title: ACTA2R179H_IPHDAC9

status: Public on Jan 13 2018

city: Boston

first: christian

middle: lacks

last: lino cardenas

state: Massachusetts

address: 185 Cambridge st Room 3224

department: division of cardiovascular

institute: Massachusetts general hospital-Harvard medical school

data_processing:
CLIP-seq reads were aligned to human UCSC h19 using standard Illumina library-type. Cufflinks 2.0.2 was run on merged bam files to assemble of transcripts and estimation of FPKM values. FPKM≤ 1.0 cutoff was used as detection threshold to generate the list of genes.
Genome_build: UCSC h19
Supplementary_files_format_and_content: FPKM values

source_name: Aortic Smooth Muscle Cells

growth_protocol: Aortic Smooth Muscle Cells were

extract_protocol: For CLIP-seq 5 million cells were UV cross-linked using 2000 µJoules/cm2 followed by extraction  of nuclear proteins. UV crosslinked lysates from vector transfected, TGFR2G357W and ACTA2R179H  transfected cells were pre-supplemented with RNAse inhibitor (1:100), protease inhibitor cocktail,   phenylmethylsulfonyl fluoride (1mM, PMSF) and treated with turbo DNAse I for 30min at 37C.  Lysates were then incubated with HDAC9 or BRG1 antibodies at 4C overnight. RNA extraction  from HDAC9 and BRG1 pull downs were performed using miRNeasy kit (Qiagen, USA) according  to the manufacturer’s instruction. RNA sequencing for human mRNA and lncRNAs were performed using Ribo-Zero™ Magnetic Kit and RnaseH is used to remove rRNA, remained RNA is then retrieved by ethonal precipitation. The retrieved RNA is fragmented using Ambion Fragmentation Solution. And according to Illumina solexa transcriptome sequencing protocol, random hexamer-primer was used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding A at 3’   end. After that, the fragments are ligated with sequencing adaptors. UNG is added before   synthesizing the second cDNA strand. After the second strand degraded, dUTP is then converted   to dTTP. Y-adaptor is added afterwards. Suitable fragments are selected as templates according   to the agarose gel electrophoresis results for PCR amplification. Generated libraries were sequenced using Illumina HiSeq™ technology.

value: Aortic Smooth Muscle Cells

tag: passage

value: ACTA2R179H mutant

tag: rip antibody


title: ACTA2R179H_IPBRG1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: genotype/variation


title: TGFR2G357W_IPBRG1

value: TGFR2G357W mutant


title: mmu_Nrep(miR-29scr) 3

status: Public on Jan 14 2018

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Basecalls performed using CASAVA for all libraries.
RNA-seq FASTQ files were mapped to the zebrafish genome version danRer7 with TopHat version 2.0.6 using the global alignment option and a seed size of 22 without allowing mismatches in this region. Only the unique best hits were kept.
FASTQ files containing the small RNA sequencing data were stripped of adapter sequences using the Reaper tool and sequences between 16-24nt were selected and mapped using a command-line variant of chimiRa to known microRNA precursors from miRBase (v21). Each sequence was assigned to a mature miRNA according to which arm (5p or 3p) of the precursor was matched and to the known mature sequence. In cases where a single sequence mapped to multiple possible loci, a random locus was assigned each time. These raw counts were assembled into a table across all microRNAs from all samples (R/BioConductor) and normalized using DESeq2. Differential expression was performed using the negative binomial Wald test (DESeq2) for differences between mutant versus wild type. All derived P-values for differential expression were multiple testing corrected using the Benjamini-Hochberg method. The trimming analysis was performed by examining the fraction of nucleotides from the annotated microRNA from miRBase that was covered by each mapped read from each sample. The mean of these values was used to compute differential trimming using a paired t-test on the derived values between 17-27nt between mutant and wild type samples for miR-29b.
Genome_build: danRer7, miRBase (v21)
Supplementary_files_format_and_content: BAM files from technical duplicates of the zebrafish libraries were merged and used to generate pileup tracks with BEDTools and UCSC tools. Tab-delimited text file includes the raw read counts for microRNA precursors for all small RNA-seq libraries.

organism: Mus musculus

source_name: ES14 male differentiated to NPCs

extract_protocol:
Total RNA was harvested from 100zebrafish embryos and >20 million mouse NPCs for each replicate using Trizol reagent. One microgram of total RNA was used for the construction of both RNA and small RNA sequencing libraries.
RNA libraries were prepared for sequencing using standard manufacturers' protocols (Illumina TruSeq kit for RNA-Seq libraries and NEBNext Multiplex small RNA library kit for small RNA libraries).

value: NPCs

tag: genotype


title: TGFR2G357W_IPHDAC9


title: WT_IPBRG1

value: WT


title: 64_SL253813

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
Sequences were trimmed of their adapters
Reads were aligned to the bovine genome , and sequences aligning to multiple places on the genome, with 5 or more mismatches were filtered out. The sequences were then marked for duplicates, and non-duplicated reads were used for gene expression study
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples
Supplementary_files_format_and_content: tab-delimited text files include count reads

organism: Bos taurus

source_name: Peripheral white blood cells

extract_protocol:
Total RNA was then isolated from PWBCs of 23 heifers using TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol
Libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina, Inc., San Diego, CA) following manufacturer’s instructions

tag: station

value: Station B

tag: pregnancy outcome


title: 36_SL253812


title: 55_SL253810


title: 39_SL253811


title: 42_SL253809


title: 58_SL253814


title: WT_IPHDAC9


title: 53_SL253806

extract_protocol:
Total RNA was then isolated from PWBCs of 24 heifers using TRIzolä reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol
Libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina, Inc., San Diego, CA) following manufacturer’s instructions


title: 62_SL253807


title: 61_SL253805


title: 59_SL253804


title: mmu_Nrep(miR-29scr) 1


title: zf_libra(del)

organism: Danio rerio

source_name: 72 hpf embryos

tag: strain

value: AB

tag: tissue

value: whole embryos

tag: age

value: 72 hours post fertilization

value: libra deletion


title: Rh2

city: FORT PIERCE

first: JINHE

last: BAI

state: FLORIDA

address: 2001 SOUTH ROCK RD

department: HORTICULTURAL RESEARCH LABORATORY

institute: USDA-ARS

description:
Healthy retain replicate 2
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that remain on the healthy trees when shaking the trees

data_processing:
The raw reads (fastq files) from Illunima HiSeq1500 were aligned to reference genome using TopHat version 1.4.1 with RefSeq annotations and the “—no-novel-juncs” option.
Ambiguous reads that mapped to more than one region in the genome and those reads with MAPQ score less than 10 were removed.
Citrus sinensis v1.1 from Phytozome v10.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Csinensis) was used as the reference genome and for transcript annotations.
Transcript quantification was performed using Partek Genomics Suite (Partek Inc, St. Louis MI), and the normalized read counts (RPKM: reads per kilobase per million mapped reads) were used to estimate the gene expression levels.
Differential expression analysis between treatments was performed using the DESeq R package. The resulting p values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR).
Genome_build: Citrus sinensis v1.1 from Phytozome v10.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Csinensis)
Supplementary_files_format_and_content: List of the mapped transcripts, reads, RPKMs

organism: Citrus sinensis

source_name: Healthy retain

growth_protocol: Six-year old ‘Hamlin’ orange trees (Citrus sinensis (L.) Osbeck), about 2.5-3.0 m tall, on 'Swingle' citrumelo (C. paradisi Macf. × Poncirus trifoliata (L) Raf.) rootstock, in a commercial grove located in Southern Florida. The trees were similar in size, and all were grown under similar agro-climatic conditions and received common cultural practices and the grower’s standard pest and disease management. Fruit were harvested on 1 Dec. 2014 (during commercial harvest season).

extract_protocol:
Total RNA was extracted from frozen AZ-C by RNeasy Plant Kit (Qiagen) following the manufacturer’s instructions. DNA was removed by on column DNase treatment with RNase-free DNase Set (Qiagen).
The purity and concentration of total RNA were determined using a 2100 bioanalyzer (Agilent). cDNA libraries were generated using the mRNA Sequencing Sample Preparation Kit following the manufacturer’s instructions (Illumina, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and cDNA was then synthesized. cDNA fragments 200 ± 25 bp in size were selected and PCR was performed with High-Fidelity DNA polymerase, universal PCR primers and Index (X) Primer. PCR products were purified and the library preparations were sequenced on the Illumina cluster station and Illumina HiSeq1500 sequencing platform.

treatment_protocol: Thirty six trees were selected for the experiment, of which eighteen were CLas negative (healthy) and the other eighteen were CLas positive (HLB), as tested by qPCR using the method of Li et al. (2006). The ground under the trees was cleaned just before shaking the trees, and trees were shaken manually. For HLB-diseased trees (d), many of the fruit dropped (Dd) upon shaking the trees. For healthy trees (h), the forces of shaking were strong enough to get enough number of dropped fruit (Dh) from the trees. The dropped fruit (Dd or Dh) were collected, and the retained fruit on HLB-diseased (Rd) or healthy trees (Rh) were hand-picked off the trees. The fruit from nine trees were pooled together as a group. There were two groups (biological replicates) for each of the Dd, Rd, Dh and Rh. Thirty fruit were randomly picked from each of the Dd, Rd, Dh and Rh groups, and the AZ-C were excised and immediately frozen in liquid nitrogen and stored at –80 ºC for RNA isolation.

tag: cultivar

value: Hamlin

tag: disease state

value: Healthy

tag: fruit status

value: retain

value: calyx abscission zone


title: Rh1

description:
Healthy retain replicate 1
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that remain on the healthy trees when shaking the trees


title: Rd1

description:
Huanglongbing retain replicate 1
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that remain on the HLB-diseased trees when shaking the trees

source_name: Huanglongbing retain

value: Huanglongbing


title: Rd2

description:
Huanglongbing retain replicate 2
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that remain on the HLB-diseased trees when shaking the trees


title: Dh2

description:
Healthy drop replicate 2
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that drop from healthy trees when vigorously shaking the trees

source_name: Healthy drop

value: drop


title: Dd2

description:
Huanglongbing drop replicate 2
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that drop from the HLB-diseased trees upon shaking the trees

source_name: Huanglongbing drop


title: Dh1

description:
Healthy drop replicate 1
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that drop from healthy trees when vigorously shaking the trees


title: Dd1

description:
Huanglongbing drop replicate 1
'Hamlin' orange (Citrus sinensis (L.) Osbeck)
fruit that drop from the HLB-diseased trees upon shaking the trees


title: 49_SL253808


title: ctrl-2

status: Public on Jan 12 2018

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

library_source: genomic

data_processing:
Illumina sequencing reads were mapped to UCSC hg19 human reference genome using bowtie program. Only uniquely mapped reads were retained for the following data analysis.
PCR duplicates were removed using samtools.
The identification of 5hmC peaks in each sample was performed using MACS, , and an IDR cutoff of  0.01 was used to filter high confident peaks.
Peaks from different samples were merged together into a unified catalog of 5hmC enriched regions using HOMER.
BigWig files were generated by deepTools with RPKM normalization method.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files for each sample was generated by deepTools with normalization to the input sample.

molecule: genomic DNA

source_name: acute myeloid leukemia

growth_protocol: ML2 cells were grown in RPMI1640 median containing 10%FBS.

extract_protocol:
Genomic DNA was extracted with Qiagen Dneasy Blood & Tissue kit according to the manufacturer's protocol.
100 ng genomic DNA extracted from ML2 cell were fragmented in 50 μL Tagmentation buffer at 55°C. Fragmented DNA was purified by Zymo DNA clean&concentrator Kit (Zymo Research, Tustin, CA). Then, the selective 5hmC chemical labeling was performed in 25 μL glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, 100 μM N3-UDP-Glc, 1 μM β-GT, and incubated at 37°C for 2 hr. After purified in 45 μL ddH2O, 1.5 μL DBCO-PEG4-Biotin (Click Chemistry Tools, 4.5 mM stored in DMSO) was added and incubated at 37°C for 2 hr. The biotin labeled DNA was pulled down by 5 µL C1 Streptavidin beads (Life Technologies, Carlsbad, CA) for 15 min at room temperature. Next, the captured DNA fragments were subjected to 13 cycles of PCR amplification using Nextera DNA sample preparation kit (Illumina, San Diego, CA). The resulting amplified product was purified by 1.0X AMPure XP beads. Input library was made by direct PCR from fragmented DNA without chemical labeling and capture. The libraries were quantified by a Qubit fluorometer (Life Technologies) and sequenced on an Illumina HiSEQ4000 sequencer with paired-end 50-bp reads.

treatment_protocol: ML2 cells were treated with 500 nM chemical compounds (370284-1/-2, and 514321-1/-2) or DMSO control (ctrl-1/-2) for 48 hrs.

tag: technology

tag: agent

value: DMSO


title: 514321-2


title: 514321-1


title: 63_SL253803


title: 370284-2


title: T84

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

description:
PolyA
Processed data file: cl_gene_counts.table.txt:

data_processing:
Trimmed adaptors using Trimmomatic, reads <50 bp removed (v0.22).
tophat -g 1 -library-type fr-firststrand hg19 <fastq.gz> (v2.0.8)
featureCounts -a gc15.woPseudoGenes.gtf -t exon -g gene_name -s 2 (subread-1.4.5-p1-Linux-x86_64)
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: cl_gene_counts.table.txt: Tab-delimited text file includes read counts for each sample.

source_name: T84 epithelial colorectal cancer cell line

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco BRL Life Technologies) supplemented with 10% fetal bovine serum (FBS; Bovogen Biologicals), 100U/ ml penicillin-streptomycin (Sigma-Aldrich) at 37°C and 5% CO2 incubator. Cells were verified to be mycoplasma free using the Lookout Mycoplasma PCR Detection kit (Sigma-Aldrich). All the cell lines were authenticated at the Australian Genome Research Facility Ltd. (AGRF) (Parkville, VIC, Australia) by STR profiling analysis using the GenePrint 10 System (Promega).

extract_protocol:
AllPrep DNA/RNA Mini kit (Qiagen).
TruSeq Stranded Total RNA Library Preparation Kit.

tag: cell line

value: epithelial colorectal cancer cell line


title: 370284-1


title: VACO5

source_name: VACO5 epithelial colorectal cancer cell line


title: V9P

source_name: V9P epithelial colorectal cancer cell line


title: SW620

source_name: SW620 epithelial colorectal cancer cell line


title: input


title: SW948

source_name: SW948 epithelial colorectal cancer cell line


title: SW480

source_name: SW480 epithelial colorectal cancer cell line


title: SNUC2B

source_name: SNUC2B epithelial colorectal cancer cell line


title: SW1116

source_name: SW1116 epithelial colorectal cancer cell line


title: VACO4S

source_name: VACO4S epithelial colorectal cancer cell line


title: SW1222

source_name: SW1222 epithelial colorectal cancer cell line


title: ctrl-1


title: RKO

source_name: RKO epithelial colorectal cancer cell line

value: RKO


title: LIM2537

source_name: LIM2537 epithelial colorectal cancer cell line


title: NCIH747

source_name: NCIH747 epithelial colorectal cancer cell line


title: SNU175

source_name: SNU175 epithelial colorectal cancer cell line


title: LIM2551

source_name: LIM2551 epithelial colorectal cancer cell line


title: LS513

source_name: LS513 epithelial colorectal cancer cell line


title: LIM2099

source_name: LIM2099 epithelial colorectal cancer cell line


title: LIM2405

source_name: LIM2405 epithelial colorectal cancer cell line


title: LIM1899

source_name: LIM1899 epithelial colorectal cancer cell line


title: LIM1863

source_name: LIM1863 epithelial colorectal cancer cell line


title: IS3

source_name: IS3 epithelial colorectal cancer cell line


title: LIM1215

source_name: LIM1215 epithelial colorectal cancer cell line


title: IS2

source_name: IS2 epithelial colorectal cancer cell line


title: IS1

source_name: IS1 epithelial colorectal cancer cell line


title: HT29

source_name: HT29 epithelial colorectal cancer cell line


title: HT55

source_name: HT55 epithelial colorectal cancer cell line


title: HT115

source_name: HT115 epithelial colorectal cancer cell line


title: HRA19

source_name: HRA19 epithelial colorectal cancer cell line


title: HCT116

source_name: HCT116 epithelial colorectal cancer cell line


title: HCT15

source_name: HCT15 epithelial colorectal cancer cell line


title: COLO205

source_name: COLO205 epithelial colorectal cancer cell line


title: HCA7

source_name: HCA7 epithelial colorectal cancer cell line


title: HCC2998

source_name: HCC2998 epithelial colorectal cancer cell line


title: DiFi

source_name: DiFi epithelial colorectal cancer cell line

value: DiFi


title: DLD1

source_name: DLD1 epithelial colorectal cancer cell line


title: GEO

source_name: GEO epithelial colorectal cancer cell line

value: GEO


title: HCT8

source_name: HCT8 epithelial colorectal cancer cell line


title: Gp5D

source_name: Gp5D epithelial colorectal cancer cell line


title: COLO201

source_name: COLO201 epithelial colorectal cancer cell line


title: CACO2

source_name: CACO2 epithelial colorectal cancer cell line


title: C135

source_name: C135 epithelial colorectal cancer cell line


title: COLO320

source_name: COLO320 epithelial colorectal cancer cell line


title: C125PM

source_name: C125PM epithelial colorectal cancer cell line


title: Ctrl_2

city: wuhan

first: linjian

last: xia

address: wuhan

country: China

institute: wuhan University

description:
ctrl-2
Rep1
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
fastq sequences were aligned to hg19 using Tophat.
Number of reads was calculated for each Entrez gene.
Differential expression analysis was performed using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Group370_vs_GroupCtrl.all.gene.result.txt: Tab-delimited text file includes expression information with genes in rows and samples in columns.

source_name: THP-1 cells, control

growth_protocol: THP-1 cells were grown in RPMI1640 medium with 10% FBS.

extract_protocol:
RNA was extracted by mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with total RNA extraction protocol. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with 50 nM NSC-370284 or DMSO control.

value: acute monocytic leukemia cell line

tag: treatment


title: Ctrl_4

description:
ctrl-4
Rep3
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt


title: Ctrl_3

description:
ctrl-3
Rep2
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt


title: JS170735

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description: Heat shock MEF negative control TimeLapse experiment with chemical treatment but no s4U treatment.

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCm38 or GRCh38 genome (MEF or K562, respectively) using STAR aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Genome_build: GRCh38

source_name: immortalized MEFs

growth_protocol: MEF cells were grown in DMEM containing 1% penicillin/streptomycin, 10% FBS, at 37°C. K562 cells were grown in RPMI containing 1% penicillin/streptomycin, 10% FBS, at 37°C.

extract_protocol:
MEF RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation. K562 RNA was harvested with a modified RNeasy protocol as described in the methods section. Chemically treated RNAs were treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in the methods section. MTS-enriched RNAs for transient transcriptome studies were prepared using a modified protocol from Duffy et al. Mol Cell (2015), as described in the methods section.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio USA, cat. 635005).

treatment_protocol: s4U plus and minus MEF cells had their media replaced with growth media supplemented with 1 mM s4U or left unsupplemented, respectively. HS and NHS cells were incubated during this 1h feed at 42°C and 37°C, respectively. For transcriptome-wide studies, s4U plus and minus K562 cells had their growth media supplemented with 100 µM s4U for 4h or left unsupplemented, respectively.  For transient transcriptome studies, s4U plus and minus K562 cells had their growth media supplemented with 1 mM s4U for 5min or left unsupplemented, respectively.

value: F1:129S1/CastEiJ x 129S1

tag: heat shock

value: Yes

tag: s4u feed

value: No

tag: chemical treatment


title: NSC-370284_4

description:
370-4
Rep2
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt

source_name: THP-1 cells, NSC-370284

tag: cell type


title: NSC-370284_5

description:
370-5
Rep3
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt


title: JS170732

description:
MEF TimeLapse experiment. For the processed data files, reads of combined replicates (JS170732 and JS170733) filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)
MEF1707-PP.0.min.bedGraph
MEF1707-PP.0.pos.bedGraph
MEF1707-PP.1.min.bedGraph
MEF1707-PP.1.pos.bedGraph
MEF1707-PP.2.min.bedGraph
MEF1707-PP.2.pos.bedGraph
MEF1707-PP.3.min.bedGraph
MEF1707-PP.3.pos.bedGraph
MEF1707-PP.4.min.bedGraph
MEF1707-PP.4.pos.bedGraph
MEF1707-PP.5.min.bedGraph
MEF1707-PP.5.pos.bedGraph


title: NSC-370284_2

description:
370-2
Rep1
PolyA RNA
Processed data file: Group370_vs_GroupCtrl.all.gene.result.txt


title: Suz12KO_129B6F1_Ezh2_ChIP

city: Copenhagen N

first: Jonas

middle: Westergaard

last: Hojfeldt

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Trimmed with Trimmomatic: SLIDINGWINDOW across 4 bases, average quality required 2
Alligned with STAR 2.4.0, built-in index mm10, default parameters
htseq-count, union mode, non-stranded, minimum alignment quality 10
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-Seq] tabular files contain gene counts
[ChIP-Seq]  No processed data.  Aligned BAM-files have been imported and analyzed/visualized within a software called Easeq (Easeq.net<http://Easeq.net>,  Nature Structural & Molecular Biology Volume 23 No 4 (April 2016), 349-357)).

source_name: Embryonic stem cells

growth_protocol: Cells grown on gelatin in 2i media

extract_protocol: NEBNext Ultra II protocol (NEB, E7645S)

tag: chip antibody

value: Ezh2 (Cell Signaling, Rabbit mAb, D2C9)

tag: genotype

value: Suz12 KO


title: Suz12DeltaVEFS_Suz12_ChIP

value: Suz12 (Cell Signaling, Rabbit mAb, D39F6)

value: SUZ12-DeltaVEFS rescue


title: Suz12VEFS_Flag_ChIP

value: Flag (Sigma, M2 affinity gel A2220)

value: SUZ12-VEFS rescue


title: Suz12rescue_Suz12_ChIP

value: SUZ12 rescue


title: Suz12WT_129B6F1_Ezh2_ChIP

value: WT


title: Suz12KO_B6_Suz12_ChIP


title: EedKO_Suz12_ChIP

value: Eed KO


title: Suz12VEFS_Suz12_ChIP


title: Suz12DeltaVEFS_Flag_ChIP


title: Suz12KO_129B6F1_Suz12_ChIP


title: C70

source_name: C70 epithelial colorectal cancer cell line

value: epithelial colorectal cancer cell line


title: E14_24h_washout_H3K27me1_ChIP

value: H3K27me1 (Takara, mouse mAb, MABI0321)


title: Suz12WT_129B6F1_Suz12_ChIP

value: Suz12 WT


title: Ezh1WT_Ezh2WT_Suz12_ChIP


title: E14_96h_washout_H3K27me1_ChIP


title: E14_16h_washout_H3K27me1_ChIP


title: E14_8h_washout_H3K27me1_ChIP


title: E14_48h_washout_H3K27me1_ChIP


title: E14_4h_washout_H3K27me1_ChIP


title: Taf1 ChIP-Exo HS3 replicate1

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

description:
Replicate 1
HS_project_extract_tag_ratio.csv

data_processing:
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Supplementary_files_format_and_content: gff, gene track peak calls using (smoothing 5bp, exclusion 10bp)
Supplementary_files_format_and_content: txt, peak pair calls filtered for significance over background
Supplementary_files_format_and_content: csv, extraction of PIP-seq, ChIP-exo tag count(or ratio to NoTag) in TSS
Supplementary_files_format_and_content: tab, tag extraction from 5' end of uniquely mapped sequencing reads, tab-delimited

organism: Saccharomyces cerevisiae

source_name: in vivo

growth_protocol: For ChIP-exo, cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
For ChIP-exo, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard SOLiD & Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo, PIP-seq

treatment_protocol: For ChIP-exo, cells were crosslinked with formaldehyde to a final concentration of 1.0%.For PIP seq 100 mMKmNO4 added.

tag: cell description

value: GRF88, MATa his4-38, S288C background


title: E14_7d_inh_H3K27me1_ChIP

tag: strain


title: E14_96h_washout_H3K27me2_ChIP

value: H3K27me2 (Cell Signaling, Rabbit mAb, D18C8)


title: E14_48h_washout_H3K27me2_ChIP


title: SUM44_LTED_repl3

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

description: SUM44 LTED replicate 3

data_processing:
Tophat (v2.1) and Cuffdiff (v2.2.1) using default parameters
Genome_build: Human Reference Genome (assembly hg19)
Supplementary_files_format_and_content: Cuffdiff output files

source_name: breast cancer cell line

growth_protocol: cultured in phenol red-free RPMI1640 medium supplemented with 10% FBS and 1 nmol/L estradiol (E2)

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
Libraries were created after Ribo-zero rRNA removal kit (Illumina) using NEBNext Ultra Directional RNA (NEB) kit

treatment_protocol: LTED cells modeling resistance to an AI were derived from  long-term culture in the presence of RPMI1640 medium containing 10% dextran charcoal stripped serum (DCC)

tag: tissue

value: breast cancer cell line

tag: biomaterial provider

value: ATCC

tag: estrogen

value: No, LTED (long term estrogen deprived)

tag: esr1 mutation


title: Ezh1KO_Ezh2KO_Suz12_ChIP

value: Ezh1/Ezh2 dKO


title: SUM44_LTED_repl2

description: SUM44 LTED replicate 2


title: SUM44_LTED_repl1

description: SUM44 LTED replicate 1


title: E14_untr_H3K27me1_ChIP


title: E14_24h_washout_H3K27me2_ChIP


title: SUM44_WT_repl2

description: SUM44 WT replicate 2

value: Yes


title: E14_8h_washout_H3K27me2_ChIP


title: SUM44_WT_repl1

description: SUM44 WT replicate 1


title: 1MWT-Stage5-Rep3

first: M.A. Saghai

last: Maroof

address: 220 Ag Quad Ln

department: Crop & Soil Environmental Sciences

data_processing:
Alignment: Reads were aligned to the latest soybean reference genome (‘Williams 82’ Wm82.a2.v1, downloaded from Phytozome (https://phytozome.jgi.doe.gov/)) with STAR (version 2.4.2) and number of reads mapped to each gene was counted using featureCount (version 1.4.6).
Feature count and normalization: Differential gene expression was analyzed using default parameters of DESeq2 (version 1.8.2) in R (version 3.2.4). Gene expression levels for each gene were normalized using DESeq2 and summarized as FPKM (Fragments Per Kilo-base pair per Million reads) values.
Differential gene expression: Four genotypes, 3mlpa, 3MWT, 1mlpa, and 1MWT, were analyzed in this data. For each pair of mutant and corresponding non-mutant, stage-wise comparison was performed to identify differentially expressed genes for each stage. For each genotype, between-stage comparisons were performed to identify differentially expressed genes between adjacent developmental stages. Differentially expressed genes were the genes with FDR adjusted p-value < 0.01 and log2 fold change > 1.
Expression clustering: The gene expression levels (FPKM values) were averaged across replicates and only differentially expressed genes were used for K-means clustering in R, and the number of clusters was determined using the minimum Bayesian Information Criteria (BIC) method.
Gene ontology and gene function analysis: GO annotation of all soybean genes was downloaded from Soybase (www.soybase.org). GO enrichment analyses were performed for each gene module. Significantly enriched GO categories were selected using Fisher’s exact test with FDR < 0.1. Transcription factor annotation was downloaded from plant TFDB. Metabolic pathway genes were downloaded from the SoyCyc 7.0 (www.plantcyc.org/databases/soycyc/7.0) database from the Plant Metabolic Network (www.plantcyc.org/tools/tools_overview.faces) website.
Network inference methods: The mean expression profile for each of the clusters (gene modules) was computed and the expression levels of transcription factors (that were differentially expressed in at least one comparison) were included to construct an expression matrix (five developmental stages for four experimental lines). Five distinct network inference algorithms: ARACNE (Margolin et al., 2006), Random Forest (Huynh-Thu et al., 2010), least angle regression (LARS) (Haury et al., 2012), partial correlation (Schafer and Strimmer, 2005b), and context likelihood relatedness (CLR) (Faith et al., 2007), were applied to this expression matrix to infer putative regulatory interactions between each transcription factor and gene modules.
Genome_build: Williams 82’ soybean reference genome (Wm82.a2.v1) downloaded from Phytozome
processed data files format and content:
Raw feature count: abundance measurement matrix table
FPKM normalized gene abundance: abundance measurement matrix table
Stage-wise-differential-expression.xlsx: differential gene expression matrix table
Between-stage differential gene expression.xlsx: differential gene expression matrix table
Gene-ontology-enrichment-analysis-results.xlsx
Predicted-regulatory-interactions.xlsx

organism: Glycine max

source_name: Developing seed

growth_protocol: Four seeds from each of experimental lines - 3mlpa, 3MWT, 1mlpa and 1MWT, were planted in each of 12 pots containing Metro-Mix® 360 (Sun Gro) media topped with GardenPro ULTRALITE soil (Redekar et al., 2015). These plants (48/line) were grown in growth chambers with 14h/10h photoperiod, 24°C/16°C temperature, 300-400 μE light and 50-60% relative humidity.

extract_protocol:
Developing seeds were sampled in triplicates for each experimental soybean line based on seed lengths corresponding to 2-4 mm (stage1), 4-6 mm (stage2), 6-8 mm (stage3), 8-10 mm (stage4), and 10-12 mm (stage5), respectively. Samples were flash frozen using liquid nitrogen and stored at -70°C. High-quality total RNA (RIN 9-10) was extracted from frozen samples using RNeasy Plant Mini Kit, with on-column DNase digestion (QIAGEN).
High quality total RNA samples were used to generate 60 mRNA libraries using standard Illumina TruSeq RNA sample preparation kit protocol.

tag: developmental stage

tag: seed length


title: E14_untr_H3K27me2_ChIP


title: E14_4h_washout_H3K27me2_ChIP


title: SUM44_WT_repl3

description: SUM44 WT replicate 3


title: E14_96h_washout_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)


title: E14_8h_washout_H3K27me3_ChIP


title: 1MWT-Stage4-Rep3


title: 1MWT-Stage3-Rep2


title: 1MWT-Stage4-Rep2


title: 1MWT-Stage5-Rep1


title: E14_16h_washout_H3K27me3_ChIP


title: 1MWT-Stage3-Rep3


title: 1MWT-Stage2-Rep3


title: 1MWT-Stage2-Rep2


title: Suz12DeltaVEFS_H3K27me1_ChIP

value: SUZ12-DeltaVEFS rescue


title: E14_16h_washout_H3K27me2_ChIP


title: E14_7d_inh_H3K27me3_ChIP


title: E14_4h_washout_H3K27me3_ChIP


title: E14_7d_inh_H3K27me2_ChIP


title: 1MWT-Stage1-Rep3


title: 1MWT-Stage5-Rep2


title: 1MWT-Stage2-Rep1


title: E14_48h_washout_H3K27me3_ChIP


title: 1MWT-Stage1-Rep2


title: Suz12rescue_H3K27me1_ChIP


title: E14_24h_washout_H3K27me3_ChIP


title: Suz12KO_H3K27me1_ChIP

value: Suz12 KO


title: 1MWT-Stage4-Rep1


title: Suz12DeltaVEFS_H3K27me2_ChIP


title: 1mlpa-Stage5-Rep3


title: 1mlpa-Stage5-Rep2


title: Suz12WT_H3K27me1_ChIP


title: Suz12VEFS_H3K27me2_ChIP

value: SUZ12-VEFS rescue


title: 1mlpa-Stage5-Rep1


title: 1mlpa-Stage4-Rep3


title: E14_untr_H3K27me3_ChIP


title: HisS5

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Sample name: HisS5
processed data file:five.rats.results.csv

data_processing:
Basic read quality was verified using summaries produced by FastQC
The reads for each sample were mapped to the rat (Rattus norvegicus) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DHR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-7 (DDT) or 1e-6 (vinclozolin) were considered DHR. The DHR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DHR. In addition to the DHR analysis, the core histones were identified using a raw read depth threshold of 150 reads. Core site edges were extended until no genomic window with a read depth > 150 remained within 1000 bp of the site.
The DHR that included at least one genomic window with an edgeR P value < 1e-6 (DDT) or 1e-7 (vinclozolin) were then selected for further analysis and annotated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values. The five.rats.results.csv.gz file includes only raw read depth counts and RPKM adjusted counts for each genomic window since no p-values were calculated.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred Hsd: Sprague Dawley SR®TM (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. The F1-F3 generation offspring were not themselves treated directly with vinclozolin or DDT. The control, vinclozolin and DDT lineage rats were housed in the same room with lighting, food and water as previously described

extract_protocol:
The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 3 ml of phosphate buffered saline (PBS) for 20 minutes at room temperature and then kept at 4ºC to immobilize the sperm. The epididymal tissue was minced and then the released sperm centrifuged at 11,000 x g and the pellet resuspended in NIM buffer and stored at -80ºC until processed further.  To isolate DNA, 100 µl of sperm suspension was combined with 820 µl DNA extraction buffer 1M Tris HC1, pH 8.0; 0.5M EDTA (ethylenediaminetetraacetic acid); 10% SDS (sodium dodecyl sulfate) and 80 µl 0.1M DTT (dithiothreitol). The sample was incubated at 65ºC for 15 minutes. Following this incubation, 80 µl proteinase K (20 mg/ml) was added and the sample incubated at 55ºC for at least 2 hours under constant rotation. Then 300 µl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 min at 4ºC. 1 ml of the supernatant was transferred to a 2 ml tube and 2 µl of Glycoblue (Invitrogen, Carlsbad, CA) and 1 ml of cold 100% isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20ºC freezer for at least one hour. After precipitation, the sample was centrifuged at 13,500 rpm for 20 min at 4ºC. The supernatant was taken off and discarded without disturbing the blue pellet. The pellet was washed with 70% cold ethanol by adding 500 µl of 70% ethanol to the pellet and returning the tube to the freezer for 20 min. After the incubation, the tube was centrifuged for 10 min at 4ºC at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then a gel loading tip was used to remove as much liquid as possible. Pellet was air-dried at RT until it looked dry (about 5 min). Pellet was then resuspended in 100 µl of nuclease free water. Equal amounts of DNA from individual sperm samples were used to produce three DNA pools for histone chromatin immunoprecipitation (ChIP). The antibody used for the H3 location ChIP was Anti-Histone H3, Ct, pan, clone A3S, manufactured by Millipore (Cat. #05-928, Lot #2780491). The antibody used for the H3K27me3 ChIP was Anti-Trymethyl-Histone H3 (Lys27 polyclonal antibody) manufactured by Millipore (Cat. #07-449, Lot #2826067).
The ChIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, San Diego, CA). The manufacturer protocol was followed.
Each pool received a separate index primer. NGS was performed at the WSU Spokane Genomics Core using Ilumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 35 million reads per pool. Six libraries were run in one lane.

treatment_protocol: On days 8 through 14 of gestation, the females were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Vinclozolin and DDT (dichlorodiphenyltrichloroethane) were obtained from Chem Service Inc. (West Chester, PA). Vinclozolin and DDT were injected in DMSO vehicle as previously described. Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. Five additional rats (samples HisS1, HisS2, HisS3, HisS5, HisS6) were neither treated nor bred. These rats provided samples that were analyzed individually, rather than being grouped together into pools.

value: Sprague-Dawley SR

value: sperm

tag: generation

tag: measurement

value: H3 location (anti-H3 histone ChIP)


title: Suz12rescue_H3K27me2_ChIP

value: SUZ12 rescue


title: HisS6

description:
Sample name: HisS6
processed data file:five.rats.results.csv

tag: treatment


title: Suz12KO_H3K27me2_ChIP


title: 1mlpa-Stage4-Rep2


title: HisS2

description:
Sample name: HisS2
processed data file:five.rats.results.csv


title: CF3P9

description:
Sample name: sP9
processed data file:F3me.DDT.results.csv.gz

value: Control

value: H3K27me3 methylation


title: 1mlpa-Stage4-Rep1


title: HisS1

description:
Sample name: HisS1
processed data file:five.rats.results.csv


title: Suz12DeltaVEFS_H3K27me3_ChIP


title: Suz12VEFS_H3K27me1_ChIP

value: H3K27me1 (Takara, mouse mAb, MABI0321)


title: CF3P8

description:
Sample name: sP8
processed data file:F3me.DDT.results.csv.gz


title: CF3P7

description:
Sample name: sP7
processed data file:F3me.DDT.results.csv.gz


title: DF3P27

description:
Sample name: sP27
processed data file:F3me.DDT.results.csv.gz

value: DDT exposed


title: DF3P26

description:
Sample name: sP26
processed data file:F3me.DDT.results.csv.gz


title: 1mlpa-Stage3-Rep3


title: Suz12VEFS_H3K27me3_ChIP


title: 1mlpa-Stage3-Rep2


title: 1mlpa-Stage3-Rep1


title: 1MWT-Stage1-Rep1


title: DF3P25

description:
Sample name: sP25
processed data file:F3me.DDT.results.csv.gz


title: H-Chip_MBM_B

description:
Sample name: sB
processed data file:F3.DDT.results.csv.gz


title: H-Chip_MBM_C

description:
Sample name: sC
processed data file:F3.DDT.results.csv.gz


title: Suz12rescue_H3K27me3_ChIP


title: Suz12KO_H3K27me3_ChIP


title: 1mlpa-Stage2-Rep3


title: Suz12WT_H3K27me3_ChIP

value: WT


title: H-Chip_MBM_A

description:
Sample name: sA
processed data file:F3.DDT.results.csv.gz


title: HisS3

description:
Sample name: HisS3
processed data file:five.rats.results.csv


title: H-Chip_MBM_E

description:
Sample name: sE
processed data file:F3.DDT.results.csv.gz


title: H-Chip_MBM_F

description:
Sample name: sF
processed data file:F3.DDT.results.csv.gz


title: Suz12WT_H3K27me2_ChIP

value: H3K27me2 (Cell Signaling, Rabbit mAb, D18C8)


title: H-Chip_MBM_D

description:
Sample name: sD
processed data file:F3.DDT.results.csv.gz


title: 1mlpa-Stage2-Rep2


title: Combination

city: Southampton

first: Sean

last: Lim

address: Southampton CRUK Cancer Research Centre, Tremona Road

institute: University of Southampton

data_processing:
basecalling - bcl2fastq
filtering, alignment - STAR aligner (v2.5.0a)
digital gene expression - Drop_Seq_tools_v1.0
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix format. (A row for each gene, and a column for each cell barcode and a UMI count matrix)

source_name: Splenocytes

growth_protocol: 10,000 BCL1 tumor cells were injected on day 0

extract_protocol:
Liberase digested spleen (Sigma)
PCR on bead then Nextera XT

treatment_protocol: Mice were treated on D4 with anti-CD20, and D5-8 with anti-CD27, spleens extracted on day 13

value: BALB/c

tag: disease state

value: B-cell lymphoma

value: anti-CD20+anti-CD27 mAb together


title: Anti-CD27

value: anti-CD27 mAb


title: 1mlpa-Stage2-Rep1


title: 1mlpa-Stage1-Rep3


title: Con2.P8

description:
Sample name: sP8
processed data file:F3.Vin.results.csv.gz


title: Con1.P7

description:
Sample name: sP7
processed data file:F3.Vin.results.csv.gz


title: Con3.P9

description:
Sample name: sP9
processed data file:F3.Vin.results.csv.gz


title: Isotype control

value: isotype control


title: Vinc3.P18

description:
Sample name: sP18
processed data file:F3.Vin.results.csv.gz

value: Vinclozolin exposed


title: 1mlpa-Stage1-Rep2


title: METAP1 knockout HAP1 cells biological replicate 2

city: Gent

first: Petra

last: Van Damme

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB

description: haploid cells

data_processing:
The 3’ adapter sequence (AGATCGGAAGAGCACAC) was trimmed using the fastx_clipper.
Reads were pre-mapped onto small nuclear RNA, tRNA and rRNA. The remaining unmapped reads were then mapped onto the human GRCh37 reference genome (Ensembl annotation bundle 75) using STAR 2.4.0i allowing only unique mapping with a maximum of two mismatches.
Separate BedGraph files were generated for the sense and antisense strand.
Reads were counted across annotated genes using HTseq set to mode “union”, feature type “exon” and minimum alignment quality of 10. For the MetAP1 KO cell line, two biological replicate samples were sequenced and for the WT cell line three.
Only protein-coding genes with ≥ 1 read per kilobase of exon per million fragments mapped (RPKM) values in all biological replicates of both conditions were retained for differential expression analysis. Differential expression analysis was performed using the Bioconductor package DESeq2 (Stanford, California, USA) in the R statistical programming environment. To determine significantly regulated genes, an adjusted p-value threshold of 0.01 was applied. The fold change calculations for differentially expressed genes was determined by DESeq2 and represent the log2 change in expression level (i.e. counts) for the MetAP1 KO versus the HAP1 control setup.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were provided for the sense and antisense strand next to supplementary file Table_S1 with processed data for all samples, including read count, RPKM values and DESeq2 differential expression analysis results.

source_name: HAP1 cell line

growth_protocol: HAP1 control cells (HAP1 WT) and CRISPR/Cas9 edited human METAP1 knockout cells (HAP1 MetAP1 KO) containing a frameshift mutation in a coding exon of METAP1D (i.e. a 179bp insertion in exon 4 of NM_015143 at chr4:99035439 ()) were obtained from Horizon Genomics GmbH (Vienna, Austria) and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% foetal bovine serum (Invitrogen, Carlsbad, CA, USA), 100 units/ml penicillin (Invitrogen) and 100 µg/ml streptomycin (Invitrogen). Cells were cultured at 37°C in a humidified atmosphere with 5% CO2 and passaged every 3-4 days.

extract_protocol:
RNA was isolated from HAP1 cells using the TRIzol reagent (Invitrogen) according to manufacturer’s instructions. RNA yields were determined using a NanoDrop spectrophotometer (Wilmington, Delaware, USA) and RNA quality was assessed by Agilent Bioanalyzer RNA 600 Nano Kit. Only samples with RIN values above 9 were accepted.
Library generation including random fragmentation, cDNA synthesis and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be) using the TruSeq stranded total RNA sample preparation kit (Illumina, San Diego, California, USA) and including a Ribo-Zero (Illumina) depletion step as to remove ribosomal RNA from total RNA by the use of biotinylated Ribo-Zero oligos. Libraries were subjected to sequencing on a NextSeq 500 instrument (Illumina) to yield 75 bp single-end reads, resulting in approximately 23-28 million 75 bp single end reads per sample.

value: METAP1 knockout


title: Vinc2.P17

description:
Sample name: sP17
processed data file:F3.Vin.results.csv.gz

value: Sprague-Dawley SR


title: 1mlpa-Stage1-Rep1


title: Vinc1.P16

description:
Sample name: sP16
processed data file:F3.Vin.results.csv.gz

value: sperm


title: 3MWT-Stage5-Rep3_re-analyzed

description:
B5-3
GSM1959616


title: wild type (parental) HAP1 cells biological replicate 3

description: haploid cells

value: wild type


title: METAP1 knockout HAP1 cells biological replicate 1

description: haploid cells


title: 3MWT-Stage5-Rep2_re-analyzed

description:
B5-2
GSM1959615


title: 3MWT-Stage5-Rep1_re-analyzed

description:
B5-1
GSM1959614


title: wild type (parental) HAP1 cells biological replicate 2

description: haploid cells


title: wild type (parental) HAP1 cells biological replicate 1

description: haploid cells


title: 3MWT-Stage4-Rep3_re-analyzed

description:
B4-3
GSM1959613


title: 3MWT-Stage4-Rep2_re-analyzed

description:
B4-2
GSM1959612


title: H3 chemical cleavage (replicate 3)

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description:
H3_CC_rep_3
Biological replicate 3
H3 chemical cleavage mapping
MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ - Δhht1/hhf1::kanMX4

data_processing:
Paired-end reads were aligned to the S. cerevisiae reference genome sacCer3, using Bowtie2 (Langmead and Salzberg 2012) with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
We analyzed the distribution of fragments with different sizes at promoters using the 2D occupancy plots (https://github.com/rchereji/plot2DO), in order to obtain the origin of each group of DNA fragments, e.g. short fragments (~50 bp long) originate from two cleavages inside the same nucleosome, medium fragments (70-130 bp) and long fragments (135-175 bp) originate from two cuts inside distinct neighboring nucleosomes, produced at consecutive or alternative cleavage sites, respectively (see the scheme of all cleavage possibilities from the paper).
The centers of the short DNA fragments (51±7 bp) were used to obtain the precise locations of the nucleosome dyads, and the long fragments (135-175 bp) were used to estimate the nucleosome repeat lengths and the linker lengths.
By stacking all the nucleosome dyad positions using MATLAB, we obtained the genome-wide dyad distributions. We computed the nucleosome occupancy profiles by symmetrically extending each dyad position to a reduced footprint of 101 bp (in order to emphasize the linkers between the clusters of alternative nucleosome positions from different cells), and then stacking these footprints. Dyad distributions and occupancy profiles were normalized such that the average for every chromosome became 1.
We used MATLAB to save the normalized profiles in wiggle (wig) files, and the wigToBigWig utility from UCSC to convert these files to the bigWig format.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: BigWig files containing the normalized occupancy and dyads profiles.

source_name: H3 chemical cleavage mapping DNA

growth_protocol: Yeast strain with HHT1/HHF1 deleted and carrying the H3Q85C mutation was grown in a volume of ~166 ml in YPD up to OD600 of 0.4-0.6.

extract_protocol:
Cells were collected by centrifugation at 3000g for 5 minutes. Cells were resuspended with 1 ml of 1 M sorbitol and spun again at 3000g for 5 minutes. Cells were resuspended with 1 ml of spheroplasting buffer containing lyticase (1 M sorbitol, 5 mM β-Mercaptoethanol, 10 mM Tris, 10 mg/ml lyticase) and gently rotated at room temperature for 5 minutes. Cells were pelleted at 3000g for 5 minutes and washed twice with 1.5 ml of Sorbitol/NP-40 buffer (1 M sorbitol, 0.2% NP-40 (Sigma-Aldrich # 74385), and 10 mM Tris pH 7.5). The cell pellet was resuspended in 400 μl of labeling buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 0.5 mM spermidine, 0.15 mM spermine, 0.2% NP-40, 0.1 mM ethylenediaminetetraacetic acid). At this point, the tubes were covered with aluminum foil to protect from light. The phenanthroline label, N-(1,10-phenanthroline-5-yl)iodoacetamide (Biotium, cat# 92015) stock solution was made fresh by dissolving the lyophilized label to a concentration of 7 mM in DMSO. The label was added to cells for a final concentration of 0.14 mM. The labeling mixture was rotated at room temperature for 2 hours and then at 4oC overnight. The cells were washed three times in 1.5 ml of Sorbitol/NP-40 buffer to remove excess label. The cells were then resuspended in 300 μl of mapping buffer (2.5 mM NaCl, 50 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 M sorbitol, 0.5 mM spermidine, 0.15 mM spermine, 0.2% NP-40), CuCl2 was added to a final concentration of 150 µM and incubated at room temperature for two minutes. Cells were spun down for 3 minutes at 3400g and then washed three times with 1.5 ml of mapping buffer. After the final wash, the cells were resuspended in 300 µl of mapping buffer. 3-mercaptopropionic acid was then added to a final concentration of 6 mM followed by H2O2 to a final concentration of 6 mM. The reaction was incubated at room temperature for 15 minutes, quenched by addition of neocuproine to 0.28 mM, and the cells were spun down at 3000g for 5 minutes. The reaction was performed four more times starting with resuspending in mapping buffer. The cells were pelleted after five reactions and resuspended in 400 μl of TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). EDTA was supplemented to final concentration of 10 mM and SDS was added to a final concentration of 0.5%. 20 μg proteinase K was added and incubated at 55oC for 2 hours. To extract DNA, two volumes (800 µl) of phenol-chloroform-isoamyl alcohol (PCI, 25:24:1) was added to the samples, mixed well and spun at max speed for 5 minutes. The aqueous phase was separated and the DNA precipitated with three volumes of 100% ethanol and 30 µg of glyco-blue as a carrier, for 30 minutes at 4oC, maximum speed. DNA pellets were washed with 1 ml of 75% ethanol and spun again. The pellets were air dried and resuspended in 50-100 µl of TE buffer. 90 µg of RNase A was added and incubated at 42oC for 30 minutes. 2 µg of cleavage material and 0.5 µg of starting material was analyzed by polyacrylamide gel electrophoresis (10% acrylamide, TBE). If the 50 bp band was observed, a final PCI extraction, chloroform cleanup, and ethanol precipitation was performed before proceeding to library preparation. For one of the samples, the 50 bp fragments were cut out from the polyacrylamide gel and purified before making libraries.
Library construction protocol: As described in Orsi et al. 2015 (PMID: 25827087).

tag: genotype/variation

value: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ - <delta>hht1/hhf1::kanMX4


title: H3 chemical cleavage (replicate 2)

description:
H3_CC_rep_2
Biological replicate 2
H3 chemical cleavage mapping
MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ - Δhht1/hhf1::kanMX4


title: H3 chemical cleavage (replicate 1)

description:
H3_CC_rep_1
Biological replicate 1
H3 chemical cleavage mapping
MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ - Δhht1/hhf1::kanMX4


title: MCF7_LTED_ESR1_Y537C_repl3

description: MCF7 LTED ESR1_Y537C replicate 3

value: breast cancer cell line

value: ATCC

tag: cell line

value: No, LTED (long term estrogen deprived)


title: MCF7_LTED_ESR1_Y537C_repl2

description: MCF7 LTED ESR1_Y537C replicate 2


title: Anti-CD20

value: anti-CD20 mAb


title: MCF7_LTED_ESR1_WT_repl3

description: MCF7 LTED ESR1_WT replicate 3


title: MCF7_LTED_ESR1_Y537C_repl1

description: MCF7 LTED ESR1_Y537C replicate 1


title: 3MWT-Stage3-Rep3_re-analyzed

description:
B3-3
GSM1959610


title: MCF7_LTED_ESR1_WT_repl2

description: MCF7 LTED ESR1_WT replicate 2


title: 3MWT-Stage3-Rep1_re-analyzed

description:
B3-1
GSM1959608


title: 3MWT-Stage3-Rep2_re-analyzed

description:
B3-2
GSM1959609


title: 3MWT-Stage2-Rep3_re-analyzed

description:
B2-3
GSM1959607


title: MCF7_WT_repl2

description: MCF7 WT replicate 2

value: Yes


title: 3MWT-Stage1-Rep3_re-analyzed

description:
B1-3
GSM1959604


title: SUM44_Input_LTED

description: Input SUM44 ESR1 mutant LTED

data_processing:
Reads were aligned to the Human Reference Genome (assembly hg19) using BWA and removing all reads with a quality score <15
Peaks were called using MACS2 (v2.1.0.20150420) 32 with default parameters
Genome_build: Human Reference Genome (assembly hg19)
Supplementary_files_format_and_content: MACS2 excel file output files

extract_protocol: Cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes and then quenched with 125 mmol/L glycine. Samples were then lysed, sonicated, and chromatin was immunoprecipitated by overnight incubation at 4C with ER antibodies prebound with Protein G magnetic dynabeads (Invitrogen). Samples were then washed vigorously with RIPA buffer and reversed crosslinked by an overnight incubation in elution buffer at 65C. DNA was digested with RNase and Proteinase K, purify precipitated with phenol chloroform and eluted in Tris-HCl pH 8.0.

tag: antibody


title: MCF7_WT_repl3

description: MCF7 WT replicate 3


title: MCF7_WT_repl1

description: MCF7 WT replicate 1


title: 3MWT-Stage4-Rep1_re-analyzed

description:
B4-1
GSM1959611


title: 3mlpa-Stage5-Rep2_re-analyzed

description:
A5-2
GSM1959600


title: SUM44_Input_WT

description: Input SUM44 ESR1 wildtype


title: 3mlpa-Stage5-Rep1_re-analyzed

description:
A5-1
GSM1959599


title: SUM44_LTED_repl2

description: ChIP SUM44 ESR1 mutant LTED

value: ESR1 (Santa-Cruz sc543)


title: SUM44_wt_repl1

description: ChIP SUM44 ESR1 wildtype


title: 3mlpa-Stage4-Rep3_re-analyzed

description:
A4-3
GSM1959598


title: MCF7 Input LTED_ESR1_Mut

description: Input MCF7 ESR1 mutant LTED

value: No, LTED (long term estrogen deprived)  ESR1 mutant


title: 3MWT-Stage2-Rep2_re-analyzed

description:
B2-2
GSM1959606


title: 3mlpa-Stage4-Rep1_re-analyzed

description:
A4-1
GSM1959596


title: MCF7 Input_LTED_WT

description: Input MCF7 ESR1 wildtype LTED

value: No, LTED (long term estrogen deprived)  ESR1 wildtype


title: MCF7 Input_WT

description: Input MCF7 ESR1 wildtype


title: 3mlpa-Stage4-Rep2_re-analyzed

description:
A4-2
GSM1959597


title: 3MWT-Stage2-Rep1_re-analyzed

description:
B2-1
GSM1959605


title: MCF7_LTED_ESR1_WT_repl1

description: MCF7 LTED ESR1_WT replicate 1


title: Ezh2rescue_replic3_RNAseq

molecule: polyA RNA

extract_protocol: TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001)

tag: chip antibody

value: EZH2 rescue


title: Ezh2rescue_replic2_RNAseq

tag: genotype


title: 3mlpa-Stage3-Rep2_re-analyzed

description:
A3-2
GSM1959594


title: SUM44_LTED_repl1

description: ChIP SUM44 ESR1 mutant LTED


title: 1MWT-Stage3-Rep1


title: Ezh2rescue_replic1_RNAseq


title: 3MWT-Stage1-Rep1_re-analyzed

description:
B1-1
GSM1959602


title: 3mlpa-Stage3-Rep1_re-analyzed

description:
A3-1
GSM1959593


title: MCF7_LTED_WT

description: ChIP MCF7 ESR1 wildtype LTED


title: SUM44_wt_repl2

description: ChIP SUM44 ESR1 wildtype


title: 3mlpa-Stage3-Rep3_re-analyzed

description:
A3-3
GSM1959595


title: Ezh1KO_Ezh2KO_replic2_RNAseq

value: Ezh1/Ezh2 dKO


title: Ezh1KO_Ezh2KO_replic1_RNAseq


title: Ezh1WT_Ezh2WT_replic3_RNAseq

value: WT


title: 3mlpa-Stage2-Rep2_re-analyzed

description:
A2-2
GSM1959591


title: Ezh1WT_Ezh2WT_replic2_RNAseq


title: PE_late_gestation

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

institute: University of Queensland

description: Preeclampsia late gestational age

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.13)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.10.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file containing raw miRNA counts

source_name: Plasma

extract_protocol:
Exosomal RNA was extracted using the RNeasy Mini Kit 50 and TRIzol LS Reagent.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 µg RNA or 100 to 300 ng of exosomal RNA was used as input for library construction.

tag: condition

value: Preeclampsia

tag: pregnancy stage

value: late gestation

tag: sample type

value: Exosome


title: Ezh1WT_Ezh2WT_replic1_RNAseq

tag: strain


title: 3mlpa-Stage2-Rep1_re-analyzed

description:
A2-1
GSM1959590


title: 3mlpa-Stage5-Rep3_re-analyzed

description:
A5-3
GSM1959601


title: PE_early_gestation

description: Preeclampsia early gestastional age

value: early gestation


title: 3mlpa-Stage1-Rep3_re-analyzed

description:
A1-3
GSM1959589


title: Ezh2rescue_H3K27me2_ChIP

extract_protocol: NEBNext Ultra protocol (NEB, E7370S)

value: H3K27me2 (Cell Signaling, Rabbit mAb, D18C8)


title: Ezh1KO_Ezh2KO_Input_ChIP


title: PE_middle_gestation

description: Preeclampsia middle gestational age

value: middle gestation


title: MCF7_LTED_MUT

description: ChIP MCF7 ESR1 mutant LTED

tag: tissue

value: breast cancer cell line

tag: biomaterial provider

tag: estrogen


title: 3mlpa-Stage1-Rep2_re-analyzed

description:
A1-2
GSM1959588

tag: developmental stage

tag: seed length


title: NP_late_gestation

description: Normal pregnancy late gestational age

value: Normal pregnancy


title: NP_early_gestation

description: Normal pregnancy early gestastional age


title: 3mlpa-Stage2-Rep3_re-analyzed

description:
A2-3
GSM1959592


title: Ezh1KO_Ezh2KO_H3K27me2_ChIP


title: Ezh1KO_Ezh2KO_H3K27me3_ChIP

value: H3K27me1 (Takara, mouse mAb, MABI0321)


title: MCF7_WT

description: ChIP MCF7 ESR1 wildtype

value: ATCC

tag: esr1 mutation


title: 3mlpa-Stage1-Rep1_re-analyzed

description:
A1-1
GSM1959587


title: Ezh1WT_Ezh2WT_H3K27me2_ChIP


title: NP_middle_gestation

description: Normal pregnancy middle gestational age


title: Ezh1WT_Ezh2WT_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)


title: SKRP1-3

city: Nanjing

first: Jie

last: Huang

state: Jiangsu

address: NO.1 Weigang

department: Plant Pathology

institute: Nanjing Agricultural University

description: hairy roots

data_processing:
The raw RNA-seq reads generated from Illumina sequence platform were filtered using the ht2-filter from HTQC package (1.92.1) with the default parameters to remove low-quality reads. Then filtered reads were aligned to the soybean genome (Gmax_275_v2.0) using tophat-2.0.11 with anchor length more than 8nt for spliced alignments.
Genome_build: Gmax_275_v2.0 (Glycine max Wm82.a2.v1)
Supplementary_files_format_and_content: bigWig

source_name: soybean

extract_protocol:
The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
These libraries were sequenced using Illumina HiSeq 4000 in paired-end mode with a read length of 150 bp.

treatment_protocol: No treatment

tag: tag

value: GFP

value: hairy roots

tag: cultivars

value: williams


title: AVR3C-3

description: hairy roots


title: SKRP1-1

description: hairy roots


title: SKRP1-2

description: hairy roots


title: 3MWT-Stage1-Rep2_re-analyzed

description:
B1-2
GSM1959603


title: GFP-3

description: hairy roots


title: GFP-2

description: hairy roots


title: AVR3C-2

description: hairy roots


title: AVR3C-1

description: hairy roots


title: GFP-1

description: hairy roots


title: Ezh1KO_Ezh2KO_H3K27me1_ChIP


title: 23_FTb1_noLPS

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) and Sooty Mangabey (Caty_1.0) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Genome_build: Caty_1.0 (GCF_000955945.1_Caty_1.0_genomic.fna,GCF_000955945.1_Caty_1.0_genomic.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Cercocebus atys

source_name: CD14+ monocytes

growth_protocol: CD14+ monocytes were isolated from Ficoll-isolated PBMCs using CD14 MicroBeads according to manufacturer’s instructions (Miltenyi Biotec)

extract_protocol:
RNA was purified using QIAGEN Micro RNEasy columns, and RNA quality assessed using Agilent Bioanalyzer
10 ng of total RNA was used as input for mRNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified mRNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits

treatment_protocol: 0.4x106 cells were stimulated for 6 h with 10 ng/ml LPS and then immediately lysed in 350 µl of QIAGEN RLT buffer

value: primary monocytes

tag: subject

tag: treatment

value: untreated


title: 22_FRb1_PlusLPS

value: LPS


title: Jurkat shLMO1 RNA-seq #1

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets of two control samples and two knockdown samples for each member of the TAL1 complex (ARID5B, TAL1, E2A, HEB, LMO1, GATA3, RUNX1, and MYB) were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
htseq-count v0.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium (BioWest) supplemented with 10% FBS (BioWest) in a CO2 incubator.

extract_protocol:
RNA was extracted using an miRNeasy kit (Qiagen) with some modifications.  The cell numbers for each sample were counted before cell pellet was collected. ERCC RNA Spike-in mix (1:10 dilution) wasthen  added to each sample according to the cell numbers (Example: 1ul was added for 1 million cells)  after the addition of Qiazol.  After the addition of chloroform, the samples were transferred to a Maxtract high-density column (Qiagen) to be spun down.  The aqueous layer was then retained for downstream RNA extraction following the manufacturer’s instructions.  The extracted RNA was subjected to DNase treatment (Turbo DNA-freeTM kit, Ambion) according to the manufacturer’s instructions to eliminate any genomic DNA present in the samples and then cleaned up using an RNeasy kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

tag: cell line

value: Jurkat

tag: knockdown


title: 24_FTb1_PlusLPS


title: Jurkat shE2A RNA-seq #2


title: 21_FRb1_noLPS


title: Jurkat shLMO1 RNA-seq #2


title: 20_FQa1_PlusLPS


title: Ezh1WT_Ezh2WT_H3K27me1_ChIP

tag: chip antibody

tag: genotype

value: WT


title: Jurkat shE2A RNA-seq #1


title: Jurkat shHEB RNA-seq #1

value: HEB


title: Jurkat shARID5B RNA-seq #2


title: 17_FKb1_noLPS


title: 18_FKB1_PlusLPS


title: 19_FQa1_noLPS


title: Jurkat shMYB RNA-seq #1

value: MYB


title: Delta-dtxR_2

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

country: Germany

institute: Bielefeld University

description: Processed data file: List_of_differentially_transcribed_genes.xlsx

data_processing:
Base calling with Illumina CASAVA.
Quality trimming with trimmomatic v0.36 from both ends (primary transcript library only from 3' end), sliding window, minimal read length 39.
Reverse complementing of R1 reads.
Mapping with bowtie2 2.2.7, --ff read orientation, default parameters.
Visualization, detection of transcription start sites, operons and gene read counting with readXplorer 2.2.3.
Analysis of differentially transcribed genes with DESeq2 in default parameters.
Genome_build: RefSeq NC_002935.1
Supplementary_files_format_and_content: List_of_differentially_transcribed_genes.xlsx contains raw counts, normalized read counts and log2foldchanges and adjusted p-values for each gene.
Supplementary_files_format_and_content: List_of_transcription_start_sites_and_operons.xlsx contains transcription start sites and operons as well as sub-operons identified with readXplorer.

organism: Corynebacterium diphtheriae NCTC 13129

source_name: Bacteria, dtxR deletion

growth_protocol: Overnight cultures of C. diphtheriae NCTC 13129 and its isogenic ΔdtxR mutant were used to inoculate fresh cultures in HIB at 37 C.

extract_protocol:
Total RNA was isolated from cells grown at exponential phase (OD600 = 0.5) using Trizol reagent (Invitrogen). The bacterial pellet obtained from 4 mL culture was resuspended in 1 mL Trizol, transferred into FastPrep Lysis Beads & Tube (MP Biomedicals) and mechanically lysed using beadbeater at a maximum speed for 20 sec 6 times. After adding 200 µL chloroform to the lysed cells followed by centrifugation at 12,000 x g for 15 min at 4 °C, the aqueous supernatant was taken and then precipitated using 500 µL isopropanol. Afterwards, crude RNA samples were treated with DNase I (Roche Diagnostics). After purification using phenol/chloroform/isoamyl alcohol (ratio 25:24:1), RNA was precipitated with ethanol. Purified total RNA pellets were dissolved in 50 µL RNase-free water.
For whole transcriptome cDNA library preparations, 2 µg total RNA from C. diphtheriae NCTC 13129 and the ΔdtxR mutant were used. Stable RNAs were depleted with the RiboZero Kit according to manufacturer's instructions (Epicentre). Afterwards, the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality with the Bioanalyzer (Agilent). Fragmentation of mRNA, reverse transcription to cDNA, adenylation of 3' ends, adapter ligation and PCR amplification were performed according to TruSeq Stranded mRNA library instructions (Illumina). Prior to paired-end sequencing of the whole transcriptome cDNA libraries on an Illumina MiSeq, the quality and concentration of the libraries were checked using the Bioanalyzer (Agilent). For the primary 5'-end cDNA library, 2× 5 µg wild type RNA was used. The preparation protocol has been described previously in detail [Pfeifer-Sancar2013]. In the present study, the experimental workflow was changed at three steps. Non-primary transcripts were digested with terminator exonuclease (Epicenre) at 30 °C for 60 min and subsequently at 42 °C for 30 min. The 5' adapter ligation was performed for 60 min at 30 °C with 1 µL 60 µM adapter. After cDNA amplification, the two libraries were purified and size-selected by gel electrophoresis for fragment sizes between 100 and 1,000 bp. The cutoff of 100 bp was chosen to reduce adapter dimers in the finished library. Due to the fact that the preparation workflow involves the use of two adapters, which together have a length of 66 nt, only transcripts smaller than 40 nt are not present in the final RNA-seq data. Sequencing was performed in single-read mode with 75 nt read length for the primary 5'-end cDNA library.

tag: strain/background

tag: genotype/variation

value: deletion of dtxR gene

tag: growth phase

value: exponential


title: Delta-dtxR_3


title: Primary transcript starts wild type

description: Processed data file: List_of_transcription_start_sites_and_operons.xlsx

source_name: Bacteria, WT

value: wild type


title: Jurkat shARID5B RNA-seq #1


title: Jurkat shMYB RNA-seq #2


title: Delta-dtxR_1


title: 8_FTy_PlusLPS

tag: tissue

value: FTy


title: 7_FTy_noLPS


title: WT_3


title: Jurkat shHEB RNA-seq #2


title: WT_2


title: 5_FJa1_noLPS


title: WT_1


title: Jurkat shRUNX1 RNA-seq #1


title: 6_FJa1_PlusLPS


title: Jurkat shGATA3 RNA-seq #2


title: Jurkat shGATA3 RNA-seq #1


title: 16_RUu10_PlusLPS

organism: Macaca mulatta


title: 15_RUu10_noLPS


title: Jurkat shTAL1 RNA-seq #2


title: 14_RRg15_PlusLPS


title: Jurkat shTAL1 RNA-seq #1


title: Lipid NRP1, biological replicate 1

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

description: Sample 11_LNRP1

data_processing:
Trimming of the raw reads: cutadapt 1.11 with Python 2.6.6, parameters: no wildcard characters, trimming 6 bases at beginning and 2 at end of each read, quality trimming of phred quality 20, poly A and Illumina adaptors.
Mapping of the data, gene counts: CLC Genomics Workbench 9.0.1, strand-specificity: reverse, others: default.
Genome_build: NC_000962.3 of Mtb strain H37Rv
Supplementary_files_format_and_content: *_GE.csv: Comma-separated values: include raw reads per gene.

organism: Mycobacterium tuberculosis H37Rv

source_name: hypoxic in vitro liquid cultures

growth_protocol: The strain was cultured in Dubos broth, without glycerol, containing 0.5% albumin, supplemented with either 0.2% dextrose or a lipid mixture (oleic acid, palmitic acid, stearic acid, at final concentration of 0.001% each, plus 0.01% cholesterol). Three growth phases of Mtb were cultivated for each carbon source (dextrose or lipids). Specifically, Mtb was grown until reaching 1) its aerobic exponential phase (DE: dextrose exponential phase and LE: lipid exponential phase), 2) its aerobic stationary phase (DS: dextrose stationary phase and LS: lipid stationary phase) and 3) its NRP1 stage of dormancy (DNRP1: dextrose NRP1 stage and LNRP1: lipid NRP1 stage).

extract_protocol:
Cell pellets were resuspended in the lysis buffer (6 M guanidinium chloride, 0.1% Tween 80, 1 mM 2-mercaptoethanol, 10 mM EDTA) and were lysed mechanically in a FastPrep cell disrupting equipment with 150 μm - to 200 μm glass beads by performing three lysis cycles of 45 s, at 4.0 m/s followed by two lysis cycles of 15 s at 6.5 m/s. Nucleic acids were extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and RNA was precipitated with 0.4 volume of absolute ethanol. Total RNA was purified three times with Trizol reagent. RNA was dissolved in DEPC-treated water and stored at -70°C.
Library preparation was performed using the 'NEBNextUltra Directional RNA Library Prep Kit for Illumina' (New England Biolabs), according to manufacturer's protocol.

tag: strain

tag: carbon source

value: cholesterol and fatty acids

value: NRP1 stage of dormancy

tag: condition

value: hypoxic


title: 13_RRg15_noLPS


title: Jurkat shRUNX1 RNA-seq #2


title: Jurkat control (shGFP) RNA-seq #1

value: control


title: Lipid stationary phase, biological replicate 2

description: Sample 10_LS

source_name: aerobic in vitro liquid cultures

value: stationary

value: aerobic


title: 12_RIo9_PlusLPS

value: primary monocytes


title: 11_RIo9_noLPS

value: untreated


title: Jurkat_WCE_ChIPSeq

data_processing:
Single end ChIP-seq reads of Jurkat were aligned to the hg19 human reference genome using Bowtie (version 1.1.1) with the following parameters: -e 70 -k 1 -m 1 -n 2 –best
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq). A p-value threshold of enrichment of 1e-9 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph output files of MACS2 was converted into bigwig file. Counts were normalized to reads per million.

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Jurkat cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and ARID5B-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
Library construction and sequencing by Illumina Hiseq 4000 were performed by BGI Tech Solutions Co., Limited (Hongkong).

treatment_protocol: Not applicable.

tag: cell type

value: Jurkat cells


title: Lipid exponential phase, biological replicate 2

description: Sample 8_LE


title: Lipid stationary phase, biological replicate 1

description: Sample 9_LS


title: Lipid exponential phase, biological replicate 1

description: Sample 7_LE


title: Jurkat_ARID5B_ChIPSeq

value: ARID5B antibody (HPA015037, Sigma)


title: 10_RBy10_PlusLPS

value: LPS


title: 9_RBy10_noLPS


title: Dextrose NRP1, biological replicate 2

description: Sample 6_DNRP1

value: dextrose


title: Dextrose stationary phase, biological replicate 2

description: Sample 4_DS


title: 4_269-02_PlusLPS


title: Dextrose exponential phase, biological replicate 2

description: Sample 2_DE


title: 3_269-02_noLPS


title: Dextrose NRP1, biological replicate 1

description: Sample 5_DNRP1


title: Lipid NRP1, biological replicate 2

description: Sample 12_LNRP1


title: 2_143-02_PlusLPS


title: Dextrose stationary phase, biological replicate 1

description: Sample 3_DS


title: 1_143-02_noLPS


title: Jurkat control (shGFP) RNA-seq #2

value: Jurkat


title: virR_C_1

status: Public on Jan 11 2018

city: Boston

first: Daniel

last: Grubaugh

state: MA

address: 77 Ave Louis Pasteur

department: MBIB

institute: Harvard Medical School

data_processing:
Base calling was performed using Illumina Real Time Analysis software
Sequences were trimmed of adaptor sequences and filtered for low quality sequence and then aligned to the Listeria monocytogenes EGD-e genome using CLCBio Genomics Workbench version 7.5.1. Reads were not mapped to rRNA features to account for  variability in rRNA-depletion efficiency between samples.
Differential gene expression analysis was performed using the DGE (edgeR) package in CLCBio Genomics Workbench version 7.5.1.
Genome_build: NC_003210.1
Supplementary_files_format_and_content: A single tab-delimited text file broken down by feature. Contains differential gene expression analysis between the two strains as well as total counts and RPKM values for each feature in each sample.

organism: Listeria monocytogenes

source_name: 10403S ΔvirR

growth_protocol: A single colony of the indicated strain was inoculated into brain-heart infusion medium (BHI) supplemented with 100μg/mL streptomycin and grown for 20h shaking at 37⁰C. Bacteria were then washed in PBS and diluted 1:100 into LB medium and grown 3.5 hours at 37⁰C shaking.

extract_protocol:
Bacteria were lysed and RNA extracted using the FastPrep RNApro solution and lysing matrix B according to the manufacturer's instructions.
Libraries were prepared by the Harvard Medical School Biopolymers Facility using Illumina kits according to the manufacturers instructions. Briefly, ribosomal RNA was removed from the samples using the Ribo-Zero™ rRNA Removal kit for Gram-positive bacteria, and the samples were the prepared for strand-specific RNA sequencing using the PrepX RNA-Seq Library Kit.

tag: strain background

value: virR deletion mutant

value: exponential growth in LB

tag: molecule subtype

value: rRNA-depleted RNA


title: Dextrose exponential phase, biological replicate 1

description: Sample 1_DE

value: exponential


title: virR_C_2


title: wt_C_1

source_name: 10403S wild type

value: wild type


title: virR_A_1


title: virR_A_2


title: wt_C_2


title: wt_B_2


title: wt_B_1


title: wt_A_2


title: wt_A_1


title: MDAMB231_LSD_ChIP

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description: ChIP-seq

data_processing:
Adapters stripped using Trimmomatic
Reads mapped with Bowtie2 using global alignment. --no-unal -q -I 100 -X 500 --fr -x
Duplicates removed using Picard
bedgraph files from HOMER, reads extended 200bp.
Peaks called with HOMER against TI -style histone -F 4 -size 300 -minDist300 and filtered on >=12.2 normalised tag count
Genome_build: hg19
Supplementary_files_format_and_content: bed files show enriched regions.

source_name: MDA-MB-231 cell line

growth_protocol: Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.

extract_protocol:
Briefly, 5 x 10^6 cells were cross-linked with formaldehyde (1%, 10 min) then quenched with glycine (125mM). Fixed cells were lysed in SDS lysis buffer and chromatin-bound DNA sheared by sonication with a Misonix Sonicator S-4000. ChIP samples were incubated overnight at 4°C with Protein A Magnetic Beads (Millipore) and 10 μg of anti-LSD1 (ab17721; Abcam) antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research).
TruSeqLT paired end

treatment_protocol: Cells were left or stimulated with PMA (1.29ng/ml) with a recombinant TGF-beta1 (5 ng/ml) for 60h.

tag: antibody


title: MCF7_PMA_TGF_LSD1_ChIP

description: ChIP-seq

source_name: MCF7 cell line

value: PMA/TGFb


title: virR_B_1


title: virR_B_2


title: X2_H327Ac_ChIPSeq

city: Houston

first: xiang

last: xiao

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75nt reads, single end) were aligned to the mm10 using the BWA algorithm (v0.6.1, default settings).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p value = 1e-7 (Zhang et al., 2008).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
ROSE (Rank Ordering of Super-Enhancers) was performed with default settings (i.e., no promoter exclusion) using MACS peaks as input (Hnisz et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: wig

source_name: In vitro Th9_OX40L treated_

growth_protocol: naïve CD4+ T cells were activated with CD3 mplus WT syngeneic APC in 96-well tissue-culture plates at 5×104 cells per well under TH9 conditions (3 ng/ml human TGF-β1 and 10 ng/ml mouse IL-4) for two days.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed by using ChIP-IT® PBMC kit (#53042, Active Motif). Briefly, targeted T cells were harvested and fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Cells were resuspended in swelling buffer with detergent for 30 mins and centrifuged for 10 mins at 3200 g at 4 0C. Cell pellets were resuspended in 500ul ChIP buffer for chromatin sonication. Genomic DNA was sonicated to an average length of 300-500 bp. An aliquot of chromatin (25-30 ug) was pre-cleaned with protein A agarose beads. Epigenetically modified or transcription factor binding genomic DNA was isolated using specific antibody (4 μg). The following antibodies against mouse antigens were used: anti-Drd4 (A301-985A50, Bethyl Laboratiories); anti-H3K27Ac (#39133, Active Motif). DNA and protein complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 0C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps for end-polishing, dA-addition and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500.

treatment_protocol: To stimulate OX40 signaling in activated T cells, OX40L transgenic APCs prepared from OX40L transgenic mice were used.

value: CD4+ T cell


title: X2_BRD4_CHIPSeq


title: RNA-seq_A549_si Negative control

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description:
control siRNA transfected
siNC

data_processing:
RNA-seq reads were trimmed down to 80 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt.

source_name: A549, si Negative control

growth_protocol: A549 cells were from Cell Resource Center for Biomedical Research, Institute of Development, Aging, and Cancer, Tohoku University. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM #11965; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin G, and 100 µg/mL streptomycin.

extract_protocol:
Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed as described (Sakurai et al., 2016, Oncogene).

treatment_protocol: A549 cells were transfected with siRNAs using Lipofectamine RNAiMAX reagent (Thermo Fisher Scientific).

tag: sirna

value: Negative control siRNA (designed by siDirect, RNAi inc., Tokyo, Japan) (5’→3’):GUACCGCACGUCAUUCGUAUC and UACGAAUGACGUGCGGUACGU

value: control

tag: histology

value: Invasive mucinous adenocarcinoma


title: X1_BRD4_CHIPSeq

source_name: In vitro Th9_Ctrl


title: input DNA

source_name: In vitro Th9_pooled


title: Cdx2-/-Eed-/- Villus RNA-seq biological rep2

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: ATAC-seq and ChIP-seq: Bowtie2; RNA-seq: Tophat, version 2.0.6
ATAC-seq and ChIP-seq peak calling: MACS2, version 2.1.1
RNA-Seq - Read counts were obtained using HTSeq and normalized using DeSeq2 with default parameters. DeSeq2 was further used for calculating differntial gene expression (q<0.01).
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with counts from HTSeq for all genotypes

source_name: Mouse intestinal villus epithelial cells

extract_protocol:
Villi were collected in TRIzol reagent (Thermo Fisher Scientific) and RNA was isolated using RNeasy kit (Qiagen) with on-column Dnase-treatment (Qiagen).
The TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed 3 days after last injection.

value: B6;129 mixed background

value: Adult differentiated jejunal epithelial cells; middle 1/3 of intestine

value: Cdx2f/f; Eedf/f; Villin-cre

tag: protocol

value: Villi from the middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were collected in TRIzol reagent and stored at -80°C for subsequent RNA isolation.


title: Eed-/- Villus RNA-seq biological rep2

description: Eed-/- Villus RNA-seq biological rep2

value: Eedf/f; Villin-cre


title: Cdx2-/-Eed-/- Villus RNA-seq biological rep1


title: MCF7_NS_LSD1_ChIP

description: ChIP-seq

tag: treatment

tag: cell line


title: X1_H3K27Ac_ChIPSeq

tag: chip antibody


title: Eed-/- Villus RNA-seq biological rep1

description: Eed-/- Villus RNA-seq biological rep1

tag: genotype


title: Cdx2-/- Villus RNA-seq biological rep3

description: Cdx2-/- Villus RNA-seq biological rep3

value: Cdx2f/f; Villin-cre


title: Cdx2-/- Villus RNA-seq biological rep2

description: Cdx2-/- Villus RNA-seq biological rep2


title: Cdx2-/- Villus RNA-seq biological rep1

description: Cdx2-/- Villus RNA-seq biological rep1


title: RNA-seq_A549_si TUFT1

description:
TUFT1 siRNA transfected
siTUFT1

source_name: A549, si TUFT1

value: TUFT1 siRNA (designed by siDirect, RNAi inc., Tokyo, Japan) (5’→3’):GGAUAUAAGUAGCAAGCUUGA and AAGCUUGCUACUUAUAUCCUC

tag: genotype/variation

value: TUFT1 knockdown


title: Wild-type Villus RNA-seq biological rep1

treatment_protocol: Mice were injected i.p. with sunflower oil (vehicle for tamoxifen) for 5 consecutive days and were sacrificed 3 days after last injection.


title: Wild-type Villus RNA-seq biological rep2


title: Cdx2-/- Villus ATAC-seq biological rep1

description:
Cdx2-/- Villus ATAC-seq biological rep1
Cdx2KO_ATAC.bw

data_processing:
Library strategy: ATAC-Seq
Alignment: ATAC-seq and ChIP-seq: Bowtie2; RNA-seq: Tophat, version 2.0.6
ATAC-seq and ChIP-seq peak calling: MACS2, version 2.1.1
RNA-Seq - Read counts were obtained using HTSeq and normalized using DeSeq2 with default parameters. DeSeq2 was further used for calculating differntial gene expression (q<0.01).
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with counts from HTSeq for all genotypes

extract_protocol:
Nuclear prep from villus cells were used for transposition reaction using Nextera Tn5 Transposase (Illumina)
The transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs), and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Villi from the middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Villi were disaggregated with 4X TrypLE in DMEM for 45 minutes at 37°C. Cells were counted, lysed and immediately used for transposase reaction.


title: Wild-type Villus Input_HCHO X-linked

description: Wild-type Villus Input_HCHO X-linked

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and a fraction was used as input.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Villi from middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were cross-linked and immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.


title: Cdx2-/- Villus ATAC-seq biological rep2

description:
Cdx2-/- Villus ATAC-seq biological rep2
Cdx2KO_ATAC.bw


description:
Wild-type Villus ATAC-seq biological rep2
WTVil_ATAC.bw


description:
Wild-type Villus ATAC-seq biological rep1
WTVil_ATAC.bw


title: Ezh1KO_Ezh2KO_replic3_RNAseq

first: Jonas

last: Hojfeldt

address: Ole Maaloes Vej 5

institute: University of Copenhagen

data_processing:
Trimmed with Trimmomatic: SLIDINGWINDOW across 4 bases, average quality required 2
Alligned with STAR 2.4.0, built-in index mm10, default parameters
htseq-count, union mode, non-stranded, minimum alignment quality 10
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-Seq] tabular files contain gene counts
[ChIP-Seq]  No processed data.  Aligned BAM-files have been imported and analyzed/visualized within a software called Easeq (Easeq.net<http://Easeq.net>,  Nature Structural & Molecular Biology Volume 23 No 4 (April 2016), 349-357)).

source_name: Embryonic stem cells

growth_protocol: Cells grown on gelatin in 2i media

value: Ezh1/Ezh2 dKO


title: Wild-type Villus Input_DSG and HCHO X-linked

extract_protocol:
Whole cell extracts from villi fixed with 2mM DSG followed by 1% formaldehyde were sonicated and used as input.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K9me3 ChIP-seq biological rep1

description: Wild-type Villus H3K9me3 X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 5 ug H3K9me3 antibody (Abcam, ab8898) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K9me3 MNase ChIP-seq biological rep1

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ug H3K9me3 antibody (Abcam, ab8898) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Villi from middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.


title: Cdx2-/- Villus H3K9me3 MNase ChIP-seq biological rep1


title: Wild-type Villus H3K27me3 ChIP-seq biological rep1

description: Wild-type Villus H3K27me3 X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 5 ug H3K27me3 antibody (EMD Millipore, 07-449) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Cdx2-/- Villus H3K27me3 ChIP-seq 5+7d biological rep1

description: Cdx2-/- Villus H3K27me3 X-linked ChIP-seq 5+7d biological rep1

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed 7 days after last injection.


title: Cdx2-/- Villus H3K9me3 ChIP-seq biological rep1

description: Cdx2-/- Villus H3K9me3 X-linked ChIP-seq biological rep1


title: Cdx2-/- Villus H3K27me3 ChIP-seq 5d biological rep1

description: Cdx2-/- Villus H3K27me3 X-linked ChIP-seq 5d biological rep1

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed the following day after last injection.


title: Wild-type Villus H3K4me3 MNase ChIP-seq biological rep1

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ug H3K4me3 antibody (Abcam, ab8580) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Cdx2-/- Villus H3K4me3 MNase ChIP-seq biological rep1


title: Cdx2-/- Villus H3K27ac MNase ChIP-seq biological rep2

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ul H3K27ac antibody (Active Motif, 39135) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K27ac MNase ChIP-seq biological rep2


title: Wild-type Villus H3K4me2 MNase ChIP-seq biological rep2

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ul H3K4me2 antibody (EMD Millipore, 07-030) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.