Tris-HCl pH 8, 5 mM EDTA, 0.2% SDS, 20 mM NaCl and 100 mg/ml Proteinase K). DNA was isolated by adding an equal volume of Phenol/Chloroform/Isoamyl to the samples and using phase-lock tubes (5PRIME Phase Lock GelTM Heavy, Quantabio), followed by an extraction with identical volume of Chloroform. DNA was precipitated with 2 volumes of 100% Ethanol plus 0.3 M NaAc, washed with 70% Ethanol and resuspended in water.
DNA libraries for RRBS analysis were prepared using the Premium RRBS kit (Diagenode) following manufacturer’s recommendations

treatment_protocol: OHT samples were treated with 4-hydroxy-tamoxifen for 6 days

tag: cell line background

value: Raslox/lox

value: FA


title: MZ_11636_early [DJ-37]


title: ERF_OHT_FA_RRBS_rep2

source_name: mouse ES cells_ERF-FA+OHT

value: FA+OHT


title: MZ_11635_late [DJ-36]


title: Ctrl_OHT_FA_RRBS_rep2

source_name: mouse ES cells_WT-FA+OHT


title: MZ_11635_early [DJ-35]


title: ERF_OHT_FA_RRBS_rep1


title: MZ_11580_early [DJ-34]


title: ChIP_Z4_REP1

value: ZC3H4 associated DNA ChIP

value: ZC3H4 associated DNA


title: MZ_11580_late [DJ-33]


title: Ctrl_OHT_FA_RRBS_rep1


title: DZ_11567_early [DJ-32]


title: Ctrl_FA_RRBS_rep1

source_name: mouse ES cells_WT-FA


title: ERF_OHT_PLO_RRBS_rep2

source_name: mouse ES cells_ERF-2iL+OHT


title: DZ_11567_late [DJ-31]


title: ChIP_Pol II_REP1

source_name: ChIP_Pol II_REP1.fq.gz

value: No variation


title: MZ_11565_early [DJ-30]


title: ERF_PLO_RRBS_rep2

source_name: mouse ES cells_ERF-2iL


title: MZ_11565_late [DJ-29]


title: MZ_11124_late [DJ-27]


title: MZ_11124_early [DJ-28]


title: DZ_11112_late [DJ-26]


title: ERF_OHT_PLO_RRBS_rep1


title: ERF_PLO_RRBS_rep1


title: MZ_11105_late [DJ-24]


title: Ctrl_FA_RRBS_rep2


title: DZ_11112_early [DJ-25]


title: Ctrl_PLO_RRBS_rep2

source_name: mouse ES cells_WT-2iL


title: ERF_FA_RRBS_rep1


title: Ctrl_OHT_PLO_RRBS_rep1

source_name: mouse ES cells_WT-2iL+OHT


title: Ctrl_PLO_RRBS_rep1


title: RASERFKO_D_RNA-seq_rep2

data_processing:
Basecalling was performed using bcl2fastq version 2.20.0
RNAseq reads were adapter trimmed using fastp v.0.20.0 (Chen et al., 2018)
Transcript expression was quantified via mapping to mouse gencode v25 transcripts using salmon (Patro et al., 2017).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files represent gene quantification files obtained from salmon.  This file is a plain-text, tab-separated file with with the following information: GeneName,LengthEffectiveLength,TPM,NumReads

molecule: total RNA

source_name: mouse ES cells_FA-OHT

growth_protocol: N-Ras−/−; H-Ras−/−; K-Rasf/f; Ubiq-CreERT2 (Raslox/lox ; Drosten et al. 2010) and wild-type (R1 and G4) ESC were grown in N2B27 media supplemented with 2i/LIF (1 mM PD0325901, 3 mM CHIR99021, 1:500 LIF, made in house). N2B27 media consisted of a 1:1 mix of DMEM/F12 and Neurobasal Medium, 1X N2 supplement, 1X B27 supplement, 0.1 mM nonessential amino acids, 55 μM β-mercaptoethanol and 1% penicillin/streptomycin (all from Life Technologies). Cells were routinely cultured in 0.1% gelatinized plates and passaged with Accutase (Gibco) unless otherwise indicated.  To induce EpiLSC differentiation, cells were grown for few passages in plates pretreated with 10 mg/ml polyL-ornithine and 5 mg/ml laminin (Corning). A total of 200,000–300,000 cells per 10 cm2 were plated on plates pretreated with 5 mg/ml Fibronectin (Millipore) in N2B27 media supplemented with 1% KOSR, 12 ng/ml FGF2 (R&D systems) and 20 ng/ml Activin A (PeproTech) for 48 hours including daily media changes.

extract_protocol:
Total RNA was isolated using Isolate II RNA Mini Kit (Bioline).
DNA libraries for RNAseq analysis were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB) according to the manufacturer’s protocol. Sequencing was performed on the Illumina NextSeq 550 (75bp pair-end reads).


title: ERFKO_D_RNA-seq_rep3

source_name: mouse ES cells_FA


title: RASERFKO_D_RNA-seq_rep3


title: MZ_11086_late [DJ-21]


title: DZ_12073_early [DJ-45]

source_name: dizygotic_twin_early death


title: RASERFKO_D_RNA-seq_rep1


title: DZ_11070_early [DJ-19]


title: DZ_11067_early [DJ-17]


title: MZ_11105_early [DJ-23]


title: RASKO_D_RNA-seq_rep3


title: DZ_10599_early [DJ-16]


title: ERFKO_D_RNA-seq_rep1


title: Ctrl_OHT_PLO_RRBS_rep2


title: WT_D_RNA-seq_rep2


title: MZ_11086_early [DJ-22]


title: ERFKO_D_RNA-seq_rep2


title: RASKO_D_RNA-seq_rep2


title: DZ_10599_late [DJ-15]


title: DZ_11070_late [DJ-20]


title: DZ_10593_early [DJ-14]


title: RASKO_D_RNA-seq_rep1


title: MZ_10572_late [DJ-12]


title: 24hrPostSensATAC_PV_IP_AMPH_Iso2_rep3

city: Durham

first: David

last: Gallegos

state: North Carolina

address: 311 Research Dr

department: Neurobiology

institute: Duke University

description:
ATAC-Seq from Immunoprecipitated PV+ Interneurons (IP) 24 hours following final dose of Saline or AMPH administered each day for 6 days
PVATAC24hrPostSensRawCounts.xlsx

data_processing:
Illumina Hi-seq 4000 and Illumina Novaseq 6000 were used for sequencing using 50-base pair single end, and paired end S-Prime protocols respectively
The quality of the raw reads was determined using FastQC v0.11.2. All adaptors and reads with quality < 30 were trimmed using cutadapt v1.8.3. The reads were then aligned using bowtie2 v2.3.4.3 against the Gencode annotation GRCm38v72 reference genome with no more than 1 mismatch. The aligned reads were sorted and we filtered out unmapped reads using bedtools v2.25.0. Samples with a fraction of reads in peaks (FRIP) <0.125 or with mapped reads <4X the mean mapped reads were excluded.
Peaks were called by converting to a bed file using bedtools, filtering duplicates, and calling broad and narrow peaks using MACS2 v 2.1.2 (parameters: --nomodel --shift 37 --ext 73) as suggested for ATAC peaks. The overhanging peak ends were clipped off the ends of chromosomes using KentUtils bedClipv302.The peaks for all samples in each comparison were merged (# peaks) to create a master peak file for a basis of comparison.
Further analysis was carried out in R 3.4.4. A peak count matrix was creating using Rsubreadv1.28.1 to read in the ATAC counts from the merged peak regions. Prior to differential expression analysis, peaks with a CPM<1 in fewer than 3 samples were filtered out. DESeq2 v1.18.1 was then used to perform the differential peak analysis using an adjusted p-value threshold of p<0.05 for significance.
For visualization these peaks were converted into bigwigs using deepTools bamCoverage at 10bpresolution (parameters: -- normalizeUsing RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet of raw counts for MACS2 called peaks
Supplementary_files_format_and_content: BigWig fiiles for track visualization

source_name: Fresh Dissected Nucleus Accumbens

growth_protocol: Adult Rosa-LSL-Sun1-GFP x Pvalb-IRES-CRE mice or Rosa-LSL-Sun1-GFP x Sst-IRES-CRE

extract_protocol:
For each experiment, the two NAc samples from each single mouse were immeditaly placed in ice-cold homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH) after dissection. The tissue was minced with a razor blade and dounce homogenized using a loose pestle in 1.5mL of homogenization buffer supplemented with 1mM DTT, 0.15mM spermine, 0.5mM spermidine, 172g/L kynurenic acid, and EDTA-free protease inhibitor. A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further dounced with eight strokes of the tight pestle. When purifying RNA, RNaseOUT was added to all buffers at 60U/mL. When isolating nuclei for ATAC-seq, sodium butyrate was added to all buffers at a final concentration of 5mM. The sample was filtered through a 40μm strainer, mixed with 1.5mL of Working Solution (1:5 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH, pH 7.8 Diluent and Optiprep Density Gradient Medium), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 10,000xg for 18min on an Sw41Ti rotor in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface and pre-cleared by incubating with 20μL of protein G magnetic Dynabeads for 10min. After removing the beads with a magnet, the mixture was diluted with wash buffer (homogenization buffer plus 0.4% IGEPAL-630) and incubated with 10μL of 0.2mg/mL rabbit monoclonal anti-GFP antibody (Thermo Fisher Scientific Cat# G10362, RRID:AB_2536526) for 30min. 60μL of Dynabeads were added, and the mixture was incubated for an additional 25 minutes. To increase yield, the bead-nuclei mixture was placed on a magnet for 30sec to 1min, completely resuspended by inversion, and placed back on the magnet. This was repeated 5-7 times. Samples were then re-placed on the magnet for 5min. 1mL of supernatant was removed as the Unbound Nuclear Fraction (UF) and placed on ice. The remaining beads were washed 3 times in 1mL of wash buffer followed by one wash in 6mL wash buffer. The 6mL was then sequentially applied to the magnet until all beads had been isolated. The final bead mixture was resuspended in 100µL wash buffer for downstream applications. All steps were performed on ice or in the cold room, and all incubations were carried out using an end-to-end rotator. 10µL of suspended UF nuclei were counted on a hemocytometer and 5000 UF nuclei were removed for use in downstream applications as an approximate reference sample to the number of PV+ nuclei harvested per mouse (calculated range 3000-5000/mouse).
Omni-ATAC-seq was done as previously described in Corces MR, et al. (Nat Methods 14, 959–962 (2017))  with the sole modification of an adjusted Tn5 volume (0.5µL/sample) to avoid over transposition in a low number of input nuclei. Briefly, 5000 UF nuclei or the entirety of the bead-bound immunoprecipitated fraction nuclei (IP) were resuspended in cold RSB buffer prior to the beginning of the Omni-ATAC procedure. Libraries were made as described with the added inclusion of a 1:1 volume library cleanup with Ampure XP beads

treatment_protocol: On day one, after habituation, mice received a mock injection and were returned to the open field. Locomotor activity was monitored as horizontal distance traveled (cm). To study acute responses to AMPH, on day 2, either saline (as a vehicle control) or 3mg/kg AMPH was administered (i.p.) and mice were returned immediately to the open field for 60min before sacrifice and harvest

tag: strain

tag: tissue

value: Brain/ Nucleus Accumbens

tag: age

tag: genotype

value: Pvalb-IRES-Cre x INTACT Compound HET

value: AMPH

tag: cell type

value: PV+


title: DZ_10175_early [DJ-10]

value: early death

value: Buffy coat DNA samples extracted from whole blood

value: DNA hydroxymethylation


title: WT_D_RNA-seq_rep1


title: RASERFKO_N_RNA-seq_rep3

source_name: mouse ES cells_2iL-OHT


title: DZ_11067_late [DJ-18]

source_name: dizygotic_twin_late death


title: ERFKO_N_RNA-seq_rep3

source_name: mouse ES cells_2iL


title: RASERFKO_N_RNA-seq_rep2


title: 24hrPostSensATAC_PV_UF_SAL_Iso2_rep2

description:
ATAC-Seq from Nac Unbound Fraction (UF) 24 hours following final dose of Saline or AMPH administered each day for 6 days
PVATAC24hrPostSensRawCounts.xlsx

value: Saline

value: PV- UF


title: MZ_10572_early [DJ-11]

source_name: monozygotic_twin_early death


title: 24hrPostSensATAC_PV_IP_SAL_Iso2_rep2


title: DZ_10593_late [DJ-13]

value: late death


title: ERFKO_N_RNA-seq_rep2


title: 24hrPostSensATAC_PV_UF_SAL_Iso2_rep1


title: DZ_10129_late [DJ-7]


title: MZ_10090_late [DJ-6]

source_name: monozygotic_twin_late death


title: RASERFKO_N_RNA-seq_rep1


title: ERFKO_N_RNA-seq_rep1


title: 24hrPostSensATAC_PV_IP_AMPH_Iso2_rep1


title: 24hrPostSensATAC_PV_IP_AMPH_Iso2_rep2


title: DZ_10129_early [DJ-8]


title: MZ_10090_early [DJ-5]


title: DZ_10175_late [DJ-9]


title: WT_N_RNA-seq_rep3


title: 24hrPostSensATAC_PV_UF_SAL_Iso1_rep1


title: 24hrPostSensATAC_PV_IP_SAL_Iso2_rep1


title: 24hrPostSensATAC_PV_IP_AMPH_Iso1_rep1


title: 24hrPostSensATAC_PV_UF_AMPH_Iso1_rep1


title: 24hrPostSensATAC_PV_UF_AMPH_Iso2_rep1


title: RASKO_N_RNA-seq_rep3


title: WT_N_RNA-seq_rep2


title: MZ_10065_early [DJ-2]


title: 24PostSenPV_UF_AMPH_Isolation2_Sample2

description:
Total Nuclear RNA from Nac Unbound Fraction 24 Hr following Repeated Saline or AMPH administration
PV24HrPostRepeatedFigureS3GEOraw_counts_filt.csv

data_processing:
Illumina Hi-seq 4000 and Illumina Novaseq 6000 were used for sequencing using 50-base pair single end, and paired end S-Prime protocols respectively. Illumina Hiseq 2500 was used for Ribo-Tag Cytoplasmic RNA samples
FASTQ-formatted data files were processed using the Trimmomatic toolkit v0.38 to trim low-quality bases and Illumina sequencing adapters from the 3′ end of the reads. Only reads that were 32nt or longer after trimming were kept for further analysis. Reads were mapped to the Gencode annotation GRCm38v72 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Gene counts were compiled using the HTSeq tool. For this analysis, we used the standard method of only counting reads that mapped to known exons and reads with mapq > 30 were used for the differential expression analysis. Prior to differential expression analysis, genes with a counts per million (CPM) <1 for any sample were excluded.
[Total RNA]  Normalization and differential expression analyses were carried out using the DESeq2 Bioconductor package with the R statistical programming environment while accounting for batch, treatment, and PCR-bottlenecking effects. The false discovery rate was calculated to control for multiple hypothesis testing. In the case of cell-type specific genes, genes with FDR<0.05 were considered significantly differentially expressed. For cell-type specific stimulus-regulated genes, an FDR<0.1 was used.
[Cytoplasmic/Ribo-Tag RNA]  Aligned and sorted by coordinate  bam files were used as the input for CuffLinks CuffDiff v2.2.1 analysis using the using the Gencode vM21 transcript annotation gtf and following syntax: fdiff -L WT_IP,WT_INPUT,KO_IP,KO_INPUT -p 8 -o (Output Directory) -dispersion-method pooled -library-type fr-firststrand (Annotation gtf path)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig fiiles for track visualization
Supplementary_files_format_and_content: csv files include raw counts for multiple samples as labeled in Title
Supplementary_files_format_and_content: Xlsx file includes processed output from Cuffdiff of all aligned Ribo-Tag samples

source_name: Dissected Nucleus Accumbens

growth_protocol: Adult Rosa-LSL-Sun1-GFP x Pvalb-IRES-CRE mice, Rosa-LSL-Sun1-GFP x Sst-IRES-CRE,  Pvalb-2A-Cre x MeCP2 Ser421Ala KI, or hemizygous WT male littermates

extract_protocol:
[Total RNA]  For each experiment, the two NAc samples from each single mouse were thawed in ice-cold homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH). The tissue was minced with a razor blade and dounce homogenized using a loose pestle in 1.5mL of homogenization buffer supplemented with 1mM DTT, 0.15mM spermine, 0.5mM spermidine, 172g/L kynurenic acid, and EDTA-free protease inhibitor. A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further dounced with eight strokes of the tight pestle. When purifying RNA, RNaseOUT was added to all buffers at 60U/mL. When isolating nuclei for ATAC-seq, sodium butyrate was added to all buffers at a final concentration of 5mM. The sample was filtered through a 40μm strainer, mixed with 1.5mL of Working Solution (1:5 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH, pH 7.8 Diluent and Optiprep Density Gradient Medium), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 10,000xg for 18min on an Sw41Ti rotor in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface and pre-cleared by incubating with 20μL of protein G magnetic Dynabeads for 10min. After removing the beads with a magnet, the mixture was diluted with wash buffer (homogenization buffer plus 0.4% IGEPAL-630) and incubated with 10μL of 0.2mg/mL rabbit monoclonal anti-GFP antibody (Thermo Fisher Scientific Cat# G10362, RRID:AB_2536526) for 30min. 60μL of Dynabeads were added, and the mixture was incubated for an additional 25 minutes. To increase yield, the bead-nuclei mixture was placed on a magnet for 30sec to 1min, completely resuspended by inversion, and placed back on the magnet. This was repeated 5-7 times. Samples were then re-placed on the magnet for 5min. 1mL of supernatant was removed as the Unbound Nuclear Fraction (UF) and placed on ice. The remaining beads were washed 3 times in 1mL of wash buffer followed by one wash in 6mL wash buffer. The 6mL was then sequentially applied to the magnet until all beads had been isolated. The final bead mixture was resuspended in 100µL wash buffer for downstream applications. All steps were performed on ice or in the cold room, and all incubations were carried out using an end-to-end rotator. 10µL of suspended UF nuclei were counted on a hemocytometer and 5000 UF nuclei were removed for use in downstream applications as an approximate reference sample to the number of PV+ nuclei harvested per mouse (calculated range 3000-5000/mouse). RNA isolation was performed using the RNaqeuous Micro kit (Thermo Fisher) according to the manufacturer’s instructions, excepting that DNase digestion was not performed at this step, as the downstream library preparation included a DNase step. RNA was eluted in 15µL elution buffer from which 4µL was used for qRT-PCR gene enrichment validation.
[RiboTag/Cytoplasmic RNA]  NAc tissue was rapidly dissected and Dounce homogenized in a tissue weight to buffer volume ratio of 5% (0.6-1mL) of homogenization buffer (HB-S, 50mM Tris, 100mM KCl, 12mM MgCl2, 1% NP-40) supplemented with 200U/mL RNAaseOUT, 1X Protease inhibitor, 1mM DTT, 100ug/mL Cyclohexamide, and 1mg/mL Heparin. Homogenate was spun down at 10,000 RPM and the supernatant was moved to the immunoprecipitation step after removal of 80µL for input vs IP comparisons. To prepare the antibody-bead mixture, Dynabeads were first washed in 1X PBS before 10µL Rabbit α-HA tag antibody (Abcam, #9110, RRID:AB_307019) was added to 300µL PBS+60µL Dynabeads and rotated at 4ºC for 4hr.  For immunoprecipitation, the remaining supernatant was subsequently combined with α-HA antibody-bead mixture and rotated overnight at 4ºC. Beads were isolated, washed 3 times in high-salt buffer, and lysed in Qiagen lysis buffer RLT for elution. RNA was subsequently extracted using the Qiagen RNeasy Mini Kit.  SMART-Seq™ v4 Ultra™ Low Input RNA Kit (Takara Bio #634888) was used to convert RNA to cDNA, which was then amplified and sequenced using an Illumina Hiseq 2500.
[Total RNA]  Nugen Ovation Solo
[RiboTag/Cytoplasmic RNA]  SMART-Seq™ v4 Ultra™ Low Input RNA Kit
Total RNA-seq
Ribo-Tag

value: 24 Hr Post 3mk/kg AMPH for 6 Days


title: 24hrPostSensATAC_PV_UF_AMPH_Iso1_rep2


title: 24hrPostSensATAC_PV_IP_SAL_Iso2_rep3


title: 24hrPostSensATAC_PV_UF_SAL_Iso1_rep2


title: 24PostSenPV_UF_AMPH_Isolation1_Sample1


title: PHx4

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

country: China

institute: Fourth Military Medical University

description: Partial hepatectomy_Day14

data_processing:
Illumina Bcl2FastQ 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 Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_exp.txt: Tab-delimited text file includes RPKM values and counts for each Sample.

source_name: liver sinusoidal endothelial cells

growth_protocol: Mouse liver sinusoidal endothelial cells were purified using Miltenyi mouse anti-CD146 magnetic beads.

extract_protocol:
Liver sinusoidal endothelial cells were isolated from sham and PHx mice, total RNA was isolated from the cells using the Trizol (invitrogen). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies, USA) and then diluted to 10pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150bp) on HiSeq 3000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver sinusoidal endothelial cells

value: 7-8 weeks

value: Partial hepatectomy

tag: time point

value: 14 days post operation


title: MZ_10085_early [DJ-3]


title: RASKO_N_RNA-seq_rep2

value: Raslox/lox


title: 24hrPostSensATAC_PV_UF_AMPH_Iso1_rep3


title: ErfKO_clone_7_OHT_H3K27ac_FA_rep2

data_processing:
library strategy: CUT&RUN
Basecalling was performed using bcl2fastq version 2.20.0
Data were processed using a modified version of Cut&RunTools (Zhu et al., 2019).  Reads were adapter trimmed using fastp v.0.20.0 (Chen et al., 2018).  An additional trimming step was performed to remove up to 6bp adapter from each read.
Next, reads were aligned to a hybrid mm10 and E. coli (MG1655) genome using bowtie2 (Langmead et al., 2012) with the ‘dovetail’ and ‘sensitive’ settings enabled.  Aligned fragments were segregated into mouse and carry-over (E. coli) subsets.  macs2 (Zhang et al., 2008) was used to call peaks with q-value cutoff < 0.01.
Normalized reads per kilobase per million (RPKM) signal tracks were generated using the ‘bamCoverage’ utility from deepTools  (Ramirez et al., 2016) with parameters ‘center_reads’ and ‘extend_reads’ options enabled.  A bin-size of 25bp and smooth length of 75bp was used for Nanog, Otx2, and Sox2 data, and bin-size 75 and smooth-length 300bp for H3K27ac data.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RPKM normalized read density.

extract_protocol:
The CUT&RUN protocol was slightly modified from (Skene et al., 2018; Meers et al., 2019). In brief, cells were washed thrice with Wash Buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche complete Protease Inhibitor tablet EDTA free) and bound to activated Concanavalin A beads (Polysciences) for 10 minutes at room temperature. Cells were then permeabilized in Digitonin Buffer (0.05 % Digitonin and 0.1% BSA in Wash Buffer) and incubated with corresponding antibodies at 4°C for 2 hours. For negative controls, Guinea Pig anti-Rabbit IgG (Antibodies-online) was used. Following antibody incubation, cells were washed with Digitonin Buffer and incubated with a hybrid protein A-protein G-Micrococcal nuclease (pAG-MNase) at 4°C for 1 hour. Samples were washed in Digitonin Buffer, resuspended in 150 μl Digitonin Buffer and equilibrated to 0°C on ice water for 5 minutes. To initiate MNase cleavage, 3 μl 100 mM CaCl2 was added to cells and after 1 hour of digestion, reactions were stopped with the addition of 150 μl 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02 % Digitonin, 50 μg/ml RNase A, 50 μg/ml Glycogen). Samples were incubated at 37°C for 10 minutes to release DNA fragments and centrifuged at 16,000 g for 5 minutes. Supernatants were collected and a mix of 1.5 μl 20% SDS / 2.25 μl 20 mg/ml Proteinase K was added to each sample and incubated at 65°C for 35 minutes. DNA was precipitated with ethanol and sodium acetate and pelleted by high-speed centrifugation at 4°C, washed, air-dried and resuspended in 10 μ 0.1x TE.
The entire precipitated DNA obtained from CUT&RUN was used to prepare Illumina compatible sequencing libraries. In brief, end-repair was performed in 50 μl of T4 ligase reaction buffer, 0.4 mM dNTPs, 3 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB) and 1 U of Klenow fragment (NEB) at 20°C for 30 minutes. End-repair reaction was cleaned using AMPure XP beads (Beckman Coulter) and eluted in 16.5 μl of Elution Buffer (10 mM Tris-HCl pH 8.5) followed by A-tailing reaction in 20 μl of dA-Tailing reaction buffer (NEB) with 2.5 U of Klenow fragment exo- (NEB) at 37°C for 30 minutes. The 20 μl of the A-tailing reaction were mixed with Quick Ligase buffer 2X (NEB), 3000 U of Quick Ligase (NEB) and 10 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 50 μl and incubated at room temperature for 20 min. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM of EDTA, cleaned with AMPure XP beads and eluted in 14 μl of Elution Buffer. All volume was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T-3′ and TruSeq barcoded primer p5 5′-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (∗ represents a phosphothiorate bond and XXXXXXXX a barcode index sequence), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a band of 300bp approximately was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq500 (75bp pair-end reads).

value: FA+OHT

tag: antibody

value: anti-H3K27Ac (Abcam, Cat# ab4729, RRID:AB_2118291)


title: RASKO_N_RNA-seq_rep1


title: SUDHL2-shEGR1#8

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

description:
SUDHL2 cells transduced with shEGR1#8 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
SUDHL2-EGR1kd-RNASEQ.txt

data_processing:
Sequence reads were filtered for average QC score>30. Reads were mapped  with Bowtie2 to the hg19 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
RNAseq fpkm were generated by HISAT, StringTie and Ballgown by following Pertea et al.(2016).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq (bigwig file); RNA-seq (txt file: gene fpkm)

source_name: ABC DLBCL cell line (SUDHL2)

growth_protocol: DLBCL cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
ChIP experiments are followed by Rui et al., 2016, PNAS 113(46): E7260-E7267; Total mRNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330); cDNA library was constructed by using Illumina Truseq RNA Library Prep Kit (RS-122-2002).

treatment_protocol: Cells transduced by shRNA was induced by Doxycycline for 48hrs.

value: ABC DLBCL cell line (SUDHL2)


title: MZ_10065_late [DJ-1]


title: PHx3

description: Partial hepatectomy_Day14


title: SUDHL2-shEGR1#9

description:
SUDHL2 cells transduced with shEGR1#9 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
SUDHL2-EGR1kd-RNASEQ.txt


title: 24PostSenPV_UF_AMPH_Isolation3_Sample2

value: Brain/ Nucleus Accumbens

value: Pvalb-IRES-Cre x INTACT Compound HET


title: SUDHL2-shsc4

description:
SUDHL2 cells transduced with control shRNA that was induced for expresion with 20 ng/ml doxycycline for 2 days.
SUDHL2-EGR1kd-RNASEQ.txt

value: control shRNA


title: Sham3

value: Sham operation


title: 24PostSenPV_UF_AMPH_Isolation3_Sample1


title: 24PostSenPV_UF_SAL_Isolation3_Sample2

value: 24 Hr Post Repeated Saline


title: TMD8-shEGR1#9

description:
TMD8 cells transduced with shEGR1#9 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
TMD8-EGR1kd-RNASEQ.txt

source_name: ABC DLBCL cell line (TMD8)

value: ABC DLBCL cell line (TMD8)


title: WT_N_RNA-seq_rep1


title: ErfKO_clone_7_H3K27ac_PLO_rep2


title: Sham1


title: 24PostSenPV_UF_AMPH_Isolation2_Sample1

value: PV- UF


title: 24PostSenPV_UF_SAL_Isolation3_Sample1


title: ErfKO_clone_7_H3K27ac_FA_rep2

value: FA


title: ErfKO_clone_7_OHT_H3K27ac_PLO_rep2


title: ErfKO_clone_7_IgG_PLO_rep4

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: TMD8-shEGR1#8

description:
TMD8 cells transduced with shEGR1#8 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
TMD8-EGR1kd-RNASEQ.txt


title: Sham4

value: Liver sinusoidal endothelial cells


title: PHx1

description: Partial hepatectomy_Day14

value: 7-8 weeks


title: 24PostSenPV_UF_SAL_Isolation2_Sample2


title: LY10-shEGR1#9-3

description:
OCI-LY10 cells transduced with shEGR1#9 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
LY10-EGR1kd-RNASEQ.txt

source_name: ABC DLBCL cell line (OCI-LY10)

value: ABC DLBCL cell line (OCI-LY10)


title: TMD8-shsc4

description:
TMD8 cells transduced with control shRNA that was induced for expresion with 20 ng/ml doxycycline for 2 days.
TMD8-EGR1kd-RNASEQ.txt


title: 24PostSenPV_UF_SAL_Isolation2_Sample1


title: ErfKO_clone_10_OHT_H3K27ac_FA_rep1


title: ErfKO_clone_10_OHT_H3K27ac_PLO_rep1


title: 24PostSenPV_UF_SAL_Isolation1_Sample1


title: ErfKO_clone_10_IgG_PLO_rep3


title: LY10-shEGR1#9-1


title: LY10-shEGR1#9-2


title: ErfKO_clone_10_H3K27ac_FA_rep1


title: 24PostSenPV_IP_AMPH_Isolation2_Sample1

description:
Total Nuclear RNA from Immunoprecipitated PV+ Interneurons 24Hr following Repeated Saline or AMPH administration
PV24HrPostRepeatedFigureS3GEOraw_counts_filt.csv

value: 24 Hr Post 3mk/kg AMPH for 6 Days

value: PV+


title: 24PostSenPV_IP_AMPH_Isolation1_Sample1


title: ErfKO_clone_10_H3K27ac_PLO_rep1

value: Raslox/lox


title: Control_clone_2_OHT_H3K27ac_PLO_rep2

value: anti-H3K27Ac (Abcam, Cat# ab4729, RRID:AB_2118291)


title: LY10-shsc4-3

description:
OCI-LY10 cells transduced with control shRNA that was induced for expresion with 20 ng/ml doxycycline for 2 days.
LY10-EGR1kd-RNASEQ.txt


title: Control_clone_2_OHT_H3K27ac_FA_rep2

value: FA+OHT


title: 24PostSenPV_IP_AMPH_Isolation2_Sample2

value: Brain/ Nucleus Accumbens


title: 24PostSenPV_IP_AMPH_Isolation3_Sample2

value: Pvalb-IRES-Cre x INTACT Compound HET


title: 24PostSenPV_IP_AMPH_Isolation3_Sample1


title: 24PostSenPV_IP_SAL_Isolation2_Sample2


title: LY10-shEGR1#8-2

description:
OCI-LY10 cells transduced with shEGR1#8 that was induced for expresion with 20 ng/ml doxycycline for 2 days.
LY10-EGR1kd-RNASEQ.txt


title: LY10-shEGR1#8-3


title: LY10-shEGR1#8-1


title: siCD271#2-2

type: RNA

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

country: Japan

institute: Miyagi Cancer Center

description: Gene expression after 48hr lipofeation of sicontrol or siCD271 in lung sqmaous cell carcinoma cell line.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction buffer containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  SurePrint G3 Human Gene Expression 8x60K(G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by Nitrogen gas.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA from MCC148c cells was purified using RNeasy Mini Kits and QIAshredder columns (Qiagen, Canada).

treatment_protocol: The siRNA (siCD271 or si control) transfections were performed using Lipofectamine® RNAiMAX Reagent (Life Technologies, CA, USA) in antibiotic-free medium for 48 h.

tag: transfection

value: human lung squamous cell carcinoma


title: siCD271#2-1

tag: cell line


title: siCD271#1-1


title: 24PostSenPV_IP_SAL_Isolation3_Sample2


title: siCD271#1-2


title: Control_clone_2_IgG_PLO_rep6

tag: genotype/variation


title: LY10-shsc4-2

tag: treatment

value: control shRNA


title: sicontrol-4

source_name: sicontrol

value: sicontrol


title: BMDM KL3

city: Hangzhou

first: Di

last: Wang

state: Zhejiang

address: Yuhgang Tang Rd No.866

department: School of Medicine

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Reads Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: BMDM

growth_protocol: Mouse bone marrow cells were flushed from tibias and femurs with chilled Dulbecco’s modified Eagle’s medium (DMEM) and then cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 10 ng/ml macrophage colony- stimulating factor (PeproTech) to generate BMDMs.

extract_protocol:
Total RNA were extracted with TRIzol and followed by ilibrary construction according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For sample C1-3 and KC1-3, BMDMs were cultured in complete DMEM medium for 4 hours. For sample L1-3 and KL1-3, BMDMs were cultured in complete DMEM medium for 4 hours in the presence of 500 ng/ml LPS.

value: Bone Marrow-Derived Macrophage (BMDM)

value: post natal week 8


title: BMDM KL2


title: 24PostSenPV_IP_SAL_Isolation3_Sample1

value: 24 Hr Post Repeated Saline


title: 24PostSenPV_IP_SAL_Isolation1_Sample1


title: BMDM KL1


title: LY10-shsc4-1


title: 3HrSST_UF_SAL_Isolation4_Sample2

description:
Total Nuclear RNA from Nac Unbound Fraction 3Hr following Saline or AMPH administration
SST3HrSalvAMPHGEOraw_counts_filt.csv

value: Sst-IRES-Cre x INTACT Compound HET

value: Saline 3 Hr

value: SST- UF


title: Control_clone_2_H3K27ac_PLO_rep2


title: 24PostSensPV_IP_SAL_Isolation2_Sample1


title: Control_clone_2_H3K27ac_FA_rep2

value: FA


title: Control_clone_1_OHT_H3K27ac_FA_rep1


title: Control_clone_1_OHT_H3K27ac_PLO_rep1


title: BMDM KC2


title: Control_clone_1_IgG_PLO_rep5

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: EGR1CHIP-TMD8

description: Genomic DNA isolicated from immunoprecipitated chromatin using EGR1 antibody.

value: ABC DLBCL cell line (TMD8)

tag: chip antibody

value: EGR1 antibody (Santa Cruz sc-110)


title: EGR1CHIP-LY10-shsc4

value: ABC DLBCL cell line (OCI-LY10)


title: BMDM L3


title: 3HrSST_UF_SAL_Isolation4_Sample1


title: EGR1INPUT-TMD8

description: Genomic DNA INPUT sample from EGR1 chromatin immunoprecipitated experiment.


title: sicontrol-2


title: BMDM KC1


title: 3HrSST_IP_SAL_Isolation4_Sample2

description:
Total Nuclear RNA from Immunoprecipitated SST+ Interneurons 3Hr following Saline or AMPH administration
SST3HrSalvAMPHGEOraw_counts_filt.csv

value: SST+


title: Control_clone_1_H3K27ac_PLO_rep1

value: Raslox/lox

value: anti-H3K27Ac (Abcam, Cat# ab4729, RRID:AB_2118291)


title: Control_clone_1_H3K27ac_FA_rep1


title: 3HrSST_UF_AMPH_Isolation2_Sample3

value: Brain/ Nucleus Accumbens

value: 3mg/kg Amph 3 Hr


title: D3-UV damaged

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

institute: The Third Xiangya Hospital of Central South Uniiversity

data_processing:
Library Preparation included: 1) 3’ -adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~134-160bp PCR amplified fragments (corresponding to ~14-40nt small RNAs).
Completed libraries were quantified using an Agilent 2100 Bioanalyzer.
DNA fragments in well mixed libraries were denatured using 0.1M NaOH to generate single-stranded DNA molecules and loaded using the NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) according to instructions provided by the manufacturer.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: skin

extract_protocol:
skin were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® was used for library preparation. The NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) was used for sequencing on the Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissure

value: skin

value: 6-8 weeks


title: BMDM L1

value: Bone Marrow-Derived Macrophage (BMDM)

value: post natal week 8


title: 3HrSST_UF_AMPH_Isolation3_Sample1

value: Sst-IRES-Cre x INTACT Compound HET


title: BMDM C2


title: 3HrSST_IP_SAL_Isolation4_Sample1

value: Saline 3 Hr


title: C2-UV damaged


title: Control_clone_2_OHT_PLO_Otx2_rep2

value: anti-Otx2 (R&D systems Cat# AF1979, RRID:AB_2157172)


title: Control_clone_2_OHT_PLO_Nanog_rep2

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: EGR1CHIP-LY10-shEGR1#9


title: Control_clone_2_PLO_Nanog_rep4


title: BMDM L2


title: D2-UV damaged


title: C3-UV damaged


title: D1-UV damaged


title: sicontrol-3

value: sicontrol

value: human lung squamous cell carcinoma


title: Sal+AMPHMulti-seqBarcoded PV Nuclei

data_processing:
fastq generation with CellRanger mkfastq (v3.0.2) from raw bcl data (Illumina NextSeq 550 mid-output)
transcriptome alignment and count matrix generation with CellRanger count (v3.0.2) and mm10-3.0.0_pre-mrna.gtf
Genome_build: mm10
Supplementary_files_format_and_content: Filtered_feature_bc_matrix - This contains the matrix, features, and bar code files for further processing
Supplementary_files_format_and_content: PV_MULTIseq_classifications.csv -  Classifications of Multi-Seq barcode calls for each nucleus.  The treatment key is Bar5 = Saline-treated, Bar6 = AMPH-treated, Doublet = two nuclei in one sample, and Negative = Multi-seq Barcode was unable to be conclusively determined.

source_name: Pooled Fresh Dissected Nucleus Accumbens

growth_protocol: Adult Rosa-LSL-Sun1-GFP x Pvalb-CRE mice

extract_protocol:
Following treatment, Nucleus Accumbens tissue was dissected fresh before nuclei were isolated and FANS sorted for DAPI + GFP co positivity. 2,125 GFP+ nuclei were sorted into final volume of 40uL before loading 10X Chromium controller with 3' Gene Expression (v3) kit for single nucleus RNA-seq
Libraries were constructed according to the 10X Genomics protocol for 3' Gene Expression (v3)
snRNA-seq

treatment_protocol: On day one, after habituation, mice received a mock injection and were returned to the open field. Locomotor activity was monitored as horizontal distance traveled (cm). To study acute responses to AMPH, on day 2, either saline (as a vehicle control) or 3mg/kg AMPH was administered (i.p.) and mice were returned immediately to the open field for 35min before sacrifice and harvest

value: PV+ Interneuron

tag: sample type

value: PV+ Interneuron nuclei

tag: Sex

value: pooled male and female

value: Pvalb-IRES-Cre x INTACT Compound HET

value: mixed sample (35 min Post Sal or 3mg/kg Amphetamine)


title: BMDM C3


title: 3HrSST_UF_SAL_Isolation2_Sample1

value: Brain/ Nucleus Accumbens

value: SST- UF


title: BMDM C1


title: sicontrol-1


title: B3-UV damaged

value: skin


title: Control_clone_2_PLO_Otx2_rep2

value: Raslox/lox


title: REH_HOB_pb_r2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
We used the subread package (PMC3664803) to map the pair-end RNA-Seq reads to the human genome (hg38) and the featureCounts function within the Rsubread R package (PMC6486549) to summarize the number of reads for genes annotated by RefSeq. Gene expression level was quantified by Reads Per Kilobase of transcript, per Million mapped reads (RPKM; PMID: 18516045).
Genome_build: hg38
Supplementary_files_format_and_content: XLS file, from left to right represent "Gene symbol", "Entrz ID", and RPKM expression values for REH cells cultured alone or co-cultured with HOB or BMSCS (n =4 ).

source_name: REH (ATCC #CRL-8286)

extract_protocol:
RNA from the REH cells was extracted using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA).

value: REH (a cell line for ALL)

tag: culture condition

value: above HOB in co-culture

tag: replicate


title: C1-UV damaged

tag: strain

value: 6-8 weeks


title: Control_clone_2_PLO_IgG_rep4

tag: cell line background

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: 3HrSST_IP_SAL_Isolation2_Sample1

tag: tissue

tag: age

value: Sst-IRES-Cre x INTACT Compound HET

value: Saline 3 Hr

value: SST+


title: Control_clone_2_OHT_PLO_IgG_rep2


title: B2-UV damaged


title: 3HrSST_UF_SAL_Isolation1_Sample1

tag: genotype

tag: cell type


title: 3HrSST_IP_SAL_Isolation1_Sample1


title: Control_clone_2_OHT_FA_Otx2_rep2

source_name: mouse ES cells_FA-OHT

value: FA+OHT

tag: antibody

value: anti-Otx2 (R&D systems Cat# AF1979, RRID:AB_2157172)


title: REH_HOB_pb_r4


title: 3HrSST_UF_AMPH_Isolation2_Sample1

value: 3mg/kg Amph 3 Hr


title: Control_clone_2_FA_Otx2_rep2

source_name: mouse ES cells_FA

value: FA


title: REH_HOB_pb_r1


title: A3-normal


title: BMDM KC3

value: Bone Marrow-Derived Macrophage (BMDM)

value: post natal week 8


title: Control_clone_2_OHT_FA_Nanog_rep2

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: Control_clone_2_FA_Nanog_rep2


title: REH_HOB_pb_r3


title: REH_BMSCs_pd_r1

value: REH

value: acute lymphoblastic leukemia cell line

value: underneath BMSCs in co-culture

tag: sample id


title: A2-normal

value: skin


title: REH_BMSCs_pd_r2

tag: cell line


title: 3HrSST_IP_AMPH_Isolation2_Sample1

value: Brain/ Nucleus Accumbens


title: Control_clone_1_PLO_Otx2_rep1

value: Raslox/lox

tag: genotype/variation


title: REH_BMSCs_pd_r3


title: 3HrSST_IP_AMPH_Isolation2_Sample2

tag: treatment


title: REH_BMSCs_pd_r4


title: REH_HOB_pd_r2

value: underneath HOB in co-culture


title: 3HrSST_IP_AMPH_Isolation2_Sample3

value: Sst-IRES-Cre x INTACT Compound HET


title: B1-UV damaged

value: 6-8 weeks


title: 598E-CD163-eGFP-plus

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Replicate 3 from pig inoculated with live-attenuated PRRSV strain, bystander PAM

data_processing:
RNA-Seq reads were first trimmed with Trim Galore version 0.6.4 with default parameters which include filtering reads shorter than 30bp (--length 30) and low-quality ends from reads (Phred score: < 20; -q 20) and the option of removing reads with Ns (--max_n 0). The quality of reads before and after trimming was checked with FastQC version 0.11.7.
The filtered reads were aligned to the Sus scrofa genome (Sscrofa11.1; GCF_000003025.6) using STAR version 2.7 with default parameters.
Alignment files generated by STAR were then used to generate raw gene abundance counts using featureCounts from the subreads 2.0 toolkit, utilizing default parameters.
A data matrix of raw gene abundance counts for all samples was created using custom Python script and the data matrix was used to run the differential gene expression analysis in DESeq2 version 1.22.1 with default parameters. The differential expression result table generated by DESeq2 was annotated with gene information obtained from Ensembl BioMart for Sus scrofa.
Comparisons between Mock vs EFGP-, Mock vs. EFGP+, and EFGP- vs. EFGP+ were made.
Genome_build: Sus scrofa 11.1 (GCF_000003025.6)
Supplementary_files_format_and_content: Tab-delimited files with gene id and raw abundance count, as well as a DESeq2 generated further annotated file with differential gene expression (fold changes, q-values, etc).

organism: Sus scrofa

source_name: Pulmonary alveolar macrophages (PAM)

growth_protocol: • Prior inoculation PRRSV was cultured and titrated on PAM cells. • Each treatment group was accommodated in a separate room in the biosecurity level 2 (BSL-2) of animal research facilities and kept on standard weaning diet.

extract_protocol:
On 7 dpi animals from both DMEM and PRRSV treatment groups were euthanized. Immediately post-euthanasia, a single-cell suspension of PAM cell was isolated aseptically and sorted in to infected and bystander group based on EGFP expression. Sorted PAM cells stored at -80 0C in TRIzol (ThermoFisher Scientific). RNA extraction, RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). Total RNA was extracted following the Trizol Reagent User Guide (Thermo Fisher Scientific). RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation. The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

treatment_protocol: At 4 weeks, the two treatment groups were intramuscularily and intra-nasally inoculated with PRRSV and DMEM, respectively.

tag: breed

value: Landrace

value: PRRSV EGFP+

tag: agent

value: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), AY545985

tag: development stage

value: 4-week-old at the time of inoculation

tag: delivery mechanism

value: Intramuscular injection (IM) and Intra-nasal (IN) with total of 1x106 TCID50/pig

tag: extraction time

value: 7 days post inoculation (dpi)


title: 3HrSST_IP_AMPH_Isolation3_Sample1

value: 3mg/kg Amph 3 Hr

value: SST+


title: Control_clone_1_OHT_PLO_Otx2_rep1

source_name: mouse ES cells_2iL-OHT

value: anti-Otx2 (R&D systems Cat# AF1979, RRID:AB_2157172)


title: LGEs, 4 (CUT&Tag)

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
Library strategy: CUT&Tag
All raw sequence data were quality trimmed to a minimum Phred score of 20 using Trimmomatic.
Apparent PCR duplicates were removed using Picard MarkDuplicates vl.107.
All reads produced by CUT&Tag of MEIS2 were aligned to the mm10 mouse genome using Bowtie2 version 2.3.4.
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 software version 2.1.4 to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites.
Peaks with a false discovery rate lower than 5% were saved to detect chromosomal regions for further analyses. Visualization of peak distribution along genomic regions of genes of interest was performed with the Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: lateral ganglionic eminence

extract_protocol:
The cells were isolated from the LGE. Then, 1x10^5 cells were washed with 500 μl of wash buffer (10× wash buffer (-), 50× protease inhibitor cocktail, ddH2O) and centrifuged at 600 rcf for 3 min at RT
For library amplification, 24 μl of DNA was mixed with 1 μl of TruePrep Amplify Enzyme (TAE, Vazyme), 10 μl of 5× TruePrep Amplify Enzyme Buffer and 5 μl of ddH2O, and 5 μl of uniquely barcoded i5 and i7 primers from TruePrep Index Kit V2 for Illumina (Vazyme).The libraries were sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated

value: lateral ganglionic eminence

value: Embryonic day 14.5

tag: cut&tag antibody


title: REH_HOB_pd_r1

value: REH

value: acute lymphoblastic leukemia cell line

tag: culture condition

tag: replicate


title: LGEs, 2 (CUT&Tag)

tag: tissue

tag: strain

value: mouse polyclonal anti-MEIS2 antibody, Santa Cruz Biotechnology


title: A1-normal

tag: tissure

value: skin

tag: age


title: 598E-CD163-eGFP-minus

value: PRRSV EGFP-


title: Control_clone_1_PLO_Nanog_rep3

source_name: mouse ES cells_2iL

tag: cell line background

value: Raslox/lox

tag: antibody

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: 503A-CD163-eGFP-plus

description: Replicate 2 from pig inoculated with live-attenuated PRRSV strain, FL12-EGFP infected PAM

value: Landrace

value: PRRSV EGFP+


title: REH_HOB_pd_r4

tag: cell line

value: underneath HOB in co-culture

tag: sample id


title: Control_clone_1_OHT_PLO_Nanog_rep1

tag: genotype/variation

tag: treatment


title: Control_clone_1_OHT_PLO_IgG_rep1

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: LGEs, 1 (CUT&Tag)


title: REH_alone_r2

value: cultured alone


title: 500B-CD163-eGFP-plus

description: Replicate 1 from pig inoculated with live-attenuated PRRSV strain, FL12-EGFP infected PAM

tag: breed

tag: agent

value: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), AY545985

value: 4-week-old at the time of inoculation

value: Intramuscular injection (IM) and Intra-nasal (IN) with total of 1x106 TCID50/pig

value: 7 days post inoculation (dpi)


title: Exp_rep1

city: Beijing

first: Jixiang

last: Zhang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
CUT&RUN reads were trimmed for adaptor sequence, and aligned to mm10 genome using bowtie v2.2.5 with default parameters
We used picard 1.131 MarkDuplicates command to mark PCR duplicates in the sam file
Data were filtered using samtools software
Narrow peaks were called using MACS2 v2.1.2
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deeptools

source_name: fresh cochlearr tissues

extract_protocol:
pA-MN cleaved fragments released Prox1-DNA complexes were isolated with antibody.
Fresh cochlear tissues performed experiment by centrifuged for 5 min at 4 ℃ at 100g. DNA was purified by phenol-chloroform extraction and ethanol precipitated. NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) was used for library construction according to manufactory’s instruction.

value: ICR


title: Control_clone_1_PLO_IgG_rep3


title: Exp_rep3


title: Control_clone_1_OHT_FA_Nanog_rep1

value: FA+OHT


title: MZ_10085_late [DJ-4]

source_name: monozygotic_twin_late death

tag: twin type

tag: twin pair

tag: discordant death (when compared their corresponding twin)

value: late death

tag: tissue/molecule

value: Buffy coat DNA samples extracted from whole blood

tag: molecule subtype

value: DNA hydroxymethylation


title: 500H-CD163-plus

description: Replicate 3, negative control

value: DMEM

tag: development stage

tag: delivery mechanism

tag: extraction time


title: 501C-CD163-plus

description: Replicate 2, negative control


title: 500B-CD163-eGFP-minus

description: Replicate 2 from pig inoculated with live-attenuated PRRSV strain, bystander PAM

value: PRRSV EGFP-


title: Control_clone_1_FA_Otx2_rep1

value: Raslox/lox

value: FA

value: anti-Otx2 (R&D systems Cat# AF1979, RRID:AB_2157172)


title: Control_clone_1_OHT_FA_Otx2_rep1


title: REH_alone_r1

value: REH

tag: tissue

value: acute lymphoblastic leukemia cell line

tag: culture condition

tag: replicate


title: 501B-CD163-plus

description: Replicate 1, negative control

value: Landrace


title: REH_alone_r3

tag: cell line

value: cultured alone


title: Control_clone_1_FA_Nanog_rep1

tag: cell line background

tag: antibody

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: ErfKO_clone_7_PLO_Sox2_rep2

tag: genotype/variation

tag: treatment

value: anti-Sox2 Antibody (Millipore, Cat# AB5603, RRID:AB_2286686)


title: REH_HOB_pd_r3

value: underneath HOB in co-culture

tag: sample id


title: Control_rep1

tag: strain

value: ICR

value: control


title: REH_alone_r4


title: ErfKO_clone_7_PLO_Nanog_rep2


title: 503A-CD163-eGFP-minus

description: Replicate 1 from pig inoculated with live-attenuated PRRSV strain, bystander PAM

tag: breed

tag: agent

value: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), AY545985

value: 4-week-old at the time of inoculation

value: Intramuscular injection (IM) and Intra-nasal (IN) with total of 1x106 TCID50/pig

value: 7 days post inoculation (dpi)


title: Control_rep2


title: gastric cancer cells, Ab-3

first: Minzhi

last: Zhao

address: zhongguancunbeiyitiao NO.11

institute: National Center for Nanoscience and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.1.0 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.1.0.
Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: SNU5 cells were cultured in 1640 Medium supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were treated with AuSP-Peg-Ab (SP treat), AuNR-Peg-Ab (NR treat) and Ramucirumab (Ab treat) with the same concentration of Ramucirumab ( (8μg/mL in Ab) for 24 hours.

tag: cell type

value: gastric cancer cell

value: Ab (Ramucirumab)


title: MDA-MB-231 cells no mitotransfer (mito-mEmerald-), macrophages with mito transfer (mitoRFP+), rep1

city: Salt Lake City

first: Minna

last: Roh-Johnson

state: UT

address: 15 N Medical Drive, 5200J Emma Eccles Jones Medical Research Building

department: Biochemistry

institute: University of Utah

description:
16067X3
mda-mb-231.h5seurat
macrophage.h5seurat

data_processing:
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 3.02 (10X Genomics)
Genome_build: GRCh38, Ensemble 93
Supplementary_files_format_and_content: The processed files are the combined expression matrix consisting of all samples combined into a single H5Seurat file that contains cells post-QC filtering and contains all the molecular and associated metadata information.  The sample column contains the information for each raw file. 16067X1 = 1A, 16067X2 = 1B, 16067X3 = 2A, 16067X4 = 2B.

source_name: MDA-MB-231 cells, human blood monocyte derived macrophages

growth_protocol: Human monocytes were isolated from healthy human leukofilters through ficoll-paque separation and then selected for using CD14+ microbeads (Miltenyi). The resultant monocytes were lentivirally transduced to express mitochondrially targeted mEmerald and differentiated into macrophages for 7 days using GM-CSF. Macrophages were then co-cultured with breast cancer cells (MDA-MB-231) expressing mitochondrially targeted RFP for 24 hours prior to being harvested for flow cytometry.

extract_protocol:
Macrophage/cancer cell cocultures were harvested for flow cytometry using trypsin and subsequently stained with BV711-CD11B. Macrophages were FACS-isolated based on CD11B and mEmerald expression, and further isolated for the presence (RFP-positive) or absence (RFP-negative) of cancer cell mitochondria. Cancer cells were FACS-isolated based on RFP expression, and further isolated for the presence (mEmerald-positive) or absence (mEmerald-negative) of macrophage mitochondria. Following FACS isolation, cells were counted and checked for viability on a hemocytometer using trypan blue. Due to the low efficiency of mitochondrial transfer, each resulting population consisted of low cell numbers. Therefore, we pooled cancer cells that received macrophage mitochondria with macrophages that did not receive cancer cell mitochondria; and pooled cancer cells that did not receive macrophage mitochondria with macrophages that did receive cancer cell mitochondria.
Libraries were prepared using the 10X genomics Single Cell 3' Gene expression Library V3 following the manufacturer's protocol.

value: mixed sample (representing MDA-MB-231 cells, macrophages)

tag: protocol

value: MDA-MB-231 cells co-cultured with human blood monocyte-derived macrophages

tag: mitorfp mitochondrial transfer

value: Positive

tag: mitomemerald mitochondrial transfer

value: Negative


title: MDA-MB-231 cells no mitotransfer (mito-mEmerald-), macrophages with mito transfer (mitoRFP+), rep2

description:
16067X4
mda-mb-231.h5seurat
macrophage.h5seurat


title: MDA-MB-231 cells with mitotransfer (mito-mEmerald+), macrophages with no mito transfer (mitoRPF-), rep2

description:
16067X2
mda-mb-231.h5seurat
macrophage.h5seurat


title: gastric cancer cells, NR-3

value: NR (gold nano-rod or AuNR-Peg-Ab)


title: gastric cancer cells, Ab-1


title: MDA-MB-231 cells with mitotransfer (mito-mEmerald+), macrophages with no mito transfer (mitoRPF-), rep1

description:
16067X1
mda-mb-231.h5seurat
macrophage.h5seurat


title: 3HrSST_UF_AMPH_Isolation2_Sample2

source_name: Dissected Nucleus Accumbens

value: Brain/ Nucleus Accumbens

tag: age

tag: genotype

value: Sst-IRES-Cre x INTACT Compound HET

value: 3mg/kg Amph 3 Hr

value: SST- UF


title: gastric cancer cells, NR-2


title: ErfKO_clone_10_PLO_Sox2_rep1

value: Raslox/lox

value: anti-Sox2 Antibody (Millipore, Cat# AB5603, RRID:AB_2286686)


title: gastric cancer cells, NR-1


title: ErfKO_clone_10_PLO_IgG_rep1

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: MeV-exposed, day 7 post-exposure, GFP-

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were aligned to a hybrid genome consisting of human genome assembly GRCh38.p13 and a measles virus containing GFP. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.h5: HDF5 format file containing counts for each gene (row) and cell barcode (column).

molecule: polyA RNA

source_name: lung

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatant was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system.

value: measles virus

tag: days post-exposure

tag: tissue

value: lung

tag: cell sorting

value: GFP-


title: SSI_A9909

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Biotinylated RNA was hybridized to Illumina Mouse RefSeq-8 v2.0 Expression BeadChip (Gene Expression Omnibus Platform GPL6885), using reagents provided according to manufacturer’s instructions

scan_protocol: imaged using the Illumina HiScan-SQ

data_processing: Signal intensities were converted to log2 scale. Detection p values were calculated as described in the GenomeStudio Gene Expression Module User Guide. Data for array probes with insufficient signal were removed from the dataset (detection was defined as at least two arrays with detection p value < 0.1). After dropping non-performing probes, quantile normalization was applied across all arrays.

label: biotin

source_name: splenic lymphocytes from co-culture with M.tb.-Infected macrophages

label_protocol: Amplification and labeling of the RNA samples were performed using the Illumina TotalPrep RNA Amplification (Applied Biosystems) using an input of 500 ng of total RNA per sample.

growth_protocol: Male C57BL/6J mice age 4 weeks were purchased from Jackson Laboratories (Bar Harbor, Maine) and were used ages 6-10 weeks.  All mice were housed in microisolator cages and were given autoclaved food and water ad libitum.  Animal studies were performed under protocols approved by the Animal Care and Use Committee (ACUC) of CBER/FDA.  Within each experiment, all animals were age and sex matched. Groups of 7-10 C57BL/6J mice were vaccinated subcutaneously with 2 x 10^2 CFU of PAS, SSI, or heat killed BCG SSI (HK) (100oC for 30 min) (REF Kurtz 2015).   Three to five C57BL/6J mice from each vaccine group, and three to five naïve control mice, were challenged aerogenically with MTB Erdman eight weeks after vaccination to assess protective efficacy.  MTB was suspended in PBS-0.04% Tween 80, and mice were challenged over a 30-min exposure in a Middlebrook Chamber (Glas Col, Terre Haute, IN) with approximately 100 CFU delivered to the lungs.  The remaining mice from each vaccine group, a minimum of 3 animals, were used for in vitro cell culture assays.

extract_protocol: Cells recovered from the supernatant of the co-culture assays were pelleted, resuspended in RNALater, and stored at -80oC until RNA purification.  RNA was extracted using Qiagen RNeasy Kits, treated with DNase to remove contaminating DNA, and then purified using QiaQuick Spin kits.  Purified RNA was quantified using a Nanodrop (ThermoFisher Scientific), and cDNA synthesis performed using commercially available kits and by following manufacturer’s instructions, as previously described (REF).  Quality of extracted RNA was verified by Bioanalyzer 2100 (Agilent) and all samples had an RNA Integrity Number (RIN) greater than 8.5

treatment_protocol: Co-cultures were performed in 24-well tissue culture plates as described previously (REF).  Briefly, mouse bone marrow macrophages (BMMØ) were cultured to confluency and infected for 2 hours with M. tb. Erdman at a multiplicity of infection (MOI) of 1:100 (bacterium-to-BMMØ) and washed extensively with antibiotic-free medium.  Single-cell suspensions of splenic lymphocytes or PBL derived from vaccinated mice (5 x 10^6/well) were added to M.tb.-infected macrophages.  Intracellular bacterial burdens in adherent infected macrophages were determined by lysing the macrophages with 1ml water + 0.05% Tween 80, and plating the lysate as previously described  (REF).

tag: immunization (of lymphocyte donor mouse)

value: SSI

value: splenocytes from mice inoculated with M. bovis BCG Copenhagen in vivo, then co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted

tag: array barcode


title: gastric cancer cells, Ab-2

value: gastric cancer cell

tag: cell line

value: Ab (Ramucirumab)


title: Mock-exposed, day 14 post-exposure

description: mock

tag: treatment

value: mock


title: ErfKO_clone_7_PLO_IgG_rep2

tag: cell line background

tag: genotype/variation

tag: antibody


title: MeV-exposed, day 14 post-exposure, GFP-


title: gastric cancer cells, SP-3

value: SP (gold nano-sphere or AuSP-Peg-Ab


title: HK_A9910

value: SSI HK

value: splenocytes from mice inoculated with heat killed BCG SSI (HK)  in vivo, then co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted


title: gastric cancer cells, SP-2


title: Control_clone_2_PLO_Nanog_rep2

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: Control_clone_2_PLO_Sox2_rep2


title: HK_A9906


title: MeV-exposed, day 7 post-exposure, GFP+

value: GFP+


title: SSI_A9905


title: PAS_A9904

value: PAS

value: splenocytes from mice inoculated with Mycobacterium bovis BCG Pasteur (PAS)  in vivo, then co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted


title: ErfKO_clone_10_PLO_Nanog_rep1

value: Raslox/lox


title: Control_clone_2_PLO_IgG_rep2

value: anti-IgG (Antibodies-Online, Cat# ABIN101961,RRID:AB_10775589)


title: PAS_A9908


title: Naive_A9903

value: Naive

value: splenocytes from naïve mice, co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted


title: HK_A9902


title: Control_clone_1_PLO_Sox2_rep1

value: anti-Sox2 Antibody (Millipore, Cat# AB5603, RRID:AB_2286686)


title: H292NC3

city: Xuzhou

first: yeqing

last: zhou

address: 99 West Huaihai Road

institute: Xuzhou Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: human cell line

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).

value: Negative control


title: SSI_A9901

value: SSI

value: splenocytes from mice inoculated with M. bovis BCG Copenhagen in vivo, then co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted


title: MeV-exposed, day 3 post-exposure, GFP+

value: measles virus

value: lung


title: MeV-exposed, day 14 post-exposure, GFP+


title: PAS_A9900


title: Exp_rep2

tag: strain

value: ICR


title: H292NC1


title: Control_rep3

value: control


title: Mock-exposed, day 3 post-exposure

value: mock


title: HFD PCN 27

city: Oulu

first: Jukka

last: Hakkola

address: Aapistie 5

department: Research Unit of Biomedicine

country: Finland

institute: University of Oulu

description:
processed data file:
Chow vs HFD PCN
HFD vs HFD PCN
HFD vehicle vs HFD PCN

data_processing:
Base calling was done with Real-Time Analysis (RTA) software version 2.
75 base pair paired-end reads were aligned to mouse Ensembl reference genome GRCm38.92 with HISAT2
Reads per gene were counted with HTSeq
Differentially expressed genes were determined with DESeq2 using Benjamini-Hochberg corrected adjusted p-value cutoff of <0.05
Genome_build: mm10
Supplementary_files_format_and_content: .txt files which include differentially expressed genes, reads per gene in all samples and log2 fold changes.

source_name: HFD PCN_liver

growth_protocol: 6-week old mice were kept on regular chow or high-fat diet for 15-weeks to induce obesity and obesity-related metabolic impairments.

extract_protocol:
Liver pieces were lysed to RNAzol RT (Sigma-Aldrich) and total RNA was extracted per manufacturer's protocol. Samples were DNAse treated with Rnase-free Dnase set (Qiagen)
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Obese mice were treated with PCN (50 mg/kg intraperitoneally) or vehicle for four days once a day.

tag: diet

value: High-fat diet (HFD)

value: 50 mg/kg PCN

value: liver


title: Control_clone_1_PLO_IgG_rep1

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI


title: MeV-exposed, day 3 post-exposure, GFP-

value: GFP-


title: H292_1_3

value: SH3PXD2A-AS1 knockdown


title: H292NC2


title: QuantSeq - body-wall muscle cells 1.5 fold embryos mir-1(luc108) #1

city: Vienna

first: Jingkui

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description:
QuantSeq, 5k cells, sorted body-wall muscles (myo-3p::YFP)
mutant_135696

data_processing:
UMIs were first extracted with UMI-tools. QuantSeq raw reads were then processed by trimming adaptors and first 4bps of low quality and mapped to the C. elegans genome (WBcel235) using STAR-aligner with the parameter max_IntronL = 50000. Duplicated mapped reads were discarded with UMI-tools and UMI counts were quantified using HTSeq-count.
Genome_build: WBcel235
Supplementary_files_format_and_content: count data as tab separated text

organism: Caenorhabditis elegans

source_name: Body-wall muscle cells - 1.5 fold embryos

growth_protocol: Wild-type and miR-1 mutant worms were grown under standard conditions at 20 degrees

extract_protocol:
RNA was extracted using Direct-zol RNA Microprep Kit (Zymo Research, cat #R2060)
QuantSeq 3’mRNA library prep kit FWD for Illumina (Lexogen)

treatment_protocol: Embryos were dissociated (using chitinase and pronase) and YFP positive muscle cells were isolated by FACS

value: lucEx1207(myo-3p::YFP); mir-1(luc108) I

tag: developmental stage

value: Embryo - 1.5 fold stage

tag: cell type

value: Body-wall muscle


title: HFD PCN 11


title: H292_1_2


title: gastric cancer cells, SP-1

value: gastric cancer cell

value: SP (gold nano-sphere or AuSP-Peg-Ab


title: HFD Vehicle 55

description:
processed data file:
Chow vs HFD Vehicle
HFD vs HFD Vehicle
HFD vehicle vs HFD PCN

source_name: HFD Vehicle_liver

value: 30% DMSOin corn oil


title: QuantSeq - body-wall muscle cells 1.5 fold embryos wt #2

description:
QuantSeq, 5k cells, sorted body-wall muscles (myo-3p::YFP)
wt_135695


title: HFD PCN 5


title: Control_clone_1_PLO_Nanog_rep1

data_processing:
library strategy: CUT&RUN
Basecalling was performed using bcl2fastq version 2.20.0
Data were processed using a modified version of Cut&RunTools (Zhu et al., 2019).  Reads were adapter trimmed using fastp v.0.20.0 (Chen et al., 2018).  An additional trimming step was performed to remove up to 6bp adapter from each read.
Next, reads were aligned to a hybrid mm10 and E. coli (MG1655) genome using bowtie2 (Langmead et al., 2012) with the ‘dovetail’ and ‘sensitive’ settings enabled.  Aligned fragments were segregated into mouse and carry-over (E. coli) subsets.  macs2 (Zhang et al., 2008) was used to call peaks with q-value cutoff < 0.01.
Normalized reads per kilobase per million (RPKM) signal tracks were generated using the ‘bamCoverage’ utility from deepTools  (Ramirez et al., 2016) with parameters ‘center_reads’ and ‘extend_reads’ options enabled.  A bin-size of 25bp and smooth length of 75bp was used for Nanog, Otx2, and Sox2 data, and bin-size 75 and smooth-length 300bp for H3K27ac data.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RPKM normalized read density.

extract_protocol:
The CUT&RUN protocol was slightly modified from (Skene et al., 2018; Meers et al., 2019). In brief, cells were washed thrice with Wash Buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche complete Protease Inhibitor tablet EDTA free) and bound to activated Concanavalin A beads (Polysciences) for 10 minutes at room temperature. Cells were then permeabilized in Digitonin Buffer (0.05 % Digitonin and 0.1% BSA in Wash Buffer) and incubated with corresponding antibodies at 4°C for 2 hours. For negative controls, Guinea Pig anti-Rabbit IgG (Antibodies-online) was used. Following antibody incubation, cells were washed with Digitonin Buffer and incubated with a hybrid protein A-protein G-Micrococcal nuclease (pAG-MNase) at 4°C for 1 hour. Samples were washed in Digitonin Buffer, resuspended in 150 μl Digitonin Buffer and equilibrated to 0°C on ice water for 5 minutes. To initiate MNase cleavage, 3 μl 100 mM CaCl2 was added to cells and after 1 hour of digestion, reactions were stopped with the addition of 150 μl 2x Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02 % Digitonin, 50 μg/ml RNase A, 50 μg/ml Glycogen). Samples were incubated at 37°C for 10 minutes to release DNA fragments and centrifuged at 16,000 g for 5 minutes. Supernatants were collected and a mix of 1.5 μl 20% SDS / 2.25 μl 20 mg/ml Proteinase K was added to each sample and incubated at 65°C for 35 minutes. DNA was precipitated with ethanol and sodium acetate and pelleted by high-speed centrifugation at 4°C, washed, air-dried and resuspended in 10 μ 0.1x TE.
The entire precipitated DNA obtained from CUT&RUN was used to prepare Illumina compatible sequencing libraries. In brief, end-repair was performed in 50 μl of T4 ligase reaction buffer, 0.4 mM dNTPs, 3 U of T4 DNA polymerase (NEB), 9 U of T4 Polynucleotide Kinase (NEB) and 1 U of Klenow fragment (NEB) at 20°C for 30 minutes. End-repair reaction was cleaned using AMPure XP beads (Beckman Coulter) and eluted in 16.5 μl of Elution Buffer (10 mM Tris-HCl pH 8.5) followed by A-tailing reaction in 20 μl of dA-Tailing reaction buffer (NEB) with 2.5 U of Klenow fragment exo- (NEB) at 37°C for 30 minutes. The 20 μl of the A-tailing reaction were mixed with Quick Ligase buffer 2X (NEB), 3000 U of Quick Ligase (NEB) and 10 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 50 μl and incubated at room temperature for 20 min. The adaptor was prepared by annealing the following HPLC-purified oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). Ligation was stopped by adding 50 mM of EDTA, cleaned with AMPure XP beads and eluted in 14 μl of Elution Buffer. All volume was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T-3′ and TruSeq barcoded primer p5 5′-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (∗ represents a phosphothiorate bond and XXXXXXXX a barcode index sequence), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a band of 300bp approximately was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina NextSeq500 (75bp pair-end reads).

value: Raslox/lox

value: anti-Nanog (Abcam, Cat# ab80892, RRID:AB_2150114)


title: H292_1_1


title: HFD Vehicle 23


title: QuantSeq - body-wall muscle cells 1.5 fold embryos wt #1

description:
QuantSeq, 5k cells, sorted body-wall muscles (myo-3p::YFP)
wt_135694


title: QuantSeq - body-wall muscle cells 1.5 fold embryos mir-1(luc108) #2

description:
QuantSeq, 5k cells, sorted body-wall muscles (myo-3p::YFP)
mutant_135697


title: HFD Vehicle 15


title: Naive_A9899

value: Naive

value: splenocytes from naïve mice, co-cultured with M. tb infected mouse bone marrow macrophages, then re-isolated and rna-extracted


title: Control 2

city: Wuhan

first: Changmin

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

description:
Bovine
C2

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Use hisat2 software (v2.0.4) to compare the reads to the cow reference genome (ARS-UCD1.2).
Then, use HTSeq software (v0.9.1) to obtain genes using edgeR software (v3.16.5) to normalize and calculate the fold change and p value between samples, screening differentially expressed lncRNA.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: LncRNA_Expression_Profiling.xlsx: Excel file includes raw counts and normalized values.

organism: Bos taurus

source_name: MAC-T cell

growth_protocol: MAC-T cells were cultured in DME/F12 medium supplemented with 10% fetal bovine serum (Gibco, United States), and cultured in a 37℃, 5% CO2 incubator.

extract_protocol:
RNA extraction protocol: Total RNA was harvested by Trizol.
Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

treatment_protocol: The two bacteria were heated in 63℃ for 30 min. After MAC-T cells were cultured for 12h in 6-well plates with 2×10^5 cells, the inactivated bacterial strains were added according to 10:1 (bacterial: cells).

value: MAC-T cell

value: untreated


title: HFD 38

description:
processed data file:
Chow vs HFD
HFD vs HFD Vehicle
HFD vs HFD PCN

value: High-fat diet (HFD)


title: Control 1

description:
Bovine
C1


title: DMSO_treatment_biological_rep3

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

description: Gene expression after 24hr in SH-SY5Y treated by DMSO

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: DMSO treatment, biological rep3

growth_protocol: Neuroblastoma SH-SY5Y cells were maintained at 37°C in the MEM or DMEM/F12 medium supplemented with 10-15% fetal bovine serum. MI-773 (Cat: S7649 Selleck, TX, USA) was dissolved in DMSO (Cat: D4540 Sigma–Aldrich, St. Louis, MO, USA)

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Arraystar Human LncRNA microarray V4.  20,730 coding transcripts and 40,173 LncRNAs and which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: SH-SY5Y cells were treated with 1uM MI-773 and control group cells were treated with the same volume of DMSO (DMSO volume < 0.1% cell culture fluid volume and its toxicity＜0.1%(v/v)). 24 hours later. Human Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.

value: DMSO


title: S. aureus group 3

description:
Bovine
S3

value: treated with S. aureus for 24 hours


title: WT2_1

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Wild type, high weight band, replicate 1.

data_processing:
Library strategy: NET-seq
Analysis of the data followed previously published protocols from the Churchman lab.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1). The FastQC results indicate the data is of a high quality value, meaning that trimming for sequence quality was not necessary.
The original fastq sequences were trimmed  using Trimmomatic v0.33 to remove potential sequencing primers and adapters.
The trimmed sequences were then collapsed to remove identical sequences which may be the result of PCR duplications using fastx_collapser v0.0.14 from the FASTX toolkit .
Sequences for rRNA genes were downloaded from SILVA 132 and tRNA genes were downloaded from GtRNAdb.  The rRNA genes were further filtered to include only Drosophila melanogaster sequences using a custom script. A star genome index was generated from the combined rRNA and tRNA sequences using STAR v20201.
The trimmed sequences for each of the eight samples were then mapped against the rRNA and tRNA database using star aligning RNA filtered reads that map to a single location in the genome.
After alignment, the resulting BAM files were split according to their strandedness using samtools v1.3.1.
The BED files were then converted to WIG files using a custom script, only accounting for the very first base in the read, which allows for a single-base resolution of the stopping point of the ribosome.
Genome_build: dm6
Supplementary_files_format_and_content: wig files representing number of unique reads beginning at each specified location on either the forward (FWD) or reverse (REV) strand

organism: Drosophila melanogaster

growth_protocol: Drosophila melanogaster S2 cells (obtained from Thermo Fisher Scientific, Waltham, MA 02451), were cultured in Schneider’s Drosophila medium (Life Technologies, Austin, TX 78744 ) supplemented with 10%  heat activated fetal bovine serum  (Sigma, St Louis, MO 63146),  100 U/ml penicillin and 100 μg/ml streptomycin at 25oC.  All experimental samples and controls were growth time and cell-density matched.

extract_protocol:
Nascent RNA isolation was performed as described at Weber et al and cap selection was done using GFP-elF4E recombinant protein generously provided by Dr. G. Zentner, Indiana University. RNA:GFP-elF4E complexes were pulled by GFP-nAb Magnetic Agarose beads (Allele Biotech) according to manufacturer’s protocol.
Sequencing library preparation for nascent RNA samples was performed according Illumina Protocol with slight modification.  After 3’- SR adaptor ligation, RNA was fragmented to 30-100 nucleotides with the RNA Fragmentation Reagent (Albion, AM8740) and purified according to Mayer et al, 2015. In order to prevent RNA fragments ligation, we performed 3’-OH phosphorylation with T4 PNK (3’ phosphatase minus) before hybridization of reverse transcription primer and 5’-SR adaptor ligation. After reverse transcription with Superscript Reverse Transcriptase (Invitrogen) we purified cDNA on 15% polyacrylamide TBE-urea gel to avoid primer dimer formation, excised gel region between 50 and 300 nt and extracted cDNA. After PCR amplification we performed quality control (QC) and size selection. To be confident on PCR products we did cloning and sequencing by using Zero Blunt TOPO PCR Cloning kit (ThermoFisher Scientific). Positive colonies were harvested, plasmid DNA was purified with QIAprep Spin Miniprep kit (Qiagen) and digested with EcoR1.  Digested products were visualized on 1% agarose gel and sent to sequence (Eurofins Scientific).

treatment_protocol: siRNA mediated PARP1 knockdown was done as described previously.  Depletion of PARP1 was confirmed by western blot (protein level) and quantitative PCR (transcript level).

value: wild type


title: S. aureus group 2

description:
Bovine
S2


title: Chow 19

description:
processed data file:
Chow vs HFD
Chow vs HFD Vehicle
Chow vs HFD PCN

value: Regular chow

value: liver


title: HFD 30


title: Chow 17


title: Control 3

description:
Bovine
C3


title: E. coli group 3

description:
Bovine
E3

value: treated with E. coli for 24 hours


title: S. aureus group 1

description:
Bovine
S1


title: HFD 4


title: KD2_2

description: PARP-1 knockdown high weight band, replicate 2.

value: PARP-1 knockdown


title: KD2_1

description: PARP-1 knockdown high weight band, replicate 1.


title: DMSO_treatment_biological_rep2

source_name: DMSO treatment, biological rep2

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)


title: WT2_2

description: Wild type, high weight band, replicate 2.


title: WT1_2

description: Wild type, low weight band, replicate 2.


title: KD1_2

description: PARP-1 knockdown low weight band, replicate 2.


title: WT1_1

description: Wild type, low weight band, replicate 1.


title: Chow 8


title: E. coli group 2

description:
Bovine
E2


title: DMSO_treatment_biological_rep1

source_name: DMSO treatment, biological rep1


title: MI-773_treatment_biological_rep3

description: Gene expression after 24hr in SH-SY5Y treated by MI-773

source_name: MI-773 treatment, biological rep3


title: E. coli group 1

description:
Bovine
E1


title: MI-773_treatment_biological_rep2

source_name: MI-773 treatment, biological rep2


title: MI-773_treatment_biological_rep1

source_name: MI-773 treatment, biological rep1