title: DU145_YAP

value: YAP


title: WT_12h_3

status: Public on Mar 28 2022

type: SRA

city: Beijing

first: Fuliang

last: Zong

state: China

address: Feitai region Dongda road

country: China

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

description: treated with ricin

library_source: transcriptomic

data_processing:
removing reads containing the sequencing adapter
removing reads with >15% low-quality base ratio (base quality ≤5)
removing reads whose unknown base ('N' base) ratio was >5%.
Clean reads were mapped to the reference genome using HISAT2 (v2.1.0). Bowtie2 (v2.2.3) was applied to align the clean reads to the reference coding gene set.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Lung tissue cells

extract_protocol:
RNAprep Pure Tissue Kit
using NovaSeq 6000 S4 Reagent kit V1.5

treatment_protocol: The ricin dose was 1.5*LD50.

tag: tissue

value: lung

tag: Sex

value: female

tag: strain

tag: treatment

value: treated with ricin

tag: time (h)

tag: genotype

value: wild type


title: siCon-HEK293-total RNA-seq-rep1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

description: Strand-specific RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were aligned to GRCh37/hg19 reference using STAR aligner.
Gene counts were calculated using FeatureCounts
Expression QC was performed using RSeQC.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes counts and RPKM values for each Sample

organism: Homo sapiens

source_name: HEK293 cells

extract_protocol:
Strand-specific RNA-seq: Total RNA was isolated using Trizol reagent. The RNA-Seq libraries were generated from 200 ng of total RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol.
Strand-specific RNA-seq: The libraries were generated using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol.

tag: sirna

value: siRNA control


title: BALBc_p53null_PLK2null_732

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
BAM files were sorted and indexed using Samtools and quality control was performed using Picard
QC: Picard 2.22.4 CollectRnaSeqMetrics
Resulting fastq files were aligned to the mouse mm10 reference genome using the STAR aligner (STAR 2.7.6a)
Transcript read counts were quantified with Salmon 1.4.0 to quantify gene expression
Gene level quantification was performed by summing transcript counts
Genome_build: Mm10
Supplementary_files_format_and_content: Matrix of salmon quantified normalized gene expressions

source_name: mammary tumor

growth_protocol: Tumors were orthotopically injected in sygeneic hosts and allowed to grow without treatment

extract_protocol:
RNA was extracted using Qiagen Rneasy kits. mRNA quality was assessed using the Agilent Bioanalyzer.
Libraries for mRNA-seq made using total RNA and the Illumina TruSeq mRNA sample preparation kit
Paired end (2x50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer at the UNC High Throughput Sequencing Facility

treatment_protocol: No Treatment

value: balb/c; p53-null; PLK2-null

value: mammary tumor


title: siZC3H4-HEK293-total RNA-seq-rep2

description: Strand-specific RNA-seq

value: siRNA ZC3H4


title: KO_4h_3

description: treated with ricin


title: KO_4h_2

description: treated with ricin


title: WT_4h_3

description: treated with ricin


title: BALBc_p53null_PLK2null_1980


title: H3K27me2_ChIP-seq_mESC_Parental

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

library_source: genomic

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters
Whole-Genome Bisulfite Sequencing (WGBS) raw reads were submitted to Bismark(version 0.22.3) for mapping and methylation calling, against mouse genome version mm10/GRCm38, discarding duplicate reads. Briefly, the methylation level at a CpG (similarly for CHH) site was the number of reads with that site methylated divided by the total number of reads covering the site. To ensure comparability of region DNA methylation levels across all samples, CpGs that overlapped with SNPs from dbSNPs or were located within the ENCODE blacklisted regions, termed DER (Duke excluded regions) were excluded and only CpGs covered by ≥ 5x in all samples were retained for the computation of DNA methylation levels. We defined the average methylation for a genomic region as the coverage-weighted mean of the methylation levels of the individual CpGs within the region.
Genome_build: mm10 and dm6 for mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

molecule: genomic DNA

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells & S2 cells

growth_protocol: Mouse embryonic stem cells were maintained on gelatin-coated plates in Knockout DMEM (Gibco) supplemented with 15% ES-cell-qualified FBS (Gemini), 0.1 mM 2-mercapoethanol, 2mM L-glutamine (Life technologies) and LIF. Drosophila S2 cells were cultured in Schneider’s Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
To obtain a soluble chromatin extract, ~2x10^7 cells were resuspended in 1 mL LB1 (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Complete protease inhibitor) and incubated rotating at 4°C for 10 min. Samples were centrifuged, resuspended in 1 mL LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Compete protease inhibitor), and incubated rotating at 4°C for 10 min. Finally, samples were centrifuged, resuspended in 1 mL LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x Complete protease inhibitor), and homogenized by passing two times through a 27-gauge needle. Chromatin extracts were sonicated for 8 min (anti-HA ChIP) or 12 min (anti-histone PTM ChIP) using a Covaris E220 focused ultra-sonicator at peak power 140, duty factor 5, and cycles/burst 200. For histone PTM ChIP-Rx, after centrifugation soluble chromatin was spiked-in with soluble chromatin from Drosophila S2 cells that was similarly prepared and equivalent to 5-10% of the mouse/human cell chromatin. The lysates were incubated with 100 μl Pierce anti-HA beads (Themo Scientific, 88836) or with anti-H3K4me1 (Abcam, ab8895), anti-H3K9me3 (Abcam, ab8898), anti-H3K27ac (Active Motif, 39133), anti-H3K27me3 (Cell Signaling Tech, 9733), anti-H3K36me2 (Cell Signaling, 2901) or anti-H3K36me3 (Active Motif, 61101) antibody bound to 75 μl protein A or protein G Dnya1 magnetic beads (Invitrogen) and incubated overnight at 4°C with 5% kept as input DNA. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). For ChIP-seq, beads were resuspended in elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10mM EDTA, 200 mM NaCl) and incubated for 30 min at 65°C. After centrifugation the eluate was reverse cross-linked overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C and with Proteinase K (Roche) for 1 hr at 55°C and DNA was recovered using Qiagen PCR purification kit.
KAPA Hyper Prep Kit

tag: chip antibody

value: H3K27me2 (Cell Signaling Technologies #9728)

tag: cell line

value: ESC line V6.5 1A

tag: cell type

value: C57BL/6 x 129S4/SvJae F1 embryo-derived embryonic stem cells

value: wild-type


title: siZC3H4-HEK293-H3K36me3-rep2

description: ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MACS2 (v2.0.10) or SICER (v0.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage signal

extract_protocol:
ChIP-seq: Lysates were clarified from Mnase/sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. . Briefly,In the first step, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by AMpure reagents. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

tag: genotype/variation

tag: antibody

tag: replicate

value: siRNAs

value: Active Motif, 61101


title: KO_4h_1

description: treated with ricin


title: KO_12h_2

description: treated with ricin


title: H3K27me2_ChIP-seq_mESC_sgNSD1

description: According to manufacturer's protocol


title: BALBc_p53null_PLK2null_1981


title: siZC3H4-HEK293-total RNA-seq-rep3

description: Strand-specific RNA-seq


title: coc90c

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 W Campus Dr

department: Animal and Poultry Sciences

institute: Virginia Tech

data_processing:
Reads were aligned to the bovine genome (ARS-UCD1.2 obtained from Ensembl) using HISAT2 (version 2.1.0)
The aligment were filterd for quality, then marked for duplicates, and non-duplicated pairs of reads (mRNA) were used for transcript quantification at the gene level. The fragments were counted against the Ensembl gene annotation (version 1.87) using featureCounts (version 1.6.0)
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Bos taurus

source_name: cumulus oocyte complex

extract_protocol:
Total RNA was isolated from individual oocytes (n=19) and groups of corresponding cumulus cells using TRIzol reagent.
Aproximatly 1ng of amplified complementary DNA was used as input for the Nextera DNA Flex Library Prep kit.

value: cumulus

tag: classification

value: BCB-


title: siCon-HEK293-total RNA-seq-rep2

description: Strand-specific RNA-seq


title: siZC3H4-HEK293-H3K27me3-rep2

description: ChIP-seq

value: Cell Signaling Technology, 9733


title: H3K27ac_ChIP-seq_mESC_Parental

description: According to manufacturer's protocol

value: H3K27ac (Active Motif #39133)


title: BALBc_p53null_PLK2null_743


title: H3K27me3_ChIP-seq_mESC_sgNSD1

description: According to manufacturer's protocol

value: H3K27me3 (Cell Signaling Technologies #9733)


title: PMBC_LateRebound_week0_A02

type: genomic

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

description:
200999740198_R01C01_Red.idat
200999740198_R01C01_Grn.idat
BCN02 clinical trial
Sample_2

hyb_protocol: Genomic DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo) following manufacturer’s protocol. 4uL of bisulfite-converted DNA were hybridized to Infinium HumanMethylationEPIC BeadChip following Illumina Infinium HD Methylation protocol

scan_protocol: Chip analysis was performed using Illumina HiScan SQ fluorescent scanner and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software

data_processing: Quality control, background correction and quantile normalization across arrays was performed using ChAMP R/Bioconductor package with functions extracted from Minfi R/Bioconductor package

label: Cy5 and Cy3

label_protocol: Standard Illumina labelling protocol.

extract_protocol: DNA and RNA were isolated simultaneously from the same sample using AllPrep DNA/RNA Mini Kit (Qiagen) and were frozen until use.

treatment_protocol: Blood samples were processed using Lymphoprep (STEMCELL technologies) and 2M dry pelleted PBMCs were frozen until use

value: PBMC

tag: rebound

value: Late

tag: time

tag: individual

value: male

tag: age


title: BALBc_p53null_PLK2null_7763

value: balb/c; p53-null; PLK2-null

tag: tissue


title: siZC3H4-HEK293-SPT5-rep2

description: ChIP-seq

value: Santa Cruz, sc-133217


title: coc91o

value: oocyte


title: coc91c


title: H3K27me3_ChIP-seq_mESC_Parental

description: According to manufacturer's protocol


title: BALBc_p53null_PLK2null_1985

tag: strain

value: mammary tumor


title: WT_0h_1

description: untreated

value: lung

tag: Sex

value: female

tag: treatment

value: untreated

value: wild type


title: siZC3H4-HEK293-S5p RNAPII-rep2

description: ChIP-seq

value: siRNA ZC3H4

value: S5p RNAPII

value: siRNAs

value: Abcam, ab5131


title: KO_0h_3

description: untreated

tag: time (h)

tag: genotype


title: coc89o

value: BCB-


title: siZC3H4-HEK293-H3K4me3-rep2

description: ChIP-seq

tag: chip antibody

value: Diagenode, C15410003


title: siZC3H4-HEK293-RNAPII-rep2

description: ChIP-seq

value: RNAPII

value: Bethyl, A300-653A


title: siZC3H4-HEK293-input-rep2

description: ChIP-seq

value: input


title: coc88c

value: cumulus


title: siCon-HEK293-total RNA-seq-rep3

description: Strand-specific RNA-seq

tag: sirna

value: siRNA control


title: WT_0h_3

description: untreated


title: siZC3H4-HEK293-H3K27me3-rep1

description: ChIP-seq

value: Cell Signaling Technology, 9733


title: coc87c


title: PMBC_FastRebound_week1_A12

description:
200999740198_R03C02_Red.idat
200999740198_R03C02_Grn.idat
BCN02 clinical trial
Sample_35

tag: cell type

value: PBMC

value: Fast

value: male


title: BALBc_p53null_PLK2null_7748

value: balb/c; p53-null; PLK2-null

value: mammary tumor


title: BALBc_p53null_PLK2null_1967


title: Angptl2_KO_2

city: shanghai

first: wenqian

last: yang

address: 280 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava2.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads FPKM(expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) were calculated using a protocol from Trapnell, Cole, et al., 2010.
Differential expression analysis,Gene Ontology (GO) and KEGG enrichment analysis.
Assembly: mmp10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Brain

extract_protocol:
Cells were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to the manufacturer's recommendations. After clean-up, RNA purity was detected by NanoDrop® spectrophotometers (Thermo Fihser, MA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumia, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X Ten platform and 150bp pired-end module.

value: total cell types in brain

value: Brain


title: Angptl2_KO_1


title: coc86c


title: KO_0h_1

description: untreated

value: lung

value: female

value: untreated


title: siZC3H4-HEK293-S2p RNAPII-rep2

description: ChIP-seq

tag: genotype/variation

value: siRNA ZC3H4

value: S2p RNAPII

value: siRNAs

value: Bethyl, A300-654A


title: KO_0h_2

description: untreated


title: coc89c

value: cumulus

value: BCB-


title: BALBc_p53null_PLK2null_1970


title: BALBc_p53null_PLK2null_1971


title: siZC3H4-HEK293-H3K36me3-rep1

description: ChIP-seq

tag: antibody

value: Active Motif, 61101


title: Angptl2_KO_3


title: WT_0h_2

description: untreated

value: wild type


title: siZC3H4-HEK293-H3K4me3-rep1

description: ChIP-seq

tag: replicate

value: Diagenode, C15410003


title: BALBc_p53null_PLK2null_1987


title: coc87o

value: oocyte

tag: classification


title: BALBc_p53null_PLK2null_7753

value: balb/c; p53-null; PLK2-null


title: coc90o


title: siZC3H4-HEK293-SPT5-rep1

description: ChIP-seq

value: Santa Cruz, sc-133217


title: BALBc_p53null_PLK2null_1984

value: mammary tumor


title: coc88o


title: BALBc_p53null_PLK2null_1986


title: siZC3H4-HEK293-S2p RNAPII-rep1

description: ChIP-seq


title: BALBc_p53null_PLK2null_7750


title: Angptl2_WT_2

value: total cell types in brain

value: Brain


title: Angptl2_WT_3


title: BALBc_p53null_PLK2null_1977


title: siZC3H4-HEK293-RNAPII-rep1

description: ChIP-seq

value: RNAPII

value: Bethyl, A300-653A


title: coc6c


title: coc86o


title: coc74c

value: BCB+


title: coc74o


title: BALBc_p53null_PLK2null_1989


title: coc73o


title: Angptl2_WT_1


title: coc73c


title: BALBc_p53null_PLK2null_1975


title: siCon-HEK293-H3K27me3-rep2

description: ChIP-seq

value: siRNA control

value: Cell Signaling Technology, 9733


title: control_Input_115

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

data_processing:
Bioinformatic processing of ATAC-seq and histone ChIP-seq data:   ATAC-seq trimming, mapping, peak calling: Following sequencing and demultiplexing, paired-end reads from each sample were first trimmed using NGmerge (with the adapter-removal flag specified) (Gaspar, 2018). Following trimming, samples were individually mapped to the Mm10 genome using Bowtie2 (Langmead, Trapnell, Pop, & Salzberg, 2009) with the following settings (--very-sensitive  -k 10) and converted to bam format and sorted using Samtools (H. Li et al., 2009). To find sites of ‘enrichment’ (i.e. peak calling) we used Genrich (https://github.com/jsh58/Genrich) with the following flags set (-j, -y, -r, -e chrM). First to identify control peaks, we used the two control replicate ATAC-seq alignment files—produced from Bowtie2/Samtools—as ‘experimental input’, with the above Genrich settings (in this approach, ‘background’ is based on the size of the analyzed genome, i.e., Mm10, minus mitochondrial DNA). We did a similar analysis using the two mutant replicate alignment files as ‘experimental input’ (rather than control)—identifying significantly enriched regions in the mutant dataset. Additionally, to compare the two datasets directly, we supplied the two control alignment files as ‘experimental’ while simultaneously supplying the two mutant alignment files as ‘background’, thus, identifying regions that were significantly enriched in controls relative to mutants. These analyses resulted in genomic coordinates of ‘peaks’ for each of the supplied datasets.    H3K4me3 histone ChIP-seq trimming, mapping, and overlapping: Following sequencing, samples were demultiplexed and mapped to the Mm10 genome build using NovoAlign (Novocraft). Mapped reads were then processed for duplicate removal using the Picard suite of tools (http://broadinstitute.github.io/picard). The resulting deduplicated mapped reads were subsequently indexed using Samtools (H. Li et al., 2009) and the resulting indexed Bam files were normalized using the bamCoverage function in deepTools (Ramirez et al., 2016). The resulting normalized bigWig files were then used with the control ATAC-seq bed file (genomic coordinates of peaks), along with the computeMatrix function in deepTools, to generate a matrix file. This matrix was then visualized using the plotHeatmap function in deepTools with a K-means cluster setting of 2, identifying ATAC-seq coordinates that had high or little to no H3K4me3 enrichment.    Multi-organ ATAC-seq dataset overlapping: First, publicly available ATAC-seq datasets were downloaded from the ENCODE consortium in bigWig file format (E11.5 heart: ENCSR820ACB; E11.5 liver: ENCSR785NEL; E11.5 hindbrain: ENCSR012YAB; E11.5 midbrain: ENCSR382RUC; E11.5 forebrain: ENCSR273UFV; E11.5 neural tube: ENCSR282YTE; E15.5 kidney: ENCSR023QZX; E15.5 intestine: ENCSR983JWA). A matrix file was then generated using all bigWig files along with the genomic coordinates obtained from the H3K4me3 clustering above (specifically the coordinates from the H3K4me3 negative cluster) using the computeMatrix function in deepTools. Once generated, the matrix file was then visualized using the plotHeatmap function, with a K-means cluster setting of 3, in deepTools.    GREAT analysis: To determine and plot the general distribution of sub-clusters and their genomic coordinates relative to transcriptional start site of genes, the GREAT algorithm (v4) (McLean et al., 2010) was used with default settings. GREAT was also utilized for identifying enriched biological pathways and gene sets within discrete sub-clusters, with the ‘Association rule settings’ limited to 100 kb distal in the ‘Basal plus extension’ setting.    Motif enrichment analysis: For motif enrichment analysis, genomic coordinates were supplied in BED file format to the HOMER software package (Heinz et al., 2010), using the “findMotifsGenome.pl” program and default settings.     Association of gene expression and ATAC-seq peaks: First, gene expression for the craniofacial ectoderm and mesenchyme, at E11.5, was calculated using our publicly available datasets profiling the facial ectoderm and mesenchyme from E10.5 through E12.5 (Hooper et al., 2020) (available through the Facebase Consortium website, www.facebase.org, under the accession number FB00000867). Expression values for all 3 craniofacial prominences (e.g. mandibular, maxillary, frontonasal) were averaged independently for the ectoderm and mesenchyme, establishing an ‘expression value’ for each tissue compartment of the entire face at E11.5. Next, an ‘ectoderm enrichment’ value was calculated for each gene by taking the quotient of the ectoderm value divided by the mesenchyme value. Concurrently, ATAC-seq peaks from various sub-clusters were associated with a corresponding gene(s) using the GREAT algorithm and these associations were downloaded using the ‘Gene -> genomic regions association table’ function in GREAT. A ‘peak-associated profile’ was then ascribed for each gene (i.e., the type and number of sub-cluster peaks associated with each gene), allowing the binning of genes based on this profile. Bins of genes, and their associated ‘ectoderm enrichment’ value were then plotted in R using the empirical cumulative distribution function (stat_ecdf) in ggplot2 and significance calculated using a Kolmogorov-Smirnov test (ks.test).    Conservation analysis: To determine the level of conversation for AP-2 dependent genomic elements (Figure 3E) the phastCons60way (scores for multiple alignments of 59 vertebrate genomes to the mouse genome) dataset was downloaded from the University of California, Santa Cruz (UCSC) genome browser in bigWig format (http://hgdownload.cse.ucsc.edu/goldenpath/mm10/phastCons60way/). A matrix file was then generated using the bigWig file along with the ‘AP-2 dependent’ genomic coordinates using the computeMatrix function in deepTools. Once generated, the matrix file was then visualized using the plotHeatmap function, with a K-means cluster setting of 2, in deepTools.
Assembly: Mm10

source_name: E11.5 facial ectoderm

extract_protocol: H3K4me3 histone ChIP: For H3K4me3 based histone ChIP-seq analysis, craniofacial ectoderm was first isolated from E10.5 and E11.5 wild-type mouse embryos, as previously described (H. Li & Williams, 2013). Once isolated and pooled, tissue/chromatin was crosslinked with 1% formaldehyde at RT for 10 minutes. Following crosslinking, reactions were quenched using 0.125 M glycine, followed by multiple PBS washes.  Samples were subsequently frozen in liquid nitrogen and stored at -80°C. Once ~ 5 mg of tissue was collected per stage (e.g., E10.5, N = ~50 embryos; or E11.5, N = ~15 embryos), samples from multiple dissections, but similar stages, were pooled and combined with 300 µl of ‘ChIP Nuclei Lysis buffer’ (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS), with 1mM PMSF and 1X proteinase inhibitor cocktail (PICT, 100X from Thermo Scientific, Prod # 1862209).  Pooled tissue was resuspended completely and subsequently incubated at RT for 10 mins.  Following incubation, chromatin was fragmented using a Bioruptor (Diagenode, Cat. No. UCD-200) with the following settings: High energy, 30 seconds on, 30 seconds off, with sonication for 45 mins. Following shearing, chromatin was assessed as ~100-500 bp in size. Next, a small portion of fragmented chromatin was saved as input, while the rest was diluted 1 in 5 in RIPA buffer (150 mM NaCl, 1% NP-40, 0.5% deoxycholate, 0.1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, plus PMSF and PICT) followed by the addition of 20 µl protein A/G agarose beads (Pierce, Thermo Scientific, Prod # 20423 ) prewashed with RIPA buffer to eliminate non-specific binding. The pre-cleaned chromatin was then incubated with 2.5 µL of monoclonal H3K4Me3 primary antibody (Millipore, cat. #04-745), while rotating at 4°C, overnight. The following day, 20 ul protein A/G beads pre-saturated with 5 mg/ml BSA in PBS (Sigma, A-3311) were washed in RIPA buffer and subsequently added to the chromatin/antibody mix at 4°C, rotating, for 2 hours. Samples were then washed twice in RIPA, four times in Szak Wash (100 mM Tris HCl pH 8.5, 500 mM LiCl, 1% NP-40, 1% deoxycholate), twice more in RIPA followed by two TE washes (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0).  Finally, the bead slurry was resuspended in 100µl TE and the remaining bound chromatin was eluted off the beads using 200 ul 1.5X  ‘Elution Buffer’ (70 mM Tris HCl pH 8.0, 1 mM EDTA, 1.5% SDS) at 65°C for 5 mins. Once eluted, crosslinks were reversed by incubating ChIP’d samples and input samples at 65°C overnight in 200 mM NaCl. Samples were then subjected to 20 ug of Proteinase K digestion at 45 ºC for 1h and DNA subsequently extracted using a standard Phenol:Chloroform, EtOH-precipitation based approach. Purified, pelleted, DNA was then resuspended in 20µl water. H3K4me3 histone ChIP-Seq library preparation and sequencing: Once purified fragments were obtained and quality and size confirmed, libraries were constructed using the Nugen ChIP Seq Library Construction Kit. Library purity, integrity, and size were then confirmed using High Sensitivity D1000 ScreenTape and subsequently sequenced using an Illumina MiSEQ platform and 50 bp single-end reads to a depth of ~25-30x106 reads per experimental sample and ~10x106 reads for input, carried out by the University of Colorado, Anschutz Medical Campus, Genomics and Microarray Core.

value: facial ectoderm

value: wild-type

tag: Stage

value: embryonic day 11.5


title: BALBc_p53null_PLK2null_1973


title: siCon-HEK293-H3K4me3-rep2

description: ChIP-seq

value: siRNAs


title: siCon-HEK293-H3K36me3-rep2

description: ChIP-seq

value: Active Motif, 61101


title: BALBc_p53null_PLK2null_7749


title: BALBc_p53null_PLK2null_1974


title: control_H3K4me3_115


title: BALBc_p53null_PLK2null_7764


title: coc72c

value: cumulus


title: siZC3H4-HEK293-S5p RNAPII-rep1

description: ChIP-seq

value: siRNA ZC3H4

value: S5p RNAPII

value: Abcam, ab5131


title: siZC3H4-HEK293-input-rep1

description: ChIP-seq

value: input


title: siCon-HEK293-S2p RNAPII-rep2

description: ChIP-seq

value: S2p RNAPII

value: Bethyl, A300-654A


title: BALBc_p53null_PLK2null_1988

value: balb/c; p53-null; PLK2-null

value: mammary tumor


title: siCon-HEK293-SPT5-rep2

description: ChIP-seq

value: Santa Cruz, sc-133217


title: siCon-HEK293-S5p RNAPII-rep2

description: ChIP-seq

value: siRNA control


title: coc72o

value: oocyte

value: BCB+


title: control_H3K4me3_105

source_name: E10.5 facial ectoderm

value: facial ectoderm

value: wild-type

value: embryonic day 10.5


title: coc71o


title: mutant_ATACseq_Rep2

data_processing:
Bioinformatic processing of ATAC-seq and histone ChIP-seq data:   ATAC-seq trimming, mapping, peak calling: Following sequencing and demultiplexing, paired-end reads from each sample were first trimmed using NGmerge (with the adapter-removal flag specified) (Gaspar, 2018). Following trimming, samples were individually mapped to the Mm10 genome using Bowtie2 (Langmead, Trapnell, Pop, & Salzberg, 2009) with the following settings (--very-sensitive  -k 10) and converted to bam format and sorted using Samtools (H. Li et al., 2009). To find sites of ‘enrichment’ (i.e. peak calling) we used Genrich (https://github.com/jsh58/Genrich) with the following flags set (-j, -y, -r, -e chrM). First to identify control peaks, we used the two control replicate ATAC-seq alignment files—produced from Bowtie2/Samtools—as ‘experimental input’, with the above Genrich settings (in this approach, ‘background’ is based on the size of the analyzed genome, i.e., Mm10, minus mitochondrial DNA). We did a similar analysis using the two mutant replicate alignment files as ‘experimental input’ (rather than control)—identifying significantly enriched regions in the mutant dataset. Additionally, to compare the two datasets directly, we supplied the two control alignment files as ‘experimental’ while simultaneously supplying the two mutant alignment files as ‘background’, thus, identifying regions that were significantly enriched in controls relative to mutants. These analyses resulted in genomic coordinates of ‘peaks’ for each of the supplied datasets.    H3K4me3 histone ChIP-seq trimming, mapping, and overlapping: Following sequencing, samples were demultiplexed and mapped to the Mm10 genome build using NovoAlign (Novocraft). Mapped reads were then processed for duplicate removal using the Picard suite of tools (http://broadinstitute.github.io/picard). The resulting deduplicated mapped reads were subsequently indexed using Samtools (H. Li et al., 2009) and the resulting indexed Bam files were normalized using the bamCoverage function in deepTools (Ramirez et al., 2016). The resulting normalized bigWig files were then used with the control ATAC-seq bed file (genomic coordinates of peaks), along with the computeMatrix function in deepTools, to generate a matrix file. This matrix was then visualized using the plotHeatmap function in deepTools with a K-means cluster setting of 2, identifying ATAC-seq coordinates that had high or little to no H3K4me3 enrichment.    Multi-organ ATAC-seq dataset overlapping: First, publicly available ATAC-seq datasets were downloaded from the ENCODE consortium in bigWig file format (E11.5 heart: ENCSR820ACB; E11.5 liver: ENCSR785NEL; E11.5 hindbrain: ENCSR012YAB; E11.5 midbrain: ENCSR382RUC; E11.5 forebrain: ENCSR273UFV; E11.5 neural tube: ENCSR282YTE; E15.5 kidney: ENCSR023QZX; E15.5 intestine: ENCSR983JWA). A matrix file was then generated using all bigWig files along with the genomic coordinates obtained from the H3K4me3 clustering above (specifically the coordinates from the H3K4me3 negative cluster) using the computeMatrix function in deepTools. Once generated, the matrix file was then visualized using the plotHeatmap function, with a K-means cluster setting of 3, in deepTools.    GREAT analysis: To determine and plot the general distribution of sub-clusters and their genomic coordinates relative to transcriptional start site of genes, the GREAT algorithm (v4) (McLean et al., 2010) was used with default settings. GREAT was also utilized for identifying enriched biological pathways and gene sets within discrete sub-clusters, with the ‘Association rule settings’ limited to 100 kb distal in the ‘Basal plus extension’ setting.    Motif enrichment analysis: For motif enrichment analysis, genomic coordinates were supplied in BED file format to the HOMER software package (Heinz et al., 2010), using the “findMotifsGenome.pl” program and default settings.     Association of gene expression and ATAC-seq peaks: First, gene expression for the craniofacial ectoderm and mesenchyme, at E11.5, was calculated using our publicly available datasets profiling the facial ectoderm and mesenchyme from E10.5 through E12.5 (Hooper et al., 2020) (available through the Facebase Consortium website, www.facebase.org, under the accession number FB00000867). Expression values for all 3 craniofacial prominences (e.g. mandibular, maxillary, frontonasal) were averaged independently for the ectoderm and mesenchyme, establishing an ‘expression value’ for each tissue compartment of the entire face at E11.5. Next, an ‘ectoderm enrichment’ value was calculated for each gene by taking the quotient of the ectoderm value divided by the mesenchyme value. Concurrently, ATAC-seq peaks from various sub-clusters were associated with a corresponding gene(s) using the GREAT algorithm and these associations were downloaded using the ‘Gene -> genomic regions association table’ function in GREAT. A ‘peak-associated profile’ was then ascribed for each gene (i.e., the type and number of sub-cluster peaks associated with each gene), allowing the binning of genes based on this profile. Bins of genes, and their associated ‘ectoderm enrichment’ value were then plotted in R using the empirical cumulative distribution function (stat_ecdf) in ggplot2 and significance calculated using a Kolmogorov-Smirnov test (ks.test).    Conservation analysis: To determine the level of conversation for AP-2 dependent genomic elements (Figure 3E) the phastCons60way (scores for multiple alignments of 59 vertebrate genomes to the mouse genome) dataset was downloaded from the University of California, Santa Cruz (UCSC) genome browser in bigWig format (http://hgdownload.cse.ucsc.edu/goldenpath/mm10/phastCons60way/). A matrix file was then generated using the bigWig file along with the ‘AP-2 dependent’ genomic coordinates using the computeMatrix function in deepTools. Once generated, the matrix file was then visualized using the plotHeatmap function, with a K-means cluster setting of 2, in deepTools.
Assembly: Mm10
Supplementary files format and content: narrow peak

extract_protocol: Tissue preparation for ATAC-seq: For ATAC-seq analysis, E11.5 embryos were dissected into ice-cold PBS and associated yolk sacs used for rapid genotyping using the Extract-N-Amp Tissue PCR kit as recommended by the manufacturer (Sigma). During genotyping, the facial prominences were carefully removed from individual embryos using a pair of insulin syringes and placed in a 24-well plate with 1 mL of 1 mg/ml Dispase II (in PBS). The samples were incubated with rocking at 37°C for 30-40 minutes and then the facial ectoderm carefully dissected away from the mesenchyme into ice-cold PBS, as described (H. Li & Williams, 2013). Facial ectoderm was then centrifuged at 4°C, 500 g, for 3 minutes in a 1.5ml Eppendorf tube, washed 1x with ice-cold PBS, and then centrifuged again. Following resuspension in 750 µL of 0.25% trypsin-EDTA, samples were incubated at 37°C for 15 minutes with gentle agitation. Following addition of 750 µL of DMEM with 10% FBS to inhibit further digestion, cells were dissociated by pipetting up and down multiple times with wide orifice pipette tips. Cells were subsequently spun at 300 g for 5 minutes and washed with PBS containing 0.4% BSA, and this step was repeated twice. Finally, the cell pellet was resuspended with 50 µL of PBS and the density of the single cell suspension quantified on a hematocytometer.    ATAC-seq transposition, library preparation, and sequencing: Following genotype analysis of embryos used for facial ectoderm isolation, EDKO (Crect; Tfap2aflox/flox; Tfap2bflox/flox) and control littermate samples lacking Crect (Tfap2aflox/+; Tfap2bflox/+) were used for the ATAC-seq protocol, largely following procedures previously described (Buenrostro et al., 2013; Buenrostro et al., 2015; Corces et al., 2017). Briefly, 50,000 cells from each sample were pelleted at 500 g for 5 minutes at 4°C. The pellet was then resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.5; 10 mM NaCl; 3 mM MgCl2; 0.1% NP-40, 0.1% Tween-20; 0.01% Digitonin) by gently pipetting ~4 times to release the nuclei which were then incubated on ice for 3 minutes. The sample was next spun at 500 g for 20 minutes at 4°C and the pelleted nuclei resuspended in Tagmentation mix (e.g. 25 µL 2x Nextera TD Buffer, 2.5 µL Nextera TD Enzyme, 0.1% Tween-20, 0.01% Digitonin, up to 50 µL with nuclease-free water) and placed at 37°C for 30 minutes in a thermocycler. Following transposition, samples were purified using the QIAGEN minElute PCR Purification Kit (Qiagen) and eluted with 11 µL of supplied Elution Buffer. Transposed DNA was next indexed with a unique barcoded sequence and amplified prior to sequencing. Briefly, 10 µL of transposed DNA was mixed with the Nextera Ad1 PCR primer as well as a unique Nextera PCR primer (e.g. Ad2.x) and NEBNext HighFidelity 2x PCR Master Mix. Samples were then amplified using the following cycling parameters: [72°C, 5 min], [98°C, 30 sec], [98°C, 10 sec; 63°C, 30 sec; 72°C, 1 min (repeat 10-12 cycles)]. Following cycle 5, an aliquot of sample was removed for Sybr-green based quantification to determine the number of remaining cycles required to reach adequate amounts for sequencing without introducing over-amplification artifacts due to library saturation. Following indexing and amplification, samples were purified using two rounds of AmpureXP bead-based size selection. Library purity, integrity, and size were then confirmed using High Sensitivity D1000 ScreenTape and subsequently sequenced using the Illumina NovaSEQ6000 platform and 150 bp paired-end reads to a depth of ~75x106 reads per sample, carried out by the University of Colorado, Anschutz Medical Campus, Genomics and Microarray Core.

value: embryonic day 11.5


title: mutant_ATACseq_Rep1


title: siCon-HEK293-RNAPII-rep2

description: ChIP-seq

value: RNAPII

value: siRNAs

value: Bethyl, A300-653A


title: BALBc_p53-null_5329_ROSEN-17

value: balb/c; p53-null


title: coc71c

value: cumulus


title: RNAseq_mESC_WT_Rep2

city: Chicago

first: Bercin

middle: K

last: Cenik

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Embryonic stem cell RNAseq

data_processing:
Basecalls were performed using  bcl2fastq v2.17.
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: V6.5 embryonic stem cells

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF). EBs were generated via the hanging drop method in serum-containing media without 2i/LIF.

extract_protocol:
For ChIP, ESCs were fixed in 1% formaldehyde, followed by quenching and cell lysis before chromatin sonication using a E220 focused-ultrasonicator (Covaris). Sheared chromatin was then subjected to immunoprecipitation, and immunoprecipitated DNA was then washed, eluted, reverse cross-linked, and purified prior to submission for library preparation. Spike-in normalized ChIP samples were mixed at a 2:1 cell count ratio (mammalian: fly) with Drosophila melanogaster S2 cells crosslinked the same way, prior to sonication.
RNA was extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions. All samples were lysed in 350ul of QIAGEN Buffer RLT prior to extraction.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit. Ribosomal RNA was depleted using QIAseq FastSelect –rRNA HMR Kit per manufacturer's instructions. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.

value: embryonic stem cell

tag: cell line

value: Wildtype/WT


title: BALBc_p53-null_5317_ROSEN-16


title: coc70o


title: BALBc_p53-null_10151_ROSEN-19


title: control_ATACseq_Rep1

value: control


title: RNAseq_mESC_WT_Rep1

description: Embryonic stem cell RNAseq


title: siCon-HEK293-input-rep2

description: ChIP-seq

value: input


title: RNAseq_mESC_ING5KO_clone2_Rep2

description: Embryonic stem cell RNAseq

value: ING5 deletion


title: BALBc_p53-null_7435_ROSEN-18

value: mammary tumor


title: control_ATACseq_Rep2


title: coc69c


title: coc68c

value: BCB-


title: RNAseq_mESC_ING5KO_clone2_Rep1

description: Embryonic stem cell RNAseq


title: siCon-HEK293-H3K36me3-rep1

description: ChIP-seq

value: siRNA control

value: Active Motif, 61101


title: coc69o

value: oocyte

value: BCB+


title: siCon-HEK293-SPT5-rep1

description: ChIP-seq

value: Santa Cruz, sc-133217


title: siCon-HEK293-S2p RNAPII-rep1

description: ChIP-seq

value: S2p RNAPII

value: Bethyl, A300-654A


title: coc70c


title: BALBc_p53-null_10152_ROSEN-20


title: BALBc_p53-null_10155_ROSEN-21


title: RNAseq_mESC_Set1AdSET_Rep1

description: Embryonic stem cell RNAseq

value: SET1A SET domain deletion


title: BALBc_p53-null_2208L_ROSEN-12

value: balb/c; p53-null


title: siCon-HEK293-H3K4me3-rep1

description: ChIP-seq

value: siRNAs

value: Diagenode, C15410003


title: RNAseq_mESC_Set1AdSET_Rep2

description: Embryonic stem cell RNAseq

value: embryonic stem cell


title: siCon-HEK293-H3K27me3-rep1

description: ChIP-seq

value: Cell Signaling Technology, 9733


title: BALBc_p53-null_2153L_ROSEN-1


title: BALBc_p53-null_2225L_ROSEN-3


title: coc19c

value: cumulus


title: siCon-HEK293-input-rep1

description: ChIP-seq

value: input


title: RNAseq_mESC_ING5KO_clone1_Rep2

description: Embryonic stem cell RNAseq

value: ING5 deletion


title: siCon-HEK293-RNAPII-rep1

description: ChIP-seq

value: RNAPII

value: Bethyl, A300-653A


title: coc68o

value: BCB-


title: RNAseq_mESC_dMutant_clone1_Rep2

description: Embryonic stem cell RNAseq

value: ING5 deletion, SET1A SET domain deletion


title: BALBc_p53-null_2396R_ROSEN-5

value: mammary tumor


title: coc66c


title: coc66o

value: oocyte


title: siCon-HEK293-S5p RNAPII-rep1

description: ChIP-seq

value: siRNA control

value: S5p RNAPII

value: Abcam, ab5131


title: HEK293-CK2a-rep2

description: ChIP-seq

value: WT

value: Abcam ab70774


title: coc65c


title: RNAseq_mESC_ING5KO_clone1_Rep1

description: Embryonic stem cell RNAseq


title: HEK293-WDR82-rep2

description: ChIP-seq


title: RNAseq_mESC_dMutant_clone2_Rep2

description: Embryonic stem cell RNAseq


title: coc6o


title: coc24o

value: BCB+


title: RNAseq_EB_WT_line1_rep5

description: Embryoid body RNAseq

value: embryoid body

value: Wildtype/WT


title: BALBc_p53-null_T11_ROSEN-10

value: balb/c; p53-null


title: HEK293-input-rep2

description: ChIP-seq

value: input


title: HEK293-SPT5-rep2

description: ChIP-seq

value: Santa Cruz, sc-133217


title: RNAseq_mESC_dMutant_clone2_Rep1

description: Embryonic stem cell RNAseq

value: embryonic stem cell


title: coc24c

value: cumulus


title: RNAseq_EB_WT_line1_rep3

description: Embryoid body RNAseq


title: BALBc_p53-null_2331L_ROSEN-14


title: coc65o

value: BCB-


title: coc17o


title: BALBc_p53-null_2224L_ROSEN-2


title: RNAseq_mESC_dMutant_clone1_Rep1

description: Embryonic stem cell RNAseq

value: ING5 deletion, SET1A SET domain deletion


title: HEK293-ZC3H4-rep2

description: ChIP-seq

value: this study


title: RNAseq_EB_WT_line1_rep4

description: Embryoid body RNAseq


title: coc19o

value: oocyte


title: RNAseq_EB_WT_line1_rep2

description: Embryoid body RNAseq


title: RNAseq_EB_WT_line1_rep6

description: Embryoid body RNAseq


title: coc17c


title: HEK293-RNAPII-rep1

description: ChIP-seq

value: RNAPII

value: Bethyl, A300-653A


title: HEK293-H3K27me3-rep1

description: ChIP-seq

value: Cell Signaling Technology, 9733


title: HEK293-H3K4me3-rep1

description: ChIP-seq

value: WT

value: Diagenode, C15410003


title: RNAseq_EB_WT_line1_rep1

description: Embryoid body RNAseq


title: RNAseq_EB_Set1AdSET_line2_rep3

description: Embryoid body RNAseq

value: SET1A SET domain deletion


title: HEK293-CK2a-rep1

description: ChIP-seq

value: Abcam, ab70774


title: RNAseq_EB_Set1AdSET_line2_rep2

description: Embryoid body RNAseq

value: embryoid body


title: RNAseq_SETlessE8_Set3_HET_8

description: E8.5 mouse embryo RNAseq

source_name: E8.5 mouse embryos

value: embryo

value: Heterozygous for SET1A SET domain deletion


title: RNAseq_SETlessE8_Set3_KO_1

description: E8.5 mouse embryo RNAseq

value: Homozygous for SET1A SET domain deletion


title: HEK293-WDR82-rep1

description: ChIP-seq


title: RNAseq_SETlessE8_Set3_WT_1

description: E8.5 mouse embryo RNAseq

value: Wildtype/WT


title: RNAseq_SETlessE8_Set3_HET_7

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set3_HET_6

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_Set1AdSET_line2_rep1

description: Embryoid body RNAseq


title: HEK293-input-rep1

description: ChIP-seq

value: input


title: HEK293-ZC3H4-rep1

description: ChIP-seq


title: RNAseq_SETlessE8_Set3_HET_5

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_Set1AdSET_line1_rep2

description: Embryoid body RNAseq


title: RNAseq_EB_Set1AdSET_line1_rep1

description: Embryoid body RNAseq


title: RNAseq_SETlessE8_Set3_HET_4

description: E8.5 mouse embryo RNAseq


title: HEK293-SPT5-rep1

description: ChIP-seq

value: Santa Cruz, sc-133217


title: RNAseq_EB_Set1AdSET_line1_rep3

description: Embryoid body RNAseq


title: RNAseq_SETlessE8_Set3_HET_3

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_ING5KO_line2_rep3

description: Embryoid body RNAseq

value: ING5 deletion


title: RNAseq_EB_ING5KO_line2_rep2

description: Embryoid body RNAseq


title: RNAseq_SETlessE8_Set3_HET_2

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set3_HET_1

description: E8.5 mouse embryo RNAseq


title: MLS402-91_siDDIT3_R2

city: Heidelberg

first: Cihan

last: Erkut

address: Im Neuenheimer Feld 581

department: Applied Functional Genomics

country: Germany

institute: German Cancer Research Center

data_processing:
Basecalling was performed using bcl2fastq 2.20.0.422.
The RNAseq data was analysed with the DKFZ/ODCF RNAseq workflow 1.3.0.
FASTQ reads for individual samples were aligned by a 2-pass alignment using the STAR aligner 2.5.3a.
Duplicate marking of the resultant main alignment file was done with sambamba 0.6.5.
The chimeric file was sorted using samtools 1.6.
BAM indexes were generated using sambamba 0.6.5.
Quality control analysis was performed using samtools flagstat and the rnaseqc tool version 1.1.8. Depth of coverage analysis for rnaseqc was turned off.
Gene-specific read counting was performed using featureCounts version 1.5.1 over exon features based on the GENCODE 19 gene models. Only unique alignments were counted. Strand specific counting was also used.
A custom script was used to calculate RPKM and TPM expression values. For total library abundance calculations, all genes on chromosomes X, Y, MT as well as rRNA and tRNA genes were omitted, as they are likely to introduce library size estimation biases.
Genome_build: 1000 Genomes Project Phase II Reference Genome (hs37d5) based on NCBI GRCh37, and GENCODE 19 gene models.
Supplementary_files_format_and_content: Tab-delimited text files with gene IDs, gene names, raw counts, RPKM and TPM values.

source_name: Myxoid liposarcoma

growth_protocol: MLS402-91 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted with an RNeasy Plus Mini Kit (QIAGEN, #74134) and DNase treated.
Illumina TruSeq Stranded kit was used for library preparation. Each sample was barcoded with an i5/i7 pair of TruSeq DNA/RNA UDI indices. The pooled library was sequenced in two lanes.

treatment_protocol: MLS402-91 cells were seeded in 6-well plates and transfected with 25 pmol YAP1 siRNA, DDIT3 siRNA or a non-targeting negative control siRNA using Lipofectamine RNAiMAX (Invitrogen). After 6h, the medium was changed to RPMI 1640 supplemented with 2% fetal bovine serum and incubated for 48h.

value: DDIT3 siRNA


title: MLS402-91_siYAP1_R1

value: YAP1 siRNA


title: MLS402-91_siDDIT3_R1


title: RNAseq_SETlessE8_Set2_WT_3

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_ING5KO_line2_rep1

description: Embryoid body RNAseq


title: MLS402-91_siCTRL_R2

value: control siRNA


title: RNAseq_EB_ING5KO_line1_rep3

description: Embryoid body RNAseq


title: RNAseq_EB_ING5KO_line1_rep2

description: Embryoid body RNAseq


title: MLS402-91_siCTRL_R1


title: RNAseq_SETlessE8_Set2_WT_1

description: E8.5 mouse embryo RNAseq


title: MLS402-91_siYAP1_R2


title: RNAseq_SETlessE8_Set2_WT_2

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set2_KO_1

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set2_HET_7

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_dMutant_line2_rep3

description: Embryoid body RNAseq

value: ING5 deletion, SET1A SET domain deletion


title: RNAseq_EB_dMutant_line2_rep2

description: Embryoid body RNAseq


title: AML59_GMP

type: RNA

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol

scan_protocol: Arrays were scanned in the Affymetrix Genearray 2500 scanner to generate flourescent images, as described in Affymetrix GeneChip protocol.

data_processing: Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA)

label: biotin

label_protocol: 2.5ug amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Untreated CMPs/GMPs sorted from BM

extract_protocol: RNeasy from Qiagen. According to manufaturer protocol.  Followed by amplification with NuGEN's WT Ovation Pico kit. Again according to manufacturer protocol.

value: Bone marrow

value: granulocyte macrophage progenitor (GMP) cells

tag: cell markers


title: AML60_GMP


title: RNAseq_EB_dMutant_line2_rep1

description: Embryoid body RNAseq


title: RNAseq_SETlessE8_Set2_HET_6

description: E8.5 mouse embryo RNAseq

tag: age


title: AML58_GMP

tag: tissue


title: RNAseq_SETlessE8_Set2_HET_5

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set2_HET_4

description: E8.5 mouse embryo RNAseq


title: RNAseq_EB_dMutant_line1_rep3

description: Embryoid body RNAseq


title: RNAseq_EB_dMutant_line1_rep2

description: Embryoid body RNAseq


title: Sample_7_CORT

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using gSnap aligner (version 2017-09-11)
Gene-read quantification was perfromed using HTSeq-count (version 0.6,0).
HTSeq-count output files were merged into the raw_gene_count_matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature according to Ensembl88 for each sample.

source_name: ventral hippocampus_Corticosterone

extract_protocol:
Total RNA was isolated from the snap-frozen ventral hippocampus samples; NucleoSpin RNA kit (Macherey-Nagel)
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

tag: strain

value: Corticosterone

tag: duration

value: 3 hours

value: ventral hippocampus


title: Sample_6_CORT

tag: treatment


title: PBMC_FastRebound_week24_B14

description:
202292320045_R07C01_Red.idat
202292320045_R07C01_Grn.idat
BCN02 clinical trial
Sample_120

value: PBMC

tag: rebound

value: Fast

tag: time

tag: individual

tag: Sex

value: male


title: Sample_8_CORT


title: PBMC_FastRebound_week24_B05

description:
202240580045_R08C01_Red.idat
202240580045_R08C01_Grn.idat
BCN02 clinical trial
Sample_80

tag: cell type


title: PBMC_LateRebound_MAP_B13

description:
202292320045_R04C01_Red.idat
202292320045_R04C01_Grn.idat
BCN02 clinical trial
Sample_111

value: Late

value: MAP


title: PBMC_LateRebound_week24_B13

description:
202292320045_R05C01_Red.idat
202292320045_R05C01_Grn.idat
BCN02 clinical trial
Sample_112


title: RNAseq_SETlessE8_Set2_HET_3

description: E8.5 mouse embryo RNAseq

value: embryo

tag: genotype/variation

value: Heterozygous for SET1A SET domain deletion


title: RNAseq_EB_ING5KO_line1_rep1

description: Embryoid body RNAseq

value: embryoid body

value: ING5 deletion


title: Sample_5_CORT


title: PBMC_FastRebound_week24_A15

description:
202240580045_R04C01_Red.idat
202240580045_R04C01_Grn.idat
BCN02 clinical trial
Sample_64


title: PBMC_FastRebound_MAP_B14

description:
202292320045_R06C01_Red.idat
202292320045_R06C01_Grn.idat
BCN02 clinical trial
Sample_119


title: ChIP_WT_Set1AdSET

description: ESC Set1A ChIPseq

value: embryonic stem cell

value: Wildtype/WT

tag: chip antibody

value: Set1A (Homemade, #919)


title: RNAseq_SETlessE8_Set2_HET_2

description: E8.5 mouse embryo RNAseq


title: Sample_4_Veh

source_name: ventral hippocampus_vehicle

value: Vehicle


title: PBMC_FastRebound_week24_B10

description:
202292320045_R03C01_Red.idat
202292320045_R03C01_Grn.idat
BCN02 clinical trial
Sample_104


title: PBMC_FastRebound_MAP_B06

description:
202240580079_R01C01_Red.idat
202240580079_R01C01_Grn.idat
BCN02 clinical trial
Sample_87


title: PBMC_FastRebound_MAP_B05

description:
202240580045_R07C01_Red.idat
202240580045_R07C01_Grn.idat
BCN02 clinical trial
Sample_79


title: PBMC_FastRebound_week24_B06

description:
202240580079_R02C01_Red.idat
202240580079_R02C01_Grn.idat
BCN02 clinical trial
Sample_88


title: RNAseq_SETlessE8_Set2_HET_1

description: E8.5 mouse embryo RNAseq


title: PBMC_LateRebound_week24_B03

description:
202240580045_R06C01_Red.idat
202240580045_R06C01_Grn.idat
BCN02 clinical trial
Sample_72


title: PBMC_LateRebound_MAP_B03

description:
202240580045_R05C01_Red.idat
202240580045_R05C01_Grn.idat
BCN02 clinical trial
Sample_71


title: Sample_3_Veh


title: ChIP_WT_ING5

description: ESC ING5 ChIPseq

value: ING5 (Proteintech, 10665-1-AP)


title: ChIP_WT_input

description: ESC ChIPseq input


title: Sample_2_Veh


title: PBMC_FastRebound_week24_A12

description:
202240580098_R06C01_Red.idat
202240580098_R06C01_Grn.idat
BCN02 clinical trial
Sample_40


title: PBMC_FastRebound_MAP_A15

description:
202240580045_R03C01_Red.idat
202240580045_R03C01_Grn.idat
BCN02 clinical trial
Sample_63


title: PBMC_LateRebound_MAP_A09

description:
202240580098_R04C01_Red.idat
202240580098_R04C01_Grn.idat
BCN02 clinical trial
Sample_31


title: PBMC_FastRebound_week24_A13

description:
202240580098_R08C01_Red.idat
202240580098_R08C01_Grn.idat
BCN02 clinical trial
Sample_48


title: RNAseq_SETlessE8_Set1_WT_1

description: E8.5 mouse embryo RNAseq


title: RNAseq_SETlessE8_Set1_WT_2

description: E8.5 mouse embryo RNAseq


title: PBMC_FastRebound_MAP_B10

description:
202240580079_R03C01_Red.idat
202240580079_R03C01_Grn.idat
BCN02 clinical trial
Sample_103


title: RNAseq_SETlessE8_Set1_KO_2

description: E8.5 mouse embryo RNAseq

value: Homozygous for SET1A SET domain deletion


title: Sample_1_Veh

value: 3 hours


title: ChIP_WT_H4K8ac

description: ESC H4K8ac ChIPseq


title: ChIP_WT_H4K5ac

description: ESC H4K5ac ChIPseq


title: Sample_acute_L36A_CORT_ENZA

data_processing:
Quality control was performed using FastQC and MultiQC
Reads were alligned to mm10 using STAR aligner (version 2.7.3a) settings: --runThreadN' '4' '--outSAMunmapped' 'Within KeepPairs' '--twopassMode' 'Basic’
Gene-read quantification was perfromed using HTSeq-count (version 0.12.4) settings: --format' 'bam' '--order' 'pos' '--stranded' 'reverse'
HTSeq-count output files were merged into the raw_gene_count_matrix.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature according to Ensembl97 for each sample.

source_name: liver

extract_protocol:
Rnease kit (Qiagen)
Total RNA was isolated from the snap-frozen liver samples.
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

value: liver

value: Corticosterone + enzalutamide

value: acute


title: RNAseq_SETlessE8_Set1_KO_1

description: E8.5 mouse embryo RNAseq


title: ChIP_WT_H3K4me3

description: ESC H3K4me3 ChIPseq

value: H3K4me3 (Homemade, #519)


title: Sample_acute_L35A_ENZA

value: Enzalutamide


title: PBMC_FastRebound_MAP_A12

description:
202240580098_R05C01_Red.idat
202240580098_R05C01_Grn.idat
BCN02 clinical trial
Sample_39

value: PBMC

value: Fast

value: MAP

value: male


title: RNAseq_SETlessE8_Set1_HET_5

description: E8.5 mouse embryo RNAseq

value: embryo

value: Heterozygous for SET1A SET domain deletion


title: ChIP_Set1AdSET_Set1AdSET

description: ESC Set1A ChIPseq

value: embryonic stem cell

value: SET1A SET domain deletion


title: H3K27me1_ChIP-seq_mESC_WT

description: According to manufacturer's protocol

growth_protocol: Cells were cultured in Knockout-DMEM (Gibco) with 15% ES qualified FBS (Gibco), ESGRO mouse LIF 1000U/mL (Millipore), 1X PenStrep (Invitrogen), 1X Glutamax (Invitrogen), 55µM b-merceptoethanol (Invitrogen), 1X non-essential amino acids (Invitrogen) and 1X Primocin (Invivogen). Cells were maintained at 37 °C and 5% CO2 on a layer of murine embryonic feeders (MEFs). Prior to collection for ChIP experiments, cells were passaged once on plates pretreated with 0.1% gelatin but without feeders. The day of collection, cells were washed with PBS followed by digestion with TrypLE 30% (for A1 lines) or trypsin 0.25% (for J1 lines) for 7 minutes at 37 °C. Trypsinizaton was terminated by addition of 1X SoyBean Trypsin inhibitor (for A1 lines) or of media (for J1 lines).

extract_protocol:
About 10 million cells per cell line were grown and directly crosslinked on the plate with 1% formaldehyde (Sigma) for 10 minutes at room temperature and the reaction was stopped using 125nM Glycine for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped off the plate, pelleted, washed twice again in ice-cold PBS, and flash frozen pellets stored at −80°C. Thawed pellets were resuspended in 500ul cell lysis buffer (5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate, EDTA-free Protease Inhibitor tablet) and incubated 30 minutes on ice. Samples were centrifugated and pellets resuspended in 500ul of nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and EDTA-free protease inhibitor tablet) and incubated 30 minutes on ice. Sonication of lysed nuclei was performed on a BioRuptor UCD-300 at max intensity for 60 cycles, 10 s on 20 s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis of a reversed cross-linked and purified aliquot. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hr, followed by 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq kit for Histone). Reverse cross-linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse cross-linked and DNA was isolated following the same protocol.
KAPA Hyper Prep Kit

value: H3K27me1 (Active Motif #61015)

value: ESC line J1

value: 129S4/SvJa embryo-derived embryonic stem cells

tag: genotype

value: wild-type


title: ChIP_WT_H3K14ac

description: ESC H3K14ac ChIPseq

value: Wildtype/WT


title: Sample_acute_L31A_Vehicle

value: liver

value: Vehicle


title: RNAseq_SETlessE8_Set1_HET_4

description: E8.5 mouse embryo RNAseq


title: Sample_acute_L32A_CORT

value: Corticosterone

value: acute


title: PBMC_LateRebound_MAP_A05

description:
202240580098_R03C01_Red.idat
202240580098_R03C01_Grn.idat
BCN02 clinical trial
Sample_23

value: PBMC

value: Late


title: RNAseq_SETlessE8_Set1_HET_3

description: E8.5 mouse embryo RNAseq


title: H3K27me2_ChIP-seq_mESC_WT

description: According to manufacturer's protocol

value: H3K27me2 (Cell Signaling Technologies #9728)


title: ChIP_Set1AdSET_ING5

description: ESC ING5 ChIPseq

value: ING5 (Proteintech, 10665-1-AP)


title: PBMC_LateRebound_week24_A02

description:
202779010020_R08C01_Red.idat
202779010020_R08C01_Grn.idat
BCN02 clinical trial
Sample_8

value: male


title: RNAseq_SETlessE8_Set1_HET_1

description: E8.5 mouse embryo RNAseq

value: embryo

value: Heterozygous for SET1A SET domain deletion


title: PBMC_FastRebound_week24_A04

description:
202240580098_R02C01_Red.idat
202240580098_R02C01_Grn.idat
BCN02 clinical trial
Sample_16

value: Fast


title: RNAseq_SETlessE8_Set1_HET_2

description: E8.5 mouse embryo RNAseq


title: Sample_acute_L29A_ENZA

value: Enzalutamide


title: Sample_acute_L26A_CORT


title: RNAseq_EB_dMutant_line1_rep1

description: Embryoid body RNAseq

value: embryoid body

value: ING5 deletion, SET1A SET domain deletion


title: H3K27me2_ChIP-seq_mESC_DNMT_TKO

description: According to manufacturer's protocol

value: ESC line J1

value: 129S4/SvJa embryo-derived embryonic stem cells


title: ChIP_Set1AdSET_input

description: ESC ChIPseq input

value: embryonic stem cell

value: SET1A SET domain deletion


title: PBMC_FastRebound_MAP_A13

description:
202240580098_R07C01_Red.idat
202240580098_R07C01_Grn.idat
BCN02 clinical trial
Sample_47

value: MAP


title: Spleen Bmem 3.2

city: Oxford

first: Oliver

last: Bannard

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Following QC analysis with the fastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), reads were aligned using STAR against GRCm38 (mm10) (Dobin,A. et al. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21. Version 2.4.0)
Gene expression levels were quantified as read counts using the featureCounts function (Liao, Y., Smyth, G.K. & Shi, W. (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930.) from the Subread package Liao,Y. and Shi,W. (2013) The Subread package: a toolkit for processing next-gen sequencing data. http://subread.sourceforge.net SourceForge package version 1.4.5.) with default parameters
The read counts were used for the identification of global differential gene expression between specified populations using the edgeR package (Robinson,M. et al. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140)
Genes were considered differentially expressed between populations if they had an adjusted p-value (FDR) of less than 0.05
The Gene Ontology analysis was performed using the goseq R package (Young, M.D. et al. (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology, 11, R14.) accounting for gene length bias and GO categories were considered significantly enriched if they had an FDR less than 0.05.
Genome_build: GRCm38 (mm10) UCSC transcripts
Supplementary_files_format_and_content: tab-delimited text files summarizing gene expression for each Sample
Supplementary_files_format_and_content: tab-delimited text file describing mapping characteristics for each sample

source_name: Spleen memory B cells (x200)

extract_protocol:
Lungs and spleen tissue were digested in 1mg/ml Collagenase D and 10ug/ml DNase1 in RPMI for 45min. After digestion, Ficoll-paque gradient was also run to enrich for lymphocyte fraction before staining and sorting.
200 cells (per sample) were sorted directly into lysis buffer and frozen at -80 prior to library construction.
Library construction was performed as previously described, using a Smart-seq2 protocol adapted to low cell numbers (Radtke 2019; PMID:30687317).
19 cycles of preamplification were used for all samples. cDNA purification was performed using Ampure XP beads (Beckman Coulter).
Libraries were analyzed with a High Sensitivity Analyser (Agilent) and cDNA tagmentation was performed with the Nextera XT DNA Sample Preparation kit (Illumina).
Libraries were quantified using PicoGreen (Illumina), sized using the High Sensitivity Analyser and equal amounts of tagmented cDNA from each library were pooled.

treatment_protocol: Animals were infected with 2x10^4 PFU X31 influenza 45d previously.

value: Spleen

tag: sorting strategy

value: Live, B220+ CD38+ AID-YFP+ GL7- Infuenza HA+


title: H3K27me1_ChIP-seq_mESC_DNMT_TKO

description: According to manufacturer's protocol

value: H3K27me1 (Active Motif #61015)


title: H3K27me3_ChIP-seq_mESC_DNMT_TKO_rep1

description: According to manufacturer's protocol

value: H3K27me3 (Cell Signaling Technologies #9733)


title: ChIP_Set1AdSET_H4K5ac

description: ESC H4K5ac ChIPseq


title: ChIP_Set1AdSET_H4K8ac

description: ESC H4K8ac ChIPseq


title: PBMC_FastRebound_MAP_A04

description:
202240580098_R01C01_Red.idat
202240580098_R01C01_Grn.idat
BCN02 clinical trial
Sample_15

value: PBMC


title: Sample_acute_L24A_CORT_ENZA

value: liver

value: Corticosterone + enzalutamide

value: acute


title: Spleen Bmem 3.1


title: Spleen Bmem 2.2


title: H3K36me2_ChIP-seq_mESC_DNMT_TKO_rep1

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Technologies #2901)


title: Sample_acute_L23A_ENZA

value: Enzalutamide


title: Spleen Bmem 2.1


title: Spleen Bmem 1.1


title: Spleen Naïve 3.2

source_name: Spleen naïve B cells (x200)

value: Live B220+ AID-YFP- CD38+ GL7-


title: Sample_acute_L19A_Vehicle

value: Vehicle


title: delta-modR H2O2 Rep 3

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

description: Supplementary Table S1.xlsx

data_processing:
Base calling with Illumina CASAVA
quality trimming with trimmomatic v0.36 from both ends with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
reverse complementing of R1 reads
mapping with bowtie2 2.2.7, --ff read orientation, default parameters
converting SAM to BAM with samtools 1.2
visualization and read counting with readXplorer 2.2.3
Analysis of differentially transcribed genes with DESeq2 in default parameters
Genome_build: ASM17889v1
Supplementary_files_format_and_content: Supplementary Table S1.xlsx contains differential expression data for each gene including log2foldchange and adjusted p-values

organism: Fusobacterium nucleatum subsp. nucleatum

source_name: bacterial culture

growth_protocol: F. nucleatum was grown in tryptic soy broth supplemented with 1% Bacto peptone plus 0.25% freshly made cysteine (TSPC) or on TSPC agar plates with 1% vitamin K1-hemin solution or BBL Columbia agar with 5% sheep blood in an anaerobic chamber (5% CO2, 2.5% H2, and 92.5% N2), as previously described

extract_protocol:
F. nucleatum RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacture’s protocol. Fusobacterial cell pellets from 3 ml log-phase culture (OD600 ~ 0.6) were harvested and resuspended into 200 μl of chilled 10 mM RNA-free TE (10 mM Tris-HCl, pH 8; 1 mM EDTA). Each suspension was transferred to a fast-protein tube (Q BIOgene), which contained 700 μl RLT buffer (RNeasy Mini Kit, Qiagen) and 7 μL β-mercaptoethanol (BME) (ThermoFischer Scientific. Cells were lysed by using Ribolyser (Hybaid), and supernatants were obtained by centrifugation at 13000 x g for 5 min at 4°C. RNA was then purified from the supernatant accordingly, and purified RNA was treated with DNAse (Qiagen) and cleaned by using an RNeasy clean up kit (Qiagen). Quality of RNA samples was determined RNA Integrity Number (RIN) values greater than 8 using an Agilent 2100 Bioanalyzer (Agilent Technologies).
2 µg total RNA from F.nucleatum parent and mutant strains 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 TrueSeq 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).

treatment_protocol: RNA samples from the parental and delta-modR mutant strains treated with or without 1 mM H2O2

value: Genes galK and modR deleted and treated with H2O2

tag: Stage

value: exponential growth


title: PBMC_LateRebound_preCART_B13

description:
202779010020_R06C01_Red.idat
202779010020_R06C01_Grn.idat
BCN02 clinical trial
Sample_105

value: Late

value: preCART

value: male


title: ChIP_Set1AdSET_H3K4me3

description: ESC H3K4me3 ChIPseq

value: embryonic stem cell

tag: cell line

value: SET1A SET domain deletion

value: H3K4me3 (Homemade, #519)


title: Sample_acute_L25A_Vehicle


title: PBMC_FastRebound_preCART_B10

description:
202779010020_R05C01_Red.idat
202779010020_R05C01_Grn.idat
BCN02 clinical trial
Sample_97

value: Fast


title: Sample_acute_L20A_CORT

value: Corticosterone


title: PBMC_FastRebound_preCART_A04

description:
202779010020_R01C01_Red.idat
202779010020_R01C01_Grn.idat
BCN02 clinical trial
Sample_9

value: PBMC


title: delta-modR H2O2 Rep 2

description: Supplementary Table S1.xlsx


title: ChIP_ING5KO_Set1AdSET

description: ESC Set1A ChIPseq

value: ING5 deletion

value: Set1A (Homemade, #919)


title: ChIP_ING5KO_input

description: ESC ChIPseq input


title: Spleen Naïve 2.2

value: Spleen


title: PBMC_FastRebound_preCART_B06

description:
202779010020_R04C01_Red.idat
202779010020_R04C01_Grn.idat
BCN02 clinical trial
Sample_81


title: ChIP_ING5KO_ING5

description: ESC ING5 ChIPseq

value: ING5 (Proteintech, 10665-1-AP)


title: Parent Strain H2O2 Rep 3

description: Supplementary Table S1.xlsx

value: Gene galK deleted and treated with H2O2


title: ChIP_ING5KO_H4K8ac

description: ESC H4K8ac ChIPseq


title: delta-modR Rep 3

description: Supplementary Table S1.xlsx

value: Genes galK and modR deleted


title: delta-modR Rep 1

description: Supplementary Table S1.xlsx


title: delta-modR Rep 2

description: Supplementary Table S1.xlsx


title: Sample_acute_L17A_ENZA

value: liver

value: Enzalutamide

value: acute


title: Spleen Naïve 2.1

value: Live B220+ AID-YFP- CD38+ GL7-


title: Spleen Naïve 3.1


title: ChIP_Set1AdSET_H3K14ac

description: ESC H3K14ac ChIPseq


title: Sample_acute_L18A_CORT_ENZA

value: Corticosterone + enzalutamide


title: delta-modR H2O2 Rep 1

description: Supplementary Table S1.xlsx

value: Genes galK and modR deleted and treated with H2O2

value: exponential growth


title: Sample_acute_L14A_CORT


title: ChIP_ING5KO_H3K4me3

description: ESC H3K4me3 ChIPseq

value: embryonic stem cell

value: H3K4me3 (Homemade, #519)


title: ChIP_ING5KO_H4K5ac

description: ESC H4K5ac ChIPseq


title: Parent Strain H2O2 Rep 1

description: Supplementary Table S1.xlsx


title: Spleen Naïve 1.1


title: ChIP_ING5KO_H3K14ac

description: ESC H3K14ac ChIPseq


title: Lung Bmem 3.2

source_name: Lung memory B cells (x200)

value: Lung

value: Live IV CD45- B220+ GL7- AID-YFP+ CD69+ infuenza HA+


title: Sample_acute_L11A_ENZA


title: ChIP_dMutant_Set1AdSET

description: ESC Set1A ChIPseq

value: ING5 deletion, SET1A SET domain deletion


title: PBMC_LateRebound_preCART_A09

description:
202779010020_R03C01_Red.idat
202779010020_R03C01_Grn.idat
BCN02 clinical trial
Sample_25

value: PBMC

value: Late

value: preCART

value: male


title: PBMC_LateRebound_preCART_A05

description:
202779010020_R02C01_Red.idat
202779010020_R02C01_Grn.idat
BCN02 clinical trial
Sample_17


title: Parent Strain Rep 3

description: Supplementary Table S1.xlsx

value: Gene galK deleted


title: Sample_acute_L30A_CORT_ENZA

value: liver


title: ChIP_dMutant_input

description: ESC ChIPseq input


title: Lung Bmem 3.1


title: Sample_acute_L13A_Vehicle

value: Vehicle


title: ChIP_dMutant_ING5

description: ESC ING5 ChIPseq

value: ING5 (Proteintech, 10665-1-AP)


title: Lung Bmem 2.2


title: Parent Strain Rep 2

description: Supplementary Table S1.xlsx


title: Lung Bmem 1.1


title: ChIP_dMutant_H4K8ac

description: ESC H4K8ac ChIPseq


title: Parent Strain Rep 1

description: Supplementary Table S1.xlsx


title: Sample_acute_L6A_CORT_ENZA

value: acute


title: Sample_acute_L12A_CORT_ENZA

value: Corticosterone + enzalutamide


title: Parent Strain H2O2 Rep 2

description: Supplementary Table S1.xlsx

value: Gene galK deleted and treated with H2O2


title: Sample_acute_L7A_Vehicle


title: ChIP_dMutant_H4K5ac

description: ESC H4K5ac ChIPseq


title: RPE-20 H2AZ Rep1

city: Amsterdam

first: Anna

last: Gonzalez Manjon

email: a.gonzalez@nki.nl, li.koob@nki.nl

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

description: ChIP in RPE-20 cells for H2AZ Rep1

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
Assembly: Hg19/Hg38

source_name: RPE-20 cells

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of specified antibody prebound to protein A beads were used.
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303 KAPA biosystems kit).

tag: technique

value: ChIP seq


title: ChIP_dMutant_H3K4me3

description: ESC H3K4me3 ChIPseq

value: embryonic stem cell


title: Sample_acute_L1A_Vehicle


title: RPE-20 H3k9me3 Rep2

description: ChIP in RPE-20 cells for H3k9me3 Rep2


title: ChIP_dMutant_H3K14ac

description: ESC H3K14ac ChIPseq


title: PBMC_LateRebound_MAP_A02

description:
202779010020_R07C01_Red.idat
202779010020_R07C01_Grn.idat
BCN02 clinical trial
Sample_7

value: MAP

tag: age


title: BMDM_Reg1_MO_LPS_rep1

city: Kyoto

first: Ka Man Carman

last: Tse

state: Kyoto

address: Yoshidakonoecho, Sakyo-ku

department: Graduate School of Medicine, Department of Medical Chemistry

country: Japan

institute: Kyoto University

data_processing:
Base-calling was performed using RTA version 1.18.54
Acquired data was analyzed using Galaxy (Afgan et al., 2018). Raw reads were preprocessed for adaptor trimming and filtering using Cutadapt (M. Marcel et al 2011) and quality check were performed using the FastQC tools (S. Andrews 2015). Reads were aligned to the reference murine genome using HiSAT2 (Galaxy version 1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Bone marrow-dervied macrophages (BMDM)

growth_protocol: Total bone marrow cells were isolated from B6 mice, and cultured in macrophage growth medium (RPMI-1640 supplemented with 10% FBS, 1% Penicillin/Streptomycin and 50 µM 2-mercaptoethanol). After 4 days, cells were washed and cultured with fresh macropahge growth medium for 3 days.

extract_protocol:
4 hours after LPS stimulation, cells were lyzed and total RNA was isolated using TRIzol reagent, followed by purifcation using the RNA clean & Concentrator-5 kit.
The cDNA libraries were prepared by NEBNext Ultra II Directional RNA Library Prep Kit (Illumia) and the samples were sequenced by NextSeq 500 (Illumina, 75 cycles) according to the manufacturer's instructions.

treatment_protocol: BMDMs were seeded on 12-well culture plates, transfected with Ctrl MO (2 µM) or Regnase-1-targeting MOs (MO1 and MO2, 2 µM) together with Endoporter (6 µl/ml), followed by stimulation with LPS (10 ng/ml) for 4 hours.

tag: stimulation

value: LPS


title: BMDM_Reg1_MO_LPS_rep2

tag: strain


title: Sample_acute_L8A_CORT

tag: tissue

value: Corticosterone

tag: duration


title: RPE-20 H3k9me3 Rep1

description: ChIP in RPE-20 cells for H3k9me3 Rep1


title: BMDM_Ctrl_MO_LPS_rep2

tag: treatment

value: Ctrl MO


title: Sample_chronic_27_CORT

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel)
Total RNA was isolated from the snap-frozen liver samples.
mRNA was enriched and purified and a stranded library was constructed for 100bp paired-end sequencing on BGI's DNBseq platform.

value: chronic


title: Lung Bmem 2.1

value: Lung

value: Live IV CD45- B220+ GL7- AID-YFP+ CD69+ infuenza HA+


title: BMDM_Ctrl_MO_LPS_rep1


title: RPE-20 H3k9me2 Rep2

description: ChIP in RPE-20 cells for H3k9me2 Rep2


title: Sample_chronic_26_CORT


title: sample_pool_2

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

description: The pool comprises of three samples labelled with hashtags and multiplexed together through a single capture channel. For sample hash tag oligo identifiers and sequences and details of the multiplexed samples see "sample.metadata.tsv".

data_processing:
1. Alignment. Sequence reads were mapped using CellRanger multi (version 6.0.0) with the 10x mouse reference transcriptome (version 2020-A)
2. Demultiplexing. Cells were demultiplexed using GMM-Demux (version 0.2.1.3)
3. Exploratory analysis. An initial, permissive, analysis was performed to help identify and remove low quality cells, contaminants and doublets. All singlet cells with > 200 genes and < 10% mitochondrial reads (n=19,146 cells) were pre-processed with SCANPY (version 1.8.1), integrated with Harmony, and clustered using pipeline_scxl.py (https://github.com/sansomlab/tenx).
4. Final QC filtering and doublet removal. Demultiplexed singlet cells (GMM-Demux confidence >= 0.8) with > 200 genes and < 5% mitochondrial genes were selected. Based on the initial exploratory analysis  (i) cells from heavily thymocyte-contaminated CLL replicate 3, (ii) cells from other replicates present in the thymocyte cluster and (iii) any remaining cells that had been identified as low-quality/apoptotic B and T cells were filtered out. Cells with scrublet scores > mean + three standard deviations were removed as likely doublets. Any remaining cells identified as B-T doublets in the initial clustering analysis were also removed. n=13,172 cells were retained for the final analysis.
5. Final data analysis. Gene expression data were total count normalised and log1p transformed with SCANPY (version 1.8.1). Highly variable genes  were identified within each sample separately (n_top_genes=2000, flavour=”Seurat_v3”, using counts) and filtered to retain the set that was discovered in at least 2 samples. The effect of total UMI number was regressed out and the data scaled.  Data were integrated with the python SCANPY implementation of Harmony (“harmony_integrate”) using n=30 principal components (“key” parameter set to the sample identifier). Integrated data were analysed using using pipeline_scxl.py (https://github.com/sansomlab/tenx). An exact neighbor graph was computed with Scikit-learn (as implemented in scVelo) using n=30 Harmony components, n=20 neighbours and the euclidean distance metric. Leiden clustering across a range of resolutions was performed and investigated.  Final cluster assignments were prepared by combining/merging the assignments from the different clustering resolutions to parsimoniously describe the major cell types/subtypes present in the different regions of the manifold for subsequent analyses.
6. ADT counts were normalized following a background aware library-size approach. The background signal for each antibody was estimated as the lower mode of a fitted bimodal distribution using the inferAmbience function implemented in the DropUtils R library .  Then, the library size factor for each cell was calculated as the median of the ratios of the features read outs in relation to the estimated backgrounds. This median-based library size factors were then used to perform scaling normalization and log-transformation using the logNormCounts function of the R scutter library. Normalization was performed independently for each sample to account for antibody background differences between staining batches. Only features with consistent profiles among staining batches were retained for down-stream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: sample.metadata.tsv: tab seperated text file with sample metadata including the hash tag oligo identifiers.
Supplementary_files_format_and_content: gmm.singlet.calls.tsv: tab seperated text file with the GMM-Demux results. The set of cells is that selected for the initial analysis.
Supplementary_files_format_and_content: matrix.mtx.gz: market matrix file with counts for gene expression, ADT and hashing antibodies. The set of cells is that selected for the initial analysis.
Supplementary_files_format_and_content: features.tsv.gz: tab separated text file of feature descriptions (for "matrix.mtx.gz")
Supplementary_files_format_and_content: barcodes.tsv.gz: tab separated text file of cell barcodes (for "matrix.mtx.gz")
Supplementary_files_format_and_content: expression-atlas.h5ad: anndata object containing the normalised (.X slot) and raw ("counts" layer) gene expression (GEX) and ADT data for the set of cells that was used for the final analysis. GEX data in the .X slot were total count normalised and log1p transformed. ADT data in the .X slot were normalised as described above with clipping of extreme values (below 2nd or above 98th quantile) to aid data visualisation. The names for the ADT features are prefixed with "AB_". The object contains additional cell metadata, cell type and cluster annotations and UMAP layouts for viewing with cellxgene.

source_name: Lung

extract_protocol:
Lung tissue was digested in 1mg/ml Collagenase D and 10ug/ml DNase1 in RPMI for 45min. After digestion, cells were FC-blocked stained and sorted.
60,000 cells (per sample) were sorted directly into FBS, then stained with TotalSeq hashing antibodies, pooled and stained with CITESeq antibodies for 30min further processing.
Approximately 20,000 cells per sample pool were loaded onto the 10X Genomics Chromium Controller (Chip K).
Gene expression and feature barcoding sequence libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B).
The final libraries were diluted to ~10nM for storage. The 10nM library was denatured and further diluted prior to loading on the NovaSeq6000 sequencing platform (Illumina, v1.5 chemistry, 28bp/98bp paired end sequencing).

treatment_protocol: Animals were infected with 2x10^4 PFU X31 influenza 42d previously. Some animals were treated with clodronated liposomes (CLL) d-3 and d-6 before rechallenge. Two groups were rechallenged 24h before collection.

value: Live IV CD45- CD45+ Cells

tag: condition

value: resting, rechallenged, CLL

value: female


title: RPE-20 H3k9me2 Rep1

description: ChIP in RPE-20 cells for H3k9me2 Rep1


title: Sample_chronic_25_CORT

value: liver


title: Zcchc8_KO_2_3Pseq_EPAP

city: Aarhus C

first: William

last: Garland

address: C.F. Møllers Allé 3

department: Molecular Biology and Genetics

institute: Aarhus University

description: QuantSeq 3'mRNA-Seq FW + UMI

data_processing:
RNA  3’end-seq data provided by Lexogen were already split by barcodes and UMI information was appended to read names, which were then quality controlled and trimmed using the bbduk.sh script from the BBMap software (v37.62) with parameters ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20. A-tails longer than 4 nucleotides on the 3’end of cleaned reads were trimmed off using a custom awk script and only reads with more than 20 nucleotides after this step were used for subsequent mapping.
A custom index, concatenating mouse genome mm10 and sequences for Lexogen ERCC and SIRV spike ins (SIRV-Set 3, Lexogen GmbH), was prepared. This merged genome was indexed using STAR (v.2.7.3a) with settings ‘--runMode genomeGenerate --genomeSAindexNbases 11’ and otherwise default settings. Reads were then mapped to this index using the STAR aligner (v2.7.3a) together with samtools (v.1.9) with settings ‘--outFilterType BySJout --outFilterMultimapNmax 1000’ to maintain multimapping reads.
Duplicate reads were removed via the included UMI information, using the dedup function from umi_tools (v1.0.1). Bam files were indexed using samtools and coverage of single mapping reads within last exons of RefSeq annotations were obtained using the multicov function from bedtools (v2.29.2) in strand-specific mode. Normalisation factors were obtained from those last exon counts using the estimateSizeFactors function from R package DESeq2 (v1.28.0), with at least a total of 100 reads summed over all libraries. Size factors were checked to be generally correlated with spike-in derived read numbers without indications for KO or EPAP treatment-specific biases.
genome build: mm10
processed data files format and content: Normalised coverage tracks were then produced using the genomecov function from bedtools with parameters ‘-bg -3 -scale 1/sizefactor’ and ‘-strand +’ or ‘-strand -’ for plus and minus strand coverage, respectively. Coverage for major mouse chromosomes was sorted using bedtools sort, the average of the 3 replicates computed and converted to bigwig format using bedGraphToBigwig function from UCSC tools (v357)

source_name: Embryonic stem cells

growth_protocol: ES cells were culturered on 0.2% gelatin coated plates in 2i/LIF containing medium

extract_protocol:
Total RNA for 3P-seq was isolated by Trizol extraction using standard procedures
3PS samples were either mock treated or incbated with E.coli Poly(A) polymerase (EPAP). rRNA was depleted using the RiboCop rRNA Depletion Kit (Lexogen). Libraries for QuantSeq 3'mRNA Seq FW + UMI were prepared by Lexogen and included the addition of spike-ins ERCC Mix1 and SIRV E0

tag: epap treatment

value: +EPAP


title: Sample_acute_L5A_ENZA

value: Enzalutamide

value: acute


title: RPE-20 H2AZ Rep2

description: ChIP in RPE-20 cells for H2AZ Rep2


title: Zcchc8_KO_3_3Pseq_EPAP

description: QuantSeq 3'mRNA-Seq FW + UMI


title: sample_pool_3

tag: Sex

value: male


title: sample_pool_1


title: RPE-20 H3k27ac Rep2

description: ChIP in RPE-20 cells for H3k27ac Rep2

value: ChIP seq


title: EAE_MO_spinal_cord_rep2

data_processing:
Raw binary base call (BCL) files were demultiplexed with the Cell Ranger pipeline (10x Genomics, default settings, Version 5.0).
Fastqs were generated using CellRanger bamtofastq from the 10X BAM files. The demultiplexed Fastq files were aligned to the mouse mm10 reference genome. Introns were included in the analysis.
Data from different GEM wells were aggregated using the Cell Ranger aggr command and analyzed together using Seurat (version 4.0).
Cells were filtered to remove low quality cells with <1500 detected UMI counts, <500 detected genes or >20% mitochondrial reads.
Harmony (version 1.0) was used to adjust PCs by GEM well ID to minimize technical batch effects between the four samples.
Genome_build: mm10
Supplementary_files_format_and_content: Contains only detected cellular barcodes, non-targeted genes are removed from the filtered matrix.

source_name: spinal cord CD45+ cells

extract_protocol:
FACS-sorted cells were loaded onto a Chromium Single cell Chip B (10x Genomics) to generate barcoded cDNA.
The gene expression sequencing libraries were generated using Chromium Single Cell 3' Library & Gel Bead kit v3 (10x Genomics). PCR (12 cycles) was performed to amplify barcoded cDNA. Index PCR was performed following cDNA fragmentation, end repair and A-tailing. The purified libraries were sequenced with a 28-bp read 1, an 8-bp index red and a 91-bp read 2 on an Illumina NovaSeq (SP Reagent Kit v1.5, 100 cycles).

treatment_protocol: On D16 after EAE immunization, spinal cord was resected and digested in buffer containing HBSS, 10% FBS, 1% Penicillin-Streptomycin, HEPES and collagenase D (160 U) at 37 degree for 35 mins, followed by densitry centrifugation using 38% Percoll to remove the myelin fraction. The isolated mononuclear cells were maintained at PBS supplemented with 2% BSA and EDTA, prior to staining with specific set of antibodies and cell sorting. The sorted cells were maintained in PBS supplemented with 2% FBS. The live cells were counted with Trypan blue dye.

tag: stain

tag: group

tag: disease state

value: EAE


title: Sample_acute_L2A_CORT


title: RPE-20 H3k27ac Rep1

description: ChIP in RPE-20 cells for H3k27ac Rep1

tag: chip antibody


title: Sample_chronic_18_CORT_ENZA

value: Corticosterone + enzalutamide


title: EAE_MO_spinal_cord_rep1


title: RPE-1 H3k9me2 Rep2

description: ChIP in RPE-1 WT cells for H3k9me2 Rep2

source_name: RPE-1 cells


title: Sample_chronic_17_CORT_ENZA


title: Sample_chronic_16_CORT_ENZA


title: Zcchc8_KO_3_3Pseq_noPAP

description: QuantSeq 3'mRNA-Seq FW + UMI

tag: genotype

value: noPAP


title: RPE-1 H3k9me2 Rep1

description: ChIP in RPE-1 WT cells for H3k9me2 Rep1


title: EAE_Ctrl_spinal_cord_rep2

value: control


title: Zcchc8_KO_2_3Pseq_noPAP

description: QuantSeq 3'mRNA-Seq FW + UMI


title: RPE-20 input Rep2

description: Input DNA in RPE-20 Replicate 2

value: none (input)


title: Zcchc8_KO_1_3Pseq_noPAP

description: QuantSeq 3'mRNA-Seq FW + UMI


title: Sample_chronic_14_Vehicle

value: Vehicle

value: chronic


title: EAE_Ctrl_spinal_cord_rep1


title: WT_3_3Pseq_EPAP

description: QuantSeq 3'mRNA-Seq FW + UMI

value: Wildtype


title: RPE-20 input Rep1

description: Input DNA in RPE-20 Replicate 1


title: RPE-1 input Rep2

description: Input DNA in RPE-1 WT replicate 2


title: Sample_chronic_12_Vehicle


title: Sample_chronic_13_Vehicle


title: WT_2_3Pseq_EPAP

description: QuantSeq 3'mRNA-Seq FW + UMI


title: Sample_chronic_11_Vehicle


title: p9

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics) against the provided GRCh38 reference genome using default parameters, including introns.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Human postmortem brain sample

extract_protocol:
Nuclei were isolated from frozen tissue, as per 10x Genomics’ recommendations, using chilled, 0.1% Nonident P40 lysis buffer with gentle homogenization and washed.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis. Libraries were sequenced using a 2x100PE configuration on a NovaSeq instrument (Illumina, San Diego, CA), targeting a depth of 50,000-100,000 reads per nucleus.

value: Substanstia nigra

value: Parkinson's Disease Dementia

tag: brain bank donor id

value: HBNX

tag: gender

value: Male

tag: race

value: White

tag: ethnicity

value: Not Hispanic or  Latino

tag: postmortem interval hours

tag: braak stage

value: Stage VI


title: non-classical_sCAD_rep3

city: Münster

first: Anika

last: Witten

address: Domagkstrasse 3

institute: Institute for Human Genetics

description: RNA isoated from flow cytometric isolated monocyte subpopulation

hyb_protocol: genechip hybridization wash and stain kit

scan_protocol: Affymetrix Fluidic Station 450, Gene Chip Scanner 3000 7G

data_processing: affymetrix expression console tm software and limma package

source_name: blood pbmc

label_protocol: affymetrix flashtag biotin hsr labeling kit

growth_protocol: patient blood samples

extract_protocol: Chloroform/Isopropanol isolation after cell lysis

treatment_protocol: total RNA was isolated from monocyte subpopulations separated by flow cytometry after antibody treatment

value: male


title: RPE-1 input Rep1

description: Input DNA in RPE-1 WT replicate 1

tag: technique

value: ChIP seq

tag: cell line


title: WT_3_3Pseq_noPAP

description: QuantSeq 3'mRNA-Seq FW + UMI


title: WT_1_3Pseq_EPAP

description: QuantSeq 3'mRNA-Seq FW + UMI

value: +EPAP


title: Sample_chronic_10_Vehicle

tag: strain

tag: tissue

value: liver

tag: treatment

tag: duration


title: p7

tag: age


title: WT_2_3Pseq_noPAP

description: QuantSeq 3'mRNA-Seq FW + UMI

tag: epap treatment

value: noPAP


title: Sample_chronic_6_CORT_ENZA

value: Corticosterone + enzalutamide


title: p5

tag: disease state

value: Unaffected Control

value: HBHF

value: Female


title: intermediate_sCAD_rep3

tag: group


title: Zcchc8_KO_1_3Pseq_EPAP

description: QuantSeq 3'mRNA-Seq FW + UMI

tag: genotype


title: classical_sCAD_rep3


title: non-classical_sCAD_rep2


title: intermediate_sCAD_rep2


title: Sample_chronic_15_Vehicle

value: Vehicle

value: chronic


title: Sample_chronic_5_CORT_ENZA


title: p4

value: Substanstia nigra

tag: brain bank donor id


title: classical_sCAD_rep2

tag: gender


title: non-classical_sCAD_rep1


title: s382-3_AP_MYC_scRNA

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

description: Single-cell RNA-seq

data_processing:
Illumina Bcl2fastq v2.18.
Reads were aligned to mm10 using STAR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *h5: Cell gene barcode matrix in HD5 format.

source_name: Hi-MYC anterior prostate

growth_protocol: FVB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified diet (Harlan Laboratories, TD.130838). Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutional Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Fresh prostatic tissues from 12-week-old mice were dissociated to form a single cell suspension. Cell preparation for 3’ barcoded scRNA-seq (#120237, Chromium V2 assay) was performed according to the manufacturer’s protocol (10X Genomics) targeting 5000 cells from single-cell suspensions of freshly processed prostate lobes.
Library construction for 3’ barcoded scRNA-seq (#120237, Chromium V2 assay) was performed according to the manufacturer’s protocol (10X Genomics).

value: anterior prostatic tissues

value: FVB

tag: genotype/variation

value: Hi-MYC

tag: Sex

value: 12 weeks