title: L3 larvae brain RNA-seq: male wild-type; replicate 3

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_male_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_male_rep3


title: C. elegans L4 rep. 1

status: Public on Jun 04 2019

type: SRA

city: Berlin

first: Ivano

last: Legnini

state: Germany

address: Robert-Rössle-Straße 10, Haus 87

department: BIMSB

country: Germany

institute: MDC

library_source: transcriptomic

data_processing:
Library strategy: FLAM-seq
CCS reads were produced with the SMRT Link browser 5.0 (minimum full pass 3, minimum predicted accuracy 90)
Fastq files were analyzed according to the FLAM-seq analysis pipeline: reads were filtered for containing at least 10 As followed by 9 Gs (or the rev. comp.), then reoriented to start with the adapter sequence, the UMI, the G tail and the poly(A) tail. Poly(A) tails were detected and removed, the remaining reads were aligned to hg38 or C. elegans WB235 genome assemblies using STARLong (Dobin et al., 2013). Each aligned read was then assigned to gene models (Ensembl GRCh38.84 for human, WBcel235_82 for worm) with FeatureCounts (Liao et al., 2014).
Genome_build: H. sapiens: hg38, C. elegans: WB235
Supplementary_files_format_and_content: Processed data contain read name, gene to which read is assigned using FeatureCounts, unique molecular identifier sequence, tail length and tail sequence

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: C. elegans L4 stage

growth_protocol: Caenorhabditis elegans animals (wild-type N2 Bristol) were cultured on OP50 bacteria, synchronized by bleaching, seeded and grown at 20 °C.

extract_protocol:
All samples were collected in Trizol and poly(A)+ RNA was extracted with the Truseq mRNA preparation kit (RS-122-21-2, Illumina).
Libraries were constructed according to the FLAM-seq protocol.

tag: genotype/variation

value: wt N2 Bristol


title: XWGBS_GM12885

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
FASTQ reads were adapter asked using cutadapt v1.9.1 for bisulfite converted adapter sequences
Masked reads were aligned to hg38+decoy+EBV using bwa-meth v0.10 with default parameters
Aligned reads were marked for duplicates using Picard v2.4.1
A custom perl script was used to filter "fill-in" artifact be qc-fail flagging reads with 3 or more methylated CHH's outside the first 11 cycles
Methylation ratios were determined, by CpG, CHG, CHH context, using MethylDackel v0.1.13 with min baseQ >= 20, min mapQ >=20 and excluding the first 11bases of R1 and R2 alignments
Genome_build: GENCODE hg38 + decoy + EBV
Supplementary_files_format_and_content: Compressed methylKit files were generated which capture CpG CHG, CHH methylation and coverage (https://github.com/al2na/methylKit); meth_10_fil_no99.rds is a serliazed R object containing filtered CpG sites with >10 read depth

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Lymphoblatoid cell lines were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
2 million cells were pelleted at 2000g for 10' and frozen at -80C until extraction of DNA. Pellets were thawed and resspended in 10mM Tris pH 8.0, 150 mM EDTA solution before the addition of SDS to a final concentration of 1%. Protein was digested overnight at 50C with 25 ug of Proteinase K, followed by an hour incubation at 37C with 5 ug of RNAse A. Extraction of genomic DNA was then achieved through two consecutive phenol:chloroform steps, selecting the aqeous phase. The DNA was then concentrated and purified via ethanol precipitation.
100 ng of genomic DNA was treated with Tn5 transposase for tagmentation, then tagged DNA was filled with methylated dCTP, dATP, dGTP, dTTP mixture. The filled DNA was bisulphite treated using EZ DNA methylation Gold kit (Zymo research). The bisulphite treated samples were amplified with custom and Illumina index adapters. The amplified products were size selected using AMPureXP beads.

tag: cell line

tag: cell type

value: EBV-transformed lymphoblastoid cell line

tag: number of cells


title: DX_female_787

type: genomic

city: Beijing

first: Xuemei

last: Deng

state: N/A = Not Applicable

address: No.2, Yuan Ming Yuan West Road, Haidian District

department: Department of animal breeding and genetics

country: China

institute: China Agricultural University

description: Dongxiang blue-shelled chicken

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations,.

data_processing: The first-step quality control and genotype calling from the raw data in the form of CEL files were performed using Affymetrix Power Tools v1.16.0 (APT) software with the criterion of dish quality control (DQC) > 0.82 and call rate > 97%. The SNP genotype was calling using Axiom™ Analysis Suite.

label: RCL

organism: Gallus gallus

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Regular quarantine inspection of the experimental farm in China Agricultural University was conducted.

extract_protocol: The genomic DNA was extracted from blood samples using the avian blood DNA extraction kit (Tiangen Co., LTD., Beijing, China).. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: tissue

value: brachial veins

tag: Sex

value: female

tag: breed

value: Dongxiang blue-shelled


title: DX_female_2330

description: Dongxiang blue-shelled chicken


title: DX_female_768

description: Dongxiang blue-shelled chicken


title: DX_female_784

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: male wild-type; replicate 1

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_male_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_male_rep1

data_processing:
MAPCap reads were further demultiplexed using the barcodes present in R2 read. Barcodes and corresponding sample names are provided as MAPCap_embryo_barcodes.tsv and MAPCap_larvae_barcodes.tsv. No demultiplexing required for RNAseq
MAPCap: Paired-end FASTQ files were trimmed for adaptors using Trimmomatic 56 (v 0.3.7). Samples were de-multiplexed by icetea (v0.99, demultiplexFastq) using provided barcode information, and mapped to the dm6 genome using Rsubread 57 (v 1.22.3, mapping wrapper provided in icetea). For de-duplication, we consider all reads mapping to the same 5’-position and having the same random barcode as duplicates and only keep the first instance of each such alignment (using icetea - filterDuplicates). BigWigs were created using deepTools 58 (v3.0.2) bamCoverage and bamCompare, with the option `--offSet 1 --binSize 1`.
RNA-seq: data was processed using snakePipes RNA-seq pipeline 65 (v1.0.0 beta) using the options ` -m alignment,deepTools_qc --star_options  --limitBAMsortRAM 60000000000 --outBAMsortingBinsN 30 dm6`. snakePipes performed alignment using STAR 66 (v2.6.1a), counting of reads on Ensembl GTF (release 79) via featureCounts 67 (v1.6.1), and quality-checks via deepTools 58 (v3.1.2). The gene-level counts obtained from featureCounts were then used for differential expression analysis via DESeq2 68 (v1.20.0).
Pipeline for processing MAPCap data is available at: https://github.com/vivekbhr/cage_pipeline
Pipeline for processing RNAseq data is available at: https://github.com/maxplanck-ie/snakepipes
Genome_build: dm6
Supplementary_files_format_and_content: bw, featureCounts, DESeq2 output

molecule: total RNA

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Fruit flies (Drosophila melanogaster) were reared on standard cornflour-molasses medium. at 25°C, 70% relative humidity and 12 hrs dark/12 hrs light cycle. mle9, cn, bw/CyO flies  (BDSC #5873) have been ordered from the Bloomington Drosophila Stock Center (BDSC) and rebalanced with the help of w; CyO, Act5C-GFP/If to generate the w; mle9, cn, bw/CyO, Act5C-GFP flies used in this study.

extract_protocol:
RNA from embryos was extracted using the Quick RNA Kit (Zymo Research). RNA from dissected brains of larvae was isolated using the DirectZol Kit (Zymo Research). RNA was eluted in 25 ul of RNase-free water.
See our manuscript for full protocol of MAPCap library construction
MAPCap: custom strategy explained in the manuscript. RNAseq: Illumina TRUseq

tag: developmental stage

value: L3 larvae (3rd Instar)

tag: genotype

value: wild-type

value: male


title: XWGBS_GM12884


title: XWGBS_GM12886


title: L3 larvae brain RNA-seq: male MLE9 mutant; replicate 3

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_vs_male.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_female_rep3

value: MLE9 mutant


title: DX_female_1934

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12883


title: DX_female_1933

description: Dongxiang blue-shelled chicken


title: DX_female_800

description: Dongxiang blue-shelled chicken


title: DX_female_798

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: male MLE9 mutant; replicate 2

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_vs_male.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_female_rep2


title: XWGBS_GM12882


title: DX_female_2350

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12881


title: DX_female_1938

description: Dongxiang blue-shelled chicken


title: DX_female_1939

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: male MLE9 mutant; replicate 1

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_vs_male.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_wt_female_rep1


title: DX_female_1945

description: Dongxiang blue-shelled chicken


title: DX_female_1943

description: Dongxiang blue-shelled chicken


title: DX_female_1940

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: female wild-type; replicate 3

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_male_rep3


title: DX_female_1951

description: Dongxiang blue-shelled chicken


title: DX_female_1953

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12878


title: L3 larvae brain RNA-seq: female wild-type; replicate 2

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_male_rep2


title: DX_female_796

description: Dongxiang blue-shelled chicken


title: DX_female_1952

description: Dongxiang blue-shelled chicken


title: DX_female_1964

description: Dongxiang blue-shelled chicken


title: L3 larvae brain RNA-seq: female MLE9 mutant; replicate 2

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KO_vs_male_KO.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_female_rep2


title: DX_female_1966

description: Dongxiang blue-shelled chicken


title: XWGBS_GM12877


title: XWGBS_GM12880


title: L3 larvae brain RNA-seq: female MLE9 mutant; replicate 3

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KO_vs_male_KO.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_female_rep3


title: L3 larvae brain RNA-seq: female MLE9 mutant; replicate 1

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KO_vs_male_KO.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_female_rep1


title: DX_female_1968

description: Dongxiang blue-shelled chicken


title: DX_female_2382

description: Dongxiang blue-shelled chicken


title: DX_female_22649

description: Dongxiang blue-shelled chicken

label: RAL


title: L3 larvae brain MAPCap: male wild-type; replicate 3

description:
MAPCap experiment performed on 3rd instar larvae
MAPCap_J-larvae_male_WT.deduplicated.bw


title: L3 larvae brain RNA-seq: female wild-type; replicate 1

description:
RNAseq performed on brains extracted from L3 larvae.
RNAseq_DEseq2_female_KOvsWT.tsv; RNAseq_featureCounts.tsv
RNAseq_larvae_mle9_male_rep1


title: XWGBS_GM12879


title: L3 larvae brain MAPCap: male wild-type; replicate 2


title: DX_female_21860

description: Dongxiang blue-shelled chicken


title: DX_female_21883

description: Dongxiang blue-shelled chicken


title: Low_Furfural_LF9

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: Furfural treated isolates LF9

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain LF9

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25-1cells were plated on YPD plates containing 0.6 g/L furfural. After growth of 4 days, colonies were picked and treaked on YPD plates without furfural. Such two steps were repeated by 10 times.

tag: strain

value: JSC-derived LF9

source_name: cell culture of JSC24-2


title: DX_female_22676

description: Dongxiang blue-shelled chicken


title: Low_Furfural_LF7

description: Furfural treated isolates LF7

source_name: cell culture of strain LF7

value: JSC-derived LF7


title: L3 larvae brain MAPCap: male wild-type; replicate 1


title: L3 larvae brain MAPCap: male MLE9 mutant; replicate 3

description:
MAPCap experiment performed on 3rd instar larvae
MAPCap_J-larvae_male_MLE9.deduplicated.bw


title: DX_female_1962

description: Dongxiang blue-shelled chicken


title: Low_Furfural_LF8

description: Furfural treated isolates LF8

source_name: cell culture of strain LF8

value: JSC-derived LF8


title: DX_female_21909

description: Dongxiang blue-shelled chicken


title: L3 larvae brain MAPCap: male MLE9 mutant; replicate 1


title: DX_female_22063

description: Dongxiang blue-shelled chicken


title: DX_female_21922

description: Dongxiang blue-shelled chicken


title: Drought kernel-2

city: qingdao

first: wang

last: baomei

state: shandong

address: school of life science，shandong university，72 binhai road， aoshanwei town， jimo city

department: school of  life science

institute: zea maize

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a re-sequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on).
Further, we also can perform deep analysis based on DEGs (We use 'FDR ≤ 0.001 and the absolute value of Log2Ratio ≥ 1' as the threshold to judge the significance of gene expression difference), including Gene Ontology (GO) enrichment analysis, pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Genome_build: maize B73 inbred line V3 version
Supplementary_files_format_and_content: files include FPKM values for each Sample

organism: Zea mays

source_name: kernel

extract_protocol:
Ears, leaves and kernels were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: 5DAP stage

tag: condition

value: Drought

value: kernel

tag: line

value: inbred line 104


title: Drought kernel-1


title: DX_female_21852

description: Dongxiang blue-shelled chicken


title: L3 larvae brain MAPCap: female wild-type; replicate 2

description:
MAPCap experiment performed on 3rd instar larvae
MAPCap_J-larvae_female_WT.deduplicated.bw


title: Drought leaf-2

source_name: leaf

value: leaf


title: L3 larvae brain MAPCap: female wild-type; replicate 3


title: L3 larvae brain MAPCap: male MLE9 mutant; replicate 2


title: DX_female_21973

description: Dongxiang blue-shelled chicken


title: L3 larvae brain MAPCap: female MLE9 mutant; replicate 3

description:
MAPCap experiment performed on 3rd instar larvae
MAPCap_J-larvae_female_MLE9.deduplicated.bw


title: DX_female_21936

description: Dongxiang blue-shelled chicken


title: Drought ear-2

source_name: ear

value: V9 stage

value: ear


title: DX_female_22657

description: Dongxiang blue-shelled chicken

value: brachial veins


title: L3 larvae brain MAPCap: female MLE9 mutant; replicate 2

value: female


title: Drought ear-1


title: Low_Furfural_LF5

description: Furfural treated isolates LF5

source_name: cell culture of strain LF5

value: JSC-derived LF5


title: DX_female_21894

description: Dongxiang blue-shelled chicken

value: Dongxiang blue-shelled


title: Low_Furfural_LF6

description: Furfural treated isolates LF6

source_name: cell culture of strain LF6

value: JSC-derived LF6


title: Control kernel-2

value: Control


title: DX_female_21912

description: Dongxiang blue-shelled chicken


title: Low_Furfural_LF3

description: Furfural treated isolates LF3

source_name: cell culture of strain LF3

value: JSC-derived LF3


title: L3 larvae brain MAPCap: female wild-type; replicate 1

value: L3 larvae (3rd Instar)

value: wild-type


title: Control kernel-1


title: Low_Furfural_LF4

description: Furfural treated isolates LF4

source_name: cell culture of strain LF4

value: JSC-derived LF4


title: Low_Furfural_LF19

description: Furfural treated isolates LF19

source_name: cell culture of strain LF19

value: JSC-derived LF19


title: Low_Furfural_LF17

description: Furfural treated isolates LF17

source_name: cell culture of strain LF17

value: JSC-derived LF17


title: Low_Furfural_LF2

description: Furfural treated isolates LF2

source_name: cell culture of strain LF2

value: JSC-derived LF2


title: Drought leaf-1

value: 5DAP stage

value: Drought

value: inbred line 104


title: Low_Furfural_LF11

description: Furfural treated isolates LF11

source_name: cell culture of strain LF11

value: JSC-derived LF11


title: DX_female_21917

description: Dongxiang blue-shelled chicken

value: brachial veins


title: Low_Furfural_LF13

description: Furfural treated isolates LF13

source_name: cell culture of strain LF13

value: JSC-derived LF13


title: Low_Furfural_LF15

description: Furfural treated isolates LF15

source_name: cell culture of strain LF15

value: JSC-derived LF15


title: Whole embryo MAPCap: replicate3

description:
MAPCap experiment performed on stage 15 embryos
MAPCap_H-embryo.deduplicated.bw

source_name: whole embryo

value: Stage 15


title: Control leaf-2

value: leaf


title: DX_female_21870

description: Dongxiang blue-shelled chicken

value: female

value: Dongxiang blue-shelled


title: L3 larvae brain MAPCap: female MLE9 mutant; replicate 1

source_name: brain

value: L3 larvae (3rd Instar)

value: MLE9 mutant


title: DX_female_21975

description: Dongxiang blue-shelled chicken


title: Control leaf-1

value: Control


title: Whole embryo MAPCap: replicate1


title: Control ear-2

value: V9 stage

value: ear


title: Low_Furfural_LF1

description: Furfural treated isolates LF1

source_name: cell culture of strain LF1

value: JSC-derived LF1

source_name: cell culture of JSC24-2


title: DX_female_21938

description: Dongxiang blue-shelled chicken


title: Stage 10.5 vegetal H3K4me1 ChIP-seq replicate 2

city: Irvine

first: Kitt

middle: D.

last: Paraiso

state: CA

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

description: processed data file: H3K4me1-st10-vegetal-peaks.bed

data_processing:
ChIP-seq peak calling: H3K4me1 ChIP-seq reads from biological replicates were concatenated and then aligned to the X. tropicalis genome v9.0 (Hellseten et al., 2010; Xenbase FTP) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 10 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.0000000001 but otherwise default options.
Genome_build: Xenopus tropicalis genome v 9.0

organism: Xenopus tropicalis

source_name: Xenopus tropicalis embryo

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.

extract_protocol:
Vegetal masses were dissected from 100 fixed embryos and were then homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 3 ug anti-H3K4me1 antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.

treatment_protocol: Embryos were cross-linked in 1% formaldehyde in 1/9x MMR at room temperature for 50 minutes with gentle rocking where each microcentrifuge tube contains 200 embryos with 1mL of the formaldehyde solution. Crosslinking reactions were neutralized by the removal of the formaldehyde solution and incubation with 1ml 125mM glycine solution for 10 minutes on ice. Embryos were then washed twice with 400mL of cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche complete protease inhibitor cocktail). Embryos were flash-frozen in liquid nitrogen and stored at -80°C.

value: Stage 10.5

value: Vegetal mass


title: Control ear-1

value: inbred line 104


title: DX_female_21859

description: Dongxiang blue-shelled chicken


title: Total RNA from CP70/shE2F6 cell line

city: Chia-Yi

first: Yu Ming

last: Chuang

address: 168 University Road,Min Hsiung

department: Department of Biomedical Science

country: Taiwan

institute: National Chung Cheng University

description: CP70 ovarian cancer cell line which the Mir193a expression is low.

data_processing:
Illumina MiSeq used for basecalling.
CLC Genomics Workbench 8.5.1 software was used.
The raw reads were cleaned by trimming of adaptor sequences.
Sequenced reads were mapped to hg19 genome using CLC Workbench default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: ovarian cancer cell line

growth_protocol: CP70 cells were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were incubated at 37˚C under a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA was extracted from each sample using TRIzol reagent.

treatment_protocol:
CP70 cells were infected with pLKO TRC005. Stable clones were selected using medium containing 2ug/ml Puromycin.
CP70 cells were infected with pLKO TRC005 shE2F6. Stable clones were selected using medium containing 2ug/ml Puromycin.
CP70 cells were infected with pLKO.1-puro shEZH2. Stable clones were selected using medium containing 2ug/ml Puromycin.

tag: shRNA


title: Whole embryo MAPCap: replicate2


title: Stage 10.5 vegetal H3K4me1 ChIP-seq replicate 1


title: Zta_N182T_5hmC_rep1

type: protein

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: Zta(N182T) PBM experiment, 5hmC

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at three power settings: 100% photomultiplier tube (PMT) voltage (high), 50% PMT (medium), and 10% PMT (low). The  resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.

molecule: protein

organism: human gammaherpesvirus 4

source_name: Zta(N182T), HK design

label_protocol: 180 ng of plasmid containing DNA binding domains of Zta or Zta(N182) mutants were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: The bZIP DNA binding domain (DBD) of wild type Zta was obtained from Dr. Timothy Hughes, University of Toronto, Canada as a GST construct cloned into a modified pDEST15 MAGIC vector (N-terminal GST) vector.  Mutant constructs of Zta (N182S, N182Q, N182T, N182I, and N182V) were generated via site-directed mutagenesis of the wild-type construct (GenScript)

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: bZIP

tag: protein

tag: double-stranding treatment


title: DX_female_21884

description: Dongxiang blue-shelled chicken

value: brachial veins


title: Zta_N182Q_5hmC_rep2

description: Zta(N182Q) PBM experiment, 5hmC

source_name: Zta(N182Q), HK design


title: Zta_N182Q_5hmC_rep1

description: Zta(N182Q) PBM experiment, 5hmC


title: DX_female_22064

description: Dongxiang blue-shelled chicken


title: DX_female_21982

description: Dongxiang blue-shelled chicken


title: Zta_N182V_5hmC_rep2

description: Zta(N182V) PBM experiment, 5hmC

source_name: Zta(N182V), HK design


title: Whole embryo MAPCap: replicate4


title: Total RNA from CP70/shEGFP cell line

value: shEGFP


title: Stage 8 Otx1 ChIP-seq replicate 2

description: processed data file: otx1-IDR-optimal-peaks.bed

data_processing:
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v9.0 (Hellsete et al., 2010; Xenbase FTP) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 8 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.001 but otherwise default options . ENCODE based irreproducibility discovery rate (IDR) was performed using the following p-value thresholds for the following comparisons: 0.01 for original biological replicates, 0.02 for pseudoreplicates of each biological replicate and 0.0025 for pseudoreplicates generated from pooled reads of biological replicates (Li et al., 2011).
Genome_build: Xenopus tropicalis genome v 9.0

extract_protocol:
The fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 4 mg anti-otx1 antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.

treatment_protocol: Embryos were cross-linked in 1% formaldehyde in 1/9x MMR at room temperature for 50 minutes with gentle rocking where each microcentrifuge tube contains 200 embryos with 1mL of the formaldehyde solution. Crosslinking reactions were neutralized by the removal of the formaldehyde solution and incubation with 1ml 125mM glycine solution for 10 minutes on ice. Embryos were then washed twice with 400mL of cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). Embryos were flash-frozen in liquid nitrogen and stored at -80°C.

value: Stage 8

value: Whole embryo


title: Stage 10 vegetal mass Double MO replicate 2

description:
processed data file: double-MO-vegt,otx1-readcounts.txt
processed data file: double-MO-vegt,otx1-TPM.txt

data_processing:
RNA-seq gene expression calling: Reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Hellsten et al., 2010; Xenbase FTP). Read counts and transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis genome v 9.0

extract_protocol:
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4°C in 2.5M LiCl to remove contaminating genomic DNA.
RNA-seq libraries were generated using Smart-seq2 cDNA synthesis followed by tagmentation, quality-tested using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina sequencers.

treatment_protocol: Vegt and otx1 MO were microinjected into 1-cell stage embryos; vegetal masses were dissected at stage 9 and RNA was harvested at stage 10.5

value: Stage 10.5 (equivalent)

value: Vegetal masses


title: DX_female_21916

description: Dongxiang blue-shelled chicken

value: female

value: Dongxiang blue-shelled


title: Total RNA from CP70/shEZH2 cell line


title: Stage 8 Vegt ChIP-seq replicate 1

description: processed data file: vegt-IDR-optimal-peaks.bed

extract_protocol:
The fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 2 mg anti-vegt antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.


title: Stage 10 vegetal mass Otx1 MO replicate 2

treatment_protocol: Otx1 MO was microinjected into 1-cell stage embryos; vegetal masses were dissected at stage 9 and RNA was harvested at stage 10.5


title: Zta_N182T_5hmC_rep2

description: Zta(N182T) PBM experiment, 5hmC


title: Zta_N182T_5mCG_rep2

description: Zta(N182T) PBM experiment, unmethylated

data_processing: For all 32,896 8-bp long DNA sequences (8-mers), a transformed median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.

treatment_protocol: The double stranded arrays were either methylated (5mCG) or unmethylated (C). The methylation of the double stranded microarray were performed using 10 μl of M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: probe state

value: methylated


title: DX_female_21997

description: Dongxiang blue-shelled chicken


title: Zta_N182S_5hmC_rep2

description: Zta(N182S) PBM experiment, 5hmC

source_name: Zta(N182S), HK design


title: Stage 10 vegetal mass uninjected replicate 2

treatment_protocol: Vegetal masses were dissected at stage 9 and RNA was harvested at stage 10.5


title: DX_female_21939

description: Dongxiang blue-shelled chicken


title: Zta_N182S_5hmC_rep1

description: Zta(N182S) PBM experiment, 5hmC


title: Zta_N182T_5mCG_rep1

description: Zta(N182T) PBM experiment, unmethylated


title: Stage 10 vegetal mass Vegt MO replicate 2

treatment_protocol: Vegt MO was microinjected into 1-cell stage embryos; vegetal masses were dissected at stage 9 and RNA was harvested at stage 10.5


title: DX_female_22067

description: Dongxiang blue-shelled chicken


title: Stage 10 vegetal mass Otx1 MO replicate 1


title: Stage 10 vegetal mass Vegt MO replicate 1


title: Zta_N182Q_5mCG_rep1

description: Zta(N182Q) PBM experiment, unmethylated


title: Zta_N182V_5hmC_rep1

description: Zta(N182V) PBM experiment, 5hmC


title: Zta_N182S_5mCG_rep2

description: Zta(N182S) PBM experiment, unmethylated


title: Zta_N182Q_5mCG_rep2

description: Zta(N182Q) PBM experiment, unmethylated


title: AGS_shGFP_2

description: genomic DNA from AGS/shGFP cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Analysis by Microsoft Excel. Raw data selected by Detection pval and removed missing values.

label: Cy5 and Cy3

source_name: Knockdown GFP in gastric cancer cell line

label_protocol: Standard Illumina Protocol

growth_protocol: AGS cells were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were incubated at 37C under a humidified atmosphere containing 5% CO2

extract_protocol: genomic DNA was extracted and purified from samples using Genomic DNA mini Kit (Geneaid) according to standard instructions

treatment_protocol: AGS cells were either transfected with pLKO.1-puro-shGFP as control or pLKO.1-puro-shSTAT3 targeting the endogenous STAT3. Stable clones were selected using medium containing 2ug/ml Puromycin.

tag: cell line

value: AGS

tag: disease

value: Adenocarcinoma

value: gastric cancer


title: Zta_N182I_5hmC_rep1

description: Zta(N182I) PBM experiment, 5hmC

source_name: Zta(N182I), HK design


title: Zta_WT_5hmC_rep2

description: Zta PBM experiment, 5hmC

source_name: Zta, HK design

value: Zta


title: DX_female_21863

description: Dongxiang blue-shelled chicken


title: AGS_shSTAT3_2

description: genomic DNA from AGS/shSTAT3 cell line

source_name: Knockdown STAT3 in gastric cancer cell line

tag: cell type


title: Stage 10 vegetal mass uninjected replicate 1

tag: tissue


title: Stage 10 vegetal mass Double MO replicate 1


title: DX_female_22068

description: Dongxiang blue-shelled chicken

tag: Sex


title: AGS_shSTAT3_1

description: genomic DNA from AGS/shSTAT3 cell line


title: Zta_N182I_5hmC_rep2

description: Zta(N182I) PBM experiment, 5hmC


title: Zta_N182I_5mCG_rep2

description: Zta(N182I) PBM experiment, unmethylated


title: Zta_N182S_5mCG_rep1

description: Zta(N182S) PBM experiment, unmethylated


title: DX_female_21928

description: Dongxiang blue-shelled chicken

tag: breed


title: DX_female_21848

description: Dongxiang blue-shelled chicken


title: DX_female_22646

description: Dongxiang blue-shelled chicken


title: Animal cap ectopic expression Vegt 100 ng, Otx1 100 ng replicate 2

description:
processed data file: ectopic-expression-vegt,otx1-readcounts.txt
processed data file: ectopic-expression-vegt,otx1-TPM.txt

treatment_protocol: vegt RNA 100 ng & otx1 RNA 100 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5

tag: developmental stage

value: Animal caps


title: Zta_N182V_5mCG_rep2

description: Zta(N182V) PBM experiment, unmethylated


title: AGS_shGFP_1

description: genomic DNA from AGS/shGFP cell line


title: DX_female_21910

description: Dongxiang blue-shelled chicken


title: Animal cap ectopic expression Vegt 100 ng, Otx1 25 ng replicate 2

treatment_protocol: vegt RNA 100 ng & otx1 RNA 25 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: DX_female_21820

description: Dongxiang blue-shelled chicken


title: Zta_N182T_5mC_rep2

description: Zta(N182T) PBM experiment, 5mC


title: Zta_N182V_5mCG_rep1

description: Zta(N182V) PBM experiment, unmethylated


title: Animal cap ectopic expression Vegt 100 ng, Otx1 50 ng replicate 2

treatment_protocol: vegt RNA 100 ng & otx1 RNA 50 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: Zta_N182V_5mC_rep2

description: Zta(N182V) PBM experiment, 5mC


title: Zta_WT_5hmC_rep1

description: Zta PBM experiment, 5hmC


title: Zta_N182T_5mC_rep1

description: Zta(N182T) PBM experiment, 5mC


title: Animal cap ectopic expression Vegt 500 ng, Otx1 0 ng replicate 2

treatment_protocol: vegt RNA 500 ng & otx1 RNA 00 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: Zta_N182Q_5mC_rep1

description: Zta(N182Q) PBM experiment, 5mC


title: DX_female_22651

description: Dongxiang blue-shelled chicken


title: DX_female_21974

description: Dongxiang blue-shelled chicken


title: Animal cap ectopic expression Vegt 200 ng, Otx1 0 ng replicate 2

treatment_protocol: vegt RNA 200 ng & otx1 RNA 00 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: Animal cap ectopic expression Vegt 50 ng, Otx1 0 ng replicate 2

treatment_protocol: vegt RNA 50 ng & otx1 RNA 00 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: DX_female_21996

description: Dongxiang blue-shelled chicken


title: Animal cap ectopic expression Vegt 100 ng, Otx1 0 ng replicate 2

treatment_protocol: vegt RNA 100 ng & otx1 RNA 00 ng were microinjected into 1-cell stage embryos; animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: Zta_N182I_5mCG_rep1

description: Zta(N182I) PBM experiment, unmethylated


title: Zta_N182Q_5mC_rep2

description: Zta(N182Q) PBM experiment, 5mC


title: Animal cap ectopic expression Vegt 0 ng, Otx1 0 ng replicate 2

treatment_protocol: Animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: DX_female_21853

description: Dongxiang blue-shelled chicken


title: DX_female_21831

description: Dongxiang blue-shelled chicken


title: Animal cap ectopic expression Vegt 100 ng, Otx1 100 ng replicate 1


title: Zta_N182T_C_rep1 (mCG)

description: Zta(N182T) PBM experiment, unmethylated

value: unmethylated


title: Zta_N182Q_C_rep1 (mCG)

description: Zta(N182Q) PBM experiment, unmethylated


title: Zta_N182T_C_rep2 (mCG)

description: Zta(N182T) PBM experiment, unmethylated


title: Zta_N182Q_C_rep2 (mCG)

description: Zta(N182Q) PBM experiment, unmethylated


title: Zta_N182I_5mC_rep2

description: Zta(N182I) PBM experiment, 5mC


title: Zta_WT_5mCG_rep1 #2

description: Zta PBM experiment, methylated


title: Animal cap ectopic expression Vegt 100 ng, Otx1 50 ng replicate 1


title: Zta_N182V_5mC_rep1

description: Zta(N182V) PBM experiment, 5mC


title: Zta_N182S_5mC_rep2

description: Zta(N182S) PBM experiment, 5mC


title: ICAM1 hi LCL donor 4

city: Durham

first: Micah

middle: Alan

last: Luftig

state: NC

address: 213 Research Drive CARL Building Room 0045

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Fastq files were aligned to the human genome (hg38) using hisat2
BAM files were converted to SAM files
Stringtie was used to assemble transcripts
Assembled transcripts were imported into the R package ballgown
Ballgown was used to determine differential gene expression and calculate RPKM
Genome_build: hg38
Supplementary_files_format_and_content: processed data contains gene level RPKMs, transcript level RPKMs and genomic locations as well as differential gene expression fold changes, pvalues and FDR q values

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: ICAM1 high sorted EBV immortalized LCL

growth_protocol: All latency III LCLs were grown in complete RPMI + 10% FBS + Pennicillin/Streptomycin/Glutamine in 5%CO2. Latency IIb cells were grown in complete RPMI + 15% FBS + Pennicillin/Streptomycin/Glutamine

extract_protocol:
RNA was isolated using a Qiagen Rneasy Kit
mRNA sequencing libraries were prepared using the Kappa Stranded RNA-seq Library Preparation Kit accoridng to the manufacturers instructions

tag: donor id

value: donor 4

tag: source cell type

value: primary human B cells

value: ICAM1 high LCL latency III

tag: ebv strain

value: EBV B95-8


title: Animal cap ectopic expression Vegt 100 ng, Otx1 25 ng replicate 1


title: Animal cap ectopic expression Vegt 500 ng, Otx1 0 ng replicate 1


title: ICAM1 lo LCL donor 4

source_name: ICAM1 low sorted EBV immortalized LCL

value: ICAM1 low LCL latency III


title: Zta_N182V_C_rep2 (mCG)

description: Zta(N182V) PBM experiment, unmethylated

value: bZIP


title: Zta_N182S_5mC_rep1

description: Zta(N182S) PBM experiment, 5mC


title: Animal cap ectopic expression Vegt 200 ng, Otx1 0 ng replicate 1

value: Stage 10.5 (equivalent)


title: ICAM1 hi LCL donor 3

value: donor 3


title: Zta_N182V_C_rep1 (mCG)

description: Zta(N182V) PBM experiment, unmethylated


title: Animal cap ectopic expression Vegt 100 ng, Otx1 0 ng replicate 1


title: day 7 donor 4

source_name: EBV infected sorted primary B cells

value: Proliferating d7 dpi latency IIB


title: Male Mdr2 WT rep3

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: caudate liver lobe biopsy from male Mdr2 WT on BALB/cJ background, treated with high-fat breeder chow days 30-45

data_processing:
Following removal of primers and barcodes, raw reads were aligned to the mm10 mouse genome with using Bowtie 2, and transcript abundances estimated using Cufflinks with FPKM as the output.
Data were normalized using DESeq and baselined to the median of all samples.
Data were filtered, requiring FPKM>3 in 100% of samples in at least one condition.
Genome_build: mm10
Supplementary_files_format_and_content: csv with gene symbol, locus, and FPKM

organism: Mus musculus

source_name: caudate liver lobe biopsy

growth_protocol: All mice were bred in-house and kept in conventional conditions, and were treated with high-fat breader chow starting at day 30.

extract_protocol:
Total hepatic RNA was isolated from biopsies using  Illumina TruSeq RNA Sample Prep Kit according to standard protocols.
Libraries were prepared with the Illumina TruSeq RNA preparation kit.

treatment_protocol: Caudate liver lobe biopsies were obtained at day 45.

value: male

tag: genotype

value: Mdr2 WT

tag: strain

value: BALB/cJ

tag: treatment

value: high-fat breeder chow days 30-45

tag: age

value: 45 days


title: Zta_N182S_C_rep2 (mCG)

description: Zta(N182S) PBM experiment, unmethylated

tag: dbd

tag: protein


title: ICAM1 mid LCL donor 4

source_name: ICAM1 mid sorted EBV immortalized LCL

value: ICAM1 mid LCL latency III


title: ICAM1 mid LCL donor 3


title: Animal cap ectopic expression Vegt 50 ng, Otx1 0 ng replicate 1

value: Animal caps


title: Zta_WT_5mC_rep2 #2

description: Zta PBM experiment, 5mC

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

value: Zta

tag: double-stranding treatment


title: Zta_N182I_5mC_rep1

description: Zta(N182I) PBM experiment, 5mC


title: Male Mdr2 KO rep3

description: caudate liver lobe biopsy from male Mdr2 KO on BALB/cJ background, treated with high-fat breeder chow days 30-45

value: Mdr2 KO


title: Zta_N182I_C_rep2 (mCG)

description: Zta(N182I) PBM experiment, unmethylated

tag: probe state

value: unmethylated


title: Zta_N182S_C_rep1 (mCG)

description: Zta(N182S) PBM experiment, unmethylated


title: Zta_N182I_C_rep1 (mCG)

description: Zta(N182I) PBM experiment, unmethylated


title: Zta_WT_5mC_rep1 #2

description: Zta PBM experiment, 5mC


title: ICAM1 lo LCL donor 3

value: primary human B cells


title: Zta_N182T_C_rep2 (mC + 5hmC)

description: Zta(N182T) PBM experiment, cytosine

value: cytosine


title: Zta_N182T_C_rep1 (mC + 5hmC)

description: Zta(N182T) PBM experiment, cytosine


title: Zta_N182Q_C_rep2 (mC + 5hmC)

description: Zta(N182Q) PBM experiment, cytosine


title: Zta_N182Q_C_rep1 (mC + 5hmC)

description: Zta(N182Q) PBM experiment, cytosine


title: Zta_N182V_C_rep1 (mC + 5hmC)

description: Zta(N182V) PBM experiment, cytosine


title: Animal cap ectopic expression Vegt 0 ng, Otx1 0 ng replicate 1

treatment_protocol: animal caps were dissected at stage 9 and RNA was harvested at stage 10.5


title: Male Mdr2 WT rep2


title: Male Mdr2 WT rep1


title: Male Mdr2 KO rep2


title: ICAM1 mid LCL donor2

value: donor 2

value: EBV B95-8


title: ICAM1 hi LCL donor 2

value: ICAM1 high LCL latency III


title: Male Mdr2 KO rep1


title: Cerebral organoids rep. 2

source_name: Cerebral organoids

growth_protocol: Cerebral organoids were generated according to the protocol described by Lancaster et al. (2014) with some modifications. Ten thousand cells were seeded per well in 96 well plates in 100 µl of EB (medium supplemented with bFGF and 50 µM ROCK inhibitor). After 4 days, the medium was replaced by EB medium and at day 6 by neural induction medium (NIM). At day 11, organoids were embedded in Matrigel (Corning, 356234) and kept in neural induction medium for two days, followed by organoid differentiation medium without retinoic acid (RA) for another four days. Next organoids were transferred to ultra-low attachment 6-well plates and culture on an orbital shaker (90 rpm) in organoid maturation medium. The composition of the original organoids maturation medium was changed by adding chemically defined lipid concentrate (1x), ascorbic acid (0.4 mM), BDNF (20 ng/ml), HEPES.

tag: cell line


title: Cerebral organoids rep. 1


title: Female Mdr2 WT rep1

description: caudate liver lobe biopsy from female Mdr2 WT on BALB/cJ background, treated with high-fat breeder chow days 30-45

value: female


title: S2 cells MAPCap; 100ng RNA

description: cDNA

data_processing:
read trimming using cutadapt (v1.16); parameters : -a AACCGGTT -m 15 -u 9 -q 5 –trim-n
mapped using subread (1.5.2); parameters :subjunc -D 500 -d 20
duplicates removed via icetea (v1.0) filterDuplicates (default options)
coverage calculated using deepTools bamCoverage (v3.0.2); parameters: --normalizeUsing CPM -p 20 -bs 1 --Offset 1 5 (for S2 cells) and –Offset 1 for femESCs
Genome_build: dm6; mm10
Supplementary_files_format_and_content: bw

source_name: S2 cells

growth_protocol: S2 cells (gift from the Butros lab, Heidelberg) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80 rpm. Cells were kept at a density of 1-16 million/ml. The hybrid mouse female embryonic stem cell line F1-21.6 (129Sv-Cast/EiJ) was grown on Attachment Factor (Gibco) coated dishes in 2i medium containing DMEM (Gibco) supplemented with 15 % KnockOut Serum Replacement (Gibco), Penicillin/Streptomycin (Sigma), 1000 U/mL LIF (Millipore), sodium pyruvate (Gibco), non-essential amino acids (Gibco), Glutamax (Gibco), 100 µM β-mercaptoethanol (Gibco), 5 µg/mL insulin (Sigma), 1 µM PD0325901 (Axon) and 3 µM CHIR99021 (Axon). Cells were maintained in a humidified incubator at 37 °C and 5 % CO2.

extract_protocol:
RNA from S2 cells was extracted using the DirectZol Kit (Zymo Research). RNA was eluted in 25 ul of RNase-free water. Mouse ESC RNA was prepared from 70-80 % confluent 10 cm dishes using Trizol (Ambion) according to manufacturer's instructions. Poly(A)-RNA was isolated from 5 µg of total RNA (mixed with spike-ins added at 0.05 % of input) using Dynabeads Oligo-(dT)25 (Thermo Fisher).
MAPCap

tag: cell type

value: S2 cell line


title: iPSCs rep. 2

source_name: iPSCs

growth_protocol: iPSCs (XMO01 clone) were cultured in E8 flex medium (Thermo Fisher, cat. A2858501) and regularly passaged with Accutase (Stem Cell Technologies, cat. 07920).


title: ICMA1 hi LCL donor 1

value: donor 1


title: ICAM1 lo LCL donor 2

value: ICAM1 low LCL latency III


title: Zta_N182V_C_rep2 (mC + 5hmC)

description: Zta(N182V) PBM experiment, cytosine

value: bZIP


title: Day 7 donor 3

value: donor 3

value: Proliferating d7 dpi latency IIB


title: S2 cells MAPCap; 1ug RNA

description: cDNA


title: Zta_N182S_C_rep2 (mC + 5hmC)

description: Zta(N182S) PBM experiment, cytosine


title: PPRH against survivin (HpsPr-WT)-24h, biological rep3

type: RNA

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: Gene expression from 24h treatment (HpsPr-WT)

hyb_protocol: Following fragmentation and terminal labeling, 5.2ug of ss-cDNA were hybridized for 16hr at 45ºC on GeneChip Human Clariom S array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneCHip Scanner 3000 System.

data_processing:
Data was processed using Genespring v14.5 software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale, using a baseline transformation to the median of control samples
Affymetrix.TranscriptomeChip.Clariom_S_Human_na36_hg38_2016-06-21

label: Biotin

source_name: PC3 prostate cancer cell line

label_protocol: Fragmented and labeled ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit user guide

growth_protocol: PC3 human prostate cancer cells (30,000) were seeded in 35 mm plates, grown in Ham's F12 medium supplemented with 7% FBS.

extract_protocol: RNA extraction with TRI reagent. extraction performed according to user's protocol.

treatment_protocol: Incubation with 100 nM of either HpsPr-WC or HpsPr-WT for 24 hours.

value: prostate cancer


title: Zta_N182I_C_rep1 (mC + 5hmC)

description: Zta(N182I) PBM experiment, cytosine


title: Zta_N182S_C_rep1 (mC + 5hmC)

description: Zta(N182S) PBM experiment, cytosine


title: Zta_N182I_C_rep2 (mC + 5hmC)

description: Zta(N182I) PBM experiment, cytosine


title: PPRH against survivin (HpsPr-WT)-24h, biological rep1


title: day 7 donor 2


title: HeLa S3 rep. 2

data_processing:
Library strategy: FLAM-seq
CCS reads were produced with the SMRT Link browser 5.0 (minimum full pass 3, minimum predicted accuracy 90)
Fastq files were analyzed according to the FLAM-seq analysis pipeline: reads were filtered for containing at least 10 As followed by 9 Gs (or the rev. comp.), then reoriented to start with the adapter sequence, the UMI, the G tail and the poly(A) tail. Poly(A) tails were detected and removed, the remaining reads were aligned to hg38 or C. elegans WB235 genome assemblies using STARLong (Dobin et al., 2013). Each aligned read was then assigned to gene models (Ensembl GRCh38.84 for human, WBcel235_82 for worm) with FeatureCounts (Liao et al., 2014).
Genome_build: H. sapiens: hg38, C. elegans: WB235
Supplementary_files_format_and_content: Processed data contain read name, gene to which read is assigned using FeatureCounts, unique molecular identifier sequence, tail length and tail sequence

source_name: HeLa S3

growth_protocol: HeLa S3 cells were cultured in DMEM high glucose (cat. 41965, Thermo Fisher) supplemented with 10% FBS (cat. 10270106, Thermo Fisher)

extract_protocol:
All samples were collected in Trizol and poly(A)+ RNA was extracted with the Truseq mRNA preparation kit (RS-122-21-2, Illumina).
Libraries were constructed according to the FLAM-seq protocol.

value: HeLa S3


title: PPRH against survivin (HpsPr-WT)-24h, biological rep2


title: Control, biological rep3

description: Gene expression from untreated control


title: HeLa S3 rep. 1


title: Negative control (HpsPr-WC)-24h, biological rep3

description: Gene expression from 24h treatment with negative control (HpsPr-WC)


title: S2 cells MAPCap; 500ng RNA

description: cDNA


title: ICAM1 mid LCL donor 1

value: ICAM1 mid LCL latency III


title: ICAM1 lo LCL donor 1


title: iPSCs rep. 1


title: cDNA standards

organism: synthetic construct

source_name: synthetic cDNA

tag: sample type

value: synthetic construct


title: NE423-V1-38-rep3

status: Public on Jun 03 2019

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

country: Italy

institute: Universita' degli Studi di Verona

description:
sample name in processed data file:
102-3

data_processing:
Bad quality read are removed, then the Scythe software removed adapters and the Sickle software the bad quality end from the reads.
Alignment was performed with TopHat 2.0.14
Expression analysis with Cufflinks 2.2.0
Genome_build: PN40024 (Jaillon et al., 2007) using the V1 12X draft, available at http://genomes.cribi.unipd.it/
Supplementary_files_format_and_content: Excel matrix with FPKM

organism: Vitis vinifera

source_name: Grapevine berries

extract_protocol:
Total RNA extraction using a commercial kit (SpectrumTM Plant Total RNA extraction kit by Sigma Aldrich)
RNA-Seq libraries were constructed from 2.5 µg of total RNA using the Illumina TruSeq® Sample Prep kit v2 (Illumina Inc., San Diego, CA, USA)

tag: cultivar

value: Nebbiolo

tag: tissue

value: berries

tag: clone

value: CVT 423

tag: vineyard


title: NE423-V1-38-rep2

description:
sample name in processed data file:
102-2

tag: developmental stage


title: day 7 donor 1

tag: donor id

tag: source cell type

value: primary human B cells

tag: ebv strain


title: NE71-V1-38-rep2

description:
sample name in processed data file:
101-2

value: CVT 71


title: NE185-V1-38-rep2

description:
sample name in processed data file:
103-2

value: CVT 185


title: NE185-V1-38-rep1

description:
sample name in processed data file:
103-1


title: NE185-V1-38-rep3

description:
sample name in processed data file:
103-3


title: NE423-V1-38-rep1

description:
sample name in processed data file:
102-1


title: Control, biological rep2

description: Gene expression from untreated control


title: NE423-V2-38-rep3

description:
sample name in processed data file:
98-3


title: Negative control (HpsPr-WC)-24h, biological rep2


title: NE423-V2-38-rep1

description:
sample name in processed data file:
98-1


title: NE71-V1-38-rep1

description:
sample name in processed data file:
101-1


title: S2 cells MAPCap; 5ug RNA

description: cDNA


title: NE71-V3-38-rep2

description:
sample name in processed data file:
97-2


title: NE71-V3-38-rep3

description:
sample name in processed data file:
97-3


title: Negative control (HpsPr-WC)-24h, biological rep1


title: NE71-V2-38-rep3

description:
sample name in processed data file:
100-3


title: NE71-V2-38-rep2

description:
sample name in processed data file:
100-2


title: NE185-V2-38-rep3

description:
sample name in processed data file:
99-3


title: Control, biological rep1

description: Gene expression from untreated control


title: NE185-V2-38-rep2

description:
sample name in processed data file:
99-2


title: NE71-V2-38-rep1

description:
sample name in processed data file:
100-1


title: NE185-V2-38-rep1

description:
sample name in processed data file:
99-1


title: NE71-V3-38-rep1

description:
sample name in processed data file:
97-1


title: NE423-V3-38-rep3

description:
sample name in processed data file:
95-3


title: NE185-V3-38-rep3

description:
sample name in processed data file:
96-3


title: NE423-V3-38-rep2

description:
sample name in processed data file:
95-2


title: NE71-V1-35-rep3

description:
sample name in processed data file:
94-6


title: NE185-V3-38-rep2

description:
sample name in processed data file:
96-2


title: NE185-V3-38-rep1

description:
sample name in processed data file:
96-1


title: NE71-V1-38-rep3

description:
sample name in processed data file:
101-3


title: NE423-V3-38-rep1

description:
sample name in processed data file:
95-1


title: NE71-V3-35-rep2

description:
sample name in processed data file:
93-2


title: NE71-V1-35-rep2

description:
sample name in processed data file:
94-5


title: NE71-V3-35-rep3

description:
sample name in processed data file:
93-3


title: NE185-V3-35-rep3

description:
sample name in processed data file:
92-6


title: NE185-V3-35-rep2

description:
sample name in processed data file:
92-4


title: NE185-V3-35-rep1

description:
sample name in processed data file:
92-3


title: NE423-V2-38-rep2

description:
sample name in processed data file:
98-2


title: NE71-V1-35-rep1

description:
sample name in processed data file:
94-4


title: NE423-V2-35-rep3

description:
sample name in processed data file:
91-3


title: NE423-V2-35-rep2

description:
sample name in processed data file:
91-2


title: NE423-V2-35-rep1

description:
sample name in processed data file:
91-1


title: NE185-V1-35-rep1

description:
sample name in processed data file:
89-1


title: NE423-V1-35-rep2

description:
sample name in processed data file:
90-2


title: NE423-V3-35-rep3

description:
sample name in processed data file:
88-3


title: NE185-V1-35-rep2

description:
sample name in processed data file:
89-4


title: NE423-V1-35-rep3

description:
sample name in processed data file:
90-3


title: NE71-V3-35-rep1

description:
sample name in processed data file:
93-1


title: NE423-V3-35-rep1

description:
sample name in processed data file:
88-1


title: NE185-V2-35-rep3

description:
sample name in processed data file:
87-3


title: NE423-V3-35-rep2

description:
sample name in processed data file:
88-2


title: NE71-V2-35-rep3

description:
sample name in processed data file:
86-3


title: NE185-V2-35-rep1

description:
sample name in processed data file:
87-1


title: NE185-V2-35-rep2

description:
sample name in processed data file:
87-2


title: NE71-V2-35-rep1

description:
sample name in processed data file:
86-1


title: NE71-V2-35-rep2

description:
sample name in processed data file:
86-2


title: NE423-V2-31-rep3

description:
sample name in processed data file:
83-3


title: NE423-V2-31-rep1

description:
sample name in processed data file:
83-1


title: NE423-V1-31-rep3

description:
sample name in processed data file:
82-3


title: NE423-V2-31-rep2

description:
sample name in processed data file:
83-2


title: NE185-V1-31-rep3

description:
sample name in processed data file:
81-3


title: NE423-V1-31-rep1

description:
sample name in processed data file:
82-1


title: NE185-V1-31-rep2

description:
sample name in processed data file:
81-2


title: NE185-V1-31-rep1

description:
sample name in processed data file:
81-1


title: NE185-V1-35-rep3

description:
sample name in processed data file:
89-5


title: NE185-V2-31-rep1

description:
sample name in processed data file:
80-1


title: NE185-V3-31-rep3

description:
sample name in processed data file:
79-3


title: NE423-V1-35-rep1

description:
sample name in processed data file:
90-1


title: NE185-V2-31-rep2

description:
sample name in processed data file:
80-2


title: NE185-V2-31-rep3

description:
sample name in processed data file:
80-3


title: NE71-V3-31-rep3

description:
sample name in processed data file:
78-3


title: NE71-V3-31-rep2

description:
sample name in processed data file:
78-2


title: NE71-V3-31-rep1

description:
sample name in processed data file:
78-1


title: NE185-V3-31-rep1

description:
sample name in processed data file:
79-1


title: NE423-V3-31-rep2

description:
sample name in processed data file:
77-2


title: NE71-V2-31-rep3

description:
sample name in processed data file:
76-3


title: NE423-V3-31-rep1

description:
sample name in processed data file:
77-1


title: NE423-V3-31-rep3

description:
sample name in processed data file:
77-3


title: NE185-V3-31-rep2

description:
sample name in processed data file:
79-2


title: NE71-V2-31-rep2

description:
sample name in processed data file:
76-2


title: NE71-V1-31-rep2

description:
sample name in processed data file:
75-2


title: NE71-V1-31-rep1

description:
sample name in processed data file:
75-1


title: NE71-V2-31-rep1

description:
sample name in processed data file:
76-1


title: NE71-V1-31-rep3

description:
sample name in processed data file:
75-3


title: U2OS_EPZM_rep2_mRNA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
For mRRBS, basecalling was performed using Illumina RTA2 software. For RNA-seq basecalls were performed using bcl2fastq v2.17.1.14
For mRRBS and RNA-seq, indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
For mRRBS, reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences. RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014).
For mRRBS, Sequence alignment to the GRCh37/hg19 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3. For RNA-seq, reads were aligned to hg19 with Tophat version 2.1.0 with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag.
Genome_build: hg19
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary_files_format_and_content: bigwig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA at a given genomic coordinate. RNA-seq bigwigs are split by strand.

growth_protocol: Cells were grown at 37 °C in DMEM, 1x glutamine, 10% serum, 1% penicillin/streptomycin, 5% CO2

extract_protocol:
Genomic DNA was obtained using the Dneasy blood/tissue Kit (Qiagen). RNA was exctracted using Rneasy plus mini Kit (Qiagen)
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.4% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles). Total RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. polyA RNA was isolated with oligo d(T)25 Magnetic Beads from NEB. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit. RNA-sequencing was performed on the NextSeq 500 or Novaseq 6000 with 50 bp reads.

treatment_protocol: HEK-293T cells were treated once with [10µM] 5-azacytidine  for 24h,48h,72h,6 days,2 weeks. HCT-116 cells for bisulfite sequencing were treated once with [10µM] 5-azacytidine  for 24h,48h,72h. HCT-116 cells for RNA-seq were treated 4 times with [10µM] 5-aza-2-deoxyazacytidine for 4 days. U2OS cells were treated with  [5µM] EPZ-6438 for 7 days, treatment every other day.

tag: exposure


title: NE423-V1-31-rep2

description:
sample name in processed data file:
82-2


title: U2OS_EPZM_rep1_mRNA


title: U2OS_DMSO rep1_mRNA

value: DMSO


title: U2OS_DMSO_rep2_mRNA


title: HCT_aza_72hr


title: HCT_aza_24hr


title: 293T_aza_2wk


title: 293T_aza_48hr


title: 293T_aza_72hr


title: 293T_6d


title: 293T_DMSO


title: 293T_aza_24hr


title: HCT_aza_48hr


title: HCT_DMSO


title: PD_RAD21L_ChIPseq

city: Cerdanyola del Vallès (Bellaterra)

first: Covadonga

last: Vara

address: Campus UAB

department: Biologia cel·lular, Fisiologia i Immunologia

institute: Universitat Autònoma de Barcelona

data_processing:
Hi-C: Reads were quality-checked and filtered using BBDuk version10/2015 and then aligned using TADbit version 0.2.0.23. Data was binned and normalised using an in-house script taht read the map files generated after filtering, obtaining matrix that were stored into a file in NPZ format (raw).
ChIP-seq: Reads were quality-checked and mapped with BWA. Mapped reads were filtered with SAMtools. Coverage files were obtained from bam files using DeepTools:bamCoverage. All the mentioned tools were used through the Galaxy server (https://usegalaxy.org/).
RNA-seq: Reads were analysed using AIR (https://transcriptomics.cloud), were reads were filtered according to quality, mapped using STAR (Dobin et al 2013) and gene expression quantification was done using featureCounts (Liao et al 2014).
Genome_build: mm10

source_name: Pachynema/Diplonema

extract_protocol:
Lysates were clarified from sonicated nuclei and RAD21L-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Pachynema/Diplonema

tag: strain

tag: chip antibody

value: RAD21L (custom)


title: PD_CTCF_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: CTCF (Millipore, #07-729)


title: RS_CTCF_ChIPseq

source_name: Round Spermatids

value: Round Spermatids


title: PD input DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and processed as other samples, but without antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols


title: PD_REC8_ChIPseq

extract_protocol:
Lysates were clarified from sonicated nuclei and REC8-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: REC8 (custom)


title: RS_RAD21L_ChIPseq


title: RS input DNA


title: E10.5_Pitx2_null_4

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
Dissociated cardiac cells
e10.5.meta.data.csv.gz
e10.5.raw.data.csv.gz
e10.5.scale.data.csv.gz

data_processing:
The scRNA data was analyzed as previously described with minor modifications (Li et al., 2018). Briefly, raw sequencing data were handled using the 10X Genomics Cell Ranger software (www.10xgenomics.com). Fastq files were mapped to the mm10 genome, and gene counts were quantified using Cellranger count function. For E10.5 we averaged 117,673 reads per cell, and detected an average of 4,104 genes per cell across all 8 experiments. For E13.5 we averaged 40,470 reads per cell, and detected 2,646 genes per cell on average across 4 experiments. Subsequently, expression matrices from each experiment were merged and then were imported into Seurat (version 2.3.4) where log normalization was performed. We corrected for batch effects by regressing out the number of molecules per cell and the batch identity with the Seurat implementation of regression (ScaleData function). Next, we performed a principle components analysis (PCA), and significant principle components (PCs) were used as input for graph-based clustering. We used UMAP for 2-dimensional visualization of the multi-dimensional data set (McInnes and Healy, 2018). Differential expression of the individual clusters was achieved by using the Wilcoxon rank sum test (FindMarkers, default). To avoid over-clustering, we merged clusters that were not transcriptionally distinct into a single cluster. Clusters composed of doublets (2 different cell types within a single droplet) were removed from the data set. And clusters that were not obviously of cardiac origin were also removed from the final analysis, including hepatocytes, and lung epithelial cells.
Supplementary_files_format_and_content: Digital gene expression (dge) files for the raw merged data, and processed and scaled data were exported directly from Seurat as csv files. Additionally, metadata is provided.

source_name: heart

extract_protocol:
Hearts were digested in trypsin to generate a single cell suspension. Following digestion, heart tissue was washed with DMEM with 10% FBS to inactivate residual trypsin activity. Next, cells were washed twice with 1X PBS containing 0.04 % BSA before being counted. Finally, cells were loaded onto the 10X Genomics Chromium instrument.
The scRNA-seq libraries were generated using the 10X Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions and were sequenced on an Illumina Nextseq500.

tag: embryonic age

tag: genotype


title: E13.5_Control_1

description:
Dissociated cardiac cells
e13.5.meta.data.csv.gz
e13.5.raw.data.csv.gz
e13.5.scale.data.csv.gz

value: Pitx2hd+/- (het) and Pitx2hd+/+ (wildtype)


title: E10.5_Control_2


title: E13.5_Pitx2_null_2


title: E10.5_Control_1


title: E10.5_Control_3


title: E10.5_Pitx2_null_1


title: E13.5_Pitx2_null_1


title: E10.5_Pitx2_null_5


title: E13.5_Control_2


title: inv(1112)d13Z_Rad21 (ChIPm-seq)

city: Lausanne

first: Fabrice

last: Darbellay

address: Station 19

department: SV/ISREC

country: Switzerland

institute: EPFL

description: metanephros E13.5 homozygote HoxD inv(11-12)d13lacZ Rad21 ChIPmentation

data_processing:
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for R1 and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for R2)
reads were then mapped using bowtie2 on the relevant wild-type or customized mm10 mutant genome (Langmead et al. 2012, v.2.2.6.2, default parameters).
reads were filtered for a MAPQ>=30
the coverage were obtained as the output of MACS2 (Zhang et al 2008, v.2.1.0.20151222)
Genome_build: mm10 for: MN_CTCF and FB_CTCF, mutant genome versions of mm10: HoxD d13lacZ for d13Z_CTCF and d13Z_Rad21, HoxD inv(11-12)d13lacZ for inv1112d13Z_CTCF and inv1112d13Z_Rad21, HoxD del(CTCF:d12d13) for del(CTCFd12d13)_CTCF (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the coverage from MACS2

source_name: E13.5 metanephros

extract_protocol:
The ChIPmentation protocol was adapted from Schmidl et al., 2015. ChIPmentation datasets were produced from 4-5 pairs of metanephros (approx. 7.5x105 cells) or from a fraction of forebrain micro-dissected from E13.5 embryos. Samples were dissociated in Collagenase (sterile filetered, C1764 Sigma). Fixation was done in a final concentration of 1% FA (w/o methanol) for 10 minutes at room temperature and cells were then stored at -80°C. Genotyping was done on brain or tail biopsies. Chromatin shearing was done using a Covaris E220 in 120 ul sonication buffer (0.25% SDS, duty cycle at 2%, peak incident power at 105W, with the amplifier engaged and a treatment of 8 minutes). The volume for the over-night IP (4°C, 25 rpm) was adjusted at 300 ul using a dilution buffer to lower the SDS concentration and buffer the pH (final concentration of 0.1% SDS, 20 mM HEPES). Following two LiCl wash, magnetic beads were then washed 2x in 1ml 10uM TrisHCl pH=7.4 and finally resuspended in 24 ul of pre-warmed tagmentation buffer (FC-121-1030, Illumina). 1 ul of TDE1 enzyme was added to the mix and the beads were incubated for 120” at 37°C.
DNA purification, quantification and Nextera library construction were done following the published ChIPmentation protocol (Schmidl, 2015) using indexed Illumina adapters (FC-121-1011, Illumina).

tag: antibody

value: anti-RAD21 (ab992, Abcam)

value: metanephros


title: del(CTCFd12d13)_CTCF (ChIPm-seq)

description: forebrain E13.5 trans-heterozygote HoxD del(CTCFd12d13)/del(8-13) CTCF ChIPmentation

source_name: E13.5 forebrain

value: HoxD del(CTCFd12d13)/del(8-13)

value: anti-CTCF (61311, Active Motif)

value: forebrain


title: E10.5_Pitx2_null_2


title: FB_CTCF (ChIPm-seq)

description: forebrain E13.5 wt CTCF ChIPmentation

value: wild type


title: RS_REC8_ChIPseq


title: Spleen macrophages

first: Wei

last: Wang

address: No.5 Dongdansantiao

institute: PUMC

data_processing:
Primary data analysis and base calling were performed by the Illumina instrument software. Individual sequence reads with the base quality scores were produced by Illumina/Solexa.
Adapter sequences were removed from both ends of Solexa reads. All identical sequences were counted and eliminated from the initial data set. The resulting set of the unique sequences with associated read counts is referred to as sequence tags.
The unique reads were mapped onto the Mouse genome of Ensembl1 using the program Bowtie2.
The perfectly matched reads were mapped onto the Mouse micorRNA precursor of Sanger miRBase3(Release 19) by Bowtie2.  Two criteria were used to define the known microRNA: 1. A unique sequence must be perfectly mapped onto the precursor.  2. The start position of the alignment must be between +2 and -2 nt of the mature microRNA on the precursor.
Similar to credibility interval approaches reported for the analysis of SAGE data10, we employed IDEG611 to identify microRNAs showing statistically significant difference in relative abundance (as reflected by total count of individual sequence reads) between the two small RNA libraries. We used the general Chi2’ method,because it resulted in the most efficient tests11. Finally, microRNA with a P value <= 0.05 and Fold change >= 1.5 were marked to be significantly different between the two samples.
Genome_build: miRBase 19.0
Supplementary_files_format_and_content: Excel files include TPM values of each known microRNA and statistic analysis for two samples

source_name: macrophage

extract_protocol:
Macrophages from mouse breast tumor or naïve mouse spleen were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  3 ug of total RNA were used for the construction of sequencing libraries.
For small RNA library construction and deep sequencing, RNA samples were prepared by using the TruSeq Small RNA Sample Preparation Kit according to the manufacture’s protocol.

value: BALB/c

value: spleen


title: inv(1112)d13Z_CTCF (ChIPm-seq)

description: metanephros E13.5 homozygote HoxD inv(11-12)d13lacZ CTCF ChIPmentation


title: d13Z_Rad21 (ChIPm-seq)

description: metanephros E13.5 homozygote HoxD d13lacZ Rad21 ChIPmentation

value: HoxD d13lacZ/d13lacZ


title: d13Z_CTCF (ChIPm-seq)

description: metanephros E13.5 homozygote HoxD d13lacZ CTCF ChIPmentation


title: E10.5_Pitx2_null_3


title: TAMs

value: breast tumor


title: R_KO2

city: New Haven

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

description:
Sdhc_expression.txt
R_KO2_005

data_processing:
Sequencing reads were aligned to the genome with STAR
Aligned reads were annotated with HTSeq to get raw read count for each gene
Normalized experssion values were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files including normalized expression of each gene

source_name: T cells

growth_protocol: Cells cultured in Th1 conditions for 5 days

extract_protocol:
RNA was extracted from sorted cell populations using Qiagen Rneasy RNA isolation kit.
llumina TruSeq RNA Sample Prep

value: Th1 cell

value: Sdhc cKO


title: R_Cont3

description:
Sdhc_expression.txt
R_Cont3_003

value: WT


title: R_KO3

description:
Sdhc_expression.txt
R_KO3_002


title: Slc25a11_1 KO

description:
Slc25a1_Slc25a11_Mg_expression.txt
25a11_01_005


title: Slc25a1_2 KO

description:
Slc25a1_Slc25a11_Mg_expression.txt
25a1_02_004

value: 25a1 KO


title: R_KO1

description:
Sdhc_expression.txt
R_KO1_004


title: R_Cont2

description:
Sdhc_expression.txt
R_Cont2_006


title: MN_CTCF (ChIPm-seq)

description: metanephros E13.5 wt CTCF ChIPmentation


title: Slc25a1_1 KO

description:
Slc25a1_Slc25a11_Mg_expression.txt
25a1_01_003


title: R_Cont1

description:
Sdhc_expression.txt
R_Cont1_001


title: MN_inv(Nsi-Itga6)_1 (ssRNA-seq)

description: metanephros E13.5 polyA RNA heterozygote HoxD inv(Nsi-Itga6)

data_processing:
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
reads were then mapped using STAR with the ENCODE settings (Dobin et al 2013, v.2.5.2b) on the relevant wild-type or customized mm10 mutant genome, with the corresponding gtf files (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
FPKM values were determined by Cufflinks (Trapnell et al 2010, v.2.2.1) with the following options: -I 600000 -F 0.05 -j 0.05—compatible-hits-norm–multi-read-correct-library-type fr-firststrand -m 45 -s 20 --min-intron-length 40
reads were filtered for uniquely mapped read (NH:i:1) and strand specific coverage was computed using BEDTools (Quinlan et al. 2010, v.2.19.1)
Genome_build: mm10 for: AUT_bal, MN_bal1, MN_bal2, MN_1, MN_2, MN_inv(Nsi-Itga6)_1, MN_inv(Nsi-Itga6)_2, MN_inv(Nsi-Itga6)del(13HD), mutant genome versions of mm10: HoxD d13lacZ for MN_d13Z, HoxD inv(11-12)d13lacZ for MN_inv1112d13Z and MN_inv1112del11d13Z, HoxD del(CTCF:d12d13) for MN_del(CTCFd12d13)_1 and MN_del(CTCFd12d13)_2, HoxD inv(11) for AUT_inv(11) and MN_inv(11), HoxD inv(12) for AUT_inv(12) and MN_inv(12) (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the strand specific coverage, txt files contains FPKM values

extract_protocol:
Whole RNA was extracted from micro-dissected tissues using RNeasy plus micro kit (Qiagen) following the manufacturer recommendations
At least 1.5ug of total RNA (RIN>9) was prepared for stranded RNA sequencing using TruSeq kits (Illumina). Samples were poly(A)-enriched.

value: HoxD inv(Nsi-Itga6)/+


title: MN_2 (ssRNA-seq)

description: metanephros E13.5 polyA RNA wild type


title: Slc25a11_2 KO

description:
Slc25a1_Slc25a11_Mg_expression.txt
25a11_02_006


title: MN_1 (ssRNA-seq)

description: metanephros E13.5 polyA RNA wild type


title: MN_inv(Nsi-Itga6)_2 (ssRNA-seq)


title: Inv(1112)d13Z_H3K4me3 (ChIP-seq)

description: metanephros E13.5 homozygote HoxD inv(11-12)d13lacZ H3K4me3 ChIP-seq

data_processing:
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
reads were then mapped using bowtie2 on the relevant customized mm10 mutant genome (Langmead et al. 2012, v.2.2.6.2, default parameters)
reads were filtered for a MAPQ>=30
the coverage were obtained as the output of MACS2 (Zhang et al 2008, v.2.1.0.20151222)
Genome_build: mutant genome versions of mm10: HoxD d13lacZ for d13Z_H3K27me3 and d13Z_H3K4me3 and HoxD inv(11-12)d13lacZ for inv1112d13Z_H3K27me3 and inv1112d13Z_H3K4me3 (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the coverage from MACS2

extract_protocol:
ChIP were produced from E13.5 metanephros. Pairs of metanephros were individually fixed in 1% Formaldehyde for 20 minutes at room temperature and stored at -80°C. Genotyping was done on tail biopsies. Shearing was performed on a Bioruptor (Diagenod) in 1% SDS. ChIP was done by over-night incubation of protA/protG magnetic beads conjugated with the desired antibody in 1.2ml dilution buffer, rotating at 30 rpm 4°C. Washes were performed in 1ml of washing buffers, incubated at 4°C for 2 minutes: 2x RIPA/2x RIPA-500mM NaCl/2x LiCl/2x TE. Beads were eluted and chromatin fixation was reversed during an over-night incubation at 65°C in presence of proteinase K. The eluate was treated with RNase A, PCI purified and precipitated.
5-10 ng of purified DNA were used to built libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumina HiSeq according to the manufacturer’s specifications.

value: anti-H3K4me3 (17-614, Millipore)


title: inv(1112)d13Z_H3K27me3 (ChIP-seq)

description: metanephros E13.5 homozygote HoxD inv(11-12)d13lacZ  H3K27me3 ChIP-seq

value: anti-H3K27me3 (17-622, Millipore)


title: Mg_01

description:
Slc25a1_Slc25a11_Mg_expression.txt
Mg_01_001

value: EV Transduced (WT)


title: d13Z_H3K4me3 (ChIP-seq)

description: metanephros E13.5 homozygote HoxD d13lacZ H3K4me3-seq

value: metanephros


title: Mg_02

description:
Slc25a1_Slc25a11_Mg_expression.txt
Mg_02_002


title: 128L:11:11TG221Liver_metformin_CCl4_m3

city: Ferrara

last: Negrini

state: Ferrara

address: 70 Via Fossato di Mortara

department: Morphology, Surgery and Experimental Medicine

institute: University of Ferrara

description: Gene expression after metformin intervention in CCl4 induced mouse model of HCC with cirrhosis background

hyb_protocol: Hybridization was performed on to Agilent mouse gene expression 8x60K microarray, according to the manufacturer's protocol (G4140-90040).

scan_protocol: Images of slides were captured by the Agilent 2565C DNA Microarray Scanner and raw microarray data was obtained by accompanying Agilent Feature Extraction Software (v10.5).

data_processing: Raw microarray were imported into Qlucore omics explorer (v3.4, Qlucore AB, Sweden), Data transformation was applied to set all the negative raw values at 1.0, followed by a Quantile normalization. FDR <0.01 and fold change >1.5 filters were applied.

source_name: Liver

label_protocol: One hundred nanograms of total RNA from each sample was used to synthesize cyanine 3-CTP (Perkin-Elmer Life Sciences, Boston, USA) labelled cRNA with Low RNA Input Linear Amplification kit (Agilent Technologies) following manufacturer’s protocol.

extract_protocol: Total RNA from snap frozen samples was extracted using Trizol Reagent (FS-881, FMB, Trevose, USA) according to manufacturer’s instructions. Quantity and quality of RNA was assessed with RNA-600 nanochip (Agilent Technologies) on Agilent 2100 Bioanalyzer. Samples with RNA integrity number above 8 were utilized for microarray.

treatment_protocol: Male miR-221 transgenic (TG221) strain with B6D2F2 background mice (4-6 wks of age) were administered 20% v/v CCl4 in olive oil by oral gavage (p.o.) three times a week for a duration of 14 wks. Metformin intervention was started after 3 wks of initiating CCl4 challenge at 300mg/kg body weight (BW) daily p.o., dissolved in distilled water. Mice were randomly assigned to the different experimental arms. At the experimental end-point (24wks) liver tissue was harvested and snap frozen in liquid nitrogen. Mice were maintained in vented cabinets at 24° C with a 12-hour light-dark cycle. Food and water were provided ad libitum. All animal procedures were performed according to the guidelines of the Italian Ministry of Health Public Health Service Policy on Care and Use of laboratory animals, and in accordance with a protocol approved by the Institutional Animal Care Committee of University of Ferrara and Italian Ministry of Health.

tag: strain background

tag: Sex

value: male

tag: genotype/variation

value: TG221 transgenic mouse

value: Liver

value: hepatocellular carcinoma (HCC)


title: 131L:11:11TG221Liver_metformin_CCl4_m6

tag: cell type


title: 43L:11:11TG221Liver_CCl4_m1

description: Gene expression in CCl4 induced mouse model of HCC with cirrhosis background

tag: tissue


title: 41L:11:11TG221Liver_CCl4_m2


title: 130L:11:11TG221Liver_metformin_CCl4_m4


title: 45L:11:11TG221Liver_CCl4_m3


title: 132L:11:11TG221Liver_metformin_CCl4_m5


title: 33L:11:11TG221Liver_CCl4_m4


title: 127L:11:11TG221Liver_metformin_CCl4_m1


title: d13Z_H3K27me3 (ChIP-seq)

description: metanephros E13.5 homozygote HoxD d13lacZ H3K27me3 ChIP-seq


title: lacZ_inv1112d13Z_G44 (4C-seq)

description: 4C-seq, viewpoint lacZ generated from metanephros E13.5 homozygote HoxD inv(11-12)13lacZ

data_processing:
de-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014). Reads were first mapped to customized mm10 mutant genome (HoxD d13lacZ for Hoxd9_d13Z_C14 and lacZ_d13Z_C44, HoxD inv(11-12)d13lacZ for Hoxd9_inv1112d13Z_G34 and lacZ_inv1112d13Z_G44) with bowtie2 (Langmead et al 2012, v.2.2.1) with parameters --end-to-end --sensitive -k 20 . segToFrag files were generated from these mapping, using customized segment libraries (available on figshare DOI: 10.6084/m9.figshare.7752065)
normalisation of segToFrag file is computed by dividing each fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample. A running mean algorithm with a window size of eleven fragments was used to smooth the normalized segtofrag file.
Genome_build: mutant genome versions of mm10: HoxD d13lacZ for , HoxD inv(11-12)d13lacZ for MN_inv1112d13Z and MN_inv1112del11d13Z (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the normalized/smoothed coverage computed from the segToFrag files

extract_protocol:
Metanephros were micro-dissected and dissociated from homozygous E13.5 mutant embryos (HoxD d13lacZ and HoxD inv(11-12)d13lacZ). Metanephric kidneys were dissociated with collagenase (Sigma Aldrich/Fluka). Cells were fixed with 2% formaldehyde (in PBS/10%FBS) for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 10 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Samples were digested again with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with barcodes allowing multiplexing. The Illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the inverse-forward primers located at the NlaII site and 5'-CAAGCAGAAGACGGCATACGA-3' for the inverse-reverse primers located at the DpnII site. Barcodes (4bp) were added between the illumina adaptor and the specific NlaIII primers when the same viewpoints were multiplexed in the same run. The barcode is mentioned in the raw file name being: C14 (CAGA), G34 (GATC), C44 (CTGT) and G44 (GCCA). Specific primer information for each viewpoint is displayed in the related publication (Darbellay et al, 2019).


title: 2586_scERα_KO

city: Minneapolis

first: Dawn

last: Lowe

state: MN

address: 420 Delaware St SE, MMC 388

department: Rehabilitation Medicine

institute: University of Minnesota

data_processing:
Illumina Casava software used for basecalling.
50bp FastQ paired-end reads (n=23.1 Million average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. In addition, headcrop was used to remove 3bp inserted at the 5' end of reads during the SMARTer Stranded pico mammalian library preparation.Quality control on raw sequence data for each sample were performed with FastQC.
RNA-seq reads were aligned to Mus musculus reference transcriptome (GRCm38/mm10) using Kallisto (Bray et al., Nature biotechnology, 2016.)(v0.44.0) quant, and the R package tximport (Soneson et al., F1000Research, 2015.)(v1.10.0) was used to convert the output to Transcript Per Million (TPM) values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files includeTPM values for each Sample

source_name: hindlimb muscles

extract_protocol:
Qiagen RNeasy Plus Universal Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice received tamoxifen injection treatment (10 mg total)

value: Adult

value: scER{alpha} KO

tag: primary cell type

value: skeletal muscle satellite cell


title: Hoxd9_d13Z_C14 (4C-seq)

description: 4C-seq, viewpoint Hoxd9 generated from metanephros E13.5 homozygote HoxD d13lacZ

value: HoxD d13lacZ/d13lacZ


title: 134L:11:11TG221Liver_metformin_CCl4_m2


title: 2587_scERα_WT

value: scER{alpha} WT


title: lacZ_d13Z_C44 (4C-seq)

description: 4C-seq, viewpoint Hoxd9 generated from metanephros E13.5 homozygote HoxD inv(11-12)13lacZ


title: 2589_scERα_WT


title: 2495_scERα_WT


title: Hoxd9_inv1112d13Z_G34 (4C-seq)

description: 4C-seq, viewpoint lacZ generated from metanephros E13.5 homozygote HoxD d13lacZ


title: In vitro derived macrophages CX3 1 5

city: Bellinzona

first: Andrea

last: Rinaldi

state: Ticino

address: via vela 6

institute: IOR - oncology institute of southern switzerland

description: In vitro derived macrophages

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

label: biotin

source_name: Bone marrow derived macrophages, CXCL3 treated

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Ex vivo macrophages or epithelial cells were isolated from the prostatic tissue of  mice and immediately processed; in vitro macrophages were obstained from bone marrow precursors upon differentiation for 7 days

extract_protocol: Total RNA was quantified by NanoDrop ND-1000 Spectro-photometer (NanoDrop Technologies, Wilming-ton, DE) and RNA quality was assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were treated with intraperitoneal injections of 100ml of the vehicle or 100ml aCXCR2 (AZD5069) from Astrazeneca, at a final concentration of 100mg/kg daily for a period of 3 weeks

value: Bone marrrow


title: In vitro derived macrophages CX3 8 5

description: In vitro derived macrophages


title: In vitro derived macrophages M2 8 5

description: In vitro derived macrophages

source_name: Bone marrow derived macrophages, IL-4/IL-13 treated


title: In vitro derived macrophages M1 8 5

description: In vitro derived macrophages

source_name: Bone marrow derived macrophages, IIFNg/LPS treated


title: In vitro derived macrophages M1

description: In vitro derived macrophages


title: In vitro derived macrophages CX2 8 5

description: In vitro derived macrophages

source_name: Bone marrow derived macrophages, CXCL2 treated


title: In vitro derived macrophages CX3

description: In vitro derived macrophages


title: 2582_scERα_KO


title: 2588_scERα_KO


title: In vitro derived macrophages M2 1 5

description: In vitro derived macrophages


title: In vitro derived macrophages CX2

description: In vitro derived macrophages