title: NSN_spk_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 113bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.  To distinguish SN from NSN oocytes without staining DNA, a previously established method was used (Inoue et al., 2007), as SN oocytes show a perivitelline space (a space between zona pellucida and the surface of the oocyte).
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.16x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

tag: developmental stage

value: Full-grown oocyte NSN


title: Sk-Hep1_scrambled siRNA_#1

status: Public on Oct 28 2020

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from Sk-Hep1 cell line transfected with a nonsense siRNA as control for 48h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of human ClariomD-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, Kernel surface background correction and Medianpolish Probeset Summary

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cell line Sk-Hep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Sk-Hep1 (ATCC; LGC Standards, Wesel, Germany) were cultured in DMEM (Sigma-Aldrich, Taufkirchen, Germany) supplemented with 10% FCS (Gibco/Life Technologies, Darmstadt, Germany) and 1 % penicillin/streptomycin (Sigma-Aldrich) at 37°C and 5% CO2.

extract_protocol: For isolation of total RNA from cultured cells, the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) was applied.

treatment_protocol: Cells were seeded in 6-well plates one day prior to transfection with siRNAs. siRNAs were received from Eurofins MWG Operon (Ebersberg, Germany) and diluted in OptiMEM (Gibco/Life Technologies) to a final concentration of 20. Oligofectamine (Life Technologies) was used as transfection reagent according to the manufacturer's protocol. After incubation at room temperature for 15 minutes, the reagents were mixed, incubated for another 10 minutes at room temperature and distributed onto the cells covered with OptiMEM. One millilitre DMEM was added after 4 hours. The medium was replaced by FCS-free medium after 24 hours. Cells and supernatant were harvested 48 hours after transfection.

tag: sirna

value: NTC


title: XEN41_control_Exp5_t=24 (DNA-seq)

type: SRA

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

library_source: genomic

data_processing:
Library strategy: WGS
Quality control assessment using FastQC
Data processing (trimming using AdapterRemoval, Alignment using BWA, variant calling using snippy)
Genome_build: GCF_000006765.1_ASM676v1
Supplementary_files_format_and_content: Variant call format (VCF)

molecule: genomic DNA

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Hydroponic experiment in Growth Minimal medium (Rathnayake, I. V. N.; Megharaj, M.; Krishnamurti, G. S. R.; Bolan, N. S.; Naidu, R., Heavy metal toxicity to bacteria – Are the existing growth media accurate enough to determine heavy metal toxicity? Chemosphere. 2013, 90, (3), 1195-1200.

extract_protocol: DNA was harvested using QIAamp® DNA Mini Kit QIAGEN

treatment_protocol: solution was removed by centrifugation and bacteria were stored at -20°C prior to DNA extraction

tag: strain

value: Xen41 Tetracycline resistant

tag: treatment

value: control

tag: time


title: XEN41_control_Exp5_t=48 (DNA-seq)


title: NSN_spk_rep1

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 112bp bin in the genome
Genome_build: mm9

organism: Mus musculus

source_name: Oocyte

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.  To distinguish SN from NSN oocytes without staining DNA, a previously established method was used (Inoue et al., 2007), as SN oocytes show a perivitelline space (a space between zona pellucida and the surface of the oocyte).
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.15x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

tag: tissue

value: Oocyte

tag: genotype

value: wild-type

tag: antibody

value: Pol2(Active Motif 102660)


title: DP_D

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: diabetes-prone

data_processing:
Raw-RNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Hisat2 v2.1.0, Cufflinks v2.2.1.
Raw-DNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Bismark v0.17.08 and MethPipe v3.4.2.
Genome_build: Reference genome file was generated by combining GRCm38.68 B6 reference and GRCm38p4 SNP file in order to exchange all B6 to NZO high quality SNPs. Non-symmetric CpGs have been withdrawn, p-values have been calculated using log-likelihood ratio test.
Supplementary_files_format_and_content: adjusted2.bed: statistic values (pval, neighbors,fdr) of all found CpGs merged by groups of all DNA samples
Supplementary_files_format_and_content: proportion_table2.txt: propotion values (found CpGs, methylated CpGs) for all DNA samples seperated
Supplementary_files_format_and_content: fpkm tracking

source_name: islet

extract_protocol:
Genomic DNA from NZO pancreatic islets was isolated with using Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol. One microgram of genomic DNA from each pool was bisulfite-converted using Zymo EZ DNA Methylation-Gold kit (Zymo Research Corporation, Irvine, CA, USA)
Carried by GATC (Konstanz, Germany)

value: NZO/HIBomDife

tag: age

value: 10 weeks

tag: Sex

value: female


title: DR_A

description: diabetes-resistent


title: DP_C

description: diabetes-prone


title: 2cell_early_total_RNA_rep1

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat 2.1.1,  transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: mm9

source_name: Preimplantation embryo

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 36 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.

value: Preimplantation embryo

value: early 2-cell


title: DP_B

description: diabetes-prone


title: DP_A

description: diabetes-prone


title: XEN41_control_Exp5_t=72 (DNA-seq)


title: DR_P15

description: diabetes-resistent

extract_protocol:
Total RNA was extracted from 100 islets (per sample) using miRNA micro kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol, with additional DNase treatment. All RNA samples with RNA integrity number RIN ≥8 (Bioanalyser, Agilent Technologies, Germany), were selected for RNA sequencing.
Carried by GATC (Konstanz, Germany)


title: DR_P14

description: diabetes-resistent


title: DR_P13

description: diabetes-resistent


title: DR_P12

description: diabetes-resistent


title: PAO1_MIC_Exp5_t=24 (DNA-seq)

value: PAO1 (Wild Type)

value: MIC


title: PAO1_MIC/10_Exp5_t=72 (DNA-seq)


title: PAO1_MIC/10_Exp5_t=24 (DNA-seq)


title: PAO1_MIC/10_Exp5_t=48 (DNA-seq)


title: PAO1_MIC_Exp5_t=72 (DNA-seq)


title: XEN41_control_Exp5_t=0 (DNA-seq)


title: PAO1_control_Exp5_t=72 (DNA-seq)


title: DP_P20

description: diabetes-prone


title: PAO1_control_Exp5_t=48 (DNA-seq)


title: mES_H3K4me3_200

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 111bp bin in the genome
Genome_build: mm9

source_name: Embryonic stem cell

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-035-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.14x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Embryonic stem cell


title: DR_P11

description: diabetes-resistent


title: mES_500_spk_Ctrl_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 109bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-033-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.12x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: DP_P19

description: diabetes-prone


title: mES_550_spk_Ctrl_rep3

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 110bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-034-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.13x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: PAO1_MIC_Exp5_t=48 (DNA-seq)


title: mES_275_spk_Ctrl_rep3

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 108bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-032-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.11x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: PAO1_control_Exp5_t=24 (DNA-seq)


title: mES_1100_spk_Ctrl_rep3

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 106bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-030-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.9x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: mES_1000_spk_Ctrl_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 105bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-029-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.8x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: mESC_H3K4me3_CUTTag_200

data_processing:
Library strategy: CUT&Tag
Basecalls performed using CASAVA version 1.8
CUT&Tag reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 109bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-028-CIR).

extract_protocol: The CUT&Tag is performed according to previously described (cite CT paper) with CUT&Tag kit (Vazyme Biotech, TD091). Briefly, cells were incubated with 10μl pre-washed ConA beads (Vazyme Biotech, TD091) in 1.5ml low-binding tube. 50μl antibody buffer (Vazyme Biotech, TD091) with 0.5μg antibody was added and cultured for 2 hours at room temperature. After twice of wash with dig-wash buffer (Vazyme Biotech, TD091), 50μl dig-wash buffer with 0.5μg secondary antibody was added and incubated at room temperature for 30min. After twice of wash with 800μl dig-wash buffer, 0.58μl pG-Tn5 was added with 100μl dig-300 buffer (Vazyme Biotech, TD091). Samples were incubated at room temperature for 1 hours and then washed twice with 800μl dig-300 buffer. 300μl tagmentation buffer was added and samples were incubated at 37°C for 1 hours. The reaction was stopped with 10μl 0.5M EDTA，3 μl 10% SDS和2.5μl 20 mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries (Vazyme Biotech, TD094).


title: YTN2 untreated 3weeks-5

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.5.2b).
Mapped reads were counted by HTSeq(version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts.

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumor tissues using TRIzol (Life technologies) and RNeasy spin columns (Qiagen) according to manufacturers' protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep (sample 1-30, 47-61) or VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina (sample 31-46) according to manufacturers' protocols.

value: untreated

tag: time point (days post tumor inoculation)


title: DP_P18

description: diabetes-prone


title: mESC_H3K4me3_CUTTag_2000

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-027-CIR).

extract_protocol: The CUT&Tag is performed according to previously described (cite CT paper) with CUT&Tag kit (Vazyme Biotech, TD091). Briefly, cells were incubated with 10μl pre-washed ConA beads (Vazyme Biotech, TD091) in 1.5ml low-binding tube. 50μl antibody buffer (Vazyme Biotech, TD091) with 0.5μg antibody was added and cultured for 2 hours at room temperature. After twice of wash with dig-wash buffer (Vazyme Biotech, TD091), 50μl dig-wash buffer with 0.5μg secondary antibody was added and incubated at room temperature for 30min. After twice of wash with 800μl dig-wash buffer, 0.58μl pG-Tn5 was added with 100μl dig-300 buffer (Vazyme Biotech, TD091). Samples were incubated at room temperature for 1 hours and then washed twice with 800μl dig-300 buffer. 300μl tagmentation buffer was added and samples were incubated at 37°C for 1 hours. The reaction was stopped with 10μl 0.5M EDTA，3 μl 10% SDS和2.5μl 20 mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries (Vazyme Biotech, TD093).


title: mESC_H3K27me3_CUTTag_2000_rep1

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-026-CIR).

extract_protocol: The CUT&Tag is performed according to previously described (cite CT paper) with CUT&Tag kit (Vazyme Biotech, TD091). Briefly, cells were incubated with 10μl pre-washed ConA beads (Vazyme Biotech, TD091) in 1.5ml low-binding tube. 50μl antibody buffer (Vazyme Biotech, TD091) with 0.5μg antibody was added and cultured for 2 hours at room temperature. After twice of wash with dig-wash buffer (Vazyme Biotech, TD091), 50μl dig-wash buffer with 0.5μg secondary antibody was added and incubated at room temperature for 30min. After twice of wash with 800μl dig-wash buffer, 0.58μl pG-Tn5 was added with 100μl dig-300 buffer (Vazyme Biotech, TD091). Samples were incubated at room temperature for 1 hours and then washed twice with 800μl dig-300 buffer. 300μl tagmentation buffer was added and samples were incubated at 37°C for 1 hours. The reaction was stopped with 10μl 0.5M EDTA，3 μl 10% SDS和2.5μl 20 mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries (Vazyme Biotech, TD092).


title: PAO1_control_Exp5_t=0 (DNA-seq)


title: mES_250_spk_Ctrl_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 107bp bin in the genome
Genome_build: mm9

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-031-CIR).

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.10x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: Sk-Hep1_scrambled siRNA_#3

extract_protocol: For isolation of total RNA from cultured cells, the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) was applied.


title: XEN41_MIC_Exp4_t=72 (DNA-seq)

extract_protocol: DNA was harvested using QIAamp® DNA Mini Kit QIAGEN


title: DP_P17

description: diabetes-prone


title: XEN41_MIC_Exp4_t=48 (DNA-seq)


title: DP_P16

description: diabetes-prone


title: XEN41_MIC_Exp4_t=24 (DNA-seq)


title: SUS3

city: Daegu

first: JA WOOK

last: KOO

address: 61 Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description: processed data file: GEO_processed.txt

data_processing:
The quality of raw sequences was checked by FastQC (Babraham Bioinformatics) and the raw 151 bp cDNA reads were then aligned to the Ensembl GRCm38.90 mouse reference genome via STAR-2.5.2b.
Raw read count values were deduced from quantitation against the Ensembl GRCm38.90 annotation features using HTSeq.
To reduce the technical variations across the samples, the raw read count values were normalized using the Relative Log Expression (RLE) method that utilizes a DESeq scaling factor for a given lane that is computed as the median of the ration (for each gene) of its read count over its geometric mean across all lanes by DESeq2 package in R.
We used parametric and nonparametric empirical Bayes frameworks in COMBAT for adjusting the batch effects that is robust to outliers in samples variation.
Using the log2-fold-changes for each comparison, we identified the genes as DEGs with absolute log2-fold changes > 1 (2-fold change). From these expressed genes, we performed the exact test in DESeq2 package. After we selected the DEGs by FDR < 0.01.
Genome_build: Version 90 of mouse reference genome GRCm38
Supplementary_files_format_and_content: GEO_processed.txt: Tab-delimited text file includes raw read count values that were deduced from quantitation against the Ensembl GRCm38.90 annotation features using HTSeq.

source_name: cholinergic interneurons

growth_protocol: Mice were housed under a 12-h light/dark cycle and allowed access to food and water ad libitum. Mice were group-housed until the catheter implantation for self-administration experiments.

extract_protocol:
On the third day from the end of the last PR session, mice were deeply anesthetized with a ketamine/xylazine mixture and cardially perfused with ice-cold PBS. Mice were then decapitated and brains were extracted. Two slices (1.0 mm thick) containing the NAc were made using an ice-cold brain matrix (ZIVIC instruments). Bilateral 12-gauge punches containing NAc were obtained, pooled from 2–3 mice per condition (susceptible, resilient, or drug-naïve), and kept in ice-cold dissociation media [Hibernate-A media (BrainBits) containing 5 μM DL-APV, 12.5 unit/ml DNase I, and 5% D-(+)-Trehalose dehydrate] until the dissociation procedure was initiated. A pure population of cholinergic interneurons was obtained via fluorescence-activated cell sorting (FACS) according to a previously published protocol, with minor modifications. Briefly, the punches were dissected out using fine forceps, chopped with scalpels, transferred into dissociation medium containing papain enzyme (1 mg/ml, Worthington), and dissociated for 45 min at 37ºC to yield single cells. Dissociated cells were triturated and filtered through a 70-µm mesh into 50 ml tubes on ice. To remove excess debris and inactivate residual papain activity, the cell suspension was subjected to centrifugation on an AOI discontinuous gradient [Hibernate-A media (BrainBits) containing 5 μM DL-APV (Sigma), 12.5 unit/ml DNase I, 5% D-(+)-Trehalose dehydrate (Sigma), and albumin ovomucoid inhibitor (AOI, 0.6 mg/ml; Worthington)] at 900 rpm for 6 min at 4ºC. The cell pellets were suspended in dissociation medium and centrifuged at 1250 rpm for 6 min at 4ºC. Cell pellets were re-suspended in ice-cold PBS and immunolabeled with Alexa Fluor 488-anti-ChAT (1:50, abcam) at 4°C for 30 min. Alexa Fluor 488-immunolabeled cells were sorted on a MoFlo® Astrios EQ high speed cell sorter (Beckman Coulter) for GFP signals (detecting Alexa Fluor 488). Cells (5–50 × 10e3 per sample) were collected using FACS. Immediately after sorting, collection tubes were vortexed and flash frozen on dry ice. Samples were stored frozen in Trizol LS at −80°C until RNA extraction and library preparation. RNA was isolated using a Directzol RNA-Mini prep (Zymo). Samples were incubated for 15 min with DNase according to the manufacturer's instructions. RNA was eluted into 12 µl H2O to ensure a viable concentration of RNA for an 8 µl library prep input volume limit.
Libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech), and validated using an Agilent Bioanalyzer (Agilent TapeStation) and PCR prior to sequencing.

treatment_protocol: After the mice were confirmed to perform stable cocaine seeking behavior [maximum 40 infusions under fixed ratio 1 schedule], breakpoints were measured daily for 10 consecutive days. Breakpoints were defined as the number of nosepoke actions that animals performed to achieve the last cocaine infusion (1.2 mg/kg/infusion) under the progressive ratio schedule. Daily progressive ratio sessions were conducted 23 h/day.

tag: strain/background

tag: genotype/variation

value: SUS

value: Male

tag: cell type

value: Nucleus accumbens cholinergic interneurons

tag: behavioral phenotype

value: Resilient to cocaine addiction


title: SUS1

description: processed data file: GEO_processed.txt


title: m1c_DRB_spk_rep1

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN2-3 embryos were harvested in M2 medium 23 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.13x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

treatment_protocol: DRB treated mitotic 1-cell embryos were obtained by using 50μM colchicine added to the culture when zygotes entering PN5 stage. These embryos were collected after 10 h culture.

value: mitotic 1-cell


title: m1c_ctrl_spk_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN2-3 embryos were harvested in M2 medium 23 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.16x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

treatment_protocol: DMSO treated mitotic 1-cell embryos were obtained by using 50μM colchicine added to the culture when zygotes entering PN5 stage. These embryos were collected after 10 h culture.


title: XEN41_MIC/10_Exp4_t=72 (DNA-seq)

value: Xen41 Tetracycline resistant


title: RES3

description: processed data file: GEO_processed.txt

value: RES

value: Susceptible to cocaine addiction


title: m1c_DRB_spk_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN2-3 embryos were harvested in M2 medium 23 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.14x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: wild-type

value: Pol2(Active Motif 102660)


title: XEN41_MIC/10_Exp4_t=48 (DNA-seq)


title: RES1

description: processed data file: GEO_processed.txt


title: XEN41_control_Exp4_t=48 (DNA-seq)

value: control


title: XEN41_control_Exp4_t=72 (DNA-seq)


title: RES2

description: processed data file: GEO_processed.txt


title: XEN41_control_Exp4_t=24 (DNA-seq)


title: XEN41_MIC/10_Exp4_t=24 (DNA-seq)


title: mESC_CUTTag_H3K27me3_2000_rep2

growth_protocol: Mouse ES cells (mESC) were cultured on 0.1% gelatin pre-coated dish in DMEM (Gibco, 11995-065) containing 15% FBS (Hyclone, SH30396.03), leukemia inhibiting factor (LIF) (Millipore, GSE1107), penicillin/streptomycin (Millipore, TMS-AB2-C), GlutaMAX (Gibco, 35050-061), nucleosides (Millipore, ES-008-D), β-mercaptoethanol (Gibco, 21985-023), and non-essential amino acids (Gibco, 25-025-CIR).

extract_protocol: The CUT&Tag is performed according to previously described (cite CT paper) with CUT&Tag kit (Vazyme Biotech, TD091). Briefly, cells were incubated with 10μl pre-washed ConA beads (Vazyme Biotech, TD091) in 1.5ml low-binding tube. 50μl antibody buffer (Vazyme Biotech, TD091) with 0.5μg antibody was added and cultured for 2 hours at room temperature. After twice of wash with dig-wash buffer (Vazyme Biotech, TD091), 50μl dig-wash buffer with 0.5μg secondary antibody was added and incubated at room temperature for 30min. After twice of wash with 800μl dig-wash buffer, 0.58μl pG-Tn5 was added with 100μl dig-300 buffer (Vazyme Biotech, TD091). Samples were incubated at room temperature for 1 hours and then washed twice with 800μl dig-300 buffer. 300μl tagmentation buffer was added and samples were incubated at 37°C for 1 hours. The reaction was stopped with 10μl 0.5M EDTA，3 μl 10% SDS和2.5μl 20 mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries (Vazyme Biotech, TD091).


title: PN5_IgG_Ctrl

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN5 embryos were harvested in M2 medium 30 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.12x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Preimplantation embryo

value: 1-cell PN5

value: IgG (Santa Cruz sc-2025)


title: PN3_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 104bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN3 embryos were harvested in M2 medium 26 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.11x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: 1-cell PN3


title: PN3_rep1

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 103bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN3 embryos were harvested in M2 medium 26 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.10x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: NSN_IgG_rep1

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 102bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.9x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Oocyte

value: Full-grown oocyte NSN


title: MII_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 101bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG.  MII oocytes were harvested in M2 medium 13 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.8x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: MII oocyte


title: WT2

description: processed data file: GEO_processed.txt

value: WT

value: Male

value: Cocaine-naive


title: MII_rep1

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG.  MII oocytes were harvested in M2 medium 13 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: WT1

description: processed data file: GEO_processed.txt

value: Nucleus accumbens cholinergic interneurons


title: SUS2

description: processed data file: GEO_processed.txt

value: SUS

value: Resilient to cocaine addiction


title: m1c_ctrl_spk_rep1

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN2-3 embryos were harvested in M2 medium 23 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.15x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: mitotic 1-cell


title: YTN16 anti-IL-17+anti-PD-1 10days-4

extract_protocol:
Total RNA was extracted from tumor tissues using TRIzol (Life technologies) and RNeasy spin columns (Qiagen) according to manufacturers' protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep (sample 1-30, 47-61) or VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina (sample 31-46) according to manufacturers' protocols.

value: anti-IL-17 and anti-PD-1


title: PAO1_MIC_Exp4_t=72 (DNA-seq)

data_processing:
Library strategy: WGS
Quality control assessment using FastQC
Data processing (trimming using AdapterRemoval, Alignment using BWA, variant calling using snippy)
Genome_build: GCF_000006765.1_ASM676v1
Supplementary_files_format_and_content: Variant call format (VCF)

value: PAO1 (Wild Type)

value: MIC


title: WT3

description: processed data file: GEO_processed.txt


title: WT_CHXANS_rep2 [re-analysis]

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

country: USA

institute: NCI

description:
Ribosome Protected mRNA (15-34 nt)
GSM3168400

data_processing:
Library strategy: Ribo-Seq
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (CTGTAGGCACCATCAAT) removed with Skewer
Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Count table for relative codon occupancies

organism: Saccharomyces cerevisiae

source_name: Whole Cells

growth_protocol: Cells were grown to an OD of ~0.5

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, a cloing linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

tag: plasmid(s)


title: YTN16 anti-IL-17+anti-PD-1 10days-3


title: PAO1_MIC/10_Exp4_t=72 (DNA-seq)


title: YTN16 anti-IL-17+anti-PD-1 10days-1


title: PAO1_MIC_Exp4_t=24 (DNA-seq)


title: YTN16 anti-IL-17+anti-PD-1 10days-2


title: PAO1_MIC/10_Exp4_t=48 (DNA-seq)


title: eEF3d_CHXANS_rep2

description: Ribosome Protected mRNA (15-34 nt)


title: PAO1_MIC/10_Exp4_t=24 (DNA-seq)


title: eEF3d_CHXTIG_rep2

description: Ribosome Protected mRNA (15-34 nt)


title: XEN41_control_Exp4_t=0 (DNA-seq)

value: Xen41 Tetracycline resistant

value: control


title: PAO1_control_Exp4_t=72 (DNA-seq)


title: WT_CHXTIG_rep1 [re-analysis]

description:
Ribosome Protected mRNA (15-34 nt)
GSM3442057


title: YTN16 anti-PD-1 10days-2


title: YTN16 anti-PD-1 10days-3


title: eEF3d_CHXTIG_rep1

description: Ribosome Protected mRNA (15-34 nt)


title: YTN16 anti-IL-17 10days-4


title: YTN16 anti-PD-1 10days-4


title: WT_CHXANS_rep1 [re-analysis]

description:
Ribosome Protected mRNA (15-34 nt)
GSM3168399


title: YTN16 anti-PD-1 10days-1


title: WT_CHXTIG_rep2

description: Ribosome Protected mRNA (15-34 nt)


title: RNA-seq_OS5K_3_rep1

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

institute: Wakayama Medical University

description: RNA-seq of neutrophils derived from mice inoculated human clear cell renal cell carcinoma cell, OS5K #3, in kidney

data_processing:
Reads per kilobase of exon permMegabase of library size (RPKM) were calculated by CLC Genomics Workbench (Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: Expression data of the four samples were summarized into a processed file.

molecule: polyA RNA

source_name: Neutrophil

growth_protocol: After 14 days from orthotopic inoculation of human clear cell renal cell carcinoma cells, OS-RC-2 and its derivatives, into BALB/c nu/nu mice, neutrophils were obtained from peripheral blood using cell sorter.

extract_protocol:
Total RNA was isolated from cultured cells with RNeasy (Qiagen, Venlo, Netherlands).
cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Shiga, Japan) and Ion Xpress Plus Fragment Library Kit (Thermo Fisher Scientific, Waltham, MA).

treatment_protocol: untreated

value: CD11b+ Ly-6G+ cells in peripheral blood

value: BALB/c nu/nu


title: RNA-seq_OS5K_3_rep2


title: PAO1_MIC_Exp4_t=48 (DNA-seq)


title: PAO1_control_Exp4_t=48 (DNA-seq)


title: YTN16 anti-IL-17 10days-2


title: RNA-seq_OS5K_2_rep2

description: RNA-seq of neutrophils derived from mice inoculated human clear cell renal cell carcinoma cell, OS5K #2, in kidney


title: eEF3d_CHXANS_rep1

description: Ribosome Protected mRNA (15-34 nt)


title: XEN41_MIC_Exp3_t=72 (DNA-seq)


title: RNA-seq_OS5K_2_rep1


title: XEN41_MIC_Exp3_t=24 (DNA-seq)


title: PAO1_control_Exp4_t=0 (DNA-seq)


title: XEN41_MIC_Exp3_t=48 (DNA-seq)


title: YTN16 untreated 10days-4

value: untreated


title: RNA-seq_OS5K_1_rep2

description: RNA-seq of neutrophils derived from mice inoculated human clear cell renal cell carcinoma cell, OS5K #1, in kidney


title: YTN16 untreated 10days-3


title: XEN41_MIC/10_Exp3_t=72 (DNA-seq)


title: RNA-seq_OSPa_rep2

description: RNA-seq of neutrophils derived from mice inoculated human clear cell renal cell carcinoma cell, OSPa, in kidney


title: PAO1_control_Exp4_t=24 (DNA-seq)


title: YTN16 untreated 10days-2


title: XEN41_MIC/10_Exp3_t=24 (DNA-seq)


title: RNA-seq_OS5K_1_rep1


title: YTN16 anti-IL-17 10days-1


title: RNA-seq_OSPa_rep1


title: YTN16 anti-IL-17 10days-3


title: RNA-seq_sham_rep2

description: RNA-seq of neutrophils derived from mice inoculated vehicle in kidney


title: XEN41_MIC/10_Exp3_t=48 (DNA-seq)


title: XEN41_control_Exp3_t=72 (DNA-seq)


title: db/m3

city: Guangzhou

first: Liting

address: Zhongshan Road 2

department: Department of Endocrinology and Metabolism

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: pancreas

extract_protocol:
Islets were isolated by collagenase digestion followed by purification on Histopaque (Sigma Aldrich, Germany) density gradient and used directly for RNA extraction.
The library for sequencing was constructed by removing ribosomal RNA from the total RNA.

value: islet cells

value: pancreas

value: wild type


title: XEN41_control_Exp3_t=48 (DNA-seq)

extract_protocol: DNA was harvested using QIAamp® DNA Mini Kit QIAGEN


title: db/m2


title: RNA-seq_sham_rep1


title: XEN41_control_Exp3_t=24 (DNA-seq)


title: db/m1


title: db/db3

value: Lepr-/-


title: C-5

city: Tartu

first: Ene

last: Reimann

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: University of Tartu

data_processing:
Sequencing was performed using a SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Three-lane sequencing was applied and 12 libraries per lane with specification of 75bp from a forward direction were sequenced. Sufficient depth of sequencing and adequate mapping rate for evaluation of the expression pattern of the transcriptome was achieved with the average 30 million reads/sample across samples.
Raw reads were processed and mapped using Lifescope 2.5.1 software (Life Technologies Corp., Carlsbad, CA, USA). This whole transcriptome analysis workflow generated output, which including gene and exon counts, alternative splicing, and fusion transcripts. Raw read counts per gene were input for further statistical analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole blood

growth_protocol: Whole blood was collected into Tempus Blood RNA Tubes (Applied Biosystems, Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol:
Total RNA extraction was performed with a commercial Tempus Spin RNA Isolation Kit (Ambion, Life Technologies Corp., Carlsbad, CA, USA) following manufacturer’s protocol. A GLOBINclear™ Kit (Ambion, Life Technologies Corp., Carlsbad, CA, USA) was used to purify the samples of globin mRNA. The quality of total RNA was assesed using a capillary electrophoresis approach Agilent 2100 Bioanalyzer and RNA 6000 Nano kit
RNA-seq library construction and RNA sequencing analysis were performed with a SOLiD 5500W protocols
SOLiD 5500 Wildfire (W) System chemistry (Life Technologies Corp., Carlsbad, CA, USA) was applied to prepare the resulting cDNA for the DNA fragment library. Next, the 12 libraries were pooled together in equal amounts to construct two different library pools. The pooled libraries were converted to SOLiD 5500W libraries.

tag: disease state

value: Healthy

tag: family


title: XEN41_control_Exp3_t=0 (DNA-seq)


title: OI-7

value: Osteogenesis Imperfecta type I

value: COL1A1, c.1128delT (p.Gly377Alafs*164)


title: PAO1_MIC_Exp3_t=72 (DNA-seq)


title: db/db2


title: db/db1


title: OI-5

value: Osteogenesis Imperfecta type III


title: C-4


title: OI-6

value: Osteogenesis Imperfecta type IV


title: YTN16 untreated 10days-1


title: PAO1_MIC/10_Exp3_t=72 (DNA-seq)