title: NiSO4 dose level 6 bio rep 2 [Ni_P1_B07_S17]

description:
96 well plate
Ni_P1_B07_S17_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to indexed FHM genome with 26,150 gene models loaded within the genome (WIOS00000000; BioSample SAMN12875914). STAR "--quantMode GeneCounts" was used to produce raw counts from the mapping; reverse strand count column was used as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with gene models are available from the authors.
Samples with <2 million raw counts and/or less than 50% unique mapping rate were removed, and within-chemical features (genes) with mean raw counts <5 across all samples were filtered from respective raw counts matrices.
For each chemical, the raw counts for the remaining features were normalized to counts per million reads (CPM), and after adding a pseudo-count of 1 to prevent taking log of zero counts, log2 transformed.
For each chemical, an MDS plot of the normalized data was generated. Individual samples separated from all remaining samples on either principle component #1 (PC1) or principle component #2 (PC2) by >2x the span of all other samples on the corresponding PC were removed from further analysis. Qualitative assessment was applied and samples with a relatively large Euclidean distance from all other remaining samples on MDS plots were also excluded, along with samples especially distant from corresponding replicates within dose.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: For each chemical, tab delimited text matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: For each sample, tab delimited text matrix table with normalized expression values for every gene and every sample that passed all filtering.

extract_protocol:
Larvae remained in their 1 mL deep wells, exposure solution was removed and replaced with lysis buffer, a bead was added to each well, and subjects were homogenized in their wells.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.


title: NiSO4 dose level 5 bio rep 2 [Ni_P1_B06_S18]

status: Public on Jan 01 2023

type: SRA

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

country: USA

description:
96 well plate
Ni_P1_B06_S18_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

library_source: transcriptomic

molecule: total RNA

organism: Pimephales promelas

source_name: whole body

treatment_protocol: For ten different chemicals, 24h post-hatch individual fathead minnow larvae were statically exposed in 96 deep well plates to controls and a half-log dilution series of treatment concentrations. Exposures were for 24 hours. Subjects from all doses that did not exhibit excessive levels of mortality were further processed.

tag: tissue

value: whole body

tag: developmental stage

value: larva

tag: age

value: 5 dpf/24 hr post hatch

tag: Sex

tag: treatment

tag: concentration

tag: time point

value: 24 hr


title: Fat Subcutaneous replicate 1

city: Tabriz

first: Sana

last: Farhadi

address: Golgasht street

country: Iran

institute: Tabriz University

data_processing:
Fastqc-Trimmomatics-Tophat-Cufflink-Cuffmerge-cuffdiff-rstudio-Enrichment analysis-Network analysis
Sequenced reads were trimmed for adaptor and low-quality sequence
Clean reads mapped to Ovis-aries whole genome using Tophat software
Assembled reads
individual transcripts were merged to form a single transcript assembly
merged transcript was used for quantification of the transcripts
Genome_build: Ovis-aries
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

organism: Ovis aries

source_name: Fat Subcutaneous

growth_protocol: All lambs were weaned at 90 days of age and then fostered under similar conditions at the research station of the Faculty of Agriculture, University of Tabriz, Tabriz, Iran (Khalatpoushan). The lambs were housed in individual pens and provided the same diet ad libitum for 120 days. Animals were slaughtered after 7 months.ll of the chicks were mintained under normal condition until 21 days of age and then cold temperature was employed to induce ascites in almost all of the ascites susceptible chickens

extract_protocol:
Total RNA was extracted using TRIzol reagent using manufacturer instractions
PolyA enriched RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: strain

value: Iranian native Sheep breed


title: NiSO4 dose level 2 bio rep 3 [Ni_P1_C03_S28]

description:
96 well plate
Ni_P1_C03_S28_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Tumor1_tRNA

city: Patras

first: Constantinos

last: Stathopoulos

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

description:
RNA from lung cancer biopsies followed by size selection
tRNAs.xlsx

data_processing:
miRNAs, tRFs and tRNAs were analyzed using an in-house build script.
human tRFs from the tRFdatabase (http://genome.bioch.virginia.edu/trfdb/) were counted directly in the fastq files.
tRNAs were mapped to an artificial tRNA genome consisting of unique sequences of hg38 tRNAs (http://gtrnadb.ucsc.edu/) using bowtie and further counted using bedtools coverage
miRNAs were mapped to an artificial miRNA genome consisting of human miRNAs from the miRdatabase (http://www.mirbase.org/)  using bowtie and further counted using bedtools coverage
Genome_build: hg38
Supplementary_files_format_and_content: abundance measurements

organism: Homo sapiens

source_name: lung cancer biopsy tissue

growth_protocol: Tumor specimens were obtained by surgical procedures

extract_protocol:
Frozen tissues were immediately lysed, and small and large RNA fractions were extracted and isolated using PureLink RNA mini Kit and mirVana miRNA Isolation Kit (Ambion)
Ion Total RNA-Seq Kit v2 protocol for small RNA sequencing

value: lung cancer biopsies


title: GL26130_CD3posP1_E03_R1

city: Boston

first: Elizabeth

last: Perez

state: MA

address: 30 Fruit Street

institute: MGH

library_source: transcriptomic single cell

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

organism: Mus musculus

source_name: brain

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain

tag: cell type

value: Tcell

value: ctrl


title: GL26130_CD3posP1_F07_R1


title: NiSO4 control bio rep 3 [Ni_P1_C01_S37]

description:
96 well plate
Ni_P1_C01_S37_L005
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Ykl-3

first: Sung-Hee

middle: Seanna

last: Yoon

address: 50 Blossom St

institute: Massachusetts General Hospital

description: Bulk-RNA Seq

data_processing:
Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR v.2.7.2b.
Transcript abundances were calculated using RSEM v.1.3.0
Differential gene expression analysis was performed using DESeq2
Supplementary files format and content: Excel table with FPKM values for all genes in all samples

source_name: whole kidney

extract_protocol:
Whole mouse kidneys were subjected to Trizol/Chloroform based RNA extraction
mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray. Libraries were sequenced on the BGISEQ500 platform.

value: whole kidney

value: male


title: Ykl-4

description: Bulk-RNA Seq


title: GL26130_CD3posP1_E02_R1


title: NiSO4 dose level 4 bio rep 2 [Ni_P1_B05_S19]

description:
96 well plate
Ni_P1_B05_S19_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Tumor5_Small

description:
RNA from lung cancer biopsies followed by size selection
miRNAs.xlsx
tRFs.xlsx


title: Ykl-2

description: Bulk-RNA Seq


title: Tumor4_Small


title: NiSO4 dose level 3 bio rep 2 [Ni_P1_B04_S20]

description:
96 well plate
Ni_P1_B04_S20_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 2 bio rep 2 [Ni_P1_B03_S6]

description:
96 well plate
Ni_P1_B03_S6_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: NiSO4 dose level 1 bio rep 2 [Ni_P1_B02_S7]

description:
96 well plate
Ni_P1_B02_S7_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Tumor2_Small


title: GL26110CD45pos_P1_F09

value: Bcell


title: Pth-8

description: Bulk-RNA Seq


title: Pth-7

description: Bulk-RNA Seq


title: NiSO4 control bio rep 2 [Ni_P1_B01_S8]

description:
96 well plate
Ni_P1_B01_S8_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26110CD45pos_P1_E09

value: NK


title: GL26110CD45pos_P1_G04


title: Tumor1_Small


title: Normal3_tRNA

description:
RNA from normal lung biopsies followed by size selection
tRNAs.xlsx

source_name: normal lung biopsy tissue

value: normal lung biopsies


title: NiSO4 dose level 9 bio rep 1 [Ni_P1_A10_S9]

description:
96 well plate
Ni_P1_A10_S9_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Normal2_tRNA


title: Pth-5

description: Bulk-RNA Seq


title: Pth-6

description: Bulk-RNA Seq


title: GL26110CD45pos_P1_B05

value: Microglia


title: GL26110CD45pos_P1_F02


title: Pth-4

description: Bulk-RNA Seq


title: NiSO4 dose level 7 bio rep 1 [Ni_P1_A08_S11]

description:
96 well plate
Ni_P1_A08_S11_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Normal1_tRNA


title: GL26110CD45pos_P1_D07


title: Ykl-1

description: Bulk-RNA Seq


title: NiSO4 dose level 6 bio rep 1 [Ni_P1_A07_S12]

description:
96 well plate
Ni_P1_A07_S12_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Normal3_Small

description:
RNA from normal lung biopsies followed by size selection
miRNAs.xlsx
tRFs.xlsx


title: Pth-2

description: Bulk-RNA Seq


title: Normal2_Small


title: GL26110CD45pos_P1_G10


title: GL26110CD45pos_P1_C12


title: NiSO4 dose level 5 bio rep 1 [Ni_P1_A06_S13]

description:
96 well plate
Ni_P1_A06_S13_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26110CD45pos_P1_B09

value: Myeloid


title: NiSO4 dose level 3 bio rep 1 [Ni_P1_A04_S3]

description:
96 well plate
Ni_P1_A04_S3_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: Pth-1

description: Bulk-RNA Seq


title: Veh-8

description: Bulk-RNA Seq

value: Veh


title: Normal1_Small


title: NiSO4 dose level 2 bio rep 1 [Ni_P1_A03_S2]

description:
96 well plate
Ni_P1_A03_S2_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: whole body


title: FUUR1_2-input

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

country: China

institute: China Agricutural University

library_source: genomic

data_processing:
single 50bp sequencing on an Illumina MiSeq platform
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 Version 2.3.4.2
peaks were called using MACS2 with following settings: -B --SPMR --pvalue=1e-2 --mfold 15 100
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using multirep_macs2_pipeline.pl; Scores represent a normalized pileup signal

molecule: genomic DNA

source_name: human ASPS cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and TARGET DNA complexes were isolated with antibody.
Library was prepared using NEBnext ChIP-seq libraray prep reagent set

tag: chip antibody

tag: cell line


title: NiSO4 dose level 8 bio rep 1 [Ni_P1_A09_S10]

description:
96 well plate
Ni_P1_A09_S10_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: larva


title: Control3,Day80

city: Guangzhou

first: HUI

last: CHEN

state: Guangdong

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ovary

growth_protocol: MBA-MD-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen) .25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on MGIseq500 platform (BGI-Shenzhen, China)

tag: strain background

value: balb/c-nude

value: ovary

tag: genotype

value: Control


title: GL26110CD45pos_P1_H06


title: Veh-6

description: Bulk-RNA Seq


title: FUUR1_2-RNAPol2

value: POLII


title: NiSO4 dose level 1 bio rep 1 [Ni_P1_A02_S1]

description:
96 well plate
Ni_P1_A02_S1_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: 24 hr


title: NiSO4 control bio rep 1 [Ni_P1_A01_S5]

description:
96 well plate
Ni_P1_A01_S5_L004
Ni.raw.counts.txt
Ni.filtered.normFinal.txt


title: GL26110CD45pos_P1_A12

value: brain


title: Imidacloprid dose level 11 bio rep 8 [Imi_R_H12_S94]

description:
96 well plate
Imi_R_H12_S94_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid


title: Pth-3

description: Bulk-RNA Seq

value: whole kidney

value: male


title: FUUR1_2-ASPSCR1


title: GL26110CD45pos_P1_A04

value: Bcell


title: FUUR1-input


title: GL26110CD45pos_P1_A08


title: Imidacloprid dose level 10 bio rep 8 [Imi_R_H11_S96]

description:
96 well plate
Imi_R_H11_S96_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26110CD45pos_P1_A03


title: Veh-4

description: Bulk-RNA Seq


title: Imidacloprid dose level 9 bio rep 8 [Imi_R_H10_S95]

description:
96 well plate
Imi_R_H10_S95_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: FUUR1-RNAPol2


title: Veh-2

description: Bulk-RNA Seq


title: GL26110CD45pos_P1_F06


title: Veh-3

description: Bulk-RNA Seq


title: FUUR1-ASPSCR1


title: GL26110CD45pos_P1_A07


title: Veh-1

description: Bulk-RNA Seq


title: Imidacloprid dose level 7 bio rep 8 [Imi_R_H08_S90]

description:
96 well plate
Imi_R_H08_S90_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Veh-5

description: Bulk-RNA Seq


title: GL26110CD45pos_P1_D03


title: GL26110CD45pos_P1_H03


title: Imidacloprid dose level 6 bio rep 8 [Imi_R_H07_S93]

description:
96 well plate
Imi_R_H07_S93_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: DENV2 2

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

institute: Tsinghua University

data_processing:
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
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.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: mouse (taxid:10088)
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...

source_name: mouse skin

growth_protocol: All mice were housed in ventilated cages (maxima six mice per cage) in a specific-pathogen-free barrier facility at Tsinghua University.

extract_protocol:
The total skin RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AG6 mice were infected with the DENV2 or ZIKV.

value: AG6 mice (ifnar1-/-ifngr1-/-)

value: mouse skin

value: post infection 4 days


title: DENV2 1


title: Imidacloprid dose level 5 bio rep 8 [Imi_R_H06_S92]

description:
96 well plate
Imi_R_H06_S92_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26110CD45pos_P1_G03

value: Microglia


title: Veh-7

description: Bulk-RNA Seq

value: Veh


title: Imidacloprid dose level 4 bio rep 8 [Imi_R_H05_S87]

description:
96 well plate
Imi_R_H05_S87_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva


title: GL26110CD45pos_P1_H04


title: ZIKV 2


title: N2_MN200_R2_ID_5_S5

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: C. elegans in vivo MNAse-Seq

data_processing:
Illumina NextSeq 1000/2000 Control Software 1.4.1.39716
The sequenced paired-end reads were mapped to C. elegans (ce11) genome using bowtie2 aligner v.2.2.9 (Langmead and Salzberg 2012) with default parameters. The resulting bam files were converted to bigwig tracks using deeptools bamCoverage (Ramírez et al. 2016) with parameters -bs 1 --extendReads 148 –normalizeUsing RPGC --effectiveGenomeSize 98259998. Additional paraments for bamCoverage was comprised of --MNase --minFragmentLength 100 --maxFragmentLength 200 --Offset 1 2 and --smoothLength 30.
Peak calling was performed with MACS2 (Zhang et al. 2008) with default parameters and reads were shifted by 75 bp to cover the nucleosome dyad and extended to 150 bp. Deeptools computeMatrix reference-point was used to compute the nucleosome density across a window spanning the TSS (500bp upstream to 700bp downstream). The TSS positions were extracted from Serizay et al. (Serizay et al., 2020), as the midpoint of the 300bp regions annotated as ”promoter”. Assignments of each promoter to Ubiquitous, Germline or Somatic was taken from these annotations. The resulting files were read in to R using the read.table function.
To produce metagene plots spanning the region surrounding the TSS, the signal at 10bp intervals across the region was averaged across all promoters within the categories above. The ”background” intensity was defined as the minimum value across each trace and was subtracted from each position across the window. A clear signal indicating the expected nucleosome density was only observed for Ubiquitous genes, as expected since somatic promoters do not show such well-defined nucleosome densities (Serizay et al., 2020) and L1s do not have extensive germline tissue (Sulston and Horvitz, 1977).
To compare the intensity of the +1 nucleosome across all ubiquitous promoters, the signal spanning from the TSS to 180bp downstream was extracted for each promoter and the signal for wild type subtracted from the mutant signal. To link changes in gene expression to changes in nucleosome density at promoters, the coordinates of the genes were extended by 500bp upstream and intersected with the 300bp promoter regions using bedtools slop and intersect respectively. Nine of the upregulated and 14 of the downregulated genes overlapped with ubiquitous promoters and the +1 signal was extracted and compared across strains.
RNA sequencing reads from the three experimental sets and RNA-seq data from Meeuse et al., (date) were treated in the same way. Raw reads were trimmed for adapters, low quality sequences and short reads with Trimmomatic (Bolger et al., 2014) (Version 0.39, parameters: ILLUMINACLIP: TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20). Remaining ribosomal RNA was removed with sortmeRNA (Kopylova, Noé, & Touzet, 2012) (Version 2.1, default parameters) and then clean reads were aligned to the C. elegans WBCel235 reference genome and gene counts quantified with salmon (Patro et al., 2018 ) (Version 1.9.0, parameters: --gcBias, --sepBias, -l A).
Assembly: ce11
Supplementary files format and content: bw files for each Sample
Supplementary files format and content: raw_counts.txt contains the raw counts produced by salmon for the RNASeq experiment

organism: Caenorhabditis elegans

source_name: C. elegans L1

growth_protocol: Synchronised C. elegans L1 larvae were obtained by bleaching of gravid adults. Embryos were left to hatch in 5ml M9 rotating on a wheel at 20°C for 24 hours to obtain a synchronised population of L1s. Approx. 60,000 L1s were seeded on NGM agar plates seeded with E. coli. Subsequently, L1s were grown at 25°C for six hours. Small frozen “worm balls” were generated from L1 pellets containing little M9 buffer. This was done by dripping small amounts of animal/M9 buffer mix into a cooled ceramic bowl placed on top of dry ice and filled with liquid nitrogen using a glass Pasteur pipette. “Worm balls” were carefully collected into 1.5 ml tubes with a cooled metal spoon and stored at -70°C.

extract_protocol:
In vivo MNAse digestion was performed on purified nuclei isolated from C. elegans (WT, swsn-1-/-, swsn-1-/-; snfc-5-/-, swsn-1-/-; snfc-5-/-; ubr-5-/-) L1 frozen popcorns. Frozen popcorns containing ~60,000 L1s for each strain was individually homogenized in liquid nitrogen and purification was optimised using sigma nuclei pure prep nuclei isolation kit (NUC-201) with modifications. Purified Nuclei of 500 ng/reaction were digested with MNAse (M0247S, NEB) concentration 200U/ml or 250U/ml for 15 mins at 37 °C to generate monoucleosomal DNA. MNase digestion was terminated by adding stop solution containing 3% SDS, 20 mM EDTA. Mononuclesomes were treated with Proteinase K (Invitrogen) and incubated at 65°C for 1 hr followed by DNA purification using Zymo clean and Concentrator. Mononucleosome bands were confirmed by D5000 ScreenTape in Agilent 2200 TapeStation system. For library preparation, DNA was measured again with Qubit dsDNA HS Assay Kit and 65 ng of mononucleosomal purified DNA was used for NEBNext Ultra II DNA Library Prep Kit for Illumina with size selection.
DNA libraries were prepared for sequencing using NEBNext Ultra II DNA Library Prep Kit for Illumina

value: L1 popcorn

value: N2 wild type

value: MNAse- 200U/ml


title: SX3622_swsn1_snfc5_MN200_R2_ID_7_S7

description: C. elegans in vivo MNAse-Seq


title: Imidacloprid dose level 8 bio rep 8 [Imi_R_H09_S91]

description:
96 well plate
Imi_R_H09_S91_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: SX3715_swsn1_snfc5_MN250

description: C. elegans in vivo MNAse-Seq

value: MNAse- 250U/ml


title: Mock-3

value: uninfection


title: GL26110CD45pos_P1_E06

value: brain


title: GL26110CD45pos_P1_A02


title: ZIKV 1


title: Imidacloprid dose level 2 bio rep 8 [Imi_R_H03_S89]

description:
96 well plate
Imi_R_H03_S89_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid

value: 24 hr


title: SX3714_swsn1_MN250

description: C. elegans in vivo MNAse-Seq


title: SX3627_swsn1_snfc5_ubr5_MN200_R2_ID_6_S6

description: C. elegans in vivo MNAse-Seq


title: GL26110CD45pos_P1_C11


title: Mock-2


title: Imidacloprid dose level 3 bio rep 8 [Imi_R_H04_S86]

description:
96 well plate
Imi_R_H04_S86_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26110CD45pos_P1_B03

value: Bcell


title: MH2354_swsn1_MN200_R2_ID_8_S8

description: C. elegans in vivo MNAse-Seq


title: Imidacloprid dose level 1 bio rep 8 [Imi_R_H02_S88]

description:
96 well plate
Imi_R_H02_S88_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: N2_MN250

description: C. elegans in vivo MNAse-Seq


title: Mock-1

value: AG6 mice (ifnar1-/-ifngr1-/-)


title: Imidacloprid control bio rep 8 [Imi_R_H01_S76]

description:
96 well plate
Imi_R_H01_S76_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26110CD45pos_P1_G09

value: NK


title: K524-E5

city: Omaha

first: Holly

last: Feser Stessman

state: NE

address: 2500 California Plaza

department: Pharmacology & Neuroscience

institute: Creighton University

data_processing:
Tuxedo standard pipeline used: Samples were mapped to the mm10 mouse reference genome  using TopHat v2.1.0 (Bowtie2 v2.2.6) followed by transcript assembly using cufflinks v2.2.1. Transcript differences were assessed using cuffdiff on merged transcriptome replicates by sex/genotype.
Genome_build: mm10
Supplementary_files_format_and_content: BAM file of assembled transcripts per sample

source_name: Embryonic brain

extract_protocol:
Brains were removed and flash frozen in liquid nitrogen. Total mRNA was extracted using the RNeasy Mini Kit including DNase I treatment (Qiagen).
RNA libraries were prepared for sequencing using standard protocols at BGI Hong Kong.

value: whole brain

value: embryonic day 14.5

value: KO

value: F


title: SX3627_swsn1_snfc5_ubr5_MN250

description: C. elegans in vivo MNAse-Seq


title: Imidacloprid dose level 10 bio rep 7 [Imi_R_G11_S74]

description:
96 well plate
Imi_R_G11_S74_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva


title: K524-E4

value: WT

value: M


title: GL26110CD45pos_P1_H08

value: Myeloid


title: GL26150CD45pos_P1_C04


title: GL26150CD45pos_P1_G03


title: Imidacloprid dose level 9 bio rep 7 [Imi_R_G10_S73]

description:
96 well plate
Imi_R_G10_S73_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: K524-E3


title: Imidacloprid dose level 8 bio rep 7 [Imi_R_G09_S80]

description:
96 well plate
Imi_R_G09_S80_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: K524-E2

value: HET


title: GL26150CD45pos_P1_E02

value: brain


title: N1IC-transduced β-Catenin-KO cells, biological rep1

type: RNA

city: Barcelona

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

country: Spain

institute: Centre for Genomic Regulation (CRG)

description: Gene Expression data from GFP+ sorted, lineage depleted (Lin-) bone marrow (BM) cells from b-Catenin-KO mice infected with pMIG-N1IC-GFP retrovirus

hyb_protocol: cRNA was hybridized on  Affymetrix GeneChip® Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files were analyzed in R (v3.1.2) with the oligo (v1.30.0) and limma (v3.22.4) packages from Bioconductor, data were normalized using RMA (Robust Multi-array Average) and expression values log2-transformed.

label: biotin

source_name: GFP+ sorted, transduced BM Lin- cells

label_protocol: 5 ug total RNA was labelled with the FL-Ovation™ cDNA Biotin Module V2 kit (NuGEN Technologies).

extract_protocol: RNA was extracted with RNEasy Micro kit (QIAGen) according to manufacturer's instructions and amplified using the Ovation™ Pico WTA System (NuGEN Technologies, San Carlos, CA) and sense transcript cDNA (ST-cDNA) was generated using the WT-Ovation™ Exon Module (NuGEN Technologies)

value: VavCre(+)β-Catenin(fl/fl)

tag: transduction


title: N1IC-transduced β-Catenin-KO cells, biological rep3


title: Imidacloprid dose level 7 bio rep 7 [Imi_R_G08_S79]

description:
96 well plate
Imi_R_G08_S79_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid

value: 24 hr


title: N1IC-transduced β-Catenin-KO cells, biological rep2


title: K524-E1


title: Control-transduced β-Catenin-KO cells, biological rep3

description: Gene Expression data from GFP+ sorted, lineage depleted (Lin-) bone marrow (BM) cells from b-Catenin-KO mice infected with pMIG-GFP (control) retrovirus

value: +pMIG-GFP


title: K477-E5


title: Control-transduced β-Catenin-KO cells, biological rep2


title: Imidacloprid dose level 6 bio rep 7 [Imi_R_G07_S78]

description:
96 well plate
Imi_R_G07_S78_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_E01

value: Microglia


title: Imidacloprid dose level 4 bio rep 7 [Imi_R_G05_S84]

description:
96 well plate
Imi_R_G05_S84_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: K477-E7

value: whole brain


title: K407-E6

value: embryonic day 14.5


title: GL26150CD45pos_P1_A01

value: NK


title: Imidacloprid dose level 11 bio rep 7 [Imi_R_G12_S75]

description:
96 well plate
Imi_R_G12_S75_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: K477-E2

value: F


title: Control-transduced β-Catenin-KO cells, biological rep1


title: GL26150CD45pos_P1_F09

value: Bcell


title: K407-E5


title: N1IC-transduced wild-type cells, biological rep3

description: Gene Expression data from GFP+ sorted, lineage depleted (Lin-) bone marrow (BM) cells from wild-type mice infected with pMIG-N1IC-GFP retrovirus

value: VavCre(+)β-Catenin(+/+)


title: GL26150CD45pos_P1_B11


title: K407-E3

value: KO


title: Imidacloprid dose level 3 bio rep 7 [Imi_R_G04_S83]

description:
96 well plate
Imi_R_G04_S83_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva


title: Imidacloprid dose level 1 bio rep 7 [Imi_R_G02_S81]

description:
96 well plate
Imi_R_G02_S81_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26150CD45pos_P1_D04


title: Control-transduced wild-type cells, biological rep2

description: Gene Expression data from GFP+ sorted, lineage depleted (Lin-) bone marrow (BM) cells from wild-type mice infected with pMIG-GFP (control) retrovirus


title: GL26150CD45pos_P1_E03


title: K407-E2

value: M


title: N1IC-transduced wild-type cells, biological rep1


title: Imidacloprid dose level 5 bio rep 7 [Imi_R_G06_S77]

description:
96 well plate
Imi_R_G06_S77_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Control-transduced wild-type cells, biological rep1


title: N1IC-transduced wild-type cells, biological rep2


title: Imidacloprid control bio rep 7 [Imi_R_G01_S85]

description:
96 well plate
Imi_R_G01_S85_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: K407-E1

value: WT


title: GL26150CD45pos_P1_A07

value: brain


title: K405-E4

value: HET


title: Overexpression rep2

first: Xin

last: Wang

address: 300 Longwood Ave,

institute: Boston children's hospital

data_processing:
We trimmed adapter sequences and low-quality sequences in RNA-seq data using the Trim Galore v0.6.6 (Martin 2011) with default parameters
Then, these high quality reads were further mapped to the mouse genome version mm10 using TopHat v2.1.1 (Kim et al. 2013) , which was guided by gene models.
Read counts for each gene were quantified by Htseq-count v0.11.2 (Anders et al. 2015) with union gene region option. Afterward, we used edgeR to normalize read counts and detect differentially expressed genes (DEGs) between mt-Ty 5’tiRNAs gapmer treatment and control, as well as between 5’ tiRNA overexpression and controls
We defined DEGs as those with a fold change greater than 1.5 and an FDR value smaller than 0.05. Gene ontology (GO) analysis was performed to check the functional enrichments of DEGs by the R package clusterProfiler v3.18.1 (Wu et al. 2021).
Gene Set Enrichment Analysis were performed by the GSEA Java software. Heatmaps and volcano plots were generated by pheatmap (Kolde 2012) and ggplots respectively.
Assembly: mm10 (GRCm38.p6 release M23)
Supplementary files format and content: txt text files including normalized

source_name: myoblast

growth_protocol: C2C12 myoblast cells (CRL-1772) were routinely cultured and maintained at 50% confluency in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin and streptomycin.

extract_protocol:
RNAs were extracted following Trizol protocol
Poly A-selected libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina), the obtained libraries were combined in equimolar amounts and loaded on a single Illumina flow cell lane, follow by paired-ended sequencing (PE150bp, GENEWIZ)

treatment_protocol: For transfection, cells were seeded at 60–70% confluency on the day, and transfectedwith gapmers or tiRNA mimics using RNAiMAX (Thermofisher Scientific 13778150) after 4h of seeding. The concentration for the treatment of gapmers and tiRNA mimics is 50 nM and 500 μM respectively.

value: myoblast

value: C2C12 myoblast cells

value: mt-Ty 5'tiRNAs Overexpression


title: Overexpression rep3


title: GL26150CD45pos_P1_F04


title: GL26150CD45pos_P1_G12

value: Microglia


title: Tumor3_Small

description:
RNA from lung cancer biopsies followed by size selection
miRNAs.xlsx
tRFs.xlsx

value: lung cancer biopsies


title: Overexpression rep4


title: Overexpression rep1


title: Imidacloprid dose level 2 bio rep 7 [Imi_R_G03_S82]

description:
96 well plate
Imi_R_G03_S82_L006
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid

value: 24 hr


title: Imidacloprid dose level 10 bio rep 6 [Imi_R_F11_S71]

description:
96 well plate
Imi_R_F11_S71_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: K405-E2

value: whole brain

value: embryonic day 14.5


title: Control rep4 (overexpression)

value: Control


title: GL26150CD45pos_P1_E04


title: Imidacloprid dose level 8 bio rep 6 [Imi_R_F09_S56]

description:
96 well plate
Imi_R_F09_S56_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body


title: Imidacloprid dose level 9 bio rep 6 [Imi_R_F10_S70]

description:
96 well plate
Imi_R_F10_S70_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva


title: K310-E4

value: F


title: Control rep3 (overexpression)


title: Imidacloprid dose level 7 bio rep 6 [Imi_R_F08_S57]

description:
96 well plate
Imi_R_F08_S57_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: GL26150CD45pos_P1_G07

value: Bcell


title: K310-E3

value: KO

value: M


title: Imidacloprid dose level 11 bio rep 6 [Imi_R_F12_S72]

description:
96 well plate
Imi_R_F12_S72_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_A08

value: brain

value: NK


title: GL26150CD45pos_P1_D10

value: Myeloid


title: K310-E7

value: WT


title: GL26150CD45pos_P1_A12


title: Imidacloprid dose level 5 bio rep 6 [Imi_R_F06_S55]

description:
96 well plate
Imi_R_F06_S55_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_E09


title: Control rep1 (overexpression)

value: myoblast

value: C2C12 myoblast cells


title: GL26150CD45pos_P1_H07

value: Microglia


title: Imidacloprid dose level 4 bio rep 6 [Imi_R_F05_S60]

description:
96 well plate
Imi_R_F05_S60_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid

value: 24 hr


title: GL26150CD45pos_P1_H03


title: CNE2 KO4-1

city: Houston

first: An

last: Xu

state: TX

institute: UThealth Houston

data_processing:
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: RNAStar for RNASeq, Bowtie2 for ChIPseq
RNAseq normalization: Featurecounts
ChIPseq sorting, normalization, and visualization: MACS2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .csv; ChIPSeq: genome browser tracks in .bigwig

growth_protocol: CNE2 cells were cells were grown in RPMI 1640 medium supplemented with 10% (vol/vol) fetal bovine serum (FBS) (Opti-Gold performance enhanced F0900-050, GenDEPOT, Barker, TX), L-glutamine, and penicillin/streptomycin.

extract_protocol:
For RNAseq, cells samples were lysed in Trizol reagent (Invitrogen, 10296010).ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A/G Dynabeads and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).
For RNASeq, library construction was performed using PE150 high-throughput sequencing. For ChIPSeq, library construction was performed using PE75 high-throughput sequencing.

value: Nasopharyngeal carcinoma (NPC)

value: Yes

value: NPC cell with p53 depletion

tag: disease state

value: NPC


title: 5' ti gapmer rep2

value: mt-Ty 5'tiRNAs KO

value: mt-Ty 5'tiRNAs gapmer treatment


title: CNE2 KO4-2


title: Control rep2 (gapmer)

value: Control


title: 5' ti gapmer rep1


title: Imidacloprid dose level 3 bio rep 6 [Imi_R_F04_S61]

description:
96 well plate
Imi_R_F04_S61_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: CNE2 Ctrl-2

value: No

value: NPC cell


title: Control rep2 (overexpression)

value: myoblast


title: CNE2 Ctrl-1


title: Control rep1 (gapmer)

value: C2C12 myoblast cells


title: Imidacloprid dose level 2 bio rep 6 [Imi_R_F03_S58]

description:
96 well plate
Imi_R_F03_S58_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_B06

value: brain

value: Microglia


title: Imidacloprid dose level 6 bio rep 6 [Imi_R_F07_S54]

description:
96 well plate
Imi_R_F07_S54_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid

value: 24 hr


title: Imidacloprid dose level 1 bio rep 6 [Imi_R_F02_S59]

description:
96 well plate
Imi_R_F02_S59_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_B09

value: NK


title: Imidacloprid control bio rep 6 [Imi_R_F01_S64]

description:
96 well plate
Imi_R_F01_S64_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_A03

value: Bcell


title: DeCi_04

city: changsha

first: min

last: liu

address: Xiangya Road, Kaifu District

institute: central south university

data_processing:
mapped to the reference genome and other sRNA database using Bowtie2.
Rfam mapping with cmsearch.
miRDeep and Piano was used to predict novel miRNA.
Differential expression analysis was using DEseq2.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Text files containing fpkm matrix.

source_name: HBV-associated decompensated cirrhosis serum EVs

extract_protocol:
The serum was separated by centrifugation at 4000R / min for 5 minutes at 4 ° C.Then centrifuged at 1500 g for 10 minutes, and 15000 g for 30 minutes. Every 5 samples in the same group were mixed into a pool, with 5 pools in each group.Exoquick-5A™ (system Biosciences, Inc., Palo Alto, CA, USA) exosome Precipitation Kit was used to enrich EVs according to the manufacturer's instructions. Total RNA was extracted from serum EVs with mirneasy Mini Kit (Qiagen #217004 total RNA) (Qiagen, Valencia, CA). After qualified RNA  quality, the library was established and sequenced.
Every 5 samples of the same group are randomly mixed into a pool. EVs RNAs were extracted from 5 pooled CHB serum samples, 5 pooled DeCi serum samples and 5 pooled healthy serum samples.

tag: sample group


title: pre-B cells, IR 30min, rep2

description:
male
ZC8

data_processing:
We trimmed adapter sequences and low-quality sequences in RNA-seq data using the Trim Galore v0.6.6 (Martin 2011) with default parameters.
To avoid rRNA homologous sequences (i.e., in the intron regions of Zc3h7a or Cdk8) prior to subsequent genomic and other RNA analysis, we first mapped the reads to mm10 rDNA sequences by TopHat v2.1.1 (Kim et al. 2013).
The unmapped reads were then further mapped to the mouse genome version mm10 and ERCC spike-in version ERCC92 using TopHat v2.1.1 (Kim et al. 2013).
Successfully mapping reads were sorted by SAMtools v1. 5.
Afterward, read counts in several types of genomic feature, i.e., protein-coding genes, rDNA and ERCCs (ERCC92.gtf), were quantified by Htseq-count v0.11.2 (Anders et al. 2015) using the union gene region option. The read number per gene was normalized based on total ERCC read numbers in each sample.  Afterward, read counts in several types of genomic feature, i.e., protein-coding genes, rDNA and ERCCs (ERCC92.gtf), were quantified by Htseq-count v0.11.2 (Anders et al. 2015) using the union gene region option. The read number per gene was normalized based on total ERCC read numbers in each sample.
Assembly: mm10 (GRCm38.p6 release M23)
Supplementary files format and content: csv text files including normalized
Library strategy: nascent RNA-seq

source_name: bone marrow

growth_protocol: Abelson virus-transformed pre-B cells were maintained in DMEM (Thermo Fisher, 11960-077) supplemented with 10% FBS, 1% Penicillin-Streptomycin, 1x nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, and 0.4% beta-mercaptoethanol in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were harvested using TRIzol reagent (Thermo Fischer, 15596018) following the manufacturer’s protocol. The click-iT reaction was performed as per manufacturer’s protocol in 50 µL total volume for 30 minutes in the dark. Subsequently, 1 µL ultrapure glycogen, 50 µL 7.5 M ammonium acetate, and 700 uL of chilled 100% EtOH were added to the reaction. The mixture was incubated at −80 °C for 16 hours. RNA pellet was spun down at 13000 ×g for 20 minutes at 4 °C, washed 2x with chilled 75% EtOH and resuspended in nuclease free water. EU-RNAs were pulled down with Dynabeads MyOne Streptavidin T1 magnetic beads and extracted with TRIzol reagents.
The same amount of ERCC spike-ins (Thermo Fisher, 4456740) were added to the purified EU-RNAs, followed by cDNA library generation using NEBNext Ultr II Directional RNA Library Prep Kit for Illumina (NEB, E7760) according to the manufacturer’s protocol

treatment_protocol: The same number of abl pre-B cells was plated in two T-25 Polystyrene flasks, one for irradiation (10 Gray) and the other for no IR control. After irradiation, both flasks of cells were recovered for 30 minutes and incubated in medium with 2 mM EU for 30 minutes

value: bone marrow

value: Abelson-transformed pre-B cells

value: WT

value: 30 min after IR (10 Gy)


title: DeCi_03

value: HBV-associated decompensated cirrhosis serum EVs


title: pre-B cells, no IR, rep2

description:
male
ZC7

value: before IR


title: Imidacloprid dose level 11 bio rep 5 [Imi_R_E12_S65]

description:
96 well plate
Imi_R_E12_S65_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: GL26150CD45pos_P1_A06


title: pre-B cells, IR 30min, rep1

description:
male
ZC6


title: Imidacloprid dose level 10 bio rep 5 [Imi_R_E11_S62]

description:
96 well plate
Imi_R_E11_S62_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: pre-B cells, no IR, rep1

description:
male
ZC5


title: DeCi_02


title: GL26150CD45pos_P1_G01


title: DeCi_01


title: GL26150CD45pos_P1_G10


title: DeCi_05


title: Imidacloprid dose level 8 bio rep 5 [Imi_R_E09_S68]

description:
96 well plate
Imi_R_E09_S68_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: CHB_04

source_name: Chronic hepatitis B serum EVs

value: Chronic hepatitis B serum EVs


title: CHB_05


title: Imidacloprid dose level 7 bio rep 5 [Imi_R_E08_S69]

description:
96 well plate
Imi_R_E08_S69_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_C10

value: Myeloid


title: Imidacloprid dose level 6 bio rep 5 [Imi_R_E07_S66]

description:
96 well plate
Imi_R_E07_S66_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_B04

value: brain


title: GL26150CD45pos_P1_C09


title: liver72_KI

first: Yuan

last: Chu

address: No. 38, kexueyuan Road, Changping District

institute: Beijing Institute of Lifeomics

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequence reads were trimmed for adaptor sequence, and  masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver, KI

growth_protocol: Male C57BL/6J mice were raised in the Specific Pathogen Free (SPF) animal room of the Animal Experiment Center at Academy of Military Medical Sciences. Mice were housed at room temperature (21-25 ˚C) with a relative humidity of 45-65%, a 12/12 hours light/dark cycle and access to food and water ad libitum

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HNF1α WT and KI mice were fed normally until 10-week-old, and their liver RNA was extracted for RNAseq

value: male

value: liver

value: HNF1alpha K117E knockin


title: liver54_WT

source_name: liver, WT


title: liver74_WT


title: liver55_KI


title: CHB_03


title: CHB_02


title: Imidacloprid dose level 5 bio rep 5 [Imi_R_E06_S67]

description:
96 well plate
Imi_R_E06_S67_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

source_name: whole body

value: Imidacloprid

value: 24 hr


title: liver19_WT


title: GL26150CD45pos_P1_A11

value: NK


title: CHB_01


title: Imidacloprid dose level 4 bio rep 5 [Imi_R_E05_S50]

description:
96 well plate
Imi_R_E05_S50_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Imidacloprid dose level 9 bio rep 5 [Imi_R_E10_S63]

description:
96 well plate
Imi_R_E10_S63_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_D11

value: Microglia


title: NC_05

source_name: normal contral serum EVs

value: normal contral serum EVs


title: Imidacloprid dose level 3 bio rep 5 [Imi_R_E04_S49]

description:
96 well plate
Imi_R_E04_S49_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_A02

source_name: brain


title: Preteated-1h-cell96

city: Shenzhen

first: Yanling

last: Peng

address: Pengfei Road 7, Dapeng new distinct

department: Animal Functional Genomics Group

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description: scTSS-seq

data_processing:
Sequencing reads are aligned to the mouse genome mm9 with bowtie2 with default parameters.
For each cell, TSSs are defined as peaks by HOMER with findpeaks function by setting parameters “-style tss -nTagthreshold 200”.
TSS clustering (TSCs) within their flanking 2bp of 5’ end peaks are determined with house python script.
TSCs are annotated to three transcript models by homer with “annotatePeaks.pl”. These models include gencode.vM1, ucsc.knownGene, refseq, respectively.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_R2.txt: peaks
Supplementary_files_format_and_content: fr.txt: focus ratio for each cell.
Supplementary_files_format_and_content: ps.txt: normalized tag count for each cell.
Supplementary_files_format_and_content: TSC.gencode.txt: TSS cluster annotation to Gencode.
Supplementary_files_format_and_content: TSC.refseq.txt: TSS cluster annotation to RefSeq.
Supplementary_files_format_and_content: TSC.ucsc.txt: TSS cluster annotation to UCSC.

growth_protocol: MEFs were cultured on uncoated plastic in DMEM supplemented with 10% of FBS.

extract_protocol:
RNA was harvested from MEFs using Trizol (Invitrogen) and purified by the RNeasy mini kit (Qiagen).
The cDNAs are processed by using Nextera XT DNA Library Prep Kit.

treatment_protocol: Cells were treated with 100 U/ml of Interferon-beta.

value: Mouse embryonic fibroblasts

tag: pretreatment

value: Pretreated

value: IFN-beta, 1h


title: NC_04


title: Imidacloprid dose level 2 bio rep 5 [Imi_R_E03_S52]

description:
96 well plate
Imi_R_E03_S52_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to indexed FHM genome with 26,150 gene models loaded within the genome (WIOS00000000; BioSample SAMN12875914). STAR "--quantMode GeneCounts" was used to produce raw counts from the mapping; reverse strand count column was used as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with gene models are available from the authors.
Samples with <2 million raw counts and/or less than 50% unique mapping rate were removed, and within-chemical features (genes) with mean raw counts <5 across all samples were filtered from respective raw counts matrices.
For each chemical, the raw counts for the remaining features were normalized to counts per million reads (CPM), and after adding a pseudo-count of 1 to prevent taking log of zero counts, log2 transformed.
For each chemical, an MDS plot of the normalized data was generated. Individual samples separated from all remaining samples on either principle component #1 (PC1) or principle component #2 (PC2) by >2x the span of all other samples on the corresponding PC were removed from further analysis. Qualitative assessment was applied and samples with a relatively large Euclidean distance from all other remaining samples on MDS plots were also excluded, along with samples especially distant from corresponding replicates within dose.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: For each chemical, tab delimited text matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: For each sample, tab delimited text matrix table with normalized expression values for every gene and every sample that passed all filtering.

extract_protocol:
Larvae remained in their 1 mL deep wells, exposure solution was removed and replaced with lysis buffer, a bead was added to each well, and subjects were homogenized in their wells.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

tag: tissue

value: whole body


title: Preteated-1h-cell95

description: scTSS-seq


title: GL26150CD45pos_P1_D02


title: Preteated-1h-cell94

description: scTSS-seq


title: Preteated-1h-cell92

description: scTSS-seq


title: Imidacloprid dose level 10 bio rep 4 [Imi_R_D11_S40]

description:
96 well plate
Imi_R_D11_S40_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: developmental stage

value: larva


title: Imidacloprid dose level 1 bio rep 5 [Imi_R_E02_S51]

description:
96 well plate
Imi_R_E02_S51_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: age

value: 5 dpf/24 hr post hatch


title: GL26150CD45pos_P1_H10

value: Bcell


title: Imidacloprid dose level 11 bio rep 4 [Imi_R_D12_S38]

description:
96 well plate
Imi_R_D12_S38_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: Sex


title: NC_02


title: Imidacloprid control bio rep 5 [Imi_R_E01_S53]

description:
96 well plate
Imi_R_E01_S53_L005
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: treatment


title: Preteated-1h-cell91

description: scTSS-seq


title: GL26150CD45pos_P1_H08


title: NC_03


title: Imidacloprid dose level 9 bio rep 4 [Imi_R_D10_S39]

description:
96 well plate
Imi_R_D10_S39_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: concentration


title: GL26150CD45pos_P1_B03


title: Preteated-1h-cell89

description: scTSS-seq


title: NC_01


title: Imidacloprid dose level 7 bio rep 4 [Imi_R_D08_S41]

description:
96 well plate
Imi_R_D08_S41_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

tag: time point


title: ESC, shTbx3, rep1

city: Chongqing

first: Chen

last: Zhang

address: 30# Gaotanyan Rd, Shapingba District

institute: Army Medical University

description:
Tbx3KD ESCs cultured in LIF/Serum culture
9TBX3

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 Hisat2.
featureCount software was used to calculate gene expression from aligned bam files
R statistical package DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: raw reads counts

growth_protocol: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the indicated medium. LIF/serum culture: DMEM supplemented with 15% FBS, 2mM GlutaMAX, 1% MEM non-essential amino acids, 0.1mM β-mercaptoethanol (all from Invitrogen) and 10 ng/ml LIF (Millipore).

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
RNA-seq transcriptome libraries were prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA), using 1μg of total RNA. Shortly, messenger RNA was isolated with polyA selection by oligo(dT) beads and fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol.

value: embryonic stem cells

value: Tbx3 knockdown

value: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the LIF/Serum medium.


title: GL26150CD45pos_P1_F07

value: brain


title: ESC, shPcgf6, rep2

description:
Pcgf6KD ESCs cultured in LIF/Serum culture
6PCGF6

value: Pcgf6 knockdown


title: GL26150CD45pos_P1_C03


title: Preteated-1h-cell88

description: scTSS-seq

tag: strain


title: Preteated-1h-cell93

description: scTSS-seq

tag: cell type


title: Preteated-1h-cell90

description: scTSS-seq


title: Imidacloprid dose level 8 bio rep 4 [Imi_R_D09_S42]

first: John

last: Martinson

description:
96 well plate
Imi_R_D09_S42_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid


title: GL26150CD45pos_P1_D01


title: ESC, shPcgf6, rep1

description:
Pcgf6KD ESCs cultured in LIF/Serum culture
5PCGF6


title: liver16_KI

value: male

value: liver

value: HNF1alpha K117E knockin


title: ESC, shTbx3, rep2

description:
Tbx3KD ESCs cultured in LIF/Serum culture
10TBX3


title: GL26150CD45pos_P1_C05

value: Microglia


title: Preteated-1h-cell87

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: ESC, shCtr9, rep1

description:
Ctr9KD ESCs cultured in LIF/Serum culture
13CTR9

value: Ctr9 knockdown


title: Imidacloprid dose level 6 bio rep 4 [Imi_R_D07_S44]

description:
96 well plate
Imi_R_D07_S44_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: Imidacloprid dose level 5 bio rep 4 [Imi_R_D06_S43]

description:
96 well plate
Imi_R_D06_S43_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body


title: ESC, shCtr9, rep2

description:
Ctr9KD ESCs cultured in LIF/Serum culture
14CTR9


title: GL26150CD45pos_P1_G06


title: GL26150CD45pos_P1_A10

value: Myeloid


title: Preteated-1h-cell85

description: scTSS-seq

value: Pretreated

value: IFN-beta, 1h


title: Imidacloprid dose level 3 bio rep 4 [Imi_R_D04_S45]

description:
96 well plate
Imi_R_D04_S45_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: Preteated-1h-cell84

description: scTSS-seq


title: GL26150CD45pos_P1_F05

value: Bcell


title: GL26150CD45pos_P1_F02

value: brain


title: Preteated-1h-cell83

description: scTSS-seq


title: GL26150CD45pos_P1_C12

value: NK


title: Imidacloprid dose level 1 bio rep 4 [Imi_R_D02_S47]

description:
96 well plate
Imi_R_D02_S47_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: Imidacloprid


title: Preteated-1h-cell82

description: scTSS-seq


title: Imidacloprid dose level 2 bio rep 4 [Imi_R_D03_S48]

description:
96 well plate
Imi_R_D03_S48_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_B10


title: Saline-2

city: Pensylvania

first: Julie A

last: Blendy

state: PA

address: 125 South 31st Street

department: Systems Pharmacology and Translational Therapeutics

institute: University of Pensylvania

data_processing:
Mapping of the reads to the mouse reference genome (Mus musculus, GRCm38/mm10) was performed using the STAR aligner (v2.6.1d). Differential expression analysis was performed with DESeq2 (v1.20.0).
Differential expression cut-offs were set at an adjusted (Adj.) p-value < 0.05 and a Log2 fold change (Log2FC) of 0.5.
Gene ontology (GO) analyses were performed via goProfiler, and the significant GO terms (p<0.05) were reduced using Revigo.
Enrichment for cell-type specific gene sets was assessed using a hypergeometric test.

source_name: mouse striatum

extract_protocol: RNA integrity was assessed with an Agilent Tapestation 4200 using the RNA ScreenTape (Agilent, Wilmington, DE). All samples had RIN values > 8. mRNA libraries were generated using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswitch, MA).

treatment_protocol:
repeated, subcutaneous (s.c.) injections of escalating doses of morphine (20mg/kg; 40mgkg; 60mg/kg; 100mg/kg, injections, twice /day injections  for 5 days)
or injections of saline

value: mouse striatum

value: Mu opioid receptor +

value: Saline


title: Saline-1


title: GL26150CD45pos_P1_D06

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)


title: Imidacloprid dose level 11 bio rep 3 [Imi_R_C12_S26]

address: 26 W. Martin L. King Drive

description:
96 well plate
Imi_R_C12_S26_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Preteated-1h-cell81

description: scTSS-seq


title: Morphine-3

value: Morphine


title: Preteated-1h-cell86

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: Imidacloprid dose level 4 bio rep 4 [Imi_R_D05_S46]

description:
96 well plate
Imi_R_D05_S46_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_C08


title: GL26150CD45pos_P1_B01


title: ESC, shControl, rep1

description:
Control ESCs cultured in LIF/Serum culture
1NG5Z

value: embryonic stem cells

value: WT

value: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the LIF/Serum medium.


title: Morphine-2


title: Preteated-1h-cell80

description: scTSS-seq


title: Preteated-1h-cell79

description: scTSS-seq


title: Imidacloprid dose level 10 bio rep 3 [Imi_R_C11_S27]

description:
96 well plate
Imi_R_C11_S27_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: 24 hr


title: Imidacloprid dose level 9 bio rep 3 [Imi_R_C10_S28]

description:
96 well plate
Imi_R_C10_S28_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Saline-3


title: GL26150CD45pos_P1_H05


title: Imidacloprid dose level 8 bio rep 3 [Imi_R_C09_S29]

description:
96 well plate
Imi_R_C09_S29_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Preteated-1h-cell78

description: scTSS-seq

value: Pretreated

value: IFN-beta, 1h


title: P31 male Bace1-fl/fl;Thy1-cre

city: Farmington

first: Riqiang

last: Yan

address: 263 Farmington Ave

institute: Uconn Health

description:
10x Genomics
SC2100090

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support)
Clustering and differential gene expression analysis was conducted using Seurat (https://satijalab.org/seurat/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Eight hippocampi from P31 and P192 male and female Bace1fl/fl and Bace1fl/fl;Thy1-cre mice were extracted and snap frozen on dry ice. Hippocampi were then homogenized and lysed in buffer containing 0.01% tween/0.01% NP-40 on ice. Debris removal (Miltenyi) step was included to remove myelin debris, and nuclei were counted and loaded onto a droplet-based 10x Chromium controller to perform single cell partitioning and barcoding.
Raw sequencing from the NovaSeq6000 was aligned and annotated using the CellRanger v3.1.0 pipeline. During FASTQ generation, reads with more than 1 mismatch in the 8bp i7 index were excluded. During alignment using STAR (62), only reads with MAPQ scores greater than 255 aligned to annotated transcripts were retained. Reads containing bases with Q30 scores below 3 were also excluded. After alignment, cell barcodes were filtered up to 1 mismatch against a whitelist of 737,500 barcodes provided by 10X Genomics. Barcodes associated with cells were distinguished from ambient mRNA using an adaptively computed UMI threshold. The raw counts matrix was filtered using cutoff values of mitochondrial transcripts below 5% and between 250 and 6,000 unique features.

value: Neurons and glia

value: hippocampus


title: ESC, shControl, rep2

description:
Control ESCs cultured in LIF/Serum culture
2NG5Z


title: GL26150CD45pos_P1_H01

first: Elizabeth

last: Perez

value: brain

value: Microglia


title: Preteated-1h-cell77

description: scTSS-seq


title: Preteated-1h-cell76

description: scTSS-seq


title: P31 male Bace1-fl/fl

description:
10x Genomics
SC2100089


title: Imidacloprid control bio rep 4 [Imi_R_D01_S25]

description:
96 well plate
Imi_R_D01_S25_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: GL26150CD45pos_P1_E10

value: Bcell


title: Imidacloprid dose level 7 bio rep 3 [Imi_R_C08_S30]

description:
96 well plate
Imi_R_C08_S30_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: P31 female Bace1-fl/fl;Thy1-cre

description:
10x Genomics
SC2100088


title: Imidacloprid dose level 6 bio rep 3 [Imi_R_C07_S31]

description:
96 well plate
Imi_R_C07_S31_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Preteated-1h-cell75

description: scTSS-seq


title: GL26150CD45pos_P1_F10


title: P31 female Bace1-fl/fl

description:
10x Genomics
SC2100087


title: Imidacloprid dose level 5 bio rep 3 [Imi_R_C06_S32]

description:
96 well plate
Imi_R_C06_S32_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Morphine-1

value: mouse striatum

value: Mu opioid receptor +

value: Morphine


title: Preteated-1h-cell74

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: Imidacloprid dose level 4 bio rep 3 [Imi_R_C05_S33]

description:
96 well plate
Imi_R_C05_S33_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_H06

value: NK


title: Preteated-1h-cell73

description: scTSS-seq


title: Imidacloprid dose level 3 bio rep 3 [Imi_R_C04_S34]

description:
96 well plate
Imi_R_C04_S34_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body


title: GL26150CD45pos_P1_D05


title: P192 female Bace1-fl/fl;Thy1-cre

description:
10x Genomics
SC2100086


title: P192 female Bace1-fl/fl

description:
10x Genomics
SC2100085


title: GL26150CD45pos_P1_D12


title: Preteated-1h-cell72

description: scTSS-seq


title: Preteated-1h-cell71

description: scTSS-seq


title: P192 male Bace1-fl/fl;Thy1-cre

description:
10x Genomics
SC2100084


title: Imidacloprid dose level 1 bio rep 3 [Imi_R_C02_S36]

description:
96 well plate
Imi_R_C02_S36_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: GL26150CD45pos_P1_B12


title: GL26150CD45pos_P1_C07


title: Preteated-1h-cell69

description: scTSS-seq

value: Pretreated


title: Imidacloprid control bio rep 3 [Imi_R_C01_S37]

description:
96 well plate
Imi_R_C01_S37_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_G02


title: Preteated-1h-cell70

description: scTSS-seq

value: IFN-beta, 1h


title: Imidacloprid dose level 11 bio rep 2 [Imi_R_B12_S22]

description:
96 well plate
Imi_R_B12_S22_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_G08


title: Preteated-1h-cell68

description: scTSS-seq


title: Preteated-1h-cell67

description: scTSS-seq


title: cochlea_WT_Rep3

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

description: KirOE_v_WT_DifferentiallyExpressedGenes.xlsx

data_processing:
NextFlow RNA pipeline
Assembly: mm10

source_name: cochlea

growth_protocol: 8 cochlea (from 4 mice) were pooled together for each sample.

extract_protocol:
RNA was harvested using Rneasy Micro kit plus (Qiagen).
mRNA was purfied using poly-T olgio attached magentic beads. After fragmentation, the frist strand cDNA was synthesized usign random hexamer primers, followed by second stand cDNA synthesis using dTTP primers. End repari, A-tailing  was reported, before adapter ligation and size seldction.

value: cochlea

value: WT


title: GL26150CD45pos_P1_B02

address: 30 Fruit Street

institute: MGH

value: brain

value: Myeloid


title: cochlea_WT_Rep1


title: GL26150CD45pos_P1_D08


title: Skin dendritic cells, uncolonized, mRNA

first: Antonin

last: Weckel

state: CA

address: 513 Parnassus

institute: UCSF

description: 3' library, aligned to the genome mms10 with Cell Ranger

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mms10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Skin

extract_protocol:
Skin was harvested and digested with collagenase. Cells were sorted to isolate dendritic cells (CD11c+ MHCII+)
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics)

treatment_protocol: None. 6 week old mice C57B/6

value: Skin

value: Dendritic cells (MHCII+CD11c+)

value: Adult


title: Imidacloprid dose level 9 bio rep 2 [Imi_R_B10_S24]

description:
96 well plate
Imi_R_B10_S24_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: Imidacloprid dose level 8 bio rep 2 [Imi_R_B09_S13]

description:
96 well plate
Imi_R_B09_S13_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Imidacloprid dose level 2 bio rep 3 [Imi_R_C03_S35]

description:
96 well plate
Imi_R_C03_S35_L004
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: cochlea_KirOE_Rep3


title: GL26150CD45pos_P1_A04


title: Preteated-1h-cell64

description: scTSS-seq


title: cochlea_KirOE_Rep1


title: Preteated-1h-cell65

description: scTSS-seq


title: Imidacloprid dose level 7 bio rep 2 [Imi_R_B08_S12]

description:
96 well plate
Imi_R_B08_S12_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_A09


title: P192 male Bace1-fl/fl

description:
10x Genomics
SC2100083

value: Neurons and glia

value: hippocampus


title: GL26150CD45pos_P1_F08

value: NK


title: GL26150CD45pos_P1_G09


title: Imidacloprid dose level 10 bio rep 2 [Imi_R_B11_S23]

description:
96 well plate
Imi_R_B11_S23_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body


title: Imidacloprid dose level 6 bio rep 2 [Imi_R_B07_S11]

description:
96 well plate
Imi_R_B07_S11_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: Imidacloprid dose level 5 bio rep 2 [Imi_R_B06_S10]

description:
96 well plate
Imi_R_B06_S10_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: cochlea_WT_Rep2


title: LAC-infected Irg1-null

city: New York

first: Kira

middle: Leigh

last: Tomlinson

state: New York

address: 650 W 168th Street, Room 4416

department: Pediatrics

institute: Columbia University

description: 10x Genomics Chromium Controller

data_processing:
FASTQ file generation, alignment, filtering, barcode counting, and UMI counting were performed with the 10X Cell Ranger software v3.
Assembly: NOT PROVIDED
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole lung

extract_protocol:
24 hours after infection, mice were euthanized and their lungs were harvested. To create a single cell suspension, the lungs were placed in an Eppendorf tube containing an enzymatic digestion solution of 2 mg/mL collagenase I (Gibco 17100-017), 20 mg/mL dispase (Gibco 17105-041), 1 mg/mL elastase (Worthington LS006365), and 1 uL/mL DNAse (Invitrogen 2224G) in PBS. The lungs were minced in the Eppendorf tube, then incubated with shaking at 37 degrees Celsius for 30 minutes. The digestion was quenched with 4 volumes of PBS supplemented with 10% heat inactivated fetal bovine serum (hiFBS; Sigma F4135), and strained over a 70-micron filter (CELLTREAT 229483). The cell suspension was centrifuged at 1400 xg for 7 minutes at 4°C. Red blood cell lysis was performed with the eBioscience RBC lysis buffer. The resulting cell pellet was resuspended in PBS supplemented with 0.04% bovine serum albumin (BSA; Sigma-Aldrich A7409) before being loaded onto the 10X Genomics Chromium Single Cell Controller.
Libraries were constructed according to manufacturer's (10X Genomics) instructions.

treatment_protocol: 8-week old WT and Irg1-/- C57BL/6NJ mice were intranasally infected with 2 x 107 USA300 LAC in 50 mL PBS or treated with PBS alone.

value: Whole lung

value: Irg1-null C57BL/6NJ

value: LAC (2e7 in 50 uL intranasal)


title: Preteated-1h-cell62

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated

value: IFN-beta, 1h


title: LAC-infected WT

description: 10x Genomics Chromium Controller

value: WT C57BL/6NJ


title: Imidacloprid dose level 4 bio rep 2 [Imi_R_B05_S9]

city: Cincinnati

description:
96 well plate
Imi_R_B05_S9_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: GL26150CD45pos_P1_D03

value: brain

value: Bcell


title: Preteated-1h-cell66

description: scTSS-seq


title: Preteated-1h-cell61

description: scTSS-seq


title: Imidacloprid dose level 3 bio rep 2 [Imi_R_B04_S8]

description:
96 well plate
Imi_R_B04_S8_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva


title: PBS-treated Irg1-null

description: 10x Genomics Chromium Controller

value: PBS (50 uL intranasal)


title: Preteated-1h-cell60

description: scTSS-seq


title: PBS-treated WT

description: 10x Genomics Chromium Controller


title: GL26150CD45pos_P1_B08


title: Preteated-1h-cell59

description: scTSS-seq


title: cochlea_KirOE_Rep2

value: cochlea


title: Imidacloprid dose level 2 bio rep 2 [Imi_R_B03_S7]

description:
96 well plate
Imi_R_B03_S7_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: GL26150CD45pos_P1_F03

value: NK


title: Preteated-1h-cell63

description: scTSS-seq


title: Imidacloprid dose level 1 bio rep 2 [Imi_R_B02_S6]

description:
96 well plate
Imi_R_B02_S6_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body


title: Preteated-1h-cell57

description: scTSS-seq


title: Imidacloprid control bio rep 2 [Imi_R_B01_S21]

description:
96 well plate
Imi_R_B01_S21_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: Microglia treated with IFNgamma and LPS [C00000_2]

first: Rafael

last: Franco

address: Avinguda Diagonal, 643

institute: Universitat de Barcelona

data_processing:
Feature Counts v1.5.0-p3 software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary Microglia culture

extract_protocol:
extraction of total RNA with the Trizol-based method using chloroform and isopropanol to purify the RNA. Quality control was assessed by measuring the 280/260 absorption ratio and the RIN in the Services of the University of Barcelona (CCiTUB: Scientific and technological centers of the Universitat de Barcelona).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Primary Microglia culture

value: WT

value: Proinflammatory components

tag: time

value: Day 3


title: Preteated-1h-cell58

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated


title: GL26150CD45pos_P1_C06


title: Imidacloprid dose level 11 bio rep 1 [Imi_R_A12_S20]

description:
96 well plate
Imi_R_A12_S20_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Microglia treated with IFNgamma, LPS and 2-Cl-IB-MECA [A30000_4]

value: Proinflammatory components + 2-Cl-IB-MECA


title: Imidacloprid dose level 10 bio rep 1 [Imi_R_A11_S19]

description:
96 well plate
Imi_R_A11_S19_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Preteated-1h-cell56

description: scTSS-seq

value: IFN-beta, 1h


title: Preteated-1h-cell55

description: scTSS-seq


title: GL26150CD45pos_P1_E07

value: brain

value: Myeloid


title: GL26150CD45pos_P1_H09


title: Imidacloprid dose level 9 bio rep 1 [Imi_R_A10_S18]

description:
96 well plate
Imi_R_A10_S18_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: larva


title: Preteated-1h-cell54

description: scTSS-seq


title: GL26140CD45pos_P1_E09

value: Bcell

value: Los


title: Microglia treated with IFNgamma and LPS [C00000_3]


title: Imidacloprid dose level 8 bio rep 1 [Imi_R_A09_S17]

description:
96 well plate
Imi_R_A09_S17_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: Microglia treated with IFNgamma, LPS and 2-Cl-IB-MECA [A30000_2]


title: Preteated-1h-cell53

description: scTSS-seq


title: GL26150CD45pos_P1_E12

value: Tcell


title: Imidacloprid dose level 7 bio rep 1 [Imi_R_A08_S16]

description:
96 well plate
Imi_R_A08_S16_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: 24 hr


title: Preteated-1h-cell52

description: scTSS-seq


title: Microglia treated with IFNgamma, LPS and 2-Cl-IB-MECA [A30000_1]

value: Primary Microglia culture

value: WT


title: Imidacloprid dose level 6 bio rep 1 [Imi_R_A07_S15]

description:
96 well plate
Imi_R_A07_S15_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: L-3

city: Nanjing

first: Weilong

last: Dai

state: jiangsu

address: Xiaoling Wei Street

institute: Nanjingagricultureuniversity

description: myoblast differentiation

data_processing:
data filtering
Base-calling
mapping
Assembly: mm39
Supplementary files format and content: Results for genomes on sample alignments, tdf

source_name: C3H C2C12 cells, 15mM lactate treatment, differentiation for 3 days

growth_protocol: C3H C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

tag: cell line

value: C3H C2C12

value: muscle stem cells

value: 15 mM lactate treatment

value: myoblast differentiation, Day 3


title: GL26140CD45pos_P1_E05

value: Microglia


title: GL26140CD45pos_P1_A07

value: brain


title: GL26140CD45pos_P1_D01

value: Myeloid


title: Preteated-1h-cell50

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated

value: IFN-beta, 1h


title: GL26140CD45pos_P1_B12

value: Los


title: L-2

description: myoblast differentiation


title: Microglia treated with IFNgamma and LPS [C00000_1]

tag: strain background

value: Proinflammatory components

value: Day 3


title: Imidacloprid dose level 5 bio rep 1 [Imi_R_A06_S14]

description:
96 well plate
Imi_R_A06_S14_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: Microglia treated with IFNgamma, LPS and 2-Cl-IB-MECA [A30000_3]

value: Primary Microglia culture

tag: genotype

value: WT

value: Proinflammatory components + 2-Cl-IB-MECA


title: Imidacloprid dose level 4 bio rep 1 [Imi_R_A05_S4]

description:
96 well plate
Imi_R_A05_S4_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: L-1

description: myoblast differentiation

value: C3H C2C12

value: muscle stem cells

value: 15 mM lactate treatment

value: myoblast differentiation, Day 3


title: GL26140CD45pos_P1_H07

value: brain

value: Microglia


title: Imidacloprid dose level 3 bio rep 1 [Imi_R_A04_S5]

description:
96 well plate
Imi_R_A04_S5_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: CT-3

description: myoblast differentiation

source_name: C3H C2C12 cells,control group, differentiation for 3 days

value: control


title: Preteated-1h-cell48

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated

value: IFN-beta, 1h


title: GL26140CD45pos_P1_D10

value: Myeloid

value: Los


title: Imidacloprid dose level 2 bio rep 1 [Imi_R_A03_S2]

description:
96 well plate
Imi_R_A03_S2_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: Imidacloprid


title: Preteated-1h-cell47

description: scTSS-seq


title: CT-2

description: myoblast differentiation


title: CT-1

description: myoblast differentiation


title: GL26140CD45pos_P1_C06


title: Imidacloprid dose level 1 bio rep 1 [Imi_R_A02_S3]

description:
96 well plate
Imi_R_A02_S3_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt

value: 24 hr


title: BMM, Day1, RANKL, Sodium acetate 1

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
Qubit 2.0, Agilent 2100, Q-PCR were used or performed to construct the library or to check the quality.
trimmomatic 0.39 was adopted to remove adaptors and low-quality reads
Alignment and read counts were performed on the mouse (GRCm38/mm10) genome using the STAR option in RSEM software (v1.3.1).
RSEM (v1.3.1) was used to count and convert the mapped reads into TPM values
DEseq2 (1.26.0) was used to count genes with differential expression in read counts quantified by RSEM.
Assembly: mm10
Supplementary files format and content: Exel files of TPM values for all the samples (genes and isoforms)
Supplementary files format and content: Exel files including raw counts of sequencing reads (genes and isoforms)
Supplementary files format and content: Exel files of FPKM values for all the samples (genes and isoforms)

source_name: Bone marrow-derevied macrophage

extract_protocol:
RNA for RNA-seq was extracted as described by the manufacturer using miRNeasy Mini Kit (217004, Qiagen), and DNase (79254, Qiagen) was treated.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bone marrow-derevied macrophage

value: Primary cell

value: RANKL, Sodium acetate


title: Preteated-1h-cell51

description: scTSS-seq


title: GL26140CD45pos_P1_E03

city: Boston


title: Preteated-1h-cell45

description: scTSS-seq


title: Preteated-1h-cell46

description: scTSS-seq


title: BMM, Day1, RANKL 1

value: RANKL


title: Preteated-1h-cell44

description: scTSS-seq


title: Fluoxetine dose level 9 bio rep 6 [Flx_P1_H10_S82]

description:
96 well plate
Flx_P1_H10_S82_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine


title: Imidacloprid control bio rep 1 [Imi_R_A01_S1]

description:
96 well plate
Imi_R_A01_S1_L003
Imi.raw.counts.txt
Imi.filtered.normFinal.txt


title: Preteated-1h-cell43

description: scTSS-seq


title: Fluoxetine dose level 8 bio rep 6 [Flx_P1_H09_S83]

description:
96 well plate
Flx_P1_H09_S83_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: BMM, Day1, RANKL


title: GL26140CD45pos_P1_B09

value: brain

value: Microglia


title: Preteated-1h-cell42

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: GL26140CD45pos_P1_D08


title: GL26140CD45pos_P1_H09


title: BMM, Day0 1


title: Preteated-1h-cell49

description: scTSS-seq

value: Pretreated


title: GL26140CD45pos_P1_C03


title: BMM, Day0


title: Preteated-1h-cell41

description: scTSS-seq

value: IFN-beta, 1h


title: Fluoxetine dose level 6 bio rep 6 [Flx_P1_H07_S81]

description:
96 well plate
Flx_P1_H07_S81_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_H01

value: Myeloid


title: BMM, Day1, RANKL, Sodium acetate


title: D3

data_processing:
Raw read QC was done with FastQC v0.11.9
Trim Galore (v0.6.4_dev) was used for Adapter trimming
BWA (v0.7.17-r1188) was used for alignment
Picard (v2.23.1) for mark duplicates was used
Picard (v2.23.1), SAMtools (v1.10), BEDTools (v2.29.2), and Pysam (v0.15.3) were used for re-mark duplicates and filtering to remove reads
HOMER (v4.11.1) was used to annotate peaks relative to gene features
Assembly: mm10
Supplementary files format and content: .bigWig files of the law data

extract_protocol:
For ATAC-seq, 50000 cells were harvested. In the case of OC (D3), 50000 cells were reseeded to a culture plate in Day2 (D2), then the whole plate was used. The cells were washed with PBS and collected in ep tubes. Then, on the ice, the cells were gently suspended and incubated in the ep tubes of 50 μl lysis buffer consisted with 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin, and the resuspension buffer containing 10mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and DW. After the 3 minutes incubation, 1 ml of wash buffer containing 990 μl of the resuspension buffer and 10 μl of 10% Tween-20 was added into the ep tube. Next, the cells were gently washed by inverting the tubes. After this wash step, the cells were centrifugated at 500 ×g for 10 minutes at 4℃. The supernatant was removed, and pelleted nuclei in each tube were gently suspended in transposition solution mix containing 25 μl 2× TD buffer (Illumina), 16.5 μl PBS, 0.1% Tween-20, 0.01 Digitonin, 2.5 μl Tn5 Transposase (Illumina), and 5 μl DW. Then the samples were incubated at 37℃ for 30 minutes on thermomixer at 1000 rpm. Transposed DNA purification was performed using DNA Clean & Concentrator (D4013, Zymo Research).
To generate library, barcoded primers  contained in a previous study (Nature Methods volume 10, pages1213–1218 (2013)) were used with NEBNext High-Fidelity 2× PCR Master Mix. The purified DNA was amplified with following conditions: 72℃ 5 minutes, 98℃ 30 seconds, after this the condition next was repeated 5 times, 98℃ 10 seconds 63℃ 30 seconds, 72℃ 60 seconds. To get saturated cycle, qPCR was performed using 100× SYBR Green 1 and 0.5 μl of primers with 5 μl of each PCR product. After getting the maximum R, PCR was conducted with 45 μl PCR product until it reaches 1/3 of the maximum R. The libraries were purified using DNA Clean & Concentrator.

value: Bone marrow-derived macrophage


title: Fluoxetine dose level 5 bio rep 6 [Flx_P1_H06_S79]

description:
96 well plate
Flx_P1_H06_S79_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body


title: Preteated-1h-cell40

description: scTSS-seq


title: Preteated-1h-cell39

description: scTSS-seq


title: Fluoxetine dose level 10 bio rep 6 [Flx_P1_H11_S84]

description:
96 well plate
Flx_P1_H11_S84_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: larva


title: D2


title: GL26140CD45pos_P1_E02

value: Los


title: GL26140CD45pos_P1_D09


title: D1


title: Preteated-1h-cell38

description: scTSS-seq


title: Fluoxetine dose level 4 bio rep 6 [Flx_P1_H05_S78]

description:
96 well plate
Flx_P1_H05_S78_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Preteated-1h-cell36

description: scTSS-seq


title: Fluoxetine dose level 7 bio rep 6 [Flx_P1_H08_S80]

description:
96 well plate
Flx_P1_H08_S80_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 24 hr


title: Fluoxetine dose level 3 bio rep 6 [Flx_P1_H04_S77]

description:
96 well plate
Flx_P1_H04_S77_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_E01


title: Fluoxetine dose level 2 bio rep 6 [Flx_P1_H03_S76]

description:
96 well plate
Flx_P1_H03_S76_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 1 bio rep 6 [Flx_P1_H02_S75]

description:
96 well plate
Flx_P1_H02_S75_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell37

description: scTSS-seq


title: GL26140CD45pos_P1_E08


title: Preteated-1h-cell35

description: scTSS-seq


title: VPR3

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description:
A2
10X Genomics

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2). The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2) in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the 10X pre-built mouse reference (mm10)  and extracted gene expression UMI counts matrix.
Genes expressed in less than 3 cells and cells expressing less than 200 genes were considered as low quality and removed from further analysis, and cells expressing more than 5,000 genes were considered as doublets and removed. Cells with more than 20 percent expression from mitochondrial genes were considered to be dead cells and removed.
Assembly: mm10
Supplementary files format and content: RawCounts.txt: Tab-separated values file and matrix file.

source_name: kidney

extract_protocol:
To induce transgene expression, VPR;Pax8-rtTa mice were fed DOX grain-based rodent diet at 7 week of age and continued for 11 weeks induction until mice were euthanized. The mice were anesthetized with Ketamine/Xylazine and perfused with chilled 1x PBS via the left ventricle. Kidneys were decapsulated, minced into 1-mm3 pieces with a sterile razor blade, and incubated in 2 mL of digestion buffer containing 1 mg/mL collagenase type II (Sigma), 1 mg/mL Pronase E (Sigma), and 50 mg/mL DNase I (Roche) at 37°C for 15 min. The partially digested tissue was then passed through a 70 mm cell strainer (Falcon) into RPMI medium supplemented with 10% FBS twice on ice and pelleted by centrifugation (200 g for 5 min). Then, the pellet was resuspended in HBSS and sheared with a 27G needle to remove large clumps. They were further filtered through a 40 mm cell strainer (Falcon) to obtain a single-cell solution. After centrifugation, the cell pellets were incubated with 3 mL of RBC lysis buffer (eBioscience 00-4333-57) to remove red blood cells on ice for 5 min. Finally, the cells were washed and resuspended in RPMI medium two times to remove debris or cell aggregates. Cell viability and number were determined using a Countess II Automated Cell Counter (Invitrogen, C10227) after staining with trypan blue. By using this method, we were able to generate single-cell suspensions with >80% viability.
Sequencing libraries were constructed according to 10x standard protocol by following the steps cDNA fragmentation, end repair and A-tailing, size selection by SPRIselect beads (Beckman Coulter), adaptor ligation, sample index PCR amplification, and repeat SPRIselect beads size selection. The final constructed single-cell libraries were sequenced by Illumina Novaseq machine with total reads per cell targeted for a minimum of 50,000.

value: kidney

value: DOX


title: D0

value: Bone marrow-derevied macrophage

value: Primary cell


title: GL26140CD45pos_P1_H11


title: GL26140CD45pos_P1_H06


title: Fluoxetine control bio rep 6 [Flx_P1_H01_S74]

description:
96 well plate
Flx_P1_H01_S74_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine


title: GL26140CD45pos_P1_B11

value: brain


title: VPR1

description:
VPR2
10X Genomics


title: WT2

description:
WT6
10X Genomics

value: WT


title: Fluoxetine dose level 9 bio rep 6 [Flx_P1_G10_S73]

description:
96 well plate
Flx_P1_G10_S73_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_E06

value: Microglia


title: Fluoxetine dose level 8 bio rep 6 [Flx_P1_G09_S72]

description:
96 well plate
Flx_P1_G09_S72_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell33

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated


title: Preteated-1h-cell32

description: scTSS-seq

value: IFN-beta, 1h


title: WT1

description:
WT5
10X Genomics


title: Fluoxetine dose level 7 bio rep 6 [Flx_P1_G08_S71]

description:
96 well plate
Flx_P1_G08_S71_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell31

description: scTSS-seq


title: GL26140CD45pos_P1_E12

value: Myeloid


title: Bap1KO_KO1_Input

city: Madison

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
bcl2fastq v2.20.0.422
H2AK119ub1 and H3K27me3 reads were mapped to the reference genome mm10 using Bowtie2.
BAM files were filtered using the NGSUtils suite for mapped and properly paired reads.
Peak tracks were generated using MACS2 callpeak and normalized to an input file.
Bedgraph files were generated using the genome coverage tool in the bedtools suite.
Assembly: mm10
Supplementary files format and content: bedgraph and peak bed files

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Six freshly dissected mouse sciatic nerves per condition (Bap1 fl/fl/Mpz-cre and Bap1 fl/fl) were minced in 1% formaldehyde for 10min then quenched for 10min with .125M glycine. Samples were incubated in LB1 for 10min, washed with LB2, then bead-homogenized using the Next Advance Bullet Blender for 5min with speed 12 (LB1, LB2, Hung et al., 2015). Samples were centrifuged to pull down nuclei-containing pellet. Pellet was resuspended in LB3 containing 0.1% SDS (LB3, Hung et al., 2015). Samples were sonicated via Bioruptor (Diagenode) on high for 2x15min cycles (30sec on/off). Sonicated chromatin was incubated with 5ug of target antibody. A 50uL aliquot of Dynabead Protein G slurry was used to pull down the protein-antibody complex. A 10% aliquot of remaining chromatin was saved for input analysis. Immunoprecipitations were washed three times in RIPA buffer and then eluted at 65 °C in reverse cross-linking buffer (50 mM Tris, 10 mM EDTA, 1% SDS). ChIP-DNA was purified using the Cell Signaling DNA Purification Kit (CST #14209S). Antibodies used for this ChIP were Rabbit IgG (Millipore, 12-370), Rabbit H3K27me3 (Active Motif, 39155), and Rabbit H2AK119ub1 (Cell Signaling, 8240P).
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.

treatment_protocol: Sciatic nerves of 4 month old mice were used immediately after dissection.

value: 4 mo.

value: Bap1 fl/fl/Mpz-cre


title: GL26140CD45pos_P1_H02

value: Los


title: VPR2

description:
A1
10X Genomics


title: Preteated-1h-cell30

description: scTSS-seq


title: Fluoxetine dose level 5 bio rep 6 [Flx_P1_G06_S69]

description:
96 well plate
Flx_P1_G06_S69_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: GL26140CD45pos_P1_F05


title: Preteated-1h-cell29

description: scTSS-seq


title: Control nerve H3K27me3

value: Bap1 fl/fl


title: Fluoxetine dose level 6 bio rep 6 [Flx_P1_G07_S70]

description:
96 well plate
Flx_P1_G07_S70_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 24 hr


title: Bap1 cKO nerve H2AK119ub1


title: Preteated-1h-cell34

description: scTSS-seq


title: Bap1 cKO nerve H3K27me3


title: GL26140CD45pos_P1_C11


title: Preteated-1h-cell28

description: scTSS-seq


title: Preteated-1h-cell27

description: scTSS-seq


title: Fluoxetine dose level 4 bio rep 6 [Flx_P1_G05_S68]

description:
96 well plate
Flx_P1_G05_S68_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell26

description: scTSS-seq


title: Control nerve H2AK119ub1


title: Fluoxetine dose level 3 bio rep 6 [Flx_P1_G04_S67]

description:
96 well plate
Flx_P1_G04_S67_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 2 bio rep 6 [Flx_P1_G03_S66]

description:
96 well plate
Flx_P1_G03_S66_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_G03


title: GL26140CD45pos_P1_F04

value: NK


title: GL26140CD45pos_P1_B05


title: Fluoxetine dose level 1 bio rep 6 [Flx_P1_G02_S65]

description:
96 well plate
Flx_P1_G02_S65_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine


title: GL26140CD45pos_P1_G05

value: brain


title: Preteated-1h-cell25

description: scTSS-seq


title: Fluoxetine control bio rep 6 [Flx_P1_G01_S85]

description:
96 well plate
Flx_P1_G01_S85_L005
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell24

description: scTSS-seq


title: GL26140CD45pos_P1_B06


title: GL26140CD45pos_P1_A01


title: Preteated-1h-cell23

description: scTSS-seq


title: IngCD, WT, Mouse7

city: Cambridge

first: David

middle: B

last: Savage

address: Addenbrooke's Hospital

department: Institute of Metabolic Science

institute: University of Cambridge

description:
WT_7
IngCD_raw_counts.csv

data_processing:
Adapter sequences were removed from raw FASTQ files using cutadapt and aligned to Mus musculus reference genome (GRCm38) using STAR.
Binary alignment/map (BAM) files were sorted using samtools and counts were performed using featureCounts
Assembly: GRCm38
Supplementary files format and content: CSV with raw counts per sample

source_name: Inguinal white adipose tissue (IngWAT)

extract_protocol:
Tissues were harvested and immediately snap frozen in liquid nitrogen and stored at -80°C. For RNA isolation, 30-50 mg of tissue was placed in Lysing Matrix D tubes and homogenized in 800 µl TRI Reagent (T9424, Sigma) using the Fastprep-24 Homogenizer for 30 s at 4-6 m/s (MP Biomedical). Homogenate was transferred to an RNase free tube and 200 µl chloroform (Sigma) added. The samples were vortexed and centrifuged at 13,000 rpm for 15 min at 4°C. The upper phase was then transferred to an RNase free tube and mixed with an equal volume of 70% ethanol before loading onto RNA isolation spin columns. RNA was extracted using a RNeasy Mini Kit (74106, Qiagen) isolation kit following the manufacturer’s instructions.
cDNA libraries were made using Illumina TruSeq RNA sample kits and sequencing was performed on Illumina NovaSeq 6000 with paired-end 150 bp reads (Novogene, Cambridge, UK). Raw reads all passed quality control for Qscore, error rate distribution, and AT/GC distribution.

treatment_protocol: Wild type (WT) and knock-in (KI) male mice aged 5 weeks were randomly allocated to HFD (45% kcal as fat, 4.7kcal/g, Research Diets D12451i) or chow (Safe Diets R105-25) 6 months

value: Inguinal white adipose tissue (IngWAT)

tag: diet

value: Chow diet

value: Wild-type


title: Fluoxetine dose level 10 bio rep 6 [Flx_P1_F11_S50]

description:
96 well plate
Flx_P1_F11_S50_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngCD, WT, Mouse6

description:
WT_6
IngCD_raw_counts.csv


title: IngCD, WT, Mouse5

description:
WT_5
IngCD_raw_counts.csv


title: Preteated-1h-cell22

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated


title: GL26140CD45pos_P1_F02

value: Myeloid


title: Fluoxetine dose level 8 bio rep 6 [Flx_P1_F09_S51]

description:
96 well plate
Flx_P1_F09_S51_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_B03

value: Microglia


title: IngCD, WT, Mouse3

description:
WT_3
IngCD_raw_counts.csv


title: Preteated-1h-cell21

description: scTSS-seq

value: IFN-beta, 1h


title: Fluoxetine dose level 7 bio rep 6 [Flx_P1_F08_S54]

description:
96 well plate
Flx_P1_F08_S54_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell20

description: scTSS-seq


title: GL26140CD45pos_P1_G09

value: Los


title: IngCD, WT, Mouse1

description:
WT_1
IngCD_raw_counts.csv


title: GL26140CD45pos_P1_E04


title: Fluoxetine dose level 6 bio rep 6 [Flx_P1_F07_S53]

description:
96 well plate
Flx_P1_F07_S53_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body


title: Preteated-1h-cell19

description: scTSS-seq


title: IngCD, KI, Mouse6

description:
KI_6
IngCD_raw_counts.csv

value: Mfn2-R707W knock-in


title: Preteated-1h-cell18

description: scTSS-seq


title: GL26140CD45pos_P1_G06


title: Fluoxetine dose level 5 bio rep 6 [Flx_P1_F06_S56]

description:
96 well plate
Flx_P1_F06_S56_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: IngCD, WT, Mouse4

description:
WT_4
IngCD_raw_counts.csv


title: Fluoxetine dose level 9 bio rep 6 [Flx_P1_F10_S52]

description:
96 well plate
Flx_P1_F10_S52_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 24 hr


title: IngCD, KI, Mouse5

description:
KI_5
IngCD_raw_counts.csv


title: GL26140CD45pos_P1_A03


title: Fluoxetine dose level 4 bio rep 6 [Flx_P1_F05_S55]

description:
96 well plate
Flx_P1_F05_S55_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngCD, KI, Mouse4

description:
KI_4
IngCD_raw_counts.csv