title: SKNMC_shFLI1_HiChIP

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Library strategy: HiChIP
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
The hichipper tool (v 0.7.7) (Lareau et al., 2018) was used for loop calling within H3K27ac ChIP-seq peak (q-value < 0.00001) regions, by applying the following parameters: --max-distance 100000000 --read-length 100
Genome_build: hg19
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). Intrachromosomal looping between anchor loci.

source_name: Ewing sarcoma cells

growth_protocol: The Ewing sarcoma cell lines A673 and SKNMC (ATCC) were grown in RPMI medium containing 10% FCS at 37°C with 5% CO2.  Primary pediatric mesenchymal stem cells were cultured in Iscove’s modified Dulbecco’s medium containing 10% fetal calf serum (FCS) and 10 ng/ml platelet-derived growth factor. shRNA mediated knock-down was used to remove EWS-FLI1 protien  from ewing cells.

extract_protocol:
Genomic DNA/ChIP DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol. H3K27ac antibody was used to pull-down ChIP following HiC and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif

treatment_protocol: Untreated

value: Ewing sarcoma cells

value: SKNMC


title: A673_shFLI1_HiChIP

status: Public on Mar 16 2023

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: treatment

value: untreated

tag: cell line


title: A673_shGFP_HiChIP


title: SKNMC_shGFP_HiChIP


title: TgTum_583202.1L

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

data_processing:
Mapping and transposon integration site identification: The expected transposon-derived sequence (5’-TAGGGTTAA-3’) was removed from the beginning of the first read (read pairs with non-matching first reads were discarded) using the preprocessReads function from the QuasR Bioconductor package (version 1.12.0). Read pairs were aligned to the mouse genome (BSgenome. Mmusculus.UCSC.mm10) using the QuasR qAlign function with the parameters alignmentParameter = “-m 1 --best --strata --maxins 1000”; this will report only uniquely mapping pairs with up to 1000 bp between-pair distance. Mapping rates were recorded, and non-mapped read pairs were further aligned against the non-mobilized transposon sequence to estimate the probable fraction of read pairs that originate from non-mobilized copies of the transposon. For each aligned read pair, the piggyBac insertion coordinate was identified as the coordinate of the first (most 5’) base of the first read.
Identification of enriched unique integration sites: For each unique integration site, the number of distinct supporting alignments (distinct read pairs, referred to as “diversity”), and the genomic sequence from the four base pairs on the same strand as the first read directly upstream of the insertion site were recorded. These diversity values were normalized by dividing trough the total alignments in a sample and then multiplied by 10^5 (normalized diversity values “divN”). Only integration sites with the expected upstream TTAA sequence were used for the downstream analysis.
Association of integration sites with genes: Coordinates of known genes (exons/introns, 5’-untranslated region [UTR], coding sequence [CDS], 3’UTR) were obtained from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package (version 3.2.2). Promoter regions were defined as regions 2000 bp upstream of known transcript start sites. Integration sites were matched against these genomic regions to identify overlaps on any strand and orientation, selecting the first overlap in the case of multiple overlaps. Integration sites were classified hierarchically as follows: sites without overlaps to any transcript were labelled as promoter sites (in the case of an overlap with a promoter region) or intergenic sites. All other sites were labelled with the first region type that they overlapped, in the following order: 5’UTR, CDS, 3’UTR, intron or ncRNA (defined as an overlap with a transcript without annotated CDS). Sites were further labelled according to their orientation with respect to the associated gene (same or opposite). Finally, sites were grouped according to the gene they overlapped (including promoter sites) or, for intergenic sites, according to the pair of flanking genes.
Identification of enriched unique integration sites: For each insert the normalized diversity values were calculated as described above. The normalized diversity values of all unique insertions sites in a gene were summed over one category of samples (divNsum). We identified a total of 61’241 insertions in the resistant samples and 98’373 insertions in the untreated controls corresponding to a total of 24’032 affected genes. We excluded 2 genes that were found in all analyzed resistance samples as a potential PCR contamination. To find putative resistance genes we focused on the genes with a higher number of unique transposon integrations in the BYL treated samples compared to the untreated samples.
Assembly: UCSC version mm10
Supplementary files format and content: PiggyBacBYLResistanceScreen_integration_sites.csv; big table that contains: insertion coordinate: is the first base downstream of the transposon sequence (first 9 bases of R1); cnt (coverage): the number of alignments starting at the insertion coordinate; cnt2 (coverage): the number of alignments of the most frequent fragment starting at the insertion coordinate (only for paired-end data); div (diversity): the number of distinct alignment-pairs starting at the insertion coordinate (only available for paired-end data); cntN, cnt2N, divN: the normalized values of cont, cnt2, div; context.5p: are the 4 genomic bases on the same strand and directly upstream of the insertion site; context.3p: are the 4 genomic bases on the same strand and directly downstream of the insertion site (including the insertion site coordinate)
Supplementary files format and content: combined_table_BYLResWAPtg-inVivoTumorWAPtg.csv; table contains: gCIS.signedNegativeLog10Pvalue: the gene centered common insertion sites  -log10 Pvalue; nInsertions.total: total number of inserteions in a gene; information on the strand where the insertion was observed; percentSamplesWithInsertionInGene: indicating the percent of samples with insertions in a given gene; divNsum: the normalized diversity values of all unique insertions sites in a gene were summed over one category of samples; all those values are given for the untreated samples and the BYL resistant samples seperatly.

organism: Mus musculus

source_name: MFP tumor

growth_protocol: Experimental mice were mated to trigger WAP expression during late pregnancy in the mammary gland resulting in the expression the PIK3CA-H1047R mutation and the PB-transposase simultaneously specifically in the mammary gland (Rad 2010, Meyer 2011).

extract_protocol:
gDNA of 94 untreated tumors and 51 resistant tumors (from a total of 53 mice) was isolated with a DNeasy Blood and Tissue Kit (Qiagen #69504) and fragmented by sonication (Covaris sonicator) to a size of 250 bp.
DNA fragments were end repaired, A-tailed, purified and then ligated to the splikerette adaptor (annealed 5’-gttcccatggtactactcatataatacgactcactataggtgacagcgagcgct-3’ with 5’-gcgctcgctgtcacctatagtgagtcgtattataatttttttttcaaaaaaa-3’). Transposon containing DNA fragments were enriched by PCR using a primer specific for the 5’-transposon arm (5’-gacggattcgcgctatttagaaagagag-3’) and the common splinkerette primer (5’-gttcccatggtactactcata-3’). An additional PCR was performed for barcoding the individual samples by using a primer specific for the 5’ arm of the transposon (5’- aatgatacggcgaccaccgagatctacacatgcgtcaattttacgcagactatc-3’) and another primer specific tor the splinkerette side (5’-caagcagaagacggcatacgagatcggtXXXXXXXXtaatacgactcactatagg-3’; Xs standing for the eight-base barcode). Purified libraries were assembled in four pools and sequenced on Illumina HiSeq 2500 (Paired-End, 2 × 100 bp, rapid run, 200 cycles).

treatment_protocol: Once tumors reached 250 mm3, animals were treated daily with 30 mg/kg BYL719. Tumors that increased in their volume over at least 3 consecutive measurements (in a total of 3 weeks) in their volume while being treated were classified as resistant. Such resistant tumors and tumors from an untreated control group were isolated once the total tumor volume of a mouse reached the allowed maximal tumor size.

tag: sample group

value: inVivoTumorWAPtg

tag: tissue

value: MFP tumor

tag: genotype


title: TgTum_583200.2R


title: SKNMC_shFLI1_HiC

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
Default settings were used to control quality, align paired reads, identify valid interactions and generate interaction matrices. The Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012) was performed for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary_files_format_and_content: HiC 40kb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiC 1mb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.

extract_protocol:
Genomic DNA was isolated from x-linked nuclei after Mbo1+HinfI restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol, and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif


title: TgTum_583202.1R


title: TgTum_583202.2L


title: TgTum_583202.5L


title: TgTum_583200.3R


title: A673_shGFP_HiC


title: TgTum_583202.4R


title: H82_IFNγ

city: Badalona

first: Pablo

last: Navajas Chocarro

state: Barcelona

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

country: Spain

institute: Josep Carreras Leukaemia Research Institute

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped against the human reference genome (GRCh38) using STAR (version 2.5.3a) (Ref1) with ENCODE parameters. Genes were quantified using RSEM (version 1.3.0) (Ref2) with default parameters. Human gene annotation file was downloaded from gencode release 27 (https://www.gencodegenes.org/ ). Mapping and quantification quality checking was performed with GEMTools (https://gemtools.github.io/ ) and custom python scripts. Multidimensional scaling plots were performed to inspect sample similarities using the ‘voom’ transformed counts. Differential gene expression was performed with ‘limma-voom’ (Ref3) and the function ‘duplicateCorrelation’ to take into account patient correlation. Genes with FDR<5% were considered significant. Functional enrichment analysis of the differentially expressed genes was performed with g:Profiler (Ref4). Heatmaps showing the scaled expression of the top 50 differentially expressed genes were performed with the pheatmap R package.
Genome_build: hg38

molecule: total RNA

source_name: ATCC

extract_protocol:
Total RNA was extracted using a Maxwell® RSC SimplyRNA Tissue Kit (Promega).
TruSeq Stranded mRNA (polyA)

value: Lung

tag: Sex

value: male

tag: age

value: 40 years adult

value: IFNg


title: A673_shFLI1_HiC


title: TgTum_586249.5RL


title: TgTum_586249.1R


title: TgTum_593199.2L


title: H69_IFNγ

value: 55 years adult


title: TgTum_586251.2R


title: H69_Untreatment


title: TgTum_383203.1L


title: H82_Untreatment


title: TgTum_383203.3R


title: A549_Untreatment

value: 58 years adult


title: TgTum_383203.1R


title: A549_IFNγ


title: DMS273_IFNγ

value: female

value: 50 years adult


title: TgTum_383203.2L


title: DMS273_Untreatment


title: DMS114_IFNγ

value: 68 years adult


title: TgTum_383203.4L


title: TgTum_383203.5L


title: TgTum_383203.4R


title: DMS114_Untreatment


title: 6 NM411

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Healthy Environments and Consumer Safety Branch

country: Canada

institute: Health Canada

hyb_protocol: Each cRNA sample and cRNA reference was mixed at an equimolar amount of 300 ng to be hybridized to Agilent 8X60K Sure Print G3 Mouse gene expression microarray for 17 h at 65°C, rotation speed of 10 rpm.

scan_protocol: Slides were washed and scanned on an Agilent Scanner G2505B.

data_processing: Expression data were extracted using Agilent Feature Extraction Software version 11.0.1.1

source_name: Lung tissue of female mice

label_protocol: The Low Input Quick Amp Labeling Kit (#5190-2331, Agilent Technologies) was used to generate double-stranded cDNA and fluorescent cRNA. cRNA was purified using RNAeasy MiniKit according to the protocol provided by the manufacturer (#74106, Qiagen).

growth_protocol: Female mice were acclimatized and housed in polypropylene cages with access to food and tap water ad libitum. Temperature (21 ± 1°C), humidity (50% ± 10%) and 12 hours light/dark period.

extract_protocol: RNA extraction was performed using TrizolTM reagent (#15596-026) and stainless-steel beads for homogenization with Retsch Mixer Mill NM400 (25.0 Hz for 2 minutes). RNA was purified using Direct-zol RNA Miniprep Kits (#R2052, Zymo Research). The RNA concentration and purity were determined through 260/280 and 260/230 absorbances using NanoDrop Spectrophotometer 2000. RNA quality and integrity were determined using the Agilent TapeStation System (Agilent). Samples showed ratios of ~2.0 and RNA integrity numbers were above 5.

treatment_protocol: Mice were exposed to CNTs by single intratracheal instillation of 6, 18 or 54 μg/mouse. The control group was instilled with NanoPure water with 2% serum. After 24 h of exposure, mice were sacrificed and the lung lobes were frozen and stored at -80°C for RNA extraction. n=8 per control group, n=5 per experimental group.

tag: strain

value: C57BL/6J BomTac

value: NM411 CNT (Pristine SWCNTs)

tag: dose

value: 6 μg/mouse

tag: time point

value: 24 hours

value: lung

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines

tag: sample type

value: Universal Mouse Reference RNA


title: TgTum_587674.3R

value: inVivoTumorWAPtg

value: untreated

value: MFP tumor


title: LXF289_Untreatment

value: Lung

value: male

value: 62 years adult


title: TgTum_593199.4R


title: H1623_IFNγ

value: 58 years adult

value: IFNg


title: TgTum_587659.3R


title: H1623_Untreatment


title: TgTum_587674.5R


title: TgTum_515714.5R


title: TgTum_515714.1L


title: Ludlu1_IFNγ

value: 72 years adult


title: Ludlu1_Untreatment


title: H522_IFNγ


title: TgTum_515714.5L


title: H522_Untreatment


title: H23_IFNγ

value: 51 years adult


title: TgTum_591633.1L


title: TgTum_591633.4L


title: H23_Untreatment


title: TgTum_587674.4R


title: LXF289_IFNγ


title: TgTum_586242.4L


title: TgTum_586242.4R


title: Mouse.608671.2.3L

value: BYLResWAPtg


title: TgTum_586242.5RL


title: DMS153_Untreatment

value: 44 years adult


title: Lu165_Untreatment

value: 50 years adult


title: TgTum_587674.2L


title: TgTum_586242.3L


title: H209_IFNγ

value: 55 years adult


title: H209_Untreatment


title: TgTum_515714.3L


title: TgTum_586250.1L


title: TgTum_586242.2L


title: TgTum_586250.3L


title: CAL12T_IFNγ

value: age unspecified


title: CAL12T_Untreatment


title: TgTum_586250.4L


title: PDC11_IFNγ

source_name: NSCLC patient derived cells

value: 67 years adult


title: TgTum_586250.4R


title: TgTum_586250.5R


title: PDC11_Untreatment


title: TgTum_586250.3R


title: DMS153_IFNγ


title: Lu165_IFNγ


title: SuppRat_siRNA3_100mkg_rep3

city: Cambridge

first: Joseph

last: Barry

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

description: SuppRat_groupsiRNA3_100mkg.vs.NaCl.DESeq2.txt

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using the ea-utils software fastq-mcf.
Filtered reads were aligned to the Mus musculus (GRCm39/mm39), Rattus norvegicus (Rnor_6.0/rn6), or Homo sapiens (hg38/GRCh38) genomes using STAR (ultrafast universal RNAseq aligner) v2.7.9a.
Differential gene expression analysis was performed by the R package DESeq2 v1.34.0 with the betaPrior parameter set to TRUE to shrink log2 fold-change estimates for noisy, low-count genes.
Assembly: GRCm39, GRCh38, Rnor_6.0
Supplementary files format and content: tab-delimited raw count files
Supplementary files format and content: tab-delimited DESeq2 tables with differential expression metrics

organism: Rattus norvegicus

source_name: liver

growth_protocol: Primary Mouse Hepatocytes (BIOIVT, Cat # M005052-P, Lot GBW) were transfected in 384-well plates (5000 cells per well) with siRNA or DPBS (mock control) at a final concentration of 50nM using Invitrogen Lipofectamine® RNAiMAX (Invitrogen, Carlsbad, CA, Catalog No. 13778-150). After 48hours, cell were lysed in lysis buffer (Tris HCl pH 7.5 100mM, LiCl 500mM, EDTA pH 8.0 10mM, LiDS 1%, DTT 5mM supplemented with TURBO™ DNase,Thermofisher #AM2238) for 30 min. Hep3B cells followed an equivalent protocol at 10nM and 24hrs for dose and time respectively.

extract_protocol:
Dynabeads Oligo (dT)25 (Thermo Fisher Scientific 61005)
Whole transcriptome mRNA-enriched RNA-Seq libraries were constructed using a KAPA mRNA Capture Kit and mRNA HyperPrep Kit (Roche) from cell lysates as per protocol but in 5x miniaturized reagent scale (except mRNA capture beads were resuspended in water prior to mix with lysate).
RNA-Seq libraries were quantified by low depth sequencing on Illumina iSeq instrument . Equal amounts of each library/sample were pooled and sequenced on a Illumina NovaSeq instrument with 2x150bp paired-end, or 1x100bp single-end settings, according to manufacturers’ instructions.

treatment_protocol: Male Sprague-Dawley rats were subcutaneously administered with TR-siRNAs or saline control at 30mg/kg or 100mg/kg (qw x 3) dose. Rats were sacrificed at D16 post- siRNA treatment.

value: liver

value: 100 mg/kg

tag: time

value: Day 16

value: transgene-regulator siRNA


title: SuppRat_siRNA3_100mkg_rep4


title: SuppRat_siRNA3_100mkg_rep1


title: SuppRat_siRNA3_100mkg_rep2


title: TgTum_586250.1R

value: inVivoTumorWAPtg

value: untreated

value: MFP tumor


title: SuppRat_siRNA3_30mkg_rep4

description: SuppRat_groupsiRNA3_30mkg.vs.NaCl.DESeq2.txt

value: 30 mg/kg


title: TgTum_578587.2L


title: TgTum_578587.3L


title: BYL-non-Rel-07_478166-3L

data_processing:
Reads were aligned to the the mouse genome (UCSC version mm10) with STAR (version STAR/2.5.2a-goolf-1.7.20) using the multi-map settings outFilterMultimapNmax = 10 and outSAMmultNmax = 1.
The output was sorted and indexed with SAMtools (for the mouse tumors: version SAMtools/1.3.1-goolf-1.7.20 and picard markDuplicates (version picard/2.9.2) was used to collapse samples run on different sequencing lanes. Stand-specific coverage tracks per sample were generated by tiling the genome in 20bp windows and counting overlapping reads in each window using the bamCount function from the Bioconductor package bamsignals (Bioconductor version 3.6). These window counts were then exporting in bigWig format using the export function rtracklayer of the Bioconductor package.
The function gQCReport of the Bioconductor package QuasR was used for assessing read and alignment quality. The number of reads (5’ ends) overlapping the exons of each gene was counted with the gCount function of QuasR, assuming an exon union model.
Differential gene expression analysis was achieved using the edgeR framework (Chen 2016).
Assembly: UCSC version mm10
Supplementary files format and content: RNAseq_WAP_tumors_annotated_counts.txt: is the gene annotated  table with raw counts after alignment

molecule: polyA RNA

source_name: tumor

extract_protocol:
Tumors of WAP-Cre/PIK3CAH1047R transgenic mice (vehicle or BYL719 treated animals) were collected, snap frozen in liquid N2, and then grinded into powder with a mortar. Total  RNA was extracted with a RNeasy Plus Mini kit (Qiagen #74136). RNA quality was analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
The library was prepared with the Illumina TruSeq stranded mRNA-seq preparation kit (Illumina #20020595) and the TruSeq RNA CD Index Plate (Illumina #20019792) according to the manufacturer’s protocol. Size and quality of the library was evaluated on the Fragment Analyzer (Advanced Analytical) with the Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-473). Then samples were pooled in equimolar ratios. Single-end libraries were sequenced with an Illumina HiSeq 2500 (50-nt read length).

value: tumor


title: SuppRat_siRNA3_30mkg_rep2


title: TgTum_585711.2R


title: BYL-Rel-07_475993-3R


title: TgTum_585711.5RL


title: TgTum_586250.2R


title: SuppRat_siRNA3_30mkg_rep3


title: Vehicle-ctr_07_459035-4L

value: DMSO


title: SuppRat_siRNA3_30mkg_rep1


title: SuppRat_siRNA2_100mkg_rep3

description: SuppRat_groupsiRNA2_100mkg.vs.NaCl.DESeq2.txt


title: SuppRat_siRNA2_100mkg_rep2


title: SuppRat_siRNA2_100mkg_rep4


title: BYL-Rel-06_478166-4L


title: SuppRat_siRNA2_100mkg_rep1


title: Vehicle-ctr_06_459035-5L


title: SuppRat_siRNA2_30mkg_rep4

description: SuppRat_groupsiRNA2_30mkg.vs.NaCl.DESeq2.txt


title: SuppRat_siRNA2_30mkg_rep3


title: BYL-Rel-05_456160-3R


title: Vehicle-ctr_05_459035-4R


title: BYL-non-Rel-04_481539-3R


title: SuppRat_siRNA2_30mkg_rep2


title: SuppRat_siRNA2_30mkg_rep1


title: SuppRat_siRNA1_100mkg_rep4

description: SuppRat_groupsiRNA1_100mkg.vs.NaCl.DESeq2.txt


title: SuppRat_siRNA1_100mkg_rep2


title: BYL-Rel-04_483119-4R


title: SuppRat_siRNA1_100mkg_rep3


title: BYL-Rel-03_488104-3R


title: BYL-non-Rel-06_499213-3R


title: Vehicle-ctr_04_480594-3L


title: Vehicle-ctr_03_480594-4R


title: SuppRat_siRNA1_30mkg_rep3

description: SuppRat_groupsiRNA1_30mkg.vs.NaCl.DESeq2.txt


title: BYL-non-Rel-05_456160-1L


title: SuppRat_siRNA1_30mkg_rep1


title: SuppRat_siRNA1_30mkg_rep2


title: SuppRat_NaCl_rep4

value: NaCl Control


title: BYL-non-Rel-01_499213-1R


title: SuppRat_NaCl_rep1


title: BYL-Rel-02_476908-5R


title: SuppRat_NaCl_rep2


title: Vehicle-ctr_02_482781-5R


title: SuppRat_NaCl_rep3


title: BYL-Rel-01_478158-3R


title: pif7-1 SH R3

city: Shanghai

first: Tongdan

last: Zhu

address: 2005 Songhu Road, Yangpu District, Shanghai

country: China

institute: Fudan university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2 2.0.1-beta release mapping to reference genome
count counting
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

extract_protocol:
Total RNA was extracted from snap-frozen tissues using the RNeasy plant mini kit (Qiagen)
RNA libraries were prepared for sequencung using standar Illumina protocols.

value: whole seedlings

value: 1 hr shade


title: Vehicle-ctr_01_482781-3R


title: H3K9ac, vel3, input, R2

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

data_processing:
Raw reads were trimmed using cutadapt-1.9.1 and mapped to Arabidopsis thaliana TAIR10 reference genome using bowtie2
H3K9ac ChIP-seq datasets were subsampled to the same read depth(25M) for each sample.
Only uniquely mapped reads were kept for downstream analysis using Samtools-1.9 and Sambamba-6.7
For data visualization, bigwig files were calculated using deepTools-3.1.1 with a bin size of 50bp, before visualization in IGV -2.12.3
Peaks were called using MACS2, based on the threshold of FDR<0.05.
Assembly: TAIR10
Supplementary files format and content: bigWig

source_name: endosperm

extract_protocol:
For H3K9ac ChIP-seq, immunoprecipitation was performed similarly as H3K27me3, except that 1.5g mature seeds were used. DNA was extracted using phenol-chloroform method.
20ng ChIP-ed DNA and input DNA were sent to Novogene (China) for sequencing, 150bp paired-end with a minimum25M clean reads per sample.

value: endosperm

tag: chip antibody


title: H3K9ac, vel3, IP, R2

value: H3K9ac (Merck Millipore, 07-352)


title: H3K9ac, vel3, IP, R1


title: pif7-1 SH R2


title: H3K9ac, vel3, input, R1


title: SuppRat_siRNA1_100mkg_rep1


title: pif7-1 WL R3

value: 1 hr white light


title: H3K9ac, Col0, IP, R2

value: wild type


title: pif7-1 WL R2


title: H3K9ac, Col0, input, R2


title: pif7-1 SH R1


title: Col-0 SH R3

value: WT


title: BYL-non-Rel-03_481539-5L


title: BYL-non-Rel-02_481539-5R


title: Col-0 SH R2


title: VEL3, IP, R2

data_processing:
For RNA-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using STAR-2.5.a (Dobin et al., 2013). featureCounts (Liao et al., 2014) was used to count the numbers of reads mapped to each gene. Sense reads were selected for downstream analysis. edgeR (Robinson et al., 2010) was used to calculate differentially expressed genes (DEGs), based on the threshold of FDR<0.05 and fold change≥2. For data visualization, bigwig files were generated using deepTools-3.1.1 (Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011).     For ChIP-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using bowtie2 (Langmead et al., 2018). Only uniquely mapped reads were kept for downstream analysis using Samtools-1.9 and Sambamba-6.7 (Li et al., 2009; Tarasov et al., 2015). For data visualization, bigwig files were calculated using deepTools-3.1.1(Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011). Peaks were called using SICER 1.1 for H3K27me3 (Zhang et al., 2009) or MACS2 for VEL3 (Zhang et al., 2008), based on the threshold of FDR<0.05. Only common peaks between two biological replicates were considered.  Different H3K27me3 peaks between Col0 and vel3 were calculated using DiffBind (Ross-Innes et al.,2012) and DESeq2 (Love et al., 2014), based on the threshold of FDR<0.05 and fold change≥2. Genes were identified for these peaks are located in genebody or 1kb promoter using bedtools-2.28.0 (Quinlan & Hall, 2010).
Supplementary files format and content: For RNA-seq, csv files with TPM are provided. For ChIP-seq, bigwig files are provided

source_name: siliques

extract_protocol:
RNA of endosperm and seeds were extracted using Qiagen RNeasy Plant Mini Kit
Libraries of RNA-seq and H3K27me3 ChIP-seq were construed by Novogene (China) and BGI (China) respectively.  For libraries of VEL3 ChIP-seq, Tn5 tagmentation was performed on 1ng ChIP-ed DNA or input DNA for 5 min at 55°C, with 0.1ul enzyme and 2.5ul buffer in 5ul reaction (Illumina, 20034197). PCR amplification was conducted using the following programs: 72°C  5min, 98°C 30s, N cycles of 98°C 10s, 63°C 30s and 72°C 1min. cycle number (N) was determined by the qpcr of each partially-amplified library. 0.8X Agencourt AMPure XP beads (Beckman Coulter, A63880) was used for the library size selection. Libraries were sequenced at Novogene (Beijing, China) using a Novaseq system, 150-bp paired-end sequences with a minimum of 30 million reads acquired per sample.

value: siliques

value: GFP-trap (Chromotek, GTMA-20)


title: H3K9ac, Col0, IP, R1


title: pif7-1 WL R1


title: H3K9ac, Col0, input, R1


title: VEL3, input, R2


title: Col-0 SH R1


title: VEL3, input, R1


title: VEL3, IP, R1


title: Col-0 WL R3


title: Col-0 WL R1


title: Cytoplasmic + Nuclear, IP, rep 2

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description:
Rapid mode
cyt.e.peaks.raw.bed
cyt.e.peaks.norm.bed
cyt.e.peaks.norm.bed.full
nuc.e.peaks.raw.bed
nuc.e.peaks.norm.bed
nuc.e.peaks.norm.bed.full

library_source: other

data_processing:
Raw fastq files underwent a first round of adapter removal/sequence trimming with cutadapt, and were split using fastx-toolkit (0.0.14-3).
Barcodes: Cytoplasmic_IP_rep1, CGTGAT; Nuclear_IP_rep1, GATCTG; Cytoplasmic_input_rep1, GCCTAA; Nuclear_input_rep1, CTGATC; Cytoplasmic_IP_rep2, ACATCG; Nuclear_IP_rep2, TCAAGT; Cytoplasmic_input_rep2, TGGTCA; Nuclear_input_rep2, AAGCTA
Split files were then merged by replicate, had a second round of cutadapt, with output sequences filtered if they had a quality of less than 25, or a length of less than 10 bases.
Mapped to custom genome using STAR v2.5.0, only allowing single-mapping reads to be output as mapped
For reads mapping to custom SINEUP contig, anything mapping to the reverse strand was removed
Clipper was used to define peaks, and peaks in IP samples were normalised by size-matched input samples
Enriched peaks in the normalised output were defined as HNRNPK binding sites, visualised using IGV
Assembly: hg38 + custom contig for SINEUP structure
Supplementary files format and content: raw.bed files are all the peaks identified by clipper
Supplementary files format and content: norm.bed files contain all peaks identified by clipper after normalising IP by input
Supplementary files format and content: norm.bed.full files are the same as above, but display additional information on direction of enrichment (peaks that are ENRICHED rather than DEPLETED are reported in the publication)
Library strategy: seCLIP

molecule: other

growth_protocol: 0.5 X 10^7 cells seeded on a 10 cm plate in DMEM Glutamax+10% FBS+1% P/S (penicillin/streptomycin) at 37°C, 5% CO2; Total three 10 cm plates

extract_protocol:
Followed Brugiolo et al., Nucleic Acids Res. 45 (18), 2017, immunoprecipitation with 15 ug of anti-hnRNPK antibody (ab39975) and seCLIP library preparation
seCLIP - Van Nostrand et al. Methods Mol Biol. 2017 ; 1648: 177–200. doi:10.1007/978-1-4939-7204-3_14

treatment_protocol: Co-transfection with sense GFP and SINEUP-GFP, 24 h post-transfection irradiated with 400 mJ/cm, 254 nm UV light then N/C separation following Brugiolo et al., Nucleic Acids Res. 45 (18), 2017.

value: Human embryonic kidney


title: Cytoplasmic + Nuclear, input, rep 1

description:
Rapid mode
cyt.i.peaks.raw.bed
nuc.i.peaks.raw.bed


title: Cytoplasmic + Nuclear, IP, rep 1


title: Cytoplasmic + Nuclear, input, rep 2


title: HMLE Input

city: Lexington

first: Ren

last: Xu

state: KENTUCKY

address: 741 S. Limestone Rd

institute: University of Kentucky

data_processing:
The sequencing data were processed by Active Motif. Briefly, the 75-nt sequence reads were mapped to the hg19 genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter,align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
MACS was used to identify the binding sites of transcription factors that bind to discrete sites. Methylated sites or  regions can be identified with MACS algorithms.
Genomic locations along with their proximities to gene annotations and other genomic features are determined by Active Motif
Assembly: hg19/GRCh37
Supplementary files format and content: bed file: Custom track for UCSC browser to see location of Intervals and Active Regions; fa file: For each sample, the 60-bp sequences surrounding the summits of the top 1,000 peaks are provided as FASTA file; genes.xlsx: This Excel file lists all genes that have at least one Interval within the chosen GeneMargin; actregs.xlsx:  lists all Active Regions (genomic regions containing 1 or multiple overlapping Intervals)

source_name: HMLE

growth_protocol: MEGM™ Mammary Epithelial Cell Growth Medium. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The genomic DNA was  extracted by Genomic DNA Purification Kit. DNA was sonicated was sonicated to 200–  1000 base pairs (bp).
ChIP-seq libraries were prepared by Ative Motif. 10 ng of DNA was used as starting material for input and ip samples.

value: HMLE

value: Human mammary epithelail

value: N/An


title: HMLE_Twist

value: 5hMC (Active Motif 39769 )


title: PDC11_IFNγ_IRF1_2

data_processing:
For ChIP-sequencing data analysis: Quality of raw reads (fastq format) was checked with FastQC (version 0.11.5).  Reads were trimmed using skewer (version 0.2.2).  Trimmed reads were mapped with bowtie2 (version 2.3.2) to the hg38 Homo sapiens genome (using release 31 of Gencode annotation).  We removed duplicated reads using Picard method “MarkDuplicates”.  Peaks were called using macs2 method “callpeak” (version 2.1.1.20160309) and next annotated with Homer’s “annotatePeaks.pl” script.  The pairwise differential binding analysis between cell lines was done with DiffBind (version 3.2.1) R (version 4.1.0) /Bioconductor package, specifying the DESeq2  method for differential binding assessment and the “DBA_BLACKLIST_HG38” blacklist. Regions were considered as differentially bound if FDR < 0.05.  Motif analysis was done per cell line using MEME-CHIP (version 5.11). Prior to motif search, only peaks present in both biological replicates of a same cell line were considered, and 50bp were taken around each side of the peak’s summit.  Gene Ontology enrichment analysis of was done using GOstats R package using a hypergeometric test p-value cutoff of 0.001. KEGG pathways enrichment was assessed with package clusterProfiler. Genes considered for functional enrichment analysis were those where a peak (i.e. peaks in common between biological duplicates) was found in the promoter region (-1500bp / + 100bp from transcription start site).
Genome_build: hg38

extract_protocol:
For ChIP, cells were grown and fixed with 1% methanol-free formaldehyde (Thermo Scientific) for 10 min and quenched by 125 mmol/L glycine for 15 min at room temperature and, after that, washed with ice-cold PBS twice. Then, the cells were centrifuged (200g at 4°C) for 5 min and the pellet resuspended in 1 mL of lysis buffer (10 mmol/L Tris-HCl, 10 mmol/L NaCl, 0.5% NP-40) containing a Halt Protease & Phosphatase Inhibitor Cocktail (Thermo Scientific; Ref: 78440) and kept rotating for 30 min at 4°C. After centrifugation, the pellet was then resuspended in 1 mL of nuclear lysis buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl pH 8.0, protease inhibitor) and kept at 4°C for 60 min. After another centrifugation, the lysate was sonicated with a Covaris M220 instrument to yield chromatin fragments of a size of 0.25–1.00 kb on average, then frozen at -20ºC for 30 min, thawed on ice and centrifuged at 2,500 g. For each ChIP reaction, 60 μL of Magna ChIP™ Protein A+G Magnetic Beads (Merck Millipore. Cat: #16-663) was used in accordance with the manufacturer’s protocol. Before addition of the sheared chromatin to the beads, Triton X-100 and Na-deoxycholate was added to a final concentration of 10% each. 1% of the chromatin volume was used for input. At least two independent ChIP experiments were performed.
Immunoprecipitated chromatin was deep sequenced in the Genomics Unit of the Centre for Genomic Regulation (CRG, Barcelona, Spain) using the Illumina HiSeq 2500 system (Illumina). Briefly, library preparation included end-repair, generation of dA overhangs, adapter ligation, size selection and removal of non-ligated adapters by agarose gene electrophoresis and amplification (18 cycles) before loading the samples into the sequencer.

value: lung; derived from metastatic site:pleural effusion

tag: antibody

value: male

value: 67 years adult

tag: source

value: Non-Small cell lung cancer

value: IFNg


title: HMLE_Ctrl


title: Col-0 WL R2

value: whole seedlings


title: PDC11_IFNγ_input_1

value: input


title: EndoC-βH1, Dexamethasone, biol_rep 3

city: Malmö

first: Lena

last: Eliasson

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

data_processing:
Quality of sequence reads was assessed with FastQC (v0.11.8)
Sequence reads were mapped to the human transcriptome (Gencode Release 27; genome assembly GRCh38) and quantified accordingly by Salmon (v0.14) (parameters: --incompatPrior 0.0 --validateMappings --gcBias --seqBias)
Read count extraction and normalization was performed by DESeq2 (v1.30.0)
Assembly: hg38
Supplementary files format and content: Excel (xlsx) file includes Deseq2 normalized values (median of ratios method) for each sample and cell type

source_name: Human pancreatic beta-cell line EndoC-betaH1

growth_protocol:
Human islets: After isolation, islets were cultured 1–7 days, free floating in CMRL 1066 culture medium (ICN Biomedicals, Costa Mesa, CA, USA) containing human serum and 5.56 mM glucose and supplemented with 10 mmol/l HEPES, 2 mmol/l 1-glutamine, 50 μg/ml gentamicin, 0.25 μg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 μg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mmol/l nicotinamide at 37 °C (5% CO2)
EndoC cells: EndoC-βH1 cells were grown in Matrigel fibronectin-coated (100 μg/mL and 2 μg/mL, respectively, Sigma–Aldrich, Steinheim, Germany) culture vessels in DMEM (Thermo Fisher Scientific, Waltham, MA, USA) containing 5.6 mM glucose, 2% BSA fraction V (Roche Diagnostics, Mannheim, Germany), 10 mM nicotinamide (Merck Millipore, Darmstadt, Germany), 50 μM 2-mercaptoethanol, 5.5 μg/mL transferrin, 6.7 ng/mL sodium selenite (Sigma–Aldrich), 100 U/mL penicillin, and 100 μg/mL streptomycin (PAA Laboratories, Pasching, Austria) at 37 °C (5% CO2)

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy isolation kit. RNA concentration and quality was determined using 2μL on a NanoDrop Spectro-photometer
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep with Ribo-Zero kit (#RS-122-2201, Illumina, CA, USA). Samples were loaded and sequenced using the Nextseq 500/550 High Output kit v2 (#FC-404-2002, Illumina, CA, USA) on an Illumina NextSeq 500 sequencer

treatment_protocol: Human islets and EndoC-βH1 cells were incubated for 48h and 24h, respectively, in cell culture media containing 2 μM dexamethasone (#D1756, Sigma-Aldrich) dissolved in DMSO (≥99.7%; 1:1000, #34869, Sigma-Aldrich) or DMSO (used as the Control condition)

value: Dexamethasone


title: EndoC-βH1, Dexamethasone, biol_rep 4

value: Human pancreatic beta-cell line EndoC-betaH1


title: Lu165_IFNγ_IRF1_1

value: Lung

value: 50 years adult

value: Small cell lung cancer


title: Lu165_IFNγ_input_2


title: Lu165_IFNγ_IRF1_2


title: Lu165_IFNγ_input_1


title: EndoC-βH1, Control, biol_rep 2

value: DMSO


title: EndoC-βH1, Dexamethasone, biol_rep 2


title: Human Islet, Dexamethasone, donor 4

source_name: Human pancreatic islets

value: Human pancreatic islets


title: EndoC-βH1, Control, biol_rep 3


title: Frozen 2

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: AmpliSeq based expression data for Frozen sample 2

data_processing:
The raw reads in FASTQ format were aligned to the human hg19 reference genome using bwa mem with default parameters: bwa mem -M -t 8 -R "@RG\tID:SampleName\tPL:ILLUMINA\tSM:SampleName" -L 5
Gene quantification was done using HTSeq using the default parameters: htseq-count -f bam -r pos -s no Sorted.bam Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf
Differential gene expression was analyzed using the DESeq2 (v.1.26.0) R/Bioconductor package
Assembly: hg19, custom annotation GTF file for targeted transcripts (Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf) received from the manufacturer
Supplementary files format and content: tab-delimited text files containing raw read counts for targeted genes.

source_name: primary human fetal kidney podocytes, Lonza CC-7224

growth_protocol: Primary human podocytes were seeded at an initial density of 30,000 cells/cm2, using RPMI 1640 basal medium with GlutaMAX and HEPES, supplemented with 10% FBS, 1% ITS, and 0.5% GA-1000. Primary cells were rinsed with HEPES-BSS during subculture and rinsing steps.

extract_protocol:
Cells were rinsed once with warm PBS prior to RNA extraction and isolation using the PicoPure RNA isolation Kit (Thermo Fisher Scientific, #KIT0204). 50 µL lysis buffer was added to each scaffold top, placed on a shaker for 5 min at room temperature, and gently scraped with a pipette tip and liquid collected while avoiding bubbles. Samples were incubated at 42˚C for 30 minutes on a heating block in microtubes. Manufacturer’s protocols were followed, with the inclusion of a DNAse treatment step (Qiagen, #79254). 21 µL of elution buffer was used in the last step, and a DeNovix spectrophotometer was used to approximate sample RNA concentration and quality. Extraction and isolation were performed in the same sitting. Isolated RNA was kept frozen at -80˚C.
Targeted whole transcriptome sequencing was done using the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, Inc) following manufacturer’s recommendations.

treatment_protocol: Groups are treated by the topographic pattern of the scaffold on which they are grown: (NT) No Topography, (RT) Round Topography, (HF) High Fractal topography. Scaffolds were coated with Porcine kidney ECM (Xylyx Bio, NativeCoat Kidney ECM surface coating kit #MTSKY201) according to manufacturer's instructions prior to cell seeding.

value: Human fetal kidney podocytes


title: Frozen 1

description: AmpliSeq based expression data for Frozen sample 1


title: EndoC-βH1, Control, biol_rep 4


title: EndoC-βH1, Control, biol_rep 1


title: EndoC-βH1, Dexamethasone, biol_rep 1


title: Frozen 3

description: AmpliSeq based expression data for Frozen sample 3


title: H82_IFNγ_IRF1_2

value: 40 years adult


title: PDC11_IFNγ_input_2


title: Human Islet, Dexamethasone, donor 3


title: PDC11_IFNγ_IRF1_1


title: 5_N_input

city: Meizhou

first: Jingyuan

last: Hou

state: CHINA

address: No. 63 Huangtang Road, Meijiang District, Meizhou

institute: Meizhou People's Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: xlsx files include FPKM values and annotation for each Sample
Supplementary files format and content: xlsx files include peak  information for each group

source_name: heart valve tissues

extract_protocol: Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: heart valve tissues

value: non-calcified


title: 5_C_input

value: calcified


title: 4_N_IP


title: H82_IFNγ_input_2

value: male


title: SKNMC_shGFP_HiC

value: Ewing sarcoma cells

value: untreated


title: 5_C_IP


title: Human Islet, Dexamethasone, donor 2


title: 5_N_IP


title: H82_IFNγ_IRF1_1

value: IFNg


title: 4_N_input


title: 4_C_input


title: H23_IFNγ_IRF1_2

value: 51 years adult

value: Non-Small cell lung cancer


title: Human Islet, Control, donor 3


title: 3_N_input


title: Human Islet, Dexamethasone, donor 1

value: Dexamethasone


title: Human Islet, Control, donor 4


title: H23_IFNγ_input_2

value: Lung

value: input


title: Human Islet, Control, donor 2


title: H82_IFNγ_input_1

value: Small cell lung cancer


title: 3_N_IP


title: 3_C_IP


title: H23_IFNγ_IRF1_1


title: 2_N_input


title: 2_N_IP


title: Human Islet, Control, donor 1

value: DMSO


title: 4_C_IP


title: 2_C_IP


title: H23_IFNγ_input_1


title: 2_C_input


title: MDA_Co_1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 algorithm against hg38 human genome version and RSEM v1.2.12 software was used to estimate read counts and RPKM values using gene information from Ensemble transcriptome version GRCh38.p12
Assembly: hg38
Supplementary files format and content: raw counts for all genes

extract_protocol:
For cells sorted from co-culture experiments, total RNA was extracted using the Direct-ZolRM RNA MiniPrep Plus (Zymo Research) according to manufacturer’s protocol.
Sequencing libraries were prepared from RNA samples using QuantSeq (Lexogen)

value: MDA231 tumor cells

tag: condition

value: cocultured


title: 1_N_input


title: MDA_Co_2

tag: cell type


title: H1993_IFNγ_IRF1_1

value: female

value: 47 years adult

tag: treatment


title: 1_C_input

value: heart valve tissues


title: 3_C_input

value: calcified


title: MDA_Al_2

tag: cell line

value: alone


title: AMC772T2

city: Utrecht

first: Michael

last: van Gerven

state: Utrecht

address: Heidelberglaan 25

department: Oncology

country: Netherlands

institute: Princess Maxima Center

data_processing:
Assembly: GRCh38
Sequences were aligned to genome build GRCh38 using STAR (v2.7.0f).
Counts were generated using the R package Rsubread.
Supplementary files format and content: *.csv: Comma-separated values files with raw counts for each sample.

source_name: Neuroblastoma

extract_protocol:
RNA was harvested with Trizol (Invitrogen) and chloroform extracted, followed by purification using NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer's protocol.
KAPA RNA HyperPrep Kit with RiboErase Kit (Roche).
RNA-seq 2x150bp

tag: tumoroid (patient-derived)

value: Neuroblastoma

value: ATRX out-of-frame exon 2-9 deletion, but exon skipping of exon 10 on mRNA resulting in in-frame product

value: Male


title: H1993_IFNγ_input_1

tag: tissue

value: IFNg


title: A549_IFNγ_IRF1_2

value: male

value: 58 years adult

value: Non-Small cell lung cancer


title: SK-N-AS ATRX knock-out clone 14 bio rep 2

data_processing:
Assembly: GRCh37
Sequences were aligned to genome build GRCh37 using STAR (v2.7.3a).
Counts were generated using the R package Rsubread.
Supplementary files format and content: *.csv: Comma-separated values files with raw counts for each sample.

source_name: SK-N-AS

extract_protocol:
RNA was harvested with Trizol (Invitrogen) and chloroform extracted, followed by purification using NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer's protocol.
The TruSeq RNA stranded RiboZeroPlus Kit (Illumina).
RNA-seq 2x50bp

value: SK-N-AS

tag: genotype

value: ATRX knock-out

value: Female


title: MDA_Al_1

value: MDA231 tumor cells


title: SK-N-AS ATRX knock-out clone 6 bio rep 1

tag: Sex


title: SK-N-AS ATRX knock-out clone 6 bio rep 2


title: A549_IFNγ_input_2

value: Lung

value: input

tag: age


title: SK-N-AS ATRX knock-out clone 14 bio rep 1


title: Astro_Co_1

source_name: Astrocytes

value: Astrocytes

value: cocultured


title: SK-N-AS ATRX wild-type clone 2

value: ATRX wild-type


title: SK-N-AS ATRX wild-type clone 6


title: NB139 ATRX exon 2-10 deletion clone 36 bio rep 4

value: ATRX in-frame exon 2-10 deletion


title: 1_C_IP

value: heart valve tissues

value: calcified


title: SK-N-AS ATRX wild-type clone 4

value: Neuroblastoma


title: NB139 ATRX exon 2-10 deletion clone 36 bio rep 2

value: Male


title: H1993_IFNγ_IRF1_2

source_name: ATCC

value: female

value: 47 years adult

value: IFNg


title: A549_IFNγ_input_1

value: male

value: 58 years adult

value: Non-Small cell lung cancer


title: SK-N-AS ATRX wild-type clone 10

value: SK-N-AS

value: Female


title: 1_N_IP

value: non-calcified


title: A549_IFNγ_IRF1_1

value: Lung


title: Astro_Al_1

value: Astrocytes

value: alone


title: NB139 ATRX exon 2-10 deletion clone 36 bio rep 1

value: ATRX in-frame exon 2-10 deletion


title: NB139 ATRX exon 2-10 deletion clone 36 bio rep 3


title: MECOM KO RNA-Seq rep2

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
RNA-Seq reads were mapped to hg19 genome assembly using tophat v2.0.12 with parameters  --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. And then the differentially expressed genes based on read counts are inferred using edgeR R package v3.12.0
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text file contains the FPKM values for each gene of each sample.

source_name: HUVEC cells

growth_protocol: HUVEC was cultured in 5% CO 2 and maintained in vitro in Endothelial Growth Basal Medium with EGM-2 SingleQuot Kit

extract_protocol:
Quick-RNA MiniPrep (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HUVEC cells

value: LentiCRISPR MECOM KO virus for 72h


title: NB139 ATRX exon 10-12 deletion clone 1 bio rep 2

value: Neuroblastoma

value: ATRX in-frame exon 10-12 deletion


title: Astro_Co_2

value: cocultured


title: ATAC-seq_pFusNmutCL-HS2-Light_rep2

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg38 using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Assembly: hg38
Supplementary files format and content: bigwig file

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM medium containing 10% FBS.

extract_protocol: ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg38) were retained for downstream data analysis.

treatment_protocol: Cells were exposed with blue light (488nM) for 5 min to induce light-activated phase separation

value: Human HeLa cells


title: ATAC-seq_pFusNmutCL-HS2-Light_rep1


title: NB139 ATRX wild-type clone 9

value: ATRX wild-type

value: Male


title: Control RNA-Seq rep2

value: LentiCRISPR V2 control virus for 72h


title: NB139 ATRX wild-type clone 8


title: Control RNA-Seq rep1


title: ATAC-seq_pFusNmutCL-HS2-Dark_rep1


title: Astro_Al_2


title: NB139 ATRX wild-type clone 7


title: ATAC-seq_BRD4LAMPS-HS2-Light_rep2


title: protonema, Wild-type

city: Tel Aviv

first: Ofir

last: Griess

address: Haim Levanon 31

department: Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

data_processing:
Identical duplicate reads and low-quality reads were filtered out using Prinseq-lite software v0-20-4
Custom Perl scripts were used to convert all the Cs in the ‘forward’ reads and reference sequence to Ts, and all the Gs in the ‘reverse’ reads and reference sequence to As
Reads were aligned to the reference genome using Bowtie2.0
Custom Perl scripts were used to recover the original sequence information and, for each C (on either strand), to count the number of times it was sequenced as a C or a T.
For each sequence context (CG, CHG, CHH),  the genomic averaged fractional methylation as well as fractional methylation within a 50 bp sliding window that were used in downstream analyses were calculated.
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents one citosine. Scores represent methylation level for each position, column 9 contains numbers of times each cytosine was sequenced as either C or T, as well as total reads coverage of the given citosine.
Separate gff files for each methylation context (CG, CHG and CHH), each entry represents 50-bp window. Scores represent methylation level for each window, column 9 contains numbers of times cytosines within the given window were sequenced as either C or T, as well as total reads coverage of citosines within the window.

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 days on BCDAT media, 25 °C,  16-h light and 8-h dark regime

extract_protocol:
Genomic DNA was extracted from 7 days old protonema using DNeasy Plant Mini Kit (Qaigen) according to manufacturer’s instructions
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to bisulfite conversion treatment using the Methylation-Gold kit (ZYMO) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and gel purified (~350-400 bp size range) prior to quantification with a Bioanalyzer (Agilent).

value: protonema

tag: strain

value: Grandsen

value: Wild-type

value: 7 days


title: MCF7_dEnh_RNA_3

city: Toronto

first: Jennifer

last: Mitchell

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

description: SOX2 enhancer-deleted replicate 3 [RNA-seq]

data_processing:
Library strategy: Ribo-seq
Adapters were removed and reads were trimmed using FastP
Reads were aligned to hg38 using STAR 2.7
Bedgraphs were generated using bedtools 2
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: MCF-7 enhancer-deleted cell line

growth_protocol: Cells were grown in phenol red free DMEM + 10% FBS with 1x PenStrep, 1x Glutamax, 1x Sodium Pyruvate and 1x non-essential aminoacids

extract_protocol:
Total RNA was extracted using Qiagen Rneasy mini kit and treated with Dneasy prior to library construction
ATAC-seq: Nuclei were isolated from tissues using gradient centrifugation as per the Omni-ATAC and were exposed to the transposase, Tn5, prior to llibrary construction.
RNA libraries were prepared using standard Illumina TruSeq protocols
ATAC-seq libraries were prepared for sequencing using standard Illumina Novaseq 6000
riboRNA-depleted TruSeq stranded library was sequenced using Illumina HiSeq 2500 with 125bp paired-ended sequencing. !Sample_extract_protocol_ch1 = ATAC-seq library was sequeced using Illumina Novaseq 6000 with 50bp paired-ended sequencing.

treatment_protocol: SOX2 enhancer was deleted using CRISPR/Cas9 and single cells were grown individually in isogenic cell lines

tag: genotype/variation

value: SOX2 enhancer-deleted

value: MCF-7 cells

tag: disease state

value: breast adenocarcinoma


title: NB139 ATRX wild-type clone 5


title: ATAC-seq_BRD4LAMPS-HS2-Light_rep1


title: protonema, ddm1_rep1

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Assembly: Ppatens v3.0 (Phypa V3 https://www.ncbi.nlm.nih.gov/assembly/GCF_000002425.4)
Supplementary files format and content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample.  The accession numbers are according to the latest P. patens genome assembly - with accessions such as Pp1c.. being genes, and numbers such as 986... being transposable elements.  These accessions can be found in the plant database, Phytozome for this assembly of P. patens.

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

tag: batch


title: MCF7_dEnh_RNA_1

description: SOX2 enhancer-deleted replicate 1 [RNA-seq]


title: MCF7_dEnh_RNA_2

description: SOX2 enhancer-deleted replicate 2 [RNA-seq]


title: GI-ME-N ATRX exon 2-10 deletion clone 39

source_name: GI-ME-N

value: GI-ME-N

value: ATRX in-frame exon 2-10 deletion

value: Female


title: ATAC-seq_BRD4LAMPS-HS2-Dark_rep2


title: protonema, ddm1_rep2


title: MECOM KO RNA-Seq rep1

value: HUVEC cells

value: LentiCRISPR MECOM KO virus for 72h


title: GI-ME-N ATRX exon 2-10 deletion clone 51

value: Neuroblastoma


title: MCF7_WT_RNA_3

description: MCF-7 wild-type replicate 3 [RNA-seq]

source_name: MCF-7 wild-type cell line

value: wild type


title: protonema, wt_rep2

value: wt


title: protonema, wt_rep1


title: NB139 ATRX exon 10-12 deletion clone 1 bio rep 1

value: ATRX in-frame exon 10-12 deletion

value: Male


title: ATAC-seq_pFusNmutCL-HS2-Dark_rep2

value: Human HeLa cells


title: GI-ME-N ATRX exon 2-10 deletion clone 48


title: MCF7_WT_RNA_2

description: MCF-7 wild-type replicate 2 [RNA-seq]


title: MSC_HiChIP

city: Charlestown

first: Rui

last: Dong

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Library strategy: HiChIP
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
The hichipper tool (v 0.7.7) (Lareau et al., 2018) was used for loop calling within H3K27ac ChIP-seq peak (q-value < 0.00001) regions, by applying the following parameters: --max-distance 100000000 --read-length 100
Genome_build: hg19
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). Intrachromosomal looping between anchor loci.

source_name: Primary Mesenchymal stem cells

extract_protocol:
Genomic DNA/ChIP DNA was isolated from x-linked nuclei after Mbo1 restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol. H3K27ac antibody was used to pull-down ChIP following HiC and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif

value: mesenchymal stem cells

value: untreated


title: protonema, ddm1

value: protonema

value: Grandsen

value: 7 days


title: MCF7_WT_RNA_1

description: MCF-7 wild-type replicate 1 [RNA-seq]

value: MCF-7 cells

value: breast adenocarcinoma


title: GI-ME-N ATRX exon 2-13 deletion clone 16

value: GI-ME-N

value: ATRX in-frame exon 2-13 deletion


title: EtOH3

city: Atlanta

first: Hyun

last: Hwang

state: Georgia

address: 2015 Uppergate Dr

department: Pediatric Cardiology

institute: Emory University School of Medicine

data_processing:
RNA quality was assessed on a Bioanalyzer instrument (Agilent, CA Technologies) and all samples had RNA integrity number >= 7.
cDNA was derived from RNA, hybridized and probe intensities were generated on Illumina HumanHT-12 v3 (Illumina, CA).
RNA sequence reads were aligned to the human reference genome (GRCh38) using HISAT2 (hierarchical indexing for spliced alignment of transcripts), followed by using UCSC reference annotation and HTSeq to estimate gene abundance.
Read count normalization was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: csv file of raw read count of genes for each sample

extract_protocol:
RNA was extracted using Aurum total RNA mini kit (Qiagen) according to manufacturer's instructions.
Library preparation and sequencing were perormed at the Parker H. Petit Institute for Bioengineering and Bioscience at the Georgia Institute of Technology.

value: iPSC-CMs

value: WT

value: EtOH treatment

tag: time

value: Day 30+


title: EtOH2


title: MSC_HiC

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
Default settings were used to control quality, align paired reads, identify valid interactions and generate interaction matrices. The Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012) was performed for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary_files_format_and_content: HiC 40kb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiC 1mb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.

extract_protocol:
Genomic DNA was isolated from x-linked nuclei after Mbo1+HinfI restriction digestion, end filling with biotin-14ATP and following ligation, according to in-situ HiC protocol, and proceed to library construction.
Followed Next Gen DNA Library Kit & Next Gen Indexing Kit from Active Motif


title: HFD_3

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2.
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include read count values for each Sample.

source_name: Whole forebrain

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent TapeStation 4000 system (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions.

value: Whole forebrain

value: HFD


title: EtOH1


title: GI-ME-N ATRX exon 2-13 deletion clone 15

value: Neuroblastoma

value: Female


title: ATAC-seq_BRD4LAMPS-HS2-Dark_rep1

value: Human HeLa cells


title: CTRL3

value: CTRL


title: VSV8h_PEP_R2

city: Beijing

first: Lu

last: Zhao

address: Dongdan Santiao 5

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: RAW264.7 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were constructed by using NEBNext® Ultra™ RNA Library Prep Kit (NEB) according to the manufacturer’s instructions.

treatment_protocol: RAW264.7 cells were pretreated with 250 μM PEP or PBS for 2 hours, followed by VSV infection for 8 hours or without infection.

value: macrophage

value: PEP, VSV


title: VSV8h_PEP_R3


title: GI-ME-N ATRX exon 2-13 deletion clone 13


title: GI-ME-N ATRX exon 2-13 deletion clone 14


title: CTRL2


title: GI-ME-N ATRX knock-out clone 3 biol rep 2

value: ATRX knock-out


title: VSV8h_PEP_R1


title: NCD_3

value: NCD


title: CTRL1


title: VSV8h_PBS_R3

value: PBS, VSV


title: NCD_2


title: GI-ME-N ATRX knock-out clone 3 biol rep 1

value: GI-ME-N


title: VSV8h_PBS_R2


title: A673_shFLI1_microC

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end microC reads were aligned against the hg19 genome using HiC-Pro.
Default settings were used to control quality, align paired reads, identify valid interactions and generate interaction matrices. The Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012) was performed for each sample.
Assembly: hg19
Supplementary files format and content: microC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary files format and content: microC 40kb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary files format and content: microC 1mb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.

source_name: Ewing sarcoma cells

extract_protocol:
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, the chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.
Dovetale MicroC kit, illumina adaptos according to the manufactors instructions

value: Ewing sarcoma cells

value: untreated


title: NCD_1

value: WT


title: GI-ME-N ATRX knock-out clone 1 biol rep 2


title: VSV8h_PBS_R1


title: GI-ME-N ATRX knock-out clone 1 biol rep 1


title: H3K27me3, vel3, IP, R2

data_processing:
For RNA-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using STAR-2.5.a (Dobin et al., 2013). featureCounts (Liao et al., 2014) was used to count the numbers of reads mapped to each gene. Sense reads were selected for downstream analysis. edgeR (Robinson et al., 2010) was used to calculate differentially expressed genes (DEGs), based on the threshold of FDR<0.05 and fold change≥2. For data visualization, bigwig files were generated using deepTools-3.1.1 (Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011).     For ChIP-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using bowtie2 (Langmead et al., 2018). Only uniquely mapped reads were kept for downstream analysis using Samtools-1.9 and Sambamba-6.7 (Li et al., 2009; Tarasov et al., 2015). For data visualization, bigwig files were calculated using deepTools-3.1.1(Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011). Peaks were called using SICER 1.1 for H3K27me3 (Zhang et al., 2009) or MACS2 for VEL3 (Zhang et al., 2008), based on the threshold of FDR<0.05. Only common peaks between two biological replicates were considered.  Different H3K27me3 peaks between Col0 and vel3 were calculated using DiffBind (Ross-Innes et al.,2012) and DESeq2 (Love et al., 2014), based on the threshold of FDR<0.05 and fold change≥2. Genes were identified for these peaks are located in genebody or 1kb promoter using bedtools-2.28.0 (Quinlan & Hall, 2010).
Supplementary files format and content: For RNA-seq, csv files with TPM are provided. For ChIP-seq, bigwig files are provided

source_name: mature endosperm

extract_protocol:
RNA of endosperm and seeds were extracted using Qiagen RNeasy Plant Mini Kit
Libraries of RNA-seq and H3K27me3 ChIP-seq were construed by Novogene (China) and BGI (China) respectively.  For libraries of VEL3 ChIP-seq, Tn5 tagmentation was performed on 1ng ChIP-ed DNA or input DNA for 5 min at 55°C, with 0.1ul enzyme and 2.5ul buffer in 5ul reaction (Illumina, 20034197). PCR amplification was conducted using the following programs: 72°C  5min, 98°C 30s, N cycles of 98°C 10s, 63°C 30s and 72°C 1min. cycle number (N) was determined by the qpcr of each partially-amplified library. 0.8X Agencourt AMPure XP beads (Beckman Coulter, A63880) was used for the library size selection. Libraries were sequenced at Novogene (Beijing, China) using a Novaseq system, 150-bp paired-end sequences with a minimum of 30 million reads acquired per sample.

value: mature endosperm

tag: chip antibody


title: A673_shGFP_microC


title: A673_shFLI1_HiC_rep

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Paired-end HiC reads were aligned against the hg19 genome using HiC-Pro.
Default settings were used to control quality, align paired reads, identify valid interactions and generate interaction matrices. The Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012) was performed for each sample.
Assembly: hg19
Supplementary files format and content: HiC all valid interaction read pairs (allValidPairs). Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size
Supplementary files format and content: HiC 40kb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary files format and content: HiC 1mb resolution Interaction matrix files (.matrix). A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.


title: Medium_PEP_R3

value: PEP


title: H3K27me3, vel3, input, R2


title: GI-ME-N ATRX wild-type clone 4

value: ATRX wild-type


title: HFD_1

value: Whole forebrain

value: HFD


title: HFD_2


title: GI-ME-N ATRX wild-type clone 3

value: Neuroblastoma

value: Female


title: H3K27me3, vel3, IP, R1


title: A673_shGFP_HiC_rep


title: Medium_PEP_R1


title: NF1_BYL_2

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

institute: University Hospital Basel

data_processing:
Reads were aligned to the human genome (UCSC version hg38AnalysisSet) with STAR (version STAR/2.5.2a-goolf-1.7.20) using the multi-map settings outFilterMultimapNmax = 10 and outSAMmultNmax = 1.
The output was sorted and indexed with SAMtools (version SAMtools/1.7-goolf-1.7.20) and picard markDuplicates (version picard/2.9.2) was used to collapse samples run on different sequencing lanes. Stand-specific coverage tracks per sample were generated by tiling the genome in 20bp windows and counting overlapping reads in each window using the bamCount function from the Bioconductor package bamsignals (Bioconductor version 3.6). These window counts were then exporting in bigWig format using the export function rtracklayer of the Bioconductor package.
The function gQCReport of the Bioconductor package QuasR was used for assessing read and alignment quality. The number of reads (5’ ends) overlapping the exons of each gene was counted with the gCount function of QuasR, assuming an exon union model.
Differential gene expression analysis was achieved using the edgeR framework (Chen 2016). Gene set enrichments were performed using CAMERA (Wu_2012)
Assembly: UCSC version hg38
Supplementary files format and content: RNAseq_T47D_CTRL_NF1KO_annotated_count_table.txt: is the gene annotated  table with raw counts after alignment

extract_protocol:
RNA was extracted with a RNeasy Plus Mini kit (Qiagen #74136). RNA quality was analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies) using the Agilent RNA 6000 Nano Chip (Agilent #5067-1511) - RIN (RNA Integrity Number) was 8.6-10 (average 9.7). RNA was quantified by Fluorometry using the QuantiFluor RNA System (Promega #E3310).
Library preparation was performed, starting from 200 ng total RNA. The library was prepared with the Illumina TruSeq stranded mRNA-seq preparation kit (Illumina #20020595) and the TruSeq RNA CD Index Plate (Illumina #20019792) according to the manufacturer’s protocol. Size and quality of the library was evaluated on the Fragment Analyzer (Advanced Analytical) with the Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-473). Samples were pooled to equimolar concentrations. Libraries complemented with 1% PhiX were sequenced Single-reads 76 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using 2 NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005).

treatment_protocol: T47D CTRL or NF1 KO cells were treated for 48 h with vehicle (DMSO) or 3 µM BYL719.

value: Breast cancer cells


title: H3K27me3, vel3, input, R1

first: Xiaochao

address: Norwich Research Park, Colney Ln

institute: John Innes Centre


title: NF1_BYL_1


title: NF1_BYL_3


title: H3K27me3, Col0, IP, R2

value: wildtype


title: Medium_PBS_R2

value: macrophage

value: PBS


title: Medium_PBS_R3


title: GI-ME-N ATRX wild-type clone 2


title: GI-ME-N ATRX wild-type clone 1


title: Medium_PBS_R1


title: NF1_Veh_3

value: DMSO


title: F-1547_G34R_P7_crx_RNA

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Bedgraph files were generated with bedtools 2.27.1 genomeCoverageBed function using a normalization factor of number of mapping read/100,000,000. Then bedGraphtoBigWig was used to convert the bedgraph files to bigwig.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4  and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: bigWig files generated with bedtools 2.27.1, read coverage for each sample over the mouse genome
Supplementary files format and content: mm10.Ensembl.raw_counts.tsv, tab-separated values file, raw counts of all the RNA-seq samples.

source_name: cortex

extract_protocol:
Total RNA was extracted from pulverized tissue using the Aurum Total RNA Mini Kit (Bio-Rad) according to manufacturer’s instructions.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre).

value: cortex

value: postnatal day 7


title: NF1_Veh_2


title: H3K27me3, Col0, IP, R1

city: Norwich

last: Chen


title: H3K27me3, Col0, input, R1


title: F-1546_WT_P7_crx_RNA


title: Medium_PEP_R2


title: H1-CAR-D7 biol rep 1

city: LOS ANGELES

first: Suwen

last: Li

state: CA

address: 610 Charles E Young Dr E, Room 3031

institute: UCLA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Transcriptome data were mapped to the GRCh38 reference genome assembly with Cell Ranger (10X Genomics) and subjected to Seurat for pre-processing and normalization using SCTransfrom. Single-cell RNA analysis (including quality control, data normalization, dimension reduction, cluster detection, and differential expression testing) were performed using Seurat 4.0 81 in R following standard workflow. Cell cycle scores, percent of mitochondrial genes, and percent of ribosomal genes were assigned and regressed out during scaling. Normalized data were integrated based on identification of ‘anchors’ between pairs of datasets with reciprocal PCA. PCA was performed and significant PCs were selected based on the elbow of standard deviations of PCs. The first 20 PCs were used for calculation of UMAP (Uniform Manifold Approximation and Projection) and the neighborhood graph for clustering. The FindAllMarkers function was used to find specific genes for each cluster, which uses the Wilcoxon rank-sum test. Cell types were annotated based on the marker genes compared to canonical markers. Clusters expressing CD7 and/or IL7R were defined as lymphoid cells and selected for further analysis. Lymphoid cells were then subjected to reclustering. To better appreciate heterogeneity within these cells, PCA was recalculated in the lymphoid subset and PC of 20 was used for UMAP projection and clustering. Differential gene expression analyses were performed with the FindMarkers function using the Wilcoxon test with a log fold-change threshold of 0.25 and a minimum expression frequency of 0.1. Pathway analysis was performed using the Single Cell Pathway Analysis (SCPA) package in R 82. Wikipathways were used as input gene sets using the msigdbr package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: in vitro differentiated cells

extract_protocol:
Day 0, 4, and 7 ATOs were harvested into single cell suspensions in MACS buffer (PBS/0.5% bovine serum album/2mM EDTA) by mechanical dissociation. Live cells were first enriched with the Dead Cell Removal Kit (Miltenyi Biotec, Cat 130–019-101). Cells were then stained and FACS-sorted as DAPI- mouse CD29- (Biolegend, San Diego, CA) to deplete residual dead cells and MS5 stromal cells, respectively.
10X 3’ RNAseq library generation from sorted cells was performed by the UCLA Technology Center for Genomics and Bioinformatics (TCGB) Core using the 10X Genomics Chromium™ Controller Single Cell Sequencing System (10X Genomics, Pleasanton, CA), per the manufacturer’s instructions and TCGB Core standard protocol

value: in vitro differentiated cells

value: human embryonic stem cell line-derived (H1 line)

value: in vitro differentiated lymphoid progenitors

value: CAR transduced

value: lymphoid differentiation

value: day 7


title: CTR_BYL_3

value: CTRL


title: H1-CAR-D7 biol rep 2

description: 10x Genomics


title: NF1_Veh_1


title: H1-CAR-D4 biol rep 2

description: 10x Genomics

value: day 4


title: H1-CAR-D4 biol rep 1

description: 10x Genomics


title: F-1545_WT_P7_crx_RNA


title: CTR_BYL_2


title: H3K27me3, Col0, input, R2

value: mature endosperm


title: CTR_BYL_1


title: H1-CAR-D0 biol rep 1

description: 10x Genomics

value: day 0


title: M-1543_G34R_P7_crx_RNA

value: Male


title: H1-CAR-D0 biol rep 2

description: 10x Genomics


title: M-1542_WT_P7_crx_RNA


title: CTR_Veh_3

value: Breast cancer cells


title: H1-D7 biol rep 1

description: 10x Genomics

value: WT


title: CTR_Veh_2


title: H1-D4 biol rep 2

description: 10x Genomics


title: M-1540_G34R_P7_crx_RNA


title: H1-D4 biol rep 1

description: 10x Genomics


title: PDX7_shOPA1

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

description: PDX7_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal

hyb_protocol: cDNA were hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours, then washed on the fluidic station FS450 (Affymetrix)

scan_protocol: GCS3000 7G (Thermo Fischer Scientific)

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v20 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples.

label: biotin

source_name: PDX AML sample transduced with expression vector

label_protocol: 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit

growth_protocol: AML cells were cultured in minimum essential medium (MEM)-α Glutamax (Life Technology, Carlsbad, CA, USA) supplemented with bovine serum albumin (BSA, Sigma-Aldrich, Saint Louis, MO, USA), 100 IU/mL penicillin and 100 µg/mL streptomycin (Life Technology) at 37°C under a 5% CO2 atmosphere.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit)

tag: tissue source

value: patient with AML


title: PDX4_shOPA1

description: PDX4_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: F-1544_G34R_P7_crx_RNA

value: Female


title: G34R 10W_rep2_multiome_ATAC

description: 10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger ARC v2.0.0 (10x Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for the multiome samples.
Sequencing reads were aligned to the mm10 genome, coupled with the Gencode vM23 (Ensembl 98) gene annotation.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes and peaks), barcodes and expression matrices generated by Cell Ranger.

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
multiome (scRNA-seq + ATAC-seq)

value: cortex

value: 10 weeks old

value: M


title: PDX5_shCTL

description: PDX5_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal

value: shCTL


title: G34R 10W_rep1_multiome_ATAC

description: 10x Genomics


title: PDX7_shCTL

description: PDX7_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX5_shOPA1

description: PDX5_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: CAPTURE-3C-seq_HUDEP1_combined

last: Xu

data_processing:
Sequencing reads were aligned to human genome assembly hg38 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (https://eg.readthedocs.io/en/latest/text.html#longrange).
Assembly: hg38
Supplementary files format and content: Pairwise Interaction Format

source_name: HUDEP1 cells

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies) with 50 ng/ml SCF, 3 IU/ml EPO, 10-6 M dexamethasone, 1 ug/ml doxycycline, and passaged every three days.

extract_protocol:
10 ng of 3C DNA was processed for library generation using the NEBNext Ultra II DNA Library prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg38) were retained for downstream data analysis.
CAPTURE-3C-seq

treatment_protocol: HeLa cells were exposed to blue light (488nM) for 5 min to induce light-activated phase separation.

value: HUDEP1 cells


title: CAPTURE-3C-seq_HUDEP1_beta3


title: PDX4_shCTL

description: PDX4_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: H1-D0 biol rep 2

description: 10x Genomics

value: in vitro differentiated cells

value: human embryonic stem cell line-derived (H1 line)

value: in vitro differentiated lymphoid progenitors


title: H1-D7 biol rep 2

description: 10x Genomics

value: lymphoid differentiation

value: day 7


title: H1-D0 biol rep 1

description: 10x Genomics


title: MCF7_dEnh_ATAC_3

description: SOX2 enhancer-deleted replicate 3 [ATAC-seq]

data_processing:
Adapters were removed and reads were trimmed using FastP
Reads were aligned to hg38 using STAR 2.7
Bedgraphs were generated using bedtools 2
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
RNA-seq: Total RNA was extracted using Qiagen Rneasy mini kit and treated with Dneasy prior to library construction. ATAC-seq: Nuclei were isolated from tissues using gradient centrifugation as per the Omni-ATAC and were exposed to the transposase, Tn5, prior to llibrary construction.
RNA-seq libraries were prepared using standard Illumina TruSeq protocols. ATAC-seq libraries were prepared for sequencing using standard Illumina Novaseq 6000
riboRNA-depleted TruSeq stranded library was sequenced using Illumina HiSeq 2500 with 125bp paired-ended sequencing. ATAC-seq library was sequeced using Illumina Novaseq 6000 with 50bp paired-ended sequencing.

value: SOX2 enhancer-deleted

value: MCF-7 cells

value: breast adenocarcinoma


title: CAPTURE-3C-seq_HUDEP1_beta1


title: PDX3_shOPA1

description: PDX3_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: WT 10W_rep1_multiome_ATAC

description: 10x Genomics


title: M-1541_WT_P7_crx_RNA

value: Male

value: postnatal day 7


title: CTR_Veh_1

value: Breast cancer cells

value: CTRL

value: DMSO


title: MCF7_dEnh_ATAC_2

description: SOX2 enhancer-deleted replicate 2 [ATAC-seq]


title: CAPTURE-3C-seq_pFusNmutCL-HS2-Light_combined

source_name: HeLa cells

value: Human HeLa cells


title: G34R P7_rep1_multiome_ATAC

description: 10x Genomics

value: cortex

value: M


title: PDX2_shCTL

description: PDX2_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal

value: patient with AML

value: shCTL


title: WT P7_rep1_multiome_ATAC

description: 10x Genomics


title: CAPTURE-3C-seq_pFusNmutCL-HS2_Dark_rep2


title: G34R 10W_rep2_multiome_snRNA

description: 10x Genomics

value: 10 weeks old


title: MCF7_dEnh_ATAC_1

description: SOX2 enhancer-deleted replicate 1 [ATAC-seq]


title: MCF7_WT_ATAC_2

description: MCF-7 wild-type replicate 2 [ATAC-seq]

value: wild type


title: PDX1_shOPA1

description: PDX1_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: WT 10W_rep2_multiome_ATAC

description: 10x Genomics


title: CAPTURE-3C-seq_pFusNmutCL-HS2-Light-rep2


title: MCF7_WT_ATAC_3

description: MCF-7 wild-type replicate 3 [ATAC-seq]


title: G34R 10W_rep1_multiome_snRNA

description: 10x Genomics


title: CAPTURE-3C-seq_pFusNmutCL-HS2_Dark_combined


title: CAPTURE-3C-seq_pFusNmutCL-HS2_Dark_rep1


title: WT 10W_rep2_multiome_snRNA

description: 10x Genomics


title: PDX2_shOPA1

description: PDX2_shOPA1_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: CAPTURE-3C-seq_pFusNmutCL-HS2-Light-rep1


title: MCF7_WT_ATAC_1

description: MCF-7 wild-type replicate 1 [ATAC-seq]


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Light_combined


title: WT 10W_rep1_multiome_snRNA

description: 10x Genomics


title: PDX3_shCTL

description: PDX3_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal