title: localized_PC_7

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

description: short RNA

hyb_protocol: Labeled samples were hybridized and washed according to the instruction manual from Toray using Human miRNA Oligo chip 4plex (5), based on miRBase 19 (Toray Industries).

scan_protocol: The intensity of each miRNA was analyzed with the 3D-Gene Scanner 3000 (Toray) with auto gain, auto focus and auto analysis settings, all according to manufacturer’s instructions.

data_processing: Background substraction was performed only on “spots” where the intensity exceeded the average value of the noise +2 standard deviations. Global normalization was applied only on miRNA spots with background sustracted data. A normalization factor was calculated based on 25 divided with the median of the signal intensity of all background normalized data. Normalized data for each probe set and sample was calculated by multiplying all background subtracted data with the normalization factor.

source_name: prostate

label_protocol: 2.2μL of each sample (Normalized to 40 ng/μL) were mixed with miRNA spike and further labeled using 3D-Gene® miRNA labeling kit (Toray Industries).

extract_protocol: Allprep RNA/DNA/Protein isolation protocol (Qiagen, Hilden, Germany) followed by Rneasy MinElute Cleanup Kit (Qiagen, Hildenm Germany).

tag: group

value: prostate


title: benign_7

status: Public on Apr 21 2023

type: RNA

country: Sweden

description: short RNA

molecule: total RNA

organism: Homo sapiens

value: benign

tag: tissue


title: genomic DNA from Blood from mouse 280626R at time point 3

type: genomic

city: Boston

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

country: USA

institute: Brigham and Women's Hospital, Harvard Medical School

description: Pregnant

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: For mammalian microarray analysis, raw methylation data were first normalized and beta values were calculated using the SeSAMe R package .

molecule: genomic DNA

organism: Mus musculus

label_protocol: Standard Illumina protocol

growth_protocol: This experiment was approved by the Mass General Brigham IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially (5 mice/cage) except during the pregnancy studies wherein male mice were housed individually after mating. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol: DNA was isolated from whole blood using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: C57Bl/6 mice (11 weeks old) were obtained from Jackson Laboratories. Three days before mating, male mice were separated into individual cages and soiled bedding from male cages was added to female cages to induce estrus (Whitten, 1956). 1:1 mating pairs were set up in the evening and left overnight. Females were removed from male cages the following morning and inspected for copulatory plugs. Pregnant females were identified by daily tracking of body weight. Blood was collected in EDTA tubes by submandibular vein puncture every two weeks to create a series of four samples per mouse: (1) 10 days before mating; (2) 4 days after mating; (3) 18 days after mating; and (4) 32 days after mating, generally corresponding to ~2 weeks postpartum. Pups were humanely euthanized shortly after birth allowing mothers to recover from pregnancy without needing to nurse. Blood was snap-frozen in liquid nitrogen immediately after collection and stored at –80°C until needed.

tag: age

tag: Sex

value: female

tag: time point

value: Pregnant

tag: mousestrain

value: Whole blood


title: Methylome capture of HG006 at lab C, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

institute: Uppsala University

description:
SAMN16727317
Whole genome bisufite converted DNA
202775690018_R05C01

hyb_protocol: Bisulfite conversion was performed using the EZ DNA Methylation Kit (Zymo Research) with 250 ng of DNA per sample. The bisulfite converted DNA was eluted in 15 μl according to the manufacturer’s protocol, evaporated to a volume of < 4 μl, and used for methylation analysis on the 850k array according to the manufacturer’s protocol (Illumina).

scan_protocol: standard Illumina protocol

data_processing: Data was normalized using several methods: No normalization (preprocessRaw minfi function) (raw.beta.txt.gz), Peak-based correction (Dedeurwaerder et al., 2011) (pbc.beta.txt.gz), SWAN (Maksimovic et al., 2012) (swan.beta.txt.gz), ENmix (Xu et al., 2016) + RCP (Niu et al., 2016) (enmix.beta.txt.gz), funnorm (Fortin et al., 2014) (funnorm.beta.txt.gz), SeSAMe (Zhou et al., 2018) (sesame.beta.txt.gz), dasen (Pidsley et al., 2013) (dasen.beta.txt.gz), dasen (Pidsley et al., 2013) + RCP (Niu et al., 2016) (dasen.rcp.beta.txt.gz).

label: Cy3, Cy5

source_name: Cell line

label_protocol: standard Illumina protocol

extract_protocol: not provided

tag: cell line

value: HG006 at lab C


title: RPM_SER_sgATP13A1

type: SRA

first: Richard

last: Sherwood

institute: Brigham & Women's Hospital

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped using the Quantseq 3' mRNA mapping pipeline as described by Lexogen to GRCh38.p12. Briefly, reads were first trimmed using bbduk from the bbmap suite (v38.79)108 trimming for low quality tails, poly-A read-through and adapter contamination using the recommended parameters. Then, reads were mapped using the STAR aligner (v2.5.2b)109 with the recommended modified-Encode settings. Finally, HT-seq (v0.9.1) count was used to obtain per-gene counts110.
Within each cell line, we conducted differential expression analysis using DESeq2 1.26.0 to identify significantly differentially expressed genes for each gene KO with respect to the control condition.
Assembly: GRCh38.p12
Supplementary files format and content: Hepg2_rnaseq_RPM.csv: matrix table containing RPMs for all samples

molecule: polyA RNA

growth_protocol: All cell lines were obtained from ATCC and were cultured in DMEM + 10% FBS

extract_protocol:
RNA was harvested from cells using the Qiagen RNEasy Plus mini kit or the Zymo Quick-RNA 96 kit
RNA libraries for RNA-seq were prepared for RNA-seq using the Lexogen QuantSeq-Pool kit, and sequenced using Illumina Nextseq at >1*10^6 reads/sample.

treatment_protocol: HepG2 Cas9NG-P2A-mChe KO cell lines were seeded at a density of 2.1x10^5 cells/cm2 on a 24 well plate with two biological replicates per serum condition and incubated overnight. The next day, the media was replaced with either DMEM + 10% FBS (serum condition) or optiMEM (serum-starved condition) and cells were incubated overnight.

tag: cell type

value: human hepatoma

tag: genotype

tag: treatment

value: SER

tag: time

value: Day 2


title: benign_6

description: short RNA


title: genomic DNA from Blood from mouse 280623R at time point 3

description: Pregnant


title: RPM_SER_sgACAD11


title: Methylome capture of HG005 at lab C, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
202775690018_R03C01

value: HG005 at lab C


title: KD2_NPCs_Rep3

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Quantification using RSEM
Assembly: mm9
Supplementary files format and content: RSEM quantification files

source_name: NPCs

growth_protocol: Neuronal differentiation was performed as previously described (Ying and Smith, 2003). Briefly, mESCs were grown for two passages in serum-based medium on MEF-free, gelatin-coated plates. Cells were then seeded on gelatin-coated plates (2x105 cells/6-well) in neuronal differentiation medium: 1:1 mixture of DMEM/F12 (Sigma) and Neurobasal medium (Gibco), supplemented with 0.5X B27 (Gibco), 0.5X N2 (Gibco), 1X Glutamax (Gibco), 0.1mM β-mercaptoethanol (Sigma), 25μg/ml BSA, and 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries). NPCs were collected after four days.

extract_protocol:
Total RNA was extracted from cells using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s instructions.
Lexogen SENSE mRNA-Seq

tag: genotype/perturbation

value: CRISPR/dCas9 KD of Meteor


title: genomic DNA from Blood from mouse 280625N at time point 3

description: Not pregnant

value: Not pregnant


title: genomic DNA from Blood from mouse 280626B at time point 3

description: Pregnant


title: Methylome capture of HG006 at lab C, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727317
Whole genome bisufite converted DNA
202775690018_R02C01


title: localized_PC_4

description: short RNA


title: KD1_NPCs_Rep3


title: RPM_SER_sgATP6V1G2


title: localized_PC_5

description: short RNA


title: Methylome capture of HG005 at lab C, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
202775690018_R01C01


title: genomic DNA from Blood from mouse 280626N at time point 3

description: Pregnant


title: Methylome capture of HG006 at lab C, replicate 3 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727317
Whole genome bisufite converted DNA
202775690018_R08C01


title: localized_PC_3

description: short RNA


title: Methylome capture of HG007 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727318
Whole genome bisufite converted DNA
201959750090_R07C01

value: HG007 at lab B


title: localized_PC_6

description: short RNA


title: Methylome capture of HG006 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727317
Whole genome bisufite converted DNA
201959750090_R06C01

value: HG006 at lab B


title: localized_PC_2

description: short RNA


title: KD1_NPCs_Rep2


title: Methylome capture of HG005 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
201959750090_R05C01

value: HG005 at lab B


title: localized_PC_1

description: short RNA


title: Methylome capture of HG002 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727313
Whole genome bisufite converted DNA
201959750090_R04C01

value: HG002 at lab B


title: genomic DNA from Blood from mouse 280623L at time point 3

description: Pregnant


title: benign_5

description: short RNA


title: KD2_NPCs_Rep1


title: benign_4

description: short RNA


title: genomic DNA from Blood from mouse 280623B at time point 3

description: Not pregnant


title: genomic DNA from Blood from mouse 280623RR at time point 2

description: Not pregnant


title: Ctrl_NPCs_Rep3

value: empty vector


title: genomic DNA from Blood from mouse 280626RR at time point 2

description: Not pregnant


title: genomic DNA from Blood from mouse 280623N at time point 2

description: Not pregnant


title: genomic DNA from Blood from mouse 280624B at time point 2

description: Pregnant


title: KD1_NPCs_Rep1


title: Gbi36L_biol rep 3

city: Hangzhou

first: Yue

last: SUN

state: Zhejiang

address: Yuhangtang Rd

country: China

institute: Zhejiang University

data_processing:
All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform. Illumina short paired-end reads produced previously were trimmed using Trimmomatic (v.0.36) with default parameters. The high-quality reads were aligned to the G. bickii genome using HISAT2 (v.2.0.4). The counts of reads aligned to each transcript were calculated with HTSeq (v.0.6.0) software, and fragments per kilobase of transcript per million mapped fragments were used to estimate the expression level of each gene.
Assembly: Gossypium bickii (G1) genome JZU_v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium bickii

source_name: cotyledons

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA was used for cDNA library construction with the NEBNext Ultra RNA Library Prep Kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). All libraries were subjected to paired-end 150-bp sequencing on the Illumina HiSeq 4000 platform.

value: cotyledons

value: 36-hours after imbibition

value: under light


title: KD2_NPCs_Rep2


title: genomic DNA from Blood from mouse 280626R at time point 2

description: Pregnant

value: female

value: Pregnant


title: benign_3

description: short RNA

value: benign

value: prostate


title: Methylome capture of HG001 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16786364
Whole genome bisufite converted DNA
201959750090_R01C01

value: HG001 at lab B


title: Ctrl_NPCs_Rep2


title: genomic DNA from Blood from mouse 280625L at time point 2

description: Pregnant

value: Whole blood


title: Ctrl_NPCs_Rep1


title: Methylome capture of HG004 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727315
Whole genome bisufite converted DNA
201959750090_R02C01

value: HG004 at lab B


title: benign_2

description: short RNA


title: Methylome capture of HG003 at lab B, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727314
Whole genome bisufite converted DNA
201959750090_R03C01

value: HG003 at lab B


title: pInv_mESCs_2i_Rep3

source_name: mESCs

growth_protocol: mESCs were routinely grown on gelatin-coated plates on MEFs in 2i medium: a 1:1 mixture of Neurobasal medium (Gibco) and Knockout DMEM (Gibco), supplemented with 1X B27 (Gibco), 1X N2 (Gibco), 1X Glutamax (Gibco), 1X Sodium pyruvate (Gibco), 1X Nonessential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), 52.5μg/ml BSA, 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries), 1μM PD 0325901 (Axon Medchem), 3μM CHIR 99021 (Axon Medchem), and 10ng/ml LIF (Weizmann Proteomics Unit). Cells were passaged with 0.25% Trypsin (Biological Industries) every 2–3 days.

value: Meteor promoter inversion


title: Methylome capture of HG002 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727313
Whole genome bisufite converted DNA
203175700087_R07C01

value: HG002 at lab A


title: benign_1

description: short RNA


title: PC_bone_met_14

description: short RNA

source_name: spine

value: spine


title: pKO2_mESCs_2i_Rep3

value: Meteor promoter KO


title: pKO1_mESCs_2i_Rep3


title: Methylome capture of HG006 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727317
Whole genome bisufite converted DNA
203175700087_R06C01

value: HG006 at lab A


title: Methylome capture of HG007 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727318
Whole genome bisufite converted DNA
203175700087_R05C01

value: HG007 at lab A


title: WT2_mESCs_2i_Rep3

value: WT


title: genomic DNA from Blood from mouse 280623B at time point 2

description: Not pregnant

value: Not pregnant


title: PC_bone_met_13

description: short RNA


title: PC_bone_met_12

description: short RNA


title: Methylome capture of HG005 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
203175700087_R04C01

value: HG005 at lab A


title: WT1_mESCs_2i_Rep3


title: Methylome capture of HG004 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727315
Whole genome bisufite converted DNA
203175700087_R03C01

value: HG004 at lab A


title: pInv_mESCs_2i_Rep2


title: genomic DNA from Blood from mouse 280626N at time point 2

description: Pregnant

value: female

value: Pregnant


title: Methylome capture of HG003 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727314
Whole genome bisufite converted DNA
203175700087_R02C01

value: HG003 at lab A


title: PC_bone_met_10

description: short RNA


title: PC_bone_met_9

description: short RNA


title: pKO2_mESCs_2i_Rep2


title: genomic DNA from Blood from mouse 280623RR at time point 1

description: Not pregnant


title: Methylome capture of HG001 at lab A, replicate 2 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16786364
Whole genome bisufite converted DNA
203175700087_R01C01

value: HG001 at lab A


title: genomic DNA from Blood from mouse 280626RR at time point 1

description: Not pregnant

value: Whole blood


title: genomic DNA from Blood from mouse 280625N at time point 2

description: Not pregnant


title: 12M_B6-HepR, liver_rep1

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using hisat v2.1.0 with parameters --threads 28 --dta -t
Read counts were computed using Rsubread using default settings
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: liver tissue

extract_protocol:
liver tissue were harvested, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HBs-HepR mice was adoptively transferred with HBsAg+ hepatocytes from HBs-Tg mice for reconstruction, and B6-HepR mice was adoptively transferred with wildtype hepatocytes from C57BL/6J mice for reconstruction.

tag: strain

value: liver

value: B6-HepR mice adoptively transferred with wildtype hepatocytes from C57BL/6J mice


title: PC_bone_met_8

description: short RNA


title: Methylome capture of HG002 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727313
Whole genome bisufite converted DNA
203175700016_R07C01


title: PC_bone_met_7

description: short RNA


title: WT2_mESCs_2i_Rep2


title: genomic DNA from Blood from mouse 280625RR at time point 1

description: Pregnant


title: PC_bone_met_11

description: short RNA


title: WT1_mESCs_2i_Rep2


title: Methylome capture of HG007 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727318
Whole genome bisufite converted DNA
203175700016_R05C01


title: pInv_mESCs_2i_Rep1

value: Meteor promoter inversion


title: PC_bone_met_5

description: short RNA


title: PC_bone_met_6

description: short RNA


title: Methylome capture of HG005 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727316
Whole genome bisufite converted DNA
203175700016_R04C01


title: genomic DNA from Blood from mouse 280626R at time point 1

description: Pregnant


title: pKO2_mESCs_2i_Rep1


title: genomic DNA from Blood from mouse 280623N at time point 1

description: Not pregnant


title: genomic DNA from Blood from mouse 280624B at time point 1

description: Pregnant


title: pKO1_mESCs_2i_Rep2


title: genomic DNA from Blood from mouse 280625N at time point 1

description: Not pregnant


title: PC_bone_met_4

description: short RNA


title: genomic DNA from Blood from mouse 280625L at time point 1

description: Pregnant


title: genomic DNA from Blood from mouse 280623R at time point 1

description: Pregnant


title: Methylome capture of HG004 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727315
Whole genome bisufite converted DNA
203175700016_R03C01


title: Methylome capture of HG003 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727314
Whole genome bisufite converted DNA
203175700016_R02C01


title: Methylome capture of HG006 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16727317
Whole genome bisufite converted DNA
203175700016_R06C01


title: Methylome capture of HG001 at lab A, replicate 1 using Illumina Infinium MethylationEPIC BeadChip (850k array)

description:
SAMN16786364
Whole genome bisufite converted DNA
203175700016_R01C01


title: WT2_mESCs_2i_Rep1


title: WT1_mESCs_2i_Rep1


title: PC_bone_met_3

description: short RNA


title: PC_bone_met_2

description: short RNA


title: liver_adult_male_dnvdra_rep4

status: Public on Apr 20 2023

first: Scott

last: Freeburg

address: 77 Ave Louis Pasteur, New Research Building #458

institute: Brigham and Women's Hospital

data_processing:
FASTQ files were mapped to GRCz11 using STAR (v2.5.3), and read counting was performed using HTSeq (v0.11.1). Read count normalization was performed using the R package DEseq2.
Assembly: GRCz11
Supplementary files format and content: .csv files containing ensembl ids, gene names, and raw read counts or normalized read counts for each experiment

organism: Danio rerio

source_name: liver (dissected)

growth_protocol: Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.

extract_protocol:
Adult livers were dissected following euthanasia, and RNA was extracted using TRIZOL reagent (ThermoFisher Scientific).
Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit (Illumina) following DNase treatment and rRNA depletion using the QIAseq® FastSelectTM−rRNA HMR kit (Qiagen).

value: liver (dissected)

value: 4.5 mpf


title: PC_bone_met_1

description: short RNA

value: spine


title: liver_adult_male_dnvdra_rep3


title: genomic DNA from Blood from mouse 280623L at time point 1

description: Pregnant


title: genomic DNA from Blood from mouse 280623B at time point 1

description: Not pregnant


title: liver_adult_male_wt_rep4

value: wt


title: genomic DNA from Blood from mouse 280626B at time point 1

description: Pregnant


title: genomic DNA from Blood from mouse 280626N at time point 1

description: Pregnant


title: liver_adult_male_dnvdra_rep2


title: liver_adult_male_dnvdra_rep1


title: pKO1_mESCs_2i_Rep1

value: Meteor promoter KO


title: hepatocytes_96hpf_dnvdra_expt1_rep4

source_name: hepatocytes (sorted)

extract_protocol:
Hepatocytes were sorted into 75 uL Buffer RLT containing b-mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on-column DNase treatment.
The SMART-Seq v4 Ultra Low Input Kit for Sequencing (Clontech) kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.

value: hepatocytes (sorted)

value: 96 hpf


title: liver_adult_male_wt_rep3


title: hepatocytes_96hpf_wt_expt1_rep2


title: hepatocytes_96hpf_dnvdra_expt1_rep2


title: hepatocytes_96hpf_wt_expt1_rep4


title: hepatocytes_96hpf_dnvdra_expt1_rep3


title: liver_adult_male_wt_rep2


title: liver_adult_male_wt_rep1


title: hepatocytes_96hpf_wt_expt1_rep3


title: hepatocytes_96hpf_dnvdra_expt1_rep1


title: hepatocytes_96hpf_wt_expt1_rep1


title: MS-67

city: Frederick

first: Venkat

middle: R

last: Pannala

state: Maryland

address: 2405 Whittier Dr, #200

department: DoD BHSAI

institute: Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.

description: Control

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the rat transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o Rat/"$sample" --single  $DATA_DIR/3105-"$sample"_1_sequence.txt.gz -l 200 -s 30 -t 20
Genome_build: Rattus norvegicus Rnor6.0 Release 84
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (New England BioLabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (KAPA Biosystems). Pooled libraries were subjected to 75-bp single-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Sprague Dawley

value: Liver

tag: time point (duration after exposure)

value: 5 h

tag: agent

value: Vehicle


title: MS-66

description: Control


title: MS-68

description: Treatment

source_name: Kidney

value: Kidney

value: Acetaminophen


title: MS-63

description: Treatment


title: MS-65

description: Treatment


title: MS-64

description: Control


title: MS-60

description: Treatment


title: MS-61

description: Control


title: MS-62

description: Treatment


title: MS-59

description: Control


title: MS-58

description: Treatment


title: MS-53

description: Control


title: MS-56

description: Treatment


title: MS-57

description: Control


title: MS-54

description: Control


title: MS-51

description: Treatment


title: MS-50

description: Control


title: MS-49

description: Control


title: MS-47

description: Control


title: MS-46

description: Treatment


title: MS-48

description: Treatment


title: MS-41

description: Control


title: MS-40

description: Treatment


title: MS-42

description: Treatment


title: MS-44

description: Treatment


title: MS-38

description: Control


title: MS-37

description: Treatment


title: genomic DNA from Blood from mouse 280625RR at time point 2

description: Pregnant

value: female

value: Pregnant

value: Whole blood


title: MS-34

description: Control


title: MS-36

description: Treatment


title: MS-35

description: Control


title: MS-29

description: Treatment


title: MS-30

description: Control


title: MS-32

description: Treatment


title: MS-28

description: Treatment


title: MS-33

description: Control


title: MS-27

description: Treatment


title: MS-52

description: Control


title: MS-24

description: Control


title: MS-23

description: Control


title: MS-22

description: Treatment


title: MS-25

description: Treatment


title: MS-43

description: Control


title: MS-21

description: Control


title: MS-20

description: Treatment


title: MS-19

description: Control


title: MS-45

description: Treatment


title: MS-17

description: Treatment


title: MS-16

description: Control


title: MS-39

description: Treatment


title: MS-12

description: Treatment


title: MS-14

description: Control


title: MS-11

description: Control


title: MS-9

description: Treatment


title: MS-10

description: Control


title: MS-7

description: Treatment


title: MS-6

description: Treatment


title: MS-4

description: Control


title: MS-5

description: Control


title: MS-3

description: Control


title: MS-1

description: Treatment


title: MS-2

description: Control


title: T8.DN.Spl2.HiC

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Drive

institute: UCSD

library_source: genomic

data_processing:
Raw Hi-C FASTQ files were aligned to the mouse genome (mm10 build), and binned Hi-C matrices generated using Juicer
Files were normalized using multiHiCcompare
Assembly: mm10
Supplementary files format and content: Raw count interaction matrices in cool format

source_name: spleen

extract_protocol: Cells were sort purified, crosslinked, digested with MboI, and underwent proximity ligation. Biotinylated DNA segments were captured, ligated to Illumina adapters, amplified by PCR, and sequenced

value: spleen

value: OT-I

value: Lm-OVA

value: Day 7


title: T8.DN.Spl1.HiC


title: MS-26

description: Treatment


title: T8.TE.Spl2.HiC


title: T8.MP.Spl1.HiC


title: T8.TE.Spl1.HiC


title: MS-18

description: Treatment


title: HCT116 Control H3K27ac HiChIP replicate 1 Technical replicate 2

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: ATCC (CCL-247)

data_processing:
library strategy: HiChIP-seq
BWA was used to align read pairs on Homo sapience genome (UCSC hg38) with "-5SP -T0".
pairtools-0.3.0 was used to remove MAPQ < 40 and duplicated pairs and rescue reads with ligation junction.
FitHiChIP was used to call loops with 'peak to all' background, FDR < 0.01 and multiple bin size (5k, 10k, and 25k). Read pairs with distance > 2M or < 100bp were excluded from loop calling.
Loops with different bin size were merged using HiCExplorer-3.7.2.
The Loops anchoring on two adjacent bins were excluded.
Assembly: hg38
Supplementary files format and content: hic files were generated from Juicer Tools pre command; BEDPE files were called loops using FitHiChIP

growth_protocol: DMEM high glucose + 10% FBS + 100 units/ml penicillin + 100 μg/ml  streptomycin  with 5 μg/ml Puromycin selection

extract_protocol:
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS. Cell pellets were incubated at -80 °C  for a day as manufacturer's instructions.
All HiChIP and sequencing libraries were generated using the Dovetail® HiChIP MNase Kit (Dovetail, #21007) as manufacturer’s instructions using H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729) antibody.

treatment_protocol: For stable cell lines, we treated pSin empty and pSin. FOXD2 full-length CDS lentivirus onto HCT116 cells. Transduced stable cells were selected by puromycin (5ug/mL) in culture medium.

value: Large intestine; Colon

tag: disease state

value: Carcinoma; Colorectal

value: pSin-Pur-MCS-Puro epmty vector

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: HCT116 Control H3K4me1 HiChIP replicate 2 Technical replicate 1

description: ATCC (CCL-247)

value: H3K4me1 (Abcam, ab8895)


title: HCT116 FOXD2 H3K4me3 HiChIP replicate 1 Technical replicate 2

description: ATCC (CCL-247)

value: pSin-FOXD2 expressing vector

value: H3K4me3 (Abcam, ab8580)


title: MS-15

description: Control

value: Sprague Dawley

value: Liver

value: Vehicle


title: HCT116 FOXD2 H3K4me1 HiChIP replicate 1 Technical replicate 2

description: ATCC (CCL-247)


title: HCT116 Control H3K4me3 HiChIP replicate 1 Technical replicate 2

description: ATCC (CCL-247)


title: HCT116 FOXD2 MLL4 Input rep2

description: ATCC (CCL-247)

data_processing:
cutadapt-3.4 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (UCSC hg38).
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
MACS2-2.2.7.1 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Assembly: hg38
Supplementary files format and content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

extract_protocol:
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS.
Crosslinked 6.0 or 10.0 × 106 HCT116 cells for 7 min at 37 °C with 1% formaldehyde. We perforemd FOXD2-flag or 6xHis ChIP with sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% NP-40, 0.01% SDS, and 0.5% sodium deoxycholate, 1mM PMSF and 1X protease inhibitor cocktail) with 4μg of antibody; MLL4/KMT2D antibody (Santa crz, sc-293217) or Anti-6X His tag® antibody [HIS.H8] (Abcam, ab18184) or Monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich, F1804). For histone ChIP using MNase without crosslinking method, we resuspended 1.0 x 106 HCT116 cells in 50ul of nuclei isolation buffer (Sigma-Aldrich, NUC101) and incubated on ice for 10 min. We then proceeded to MNase digestion with final concentration 2 units/μl (NEB, M0247), pre-clearing and immunoprecipitated chromatin in ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, and 1 mM PMSF) with 2μg of antibody; H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).

value: pSin-FOXD2 epxressing vector


title: HCT116 Control H3K4me1 HiChIP replicate 1 Technical replicate 2

description: ATCC (CCL-247)


title: HCT116 Control MLL4 Input rep2

description: ATCC (CCL-247)


title: HCT116 FOXD2 MLL4 ChIP rep2

description: ATCC (CCL-247)

value: ML4/KMT2D (Santa crz, sc-293217)


title: Ctrl_basal

city: Wuhan

first: Yu

last: Zhou

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China.

institute: Medical Research Institute, Wuhan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cell

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

value: primary cell

value: mammary epithelial cells

value: WT


title: HCT116 Control MLL4 ChIP rep2

description: ATCC (CCL-247)


title: Large intestinal stem cell

data_processing:
The Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
The reads were aligned to mm10 reference provided by 10X Genomics.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv: barcode ids for each sample; features.tsv: gene ids for each sample; mtx: count matrix in a sparse matrix format

source_name: Large intestine

growth_protocol: primary cell isolates from Lgr5-EGFP reporter mouse

extract_protocol:
Lgr5-EGFP+ large intestinal stem cells were enriched from FACS
Cellular suspensions were loaded on a Chromium Controller (10x Genomics) to generate single-cell GEMs for the "LISC" sample. Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single cell 3’ Reagent Kit v3.1 following the manufacturer's protocol (PN-1000128, PN-1000127, and PN-220103).
scRNA-seq

value: Large intestine


title: CL_basal

value: clodronate liposome (CL)

value: Day 7


title: T8.MP.Spl2.HiC

value: spleen

value: OT-I

value: Lm-OVA


title: 7_4_BAT

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description:
BAT.counts.txt
BAT.TPM.txt

data_processing:
Quality inspection of raw RNA-Seq reads was performed with FastQC v0.11.9.
Counts and TPM values were obtained using kallisto v0.45 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

source_name: brown adipose tissue

extract_protocol:
Whole quadriceps, gonadal white adipose tissue, heart, brown adipose tissue, and a portion of  the liver were pulverized at the temperature of liquid nitrogen. Tissue was homogenized in Trizol  (Invitrogen, Carlsbad, CA, USA), RNA was isolated using the RNeasy Isolation Kit (Qiagen, Hilden,  Germany), and RNA concentration and quality were assessed (RIN > 7.0 used in downstream  applications)
Libraries were prepared using KAPA mRNA HyperPrep Kits and KAPA Dual Index Adapters (Roche, Basel, Switzerland) per manufacturer’s instructions. A total of 800-1000 ng of RNA was used for library preparation with settings 200-300 bp and 12 PCR cycles. The resultant libraries were tested for quality.

value: brown adipose tissue

value: female

value: PL/J

tag: exercise group

value: Exercised


title: 8_15_BAT

description:
BAT.counts.txt
BAT.TPM.txt

tag: tissue

value: FVB/NJ

value: Sedentary


title: 9_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: SWR/J


title: 6_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: BALB/cJ


title: 6_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 8_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 9_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 50_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: LP/J


title: 7_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 5_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: CBA/J


title: HCT116 FOXD2 H3K4me1 HiChIP replicate 2 Technical replicate 1

description: ATCC (CCL-247)

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: pSin-FOXD2 expressing vector

value: H3K4me1 (Abcam, ab8895)


title: HCT116 FOXD2 H3K27ac HiChIP replicate 1 Technical replicate 2

description: ATCC (CCL-247)

value: H3K27ac (Abcam, ab4729)


title: 49_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: NZB/BlNJ


title: 50_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 49_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 47_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: NZW/LacJ


title: 48_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: brown adipose tissue

value: BTBR T<+> tf/J


title: 48_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: female


title: 45_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 47_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: Exercised


title: 46_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: NOD/ShiLtJ


title: 44_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: Sedentary


title: 45_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 44_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 43_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 43_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 42_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 42_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 5_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 40_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 4_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: AKR/J


title: 40_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 4_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 41_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 38_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 39_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 38_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 46_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 36_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 35_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 37_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 37_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 35_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 36_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 34_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: SJL/J


title: 34_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 33_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 32_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 33_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 32_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 31_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: I/LnJ


title: 30_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 31_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 30_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 41_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 3_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: A/J


title: 29_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 39_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 29_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 28_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 27_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: SEA/GnJ


title: 28_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 27_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 26_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: RIIIS/J


title: 25_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 26_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 24_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 23_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 25_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 23_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 22_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 20_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 21_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 24_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 22_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 21_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 20_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 2_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 2_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 19_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 18_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 18_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 19_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 3_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 17_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 17_4_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 16_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 16_8_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 15_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: SM/J


title: 15_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 14_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 13_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 13_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 12_5_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 12_3_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 11_6_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 10_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 11_2_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 10_1_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 1_26_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: 1_34_BAT

description:
BAT.counts.txt
BAT.TPM.txt


title: LPSPparafl2

city: Beijing

first: Xinxin

last: Zhu

address: 10 You’anmen Outer West 1st Street

department: Department of Physiology and Pathophysiology

institute: Capital medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through fastp v0.23.2 soft.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.1.0 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.1.0.
stringtie v1.3.3b was used to count the reads numbers mapped to each gene.And then COUNT of each gene was calculated based on the length of the gene and readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.30.1).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include COUNT values for each Sample

source_name: heart tissue

growth_protocol: Ppara-Flox and cardiomyocyte PPARα dificient mice on a C57BL/6J background were generated as described previously. All mice were kept on a standard 12-hour light/dark cycle with free access to normal chow diet and water. All experimental procedures conformed to the US National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and under a project license (AEEI-2018-127) granted by the ethics board of Capital Medical University.

extract_protocol:
The isolated islets are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

treatment_protocol: Eight- to twelve-week-old male mice were injected intraperitoneally with LPS (Sigma Aldrich, St. Louis, USA), (5 mg/kg) dissolved in phosphate buffered saline (PBS) or PBS alone as their control mice as described previously. After twelve hours- LPS treatment, the heart tissue were collected and stored at -80 ℃ for RNA sequencing.

value: heart tissue

tag: background strain

value: male

value: PPARa-Flox

value: LPS


title: PBSPparaCM2

tag: Sex

value: PPARa deficient

value: PBS


title: PBSPparaCM1


title: 14_7_BAT

description:
BAT.counts.txt
BAT.TPM.txt

value: brown adipose tissue

value: female


title: PBSPparafl4


title: LPSPparaCM2


title: LPSPparaCM3


title: PBSPparafl3


title: PBSPparafl2


title: LPSPparaCM1


title: LPSPparafl1


title: LPSPparaCM4


title: PBSPparafl1


title: DKO-Dnmt-null-SC-3

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

data_processing:
The adapter sequences were removed from the 3’ end of the sequenced reads using the fastp program (version 0.20.1) with parameters “-l 15 --length_limit 40”
The remaining reads were mapped to the mouse genome (version GRCm38) using bowtie (version 1.2.1.1) first.
The mapped reads were mapped again to the mature miRNA sequences annotated in miRbase (version 21), allowing -2 or +2 nt to be templated by the corresponding genomic sequence at the 3’ end to determine the expression level of each miRNA.
The differential expression analysis of each miRNA were performed by R package DESeq2 (version 1.30.1).
The miRNAs with foldchange >1.414 and P-value <0.05 were defined as significant different expressed miRNAs.
Assembly: GRCm38
Supplementary files format and content: txt

source_name: semi-cloned embryo

extract_protocol:
Total RNA was extracted from E6.5 and E7.5 embryos and AG-haESCs by using miRNeasy Micro Kit (QIAGEN, Cat#217084) according to the manufacturer's instructions.
The preparation of CAS-seq cDNA library was mainly followed the published protocol (Yang. Q., et al., 2019, Nature Communications). The extracted RNA (100 pg) underwent the following steps to construct small RNA libraries: adapter ligation, first-strand cDNA synthesis, Cas9/sgRNA treatment, on-bead in vitro transcription, second RT and PCR amplification and gel purification. An Illumina NovaSeq 6000 System was used to sequence the small RNA libraries at the MingmaTechnologies Co., Ltd., China

value: semi-cloned embryo

tag: developmental stage

value: C57BL/6 male X F1 female

value: DKO-Dnmt-null-SC


title: DKO-Dnmt-null-SC-1


title: LPSPparafl3


title: LPSPparafl4


title: 11C_M_2982

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age


title: 11C_M_2981


title: 11C_M_2978


title: PBSPparaCM4


title: 11C_M_2977


title: PBSPparaCM3


title: 11C_M_2975


title: 11C_M_2980


title: 11C_M_2971


title: 11C_M_2969


title: 11C_M_2972


title: 11C_M_2985


title: 11C_M_2964


title: 11C_M_2962


title: 11C_M_2966


title: DKO-Dnmt-null-SC-2


title: 11C_M_2983


title: 11C_M_2965


title: 11C_M_2967


title: 11C_M_2961


title: 11C_M_2974


title: 11C_M_2959


title: 11C_M_2963


title: 11C_M_2976


title: 11C_M_2968


title: 11C_M_2960


title: 11C_M_2957


title: 11C_M_2984


title: 11C_M_2956


title: 11C_M_2953


title: 11C_M_2954


title: 11C_M_2950


title: 11C_M_2970


title: 11C_M_2949


title: 11C_M_2958


title: 11C_M_2948


title: 11C_M_2951


title: 11C_M_2973


title: 11C_M_2947


title: 11C_M_2946


title: 11C_M_2942


title: 11C_M_2944


title: 11C_M_2945


title: 11C_M_2940


title: 11C_M_2943


title: 11C_M_2939


title: 11C_M_2938


title: 11C_M_2936


title: 11C_M_2937


title: 11C_M_2934


title: 11C_M_2933


title: 11C_M_2924


title: 11C_M_2928


title: 11C_M_2930


title: 11C_M_2925


title: 11C_M_2931


title: 11C_M_2926


title: 11C_M_2922


title: 11C_M_2932


title: 11C_M_2918


title: 11C_M_2920


title: 11C_M_2923


title: 11C_M_2919


title: 11C_M_2921


title: 11C_M_2916


title: 11C_M_2915


title: 11C_M_2935


title: 11C_M_2913


title: 11C_M_2911


title: 11C_M_2912


title: 11C_M_2910


title: 11C_M_2909


title: 11C_M_2914


title: 11C_M_2907


title: 11C_M_2905


title: 11C_M_2929


title: 11C_M_2904


title: 11C_M_2906


title: 11C_M_2903


title: 11C_M_2899


title: 11C_M_2901


title: 11C_M_2898


title: 11C_M_2900


title: 11C_M_2897


title: 11C_M_2894


title: 11C_M_2896


title: 11C_M_2888


title: 11C_M_2889


title: 11C_M_2890


title: 11C_M_2902


title: 11C_M_2891


title: 11C_M_2892


title: 11C_M_2887


title: 11C_M_2893


title: 11C_M_2886


title: 11C_M_2908


title: 11C_M_2880


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title: 11C_M_2881


title: 11C_M_2882


title: 11C_M_2885


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title: 11C_M_2878


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title: 11C_M_2876


title: 11C_M_2873


title: 11C_M_2875


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title: 11C_M_2870


title: 11C_M_2868


title: 11C_M_2867


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title: 11C_M_2874


title: 11C_M_2865


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title: 11C_M_2686


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title: 11C_M_2306


title: 11C_M_2305


title: 11C_M_2333


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title: 11C_M_2290


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title: 11C_M_2292


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