title: EV@FGF2-RSG_4

city: nanjing

first: qiang

last: tian

address: School of Life Sciences, Nanjing University, Nanjing, 210023, China.

department: the school of life sciences

institute: nanjing university

description: Library name: Sample12

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Liver tissue

value: primary cell

value: Hepatic parenchymal cells and non parenchymal cells

value: WT

value: C57BL/6J mice treated with EV@FGF2-RSG


title: EV@FGF2-RSG_3

status: Public on Jan 15 2025

type: SRA

country: China

description: Library name: Sample11

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: EV@FGF2-RSG_1

description: Library name: Sample9


title: EV_3

description: Library name: Sample7

value: C57BL/6J mice treated with EV


title: EV_4

description: Library name: Sample8


title: EV_2

description: Library name: Sample6


title: Saline_4

description: Library name: Sample4

value: C57BL/6J mice treated with Saline


title: Saline_3

description: Library name: Sample3


title: Saline_1

description: Library name: Sample1


title: Saline_2

description: Library name: Sample2


title: C/EBPB -/-_UVB [JH14_S14]

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

country: USA

institute: NCSU

description:
Library name: JH14_S14
JH14_S14

data_processing:
The quality of raw sequence data was assessed using FastQC and the first 12 poor-quality bases were trimmed based on the quality matrix from the FastQC, application. Reads were aligned to the mouse reference genome (mm38 version 87) using STAR  aligner. For each replicate sample, per-gene counts of uniquely mapped reads were calculated using htseq-count script from the HTSeq python package. The count matrix was imported and normalized for sequence depth and distortion, and dispersion was estimated using DESeq2. Bioconductor package in the R statistical computing environment.  Differentially expressed genes were identified after applying multiple testing correction using the Benjamini-Hockeberg procedure(FDR < 0.1).
mm38 version 87 from Ensembl
Supplementary files format and content: raw count merged for all samples

source_name: mouse epidermis

growth_protocol: RNA was isolated from 8-12 week old SKH-1 mice. Epidermis was collected via heat shock method.

extract_protocol:
Total RNA was isolated from heat shock isolated mouse epidermis and purified  using QiaZOL lysis (Qiagen), followed by DNase I digestion, and column clean up (Zymo).
cDNA libraries for Illumina sequencing were constructed via the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s protocol.

value: mouse epidermis

value: tissue

value: Epidermal specific knockout of C/EBPB collected 6h post 100mJ/cm2 UVB


title: C/EBPB -/-_UVB [JH13_S13]

description:
Library name: JH13_S13
JH13_S13


title: K5Cre_UVB [JH12_S12]

description:
Library name: JH12_S12
JH12_S12

value: Collected  6h post 100mJ/cm2 UVB


title: K5Cre_UVB [JH10_S10]

description:
Library name: JH10_S10
JH10_S10


title: K5Cre_UVB [JH11_S11]

description:
Library name: JH11_S11
JH11_S11


title: K5Cre_UVB [JH9_S9]

description:
Library name: JH9_S9
JH9_S9


title: C/EBPB -/- [JH7_S7]

description:
Library name: JH7_S7
JH7_S7

value: Epidermal specific knockout of C/EBPB


title: C/EBPB -/- [JH8_S8]

description:
Library name: JH8_S8
JH8_S8


title: K5Cre [JH4_S4]

description:
Library name: JH4_S4
JH4_S4

value: Untreated K5Cre control


title: C/EBPB -/- [JH5_S5]

description:
Library name: JH5_S5
JH5_S5


title: EV@FGF2-RSG_2

description: Library name: Sample10


title: K5Cre [JH3_S3]

description:
Library name: JH3_S3
JH3_S3


title: K5Cre [JH2_S2]

description:
Library name: JH2_S2
JH2_S2


title: HSTC_pmef_siWtap_frac_rna_seq_nuc_hs90

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_nuc_hs90

data_processing:
mRNA samples from human and mouse were aligned to the mm9/hg19 genome using STAR v.2.5.3a with default settings (‘--alignIntronMax 1000000’) (Dobin et al., 2013). For gene expression (TPM) and read counts, rsem-calculate-expression (rsem/1.3.3) was employed (Li and Dewey, 2011). m6A-GI and m6A-SI metrics were derived using the bam2ReadEnds.R script (Garcia-Campos et al., 2019) as per Dierks et al. 2021, calculating m6A IP enrichment against input coverage.
Assembly: mm9 & hg19
Supplementary files format and content: Processed data includes BAM alignment files from STAR alignemnt as described in the manuscriot

molecule: polyA RNA

source_name: pMEF

growth_protocol: Mammalian cell lines were grown at 37°C and 5 % CO2 in DMEM (10% FBS, with Antibiotics Penn/Strep)

extract_protocol:
Nucleozol total RNA extraction protocol according to the manufacturers protocol.
All libraries were conducted according to the libraray preparation protocol in Dierks et al. 2021. For RNA-seq, the protocol was performed as in Dierks 2021, excluding the m6A IP step, (performed as if only is the input sample.
m6A-seq2 & RNA-seq (m6A-seq2 protocol exluding the m6A IP section)

value: pMEF

value: primary cells


title: C/EBPB -/- [JH6_S6]

description:
Library name: JH6_S6
JH6_S6


title: K5Cre [JH1_S1]

description:
Library name: JH1_S1
JH1_S1


title: HSTC_pmef_siWtap_frac_rna_seq_cyt_r1

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_cyt_r1


title: HSTC_pmef_siWtap_frac_rna_seq_nuc_r1

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_nuc_r1


title: HSTC_pmef_siWtap_frac_rna_seq_cyt_ctrl

description: Library name: HSTC_pmef_sisiWtapap_frac_rna_seq_cyt_ctrl


title: HSTC_pmef_siWtap_frac_rna_seq_cyt_hs90

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_cyt_hs90


title: EV_1

description: Library name: Sample5


title: C/EBPB -/-_UVB [JH16_S16]

description:
Library name: JH16_S16
JH16_S16


title: EACBEwt-Rag1ko-DP-ChIP-Rad21-rep1

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

description: Library name: Sample 6

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ChIP-Seq data process pipline. The raw data were processed and analyzed according to the following procedure. First, SRA files were converted to fastq format, then aligned to mouse genome (mm10) using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8) (http://broadinstitute.github.io/picard). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. Peaks were identified by HOMER (v4.10.4) . FRiP (Fragments Ratio in Peaks) value was calculated using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) (https://github.com/deeptools/deepTools) to generate bigWig file with CPM normalization. Profiles were obtained on a region of ±0.2 Mb from the center of peaks, and average scores were plotted to generate averaged read density around peaks using deepTools(v3.5.0) plotProfile.
Assembly: mm10
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

molecule: genomic DNA

source_name: Thymus

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For 3C-HTGTS, mouse thymus were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer.The detailed primers used in this study are also listed in Supplementary information, Table S1.  And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For ChIP-Seq, Chromatin immunoprecipitation (ChIP) was performed on DN thymocytes from 3-4 Rag1-/- mice and 10 million anti-CD3 antibody-stimulated DP thymocytes from Rag1-/- mice per experiment. Cells were crosslinked with a final concentration of 1% formaldehyde on ice for 10 minutes and quenched with glycine (final concentration 0.125 M) on ice for 5 minutes. Cells were washed in 1x PBS once. The subsequent steps were carried out as ABclonal Sonication ChIP Kit (RK20258) with some modifications. After lysed and sonicated, chromosomal DNA was incubated with 5μg of specific antibody (anti-CTCF 07-729 from Millipore, anti-Rad21 Ab992 from Abcam) or isotype-matched IgG for 5 hours at 4°C, followed by addition of 15μl protein A/G magnetic beads for an additional 2 hours at 4°C. After washing and reversal of cross-linking, Immunoprecipitates place tube on magnet and collect supernatant to a new tube.The product was purified by PCR purification kit. Immunoprecipitated and input DNAs were quantified by real time PCR or sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp pair-end reads.
Construction of libraries were described as the above extract protocol

treatment_protocol: Three week-old mice were intraperitoneally injected with 150ug of CD3 antibody and thymic DP cells were taken 10 days later.

value: Thymus

value: T-cell

value: DP thymocytes

value: anti-CD3 antibody-stimulation


title: EACBEwt-Rag1ko-DP-ChIP-input-rep1

description: Library name: Sample 5


title: C/EBPB -/-_UVB [JH15_S15]

description:
Library name: JH15_S15
JH15_S15


title: HSTC_pmef_siWtap_frac_rna_seq_cyt_r4

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_cyt_r4


title: EACBEwt-Rag1ko-DN-ChIP-input-rep1

description: Library name: Sample 3

value: DN thymocytes


title: EACBEwt-Rag1ko-DN-ChIP-Rad21-rep1

description: Library name: Sample 4


title: EACBEwt-Rag1ko-DP-Tcrb-CBE3-3C-HTGTS-rep1

description: Library name: Sample 2


title: RiboTag, CA1, Control, IP, replicate 3

city: New York

first: Ruth

middle: A

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

description:
Library name: RiboTag_Control_IP_Rep3
S1 Flowcell 2 x 150

data_processing:
Illumina's bcl2fastq2 Conversion Software was used for basecalling. Salmon quantifications were derived using Salmon from raw FastQ against the mm10 transcriptome sequences. Differential expression analysis was performed directly from Salmon quantifications using Tximport and DESeq2
Assembly: mm10
Supplementary files format and content: Salmon transcript quantifications against the mm10 transcriptome sequences

source_name: CA1 hippocampus

extract_protocol:
30 minutes after optogenetic activation, tissue was dissected from acute brain slices in HBSS with 0.1 mg/mL cycloheximide and then resuspended in 5% w/v ice-cold polysome buffer (20 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 0.5 mM DTT) freshly supplemented with 40 U/ml RNasin Plus (Promega), cOmplete protease inhibitors (Roche), 0.1 mg/mL cycloheximide, and 0.5 mM DTT) and homogenized by dounce homogenization (40 strokes type A pestle followed by 40 strokes type B pestle). NP-40 was added to 1% final concentration and lysate was incubated on ice for 10 min. Supernatant was subsequently centrifuged at 2000 x g for 10 min at 4°C followed by 20,000 x g for 10 min at 4°C. 10% of the resulting lysate was used as input and the remaining lysate was pre-cleared by rotation with 50 μl Protein G Dynabeads (Invitrogen) (washed in polysome buffer) for 45 min at 4°C. HA-tagged ribosomes were collected by indirect IP by adding mouse anti-HA (8 μl antibody per mL lysate; Biolegend; MMS-101R) antibody directly to the lysate, rotating the mixture at 4°C for 4 hours, and adding 150 μl Protein G dynabeads to the lysate + antibody followed by overnight rotation at 4°C. Beads were washed twice with polysome buffer containing 1% NP-40 and three times with high salt wash buffer (20 mM HEPES, 5 mM MgCl2, 350 mM KCl, 1% NP-40) freshly supplemented with 0.1 mg/mL cycloheximide, and 1 mM DTT. All washes were 5 minutes with rotation at 4°C. RNA was extracted from input and IP samples by incubation with 1 mL Trizol at room temperature for 5 minutes and then RNeasy Lipid Tissue Mini Kit (Qiagen) via the manufacturer’s protocol with on-column DNase treatment (Roche). RNA quantity and quality were obtained by the Agilent 2100 Pico Bioanalyzer system.
The libraries were prepared by Illumina Stranded Total RNA Prep with Ribo-Zero Plus following the manufacturer’s instructions. High-throughput sequencing was performed on NovaSeq (Illumina) to obtain 150 nucleotide paired-end reads.

value: CA1 hippocampus

value: Camk2a-Cre x Rpl22-HA

value: AAV-Control


title: RiboTag, CA1, Control, IP, replicate 2

description:
Library name: RiboTag_Control_IP_Rep2
S1 Flowcell 2 x 150


title: RiboTag, CA1, Control, IP, replicate 1

description:
Library name: RiboTag_Control_IP_Rep1
S1 Flowcell 2 x 150


title: EACBEwt-Rag1ko-DN-Tcrb-CBE3-3C-HTGTS-rep1

description: Library name: Sample 1


title: RiboTag, CA1, Control, Input, replicate 3

description:
Library name: RiboTag_Control_Input_Rep3
S1 Flowcell 2 x 150


title: RiboTag, CA1, Opto, IP, replicate 3

description:
Library name: RiboTag_ChR2_IP_Rep3
S1 Flowcell 2 x 150


title: RiboTag, CA1, Control, Input, replicate 1

description:
Library name: RiboTag_Control_Input_Rep1
S1 Flowcell 2 x 150


title: RiboTag, CA1, Opto, IP, replicate 2

description:
Library name: RiboTag_ChR2_IP_Rep2
S1 Flowcell 2 x 150


title: RiboTag, CA1, Opto, IP, replicate 1

description:
Library name: RiboTag_ChR2_IP_Rep1
S1 Flowcell 2 x 150


title: HSTC_pmef_siWtap_frac_rna_seq_nuc_ctrl

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_nuc_ctrl


title: RiboTag, CA1, Opto, Input, replicate 3

description:
Library name: RiboTag_ChR2_Input_Rep3
S1 Flowcell 2 x 150


title: HSTC_pmef_siWtap_frac_rna_seq_nuc_r4

description: Library name: HSTC_pmef_siWtap_frac_rna_seq_nuc_r4


title: RiboTag, CA1, Opto, Input, replicate 1

description:
Library name: RiboTag_ChR2_Input_Rep1
S1 Flowcell 2 x 150


title: DTa_1704257_2 mg/kg_3 Days_liver_G-1_B13

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Library name: 243309

data_processing:
Reads were aligned to the specified genome (Ensembl build 96) using STAR
Gene counts were tabulated using salmon v0.7 using default parameters (pseudoalignment mode)
Assembly: mm10, hg39
Supplementary files format and content: tab-delimited default salmon output including raw counts for each sample

source_name: liver

extract_protocol:
Total RNA was isolated using the PureLink Pro 96 Total RNA Purification Kit (Life Technologies, Carlsbad, CA)
Tag-Seq performed using lexogen 3' QuantSeq kit FWD

value: liver


title: DTa_1704257_2 mg/kg_3 Days_liver_Z-2_G11

description: Library name: 243350


title: DTa_1828763_2 mg/kg_3 Days_liver_K-2_C11

description: Library name: 243368


title: DTa_1828763_2 mg/kg_3 Days_liver_K-1_C9

description: Library name: 243356


title: DTa_1828763_10 mg/kg_3 Days_liver_J-3_C5

description: Library name: 243314


title: DTa_1828763_10 mg/kg_3 Days_liver_J-4_C7

description: Library name: 243349


title: DTa_1704257_10 mg/kg_3 Days_liver_Y-3_G5

description: Library name: 243375


title: DTa_1704257_10 mg/kg_3 Days_liver_Y-4_G7

description: Library name: 243338


title: DTa_1704257_2 mg/kg_3 Days_liver_G-2_B15

description: Library name: 243379


title: DTa_1704257_10 mg/kg_3 Days_liver_Y-2_G3

description: Library name: 243320


title: DTa_1704257_10 mg/kg_3 Days_liver_F-3_B9

description: Library name: 243353


title: DTa_1704257_2 mg/kg_3 Days_liver_Z-1_G9

description: Library name: 243369


title: RiboTag, CA1, Control, Input, replicate 2

description:
Library name: RiboTag_Control_Input_Rep2
S1 Flowcell 2 x 150


title: DTa_1704257_10 mg/kg_3 Days_liver_F-2_B7

description: Library name: 243362


title: DTa_1704257_10 mg/kg_3 Days_liver_F-4_B11

description: Library name: 243305


title: DTa_1828763_0.4 mg/kg_3 Days_liver_L-1_C13

description: Library name: 243315


title: DTa_1704257_10 mg/kg_3 Days_liver_Y-1_G1

description: Library name: 243324


title: RiboTag, CA1, Opto, Input, replicate 2

description:
Library name: RiboTag_ChR2_Input_Rep2
S1 Flowcell 2 x 150


title: DTa_1828763_0.4 mg/kg_3 Days_liver_L-2_C15

description: Library name: 243341


title: DTa_1704257_10 mg/kg_3 Days_liver_F-1_B5

description: Library name: 243333


title: DTa_1704257_0.4 mg/kg_3 Days_liver_H-2_B19

description: Library name: 243325


title: DTa_PBS_0 mg/kg_3 Days_liver_T-1_E21

description: Library name: 243302

value: UTC


title: DTa_1704257_0.4 mg/kg_3 Days_liver_AA-1_G13

description: Library name: 243334


title: DTa_1704257_0.4 mg/kg_3 Days_liver_AA-2_G15

description: Library name: 243347


title: DTa_1704257_0.4 mg/kg_3 Days_liver_H-1_B17

description: Library name: 243377


title: DTa_PBS_0 mg/kg_3 Days_liver_T-3_F1

description: Library name: 243318


title: DTa_PBS_0 mg/kg_3 Days_liver_A-3_A5

description: Library name: 243342


title: DTa_1828763_10 mg/kg_3 Days_liver_J-1_C1

description: Library name: 243360


title: DTa_1828763_10 mg/kg_3 Days_liver_J-2_C3

description: Library name: 243373


title: DTa_PBS_0 mg/kg_3 Days_liver_A-4_A7

description: Library name: 243297


title: DTa_PBS_0 mg/kg_3 Days_liver_T-4_F3

description: Library name: 243311


title: DTa_PBS_0 mg/kg_3 Days_liver_A-2_A3

description: Library name: 243330


title: ALow_MD303_1735511_30 mg/kg_N-1_I1

description: Library name: 181687

value: Ttr-iBu


title: DTa_PBS_0 mg/kg_3 Days_liver_T-2_E23

description: Library name: 243384


title: ALow_MD303_1735511_30 mg/kg_N-4_I4

description: Library name: 181638


title: ALow_MD303_1735511_30 mg/kg_N-2_I2

description: Library name: 181636


title: ALow_MD303_1715157_30 mg/kg_G-1_G21

description: Library name: 181621

value: Ttr-MOP


title: ALow_MD303_1715157_30 mg/kg_G-4_G24

description: Library name: 181649


title: ALow_MD303_1735511_30 mg/kg_N-3_I3

description: Library name: 181671


title: ALow_MD303_1715157_30 mg/kg_G-2_G22

description: Library name: 181640


title: ALow_MD303_1735511_100 mg/kg_O-1_I5

description: Library name: 181643


title: ALow_MD303_1735511_100 mg/kg_O-3_I7

description: Library name: 181648


title: DTa_PBS_0 mg/kg_3 Days_liver_A-1_A1

description: Library name: 243344


title: ALow_MD303_1735511_100 mg/kg_O-2_I6

description: Library name: 181633


title: ALow_MD303_1715157_100 mg/kg_H-1_H1

description: Library name: 181629


title: ALow_MD303_1715157_100 mg/kg_H-3_H3

description: Library name: 181631


title: ALow_MD303_1735511_100 mg/kg_O-4_I8

description: Library name: 181688


title: ALow_MD303_1715157_100 mg/kg_H-2_H2

description: Library name: 181632


title: ALow_MD303_1735511_10 mg/kg_M-3_H23

description: Library name: 181666


title: ALow_MD303_1735511_10 mg/kg_M-4_H24

description: Library name: 181684


title: ALow_MD303_1715157_100 mg/kg_H-4_H4

description: Library name: 181655


title: ALow_MD303_1715157_10 mg/kg_F-4_G20

description: Library name: 181680


title: ALow_MD303_1715157_10 mg/kg_F-3_G19

description: Library name: 181639


title: ALow_MD303_1735511_10 mg/kg_M-2_H22

description: Library name: 181665


title: ALow_MD303_1715157_10 mg/kg_F-2_G18

description: Library name: 181660


title: ALow_MD303_1715157_10 mg/kg_F-1_G17

description: Library name: 181694


title: ALow_MD302_1708616_30 mg/kg_7 Days_liver_G-1_B21

description: Library name: 181436

value: Ttr-Parent


title: ALow_MD302_1708616_30 mg/kg_7 Days_liver_G-4_B24

description: Library name: 181461


title: ALow_MD302_1708616_30 mg/kg_7 Days_liver_G-2_B22

description: Library name: 181479


title: ALow_MD302_1708616_100 mg/kg_7 Days_liver_H-4_C4

description: Library name: 181413


title: ALow_MD302_1708616_100 mg/kg_7 Days_liver_H-2_C2

description: Library name: 181421


title: ALow_MD302_1708616_10 mg/kg_7 Days_liver_F-1_B17

description: Library name: 181419


title: ALow_MD302_1708616_10 mg/kg_7 Days_liver_F-4_B20

description: Library name: 181422


title: ALow_MD302_1708616_100 mg/kg_7 Days_liver_H-3_C3

description: Library name: 181482


title: ALow_MD303_1715157_30 mg/kg_G-3_G23

description: Library name: 181624


title: C56BL/6 rage knockout mice, muscles, CLP-3d-2

city: nanning

first: dongqin

last: huang

address: No. 50 Liangyu Avenue, Wuxiang New District,

department: aneashesiology department

institute: guang xi medical universty cancer hospital

description:
Library name: KO_CLP2
Column name in 1_genes_fpkm_expression.txt: FPKM.KO_CLP2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: anterior tibialis and gastrocnemius muscles

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: After CLP surgery or sham surgery, the mice were resuscitated with 1ml normal saline on a heat preservation blanket. After the mice were fully awake, food and water were given as usual. Samples were taken 3 days after surgery.

tag: strain

value: tissue

value: rage knockout

value: Day3 of cecal ligation and puncture (CLP) operation

tag: batch


title: C56BL/6 rage knockout mice, muscles, CLP-3d-3

description:
Library name: KO_CLP3
Column name in 1_genes_fpkm_expression.txt: FPKM.KO_CLP3

value: anterior tibialis and gastrocnemius muscles


title: C56BL/6 rage knockout mice, muscles, CLP-3d-1

description:
Library name: KO_CLP1
Column name in 1_genes_fpkm_expression.txt: FPKM.KO_CLP1


title: C56BL/6 WT mice, muscles, sham-3d-3

description:
Library name: sham3
Column name in 1_genes_fpkm_expression.txt: FPKM.sham3

value: wildtype

value: Day3 of sham operation


title: C56BL/6 WT mice, muscles, CLP-3d-4

description:
Library name: WT_CLP1
Column name in 1_genes_fpkm_expression.txt: FPKM.WT_CLP1


title: ALow_MD303_1735511_10 mg/kg_M-1_H21

description: Library name: 181685


title: C56BL/6 WT mice, muscles, CLP-3d-6

description:
Library name: WT_CLP3
Column name in 1_genes_fpkm_expression.txt: FPKM.WT_CLP3


title: C56BL/6 WT mice, muscles, sham-3d-2

description:
Library name: sham2
Column name in 1_genes_fpkm_expression.txt: FPKM.sham2


title: C56BL/6 WT mice, muscles, CLP-3d-2

description:
Library name: CLP2
Column name in 1_genes_fpkm_expression.txt: FPKM.CLP2


title: C56BL/6 WT mice, muscles, sham-3d-1

description:
Library name: sham1
Column name in 1_genes_fpkm_expression.txt: FPKM.sham1


title: C56BL/6 WT mice, muscles, CLP-3d-1

description:
Library name: CLP1
Column name in 1_genes_fpkm_expression.txt: FPKM.CLP1


title: CastratedMouseProstate_C57BL6_ATAC

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description: Library name: SI_32228

library_source: genomic single cell

data_processing:
Following sequencing, raw reads were processed with the 10X Genomics Cell Ranger ARC pipeline (version 2.0). Filtered RNA count matrix and ATAC fragments were used as input for downstream analyses.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: Per-sample non-zero count matrix files in H5 format.
Supplementary files format and content: atac_fragments.tsv.gz: Per-sample tab-separataed fragments.
Supplementary files format and content: multiome.annotation.GEO.csv: Metadata table with the cell type annotation of each cell in the GEX samples.

source_name: prostate

extract_protocol:
Mouse prostate tissues from both intact and castrated mice were used to generate Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (10x Genomics) libraries following manufacturer’s protocol. Briefly, nuclei were prepared from single cells derived from tissue dissociation following the manufacturer's recommended protocol for primary cells as described in CG000365 and nuclei numbers were estimated using Countess II FL automated cell counter. Nuclei transposition were performed for ~6000 targeted nuclei recovery.
Following transposition, sequential GEM (Gel Beads-in-emulsion) generation and barcoding steps enables the production of barcoded, full-length cDNA from poly-adenylated mRNA for geneexpression (GEX) library and attachment of a Spacer sequence with barcode to transposed DNA fragments for ATAC library. Post GEM lysis and cleanup, a preamplification PCR step fills gaps and generates sufficient mass for library construction. From this juncture the preamplified product was split to generate ATAC library (where P5 and P7 sequences used for Illumina bridge amplification were added) and GEX library constructions. The GEX library construction step entails enzymatic fragmentation, size selection, and addition of P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) via End Repair, A-tailing, Adaptor Ligation, and PCR steps. The generated libraries’ size and quality were estimated using BioAnalyzer high sensitivity chip. Multiome ATAC libraries comprise double stranded DNA with standard Illumina® paired-end constructs which begin with P5 and end with P7,  Multiome GEX libraries comprise cDNA insert with standard Illumina® paired-end constructs which begin with P5 and end with P7. Sequencing was carried out on an Illumina platform, and data analysis was executed using the 10x Genomics Cell Ranger software, which provided demultiplexing, alignment, and gene quantification against the mm10 mouse genome reference.

value: prostate

value: mixed

value: castration


title: C56BL/6 WT mice, muscles, CLP-3d-3

description:
Library name: CLP3
Column name in 1_genes_fpkm_expression.txt: FPKM.CLP3


title: IntactMouseProstate_C57BL6_ATAC

description: Library name: SI_32227


title: CastratedMouseProstate_C57BL6_GEX

description: Library name: SI_32222

library_source: transcriptomic single cell

molecule: nuclear RNA


title: ALow_MD302_1708616_30 mg/kg_7 Days_liver_G-3_B23

description: Library name: 181430


title: ALow_MD302_1708616_100 mg/kg_7 Days_liver_H-1_C1

description: Library name: 181474


title: Slide3C_CastratedD15_MouseProstate_C57BL6_rep3

description: Library name: Slide 3C

data_processing:
Raw Sequencing data were processed using the 10x genomics space ranger pipeline to generate FastQs
Sequences were aligned to mm10 genome to gene expression count using Space Ranger default settings
Gene expression levels of Refseq coding genes were quantifed using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered count matrix
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

growth_protocol: Male C57BL/6 mice 10 to 18 weeks old were either purchased from The Jackson Laboratory, or bred in-house from purchased mice

extract_protocol:
Slides in quadruplet on mice FFPE samples from two timepoints for a total of eight sections on two slides. Tissue sections of each sample type were analyzed for RNA integrity prior to placement on Spatial Tissue Optimization slides. Optimization was performed only for samples with RIN greater than or equal to 7. Spatial gene expression slides specific for either cryosections or FFPE sections were used (10X Genomics, Pleasanton, CA) and were submitted to the Advanced Genomics Core, (AGC, University of Michigan ILAB Core) for tissue optimization / permeabilization and Library Construction. Tissue was processed and placed the according to the manufacturer's instructions(CG000408 Visium Spatial Gene Expression for FFPE –Tissue Preparation Guide and CG000407 Visium Spatial Gene Expression for FFPE User Guide). Samples were stained lightly with H&E on the Spatial Gene Expression slides using a standard protocol CG000409 Visium Spatial Gene Expression for FFPE –Deparaffinization, H&E Staining, Imaging & Decrosslinkingand images scanned at high resolution and then probed with  the Visium Mouse Transcriptome Probe Set (Visium Mouse Transcriptome Probe Set v1.0).
Visium sequencing depth for probe set assay was 100m reads/sample. All sequencing was performed at the University of Michigan Advanced Sequencing core on the NovaSeq6000 with 300 cycles and paired end 150. Each sequenced library was demultiplexed to FASTQ files and aligned to reads to the mm10 mouse transcriptomewith tr the Spatial Space Ranger 1.3

treatment_protocol: Mice were orchiectomized  and prostates harvested 15 or 20 days later. Upon removal of adhering fats, dissected whole prostates were placed in histocassettes sandwiched between sponges (Fisher) and fixed in 10% Formaldehyde for 4 hours and paraffin embedded within 24 hrs. Cryosections 5 to 7µm and 5um paraffin sections for FFPE were performed by ULAM-IVAC (University of Michigan ILAB Core).

value: Castracted D15


title: IntactMouseProstate_C57BL6_GEX

description: Library name: SI_32221


title: Slide3B_CastratedD15_MouseProstate_C57BL6_rep2

description: Library name: Slide 3B


title: ALow_MD302_1708616_10 mg/kg_7 Days_liver_F-2_B18

description: Library name: 181425


title: Slide3A_CastratedD15_MouseProstate_C57BL6_rep1

description: Library name: Slide 3A


title: ALow_MD302_1708616_10 mg/kg_7 Days_liver_F-3_B19

description: Library name: 181433


title: Slide1D_IntactMouseProstate_C57BL6_rep4

description: Library name: Slide 1D

value: Intact


title: Slide1C_IntactMouseProstate_C57BL6_rep3

description: Library name: Slide 1C


title: Slide1B_IntactMouseProstate_C57BL6_rep2

description: Library name: Slide 1B


title: Slide1A_IntactMouseProstate_C57BL6_rep1

description: Library name: Slide 1A


title: B16F10_3

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

country: Japan

institute: National Cancer Center

data_processing:
Low quality bases and adapter sequences were removed from the raw Fastq read sequences by Trim Galore v 0.6.5. In addition, reads mapped to rRNA genes were removed using Bowite2 v 2.4.1.
The filtered Fastq sequence reads were then aligned to the mouse genome using STAR v 2.7.3a.
Gene expression values were calculated as TPM using Stringtie (v 2.1.2)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: CD45+ tumor-infiltrating immune cells

growth_protocol: BALB/cJ mice or C57BL/6J mice were subcutaneously inoculated with each cell lines.

extract_protocol:
When tumors reached 10 mm in length, tumor tissues were minced and treated with TTDR (BD Biosciences), and RNA was prepared from single cell suspensions. Total RNA was extracted using TRIzol (Thermo Fisher Scientific)  according to the manufacturer’s instructions.
cDNA libraries were prepared from the TruSeq Stranded mRNA Sample Prep (Illumina, San Diego, CA).

treatment_protocol: Mice were treated with/without OK-432 into the tumors for 24 hours.

value: CD45+ tumor-infiltrating immune cells


title: C56BL/6 WT mice, muscles, CLP-3d-5

description:
Library name: WT_CLP2
Column name in 1_genes_fpkm_expression.txt: FPKM.WT_CLP2


title: Slide3D_CastratedD15_MouseProstate_C57BL6_rep4

description: Library name: Slide 3D


title: B16F10_2


title: B16F10_1


title: B16F1_1


title: Renca_3


title: B16F1_3


title: Renca_2


title: B16F1_2


title: Renca_1


title: CMS5a_3


title: CMS5a_2


title: CMS5a_1


title: CT26NYESO1_3


title: CT26_2


title: CT26NYESO1_2


title: CT26NYESO1_1


title: CT26_3


title: CT26_1


title: LL2_3


title: LL2_2


title: EMT6_3


title: LL2_1


title: EMT6_2


title: EMT6_1


title: MC38OVA_2


title: MC38OVA_1


title: MC38_2


title: MC38_1


title: LL2_OK432_3

source_name: TME of LL-2 tumor

growth_protocol: BALB/cJ mice or C57BL/6J mice were subcutaneously inoculated with CT26, CT26-NY-ESO-1 or LL/2 cells.

extract_protocol:
On Day 14, mice were sacrificed, and tumors were collected for bulk RNA-seq. Total RNA was extracted using TRIzol (Thermo Fisher Scientific) according to the manufacturer’s instructions.
cDNA libraries were prepared from the TruSeq Stranded mRNA Sample Prep (Illumina, San Diego, CA).

value: TME of LL-2 tumor


title: LL2_OK432_2


title: LL2_OK432_1


title: LL2_Ctrl_3

value: Ctrl


title: LL2_Ctrl_2


title: CT26NYESO1_OK432_3

source_name: TME of CT26-NY-ESO-1 tumor

value: TME of CT26-NY-ESO-1 tumor


title: LL2_Ctrl_1


title: CT26NYESO1_OK432_1


title: CT26NYESO1_Ctrl_3


title: CT26NYESO1_Ctrl_2


title: CT26NYESO1_Ctrl_1


title: CT26NYESO1_OK432_2


title: CT26_OK432_3

source_name: TME of CT26 tumor

value: TME of CT26 tumor


title: CT26_OK432_1


title: CT26_Ctrl_2


title: CT26_OK432_2


title: CT26_Ctrl_3


title: CT26_Ctrl_1


title: e2Merv_dtag_gfpPos_72hr_rna_rep3

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

data_processing:
Biological and technical replicates were merged using zcat
Reads were trimmed to remove adapter sequences using trim galore v0.6.7 with parameters: --phred33 --quality 0 --stringency 10 --length 20
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
TE Counts v2.2.3 was used to assign mapped reads to genes and repeats with default parameters. GTFs from GENCODE (vM25) and a repeat file from TE Counts were used.
Bigwigs were made from bed files using deeptools v3.5.1 using parameters: -p 10 --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize  2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Differential gene expression was performed in R v4.1.0 using DESeq2 v1.34.0 with parameters: geneField = 'ensembl'
Assembly: mm10, GRCm38 vM25
Supplementary files format and content: CSVs of DESeq2 normalized counts for each round of RNAseq
Supplementary files format and content: CSVs of DESeq2 normalized counts for transposable elements (TEs) for each round of RNAseq
Supplementary files format and content: CSVs of DESeq2 results for relevant, pairwise comparisons
Supplementary files format and content: Bigwigs normalized to sequencing depth for read 1 and read 2

growth_protocol: Cells were cultured in FBS/LIF conditions at 37C at 5%CO2.

extract_protocol:
RNA was extracted using the  Trizol extraction method and then purified using the Zymo Rna Clean and concentrator kit.
Sequencing libraries were prepared using TruSeq Stranded mRNA Library Preparation (Poly-A selection and Stranded RNA-Seq)(Illumina)following the manufacturer’s instructions. High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform. Low input RNA-seq librarier were made by Novogene and sequenced on NovaSeq 6000

treatment_protocol: Cells treated with DMSO or dTAG for 24 hours, 7 days or 15days. To assess transcriotional recovery cells were  treated with dTAG for 7 days  followed by 8 days of recovery.  RNA was collected at the endpoint of all the aforementioned treatment cycles.Mervl cells were sorted for GFP+ and -ve populatios after treatment with DMSO/dTAG-13 for 72hrs , RNA collected for 200000 sorted cells.

value: ESC

value: dTAG

tag: time


title: e2Merv_dtag_gfpPos_72hr_rna_rep2


title: MC38OVA_3


title: MC38_3


title: e2Merv_dtag_gfpNeg_72hr_rna_rep2


title: e2Merv_dtag_gfpNeg_72hr_rna_rep1


title: e2Merv_dtag_gfpPos_72hr_rna_rep1


title: e2Merv_dmso_gfpPos_72hr_rna_rep3

value: DMSO


title: e2Merv_dmso_gfpPos_72hr_rna_rep2


title: e2Merv_dmso_gfpPos_72hr_rna_rep1


title: E2-K71-RECOVERY 8 DAYS

value: dTAG+DMSO

value: 8 days


title: E2-17-RECOVERY 8 DAYS


title: e2Merv_dmso_gfpNeg_72hr_rna_rep1


title: e2Merv_dmso_gfpNeg_72hr_rna_rep3


title: E2-20-RECOVERY 8 DAYS


title: E2-K71-DTAG 15 DAYS


title: e2Merv_dmso_gfpNeg_72hr_rna_rep2


title: E2-20-DTAG 15 DAYS


title: E2-17-DTAG 15 DAYS


title: E2-17-DMSO-15days


title: E2-K71-dTAG 7 day

value: 7 days


title: E2-20-DMSO-15days


title: E2-17-dTAG 7 day


title: E2-20-dTAG 7 day


title: E2-K71-7 days -DMSO


title: E2-20-7 days -DMSO


title: E2-K71-dTAG 24hr


title: E2-17-7 days -DMSO


title: e2Merv_dtag_gfpNeg_72hr_rna_rep3


title: E2-K71 24h-DMSO


title: E2-K71-DMSO 15DAYS


title: e2_dmso_24hr_chip_aHA-CST_rep4_20

data_processing:
Biological and technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Peaks were called on bed files using MACS2 v2.2.6 using parameters: -f BEDPE --nomodel --seed 123 --keep-dup all -p 0.05
After peak calling with MACS2, peak files were filtered to only include peaks with q-value < 0.05 using a custom python script.
Bigwigs were made from bed files using deeptools v3.5.1 using parameters: --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Bigwigs were z-normalized per chromsome arm using a custom R script (v4.1.2 "Bird Hippie").
Assembly: mm10
Supplementary files format and content: z-normalized bigwigs for merged replicates.
Supplementary files format and content: narrowpeak files of called peaks

growth_protocol: ESCs were cultured  in KO-DMEM (Invitrogen) supplemented with L-Glutamine, penicillin-streptomycin, nonessential amino acids, β-mercaptoethanol, LIF and heat-inactivated fetal bovine serum (FBS).

extract_protocol:
For HA CHIP 30M treated cells were first fixed with DSG for 50 followed by  1% formaldehyde fixation at room temperature (RT) for 10 minutes and quenched with 125mM glycine 5 mins at RT.Cell pellets were washed twice in PBS and resuspended in 400ul lysis buffer per 20 million cells (10mM Tris pH8, 1mM EDTA, 0.5% SDS). Cells were sonicated in a bioruptor device and spin down 10 minutes at 4 degrees at maximum speed. Supernatants were diluted 5 times with dilution buffer (0.01%SDS, 1.1% triton,1.2mM EDTA,16.7mM Tris pH8, 167mM NaCl) and incubated with the respective antibody (2-3ug/10M cells) O/N with rotation at 4oC. Next day, protein G Dynabeads (ThermoScientific) preblocked with BSA protein (100ng per 10ul Dynabeads) were added (10ul blocked Dynabeads per 10 million cells) and incubated for 2-3 hours at 4oC. Beads were immobilized on magnet and washed twice in low salt buffer (0.1% SDS,1% triton, 2mM EDTA, 150mM NaCl, 20mM Tris pH8), twice in high salt buffer (0.1% SDS,1% triton, 2mM EDTA, 500mM NaCl, 20mM Tris pH8), twice in LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris pH8) and once in TE. DNA was then eluted from the beads by incubating with 150ul elution buffer (1% SDS, 100mM NaHCO3) for 20 minutes at 65 degrees (vortex every 10min). Supernatants were collected and reverse-crosslinked by incubation at 65 degrees O/N in presence of proteinase K. After Rnase A treatment for 1hr at 37oC, DNA was purified using the Qiagen minElute kit. 6-10ng of immunoprecipitated material was used for ChIP-seq.
ChIP-seq library preparation using the KAPA Hyper prep kit from KAPA Biosystems. Libraries were sequenced on an NovaSeq 6000. PE x100

treatment_protocol: Cells were treated with DMSO for 24 hours.

value: BL6/129 hybrid

tag: antibody


title: e2_dmso_24hr_input_aHA-CST_rep5_k71


title: e2_dmso_chipExo1_aHA-EHMT2_rep1_17

data_processing:
Biological and technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Peaks were called on bed files using MACS2 v2.2.6 using parameters: -f BEDPE --nomodel --seed 123 --keep-dup all -p 0.05
After peak calling with MACS2, peak files were filtered to only include peaks with q-value < 0.05 using a custom python script.
Bigwigs were made from bed files using deeptools v3.5.1 using parameters: --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Bigwigs were z-normalized per chromsome arm using a custom R script.
Assembly: mm10
Supplementary files format and content: z-normalized bigwigs for merged replicates.
Supplementary files format and content: narrowpeak files of called peaks
Library strategy: CHIP-exo

extract_protocol:
EHMT-dTAG ESC cells were cultured at 37˚C on feeders in FBS/LIF  conditions. Cells were collected by trypsinization for 3 mins and were washed with PBS followed by centrifugation (500 g, 5 mins, 4˚C). 10 M cells were used per each replicate of library. Pellet was resuspended to have 1 million cells per mL in PBS (RT). Cells were crosslinked with 1% formaldehyde in RT for 10 mins on platform shaker. Crosslinking was quenched with 125 mM glycine for 5 min at RT on platform shaker. Crosslinked cells were centrifuged (500 g, 5 mins, 4˚C) and was washed twice with ice cold PBS. After the final wash and centrifuge, the pellet was snap frozen before extraction. Frozen cell pellets were processed by the Lai lab at Cornell University, Ithaca as described previously in ChIP-exo 5.0 protocol (PMID: 30030442).
Frozen cell pellets were processed as described previously in ChIP-exo 5.0 protocol (Rossi et al.).  anti-HA antibody (Abcam 9110) was used for o/n chromatin immunoprecipitation at 4˚C.Immunoprecipitated material was processed as described previously in ChIP-exo 5.0 protocol (Rossi)


title: e2_dmso_24hr_atac_rep1_20

data_processing:
Biological and technical replicates were merged using zcat
Reads were trimmed to remove adapters using bbmap v38.95, with parameters: ktrim=4 ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe
To correct for the tn5 cut position, fragments were shifted +4bp and -5bp for reads mapping to the + and - strand, respectively, using a custom awk script.
Peaks were called on bed files using MACS2 v2.2.6 using parameters: -f AUTO -g 2652783500 -p 0.05 --keep-dup all
After peak calling with MACS2, peak files were filtered to only include peaks with q-value < 0.05 using a custom python script.
Bigwigs were made from bed files using bedtools genomecov v2.30.0.
Bigwigs were z-normalized per chromsome arm using a custom R script.
Assembly: mm10
Supplementary files format and content: z-normalized bigwigs for merged replicates.
Supplementary files format and content: narrowpeak files of called peaks

growth_protocol: All cells cultured at 37C, 5% CO2.  ESC's were cultured in DMEM KO media containing FBS/LIF.

extract_protocol:
ATACseq was performed on 50,000 cells per sample using the Nextera DNA library preparation kit (Illumina FC121103) according to the manufacturer's instructions.
Libraries were constructed using the Nextera DNA library preparation kit (Illumina FC121103) and NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) according to the manufacturer's instructions. Cycles for PCR amplification were determined individually for each sample by qPCR Libraries were size selected (0.55–1.5x) using SPRI beads (Beckman Coulter)

treatment_protocol: EHMT-dTAG cells were treate with DMSO for 24 hrs.


title: Sample_28_Non-tau E4_Control

city: Boston

first: Wesley

last: Nogueira Brandao

state: Massachusetts

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Basecalls and demultiplexing were performed withIllumina’s bcl2fastq software and a customPythondemultiplexing program with a maximum ofone mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101primary assembly with STAR version 2.7.9a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Assembly: Ensembl 101 GRCm38
Supplementary files format and content: counts file per sample from featureCounts

source_name: Hippocampus

growth_protocol: P301S Tau transgenic mice (Stock No. 008169, Jackson Laboratories) mice were purchased from the Jackson Laboratory. APOE4 (E4) was generated by replacing the mouse genomic sequence from the translation initiation codon in exon 2 to the termination codon in exon 4 with its human counterparts flanked by loxP sites All animal procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital, Harvard Medical School, and Washington University School of Medicine.

extract_protocol:
Hipocampus tissue was extracted.
Samples were prepared according to the library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: We utilized a newly designed inhalation chamber to house up to 12 mice with an airtight 8L volume and a gas recirculation system. Continuous monitoring of Xe, O2, and CO2 concentrations was conducted, with a CO2 absorbent used to maintain CO2 levels between 600-900 ppm. This new system maintained stable gas 30% Xenon concentrations throughout the 40-minute treatment period. The animals were treated once a week from 6 to 9.5 months of age.

value: Hippocampus

value: Non-tau E4

tag: Sex

value: Male

value: Control

tag: age

value: 9.5 Months


title: Sample_24_TE4_Xenon

value: Xenon


title: Sample_29_Non-tau E4_Control


title: e2_dmso_chipExo1_aHA-EHMT2_rep2_20


title: E2-17 24h-DMSO


title: Sample_22_TE4_Xenon


title: e2_dmso_24hr_atac_rep2_k71


title: Sample_23_TE4_Xenon


title: Sample_25_Non-tau E4_Control


title: e2_dmso_24hr_chip_aHA-CST_rep5


title: Sample_21_TE4_Xenon


title: e2_dmso_24hr_input_aHA-CST_rep4_20


title: Sample_18_TE4_Xenon


title: Sample_16_TE4_Xenon


title: E2-20 24h-DMSO


title: Sample_20_TE4_Xenon


title: E2-20-dTAG 24hr


title: Sample_14_TE4_Xenon


title: Sample_17_TE4_Xenon


title: E2-17-dTAG 24hr


title: Sample_13_TE4_Xenon


title: Sample_19_TE4_Xenon


title: Sample_26_Non-tau E4_Control


title: Sample_27_Non-tau E4_Control


title: Sample_12_TE4_Control


title: Sample_10_TE4_Control


title: Sample_11_TE4_Control


title: Sample_9_TE4_Control


title: Sample_6_TE4_Control


title: Sample_5_TE4_Control


title: Sample_7_TE4_Control


title: Sample_8_TE4_Control


title: Sample_4_TE4_Control


title: PVN, Otp, CUT&RUN

city: Dallas

first: Baijie

last: Xu

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Paired-end reads were trimmed with Trimmomatic and aligned to mm10 using Bowtie2.
After alignment, duplicate reads were removed using Picard MarkDuplicates.
Deduplicated reads were filtered using SAMtools.
After filtering, peaks were called using MACS2 and visualized with the Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&RUN

source_name: PVN

extract_protocol:
Nuclei from each sample was isolated separately with 1 ml homogenization buffer in a 2-ml dounce homogenizer. Use Pestle B to dounce it 20 times to ensure isolation of nuclei from cells with minimal damage. Transfer the lysis solution and 3 ml homogenization buffer to individual NalgeneTM centrifuge tubes containing 8 ml Sucrose Cushion buffer. Centrifuge for 1 h at 20,000 rpm, 4°C. Carefully remove the middle layer, which contains a lot of white particles. Discard all the supernatants.
After discarding the supernatants, nuclei were resuspended in 100 µl of cold nuclear extraction buffer and proceeded to the ConA bead conjugation step following the standard protocol in the CUT&RUN Kit from Epicypher (EpiCypher, #14-1048).

value: PVN

value: neurons

value: WT

value: Otp


title: Sample_15_TE4_Xenon


title: PRDM16, IgG

city: Ann Anrbor

first: Zhenguo

last: Wang

state: MI

address: 2800 Plymouth Road

department: Internal Medicine

data_processing:
For RNA-seq, Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files. The reads were trimmed using Cutadapt v2.3. The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq. QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7.
For ChIP-Seq, we use FastQC(FastQC)(v0.11.8) to assess the overall quality of each sequenced sample; We use TrimGalore(TrimGalore)(v0.4.5) and cutadapt(Martin)(v1.15) with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20; We align trimmed reads to mm10 with Bowtie2(Langmead and Salzberg, 2012)(v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches; The reads were mapped to the mouse genome (NCBI GRCm38) with bowtie2. The peak calling was done with MACS2 (with the following settings: -f BAMPE –g hs –B --SPMR –q 0.01). Peaks were aligned to the nearest transcription start site (TSS) with Homer v4.11 (http://homer.ucsd.edu/homer/).
Assembly: mm10
Supplementary files format and content: Matrix table with transcripts per kilobase million (tpm) for every gene and every sample
Supplementary files format and content: bed(peak)

source_name: Vascualr fibroblast

extract_protocol:
Total RNA from thoracic aorta were isolated with the RNeasy® micro kit (catalog #74004, Qiagen). ChIP assay was performed with the SimpleChIP® Enzymatic Chromatin IP Kit (catalog #9003, Cell Signaling Technology)
The RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) with poly A selection. This pool was subjected to 151 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). An average of 40 million paired-reads per samples were generated. The DNA library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 101 bp reads. An average of 25 million paired reads was generated for each sample

value: Vascualr fibroblast

value: Primary

value: Fibroblast

value: Wild type


title: 8.3kb-EAAT2-tdT mice PND1

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
CellRanger Software version 6.0.2 was use to generate the FASTQ files, aligned fastq files to the mouse reference genome (refdata-gex-mm10-2020-A)
Data filtering: mRNA contamination was removed using Soupx v1.3.0, nCount_RNA >= 500 & nFeature_RNA > 200 & nFeature_RNA < 6500 & percent.mt < 15
Assembly: mm10
Supplementary files format and content: Barcodes, features and matrix file for each sample

source_name: Dorsal-anterior Forebrain

extract_protocol:
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pCapture
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pLibraryPrep

value: Dorsal-anterior Forebrain

value: tissue


title: Vector, IgG


title: Sample_1_TE4_Control


title: Prdm16SMKO, rep.3

source_name: Thoracic aorta

value: Thoracic aorta

value: Tissue

value: Prdm16f/f, SMMHC-CreERT2


title: PVN, Negative, CUT&RUN

value: IgG


title: BAC-GLT1-eGFP mice PND1


title: Control, rep.2


title: Control, rep.3


title: Control, rep.1


title: Prdm16SMKO, rep.1


title: Vector, Flag


title: Prdm16SMKO, rep.2


title: Control mice liver1,scRNAseq

city: Changzhou

first: Chao

last: Tu

state: Jiangsu

address: 185 Juqian Road

department: Department of Internal Medicine

institute: The Third Affiliated Hospital of Soochow University

description:
L_Control1
10x Genomics

data_processing:
The raw reads were mapped to the mouse reference genome (mm10) using CellRanger count (v7.0.0) with default  parameters, the digital expression matrix was extracted from the folder outputted by the CellRanger count pipeline.
Assembly: mm10
Supplementary files format and content: filltered expression matrices with corresponding gene names (.tsv) and barcodes (.tsv)

extract_protocol:
Samples were minced with a sterile scalpel into 1 mm3 fragments, suspended in 5ml of digestion buffer consisting of 2 mg/mL Collagenase type II (Sigma, C6885) and 200U/ml DNase I (Worthington, LS006344) in RPMI medium (Coring,10-040-CV), and incubated in 37℃ water bath with shaking for 45 min.The suspension was passed through a 100 μm filter (Falcon,3523260) and centrifugated (400g, 10 min, 4℃). Pelleted cells were resuspended in red blood cell lysis buffer (Solarbio,R1010), incubated for 2 min, passed through a 40 μm filter (Falcon,3523240), collected by centrifugation (400g, 10 min, 4℃) and resuspended in PBS (BI, 02-024-1ACS)  containing 0.04% BSA (Sigma,B2064). Cells were manually counted by Trypan blue (Thermo, T10282) and AO-PI (LUNA, D23001) after each centrifugation (400g, 10 min, 4℃) and resuspended. Single cells were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
By using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics, 1000268) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, 1000120), we performed single cell 3’gene expression profiling. The cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.

value: liver

value: Control mice


title: Tig treated mice liver1,scRNAseq

description:
L_Tigulixostat1
10x Genomics

value: Tig treated mice


title: Hyperuricemia mice liver1,scRNAseq

description:
L_Uox_KO1
10x Genomics

value: Hyperuricemia mice


title: Sample_2_TE4_Control

value: Hippocampus

value: Male

value: Control

value: 9.5 Months


title: Sample_3_TE4_Control


title: Tig treated mice kidney1,scRNAseq

description:
K_Tigulixostat1
10x Genomics

source_name: kidney

value: kidney


title: 4F treatment

city: Houston

first: Tamer

last: Mohamed

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

description: 10X genomics

data_processing:
All cells with at least three detected genes and less than 30% of reads from mitochondrial genes and all detected genes in at least 200 cells were used in the further analyses. The remaining data were normalized using the "LogNormaliz" method. Principal Component Analysis for the subset of the 2000 most variable genes (Seurat function FindVariableFeatures) was then performed on the scaled data. The cells were clustered using the Louvain Algorithm with the resolution parameter value of 0.5 (Seurat function FindClusters) after determining the shared nearest neighbor graph using the first ten principal components (Seurat function FindNeighbors). The data were visualized using the UMAP algorithm with the first ten principal components as input (Seurat function RunUMAP). The cells were grouped into ten clusters based on the distribution of expression of the cell cycle genes of interest. Differential analysis between all pairs of clusters was performed using the Wilcoxon rank-sum test to identify the differentially expressed genes (Seurat function FindMarkers).
Assembly: mm10

source_name: heart

extract_protocol:
P1 cardiomyocytes either infected with LacZ or 4F for the indicated time were filtered using a 70µM filter, resuspended in 1% B.S.A. in PBS, and counted immediately before library preparation.
G.E.M. Generation and Barcoding were performed following the Chromium Single Cell" Reagents Kits v3 Rev A User Guide with Chromium Single Cell" G.E.M., Library and Gel Bead Kit v3 (10X Cat # 1000092).
The Chromium chip was loaded, and the Chromium Single Cell B program was selected. The chip was ejected immediately following the completion of the program. 100 µL of recovered G.E.M.s was slowly pipetted and transferred to tubes precooled on ice. The G.E.M.s were then incubated for the R.T. reaction using a thermal cycler at 53˚C for 45 min, then 85˚C for 5 min, followed by a 4˚C hold. Samples were then stored at -20˚C overnight. All libraries were pooled and sequenced using the NovaSeq to a read depth of at least 50,000 reads per cell. The sequenced reads for each sample were mapped to the GRCh38 genome to generate the (geneby-cell) count matrix using cell ranger count (Cell Ranger version 3.1.0 from 10x Genomics) with default parameters. The counts" matrices across the samples were aggregated using cell ranger aggr. The resulting files were processed in R using the package Seurat (version 3.1.3)

value: heart

value: P1 cardiomyocytes

value: 4F adenovirus


title: PRDM16, Flag

value: Vascualr fibroblast

value: Primary

value: Fibroblast

value: Wild type


title: LacZ control

description: 10X genomics

value: LacZ adenovirus


title: RNA, liver, Tfam KO biol rep3

first: Emily

last: Walker

address: 1000 Wall Street

data_processing:
Alignment options followed ENCODE standards for RNA-seq. FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Reads were preprocessed by BBDuk which removes adapters, trims reads for quality from the 3′ end, and discards reads that are too short after trimming. Preprocessed reads were aligned by STAR aligner and quantification was done using featureCounts. FastQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool.Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model (thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with Genialis (Boston, MA, USA).
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Supplementary files format and content: Tab-delimited text files include raw counts

growth_protocol: Islets were cultured overnight after isolation prior to RNA isolation. Liver was flash frozen prior to RNA isolation.

extract_protocol:
For both islets and liver: Total RNA was isolated from cultured islets or frozen liver samples and DNase treated using commercially available kits (Omega Biotek and Ambion, respectively).
Libraries were constructed and subsequently subjected to 151 bp paired-end cycles on the NovaSeq-6000 platform (Illumina). FastQC (v0.11.8) was used to ensure the quality of data.
RNA-sequencing was performed by the Advanced Genomics Core at University of Michigan Medical School.

value: liver

value: Tfam KO


title: RNA, liver, Tfam KO biol rep1


title: RNA, liver, Mfn DKO biol rep2

value: Mfn DKO


title: RNA, liver, Mfn DKO biol rep4


title: RNA, liver, Mfn DKO biol rep1


title: RNA, liver, control biol rep5

value: control


title: RNA, islets, Tfam KO biol rep5

source_name: islets

value: islets

value: male


title: RNA, islets, Tfam KO biol rep4

value: female


title: RNA, liver, control biol rep3


title: RNA, islets, Tfam KO biol rep6


title: RNA, islets, Tfam KO biol rep2


title: RNA, liver, control biol rep6


title: RNA, islets, Tfam control biol rep8

value: Tfam control


title: RNA, islets, Tfam KO biol rep3


title: RNA, liver, control biol rep4


title: RNA, liver, control biol rep2


title: RNA, islets, Tfam control biol rep6


title: RNA, islets, Tfam control biol rep5


title: RNA, islets, Tfam control biol rep4


title: RNA, islets, Tfam KO biol rep1


title: RNA, islets, Tfam control biol rep7


title: RNA, liver, Tfam KO biol rep2


title: RNA, liver, Mfn DKO biol rep3


title: RNA, islets, Tfam control biol rep3


title: RNA, islets, Tfam control biol rep2


title: RNA, islets, Tfam control biol rep1


title: RNA, liver, control biol rep1


title: Control mice2,scRNAseq

description:
Control2
10x Genomics

value: kidney

tag: strain background

value: wild type


title: Control mice1,scRNAseq

description:
Control1
10x Genomics


title: Hyperuricemia mice1,scRNAseq

description:
Uox_KO1
10x Genomics

value: urate oxidase knockout (Uox-KO)


title: Hyperuricemia mice2,scRNAseq

description:
Uox_KO2
10x Genomics


title: Postmitotic_Foxg1_LOF_Mutant_3

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description:
FN_mutant_3
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv

data_processing:
Read alignment software - HISAT2
Read mapping tool - FeatureCounts
Read normalization - DESeq2
Assembly: mm10
Supplementary files format and content: CSV file format; Raw Counts
Supplementary files format and content: CSV file format; Normalized Counts

source_name: Cerebral Cortex

growth_protocol: in vivo cortical progenitors or neurons isolated using microdissection and FACS purification.

extract_protocol:
Trypsin-based tissue dissociation and PCI-based RNA isolation
NEBNext RNA Ultra II directional protocol 2x150bp

treatment_protocol: FACS purification of recombined cells using 561 or 488 lazers.

value: Cerebral Cortex

value: NexCre/+; Foxg1lox/lox


title: Postmitotic_Foxg1_LOF_Mutant_4

description:
FN_mutant_4
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: Postmitotic_Foxg1_LOF_Mutant_1

description:
FN_mutant_1
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: Postmitotic_Foxg1_LOF_Mutant_2

description:
FN_mutant_2
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: Postmitotic_Foxg1_LOF_Control_4

description:
FN_Control_4
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: posControl_s2

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
10x Genomics
Protocol 2

data_processing:
human
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). Cellranger “mkfastq” command was used to demultiplex the different samples and Cellranger “count” command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender(v0.2.0)with standard parameters. Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates(PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples ((Neg_C_PDAC, Neg_Control, Neg_WS_PDAC) and positive samples (Pos_C_PDAC, Pos_Control, Pos_WS_PDAC) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 5796 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).  Negative Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 11527 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9). Differential expression analysis: To identify differentially expressed genes in Negatives and Positive samples. 1. Neg Control vs Neg Cachetic PDAC (Neg_Control  vs Neg_C_PDAC)  2. Neg Control vs Neg Weight Stable PDAC (Neg_Control  vs Neg_WS_PDAC)  3.  Neg Cachetic PDAC  vs Neg Weight Stable PDAC (Neg_C_PDAC  vs Neg_WS_PDAC) 4. Pos Control vs Pos Cachetic PDAC (Pos_Control  vs Pos_C_PDAC)  5. Pos Control vs Pos Weight Stable PDAC (Pos_Control  vs Pos_WS_PDAC)  6.  Pos Cachetic PDAC  vs Pos Weight Stable PDAC (Pos_C_PDAC  vs Pos_WS_PDAC) in each defined cell types, the R package LIBRA (v1.0.0) with option wilcox was used to perform zero-inflated regression analysis (PMID: 34584091). Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2.
Assembly: Homo Sapiens hg38
Supplementary files format and content: HDF5 Feature-Barcode Matrix
mouse
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). Cellranger “mkfastq” command was used to demultiplex the different samples and Cellranger “count” command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender(v0.2.0)with standard parameters. Mouse Genome mm10 was used for the alignment and gencode vM25 was used for gene annotation and coordinates (PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples (CtrlNeg and KppNeg) were merged into a unique single cell object and positive samples (CtrlPos and KppPos) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 17462 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).   Negative Samples: Cells with <10000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 35352 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: Skeletal Muscle

extract_protocol: Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Skeletal Muscle

value: Mononuclear cells

value: 14 weeks


title: Kpp_Neg

description:
10x Genomics
Protocol 2

value: 5 months


title: posControl_s1

description:
10x Genomics
Protocol 2


title: Kpp_Pos

description:
10x Genomics
Protocol 2


title: Postmitotic_Foxg1_LOF_Control_2

description:
FN_Control_2
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: Ctrl_Pos

description:
10x Genomics
Protocol 2


title: C26neg_s1

description:
10x Genomics
Protocol 2


title: Postmitotic_Foxg1_LOF_Control_1

description:
FN_Control_1
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: Ctrl_Neg

description:
10x Genomics
Protocol 2


title: C26pos_s2

description:
10x Genomics
Protocol 2


title: Postmitotic_Foxg1_LOF_Control_3

description:
FN_Control_3
P1_Foxg1_Postmitotic_CountMatrix.csv
P1_Foxg1_Postmitotic_DESeq2_results.csv


title: negControl_s1

description:
10x Genomics
Protocol 2


title: C26pos_s1

description:
10x Genomics
Protocol 2


title: ConMLDL1

city: Beijing

first: MingYi

address: No.28 Fuxing Road, Haidian District,

institute: The First Medical Center of Chinese PLA General Hospital

data_processing:
Clean reads were aligned to reference genome with orientation mode using HISAT2 software v 2.2.1 to obtain mapped reads
FeatureCounts v 2.0.3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 v 3.17, DEGs with | log2FC | > 1 and Padj < 0.05 were considered to be significantly different expressed genes.
We use clusterProfiler R v 4.2.1 software package for GO function enrichment and KEGG pathway enrichment analysis. When P<0.05, it is considered that the GO or KEGG function is significantly enriched.
Assembly: GRCm39
Supplementary files format and content: Excel file includes raw counts for each Sample.
Supplementary files format and content: Excel file includes FPKM values for each Sample.

growth_protocol: IL10M and ConM were maintained in RPMI-1640 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol® agent(Magen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using ABclonal mRNA-seq Lib Prep Kit(ABclonal, China) following manufacturer's protocols.

value: macrophage

value: WT

value: oxidized low density lipoprotein(oxLDL) treatment


title: IL10MLDL3

value: IL-10 overexpression


title: IL10MLDL2


title: ConMLDL3


title: ConMLDL2


title: IL10MLDL1


title: ConMLPS3

value: lipopolysaccharide(LPS) stimulaiton


title: C26neg_s2

description:
10x Genomics
Protocol 2


title: IL10MLPS3


title: IL10MLPS2


title: ConMLPS1


title: IL10MLPS1


title: ConM2

value: No treatment


title: ConM1


title: ConM3


title: IL10M3


title: IL10M2


title: AAV-GFP 2

data_processing:
Analysing Sequence Quality with FastQC
Removing Low Quality Sequences with Trim_Galore!
Removing rRNA Sequences with SortMeRNA
Aligning to Genome with STAR-aligner
Summarizing Gene Counts with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample

source_name: PVH

extract_protocol:
Cells were sorted into the tubes containing Trizol and total RNA was isolated using chloroform extraction and was cleaned using NucleoSpin RNA XS RNA Isolation kit (Takara).
RNA libraries were prepared using SMART-Seq mRNA LP Kit (Clonetech # 634768).

treatment_protocol: For adult AAV virus injection mice, the paraventricular nucleuses were dissected after 12 weeks injection. TOM positive and GFP positive cells were sorted for AAV-Cre injection and AAV-GFP injection individually.

value: PVH

value: 26 weeks old

value: Otp fl/fl; Ai14

value: AAV-GFP injection

tag: sorting

value: GFP positive


title: hα-syn（A53T)-1

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

institute: Nanjing First hospital

data_processing:
Sequencing was conducted with NovaSeq platform (Illumina) which producing 150bp paired-end reads. Bowtie-v1.2.3 was used to match clean reads to the reference genome. DESeq2-v1.10.1 was used to normalize the mapped reads and analyze differential expression of miRNA. |log2(fold change)|≥1 was regard as differentially expressed miRNAs and P＜0.0001 was defined significantly differentially expressed miRNAs
Assembly: mm9

source_name: right SNpc tissues

extract_protocol:
RNA was isolated from the right SN of mice using Trizol
RNA library was prepared with 1 μg of DNase-treated total RNA as input, and quantified with ABI 9700HT Fast Real-Time PCR system.

value: human alpha-syn (A53T) overexpressing mice

value: Supranigral injection with 0.25uL/hour artificial cerebrospinal fluid by osmotic pumps for 4 weeks

value: brain


title: IL10M1


title: hα-syn（A53T)+Ang（1-7）-1

value: Supranigral injection with 1.1 nmol/0.25uL/hour Ang-(1-7) by osmotic pumps for 4 weeks


title: hα-syn（A53T)-3


title: AAV-GFP 3


title: AAV-GFP 1


title: hα-syn（A53T)+Ang（1-7）-3


title: AAV-Cre 1

value: AAV-Cre injection

value: TOM positive


title: Mc4r_TOM neg2

source_name: hypothalamus

value: hypothalamus

value: 4 weeks old

value: Mc4r-Cre; Ai14

value: TOM negative


title: Mc4r_TOM neg1


title: ConMLPS2

value: macrophage

value: WT

value: lipopolysaccharide(LPS) stimulaiton


title: Mc4r_TOM pos2


title: AAV-Cre 2

value: PVH

value: 26 weeks old


title: Mc4r_TOM neg3


title: Mc4r_TOM pos3


title: AAV-Cre 3

value: Otp fl/fl; Ai14


title: Mc4r_TOM pos1


title: AAV_Cre_2, ATAC

data_processing:
QUALITY CONTROL by fastqc and trimmed via trim_galore
Align to reference genome using bowtie2
Remove mtDNA reads
Estimate fraction of library to subsample to achieve uniform number of unique fragments and subsample based on library complexity estimates
Remove PCR duplicates
Fix read mates and bedpe conversion and followed by Tn5 shift
Call narrow peaks on each individual replicate using MACS2
Compute naive overlap
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
Nuclei from each sample was isolated separately with 1 ml homogenization buffer in a 2-ml dounce homogenizer. Use Pestle B to dounce it 20 times to ensure isolation of nuclei from cells with minimal damage. Transfer the lysis solution and 3 ml homogenization buffer to individual NalgeneTM centrifuge tubes containing 8 ml Sucrose Cushion buffer. Centrifuge for 1 h at 20,000 rpm, 4°C. Carefully remove the middle layer, which contains a lot of white particles. Discard all the supernatants.
Resuspend nuclei in 40 µl Pre-Tagmentation Master Mix for tagmentation reaction. ATAC libraries were prepared using ATAC-Seq Kit (Active Motif # 53150).

treatment_protocol: For adult AAV virus injection mice, the paraventricular nucleuses were dissected after 4 weeks injection.

value: 12 weeks old


title: AAV_Cre_1, ATAC


title: AAV-GFP_1, ATAC

value: AAV-GFP injection


title: FF-10101_3

city: Nagoya

first: Takahiko

last: Sato

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Department of Hematology

institute: Nagoya University Graduate School of Medicine

data_processing:
Raw FASTQ files were processed using fastp version 0.19.5,  and transcript abundance was quantified using Salmon version 1.5.1
Gene expression was analyzed with normalized count data calculated by DESeq2 version 1.22.1.
Assembly: GENCODE vM27
Supplementary files format and content: Comma separated value (csv) file includes VST normalized counts for all samples.

source_name: Subcutaneous tumor collected on day 8 after inoculation

extract_protocol:
Tumor samples were collected into RNAlater Stabilization Solution (Thermo Fisher Scientific; Cat. #AM7024), and total RNA were extracted using a RNeasy® Plus Mini Kit (QIAGN, Venlo, Netherland; Cat. #74134).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Mice were inoculated subcutaneously with a suspension of 1 × 10^6 tumor cells in 100 microL of PBS(-) at the right flank (day 0). MilliQ water or 0.1 mg/mL of FF-10101 were administered by water supplement bottle from day 1 to day 8.

value: fibrosarcoma

value: Day 8


title: FF-10101_2

value: Subcutaneous tumor collected on day 8 after inoculation


title: Control_3

value: milliQ water


title: hα-syn（A53T)+Ang（1-7）-2

value: human alpha-syn (A53T) overexpressing mice

value: Supranigral injection with 1.1 nmol/0.25uL/hour Ang-(1-7) by osmotic pumps for 4 weeks

value: brain


title: hα-syn（A53T)-2

value: Supranigral injection with 0.25uL/hour artificial cerebrospinal fluid by osmotic pumps for 4 weeks


title: Control_1


title: Th9, SPC, Day3 n=2

city: Suwon-si

first: Ji Cheol

last: Kim

state: Gyeonggi-do

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

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

source_name: Naive CD4+ T cells from mouse spleen

growth_protocol: Mouse naïve CD4+ T cells (using MagnisortTM mouse CD4 naïve T cell enrichment kit, Invitrogen) isolated from C57BL/6N mouse spleen were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 1% antibiotics-antimycotic and 2-mercaptoethanol (50 μM) in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: Mouse naïve CD4+ T cells were cultured in in flat-bottom 96 well plates and stimulated with plate-bound anti-CD3e (1 μg/ml) and soluble anti-CD28 (1 μg/ml) together with IL-4 (10 ng/ml), TGF-β1 (2 ng/ml), and anti-IFN-γ (10 μg/ml) in the presence or absence of SPC (d18:1, 30 μM) for 3 days

value: Naive CD4+ T cells from mouse spleen

value: Wild-type

value: Day 3


title: Th9, SPC, Day3 n=1


title: Th9, SPC, Day3 n=3


title: circadian disruption fetus ZT18 rep3

city: Irvine

first: Kousha

last: Changizi Ashtiani

state: California

address: Institute for Genomics and Bioinformatics 243, Info & Computer Science Building 2

department: ICS

institute: University of California, Irvine

description:
ZT_18_REP_2
PF.tsv

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

value: Liver

tag: maternal stress

value: circadian disruption

tag: developmental stage

value: fetus


title: Th9, Control, Day3 n=2


title: Th9, Control, Day3 n=1


title: Th9, Control, Day3 n=3


title: circadian disruption fetus ZT18 rep2

description:
ZT_18_REP_1
PF.tsv


title: circadian disruption fetus ZT18 rep1

description:
ZT_18_REP_0
PF.tsv


title: circadian disruption fetus ZT12 rep3

description:
ZT_12_REP_2
PF.tsv


title: circadian disruption fetus ZT12 rep1

description:
ZT_12_REP_0
PF.tsv


title: AAV-GFP_2, ATAC

value: PVH

value: Otp fl/fl; Ai14


title: circadian disruption fetus ZT0 rep2

description:
ZT_0_REP_1
PF.tsv


title: circadian disruption fetus ZT6 rep3

description:
ZT_6_REP_2
PF.tsv


title: circadian disruption fetus ZT12 rep2

description:
ZT_12_REP_1
PF.tsv


title: circadian disruption fetus ZT6 rep1

description:
ZT_6_REP_0
PF.tsv


title: circadian disruption mother ZT18 rep2

description:
ZT_18_REP_1
P.tsv

value: mother


title: circadian disruption mother ZT18 rep1

description:
ZT_18_REP_0
P.tsv


title: Control_2

value: fibrosarcoma


title: circadian disruption mother ZT12 rep3

description:
ZT_12_REP_2
P.tsv


title: circadian disruption fetus ZT6 rep2

description:
ZT_6_REP_1
PF.tsv


title: circadian disruption fetus ZT0 rep3

description:
ZT_0_REP_2
PF.tsv


title: circadian disruption mother ZT6 rep1

description:
ZT_6_REP_0
P.tsv


title: circadian disruption fetus ZT0 rep1

description:
ZT_0_REP_0
PF.tsv


title: circadian disruption mother ZT18 rep3

description:
ZT_18_REP_2
P.tsv


title: circadian disruption mother ZT6 rep2

description:
ZT_6_REP_1
P.tsv


title: FF-10101_1

value: Day 8


title: circadian disruption mother ZT12 rep1

description:
ZT_12_REP_0
P.tsv


title: circadian disruption mother ZT6 rep3

description:
ZT_6_REP_2
P.tsv


title: circadian disruption mother ZT0 rep1

description:
ZT_0_REP_0
P.tsv


title: circadian disruption mother ZT0 rep3

description:
ZT_0_REP_2
P.tsv


title: control fetus ZT18 rep3

description:
ZT_18_REP_2
CF.tsv

value: control


title: control fetus ZT18 rep2

description:
ZT_18_REP_1
CF.tsv


title: control fetus ZT18 rep1

description:
ZT_18_REP_0
CF.tsv


title: control fetus ZT6 rep3

description:
ZT_6_REP_2
CF.tsv


title: control fetus ZT12 rep1

description:
ZT_12_REP_0
CF.tsv


title: control fetus ZT6 rep2

description:
ZT_6_REP_1
CF.tsv


title: circadian disruption mother ZT0 rep2

description:
ZT_0_REP_1
P.tsv


title: control fetus ZT12 rep2

description:
ZT_12_REP_1
CF.tsv


title: control fetus ZT0 rep1

description:
ZT_0_REP_0
CF.tsv


title: control fetus ZT0 rep3

description:
ZT_0_REP_2
CF.tsv


title: control fetus ZT6 rep1

description:
ZT_6_REP_0
CF.tsv


title: control mother ZT18 rep3

description:
ZT_18_REP_2
C.tsv