title: Fluoxetine dose level 3 bio rep 6 [Flx_P1_F04_S58]

description:
96 well plate
Flx_P1_F04_S58_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell17

status: Public on Jan 01 2023

type: SRA

city: Shenzhen

first: Yanling

last: Peng

address: Pengfei Road 7, Dapeng new distinct

department: Animal Functional Genomics Group

country: China

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

description: scTSS-seq

library_source: transcriptomic

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.

molecule: polyA RNA

organism: Mus musculus

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.

tag: strain

tag: cell type

value: Mouse embryonic fibroblasts

tag: pretreatment

value: Pretreated

tag: treatment

value: IFN-beta, 1h


title: GL26140CD45pos_P1_C01

city: Boston

first: Elizabeth

last: Perez

state: MA

address: 30 Fruit Street

country: USA

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)

molecule: total RNA

source_name: brain

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

tag: tissue

value: brain

value: Myeloid

value: Los


title: Preteated-1h-cell16

description: scTSS-seq


title: IngCD, KI, Mouse3

city: Cambridge

first: David

middle: B

last: Savage

address: Addenbrooke's Hospital

department: Institute of Metabolic Science

country: United Kingdom

institute: University of Cambridge

description:
KI_3
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

tag: genotype

value: Mfn2-R707W knock-in


title: GL26140CD45pos_P1_D03

value: Microglia


title: Preteated-1h-cell15

description: scTSS-seq


title: Fluoxetine dose level 2 bio rep 6 [Flx_P1_F03_S57]

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

description:
96 well plate
Flx_P1_F03_S57_L004
Flx.raw.counts.txt
Flx.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.

organism: Pimephales promelas

source_name: whole body

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.

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.

value: whole body

tag: developmental stage

value: larva

tag: age

value: 5 dpf/24 hr post hatch

tag: Sex

value: Fluoxetine

tag: concentration

tag: time point

value: 24 hr


title: IngCD, KI, Mouse2

description:
KI_2
IngCD_raw_counts.csv


title: IngCD, WT, Mouse2

description:
WT_2
IngCD_raw_counts.csv

value: Wild-type


title: Fluoxetine dose level 1 bio rep 6 [Flx_P1_F02_S60]

description:
96 well plate
Flx_P1_F02_S60_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_D06


title: BAT, WT, Mouse6

description:
WT_6
BAT_raw_counts.csv

source_name: Brown adipose tissue (BAT)

value: Brown adipose tissue (BAT)

value: High fat diet


title: Fluoxetine dose level 10 bio rep 5 [Flx_P1_E11_S62]

description:
96 well plate
Flx_P1_E11_S62_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell14

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated


title: GL26140CD45pos_P1_C08

value: brain

value: NK


title: GL26140CD45pos_P1_A09

value: Myeloid

value: Los


title: Preteated-1h-cell12

description: scTSS-seq

value: IFN-beta, 1h


title: Preteated-1h-cell13

description: scTSS-seq


title: Fluoxetine dose level 8 bio rep 5 [Flx_P1_E09_S64]

description:
96 well plate
Flx_P1_E09_S64_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_E11


title: Preteated-1h-cell11

description: scTSS-seq


title: Fluoxetine dose level 9 bio rep 5 [Flx_P1_E10_S61]

description:
96 well plate
Flx_P1_E10_S61_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell10

description: scTSS-seq


title: GL26140CD45pos_P1_D07


title: Fluoxetine dose level 7 bio rep 5 [Flx_P1_E08_S63]

description:
96 well plate
Flx_P1_E08_S63_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell9

description: scTSS-seq


title: BAT, WT, Mouse4

description:
WT_4
BAT_raw_counts.csv


title: GL26140CD45pos_P1_F10


title: BAT, WT, Mouse3

description:
WT_3
BAT_raw_counts.csv


title: Fluoxetine dose level 6 bio rep 5 [Flx_P1_E07_S43]

description:
96 well plate
Flx_P1_E07_S43_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngCD, KI, Mouse1

description:
KI_1
IngCD_raw_counts.csv

value: Inguinal white adipose tissue (IngWAT)

value: Chow diet

value: Mfn2-R707W knock-in


title: BAT, WT, Mouse2

description:
WT_2
BAT_raw_counts.csv


title: GL26140CD45pos_P1_G11

value: Microglia


title: BAT, WT, Mouse1

description:
WT_1
BAT_raw_counts.csv


title: Fluoxetine control bio rep 6 [Flx_P1_F01_S59]

description:
96 well plate
Flx_P1_F01_S59_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: Preteated-1h-cell8

description: scTSS-seq


title: Preteated-1h-cell7

description: scTSS-seq


title: BAT, KI, Mouse6

description:
KI_6
BAT_raw_counts.csv


title: Preteated-1h-cell6

description: scTSS-seq


title: Fluoxetine dose level 5 bio rep 5 [Flx_P1_E06_S44]

description:
96 well plate
Flx_P1_E06_S44_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine

value: 24 hr


title: GL26140CD45pos_P1_F01


title: GL26140CD45pos_P1_B01


title: GL26140CD45pos_P1_F11


title: Fluoxetine dose level 4 bio rep 5 [Flx_P1_E05_S45]

description:
96 well plate
Flx_P1_E05_S45_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell5

description: scTSS-seq


title: BAT, KI, Mouse4

description:
KI_4
BAT_raw_counts.csv

value: Brown adipose tissue (BAT)

value: High fat diet


title: Fluoxetine dose level 2 bio rep 5 [Flx_P1_E03_S47]

description:
96 well plate
Flx_P1_E03_S47_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell4

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Pretreated


title: Preteated-1h-cell3

description: scTSS-seq


title: GL26140CD45pos_P1_E07

value: brain


title: GL26140CD45pos_P1_B02

value: Myeloid


title: BAT, KI, Mouse1

description:
KI_1
BAT_raw_counts.csv


title: BAT, KI, Mouse3

description:
KI_3
BAT_raw_counts.csv


title: Fluoxetine dose level 10 bio rep 4 [Flx_P1_D11_S34]

description:
96 well plate
Flx_P1_D11_S34_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine control bio rep 5 [Flx_P1_E01_S49]

description:
96 well plate
Flx_P1_E01_S49_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Preteated-1h-cell1

description: scTSS-seq


title: Preteated-1h-cell2

description: scTSS-seq


title: Fluoxetine dose level 9 bio rep 4 [Flx_P1_D10_S35]

description:
96 well plate
Flx_P1_D10_S35_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, WT, Mouse8, Rep2

description:
WT_8
IngHFD_raw_counts.csv

value: Wild-type


title: BAT, KI, Mouse5

description:
KI_5
BAT_raw_counts.csv


title: Fluoxetine dose level 3 bio rep 5 [Flx_P1_E04_S46]

description:
96 well plate
Flx_P1_E04_S46_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, WT, Mouse8, Rep1

description:
WT_8
IngHFD_raw_counts.csv


title: Naïve-1h-cell96

description: scTSS-seq

value: Naive

value: IFN-beta, 1h


title: Naïve-1h-cell95

description: scTSS-seq


title: Fluoxetine dose level 1 bio rep 5 [Flx_P1_E02_S48]

description:
96 well plate
Flx_P1_E02_S48_L004
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 7 bio rep 4 [Flx_P1_D08_S37]

description:
96 well plate
Flx_P1_D08_S37_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, WT, Mouse7, Rep2

description:
WT_7
IngHFD_raw_counts.csv

value: Inguinal white adipose tissue (IngWAT)


title: GL26140CD45pos_P1_A05

value: Los


title: Naïve-1h-cell94

description: scTSS-seq


title: Fluoxetine dose level 8 bio rep 4 [Flx_P1_D09_S36]

description:
96 well plate
Flx_P1_D09_S36_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_C12

value: Microglia


title: GL26140CD45pos_P1_G12


title: IngHFD, WT, Mouse7, Rep1

description:
WT_7
IngHFD_raw_counts.csv


title: Fluoxetine dose level 6 bio rep 4 [Flx_P1_D07_S38]

description:
96 well plate
Flx_P1_D07_S38_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body


title: Naïve-1h-cell93

description: scTSS-seq


title: GL26140CD45pos_P1_H08


title: IngHFD, WT, Mouse6, Rep2

description:
WT_6
IngHFD_raw_counts.csv


title: BAT, KI, Mouse2

description:
KI_2
BAT_raw_counts.csv

value: Mfn2-R707W knock-in


title: GL26140CD45pos_P1_G01


title: Naïve-1h-cell92

description: scTSS-seq


title: Fluoxetine dose level 5 bio rep 4 [Flx_P1_D06_S39]

description:
96 well plate
Flx_P1_D06_S39_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: IngHFD, WT, Mouse6, Rep1

description:
WT_6
IngHFD_raw_counts.csv


title: Naïve-1h-cell91

description: scTSS-seq


title: GL26140CD45pos_P1_F09


title: Naïve-1h-cell90

description: scTSS-seq


title: Fluoxetine dose level 4 bio rep 4 [Flx_P1_D05_S40]

description:
96 well plate
Flx_P1_D05_S40_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine

value: 24 hr


title: GL26140CD45pos_P1_F06


title: IngHFD, WT, Mouse5, Rep2

description:
WT_5
IngHFD_raw_counts.csv

value: High fat diet


title: GL26140CD45pos_P1_G04


title: Fluoxetine dose level 3 bio rep 4 [Flx_P1_D04_S41]

description:
96 well plate
Flx_P1_D04_S41_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 1 bio rep 4 [Flx_P1_D02_S25]

description:
96 well plate
Flx_P1_D02_S25_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_H12


title: IngHFD, WT, Mouse5, Rep1

description:
WT_5
IngHFD_raw_counts.csv


title: Fluoxetine dose level 2 bio rep 4 [Flx_P1_D03_S42]

description:
96 well plate
Flx_P1_D03_S42_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Naïve-1h-cell89

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: Naïve-1h-cell87

description: scTSS-seq


title: IngHFD, WT, Mouse4, Rep2

description:
WT_4
IngHFD_raw_counts.csv


title: Naïve-1h-cell88

description: scTSS-seq


title: GL26140CD45pos_P1_A04


title: Fluoxetine dose level 9 bio rep 3 [Flx_P1_C10_S22]

description:
96 well plate
Flx_P1_C10_S22_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine control bio rep 4 [Flx_P1_D01_S24]

description:
96 well plate
Flx_P1_D01_S24_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_D11


title: Fluoxetine dose level 8 bio rep 3 [Flx_P1_C09_S29]

description:
96 well plate
Flx_P1_C09_S29_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, WT, Mouse4, Rep1

description:
WT_4
IngHFD_raw_counts.csv


title: Naïve-1h-cell86

description: scTSS-seq


title: IngHFD, WT, Mouse3, Rep2

description:
WT_3
IngHFD_raw_counts.csv


title: GL26140CD45pos_P1_A11

value: Bcell


title: IngHFD, WT, Mouse3, Rep1

description:
WT_3
IngHFD_raw_counts.csv


title: Fluoxetine dose level 7 bio rep 3 [Flx_P1_C08_S28]

description:
96 well plate
Flx_P1_C08_S28_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 10 bio rep 3 [Flx_P1_C11_S23]

description:
96 well plate
Flx_P1_C11_S23_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Naïve-1h-cell82

description: scTSS-seq


title: IngHFD, WT, Mouse2, Rep2

description:
WT_2
IngHFD_raw_counts.csv


title: Naïve-1h-cell85

description: scTSS-seq


title: Naïve-1h-cell83

description: scTSS-seq


title: IngHFD, WT, Mouse1, Rep2

description:
WT_1
IngHFD_raw_counts.csv


title: IngHFD, WT, Mouse1, Rep1

description:
WT_1
IngHFD_raw_counts.csv


title: Naïve-1h-cell84

description: scTSS-seq


title: Fluoxetine dose level 5 bio rep 3 [Flx_P1_C06_S26]

description:
96 well plate
Flx_P1_C06_S26_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_C04

value: brain


title: Naïve-1h-cell81

description: scTSS-seq


title: GL26140CD45pos_P1_D05

value: NK


title: IngHFD, KI, Mouse8, Rep2

description:
KI_8
IngHFD_raw_counts.csv


title: Naïve-1h-cell80

description: scTSS-seq


title: GL26140CD45pos_P1_B08


title: Fluoxetine dose level 2 bio rep 3 [Flx_P1_C03_S31]

description:
96 well plate
Flx_P1_C03_S31_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_B05

value: ctrl


title: IngHFD, WT, Mouse2, Rep1

description:
WT_2
IngHFD_raw_counts.csv

value: Wild-type


title: IngHFD, KI, Mouse7, Rep2

description:
KI_7
IngHFD_raw_counts.csv


title: Naïve-1h-cell79

description: scTSS-seq

value: Naive

value: IFN-beta, 1h


title: GL26140CD45pos_P1_G07

value: Los


title: GL26130CD45pos_P1_E04

value: Myeloid


title: Fluoxetine dose level 1 bio rep 3 [Flx_P1_C02_S30]

description:
96 well plate
Flx_P1_C02_S30_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body


title: Naïve-1h-cell78

description: scTSS-seq


title: GL26140CD45pos_P1_D04


title: Fluoxetine dose level 6 bio rep 3 [Flx_P1_C07_S27]

description:
96 well plate
Flx_P1_C07_S27_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, KI, Mouse7, Rep1

description:
KI_7
IngHFD_raw_counts.csv

value: Inguinal white adipose tissue (IngWAT)

value: Mfn2-R707W knock-in


title: Naïve-1h-cell77

description: scTSS-seq


title: Fluoxetine dose level 10 bio rep 2 [Flx_P1_B11_S21]

description:
96 well plate
Flx_P1_B11_S21_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: Naïve-1h-cell76

description: scTSS-seq


title: IngHFD, KI, Mouse6, Rep1

description:
KI_6
IngHFD_raw_counts.csv


title: IngHFD, KI, Mouse8, Rep1

description:
KI_8
IngHFD_raw_counts.csv


title: IngHFD, KI, Mouse6, Rep2

description:
KI_6
IngHFD_raw_counts.csv


title: GL26130CD45pos_P1_A09


title: GL26140CD45pos_P1_A06


title: GL26130CD45pos_P1_F06

value: Microglia


title: GL26130CD45pos_P1_F01


title: Fluoxetine dose level 3 bio rep 3 [Flx_P1_C04_S32]

description:
96 well plate
Flx_P1_C04_S32_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine

value: 24 hr


title: Fluoxetine dose level 8 bio rep 2 [Flx_P1_B09_S19]

description:
96 well plate
Flx_P1_B09_S19_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, KI, Mouse5, Rep1

description:
KI_5
IngHFD_raw_counts.csv

value: High fat diet


title: GL26130CD45pos_P1_C03

value: brain


title: Naïve-1h-cell72

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: Fluoxetine dose level 6 bio rep 2 [Flx_P1_B07_S11]

description:
96 well plate
Flx_P1_B07_S11_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_E11

value: ctrl


title: IngHFD, KI, Mouse4, Rep2

description:
KI_4
IngHFD_raw_counts.csv


title: IngHFD, KI, Mouse5, Rep2

description:
KI_5
IngHFD_raw_counts.csv


title: Naïve-1h-cell74

description: scTSS-seq


title: GL26130CD45pos_P1_F10


title: Fluoxetine dose level 9 bio rep 2 [Flx_P1_B10_S20]

description:
96 well plate
Flx_P1_B10_S20_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Naïve-1h-cell75

description: scTSS-seq


title: GL26130CD45pos_P1_A11

value: NK


title: BAT, WT, Mouse5

description:
WT_5
BAT_raw_counts.csv

value: Brown adipose tissue (BAT)

value: Wild-type


title: GL26130CD45pos_P1_C10


title: Naïve-1h-cell73

description: scTSS-seq

value: Naive

value: IFN-beta, 1h


title: Naïve-1h-cell70

description: scTSS-seq


title: Naïve-1h-cell69

description: scTSS-seq


title: Naïve-1h-cell68

description: scTSS-seq


title: Fluoxetine control bio rep 3 [Flx_P1_C01_S33]

description:
96 well plate
Flx_P1_C01_S33_L003
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body


title: Fluoxetine dose level 1 bio rep 2 [Flx_P1_B02_S12]

description:
96 well plate
Flx_P1_B02_S12_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 5 bio rep 2 [Flx_P1_B06_S9]

description:
96 well plate
Flx_P1_B06_S9_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: IngHFD, KI, Mouse2, Rep1

description:
KI_2
IngHFD_raw_counts.csv

value: Inguinal white adipose tissue (IngWAT)


title: IngHFD, KI, Mouse4, Rep1

description:
KI_4
IngHFD_raw_counts.csv

value: Mfn2-R707W knock-in


title: Naïve-1h-cell71

description: scTSS-seq


title: Naïve-1h-cell67

description: scTSS-seq


title: GL26130CD45pos_P1_C04


title: Fluoxetine dose level 3 bio rep 2 [Flx_P1_B04_S14]

description:
96 well plate
Flx_P1_B04_S14_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: larva


title: IngHFD, KI, Mouse3, Rep2

description:
KI_3
IngHFD_raw_counts.csv


title: GL26130CD45pos_P1_D05

value: Myeloid


title: Naïve-1h-cell66

description: scTSS-seq


title: Fluoxetine dose level 9 bio rep 1 [Flx_P1_A10_S18]

description:
96 well plate
Flx_P1_A10_S18_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Fluoxetine dose level 2 bio rep 2 [Flx_P1_B03_S15]

description:
96 well plate
Flx_P1_B03_S15_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: Fluoxetine


title: GL26130CD45pos_P1_G10


title: GL26130CD45pos_P1_B02


title: Fluoxetine dose level 7 bio rep 2 [Flx_P1_B08_S10]

description:
96 well plate
Flx_P1_B08_S10_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: 24 hr


title: Naïve-1h-cell65

description: scTSS-seq


title: IngHFD, KI, Mouse1, Rep2

description:
KI_1
IngHFD_raw_counts.csv

value: High fat diet


title: IngHFD, KI, Mouse3, Rep1

description:
KI_3
IngHFD_raw_counts.csv


title: IngHFD, KI, Mouse2, Rep2

description:
KI_2
IngHFD_raw_counts.csv


title: Fluoxetine control bio rep 2 [Flx_P1_B01_S13]

description:
96 well plate
Flx_P1_B01_S13_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_F11

value: brain

value: Microglia


title: Fluoxetine dose level 8 bio rep 1 [Flx_P1_A09_S16]

description:
96 well plate
Flx_P1_A09_S16_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 10 bio rep 1 [Flx_P1_A11_S17]

description:
96 well plate
Flx_P1_A11_S17_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Fluoxetine dose level 7 bio rep 1 [Flx_P1_A08_S8]

description:
96 well plate
Flx_P1_A08_S8_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26140CD45pos_P1_F08

value: Los


title: MCC-Sparcl1

city: Shanghai

first: Yu

last: Miao

address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
Quality distribution plot and base content distribution were generated by FASTQC.
STAR is used to align clean reads to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: primary chondrocyte

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; HyClone) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin cocktail and maintained in a humidified incubator containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA from  MCCs were extracted using EZ-press RNA Purification Kit (EZBioscience) in line with the user manual and quantified on a NanoDrop 2000 (Thermo, Waltham, USA).
RNA libraries were prepared for sequencing using NEBNext UltraTM RNA Library Prep Kit for Novaseq 6000 according to the manufacturer’s instructions.

treatment_protocol: MCC cells were treated with PBS (ctrl) or recombinant mouse Sparcl1 protein (R&D)(50ng/ml) for 3 days.

value: primary chondrocyte

value: WT

value: Recombinant Sparcl1 protein

tag: time

value: 3 days


title: Naïve-1h-cell64

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Naive

value: IFN-beta, 1h


title: GL26130CD45pos_P1_F03

value: Bcell

value: ctrl


title: GL26130CD45pos_P1_C01


title: Naïve-1h-cell63

description: scTSS-seq


title: GL26130CD45pos_P1_G12


title: BCR seq of  MRL/lpr Naive cells

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: BCR seq of MRL/lpr bone marrow Fr E and spleen FO B cells

data_processing:
The 10x raw data from each sample were demultiplexed and FASTQ files were generated using the “mkfastq” Cell Ranger pipeline (v5.0.0, 10X Genomics).
Cell Ranger “count” was used to align reads to the mm10 reference genome, and mRNA transcript, and HTO unique molecular identifier (UMI) quantification tables were generated.
The raw barcode matrix files generated from the Cell Ranger pipeline were further utilized for downstream analysis using the Seurat package (v4.0.0) in R (v3.4.3).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: Raw count output file from Cellranger.

source_name: Bone marrow, Spleen

extract_protocol:
Cells were loaded into the 10x Chromium system and RNA was isolated using the Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 with Feature Barcoding Technology for Cell Surface Protein following manufacturers' instructions
Libraries were normalized and pooled at a ratio of 1 part BCR and 1 part HTO library to 4 parts GEX library and sequenced on the Illumina HiSeq platform

treatment_protocol: Cells were isolated from bone marrow and surface stained for B220, CD93 and IgM.  Fraction E (B220+CD93+IgM+) B cells were isolated by sorting.  Splenocytes were isolated and surface stained for CD19, TCRb, CD21/35 and CD23.  CD19+CD23+CD21/35- FO B cells were isolated by sorting.  Following the sort, samples were stained with sample-hashing oligo tagged antibodies.

value: MRL/lpr (MRL.Faslpr)

value: Bone marrow, Spleen


title: IngHFD, KI, Mouse1, Rep1

description:
KI_1
IngHFD_raw_counts.csv

value: Inguinal white adipose tissue (IngWAT)

value: Mfn2-R707W knock-in


title: Fluoxetine dose level 6 bio rep 1 [Flx_P1_A07_S7]

description:
96 well plate
Flx_P1_A07_S7_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: Fluoxetine

value: 24 hr


title: BCR seq of  MRL/lpr B cells

description: BCR seq of  MRL/lpr B cellsSpleen

source_name: Spleen

treatment_protocol: Cells were isolated from spleen, surfaced stained using antibodies for flow cytometry, and sorted on BD FacsAria for CD19+TCRb-DAPI- cells.  Following the sort, cells were stained with sample hashing antibodies per mouse together with a cocktail of TotalSeq-C surface feature antibodies (against CD21/35, CD23, CD44, CD138, CD11c, CD11b, CD80, CD273, CD73 and IgM)

value: Spleen


title: MRL/lpr sorted B cells

description: MRL/lpr sorted B cellsSpleen


title: Fluoxetine dose level 4 bio rep 1 [Flx_P1_A05_S3]

description:
96 well plate
Flx_P1_A05_S3_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_G07

value: brain

value: Myeloid


title: GL26130CD45pos_P1_F05


title: Naïve-1h-cell62

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: GL26130CD45pos_P1_E03

value: Microglia


title: Fluoxetine dose level 5 bio rep 1 [Flx_P1_A06_S6]

description:
96 well plate
Flx_P1_A06_S6_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_B11

value: NK


title: MCC-Ctrl

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

value: primary chondrocyte

value: WT

value: control

value: 3 days


title: Fluoxetine dose level 2 bio rep 1 [Flx_P1_A03_S5]

description:
96 well plate
Flx_P1_A03_S5_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: Young_rep4

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
10X Genomics
3' scRNA-seq

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics mm10 reference build (version 2020-A, GRCm38 assembly with GENCODE M23 annotations) using 10X Genomics CellRanger count version 6.0.0  for all samples.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
The resultant counts matrices were input into PartekFlow (version 10.0.22.0428) for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: column labels (cell barcodes) of gene expression counts matrix
Supplementary files format and content: features.tsv.gz: row labels (genes) of gene expression counts matrix
Supplementary files format and content: matrix.mtx.gz: digital counts matrix for gene expression (matrix market format)

source_name: Bone Marrow

extract_protocol:
5 young and 9 middle-age B6 mice harvested. Single cell suspensions from each mouse were prepared by crushing spines, sternums, humeri, tibias, femurs, and iliac crests.  Niche cells were submitted to enzymatic digest, stained, and sorted on a FACSympony S6 sorter. Hematopoietic cells pass through a ficoll gradient, stained, and sorted on a FACSAria II sorter.
The cells were immediately processed as follows. Cells were counted on a Countess II automated cell counter (ThermoFisher), and 12,000 cells were loaded into one lane of a 10X Chromium microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Chromium version 3.1 NEXTGEM chemistry, according to the manufacturer’s protocol (#CG000315). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing. each gene expression library was sequenced at 18.75% of an Illumina NovaSeq 6000 S4 flow cell lane, targeting 6,000 barcoded cells with an average sequencing depth of 75,000 reads per cell.

value: Bone Marrow

value: hematopoietic and niche cells

value: young


title: Young_rep3

description:
10X Genomics
3' scRNA-seq


title: Young_rep5

description:
10X Genomics
3' scRNA-seq


title: Naïve-1h-cell57

description: scTSS-seq

value: Naive

value: IFN-beta, 1h


title: Young_rep2

description:
10X Genomics
3' scRNA-seq


title: Fluoxetine control bio rep 1 [Flx_P1_A01_S1]

description:
96 well plate
Flx_P1_A01_S1_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: Fluoxetine


title: Naïve-1h-cell60

description: scTSS-seq


title: Naïve-1h-cell56

description: scTSS-seq


title: Young_rep1

description:
10X Genomics
3' scRNA-seq


title: Flupyradifurone dose level 11 bio rep 6 [Flp_R_H12_S62]

description:
96 well plate
Flp_R_H12_S62_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone

value: 24 hr


title: Naïve-1h-cell59

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: Fluoxetine dose level 3 bio rep 1 [Flx_P1_A04_S2]

description:
96 well plate
Flx_P1_A04_S2_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: GL26130CD45pos_P1_H07

value: brain

value: Microglia

value: ctrl


title: MA_rep9

description:
10X Genomics
3' scRNA-seq

value: middle-age


title: Naïve-1h-cell58

description: scTSS-seq


title: Flupyradifurone dose level 10 bio rep 6 [Flp_R_H11_S64]

description:
96 well plate
Flp_R_H11_S64_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26130CD45pos_P1_E02

value: Myeloid


title: GL26130CD45pos_P1_B12


title: Flupyradifurone dose level 9 bio rep 6 [Flp_R_H10_S63]

description:
96 well plate
Flp_R_H10_S63_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell54

description: scTSS-seq


title: GL26130CD45pos_P1_C12


title: Naïve-1h-cell53

description: scTSS-seq


title: GL26130CD45pos_P1_G01


title: Naïve-1h-cell55

description: scTSS-seq


title: Flupyradifurone dose level 8 bio rep 6 [Flp_R_H09_S70]

description:
96 well plate
Flp_R_H09_S70_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell52

description: scTSS-seq


title: Fluoxetine dose level 1 bio rep 1 [Flx_P1_A02_S4]

description:
96 well plate
Flx_P1_A02_S4_L002
Flx.raw.counts.txt
Flx.filtered.normFinal.txt


title: MA_rep8

description:
10X Genomics
3' scRNA-seq

value: Bone Marrow


title: MA_rep7

description:
10X Genomics
3' scRNA-seq

value: hematopoietic and niche cells


title: MA_rep6

description:
10X Genomics
3' scRNA-seq


title: Flupyradifurone dose level 7 bio rep 6 [Flp_R_H08_S69]

description:
96 well plate
Flp_R_H08_S69_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26130CD45pos_P1_H12

value: Bcell


title: Naïve-1h-cell61

description: scTSS-seq

value: Naive


title: Naïve-1h-cell51

description: scTSS-seq

value: IFN-beta, 1h


title: GL26130CD45pos_P1_A07

value: NK


title: MA_rep5

description:
10X Genomics
3' scRNA-seq


title: Flupyradifurone dose level 6 bio rep 6 [Flp_R_H07_S72]

description:
96 well plate
Flp_R_H07_S72_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body

value: larva


title: GL26130CD45pos_P1_D01


title: Naïve-1h-cell50

description: scTSS-seq


title: Naïve-1h-cell49

description: scTSS-seq


title: MA_rep4

description:
10X Genomics
3' scRNA-seq


title: GL26130CD45pos_P1_E01


title: Flupyradifurone dose level 4 bio rep 6 [Flp_R_H05_S66]

description:
96 well plate
Flp_R_H05_S66_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Flupyradifurone dose level 3 bio rep 6 [Flp_R_H04_S65]

description:
96 well plate
Flp_R_H04_S65_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone


title: MA_rep3

description:
10X Genomics
3' scRNA-seq


title: Flupyradifurone dose level 5 bio rep 6 [Flp_R_H06_S71]

description:
96 well plate
Flp_R_H06_S71_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: Naïve-1h-cell47

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: GL26130CD45pos_P1_D02

value: brain


title: GL26130CD45pos_P1_G09


title: Flupyradifurone dose level 2 bio rep 6 [Flp_R_H03_S68]

description:
96 well plate
Flp_R_H03_S68_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell46

description: scTSS-seq


title: GL26130CD45pos_P1_D07


title: MA_rep1

description:
10X Genomics
3' scRNA-seq


title: MA_rep2

description:
10X Genomics
3' scRNA-seq


title: scRNA-seq of WT iPSCs

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

description: 10x Genomics

data_processing:
Sequences from scRNA-seq were processed with Cellranger (v.2.0.0) software (10x Genomics).
Further analysis—including data cleaning, normalization, scaling quality and filtering was performed using the Seurat v3.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSCs

growth_protocol: Mouse iPSCs with SRFΔ/Δ (KO) and SRFf/f (WT) were generated and cultured in serum containing medium follow our previous work (Hu et al., 2019).

extract_protocol:
Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.).
10x Genomics Chromium platform was used to capture and barcode cells to generate single-cell Gel Beads-in-Emulsion (GEMs) by following the manufacturer’s protocol. The resulting libraries were sequenced on an Illumina NovaSeq 6000 System.

value: iPSCs

value: WT iPSCs


title: Flupyradifurone dose level 1 bio rep 6 [Flp_R_H02_S67]

description:
96 well plate
Flp_R_H02_S67_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26130CD45pos_P1_A02

value: ctrl


title: Naïve-1h-cell44

description: scTSS-seq


title: scRNA-seq of SRF KO iPSCs

description: 10x Genomics

treatment_protocol: Total RNA was extracted from cells for RNA-seq using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.).

value: SRF KO iPSCs


title: Flupyradifurone control bio rep 6 [Flp_R_H01_S53]

description:
96 well plate
Flp_R_H01_S53_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: KO, stress, mouse 3 [Case_12_S12]

city: Bryan

first: Adam

middle: J

last: Case

state: TX

address: 8447 Riverside Pkwy

department: Psychiatry and Behavioral Sciences

institute: Texas A&M University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Html, TSV

extract_protocol:
Spleens were isolated from all 12 mice, physically dissociated into single cell suspension, erythrocytes lysed, and cells resuspended in RPMI + 10% FBS. Cells were counted and tested for viability (all samples >85% live), and immediately taken to the DNA core facility for library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Spleen

value: Splenocytes

value: Repeated social defeat stress


title: Naïve-1h-cell43

description: scTSS-seq

value: Naive


title: GL26130CD45pos_P1_G04

value: Myeloid


title: Naïve-1h-cell48

description: scTSS-seq

value: IFN-beta, 1h


title: Flupyradifurone dose level 10 bio rep 6 [Flp_R_G11_S55]

description:
96 well plate
Flp_R_G11_S55_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: KO, stress, mouse 2 [Case_11_S11]

description: 10x Genomics


title: KO, stress, mouse 1 [Case_10_S10]

description: 10x Genomics


title: GL26130CD45pos_P1_D10


title: Flupyradifurone dose level 9 bio rep 6 [Flp_R_G10_S56]

description:
96 well plate
Flp_R_G10_S56_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva


title: GL26130CD45pos_P1_H06

value: Microglia


title: Naïve-1h-cell40

description: scTSS-seq


title: WT, stress, mouse 3 [Case_9_S9]

description: 10x Genomics


title: Naïve-1h-cell39

description: scTSS-seq


title: Flupyradifurone dose level 8 bio rep 6 [Flp_R_G09_S49]

description:
96 well plate
Flp_R_G09_S49_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Flupyradifurone


title: Flupyradifurone dose level 6 bio rep 6 [Flp_R_G07_S51]

description:
96 well plate
Flp_R_G07_S51_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: Naïve-1h-cell42

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: GL26130CD45pos_P1_G05

value: brain


title: WT, stress, mouse 2 [Case_8_S8]

description: 10x Genomics


title: Naïve-1h-cell41

description: scTSS-seq


title: GL26130CD45pos_P1_B04


title: WT, stress, mouse 1 [Case_7_S7]

description: 10x Genomics


title: Flupyradifurone dose level 7 bio rep 6 [Flp_R_G08_S50]

description:
96 well plate
Flp_R_G08_S50_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell45

description: scTSS-seq


title: GL26130CD45pos_P1_G03


title: Flupyradifurone dose level 5 bio rep 6 [Flp_R_G06_S52]

description:
96 well plate
Flp_R_G06_S52_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: KO, control, mouse 3 [Case_6_S6]

description: 10x Genomics

value: No stress


title: GL26130CD45pos_P1_C02

value: ctrl


title: Naïve-1h-cell37

description: scTSS-seq


title: Flupyradifurone dose level 11 bio rep 6 [Flp_R_G12_S54]

description:
96 well plate
Flp_R_G12_S54_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 4 bio rep 6 [Flp_R_G05_S58]

description:
96 well plate
Flp_R_G05_S58_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: KO, control, mouse 2 [Case_5_S5]

description: 10x Genomics


title: GL26130CD45pos_P1_F09


title: Naïve-1h-cell36

description: scTSS-seq


title: Naïve-1h-cell38

description: scTSS-seq


title: GL26130CD45pos_P1_G02


title: Flupyradifurone dose level 3 bio rep 6 [Flp_R_G04_S59]

description:
96 well plate
Flp_R_G04_S59_L007
Flp.raw.counts.txt
na


title: Naïve-1h-cell35

description: scTSS-seq


title: Naïve-1h-cell34

description: scTSS-seq


title: WT, control, mouse 2 [Case_2_S2]

description: 10x Genomics


title: GL26130CD45pos_P1_A03


title: GL26130CD45pos_P1_B06


title: WT, control, mouse 3 [Case_3_S3]

description: 10x Genomics


title: GL26130CD45pos_P1_E10


title: Flupyradifurone dose level 1 bio rep 6 [Flp_R_G02_S61]

description:
96 well plate
Flp_R_G02_S61_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell32

description: scTSS-seq


title: WT, control, mouse 1 [Case_1_S1]

description: 10x Genomics


title: GL26130CD45pos_P1_G06


title: Flupyradifurone control bio rep 6 [Flp_R_G01_S57]

description:
96 well plate
Flp_R_G01_S57_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell33

description: scTSS-seq


title: GL26130CD45pos_P1_E05


title: Naïve-1h-cell31

description: scTSS-seq


title: Flupyradifurone dose level 11 bio rep 6 [Flp_R_F12_S46]

description:
96 well plate
Flp_R_F12_S46_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: AW75-LN_HTO

city: San Francisco

first: Antonin

last: Weckel

state: CA

address: 513 Parnassus

institute: UCSF

description:
SDLN migratory dendritic cells,CT-subpop/SEneg_subpop/SEpos_subpop/SAneg_subpop/SApos_subpop, cDNA
Hashtag-derived oligonucleotide (HTO)

data_processing:
Cellranger. Barcodes to assemble HTO and ADT can be recovered for alignment with the supplementary files AW75_Feature_Reference
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Skin draining lymph nodes

extract_protocol:
Skin was minced and digested with collagenase. Cells (Live CD45 MHCII+ CD11c+) were sorted, stained for Citeseq, hashtagged and and submitted for 10X
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) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics).
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

treatment_protocol: Colonized mice: Staphylococcus epidermidis Tu3298 was applied to the back skin of D10 C57BL/6J mice and tissue were processed according to material and methods 16h after colonization

value: Skin draining lymph nodes

value: dendritic cells

tag: library type

value: HTO

tag: antibodies/tags


title: Naïve-1h-cell30

description: scTSS-seq


title: AW75-LN_ADT

description:
SDLN migratory dendritic cells,CT-subpop/SEneg_subpop/SEpos_subpop/SAneg_subpop/SApos_subpop, cDNA
Antibody-derived oligonucleotide (ADT)

value: ADT

value: CD103/TotalSeq-A0201, CD11b/TotalSeq-A0014, CD301b/TotalSeq-A0566, PD-L1/TotalSeq-A0190 ,EpCAM/TotalSeq-A0449  , CD86/TotalSeq-A0200


title: GL26130CD45pos_P1_H11


title: AW75-Skin-SE_HTO

description:
Skin dermal dendritic cells, CT-subpop/SEneg_subpop/Sepos_subpop, cDNA
Hashtag-derived oligonucleotide (HTO)

source_name: skin

value: skin


title: Naïve-1h-cell29

description: scTSS-seq

value: Naive

value: IFN-beta, 1h


title: AW75-Skin-SE_ADT

description:
Skin dermal dendritic cells, CT-subpop/SEneg_subpop/Sepos_subpop, cDNA
Antibody-derived oligonucleotide (ADT)


title: GL26130CD45pos_P1_A10

value: Myeloid


title: GL26130CD45pos_P1_B07

value: Bcell


title: Flupyradifurone dose level 2 bio rep 6 [Flp_R_G03_S60]

description:
96 well plate
Flp_R_G03_S60_L007
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body

value: larva

value: 5 dpf/24 hr post hatch


title: Flupyradifurone dose level 8 bio rep 6 [Flp_R_F09_S33]

description:
96 well plate
Flp_R_F09_S33_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone

value: 24 hr


title: KO, control, mouse 1 [Case_4_S4]

description: 10x Genomics

value: Spleen

value: Splenocytes

value: No stress


title: GL26130CD45pos_P1_C09

value: brain

value: Microglia

value: ctrl


title: AW75-LN

description:
SDLN migratory dendritic cells,CT-subpop/SEneg_subpop/SEpos_subpop/SAneg_subpop/SApos_subpop, mRNA
3' library, aligned to the genome mms10 with Cell Ranger

value: Skin draining lymph nodes

value: dendritic cells

value: mRNA


title: Naïve-1h-cell26

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Naive

value: IFN-beta, 1h


title: Flupyradifurone dose level 6 bio rep 6 [Flp_R_F07_S31]

description:
96 well plate
Flp_R_F07_S31_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: Naïve-1h-cell27

description: scTSS-seq


title: AW75-Skin-SE

description:
Skin dermal dendritic cells, CT-subpop/SEneg_subpop/Sepos_subpop, mRNA
3' library, aligned to the genome mms10 with Cell Ranger

value: skin


title: Skin dermal dendritic cells, loaded cells from colonized mice with S.epidermidis-zsgreen, mRNA

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+), and for colonized mice loaded cells (zsgreen+) and non loaded dendritic cells (zsgreen_neg)
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: Colonization with Staphylococcus epidermidis-zsgreen for 16h on the back of D10 C57BJ mice.

value: Skin

value: Dendritic cells (MHCII+CD11c+)

value: colonized

tag: loading status

value: loaded (zsgreen-pos)


title: Flupyradifurone dose level 5 bio rep 6 [Flp_R_F06_S30]

description:
96 well plate
Flp_R_F06_S30_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch

value: Flupyradifurone

value: 24 hr


title: Naïve-1h-cell25

description: scTSS-seq


title: GL26130CD45pos_P1_A05

value: brain

value: Microglia

value: ctrl


title: Flupyradifurone dose level 10 bio rep 6 [Flp_R_F11_S47]

description:
96 well plate
Flp_R_F11_S47_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 4 bio rep 6 [Flp_R_F05_S37]

description:
96 well plate
Flp_R_F05_S37_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 9 bio rep 6 [Flp_R_F10_S48]

description:
96 well plate
Flp_R_F10_S48_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell24

description: scTSS-seq


title: Skin dermal dendritic cells, non-loaded cells from colonized mice with S.epidermidis-zsgreen, mRNA

value: not loaded (zsgreen-neg)


title: Skin dermal dendritic cells, uncolonized, mRNA

value: CT


title: Flupyradifurone dose level 3 bio rep 6 [Flp_R_F04_S36]

description:
96 well plate
Flp_R_F04_S36_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell28

description: scTSS-seq

value: Mouse embryonic fibroblasts

value: Naive


title: Naïve-1h-cell23

description: scTSS-seq

value: IFN-beta, 1h


title: GL26130CD45pos_P1_F12

value: Myeloid


title: SYN14

city: Worcester

first: Huiya

last: Yang

address: 368 Plantation street

department: Gene therapy center

institute: UMass Chan Medical School

data_processing:
3′ adapter sequence was removed using Trimmomatic (with parameters ILLUMINACLIP, min_length, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5)
Then, reads were mapped to mouse_mm10_gencode_ using STAR
To estimate expression levels, RSEM55 was used to align reads to a predefined set of transcripts from GENCODE.
The RSEM quantification matrix, i.e., estimated counts for each gene and/or for each annotated isoform, was used for differential gene expression analysis. Count matrix was loaded into DEBrowser software for interactive analysis. Data analysis was performed on the RNA-seq pipeline of the DolphinNext
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: liver

extract_protocol:
mRNA from mouse liver samples was extracted and enriched using oligo(dT) beads followed by rRNA removal using the Ribo-Zero kit.
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X) (New England BioLabs).  First strand cDNA was synthesized using random hexamer primer and M-MuL V Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Final libraries quantity was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples were performed on a cBot Cluster Generation System using PEE Cluster Kit cBot-HS (Illumina, California, USA) according to the manufacturer’s instructions.

treatment_protocol: P1 male C57BL/6 pups were injected with PBS or AAV9.empty, or AAV9.CB.EGFP, or AAV9.CB.hST3GAL5, or AAV9.CB.hST3GAL5_E332K or AAV9.Syn1.hST3GAL5.miR122BS vectors by IV. 36 hours post injection,  mice were sacrificed, and liver were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

value: liver

value: male

value: WT


title: Naïve-1h-cell21

description: scTSS-seq


title: Naïve-1h-cell22

description: scTSS-seq


title: Flupyradifurone dose level 1 bio rep 6 [Flp_R_F02_S34]

description:
96 well plate
Flp_R_F02_S34_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: Flupyradifurone dose level 2 bio rep 6 [Flp_R_F03_S35]

description:
96 well plate
Flp_R_F03_S35_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva


title: SYN13


title: GL26130CD45pos_P1_H02


title: GL26130CD45pos_P1_A01


title: GL26130CD45pos_P1_H03

value: Bcell


title: Flupyradifurone control bio rep 6 [Flp_R_F01_S41]

description:
96 well plate
Flp_R_F01_S41_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch

value: Flupyradifurone


title: GL26130CD45pos_P1_G11

value: brain

value: NK


title: GL26130CD45pos_P1_D11

value: ctrl


title: SYN12


title: GL26130CD45pos_P1_H10


title: Naïve-1h-cell19

description: scTSS-seq


title: Flupyradifurone dose level 10 bio rep 5 [Flp_R_E11_S39]

description:
96 well plate
Flp_R_E11_S39_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: E332K2


title: GL26130CD45pos_P1_F07


title: GL26130CD45pos_P1_F02

value: Microglia


title: Naïve-1h-cell17

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: E332K1


title: E332K3


title: Naïve-1h-cell16

description: scTSS-seq

value: Naive


title: Naïve-1h-cell18

description: scTSS-seq

value: IFN-beta, 1h


title: SYN11


title: Flupyradifurone dose level 8 bio rep 5 [Flp_R_E09_S45]

description:
96 well plate
Flp_R_E09_S45_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell15

description: scTSS-seq


title: Flupyradifurone dose level 6 bio rep 5 [Flp_R_E07_S43]

description:
96 well plate
Flp_R_E07_S43_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 11 bio rep 5 [Flp_R_E12_S40]

description:
96 well plate
Flp_R_E12_S40_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell14

description: scTSS-seq


title: Flupyradifurone dose level 7 bio rep 5 [Flp_R_E08_S44]

description:
96 well plate
Flp_R_E08_S44_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26130CD45pos_P1_A12


title: CB1


title: Naïve-1h-cell20

description: scTSS-seq


title: CB2


title: Flupyradifurone dose level 9 bio rep 5 [Flp_R_E10_S38]

description:
96 well plate
Flp_R_E10_S38_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26130CD45pos_P1_E07


title: EGFP4


title: Naïve-1h-cell12

description: scTSS-seq


title: GL26130CD45pos_P1_H09


title: Naïve-1h-cell13

description: scTSS-seq


title: EGFP2


title: GL26130CD45pos_P1_B03

value: Tcell


title: Flupyradifurone dose level 4 bio rep 5 [Flp_R_E05_S27]

description:
96 well plate
Flp_R_E05_S27_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: EGFP3

value: liver


title: GL26130CD45pos_P1_C05

value: Myeloid


title: Flupyradifurone dose level 7 bio rep 6 [Flp_R_F08_S32]

description:
96 well plate
Flp_R_F08_S32_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell11

description: scTSS-seq


title: EGFP1

value: male

value: WT


title: Naïve-1h-cell9

description: scTSS-seq


title: Flupyradifurone dose level 3 bio rep 5 [Flp_R_E04_S28]

description:
96 well plate
Flp_R_E04_S28_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body

value: larva


title: GL26130CD45pos_P1_E06


title: CB3


title: Flupyradifurone dose level 2 bio rep 5 [Flp_R_E03_S25]

description:
96 well plate
Flp_R_E03_S25_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: Flupyradifurone control bio rep 5 [Flp_R_E01_S29]

description:
96 well plate
Flp_R_E01_S29_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone


title: AAV94


title: Naïve-1h-cell10

description: scTSS-seq


title: GL26110CD45neg_P2_H06

value: brain

value: Oligodendrocytes


title: GL26130CD45pos_P1_F04

value: ctrl


title: Naïve-1h-cell7

description: scTSS-seq


title: GL26110CD45neg_P2_A07


title: Flupyradifurone dose level 11 bio rep 4 [Flp_R_D12_S3]

description:
96 well plate
Flp_R_D12_S3_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: AAV92


title: PBS4

value: PBS


title: AAV91


title: AAV93


title: Flupyradifurone dose level 1 bio rep 5 [Flp_R_E02_S26]

description:
96 well plate
Flp_R_E02_S26_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell6

description: scTSS-seq

value: Mouse embryonic fibroblasts


title: GL26110CD45neg_P2_F10


title: GL26110CD45neg_P2_B01


title: Naïve-1h-cell4

description: scTSS-seq

value: Naive


title: Flupyradifurone dose level 10 bio rep 4 [Flp_R_D11_S1]

description:
96 well plate
Flp_R_D11_S1_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell5

description: scTSS-seq

value: IFN-beta, 1h


title: Flupyradifurone dose level 7 bio rep 4 [Flp_R_D08_S7]

description:
96 well plate
Flp_R_D08_S7_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 9 bio rep 4 [Flp_R_D10_S2]

description:
96 well plate
Flp_R_D10_S2_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell2

description: scTSS-seq


title: GL26110CD45neg_P2_G12


title: Flupyradifurone dose level 8 bio rep 4 [Flp_R_D09_S6]

description:
96 well plate
Flp_R_D09_S6_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Naïve-1h-cell8

description: scTSS-seq


title: Naïve-1h-cell3

description: scTSS-seq


title: GL26110CD45neg_P2_F04


title: Flupyradifurone dose level 6 bio rep 4 [Flp_R_D07_S4]

description:
96 well plate
Flp_R_D07_S4_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: PBS2


title: PBS1


title: Flupyradifurone dose level 5 bio rep 4 [Flp_R_D06_S5]

description:
96 well plate
Flp_R_D06_S5_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: PBS3


title: GL26110CD45neg_P2_B10

value: Malignant


title: Flupyradifurone dose level 5 bio rep 5 [Flp_R_E06_S42]

description:
96 well plate
Flp_R_E06_S42_L006
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 3 bio rep 4 [Flp_R_D04_S11]

description:
96 well plate
Flp_R_D04_S11_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Pretreated-0h

description: scTSS-seq

data_processing:
The obtained sequences are aligned to the mouse genome mm9 using Tophat.
Transcript abundance is quantified using Cufflinks 1.2.1.
Genes showing significantly (p value < 0.01) higher transcript expression (RPKM) in treated cells following IFN treatment (1h) over untreated cells (0h) are considered up-regulated genes (ISGs) and are analyzed further.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include differential expression analysis and RPKM values for the used samples.
Supplementary_files_format_and_content: N0N1-gene_exp.diff: naïve 0 and naïve 1 h differential expression analysis.
Supplementary_files_format_and_content: P0P1-gene_exp.diff: pretreated 0 and pretreated 1 h differential expression analysis.
Supplementary_files_format_and_content: N1P1-FPKM.csv: RPKM values for naïve 1h and pretreated 1h MEFs.

growth_protocol: MEFs derived from H3.3-HA knockin mice in which the H3f3b locus was replaced by a H3.3-HA cDNA 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).
RNA library were prepared for sequencing using standard Illumina protocols.

value: H3.3-HA knock-in

value: Pretreated


title: Mouse, Control, 8 weeks, aortic arch

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

description:
WT_mouse
Single Lane (2 total raw files).

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite’. Raw, indexed base-call files from NovaSeq 6000 runs were demultiplexed to generate FASTQ files (included here as raw data files) using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) or human (hg19) genome as appropriate. Cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline.
Output files from the Cellranger pipeline (individual cell barcode, feature, and matrix files for each sample) are included in this repository as processed data files.
Assembly: mm10, hg19
Supplementary files format and content: 'barcodes.tsv.gz' is a column of unique barcodes corresponding to individual cells in the dataset.
Supplementary files format and content: 'features.tsv.gz' is a column of gene name identifiers from the specified genome build to which the samples were aligned.
Supplementary files format and content: 'matrix.mtx.gz' is a matrix of gene counts per cell with cell identifier barcodes arranged in columns and gene names (features) arranged in rows.

source_name: Aortic arch

extract_protocol:
Aortic tissues were cleaned and rinsed with saline to remove residual blood. Tissues were finely minced and digested enzymatically in collagenase/elastase cocktail. Single cell suspensions were then pelleted, washed, and sorted for live cells using fluorescence-activated cell sorting.
Individual sample libraries were generated from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Aortic arch

value: Control

value: 8 weeks


title: GL26110CD45neg_P2_C12


title: Naïve-1h-cell1

description: scTSS-seq


title: TKO_FL_d0

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

data_processing:
Raw sequence reads were trimmed to remove low-quality reads and adapter sequences using Trim Galore! and then mapped to the mm10 genome using HISAT2 with default parameter.
The Sam file was converted to a bam file using the Samtools.
Expression data were obtained using the subread package Featurecounts, and then transcripts per million (TPM) was calculated. The bam file for WT ESCs was reanalysed from previous study (GSM5403455).
Assembly: mm10
Supplementary files format and content: tab-delimited .txt files containing TPM value for each samples

source_name: Embryonic stem cells

growth_protocol: All ESCs were cultured on mitomycin C-treated mouse embryonic fibroblasts (MEFs) in ESC medium [D-MEM/Ham’s F12 (Wako, Osaka, Japan), 10% fetal bovine serum (Corning, NY, USA), 1× penicillin-streptomycin and 2 mM L-glutamate (Gibco®, Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Signa-Aldrich), and 10^3 U/ml ESGRO® LIF (Merck, Kenilworth, NJ, USA)] and grown under 5% CO2 at 37˚C. The medium was changed daily.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
After the QC process, mRNA was enriched using oligo(dT) beads. First, mRNA was randomly fragmented by adding fragmentation buffer, cDNA was synthesized using mRNA template and random hexamer primer, and custom double-strand synthesis buffer (Illumina), dNTPs, RNase H, DNA polymerase Synthesis was performed. Next, end repair, A-ligation, sequencing adapter ligation, size selection, and PCR enrichment were performed to complete the double-stranded cDNA library.

tag: cell line

tag: day

value: day 0


title: GL26110CD45neg_P2_E06

tag: cell type


title: Mouse, Aca2 R179C induced, 8 weeks, aortic arch

description:
Acta2_mouse
Single Lane (2 total raw files).

value: SMC Acta2 R179C induced


title: Naïve-0h

description: scTSS-seq

tag: strain

tag: pretreatment


title: GL26110CD45neg_P2_B03

tag: tissue

tag: treatment


title: Pretreated-1h

description: scTSS-seq

tag: genotype


title: Flupyradifurone dose level 2 bio rep 4 [Flp_R_D03_S8]

description:
96 well plate
Flp_R_D03_S8_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body

tag: developmental stage

value: larva

value: 5 dpf/24 hr post hatch

value: Flupyradifurone


title: Naïve-1h

description: scTSS-seq


title: GL26110CD45neg_P2_H08

value: brain

value: Oligodendrocytes


title: TKO_d0

value: TKO


title: GL26110CD45neg_P2_F02


title: Flupyradifurone dose level 1 bio rep 4 [Flp_R_D02_S9]

description:
96 well plate
Flp_R_D02_S9_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

tag: age

value: 24 hr


title: Flupyradifurone dose level 4 bio rep 4 [Flp_R_D05_S10]

description:
96 well plate
Flp_R_D05_S10_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

tag: Sex


title: GL26110CD45neg_P2_C03


title: Flupyradifurone control bio rep 4 [Flp_R_D01_S13]

description:
96 well plate
Flp_R_D01_S13_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

tag: concentration


title: Mouse dorsolateral prostate Ghr deletion replicate 2

city: Madison

first: Paul

last: Marker

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

data_processing:
Fastq files generated with bcl2fastq v2.20.422
Alignment to Mus musculus GRCm38 genome with STAR aligner v 2.5.3a with defulat settings
Read counts calculated with RSEM v. 1.3.0 with default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM files that contain expected read counts, TPM and FPKM

source_name: Mouse dorsolateral prostate

growth_protocol: Mice were housed in polysulfone cages containing corn cob bedding and maintained on a 12 hr light and dark cycle at 20.5 ± 5°C and 30-70% relative humidity. Mice were fed a 5015 Diet (PMI Nutrition International, Brentwood MO) from conception through weaning (post-natal day 21) and an 8604 Teklad Rodent Diet thereafter (Harlan Laboratories, Madison WI). Feed and water were available ad libitum.

extract_protocol:
RNA was extracted from flash frozen tissue using a NuceloSpin® RNA extraction kit (740955, Machery-Nagel, Düren, Germany) per the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA Sample Preparation Guide

treatment_protocol: 250 mg/kg tamoxifen daily for five days. DLP collected one month after final tamoxfien injection.

tag: host age

value: 7 Months

tag: host sex

value: Male

tag: mouse genetics

value: 250 mg/kg tamoxifen daily for five days


title: Mouse dorsolateral prostate Ghr deletion replicate 3

description: DLP collected one month after final tamoxfien injection


title: GL26110CD45neg_P2_H02


title: Mouse dorsolateral prostate Ghr deletion replicate 1


title: GL26110CD45neg_P2_G09


title: Empty pIC Rep2

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

description: pIC activation (Control)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were checked for quality using FastQC v0.11.5, then mapped to mm10 whole genome using TopHat v2.1.0 with defult parameters
Fragment Per Kilobase of exon per Megabase of library size (FPKM)  were calculated using cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file is output from cufflinks that includes FPKM values of genes after pIC activation at 6hr

source_name: DC1940 cell line

growth_protocol: The CD8α+ DC lines were grown in IMDM medium supplemented with 10% FBS and antibiotic solution (Gibco), 5x10-5M 2-mercaptoethanol,sodiumbicarbonate, hepes. The cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
The cells were thawed by placing the plates/tubes on ice. Total RNA was isolated using RNeasy plus kit (Qiagen) according to vendor recommended protocol. RNA concentration was estimated by nanodrop (Thermo)
2 ug of total RNA was used to isolate mRNA through magnetic beads using mRNA isolation kit (PolyA mRNA isolation Module, NEB) followed by RNA-seq library preparation using mRNA library preparation kit (NEB) strictly following the vendor recommended protoco.l

treatment_protocol: DCs were plated in 6 well plates at a density of 5 x 106 cells/ml overnight. Cells were challenged with different activation media containing TLR3 agonist pIC for different time points. cells were washed in the plate once with PBS followed by addition of RNA-later (RLT) buffer (Qiagen) for lysis of cells. The plates were then stored at -80oC until further RNA isolation and processing of samples.

value: Dendritic cell

tag: genotype/variation

value: wild type


title: Empty pIC Rep1

description: pIC activation (Control)


title: Mouse dorsolateral prostate Tamoxifen-control replicate 2

value: Ghrflox/flox;SV40 C3(1) T-antigen+/0


title: GL26110CD45neg_P2_E05

source_name: brain


title: Flupyradifurone dose level 9 bio rep 3 [Flp_R_C10_S14]

description:
96 well plate
Flp_R_C10_S14_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

tag: time point


title: K10_1

city: wuhan

first: Xiaomeng

last: Dai

address: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China

description: KN93 10uM treating

data_processing:
Illunima HiSeqTM2000/ Miseq software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated, then mapped to Mus_musculus.GRCm38.94 whole genome using Hisat2
The number of perfect clean tags for each gene was calculated and then normalized infragments per kilo bases per million mapped Reads (FPKM) using the described method.
Genome_build: Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: text files include FPKM values for each Sample ...

source_name: bone marrow

extract_protocol:
Total RNA was extracted from mice BMDMs treated with PBS or KN93 at different concentrations using a TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow


title: GL26110CD45neg_P2_F03

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)

value: Malignant


title: K10

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China

description: KN93 10uM treating


title: Mouse dorsolateral prostate Tamoxifen-control replicate 1


title: GL26110CD45neg_P2_A11


title: K5_1

description: KN93 5uM treating


title: Flupyradifurone dose level 6 bio rep 3 [Flp_R_C07_S19]

description:
96 well plate
Flp_R_C07_S19_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

source_name: whole body


title: Flupyradifurone dose level 8 bio rep 3 [Flp_R_C09_S17]

description:
96 well plate
Flp_R_C09_S17_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: 0_1

description: PBS treating


title: Ghr deletion replicate 2

tag: mouse age

value: 3 months


title: Flupyradifurone dose level 7 bio rep 3 [Flp_R_C08_S16]

description:
96 well plate
Flp_R_C08_S16_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: Tamoxifen-control replicate 3

value: Ghrflox/flox


title: Flupyradifurone dose level 11 bio rep 3 [Flp_R_C12_S12]

description:
96 well plate
Flp_R_C12_S12_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: Flupyradifurone dose level 5 bio rep 3 [Flp_R_C06_S18]

description:
96 well plate
Flp_R_C06_S18_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone


title: Flupyradifurone dose level 10 bio rep 3 [Flp_R_C11_S15]

description:
96 well plate
Flp_R_C11_S15_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Tamoxifen-control replicate 2


title: 0

description: PBS treating


title: GL26110CD45neg_P2_F06

value: brain

value: Oligodendrocytes


title: GL26110CD45neg_P2_D04


title: Flupyradifurone dose level 4 bio rep 3 [Flp_R_C05_S21]

description:
96 well plate
Flp_R_C05_S21_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: 994_S45

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
Data mapping using hisat2 (version 2.0.6) with paramters:--very-sensitive --score-min=C,-15,0 --seed 19
Read count extraction using htseq-count version 0.13.5
Assembly: mm10
Supplementary files format and content: csv  text files include raw counts values for each sample

source_name: hearts from female mice

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks. PMID: 23312289

extract_protocol:
Qiagen miRNAeasy kit
QIAseq miRNA Library Kit

value: hearts from female mice

value: female

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: Flupyradifurone dose level 3 bio rep 3 [Flp_R_C04_S20]

description:
96 well plate
Flp_R_C04_S20_L005
Flp.raw.counts.txt
Flp.sansG4.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: GL26110CD45neg_P2_F07

value: Tcell


title: 987_S44


title: GL26110CD45neg_P2_G10


title: Flupyradifurone dose level 2 bio rep 3 [Flp_R_C03_S23]

description:
96 well plate
Flp_R_C03_S23_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: K5

description: KN93 5uM treating


title: GL26110CD45neg_P2_C04


title: 984_S43


title: Tamoxifen-control replicate 1

value: Male

value: 250 mg/kg tamoxifen daily for five days


title: MC3T3_D3_EPZ6438_rep3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using FastQC
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
ChIP-seq peaks are called using the broad-peak function in MACS2 software (doi:10.1038 /nprot.2012.10127).
Duplicates were removed using Picard (https://broadinstitute.github.io/picard/).
For basic annotation of identified peaks, the HOMER function annotatePeaks.pl was used (10.1016/j.molcel.2010.05.004).
The differential peak calling was using DiffBind tool from MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with Chip-Seq peak coordinates and RNA-Seq gene expression respectively

source_name: Calvaria Pre-Osteoblasts

growth_protocol: Cells were maintained in α-minimal essential medium without ascorbic acid (Gibco) containing 10% fetal bovine serum (Atlanta Biologicals), 100 units/ml penicillin and 100 μg/ml streptomycin (Gibco).

extract_protocol:
Direct-zol™ RNA kit (Zymo Research) and TRIzol reagent (Invitrogen)
mRNA version 2 library prep kit (Illumina)
Direct-zol™ RNA kit (Zymo Research) and TRIzol reagent (Invitrogen)

treatment_protocol: Cells were treated with vehicle (DMSO) or 2.5µM EPZ6438 (MedChem, HY-13803) in osteogenic medium for 3 days.

tag: cell line_passage_strain

value: MC3T3-E1 subclone 4 cells_P9_C57BL/6

value: Treated with EPZ6438 (2.5uM) for 3 days in Osteogenic Media


title: MC3T3_D3_DMSO_rep3

value: Treated with 0.25% DMSO for 3 days in Osteogenic Media


title: Flupyradifurone dose level 1 bio rep 3 [Flp_R_C02_S22]

description:
96 well plate
Flp_R_C02_S22_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: GL26110CD45neg_P2_D12

city: Boston

first: Elizabeth

last: Perez

address: 30 Fruit Street

tag: cell type


title: GL26110CD45neg_P2_H12

value: Malignant


title: Ghr deletion replicate 1

value: 3 months


title: 951_S41


title: 974_S42


title: Flupyradifurone control bio rep 3 [Flp_R_C01_S24]

description:
96 well plate
Flp_R_C01_S24_L005
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: MC3T3_D3_EPZ6438_rep2


title: GL26110CD45neg_P2_F12

value: brain


title: Flupyradifurone dose level 11 bio rep 2 [Flp_R_B12_S22]

description:
96 well plate
Flp_R_B12_S22_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone


title: MC3T3_D3_DMSO_rep2


title: 931_S40


title: GL26110CD45neg_P2_C01


title: Flupyradifurone dose level 10 bio rep 2 [Flp_R_B11_S24]

description:
96 well plate
Flp_R_B11_S24_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: 920_S39

value: hearts from female mice


title: GL26110CD45neg_P2_B07

value: Oligodendrocytes


title: MC3T3_D3_DMSO_rep1


title: 903_S38

value: female

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: GL26110CD45neg_P2_C07


title: Flupyradifurone dose level 8 bio rep 2 [Flp_R_B09_S6]

description:
96 well plate
Flp_R_B09_S6_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 9 bio rep 2 [Flp_R_B10_S23]

description:
96 well plate
Flp_R_B10_S23_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: MC3T3_D3_EPZ6438_Input_rep2

library_source: genomic

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared from 10 ng of ChIP and input DNAs with the Ovation Ultralow DR Multiplex system (NuGEN, San Carlos, CA).
Direct-zol™ RNA kit (Zymo Research) and TRIzol reagent (Invitrogen)


title: 885_S37


title: MC3T3_D3_EPZ6438_K27me3_rep2


title: GL26110CD45neg_P2_F11


title: 876_S36


title: GL26110CD45neg_P2_H04


title: MC3T3_D3_EPZ6438_K4me3_rep2

value: H3K4me3, Abcam, ab8580


title: Flupyradifurone dose level 7 bio rep 2 [Flp_R_B08_S7]

description:
96 well plate
Flp_R_B08_S7_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: 863_S35


title: Flupyradifurone dose level 6 bio rep 2 [Flp_R_B07_S8]

description:
96 well plate
Flp_R_B07_S8_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26110CD45neg_P2_E04


title: GL26110CD45neg_P2_E08


title: 758_S34


title: 747_S33


title: Flupyradifurone dose level 4 bio rep 2 [Flp_R_B05_S10]

description:
96 well plate
Flp_R_B05_S10_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: MC3T3_D3_DMSO_K27me3_rep2


title: MC3T3_D3_EPZ6438_rep1


title: MC3T3_D3_DMSO_Input_rep2


title: Flupyradifurone dose level 3 bio rep 2 [Flp_R_B04_S11]

description:
96 well plate
Flp_R_B04_S11_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: 742_S32


title: GL26110CD45neg_P2_A02


title: Flupyradifurone dose level 2 bio rep 2 [Flp_R_B03_S12]

description:
96 well plate
Flp_R_B03_S12_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: 734_S31


title: MC3T3_D3_EPZ6438_K27me3_rep1


title: 732_S30


title: GL26110CD45neg_P2_D02


title: Flupyradifurone dose level 1 bio rep 2 [Flp_R_B02_S13]

description:
96 well plate
Flp_R_B02_S13_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone control bio rep 2 [Flp_R_B01_S14]

description:
96 well plate
Flp_R_B01_S14_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26110CD45neg_P2_C11


title: MC3T3_D3_EPZ6438_K4me3_rep1


title: Flupyradifurone dose level 5 bio rep 2 [Flp_R_B06_S9]

description:
96 well plate
Flp_R_B06_S9_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: MC3T3_D3_DMSO_Input_rep1


title: 722_S29


title: GL26110CD45neg_P2_A04


title: MC3T3_D3_DMSO_K27me3_rep1


title: Flupyradifurone dose level 11 bio rep 1 [Flp_R_A12_S15]

description:
96 well plate
Flp_R_A12_S15_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 10 bio rep 1 [Flp_R_A11_S16]

description:
96 well plate
Flp_R_A11_S16_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26110CD45neg_P2_G05


title: MC3T3_D3_DMSO_K4me3_rep2


title: 714_S27


title: Flupyradifurone dose level 9 bio rep 1 [Flp_R_A10_S17]

description:
96 well plate
Flp_R_A10_S17_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26110CD45neg_P2_D07


title: 716_S28


title: GL26110CD45neg_P2_A05


title: MC3T3_D3_DMSO_K4me3_rep1


title: DM_T177

city: New York

first: Jordi

last: Creus Muncunill

state: NY

address: 1391 Madison Ave, Apt. 3F

institute: Mount Sinai

data_processing:
Paired-end reads were aligned to the reference genome using STAR
FeatureCounts was used to count the read numbers mapped per gene
Readcounts were adjusted by TMM normalisation
DESeq2 R package was used to perform differential expression analysis.
P-values were adjusted using Benjamini Hochberg method
Genome_build: Mus musculus Grch38
Supplementary_files_format_and_content: .txt file containing a matrix of genes with readcounts against samples

source_name: striatum

extract_protocol:
The striatum  from one hemisphere was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA sequencing was performed by Novogene (https://en.novogene.com) on an Illumina Novaseq 6000 S4 flow cells platform

value: Q175 heterozygote;Tyrobp-KO

tag: strain

value: Female


title: 695_S26


title: MC3T3_D3_EPZ6438_Input_rep1

value: MC3T3-E1 subclone 4 cells_P9_C57BL/6

value: Treated with EPZ6438 (2.5uM) for 3 days in Osteogenic Media


title: GL26110CD45neg_P2_D01

institute: MGH


title: GL26110CD45neg_P2_A12


title: DM_T175


title: Flupyradifurone dose level 7 bio rep 1 [Flp_R_A08_S19]

city: Cincinnati

first: John

last: Martinson

address: 26 W. Martin L. King Drive

description:
96 well plate
Flp_R_A08_S19_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: whole body


title: GL26140CD45neg_P2_H01

value: Malignant

value: Los


title: 682_S23


title: 686_S24


title: DM_T174

value: Male


title: Flupyradifurone dose level 5 bio rep 1 [Flp_R_A06_S21]

description:
96 well plate
Flp_R_A06_S21_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: 673_S22


title: DM_T165


title: Flupyradifurone dose level 4 bio rep 1 [Flp_R_A05_S1]

description:
96 well plate
Flp_R_A05_S1_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: Flupyradifurone


title: GL26140CD45neg_P2_C01

value: brain


title: DM_T158


title: GL26140CD45neg_P2_E02


title: DM_T152


title: Flupyradifurone dose level 6 bio rep 1 [Flp_R_A07_S20]

description:
96 well plate
Flp_R_A07_S20_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt

value: 24 hr


title: Flupyradifurone dose level 8 bio rep 1 [Flp_R_A09_S18]

description:
96 well plate
Flp_R_A09_S18_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: 692_S25

value: hearts from female mice


title: Q175_Q173

value: Q175 heterozygote


title: GL26140CD45neg_P2_B05


title: 614_S20

value: female

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: Flupyradifurone dose level 3 bio rep 1 [Flp_R_A04_S2]

description:
96 well plate
Flp_R_A04_S2_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 1 bio rep 1 [Flp_R_A02_S4]

description:
96 well plate
Flp_R_A02_S4_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Flupyradifurone dose level 2 bio rep 1 [Flp_R_A03_S3]

description:
96 well plate
Flp_R_A03_S3_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: GL26140CD45neg_P2_D06


title: 575_S18


title: GL26110CD45neg_P2_D09

value: Oligodendrocytes


title: GL26140CD45neg_P2_H12


title: Flupyradifurone control bio rep 1 [Flp_R_A01_S5]

description:
96 well plate
Flp_R_A01_S5_L008
Flp.raw.counts.txt
Flp.sansG4.filtered.normFinal.txt


title: Q175_Q172

value: Female


title: Q175_Q163


title: 567_S17


title: GL26140CD45neg_P2_C02


title: Q175_Q183


title: 645_S21


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_H9_S85]

description:
96 well plate
Cu_P1_H9_S85_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 563_S16


title: Q175_Q174


title: GL26140CD45neg_P2_C03


title: 550_S15


title: 583_S19


title: Q175_Q182


title: GL26140CD45neg_P2_D11


title: KO_T176

value: Tyrobp-KO


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_H8_S84]

description:
96 well plate
Cu_P1_H8_S84_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_H7_S83]

description:
96 well plate
Cu_P1_H7_S83_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_E08


title: 538_S14


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_H5_S81]

description:
96 well plate
Cu_P1_H5_S81_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_H6_S82]

description:
96 well plate
Cu_P1_H6_S82_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_F10


title: 521_S12


title: KO_T171


title: KO_T160


title: 524_S13


title: GL26140CD45neg_P2_G06


title: CuSO4 dose level 3 bio rep 3 [Cu_P1_H4_S80]

description:
96 well plate
Cu_P1_H4_S80_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: KO_T173


title: 393_S11


title: 302_S10


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_H3_S79]

description:
96 well plate
Cu_P1_H3_S79_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_G08


title: GL26140CD45neg_P2_C04


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_H2_S78]

description:
96 well plate
Cu_P1_H2_S78_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 control bio rep 3 [Cu_P1_H1_S77]

description:
96 well plate
Cu_P1_H1_S77_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 218_S9


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_H10_S86]

description:
96 well plate
Cu_P1_H10_S86_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_D12


title: GL26140CD45neg_P2_C06


title: 196_S7


title: WT_WT25

value: WT


title: 211_S8


title: GL26140CD45neg_P2_G11


title: GL26140CD45neg_P2_F01


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_G9_S75]

description:
96 well plate
Cu_P1_G9_S75_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: whole body


title: 183_S6


title: WT_WT24


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_G8_S74]

description:
96 well plate
Cu_P1_G8_S74_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: WT_Q175


title: 180_S5


title: 166_S4


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_G7_S73]

description:
96 well plate
Cu_P1_G7_S73_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_F02

value: Malignant


title: WT_WT30


title: 161_S3


title: KO_T162

value: male


title: GL26140CD45neg_P2_G12

value: Los


title: WT_WT27

value: Male


title: KO_T154


title: GL26140CD45neg_P2_C07


title: 1489_S85


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_G5_S71]

description:
96 well plate
Cu_P1_G5_S71_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: larva

value: 5 dpf/24 hr post hatch


title: WT_WT577


title: CuSO4 dose level 3 bio rep 3 [Cu_P1_G4_S70]

description:
96 well plate
Cu_P1_G4_S70_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: SePC-La 2

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

institute: Anhui University

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes the expression values of this transcript for each Sample

source_name: lung cancer tissue

growth_protocol: Male C57BL/6 mice (18-20g) were selected and inoculated with 100μ L LLC-luc cells (2x10^7 cells/mL) subcutaneously in the axillary region of the left chest of the mouse to construct the mouse model of lung cancer.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SePC and PC were injected into the tumor once every 5 days. Four hours after the injection, a 620nm laser was irradiated for 10 minutes.

value: lung cancer tissue

value: SePC-laser


title: 1484_S84

value: hearts from female mice


title: SePC-La 1


title: 1476_S83


title: GL26140CD45neg_P2_B02

value: brain


title: GL26140CD45neg_P2_F03


title: PC-La 2

value: PC-laser


title: PC-La 1


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_G3_S69]

description:
96 well plate
Cu_P1_G3_S69_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: 24 hr


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_G2_S68]

description:
96 well plate
Cu_P1_G2_S68_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1464_S82

value: female

value: chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks


title: GL26140CD45neg_P2_A02


title: 1446_S81


title: GL26140CD45neg_P2_H07


title: CuSO4 control bio rep 3 [Cu_P1_G1_S67]

description:
96 well plate
Cu_P1_G1_S67_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_G6_S72]

description:
96 well plate
Cu_P1_G6_S72_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: Laser 2

value: Laser


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_G10_S76]

description:
96 well plate
Cu_P1_G10_S76_L006
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1433_S79


title: GL26140CD45neg_P2_D09


title: Laser 1


title: 1435_S80


title: GL26140CD45neg_P2_E11


title: GL26140CD45neg_P2_A01


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_F8_S62]

description:
96 well plate
Cu_P1_F8_S62_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1410_S78


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_F6_S60]

description:
96 well plate
Cu_P1_F6_S60_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1404_S77


title: GL26140CD45neg_P2_H10


title: GL26140CD45neg_P2_E09


title: 1394_S76


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_F7_S61]

description:
96 well plate
Cu_P1_F7_S61_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_D01


title: CuSO4 dose level 4 bio rep 3 [Cu_P1_F5_S59]

description:
96 well plate
Cu_P1_F5_S59_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: 1366_S74


title: CuSO4 dose level 3 bio rep 3 [Cu_P1_F4_S58]

description:
96 well plate
Cu_P1_F4_S58_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_B06


title: CuSO4 dose level 1 bio rep 3 [Cu_P1_F2_S56]

description:
96 well plate
Cu_P1_F2_S56_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_D07


title: GL26140CD45neg_P2_A05


title: 1355_S72


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_F9_S63]

description:
96 well plate
Cu_P1_F9_S63_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: CuSO4 control bio rep 3 [Cu_P1_F1_S55]

description:
96 well plate
Cu_P1_F1_S55_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_G03


title: 1364_S73


title: MG21hHF6

department: School of life sciences

data_processing:
PE150 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Bidirectional clustering analysis was performed for all different genes in the samples using R language Pheatmap(1.0.8) software package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes the expression values of transcripts for each Sample

growth_protocol: 6 to 8-week-old male C57BL/6 mice (purchased from Charles River Laboratories, Beijing, China) were housed under a 12-hour light/12-hour dark (LD) cycle. After adaptively fed for 1 week, the mice were randomly divided into two groups.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice in the treatment group (the HF group） were fed with a high-fat diet (D12492, Xietong Pharmaceutical Bio-engineering Co. Ltd., Jiangsu, China; 60 kcal% fat) for 3 months, and the age-matched mice in the control group (the CT group) were fed with a standard-fat diet (1010009, Xietong Pharmaceutical Bio-engineering Co. Ltd., Jiangsu, China; 10 kcal% fat) for 3 months.

value: meibomian gland

value: high-fat diet for 3 months

tag: time


title: GL26140CD45neg_P2_D02

tag: tissue

value: Malignant


title: 1338_S70

tag: treatment


title: CuSO4 dose level 9 bio rep 3 [Cu_P1_F10_S64]

description:
96 well plate
Cu_P1_F10_S64_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: whole body


title: MG21hHF3

value: male


title: 1334_S69


title: CuSO4 dose level 8 bio rep 3 [Cu_P1_E9_S53]

description:
96 well plate
Cu_P1_E9_S53_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_F07

value: Los


title: 1347_S71


title: 1379_S75


title: GL26140CD45neg_P2_H06


title: CuSO4 dose level 7 bio rep 3 [Cu_P1_E8_S52]

description:
96 well plate
Cu_P1_E8_S52_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: larva


title: CuSO4 dose level 2 bio rep 3 [Cu_P1_F3_S57]

description:
96 well plate
Cu_P1_F3_S57_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt

value: 5 dpf/24 hr post hatch


title: 1329_S68


title: CuSO4 dose level 6 bio rep 3 [Cu_P1_E7_S51]

description:
96 well plate
Cu_P1_E7_S51_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_B04


title: MG21hCTL1

value: standard-fat diet for 3 months


title: MG15hHF2


title: CuSO4 dose level 5 bio rep 3 [Cu_P1_E6_S50]

description:
96 well plate
Cu_P1_E6_S50_L005
Cu.raw.counts.txt
Cu.96wOnlySansD3.filtered.normFinal.txt


title: GL26140CD45neg_P2_H04


title: GL26140CD45neg_P2_C11


title: 1312_S67


title: 1265_S65


title: 1272_S66


title: MG15hHF6


title: MG15hCTL3


title: GL26140CD45neg_P2_F06


title: GL26140CD45neg_P2_H11