title: Tinaja_H3K27ac_ip_2005_B

description: processed data file: tinaja_H3K27Ac.bed

source_name: Tinaja cave_liver_H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: Tinaja_H3K4me3_ip_2005_A

status: Public on Sep 07 2021

type: SRA

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

country: USA

institute: Stowers Institute

description: processed data file: tinaja_H3K4me3.bed

library_source: genomic

data_processing:
Following sequencing, Illumina Real Time Analysis version 1.18.64 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
FASTQ files for each chromatin mark were aligned to astMex_2.0 using bowtie2 under default parameters.
Reads mapping to the mitochondrial chromosome were filtered out using samtools prior to calling peaks with MACS2 under default parameters.
Overlapping peaks observed in at least 2 replicates were reduced using the GenomicRanges library in R.
Genome_build: astMex_2.0
Supplementary_files_format_and_content: BED files representing reproducible peak locations

molecule: genomic DNA

organism: Astyanax mexicanus

source_name: Tinaja cave_liver_H3K4me3

extract_protocol:
Adult livers were dissected and fixed in 1% formaldehyde for 15 min. Chromatin was prepared using MAGnify Low Cell ChIP-Seq Kit (Thermo Fischer) and ChIP was done for H3K4me3 (Millipore, # 07-473), H3K27ac (Abcam, # ab4729), H3K27me3 (Abcam, # ab195477). 200,000 cells and 1ug of antibody was used for each sample.
Libraries were prepared using the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies).  Post amplification size selection was performed on all libraries using a Pippin Prep (Sage Science). Libraries were re-quantified, normalized, pooled and sequenced on Illumina Illumina HiSeq 2500 instrument as 50-bp single read.

tag: FISH type

value: Tinaja cave

tag: tissue

value: liver

tag: chip antibody

value: H3K4me3 (Millipore, #07-473)

tag: sample type

value: ip

tag: replicate

tag: background sample


title: Testis, Control  2

status: Public on Sep 08 2021

city: Fuzhou

first: Lihong

last: Zhang

state: Fujian

address: No. 1 Xueyuan Road, Minhou County

country: China

institute: Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University

description:
One8
lncRNA and mRNA

library_source: transcriptomic

data_processing:
Basecalls performed using  Solexa pipeline v1.8.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5) software.
The transcript abundances for each sample was estimated with StringTie (1.3.1c).
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file.xlsx reports transcript abundances for each sample estimated with StringTie

molecule: total RNA

organism: Rattus norvegicus

source_name: Testis

growth_protocol: The rats used in this study were purchased and kept in the Laboratory Animal Center of Fujian Medical University. All the procedures conformed to Guidelines for the Care and Use of Laboratory Animals, which is established by Fujian Medical University and the Animal Approval Committee number is # SYXK-2012-0001.

extract_protocol:
Left testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment;2)Random primed first strand cDNA synthesis;3)dUTP based second strand cDNA synthesis; 4)Adaptor ligation and PCR amplification.

treatment_protocol: MOP, the polysaccharide in dried root (M. officinalis, Bajitian in Chinese) were extracted according to the specific protocol, the classical water extracting and alcohol precipitating method. In brief, after being grinded, the dried root was boiled in ethyl alcohol to remove oligosaccharide and lipid substance, then be extracted using deionized water, next be precipitated with 60% alcohol, the last Sevag reagent was added to remove protein. The experimental varicocele operation was done on the male rats to model varicocele by ligating the left vein of kidney partially. The same operation was conducted except the partial ligation on the rats in control group, and followed by 12 weeks conventional feeding. After the operation by 8 weeks, about 2 mL normal saline was administrated to the VC group rats daily for 4 weeks; 300 mg kg-1 MOP was given to VC+MOP group rats per day also lasting 4 weeks, and both by gavage. After being anesthetized (using 4–6 mg kg-1 chloral hydrat), the rats sacrificed to gain the left testicular tissue, and followed by being set into liquid nitrogen immediately. If the vascular dilation didn’t form or left kidney atrophy occurred in varicocele operation rats, the animals should be removed from the follow-up experiment.

tag: strain

value: Sprague Dawley

value: testis

tag: Sex

value: male

tag: age

value: 6-7 weeks

tag: condition

value: control

tag: treatment


title: Pachon_H3K27me3_ip_2399_b

description: processed data file: pachon_H3K27me3.bed

source_name: Pachon cave_liver_H3K27me3

value: Pachon cave


title: Tinaja_H3K27me3_ip_2399_b

description: processed data file: tinaja_H3K27me3.bed

source_name: Tinaja cave_liver_H3K27me3


title: Tinaja_H3K4me3_ip_1934_a

description: processed data file: tinaja_H3K4me3.bed


title: Tinaja_H3K27ac_ip_2005_A

description: processed data file: tinaja_H3K27Ac.bed


title: Pachon_1 [RNA-seq]

data_processing:
Following sequencing, Illumina Real Time Analysis version 1.18.64 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
FASTQ files were aligned to astMex_2.0 using STAR under default parameters and --quantMode with gene models from Ensembl 96 to generate gene counts.
Genome_build: astMex_2.0
Supplementary_files_format_and_content: Tab-delimited text file of stranded Ensembl96 gene counts for each fish.

molecule: polyA RNA

source_name: Pachon cave_liver

extract_protocol:
RNA was extracted from Liver tissue and purified using the Qiagen RNeasy kit.
Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina).

tag: morphotype/population


title: Surface_H3K27ac_ip_1930_2

description: processed data file: surface_H3K27Ac.bed

value: Surface


title: Pachon_tc_1889

source_name: Pachon cave_liver_total chromatin

value: total chromatin


title: Pachon_H3K27ac_1ug_ip_1934_b

description: processed data file: pachon_H3K27Ac.bed

source_name: Pachon cave_liver_H3K27ac


title: Surface_H3K4me3_ip_1930_1

description: processed data file: surface_H3K4me3.bed


title: Pachon_2 [RNA-seq]


title: Pachon_H3K27ac_1ug_ip_1889

description: processed data file: pachon_H3K27Ac.bed


title: Tinaja_H3K27ac_ip_1934_b

description: processed data file: tinaja_H3K27Ac.bed


title: Surface_H3K27ac_ip_1930_1


title: DMC1 B6xSPRETUS (Prdm9 HUM/SPRETUS)

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

country: United Kingdom

institute: Oxford University

data_processing:
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm (described in Davies et al Nature 2016). R code available at https://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al Science 2019)
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al Science 2019)
Genome_build: mm10
Supplementary_files_format_and_content: text file with column descriptions in commented header; each line corresponds to one hotspot

organism: Mus musculus

source_name: whole adult testis

growth_protocol: Data were generated from in vivo tissue samples from adult male mice - no culturing was performed.

extract_protocol:
Testes samples were stripped of the tunica and processed as described in Khil et al, Genome Research, 2012). Single-stranded DNA sequencing and double-strand break detection were performed using a modified ssDNA ChIPseq protocol. Full experimental procedures are reported in accompanying manuscript (Davies et al).
Libraries were prepared according to Illumina's instructions

tag: prdm9 genotype

value: HUM/SPRETUS


title: DMC1 B6xSPRETUS (Prdm9 CAST/SPRETUS)

value: CAST/SPRETUS


title: DMC1 B6xSTUS


title: DMC1 B6xSPRETUS


title: 5 - nanoparticle negative tumour endothelial cells

city: Toronto

first: Warren

last: Chan

state: ON

address: 160 College St.

country: Canada

institute: University of Toronto

data_processing:
Trim sequences to remove adapter sequences and nucleotides that were poor quality using Trimmomatic v.0.036
Map trimmed reads to mus musculus genome available on the ENSEMBL database (GRCm38) and use STAR aligner (v2.5.2b) to align reads and generate BAM files
Generate unique hit counts using featureCounts and the Subread package (v.1.5.2) and report using the gene_id feature
Perform differential gene expression between nanoparticle positive and nanoparticle negative tumour endothelial cells using DESeq2 using the Wald test to generate log2 fold change values and adjusted p-values
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw counts are provided in .txt files
Supplementary_files_format_and_content: Differential gene expression analysis from DESeq2 for all samples is provided in the .csv file

source_name: 4T1 mouse mammary tumour endothelial cells

growth_protocol: 4T1 tumours induced in 8 week old female Balb/c mice using 1 million cells into the inguinal mammary fat pad. Grown for 2 weeks.

extract_protocol:
Tumours removed, mechanically and enzymatically digested into a single cell suspension. Tumour endothelial cells were enriched using Miltenyi MACS system by first depleating CD45+ cells, and then selection CD31+ cells. The enriched tumour endothelial cells were then sorted into nanoparticle positive and nanoparticle negative fractions using FACS. The isolated cells were then frozen at -80C in Trizol. RNA extraction done using the Qiagen RNeasy Plus Mini Kit.
cDNA synthesis and amplification were done using the SMART-Seq v4 Ultra Low Input Kit for Sequencing from Clontech. Sequencing was done by 2x150bp paired end reads.

treatment_protocol: Dose: 1E12 nanoparticles; Formulation: 50 nm gold nanoparticles 5K mPEG, with Cy5. Injected via tail vein. Tumours harvested 1 hour post injection.

tag: sorting

value: Balb/c

value: 4T1 tumour

value: 10 weeks

tag: tumour age

value: 2 weeks


title: 6 - nanoparticle negative tumour endothelial cells


title: 4 - nanoparticle negative tumour endothelial cells


title: Pool14: mouse stress + untreated monocyte RNA-seq

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
Quality control was assessed using FastQC (version 0.11.7). Low-quality base noise in the beginning of the reads was trimmed using FASTX-Toolkit fastx_trimmer (version 0.0.13) using flags -Q33 -f 11. Reads were mapped to mouse reference genome mm10 using STAR (version 2.6.1d). Genomic features were assigned using Subread featureCounts (version v1.6.3).
genome build: mm10
processed data files format and content: rawcounts.txt files contain comma separated raw counts

source_name: isolated bone marrow monocytes

extract_protocol: RNA was isolated from bone marrow monocytes isolated by negative selection using magnetic-activated cell sorting (MACS, Miltenyi Biotec) according to manufacturers instructions. RNA was used to generate barcoded cDNA libraries using the NEBNext Ultra RNA library prep with rRNA depletion. Indexed libraries were sequenced in the 2x150bp configuration on the Illumina HiSeq2500 platform.

value: 8-12 weeks

tag: group

value: stress + untreated

tag: cell type

value: monocytes


title: 1 - nanoparticle positive tumour endothelial cells


title: 2 - nanoparticle positive tumour endothelial cells


title: Pool12: mouse stress + untreated monocyte RNA-seq


title: Pool7: mouse control + LPS monocyte RNA-seq

value: control + LPS


title: Pool5: mouse control + LPS monocyte RNA-seq


title: Pool9: mouse control + untreated monocyte RNA-seq

value: control + untreated


title: 3 - nanoparticle positive tumour endothelial cells


title: Pool15: mouse control + untreated monocyte RNA-seq


title: Pool3: mouse control + LPS monocyte RNA-seq


title: Pool16: mouse stress + untreated monocyte RNA-seq


title: Pool6: mouse stress + LPS monocyte RNA-seq

value: stress + LPS


title: Pool10: mouse stress + untreated monocyte RNA-seq


title: DMC1 B6xSTUS (Prdm9 HUM/STUS)

value: testis

value: HUM/STUS


title: Pool2: mouse stress + LPS monocyte RNA-seq


title: M16: mouse stress monocyte ATAC-seq

data_processing:
Per-read per-sample FASTQ files were generated using the bcl2fastq Conversion software (v.2.20) to convert per-cycle BCL base call files outputted by the sequencing instrument into the FASTQ format. The alignment program, Bowtie2 (v.2.3.4.1), was used for mapping sequenced reads from the mouse samples to the mouse reference genome mm10 and the application Sambamba (v.0.6.7) was utilized to remove duplicate reads. The algorithm, MACS (in Python v.2.7.3), was used to call peaks of signal for annotated genomic features.
genome build: mm10
processed data files format and content: peak files generated by macs for ATACseq data

extract_protocol: Chromatin profiling was performed by ATAC-Seq as described previously.(Buenrostro et al., 2013) Briefly, 50,000 to 100,000 cells were washed in cold PBS and lysed. Transposition was performed at 42C for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5 ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).

value: stress


title: Pool13: mouse control + untreated monocyte RNA-seq


title: Pool8: mouse stress + LPS monocyte RNA-seq


title: M1: mouse control monocyte ATAC-seq

value: control


title: Pool1: mouse control + LPS monocyte RNA-seq


title: M15: mouse stress monocyte ATAC-seq


title: Pool4: mouse stress + LPS monocyte RNA-seq


title: Pachon_H3K4me3_1ug_ip_1889

description: processed data file: pachon_H3K4me3.bed

source_name: Pachon cave_liver_H3K4me3

tag: FISH type

value: Pachon cave

value: liver

value: H3K4me3 (Millipore, #07-473)

value: ip


title: M14: mouse stress monocyte ATAC-seq


title: M14: mouse stress monocyte RNA-seq

data_processing:
data was processed and analyzed with Basepair software (www.basepairtech.com) using their default parameters
genome build: mm10
processed data files format and content: RNAraw.txt files contain comma separated counts, fpkm, and tpm for each sample, generated by basepair website


title: M4: mouse control monocyte ATAC-seq


title: M16: mouse stress monocyte RNA-seq


title: Pool11: mouse control + untreated monocyte RNA-seq


title: CS38.25.CD28_D16#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the human reference genome (GRCh38) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v34)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

organism: Homo sapiens

extract_protocol:
CD25+ naive Tregs from healthy donors were sorted, activated, transduced with lentiviral vector for CAR+CD28/4-1BB expression and expanded for 16 days, with a CAR-negative sorting (CD25-NT) or CAR-positive sorting (CD25+28/25+BB) at D11 of culture. At D16 cells were stained and sorted by flow cytometry as DAPI– CD4+CD25+ FVD-EGFR+ or FVD-EGFR- (CD25-NT). 1,000 cells were double-sorted directly into lysis buffer for RNA-seq (Smart-seq2)  library preparation following the standard ImmGen low-input protocol (www.immgen.org). Samples were collected in independent experiments and sequenced in the same RNAseq batch.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: genotype

value: HD

tag: tissue

value: Blood

value: WT

tag: experiment

value: male

tag: donor

value: CD4 TReg Cell

tag: cell population

value: CD28 CAR-Tregs were sorted as  DAPI– CD4+CD25+ FVD-EGFR+


title: CS41.25.CD28_D16#1

value: female


title: M3: mouse control monocyte RNA-seq

tag: strain

value: 8-12 weeks

value: monocytes


title: Rep3_siCNOT1_ER

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

data_processing:
fastp v0.19.5 was used for adapter and quality trimming
cd-hit-dup v4.6.6 was used to deduplicate reads based on the 12nt UMI
alignment using STAR v2.6 was used for alignments
featureCounts v1.6.4 was used to obtain read counts
Genome_build: hg38, gencode v27
Supplementary_files_format_and_content: csv file containing the mRNA localisation cluster determined using kmeans clustering on the control data as well as log2FC RNA in the cytosol and log2FC RNA in the ER (siCNOT1/siControl)

source_name: HEK293 cells

growth_protocol: HEK293 cells grown in DMEM with 10% FBS and 2mM L-glutamine

extract_protocol:
Cells were washed with ice-cold PBS and Trizol added directly to the well. The RNA was extracted with Trizol purification
Total RNA was rRNA depleted using lexogen RiboCop and then input into the lexogen CORALL Total RNA-seq kit

treatment_protocol: Cells treated with 30nM of control or CNOT1-targeting siRNA for 48 hrs

tag: sirna

value: CNOT1 siRNA

tag: fraction

value: ER


title: Rep2_siCNOT1_ER


title: M15: mouse stress monocyte RNA-seq

tag: age

value: stress


title: CS38.25.CD137_D16#1

tag: Sex

value: 4-1BB CAR-Tregs were sorted as  DAPI– CD4+CD25+ FVD-EGFR+


title: Rep3_siControl_cyto

value: control siRNA

value: cytosol


title: Rep3_siCNOT1_cyto


title: CS38.25.NT_D16#1

value: Untransduced Tregs were sorted  as DAPI– CD4+CD25+ FVD-EGFR-


title: CS41.25.CD137_D16#1


title: Rep2_siCNOT1_cyto


title: CS41.25.NT_D16#1


title: M3: mouse control monocyte ATAC-seq

value: control


title: Rep1_siCNOT1_ER


title: M1: mouse control monocyte RNA-seq


title: Rep2_siControl_ER


title: Rep1_siControl_ER


title: Rep1_siCNOT1_cyto


title: Rep3_siControl_ER


title: Blood patient 18

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
The stranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: peripheral blood

extract_protocol:
T cells from BAL, tonsil and PBMC and healthy donor controls were sorted on an ARIA II flow sorter (Becton Dickinson) as DAPI- CD14- CD16- CD19- CD3+ CD4+ CD45RA- CD45RO+. Tonsillar T cell were further sorted for CXCR5/PD-1 double-positive or -negative to discriminate Tfh and non-Tfh cells. RNA was isolated using a Qiagen (Hilden, Germany) RNeasy Micro Kit. RNA quality was determined on an Agilent Fragment Analyzer System using the HS RNA 15nt Kit.
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions

value: peripheral blood

tag: patient diagnosis

value: sarcoidosis

tag: cells

value: CD4+ CD45RO+ T cells

tag: condition

value: CD4+ effector/memory


title: Rep1_siControl_cyto


title: Blood patient 22


title: Rep2_siControl_cyto


title: M4: mouse control monocyte RNA-seq


title: Blood patient 14


title: Tonsil patient 6 non-Tfh

source_name: palatine tonsil

value: palatine tonsil

value: CD4+ CD45RO+ CXCR5- PD-1- T cells

value: CD4+ effector/memory non-Tfh


title: Blood healthy donor 199

value: healthy


title: Tonsil patient 1 non-Tfh


title: Tonsil patient 6 Tfh

value: CD4+ CD45RO+ CXCR5+ PD-1+ T cells

value: CD4+ effector/memory Tfh


title: Blood healthy donor 197


title: Tonsil patient 1 Tfh


title: BAL patient 16

source_name: bronchoalveolar lavage

value: bronchoalveolar lavage


title: Blood healthy donor 196


title: BAL patient 14


title: BAL patient 15


title: BAL patient 18


title: BAL patient 22


title: IL7R Dox induced IL7R 9

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
Kallisto was used to quantify abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment (Nat Biotechnol. 2016 May;34(5):525-7).
Genome_build: mm10
Supplementary_files_format_and_content: tsv

source_name: IL7R Dox induced IL7R_thymus

extract_protocol:
Total RNA was extracted with trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq libraries were sequenced as paired-end 75-bp sequence tags using the standard Illumina pipeline

tag: genotype/variation

value: tetracycline-inducible expression of IL-7R{alpha}

value: Thymus


title: IL7R Dox induced IL7R 8


title: TREATED_rep1 (cobalt)

type: RNA

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: cobalt treated tumor M. musculus sample

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Rat Genome 230 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA). Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Affymetrix Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm. Data were normalized across all three groups.

label: biotin

source_name: lung, cobalt treated tumor

label_protocol: One hundred nanograms of total RNA was amplified as directed in the Affymetrix 3′ IVT Plus kit protocol. Fifteen micrograms of amplified biotin-aRNAs was fragmented, and 12.5 μg was hybridized to each array for 16 h at 45 °C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

growth_protocol: At the start of the study, the animals were 5–6 weeks of age. The animals were housed 2 per cage. Tap water and NTP-2000 diet (Zeigler Brothers, Inc. Gardners, PA) were made available ad libitum. The care of animals on this study was according to National Institutes of Health (NIH) procedures as described in the ‘‘The U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals,’’ available from the Office of Laboratory Animal Welfare, NIH, Department of Health and Human Services, RKLI, Bethesda, MD or online at http://grants.nih.gov/grants/olaw/olaw.htm#pol.

extract_protocol: The lung was harvested and weighed, and then, a representative sections are collected and fixed in 10 % neutral buffered formalin for histology. Hematoxylin and eosin (H&E)-stained sections (5 μm) were examined by a board certified pathologist. Selected lung tumors are dissected from the remaining lung parenchyma and flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. RNA was extracted from frozen samples using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A, Carlsbad, CA) according to the manufacturer’s protocol. RNA concentration and quality were measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples were aliquoted and stored at −80 °C until they were analyzed for gene expression studies.

treatment_protocol: Cobalt metal dust was produced by OMG Kokkola Chemicals Oy (Kokkola, Finland) and was provided by the Cobalt Development Institute via PEL Technologies in one lot (P32 3040-1) that was used in the 2-week, 3-month, and 2-year studies.  Groups of 50 male and 50 female mice were exposed to cobalt metal particulate aerosol by inhalation at concentrations of 0, 1.25, 2.5, or 5 mg/m3, 6 hours plus T90 (12 minutes) per day, 5 days per week for up to 105 weeks.

tag: group

value: cobalt_Treated Tumor


title: TREATED_rep6 (cobalt)

description: cobalt treated tumor M. musculus sample


title: IL7R Dox induced IL7R 7


title: TREATED_rep2 (cobalt)

description: cobalt treated tumor M. musculus sample


title: IL7R Dox induced IL7R 4


title: TREATED_rep5 (cobalt)

description: cobalt treated tumor M. musculus sample


title: SPONT_rep4 (cobalt)

description: cobalt spontaneous tumor M. musculus sample

source_name: lung, spontaneous tumor

value: cobalt_Spontaneous Tumor


title: TREATED_rep4 (cobalt)

description: cobalt treated tumor M. musculus sample


title: SPONT_rep1 (cobalt)


title: SPONT_rep2 (cobalt)


title: IL7R Dox induced IL7R 2


title: IL7R Dox induced IL7R 1


title: TREATED_rep3 (cobalt)

description: cobalt treated tumor M. musculus sample


title: IL7R Dox induced IL7R 5


title: Control 3

source_name: healthy control_thymus


title: IL7R Dox induced IL7R 6


title: SPONT_rep6 (cobalt)


title: CONTROL_rep4 (cobalt)

description: M. musculus vehicle control sample

source_name: lung, vehicle control


title: CONTROL_rep5 (cobalt)

description: M. musculus vehicle control sample


title: Control 2


title: CONTROL_rep2 (cobalt)

description: M. musculus vehicle control sample


title: CONTROL_rep1 (cobalt)

description: M. musculus vehicle control sample


title: SPONT_rep5 (cobalt)


title: IL7R Dox induced IL7R 3


title: SPONT_rep3 (cobalt)


title: CONTROL_rep3 (cobalt)

description: M. musculus vehicle control sample


title: CONTROL_rep6 (cobalt)


title: Control 1


title: 293T-WT-rep3

city: Hangzhou

first: Fan

last: Wang

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio is more than 20%; (3) Removing reads whose unknow base ratio is more than 5%. Afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: GCF_000001405.38_GRCh38.p12

source_name: 293T cells

growth_protocol: WT and HVCN1-/- 293T cells were cultured in DMEM containing 10% FBS.

extract_protocol:
Total RNA was extracted from 293T cells using TRIzolTM Reagent (#15596026, InvitrogenTM). Then mRNA was purified from total RNA using oligo(dT)-attached magnetic beads.
First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adapters were ligated to the ends of these 3' adenylated cDNA fragments. The products were amplyfied, purified with Ampture XP Beads (AGENCOURT) and circularized by splint oligo sequence.The single strand circle DNA (ssCir DNA) were formatted as the final library.

treatment_protocol: no treatment.

tag: cell type

value: human embryonic kidney cell line


title: 293T-HVCN1 KO-rep1


title: 293T-WT-rep1


title: 293T-HVCN1 KO-rep2


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_027_DX]

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

description:
MNC_027_DX
mRNA profiles of the corresponding sample

data_processing:
Sequenced reads were quality and adapter trimmed using Trim Galore v0.6.6 with extra parameters --quality 10 --length 20.
Reads were aligned against Ensembl GRCh38.p13 v102 genome using HiSat2 v2.2.1 with parameter -U for unpaired reads to be aligned.
Aligned reads were assigned to gene counts using featureCounts v2.0.1 with extra parameters -s 0 for unstranded and -s 2 for stranded protocol.
Genome_build: Ensembl GRCh38.p13 v102
Supplementary_files_format_and_content: *processed_data_countdata.tsv: Tab-delimited text file with raw gene counts for every gene and every sample.

source_name: Bone marrow

growth_protocol: The complete mononuclear cell fraction was fresh frozen upon density gradient separation. After thawing, the sample was DTC depleted.

extract_protocol:
miRNeasy Micro Kit.
New England Biolab kit with polyA enrichment: directional or non-directional.

treatment_protocol: No treatment.

tag: diagnosis

value: neuroblastoma


title: 293T-WT-rep2


title: 293T-HVCN1 KO-rep3


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_030_DX]

description:
MNC_030_DX
mRNA profiles of the corresponding sample


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_028_DX]

description:
MNC_028_DX
mRNA profiles of the corresponding sample


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_031_DX]

description:
MNC_031_DX
mRNA profiles of the corresponding sample


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_033_DX]

description:
MNC_033_DX
mRNA profiles of the corresponding sample


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_008_DX]

description:
MNC_008_DX
mRNA profiles of the corresponding sample


title: FRS2beta_hetero_rep3

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

description: gene expression of spheres

hyb_protocol: Cy3-labelled cRNA was fragmented  and then hybridized to array following the manufacturer's instructions.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2539A).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol: GE1_107_Sep09, and Grid: 028005_D_F_20120201.) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software 14 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in more than two replicates in both conditions, the probe was excluded. In the second filter, when the flag of a probe was compromised in more than two replicates in at least one condition, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: FRS2beta hetero, replicate3

label_protocol: RNA samples were labeled with Cy3 exploitng Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Spheres were grown in sphere culture medium (SCM), composed of DMEM/F12 (GIBCO), B27 Supplement (GIBCO), 20 ng/mL EGF (Millipore), 20 ng/mL bFGF (PEPROTECH), 2 mg/mL heparin (Stemcell Technologies).

extract_protocol: Total RNA was extracted with Trizol reagent (ThermoFisher Scientific) according to the manufacturer's instructions.

value: mammary tumor

tag: genotype

value: FRS2beta hetero


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_010_DX]

description:
MNC_010_DX
mRNA profiles of the corresponding sample

tag: tissue


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_006_DX]

description:
MNC_006_DX
mRNA profiles of the corresponding sample


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_003_DX]

description:
MNC_003_DX
mRNA profiles of the corresponding sample


title: FRS2beta_ko_rep1

description: gene expression of spheres

source_name: FRS2beta ko, replicate1

value: FRS2beta knock-out


title: FRS2beta_ko_rep3

description: gene expression of spheres

source_name: FRS2beta ko, replicate3


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_001_DX]

description:
MNC_001_DX
mRNA profiles of the corresponding sample


title: FRS2beta_ko_rep2

description: gene expression of spheres

source_name: FRS2beta ko, replicate2


title: FRS2beta_hetero_rep1

description: gene expression of spheres

source_name: FRS2beta hetero, replicate1


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_007_DX]

description:
MNC_007_DX
mRNA profiles of the corresponding sample


title: FRS2beta_hetero_rep2

description: gene expression of spheres

source_name: FRS2beta hetero, replicate2


title: 9_RNAseq_mESC_PD rep3

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description: 2_transformed(wtAsh1L)_transformed(Ash1LKO).diff

data_processing:
For the RNA-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Tophat2.
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 1.5-fold RPKM change between samples.
Genome_build: mm9

source_name: MLL-AF9-transformed cells

growth_protocol: HPCs cells were maintained in RMPI1640 medium supplemented with 10% FBS, 1% MEM non-essential amino acids, 1% Glutamax, 10 ng/mL, 2-mercaptoethanol, and 50 ng/mL mSCF (PeproTech), 10 ng/mL mIL-6 (PeproTech), and 10 ng/mL mIL-3 (PeproTech). The MLL-AF9-transformed cells were maintained in RMPI1640 medium supplemented with 10% FBS, 1% MEM non-essential amino acids, 1% Glutamax, 10 ng/mL, 2-mercaptoethanol 10 ng/mL mIL-3 (PeproTech).

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA (1 µg) was used to generate RNA-seq library using NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated cDNA was amplified by PCR and followed by size selection using agarose gel electrophoresis. The DNA was purified using Qiaquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The libraries were diluted to a working concentration of 10nM prior to sequencing. Sequencing on an Illumina HiSeq4000 instrument was carried out by the Genomics Core Facility at Michigan State University.

treatment_protocol: Retroviral and lentiviral transduction of HPCs was performed by spin inoculation for 1 hour at 800g.

tag: modification

value: no modifications

value: Ash1L knockout


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_004_DX]

description:
MNC_004_DX
mRNA profiles of the corresponding sample


title: 6_RNAseq_mESC_serum rep3

value: Ash1L wild-type


title: 5_RNAseq_mESC_serum rep2


title: 7_RNAseq_mESC_PD rep1


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_002_DX]

description:
MNC_002_DX
mRNA profiles of the corresponding sample


title: 4_RNAseq_mESC_serum rep1


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_061_DX_2]

description:
MNC_061_DX_2
mRNA profiles of the corresponding sample


title: 3_normalHPC rep3

source_name: c-kit+ hematopoietic progenitor cells

value: wild-type


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_005_DX]

description:
MNC_005_DX
mRNA profiles of the corresponding sample


title: 8_RNAseq_mESC_PD rep2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_978_DX]

description:
BMn_978_DX
mRNA profiles of the corresponding sample

growth_protocol: The complete mononuclear cell fraction was fresh frozen upon density gradient separation.

value: Non/low infiltrated bone marrow


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BM_059_NA]

description:
BM_059_NA
mRNA profiles of the corresponding sample


title: 1_normalHPC rep1


title: DTC-depleted bone marrow fraction (MNCs) of a neuroblastoma patient [MNC_517_DX_2]

description:
MNC_517_DX_2
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_990_DX]

description:
BMn_990_DX
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_963_DX]

description:
BMn_963_DX
mRNA profiles of the corresponding sample


title: Tf_E12_PAX6_1

city: San Francisco

first: Kenneth

last: Lim

state: CA

department: Psychiatry

institute: UCSF

description: Protocol 2

data_processing:
ATACseq, Histone ChIPseq and Transcription Factor ChIPseq reads were aligned to mm9 (UCSC) genome assembly using BWA mem (v0.7.17).
Aligned reads were filtered using samtools view version 1.10 with a MAPQ cutoff of 30.
bigwig files were generated using deepTools bamCoverage (v3.4.3) with the following parameters: output type=bigwig, bin-size=10, fragment extension=200, normalize=RPKM, ignore duplicates=active.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files generated using deepTools. Scores represent RPKM.

source_name: cerebral cortex

growth_protocol:
Cerebral cortex tissue was dissected from WT or mutant E12.5 littermate embryos. Ftag was injected into the lateral ventricles for 20 minutes and the cortex was then dissecte..
Cerebral cortex tissue was dissected from WT or mutant E12.5 embryos. For TF ChIP-seq, samples represent pooled tissue from 2-3 litters.

extract_protocol:
Nuclear extracts were prepared from sorted cells and digested with MNase to obtain mono- and di-nucleotide fragments. Digested chromatin was dialysed overnight. Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against H3K27ac (Abcam, ab472) or H3K27me3 (Active motif, 39157). Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction.
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).
Nuclear extracts were prepared from  cells and sheared using a bioruptor (18-40 cylces; 30s ON and 45s OFF). Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against the relevant TF or IgG or a blocking peptide overnight at 4C.  Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction.
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).

treatment_protocol:
The tissue was dissociated using the Papain Dissociation System (Worthington) according to the manufacturer’s instructions. Dissociated cells were separated by fluorescence activated cell sorting on a FACSAria II machine (BD Biosciences). Sorted GFP-positive ventricular zone cortical cells were collected.
The tissue was dissociated by pipetting and fixed for 10-20 mins in 1-1.5% PFA for 10-20 minutes.

tag: experiment

value: TranscriptionFactorChIPseq

value: Cortex

tag: chip antibody

tag: replicate

value: WT


title: Tf_E12_LHX2

description: Protocol 2


title: Tf_E12_PAX6_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_696_DX]

description:
BMn_696_DX
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a ganglioneuroma patient [BMn_966_DX]

description:
BMn_966_DX
mRNA profiles of the corresponding sample

value: ganglioneuroma


title: 2_normalHPC rep2

tag: strain


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_964_DX]

description:
BMn_964_DX
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_693_DX]

description:
BMn_693_DX
mRNA profiles of the corresponding sample


title: Tf_E12_EMX2_1

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_962_DX]

description:
BMn_962_DX
mRNA profiles of the corresponding sample


title: Tf_E12_EMX2_2

description: Protocol 2


title: Tf_E12_CTF1_3

description: Protocol 2


title: Tf_Input_E12_EMX2_1

description: Protocol 2

value: Input


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_960_DX]

description:
BMn_960_DX
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_524_DX]

description:
BMn_524_DX
mRNA profiles of the corresponding sample


title: Tf_E12_CTF1_1

description: Protocol 2


title: Tf_Input_E12_3

description: Protocol 2


title: Tf_E12_CTF1_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_397_DX]

description:
BMn_397_DX
mRNA profiles of the corresponding sample


title: Tf_Input_E12_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_626_DX_2]

description:
BMn_626_DX_2
mRNA profiles of the corresponding sample


title: Tf_Input_E12_EMX2_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_529_DX]

description:
BMn_529_DX
mRNA profiles of the corresponding sample


title: Tf_Input_E12_5

description: Protocol 2


title: Tf_Input_E12_1

description: Protocol 2


title: Tf_Input_E12_CTF1

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_528_DX]

description:
BMn_528_DX
mRNA profiles of the corresponding sample


title: Tf_Input_E12_4

description: Protocol 2


title: Tf_IgG_E12_EMX2

description: Protocol 2

value: IgG


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_121_DX]

description:
BMn_121_DX
mRNA profiles of the corresponding sample


title: Non/low infiltrated bone marrow of a ganglioneuroblastoma patient [BMn_507_DX]

description:
BMn_507_DX
mRNA profiles of the corresponding sample

value: ganglioneuroblastoma


title: Tf_IgG_E12_CTF1_1

description: Protocol 2


title: Tf_IgG_E12_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_723_DX]

description:
BMn_723_DX
mRNA profiles of the corresponding sample


title: Tf_IgG_E12_CTF1_2

description: Protocol 2


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_366_DX_2]

description:
BMn_366_DX_2
mRNA profiles of the corresponding sample


title: Tinaja_2 [ATAC-seq]

description:
Tinaja_2_HGNK2AFXX
Tinaja_2_HH3NMAFXX

data_processing:
Following sequencing, Illumina Real Time Analysis version 1.18.64 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
Paired-end fastq data was aligned to astMex_2.0 using bowtie2 -X 2000 --very-sensitive
Reads mapping to the mitochondrial chromosome were filtered out using samtools prior to calling peaks with MACS2 under default parameters.
Overlapping peaks from each replicate were reduced using the GenomicRanges package in R to give a single peak set for each fish type.
Genome_build: astMex_2.0
Supplementary_files_format_and_content: BED files representing ATAC peak locations

source_name: Tinaja cave_liver

extract_protocol:
ATAC was performed as per Buenos et al. with some modifications to accommodate the use of whole tissues as starting material instead of cells. Livers were homogenized (30-40 strokes) using the loose pestle of Dounce homogenizer in lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl, 3 mMMgCl2, 0.1% (v/v) Igepal CA-630) to prepare nuclei. Rupturing of cell membrane and obtainment of nuclei was confirmed using Trypan blue staining under a phase contrast microscope. ~70000 nuclei were taken and spun down at 1500g at 4deg.
Nuclei were resuspended in transposition mixture (25 μl TD of 2× reaction buffer from Nextera kit, 2.5 μl TDE1 Tn5 Transposase, 22.5 μl nuclease-free water) and incubated at 37deg for 22-24 min. The reaction was purified, and library was prepared following manufacturer instructions. Paired-end sequencing was done in Illumina Next-seq Mid-output mode.

tag: FISH type

value: Tinaja cave

value: liver


title: Surface_2 [ATAC-seq]

description:
Surface_2_HGNK2AFXX
Surface_2_HH3NMAFXX

value: Surface


title: Tf_IgG_E12_3

description: Protocol 2

tag: age


title: Hinput_E12_ftag_PAX6_pos1

description: Protocol 1

value: HistoneChIPseq


title: Non/low infiltrated bone marrow of a neuroblastoma patient [BMn_137_DX]

description:
BMn_137_DX
mRNA profiles of the corresponding sample

value: neuroblastoma


title: Surface_1 [ATAC-seq]

description:
Surface_1_HGNK2AFXX
Surface_1_HH3NMAFXX


title: Pachon_2 [ATAC-seq]

description:
Pachon_2_HGNK2AFXX
Pachon_2_HH3NMAFXX

source_name: Pachon cave_liver

value: Pachon cave


title: Hinput_E12_ftag_PAX6_pos2

description: Protocol 1


title: Non/low infiltrated bone marrow of a ganglioneuroblastoma patient [BMn_139_DX]

description:
BMn_139_DX
mRNA profiles of the corresponding sample


title: Pachon_1 [ATAC-seq]

description:
Pachon_1_HGNK2AFXX
Pachon_1_HH3NMAFXX


title: Hinput_E12_ftag_EMX2_pos1

description: Protocol 1


title: Hinput_E12_ftag_EMX2_pos2

description: Protocol 1


title: Tf_BP_E12_EMX2

description: Protocol 2


title: Hinput_E12_ftag_PAX6_neg2

description: Protocol 1


title: Hinput_E12_ftag_PAX6_neg1

description: Protocol 1


title: Hinput_E12_ftag_EMX2_neg2

description: Protocol 1


title: Non/low infiltrated bone marrow of a ganglioneuroblastoma patient [BMn_247_DX]

description:
BMn_247_DX
mRNA profiles of the corresponding sample


title: Tf_IgG_E12_1

description: Protocol 2


title: Tinaja_1 [ATAC-seq]

description:
Tinaja_1_HGNK2AFXX
Tinaja_1_HH3NMAFXX


title: Hinput_E12_ftag_CTF1_pos1

description: Protocol 1


title: Hinput_E12_ftag_CTF1_neg2

description: Protocol 1


title: Hinput_E12_ftag_EMX2_neg1

description: Protocol 1


title: Hinput_E12_ftag_CTF1_pos2

description: Protocol 1


title: RPI29 9s

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Unique molecular identifiers (UMIs) and sample barcodes were extracted from the first read of each read pair using a custom R script. The second read of each read pair were aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted.
Genome_build: AgpV4
Supplementary_files_format_and_content: BeyondProto.UMI.matrix.csv: Comma-separated text file containing transcript counts for each gene and cell sample.

organism: Zea mays

source_name: isolated maize anther cell

growth_protocol: Maize (Zea mays) inbred line W23 bz2 was grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle.

extract_protocol:
Maize anthers were dissected, fixed in Farmer's Solution and digested in protoplasting enzymes. Isolated cells were sorted via BioSorter (Union Biometrica) or Hana (Namocell).
Library protocol based on CEL-Seq2 with modifications similar to Nelms & Walbot 2019.

value: anther

tag: inbred line


title: RPI29 94s


title: RPI29 92s


title: Hinput_E12_ftag_CTF1_neg1

description: Protocol 1


title: RPI29 93s


title: H27me3_E12_ftag_PAX6_pos1

description: Protocol 1


title: H27me3_E12_ftag_PAX6_neg2

description: Protocol 1


title: RPI29 96s


title: RPI29 91s


title: H27me3_E12_ftag_EMX2_pos1

description: Protocol 1


title: H27me3_E12_ftag_PAX6_neg1

description: Protocol 1


title: H27me3_E12_ftag_PAX6_pos2

description: Protocol 1


title: H-cleft palate only-ctrl

city: Lanzhou

first: Baoping

address: Donggang 199

department: School of Stomatology

institute: Lanzhou University

hyb_protocol: Kit and Instruments:Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):10X Blocking Agent, 25X Fragmentation Buffer, 2x GEx Hybridization Buffer HI-RPM, Hybridization Chamber, stainless (Agilent p/n G2534A), Hybridization Chamber gasket slides (Agilent p/n G2534-60003), Hybridization oven (Agilent p/n G2545A), Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029).  Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube according to manu  4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: Instrument:Agilent Microarray Scanner (Agilent p/n G2565BA)  Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Software:Agilent Feature Extraction  Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: normal tissue of the patient of cleft palate only

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from tissues was extracted by TRIzol® reagent (10296028, Thermo Fisher Scientific, Inc.) based on manufacturer's instructions. The quality and quantity of RNA were evaluated via a NanoDrop (ND-1000, Implen, Inc., Westlake Village, CA, USA). RNA integrity was evaluated using a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Fresh tissue excised from the trimmed wound edge was reserved to serve as experimental samples, and frozen at -80 °C with RNAlater® Stabilization Solution (AM7021, Thermo Fisher Scientific, Inc., USA)

value: tissue

value: 14 months


title: L-cleft lip with cleft palate-ctrl

source_name: normal tissue of the patient of cleft lip with cleft palate

value: 7 months


title: H-cleft palate only

source_name: tissues of the patient of cleft palate only


title: L-cleft lip with cleft palate

source_name: tissues of the patient of cleft lip with cleft palate


title: T- left lip without cleft palate

source_name: tissues of the patient of left lip without cleft palate

value: 6 months


title: T-cleft lip without cleft palate-ctrl

source_name: normal tissue of the patient of left lip without cleft palate


title: RPI29 85s


title: H27me3_E12_ftag_EMX2_neg1

description: Protocol 1

value: Cortex


title: H27me3_E12_ftag_EMX2_pos2

description: Protocol 1


title: RPI29 90s


title: H27me3_E12_ftag_CTF1_pos1

description: Protocol 1


title: RPI29 88s


title: RPI29 86s


title: RPI29 83s


title: RPI29 81s


title: RPI29 87s


title: H27me3_E12_ftag_CTF1_pos2

description: Protocol 1


title: RPI29 84s


title: H27me3_E12_ftag_EMX2_neg2

description: Protocol 1


title: RPI29 80s


title: RPI29 75s


title: H27me3_E12_ftag_CTF1_neg2

description: Protocol 1


title: RPI29 77s


title: H27ac_E12_ftag_PAX6_neg

description: Protocol 1


title: RPI29 79s


title: RPI29 89s


title: H27ac_E12_ftag_CTF1_neg2

description: Protocol 1


title: H27ac_E12_ftag_CTF1_pos1

description: Protocol 1


title: RPI29 74s


title: H27me3_E12_ftag_CTF1_neg1

description: Protocol 1


title: RPI29 7s


title: H27ac_E12_ftag_CTF1_pos2

description: Protocol 1


title: RPI29 78s


title: H27ac_E12_ftag_EMX2_neg1

description: Protocol 1


title: H27ac_E12_ftag_EMX2_pos2

description: Protocol 1


title: H27ac_E12_ftag_PAX6_pos2

description: Protocol 1


title: H27ac_E12_ftag_EMX2_pos1

description: Protocol 1


title: RPI29 72s


title: RPI29 73s


title: RPI29 76s


title: RPI29 82s


title: H27ac_E12_ftag_PAX6_pos1

description: Protocol 1


title: H27ac_E12_ftag_CTF1_neg1

description: Protocol 1


title: H27ac_E12_ftag_EMX2_neg2

description: Protocol 1


title: RPI29 71s


title: Atac_E12_ftag_PAX6_pos1

description: Protocol 1

value: ATACseq


title: Atac_E12_ftag_PAX6_neg3

description: Protocol 1


title: RPI29 69s


title: RPI29 6s


title: RPI29 70s


title: RPI29 68s


title: RPI29 67s


title: RPI29 64s


title: RPI29 62s


title: Atac_E12_ftag_CTF1_neg1

description: Protocol 1


title: RPI29 60s


title: B6xSPRET_hum_spret_H3K4me3_input_rep2

data_processing:
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm (described in Davies et al Nature 2016). R code available at https://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al Science 2019)
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al Science 2019)
Genome_build: mm10
Supplementary_files_format_and_content: text file with column descriptions in commented header; each line corresponds to one hotspot

source_name: whole adult testis

extract_protocol:
Testes samples were stripped of the tunica and processed as described in Khil et al, Genome Research, 2012). Single-stranded DNA sequencing and double-strand break detection were performed using a modified ssDNA ChIPseq protocol. Full experimental procedures are reported in accompanying manuscript (Davies et al).
Libraries were prepared according to Illumina's instructions

value: testis

tag: prdm9 genotype

value: HUM/SPRETUS


title: Atac_E12_ftag_EMX2_neg1

description: Protocol 1


title: Atac_E12_ftag_EMX2_pos2

description: Protocol 1


title: Atac_E12_ftag_PAX6_neg2

description: Protocol 1


title: Atac_E12_ftag_CTF1_pos2

description: Protocol 1


title: RPI29 63s


title: Atac_E12_ftag_EMX2_pos1

description: Protocol 1


title: B6xSPRET_hum_spret_H3K4me3_input_rep1b


title: Atac_E12_ftag_PAX6_neg1

description: Protocol 1


title: RPI29 59s


title: RPI29 65s


title: Atac_E12_ftag_CTF1_neg2

description: Protocol 1


title: Atac_E12_ftag_CTF1_pos1

description: Protocol 1


title: B6xSPRET_hum_spret_H3K4me3_ChIPseq_rep1b


title: RPI29 61s


title: WSB/EiJ m HFD BXD-012014

city: Lausanne

first: Jean-David

middle: Horacio

last: Morel

state: Vaud

address: Station 15

department: SV/IBI

country: Switzerland

institute: Ecole Ploytechnique Fédérale de Lausanne

description:
Liver from WSB/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012014

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
A threshold of BH-corrected false discovery rate smaller than 0.05 was considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: rnm10
Supplementary_files_format_and_content: tab-delimited text file includes mapped read counts per feature, normalized with the TMM (Trimmed Mean of M-values) method (generated by STAR - per strand and combined strands)

source_name: Liver

growth_protocol: Mouse strains were imported from Charles River and bred at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for more than two generations before incorporation into the study. We examined 15 cohorts of 9 mouse inbred strains fed a CD or HFD separated into two groups of five mice (3 for RNAseq) for each diet. Strains were entered into the phenotyping program randomly and had staggered entry, typically by 1 or 2 weeks. HFD feeding started at 8 weeks of age. CD is Harlan 2018 (6% kCal of fat, 20% kCal of protein, and 74% kCal of carbohydrates), and HFD is Harlan 06414 (60% kCal of fat, 20% kCal of protein, and 20% kCal of carbohydrates). All mice were housed under 12 hours of light alternated with 12 hours of dark, with ad libitum access to food and water at all times. Body weight was measured weekly from 8 weeks of age until killing. The sacrifices took place from 8:30 a.m. until 10:30 a.m., with isoflurane anesthesia followed by a complete blood draw (~1 mL) from the vena cava, followed by perfusion with phosphate-buffered saline, followed immediately by collection of the liver. Gallbladders were removed, and the livers were cut into small pieces before freezing in liquid nitrogen until preparation into mRNA, protein, or metabolite samples. Livers were then stored at –80°C until analysis. All research was approved by the Swiss cantonal veterinary authorities of Vaud under licenses 2257.2.

extract_protocol:
Liver tissue were crushed in liquid nitrogen and then 10 mg of tissues were suspended in TRIzol (Invitrogen) and homogenized with stainless steel beads using a TissueLyser II (Qiagen) at 30 Hz for 2 min. RNA was extracted and purified using Direct-zol-96 RNA kits (Zymo Research). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: Mice received no treatments in this study.

value: WSB/EiJ

tag: Sex

value: m

tag: age (weeks)

tag: diet

value: HFD


title: RPI29 54s


title: RPI29 5s


title: B6xSPRET_cast_spret_H3K4me3_input_rep2

value: CAST/SPRETUS


title: B6xSPRET_hum_spret_H3K4me3_input_rep1


title: RPI29 66s


title: B6xSPRET_H3K4me3_input_rep2


title: RPI29 53s


title: WSB/EiJ f CD BXD-011375

description:
Liver from WSB/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-011375

value: f

value: CD


title: WSB/EiJ m HFD BXD-012010

description:
Liver from WSB/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012010


title: RPI29 52s


title: WSB/EiJ f CD BXD-011372

description:
Liver from WSB/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-011372


title: WSB/EiJ m CD BXD-010949

description:
Liver from WSB/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-010949


title: WSB/EiJ f CD BXD-011371

description:
Liver from WSB/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-011371


title: WSB/EiJ m HFD BXD-012011

description:
Liver from WSB/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012011


title: B6xSPRET_hum_spret_H3K4me3_ChIPseq_rep2


title: Atac_E12_ftag_EMX2_neg2

description: Protocol 1


title: B6xSPRET_hum_spret_H3K4me3_ChIPseq_rep1


title: RPI29 51s


title: RPI29 56s


title: B6xSPRET_H3K4me3_input_rep1


title: WSB/EiJ m CD BXD-010948

description:
Liver from WSB/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-010948


title: RPI29 57s


title: RPI29 55s


title: B6xSPRET_cast_spret_H3K4me3_input_rep1


title: RPI29 58s


title: WSB/EiJ f HFD BXD-010944

description:
Liver from WSB/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010944


title: WSB/EiJ f HFD BXD-010942

description:
Liver from WSB/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010942


title: WSB/EiJ m CD BXD-010950

description:
Liver from WSB/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-010950


title: B6xSPRET_H3K4me3_ChIPseq_rep1


title: WSB/EiJ f HFD BXD-010940

description:
Liver from WSB/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010940


title: PWK/PhJ m CD BXD-011029

description:
Liver from PWK/PhJ male mice fed a chow diet from 8 to 21 weeks
BXD-011029

value: PWK/PhJ


title: PWK/PhJ m HFD BXD-010976

description:
Liver from PWK/PhJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010976


title: RPI29 50s


title: WT

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

data_processing:
Library strategy: Ribo-seq (ribosome profiling)
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using bowtie (1.2.2), parameters: -l 16 -n 1 -e 50 -m 1—strata—best y
Read counting using HTSeq, version 0.9.1
Genome_build: Mus Musculus Ensemble build GRCm38
Supplementary_files_format_and_content: Unique read counts per gene per kilobase and million mapped reads RPKM

source_name: Wild Type_mouse spinal cord

extract_protocol:
Spinal cord of three heterozygous GarsC201R/+ or three wildtype mice, flash frozen and immediately lysed by grinding in 10mM Tris-HCL pH 7.4, 5mM MgCl2, 100mM KCL, 1% NP-40, 2% sodium deoxycholate.The lysates from three animals each were pooled.
Isolation of mRNA-bound ribosome complexes, RNase I digestion-derived ribosome-protected fragments (RPFs), RNA-size selection and generation of the cDNA libraries was performed as described (Guo et al, 2010; doi: 10.1038/nature09267 )

value: spinal cord

value: WT


title: PWK/PhJ m CD BXD-011025

description:
Liver from PWK/PhJ male mice fed a chow diet from 8 to 21 weeks
BXD-011025


title: B6xSPRET_cast_spret_H3K4me3_ChIPseq_rep2

city: Oxford

first: Anjali

institute: Oxford University


title: PWK/PhJ f CD BXD-010434

description:
Liver from PWK/PhJ female mice fed a chow diet from 8 to 21 weeks
BXD-010434


title: RPI29 44s

value: anther


title: B6xSPRET_cast_spret_H3K4me3_ChIPseq_rep1


title: RPI29 4s


title: RPI29 49s


title: HET

source_name: Heterezygous GarsC201R/+  mouse spinal cord


title: PWK/PhJ m CD BXD-011052

description:
Liver from PWK/PhJ male mice fed a chow diet from 8 to 21 weeks
BXD-011052


title: RPI29 48s


title: RPI29 42s


title: PWK/PhJ f HFD BXD-010122

description:
Liver from PWK/PhJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010122


title: RPI29 47s


title: 48hpa_ctrl

city: Bethesda

first: Jason

last: Sinclair

state: MD

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

description: mRNA

data_processing:
Binary Base Call (BCL) files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 (10x Genomics).
Cell Ranger Version 3.0.2. was used to demultiplex, for barcode processing, for single cell gene counts, and aggregating files.
Further analyses of the samples was performed using Loupe Cell Browser (10x Genomics).
Genome_build: Danio_Rerio_11 (danRer11, GRCz11)
Supplementary_files_format_and_content: cloupe files are provided which can be visualized with the Loupe Cell Browser (10x Genomics).
Supplementary_files_format_and_content: hd5 files.

organism: Danio rerio

source_name: Regenerating embryonic zebrafish tail

extract_protocol:
Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase.
cDNA libraries were generated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics).

value: Regenerating embryonic tail

tag: embryo age

value: 5 days post-fertilization

tag: treatment

tag: time point


title: NZO/HlLtJ m HFD BXD-012761

description:
Liver from NZO/HlLtJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012761

value: NZO/HlLtJ


title: PWK/PhJ m HFD BXD-010975

description:
Liver from PWK/PhJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010975


title: PWK/PhJ m HFD BXD-010968

description:
Liver from PWK/PhJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010968


title: B6xSPRET_H3K4me3_ChIPseq_rep2

last: Hinch

address: Roosevelt Drive


title: RPI29 43s


title: PWK/PhJ f CD BXD-010283

description:
Liver from PWK/PhJ female mice fed a chow diet from 8 to 21 weeks
BXD-010283


title: PWK/PhJ f CD BXD-010433

description:
Liver from PWK/PhJ female mice fed a chow diet from 8 to 21 weeks
BXD-010433


title: RPI29 40s


title: NZO/HlLtJ m CD BXD-012210

description:
Liver from NZO/HlLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-012210


title: NZO/HlLtJ f HFD BXD-012203

description:
Liver from NZO/HlLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012203


title: PWK/PhJ f HFD BXD-010126

description:
Liver from PWK/PhJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010126


title: PWK/PhJ f HFD BXD-010125

description:
Liver from PWK/PhJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010125


title: 48hpa_2DG

description: mRNA

value: 100 mM 2-deoxyglucose


title: RPI29 3s


title: NZO/HlLtJ m CD BXD-012212

description:
Liver from NZO/HlLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-012212


title: RPI29 41s


title: NZO/HlLtJ f HFD BXD-012158

description:
Liver from NZO/HlLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012158


title: NZO/HlLtJ f HFD BXD-012201

description:
Liver from NZO/HlLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012201


title: RPI29 39s


title: NZO/HlLtJ m CD BXD-012156

description:
Liver from NZO/HlLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-012156


title: 24hpa_ctrl

description: mRNA

value: 4 days post-fertilization


title: 24hpa_2DG

description: mRNA


title: NZO/HlLtJ f CD BXD-012052

description:
Liver from NZO/HlLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-012052


title: NZO/HlLtJ f CD BXD-012053

description:
Liver from NZO/HlLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-012053


title: RPI29 38s


title: NOD/ShiLtJ f HFD BXD-012801

description:
Liver from NOD/ShiLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012801

value: NOD/ShiLtJ


title: NOD/ShiLtJ f HFD BXD-012804

description:
Liver from NOD/ShiLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012804


title: NZO/HlLtJ f CD BXD-012051

description:
Liver from NZO/HlLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-012051


title: NOD/ShiLtJ f HFD BXD-012802

description:
Liver from NOD/ShiLtJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-012802


title: RPI29 36s


title: RPI29 35s


title: RPI29 34s


title: NOD/ShiLtJ m HFD BXD-011434

description:
Liver from NOD/ShiLtJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011434


title: NOD/ShiLtJ m CD BXD-011717

description:
Liver from NOD/ShiLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-011717


title: RPI29 33s


title: L3

city: Shanghai

first: Tiansheng

last: Xu

address: No. 138 Xinjunhuan Road

institute: OE

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: HepG2.2.15 cell

label_protocol: standard Agilent protocol

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer's standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

value: liver


title: L2


title: NOD/ShiLtJ f CD BXD-011431

description:
Liver from NOD/ShiLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-011431


title: NOD/ShiLtJ m HFD BXD-011426

description:
Liver from NOD/ShiLtJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011426


title: NOD/ShiLtJ m HFD BXD-011425

description:
Liver from NOD/ShiLtJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011425


title: L1


title: RPI29 37s


title: T3


title: NOD/ShiLtJ f CD BXD-010391

description:
Liver from NOD/ShiLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-010391


title: T1


title: NOD/ShiLtJ f CD BXD-010393

description:
Liver from NOD/ShiLtJ female mice fed a chow diet from 8 to 21 weeks
BXD-010393


title: T2


title: RPI29 32s


title: CAST/EiJ m HFD BXD-012091

description:
Liver from CAST/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012091

value: CAST/EiJ


title: NOD/ShiLtJ m CD BXD-011718

description:
Liver from NOD/ShiLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-011718

value: m


title: NOD/ShiLtJ m CD BXD-011720

description:
Liver from NOD/ShiLtJ male mice fed a chow diet from 8 to 21 weeks
BXD-011720


title: RPI29 31s


title: C3


title: CAST/EiJ m HFD BXD-012090

description:
Liver from CAST/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012090

value: HFD


title: Donor_fibroblast_cell_mCG_rep2

city: Boston

first: Wenhao

last: Zhang

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

data_processing:
genome build: rheMac8
Adaptors were firstly trimmed by Trim Galore with parameters --illumina. Adaptor trimmed reads were mapped to rheMac8 using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Duplicated reads were removed using Picard MarkDuplicates and methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For calculating of 5mC levels at base resolution, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC levels for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on this CpG site.
Tab-delimited text files for bisulfite-seq including the average mCG level in single base

organism: Macaca mulatta

source_name: Fibroblast

extract_protocol: The extracted DNA was mixed with lambda DNA (1:200) and sonicated into an average of 300 bp fragments using Covaris (M220). Sonicated DNA fragments were added by T4 DNA Ligase Buffer (Thermo Scientific), dNTP (10 mM), ATP (10 mM) and END Repair Enzyme Mix, and incubated at room temperature for 1 hour. Then, DNA was purified and added by Klenow Buffer, dATP and Klenow exo- enzyme and incubated at 37°C for 30 minutes. DNA was then purified and added by Quick Ligase Buffer (NEB), Quick Ligase (NEB) and Methylated Adaptors for Illumina Sequencing (Synthesized with all cytosines methylated) and incubated at room temperature for 3 hours. Then, ligated DNA was purified and subjected to sodium bisulfite conversion using the Zymo EZ DNA Methylation-Direct Kit (Zymo Research) following the manufacturer’s instruction. Finally, bisulfite converted fragments were PCR amplified using KAPA HiFi Uracil+ Kit following manufacturer’s instruction and the libraries were purified and sequenced.

tag: chip-antibody


title: CAST/EiJ m HFD BXD-012044

description:
Liver from CAST/EiJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-012044


title: C2

tag: tissue


title: CAST/EiJ m CD BXD-011960

description:
Liver from CAST/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-011960


title: RPI29 30s


title: CAST/EiJ m CD BXD-011923

description:
Liver from CAST/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-011923


title: CAST/EiJ m CD BXD-011924

description:
Liver from CAST/EiJ male mice fed a chow diet from 8 to 21 weeks
BXD-011924


title: RPI29 2s


title: CAST/EiJ f HFD BXD-011197

description:
Liver from CAST/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011197


title: RheMac_WT_Placenta_RNA

data_processing:
genome build: rheMac8
Adaptors were firstly trimmed by Trim Galore with parameters --illumina --paired. Adaptor trimmed reads were mapped to rheMac8 using TopHat (v2.1.1) with parameter -p 2 -g 1 --no-coverage-search. Then, expression values represented by Fragments per Kilobase per Million (FPKM) of the protein-coding genes were calculated by Cufflinks (v2.2.1) based on annotations from Ensembl database.
Tab-delimited text files for RNA seq including FPKM values for each gene

source_name: Placenta

extract_protocol: The mRNA was purified from total RNA using oligo-dT attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer. Then, the first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (NEB). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease and polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. USER Enzyme (NEB) was used to release the looped adaptors. Then the adaptor-ligated DNA was amplified with Phusion High-Fidelity DNA polymerase and purified for sequencing.

tag: genotype


title: RheMac_SCNT_Placenta_RNA

value: SCNT


title: RPI29 29s


title: RheMac_SCNT_Placenta_mCG

data_processing:
genome build: rheMac8
Adaptors were firstly trimmed by Trim Galore with parameters --illumina. Adaptor trimmed reads were mapped to rheMac8 using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Duplicated reads were removed using Picard MarkDuplicates and methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For calculating of 5mC levels at base resolution, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC levels for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on this CpG site.
Tab-delimited text files for bisulfite-seq including the average mCG level in 200bp bins.


title: CAST/EiJ f CD BXD-009846

description:
Liver from CAST/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-009846

value: f


title: Donor_fibroblast_cell_mCG_rep1


title: RPI29 28s


title: CAST/EiJ f HFD BXD-011194

description:
Liver from CAST/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011194


title: C1


title: A/J f HFD BXD-010592

description:
Liver from A/J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010592

value: A/J


title: A/J f HFD BXD-010591

description:
Liver from A/J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010591


title: RPI29 26s


title: A/J f HFD BXD-010597

description:
Liver from A/J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-010597


title: CAST/EiJ f HFD BXD-011196

description:
Liver from CAST/EiJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011196


title: A/J m HFD BXD-010579

description:
Liver from A/J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010579


title: RPI29 22s


title: A/J f CD BXD-010399

description:
Liver from A/J female mice fed a chow diet from 8 to 21 weeks
BXD-010399

value: CD


title: A/J f CD BXD-010400

description:
Liver from A/J female mice fed a chow diet from 8 to 21 weeks
BXD-010400


title: A/J m CD BXD-009775

description:
Liver from A/J male mice fed a chow diet from 8 to 21 weeks
BXD-009775


title: A/J m HFD BXD-010586

description:
Liver from A/J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010586


title: A/J m HFD BXD-010585

description:
Liver from A/J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-010585


title: RPI29 24s


title: CAST/EiJ f CD BXD-009845

description:
Liver from CAST/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-009845


title: A/J m CD BXD-009771

description:
Liver from A/J male mice fed a chow diet from 8 to 21 weeks
BXD-009771


title: RPI29 27s


title: RPI29 23s


title: RPI29 20s


title: RPI29 21s


title: RheMac_WT_Placenta_mCG


title: RPI29 18s


title: A/J m CD BXD-009773

description:
Liver from A/J male mice fed a chow diet from 8 to 21 weeks
BXD-009773


title: 129S1/SvImJ f CD BXD-011073

description:
Liver from 129S1/SvImJ female mice fed a chow diet from 8 to 21 weeks
BXD-011073


title: 129S1/SvImJ m CD BXD-010573

description:
Liver from 129S1/SvImJ male mice fed a chow diet from 8 to 21 weeks
BXD-010573


title: 129S1/SvImJ f HFD BXD-011750

description:
Liver from 129S1/SvImJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011750


title: RPI29 19s


title: CAST/EiJ f CD BXD-009842

description:
Liver from CAST/EiJ female mice fed a chow diet from 8 to 21 weeks
BXD-009842


title: 129S1/SvImJ f HFD BXD-011747

description:
Liver from 129S1/SvImJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011747


title: RPI29 1s


title: 129S1/SvImJ m HFD BXD-009938

description:
Liver from 129S1/SvImJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-009938


title: 129S1/SvImJ f CD BXD-011082

description:
Liver from 129S1/SvImJ female mice fed a chow diet from 8 to 21 weeks
BXD-011082


title: 129S1/SvImJ m HFD BXD-009936

description:
Liver from 129S1/SvImJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-009936


title: A/J f CD BXD-010401

description:
Liver from A/J female mice fed a chow diet from 8 to 21 weeks
BXD-010401


title: 129S1/SvImJ f HFD BXD-011746

description:
Liver from 129S1/SvImJ female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011746


title: 129S1/SvImJ f CD BXD-011078

description:
Liver from 129S1/SvImJ female mice fed a chow diet from 8 to 21 weeks
BXD-011078


title: 129S1/SvImJ m CD BXD-010571

description:
Liver from 129S1/SvImJ male mice fed a chow diet from 8 to 21 weeks
BXD-010571


title: RPI29 17s


title: DBA/2J f CD BXD-011970

description:
Liver from DBA/2J female mice fed a chow diet from 8 to 21 weeks
BXD-011970


title: DBA/2J m CD BXD-011867

description:
Liver from DBA/2J male mice fed a chow diet from 8 to 21 weeks
BXD-011867


title: 129S1/SvImJ m CD BXD-010569

description:
Liver from 129S1/SvImJ male mice fed a chow diet from 8 to 21 weeks
BXD-010569


title: RPI29 12s


title: RPI29 15s


title: RPI29 16s


title: RPI29 14s


title: DBA/2J f CD BXD-011981

description:
Liver from DBA/2J female mice fed a chow diet from 8 to 21 weeks
BXD-011981


title: 129S1/SvImJ m HFD BXD-009943

description:
Liver from 129S1/SvImJ male mice fed a high-fat-diet from 8 to 21 weeks
BXD-009943


title: DBA/2J m CD BXD-011864

description:
Liver from DBA/2J male mice fed a chow diet from 8 to 21 weeks
BXD-011864


title: RPI29 11s


title: DBA/2J f HFD BXD-011755

description:
Liver from DBA/2J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011755


title: RPI29 13s


title: DBA/2J f CD BXD-011980

description:
Liver from DBA/2J female mice fed a chow diet from 8 to 21 weeks
BXD-011980


title: DBA/2J m CD BXD-011868

description:
Liver from DBA/2J male mice fed a chow diet from 8 to 21 weeks
BXD-011868


title: DBA/2J f HFD BXD-011752

description:
Liver from DBA/2J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011752


title: DBA/2J f HFD BXD-011751

description:
Liver from DBA/2J female mice fed a high-fat-diet from 8 to 21 weeks
BXD-011751


title: RPI29 10s


title: DBA/2J m HFD BXD-011220

description:
Liver from DBA/2J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011220


title: DBA/2J m HFD BXD-011225

description:
Liver from DBA/2J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011225


title: RPI28 9s


title: DBA/2J m HFD BXD-011219

description:
Liver from DBA/2J male mice fed a high-fat-diet from 8 to 21 weeks
BXD-011219


title: C57BL/6J f CD LIM-J17736

description:
Liver from C57BL/6J female mice fed a chow diet from 8 to 21 weeks
LIM-J17736


title: RPI28 95s


title: RPI28 94s


title: C57BL/6J f CD LIM-J17735

description:
Liver from C57BL/6J female mice fed a chow diet from 8 to 21 weeks
LIM-J17735


title: RPI28 92s


title: C57BL/6J m HFD LIM-J17556

description:
Liver from C57BL/6J male mice fed a high-fat-diet from 8 to 21 weeks
LIM-J17556


title: C57BL/6J m HFD LIM-J17543

description:
Liver from C57BL/6J male mice fed a high-fat-diet from 8 to 21 weeks
LIM-J17543


title: C57BL/6J m HFD LIM-J17544

description:
Liver from C57BL/6J male mice fed a high-fat-diet from 8 to 21 weeks
LIM-J17544


title: C57BL/6J f HFD LIM-J16811

description:
Liver from C57BL/6J female mice fed a high-fat-diet from 8 to 21 weeks
LIM-J16811


title: C57BL/6J f HFD LIM-J16807

description:
Liver from C57BL/6J female mice fed a high-fat-diet from 8 to 21 weeks
LIM-J16807


title: C57BL/6J f HFD LIM-J16808

description:
Liver from C57BL/6J female mice fed a high-fat-diet from 8 to 21 weeks
LIM-J16808


title: C57BL/6J m CD LIM-J16802

description:
Liver from C57BL/6J male mice fed a chow diet from 8 to 21 weeks
LIM-J16802


title: C57BL/6J m CD LIM-J16801

description:
Liver from C57BL/6J male mice fed a chow diet from 8 to 21 weeks
LIM-J16801


title: Monkey_Intestine_mCG

data_processing:
genome build: macFas5
For PBAT libraries, the paired-end sequenced reads were mixed and processed as single-end sequenced reads. Adaptors were firstly trimmed by Trim Galore with parameters --dont_gzip --clip_R1 9 --three_prime_clip_R1 9. Adaptor trimmed reads were mapped to macFas5 using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Duplicated reads were removed using Picard MarkDuplicates and methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For calculating of 5mC levels at base resolution, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC levels for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on this CpG site.
Tab-delimited text files for bisulfite-seq including the average mCG level in 200bp bins.

organism: Macaca fascicularis

source_name: Small intestine

extract_protocol: The methylome extraction is majorly based on post-bisulfite adaptor tagging (PBAT). DNA from tissues are extracted by phenol/chloroform/isoamylalcohol followed by isopropanol precipitation. Then extracted DNA was mixed with lambda DNA (1:200) and subjected to sodium bisulfite conversion using the Zymo EZ DNA Methylation-Direct Kit (Zymo Research) following the manufacturer’s instruction. The eluted bisulfite-converted DNA was then subject to preamplification by Klenow exo- with adaptor-marked oligos on both strands. Then, the double-tagged DNA was purified by SPRIbeads and amplified using KAPA HiFi Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Multiplex Oligos for Illumina (New England BioLabs).

value: Small intestine


title: RPI28 89s


title: RPI28 90s


title: RPI28 8s


title: C57BL/6J m CD LIM-J16800

description:
Liver from C57BL/6J male mice fed a chow diet from 8 to 21 weeks
LIM-J16800


title: Monkey_Placenta_mCG

data_processing:
genome build: macFas5
Adaptors were firstly trimmed by Trim Galore with parameters --illumina. Adaptor trimmed reads were mapped to macFas5 using Bismark (v0.20.0) using parameters --fastq -L 30 -N 1 --non_directional. Duplicated reads were removed using Picard MarkDuplicates and methylated CpGs were interpreted by bismark_methylation_extractor with parameters -s --no_overlap --report --bedGraph. For calculating of 5mC levels at base resolution, a cutoff of minimal 3× coverage was required for each CpG site. The 5mC levels for certain CpG was calculated using the number of methylated CpGs to divide the number of total CpGs detected on this CpG site.
Tab-delimited text files for bisulfite-seq including the average mCG level in 200bp bins.

value: Placenta


title: RPI28 88s

value: anther


title: Monkey_Heart_mCG

source_name: Heart

value: Heart


title: Monkey_Cerebellum_mCG

source_name: Cerebellum

value: Cerebellum


title: Monkey_Cortex_mCG

source_name: Cortex

value: Cortex


title: Monkey_Liver_mCG

value: Liver


title: RPI28 93s

source_name: isolated maize anther cell


title: Monkey_16cell_PG_mCG

source_name: Parthenogenetic 16-cell embryos

extract_protocol: The methylome extraction is majorly based on post-bisulfite adaptor tagging (PBAT). Early embryos were pre-treated by lysed in Buffer RLT Plus (Qiagen). Then lysed embryos were mixed with lambda DNA (1:200) and subjected to sodium bisulfite conversion using the Zymo EZ DNA Methylation-Direct Kit (Zymo Research) following the manufacturer’s instruction. The eluted bisulfite-converted DNA was then subject to preamplification by Klenow exo- with adaptor-marked oligos on both strands. Then, the double-tagged DNA was purified by SPRIbeads and amplified using KAPA HiFi Uracil+ ReadyMix (Kapa Biosystems) and NEBNext Multiplex Oligos for Illumina (New England BioLabs).

tag: developmental stage

value: Parthenogenetic 16-cell embryos


title: RPI28 91s


title: RPI28 87s


title: RPI28 84s


title: Monkey_16cell_AG_mCG

source_name: Androgenetic 16-cell embryos

value: Androgenetic 16-cell embryos


title: RPI28 85s


title: Monkey_Kidney_mCG

source_name: Kidney

value: Kidney


title: RPI28 81s


title: Monkey_blast_ICSI_H3K27me3_rep2

data_processing:
genome build: macFas5
Adaptors were firstly trimmed by Trim Galore with parameters --illumina --paired. Libraries were sequenced in paired-end manner and adaptor trimmed reads were mapped to macFas5 using Bowtie2 (v2.3.4.1) with parameters -t -q -p 4 -N 1 -L 25 -X 2000 --no-mixed --no-discordant. Duplicated reads were removed using Picard MarkDuplicates and the remaining paired-end reads with inserted fragments over 150 bp were kept for further analysis. For calculating H3K27me3 enrichment, the whole genome was divided into bins with 100 bp length. The values represented by Reads per Kilobase per Million (RPKM) was then calculated in each bin.
Tab-delimited bed files including number of reads in 100bp bin in the genome for each ChIP-seq sample

source_name: Blastocyst

extract_protocol: H3K27me3 profling in early embryos are majorly based on a previously reported method cleavage under targests and release using nuclease (CUT&RUN). Briefly, several embryos containing total 200 ~ 300 cells were combined and transferred in a 1.5-ml tube containing 50 ul wash buffer. The embryos were then captured with BioMagPlus Concanavalin A, and incubated with a rabbit anti-H3K27me3 antibody for 16 hours at 4°C. After unbound antibodies were washed away, protein A-MNase was added and incubated for 3 hours at 4°C. After washes, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, and the reaction was carried out for 20 min at 4°C and then stopped by addition of STOP buffer. The protein-DNA complexes were released by 10 min incubation at 37°C followed by centrifugation for 5 min at 16,000 g at 4°C. After transferring the supernatant to a new Lo-bound tube, SDS and Proteinase K were added and incubated at 55°C for at least 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen, and then dissolved in water. The purified DNA was prepared into library for sequencing using NEBNext UltraTM II DNA Libarary Prep Kit for Illumina according to manufacturer’s instructions.

value: Blastocyst

tag: chip antibody

value: Diagenode, C15410069


title: Monkey_blast_ICSI_H3K27me3_rep1


title: RPI28 83s


title: Monkey_16cell_ICSI_H3K27me3_rep1

source_name: 16-cell embryos

value: 16-cell embryos


title: Monkey_16cell_ICSI_H3K27me3_rep2


title: Monkey_16cell_PG_H3K27me3


title: Monkey_16cell_AG_H3K27me3


title: Monkey_16cell_PG_RNA_rep3

data_processing:
genome build: macFas5
Adaptors were firstly trimmed by Trim Galore with parameters --illumina --paired. Adaptor trimmed reads were mapped to macFas5 using TopHat (v2.1.1) with parameter -p 2 -g 1 --no-coverage-search. Then, expression values represented by Fragments per Kilobase per Million (FPKM) of the protein-coding genes were calculated by Cufflinks (v2.2.1) based on annotations from Ensembl database.
Tab-delimited text files for RNA seq including FPKM values for each gene

extract_protocol: SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) was used and experiments were performed according to manufacturer’s instructions. Briefly, single embryo was incubated in lysis buffer with RNase Inhibitor on dry ice for 1 minutes, and then thawed at room temperature. First-Strand Buffer, SMART-Seq v4 Oligonucleotide, 3’ SMART-Seq CDS primer II and RNase Inhibitor was added into the lysed cells and incubated at 72°C for 3 minutes then put on ice immediately. Incubating was performed after adding SMARTScribe II Reverse Transcriptase as following: 42°C for 90 minutes then 70°C for 10 minutes. Without purification, SeqAmp PCR Buffer, PCR Primer II A and SeqAmp DNA Polymerase was added for pre-amplification using thermal cycler for 12 cycles following the manufacturer’s instruction. The amplified cDNA was then purified by 1.8× volume of SPRIselect beads and fragmented into an average of 200 bp by sonication using Covaris. Then, the cDNA was prepared into library for sequencing using  NEBNext UltraTM II DNA  Prep Kit for Illumina (NEB, E7103) according to manufacturer’s instruction.


title: C57BL/6J f CD LIM-J17744

description:
Liver from C57BL/6J female mice fed a chow diet from 8 to 21 weeks
LIM-J17744

source_name: Liver


title: RPI28 80s


title: Monkey_16cell_PG_RNA_rep4


title: Monkey_16cell_PG_RNA_rep1


title: Monkey_16cell_PG_RNA_rep2


title: RPI28 7s


title: RPI28 77s


title: RPI6 96s


title: RPI28 78s


title: Monkey_16cell_AG_RNA_rep3


title: RPI6 9s


title: RPI6 94s


title: RPI28 79s


title: RPI28 75s


title: RPI6 89s


title: RPI6 93s


title: RPI6 88s


title: RPI6 86s


title: RPI28 73s


title: RPI6 90s


title: RPI6 83s


title: RPI6 84s


title: Monkey_16cell_AG_RNA_rep4


title: RPI6 87s


title: RPI28 74s


title: RPI6 81s


title: Monkey_16cell_AG_RNA_rep1


title: RPI6 82s


title: Monkey_16cell_AG_RNA_rep2


title: RPI28 72s


title: RPI28 76s


title: RPI6 79s


title: RPI6 78s


title: RPI28 71s


title: RPI28 70s


title: RPI6 91s


title: RPI6 74s


title: RPI6 80s


title: RPI6 69s


title: RPI6 75s


title: RPI6 66s


title: RPI6 63s


title: RPI6 77s


title: RPI28 61s


title: RPI28 60s


title: RPI6 68s


title: RPI28 6s


title: RPI28 5s


title: RPI6 64s


title: RPI6 70s


title: RPI6 73s


title: RPI28 69s


title: RPI6 5s


title: RPI28 62s


title: RPI28 65s


title: RPI6 59s


title: RPI6 3s


title: RPI6 61s


title: RPI28 58s


title: RPI6 67s


title: RPI6 32s


title: RPI28 56s


title: RPI6 58s


title: RPI28 64s


title: RPI6 39s


title: RPI28 52s


title: RPI6 28s


title: RPI6 4s


title: RPI6 27s


title: RPI28 59s


title: RPI6 43s


title: RPI6 41s


title: RPI6 36s


title: RPI28 57s


title: RPI28 68s


title: RPI6 57s


title: RPI6 56s


title: RPI6 16s


title: RPI6 30s


title: RPI28 55s


title: RPI6 21s


title: RPI28 51s


title: RPI6 24s


title: RPI28 50s


title: RPI6 2s


title: RPI6 29s


title: RPI6 12s


title: RPI6 14s


title: RPI28 4s


title: RPI6 11s


title: RPI28 49s


title: RPI28 47s


title: RPI6 1s


title: RPI28 46s


title: RPI28 45s


title: RPI11 95s


title: RPI11 94s


title: RPI11 9s


title: RPI11 93s


title: RPI11 96s


title: RPI11 92s


title: RPI28 44s


title: RPI11 8s


title: RPI6 34s


title: RPI11 91s


title: RPI11 89s


title: RPI28 42s


title: RPI11 84s


title: RPI11 90s


title: RPI28 41s


title: RPI11 87s


title: RPI28 40s


title: RPI11 82s


title: RPI11 83s


title: RPI11 85s


title: RPI11 81s


title: RPI28 39s


title: RPI11 80s


title: RPI11 7s


title: RPI28 38s


title: RPI11 88s


title: RPI11 75s


title: RPI6 15s


title: RPI11 74s


title: RPI11 77s


title: RPI28 36s


title: RPI11 78s


title: RPI28 3s


title: RPI11 6s


title: RPI11 67s


title: RPI28 30s


title: RPI11 69s


title: RPI11 63s


title: RPI11 79s


title: RPI28 34s


title: RPI28 33s


title: RPI11 65s


title: RPI28 32s


title: RPI11 64s


title: RPI11 66s


title: RPI11 61s


title: RPI11 62s


title: RPI28 37s


title: RPI28 31s


title: RPI11 60s


title: RPI11 68s


title: RPI11 5s


title: RPI28 29s


title: RPI11 59s


title: RPI28 28s


title: RPI11 73s


title: RPI11 56s


title: RPI11 55s


title: RPI11 46s


title: RPI28 27s


title: RPI28 25s


title: RPI11 57s


title: RPI11 4s


title: RPI11 41s


title: RPI28 2s


title: RPI28 26s


title: RPI11 40s


title: RPI28 24s


title: RPI11 39s


title: RPI28 1s


title: RPI11 3s


title: RPI11 43s


title: RPI11 38s


title: RPI11 37s


title: RPI11 42s


title: RPI28 23s


title: RPI28 19s


title: RPI11 34s


title: RPI11 36s


title: RPI11 33s


title: RPI11 58s


title: RPI11 32s


title: RPI28 14s


title: RPI11 2s


title: RPI11 31s


title: RPI11 30s


title: RPI28 15s


title: RPI11 29s


title: RPI28 12s


title: RPI11 27s


title: RPI11 26s


title: RPI11 25s


title: RPI11 24s


title: RPI28 10s


title: RPI28 11s


title: RPI11 1s


title: RPI11 23s


title: Day6_Rab9_Rep4

city: Washington DC

first: Xiujie

last: Sun

state: DC

address: 2300 I ST NW, Room 433

institute: The George Washington University

data_processing:
Basecalls performed using Illuminal CASAVA software.
Reads were aligned to mm10 genome assembly using Tophat.
Differentially expressed genes were detected by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads counts for each Sample

source_name: E0771 mammary tumor

extract_protocol:
RNA was harvested using Trizol reagent. About 500 ng RNA was used for the construction of sequencing libraries.
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.

value: E0771 mammary tumor

value: hDDR1 ECD antibody treatment


title: Day6_Ctrl_Rep4

value: IgG treatment