title: BORIS-ko_SC_CTCF_ChIP-seq_INPUT

description: Chip-seq

data_processing:
For Ion torrent sequencing, RNA-seq FASTQ files were mapped to UCSC mouse reference (build mm9) using two-step alignments. First, the reads were aligned with TopHat2. Second, the unmapped reads from the first step are then extracted and aligned with Bowtie2 with –local mode and --very-sensitive-local option. For Illumina RNA-seq, FASTQ files were mapped to UCSC mouse reference (build mm9) using STAR with default settings.   Diferentyally expressed genes (DEG) were obtained with the R package DESeq2. The genes with an p-adjusted < 0.001 and Fold change > 2 were consider as significant differentially expressed genes. Chip-seq sequences generated by the Illumina genome analyzer (50bp reads) were aligned against mouse (build mm9) genome using Bowtie program (http://bowtie-bio.sourceforge.net).  The alignment was performed with default parameters except the sequence tags that mapped to more than one location in the genome were excluded from the analysis using –m1 option. Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (part of MACS) to call sub-peaks, summit of peaks and improve peak resolution
Genome_build: mm9
Supplementary_files_format_and_content: Peak bed files and wig files for Chip-seq. Total raw counts for RNA-seq

source_name: Mouse spermatocytes

extract_protocol:
Germ cells enriched preparations were prepared as follows. Decapsulated testes were treated with collagenase to digest interstitial tissue and release single tubules in suspension. The tubules were next treatment with trypsin to generate a germ cells enriched single cells suspension. The supernatants were then filtered in PVDF 100 um filter to discard tissue debris and washed with PBS. In order to obtain a better cell representation of the phenotypes observed, we included 4 different mice in each germ cells preparation. Spermatocytes and round spermatids were purified by centrifugal elutriation as described previously 3 followed by flow cytometric sorting of cells stained with Vybrant DyeCycle Green (Invitrogen, Carlsbad, CA) to obtain cell fractions with high purity. Briefly, decapsulated testes were treated with 1 mg/ml collagenase followed by treatment with 0.5 ug/ml trypsin, and the dissociated cells were used for centrifugal elutriation. Partially purified spermatocytes and the round spermatids fractions were incubated with 10 μM Vybrant DyeCycle Green for 30 min at 32°C followed by 4,6-diamidino-2-phenylindole (DAPI) staining. Cells were then sorted on a FACS-Aria (Becton Dickinson) to purify spermatocytes and round spermatids. DAPI-positive dead cells were eliminated. The purity of cells was confirmed by flow cytometry analysis of DNA content using sorted cells and by cell morphology analysis. The purification of round spermatids fraction was estimated to be approximately 93.7% ± 2.3%. The purification of spermatocytes was estimated to be approximately 81.5 ± 3.7%, based on the immunostaining with anti-SYCP3 abs. The expression of genes specific for spermatocytes and round spermatids was confirmed by RNA-seq.  For Chip-seq, germ cells enriched preparations were obtained as described before.  60 million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication. After overnight incubation with DiaMag magnetic beads (Diagenode, Inc.) and antibodies, precipitated chromatin was then washed, decrosslinked, and digested with proteinase K.  The resulting DNA was purified using phenol/chloroform/isoamyl alcohol. DNA concentration was assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries. For CTCF Chip-seq, we used an equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from cell signaling: anti-CTCF (07-727) from Millipore: anti-CTCF (70303) from Abcam: anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus. For Pol2 Chip-seq, we used the Anti-Pol2(4H8) antibodies from Abcam (ab5408). For H3K4m3 Chip-seq, we used the  Anti-H3 (tri methyl K4) antibodies from Abcam (ab8580)
For RNA-seq Ion Torrent libraries,  rRNA-depleted RNA from 3 independents germ cells preparations (4 mice in each preparation) was prepared using the RiboMinus Eukaryote System v2 kit (Life Technologies) according to the manufacture recommendations. For RNA-seq Ion Torrent libraries, 500 ng of rRNA-depleted RNA was used for library preparation using the Ion Total RNA-seq v2 kit. The enriched libraries were diluted to a final concentration of 11 pM and subjected to sequencing from a single end in Ion Proton Sequencer.For RNA-seq from spermatocytes and round spermatids, total RNA was extracted from cells using Trizol (Life Technologies) according to the protocol provided by the manufacturer. The RNA quality was assessed using the Agilent Bioanalyzer 2100. The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols with minor modifications. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM. Each sample was subjected to 75 cycles of sequencing from a single end in Illumina Hiseq2000 Sequencer.  ChIP DNA was amplified using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). Briefly, the immunoprecipitated material was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 15 cycles of PCR, and size selected (200–400 bp) followed by single end sequencing on an Illumina Genome Analyzer according to the manufacturer's recommendations.

tag: strain

value: Testis

tag: genotype

value: BORIS KO

value: 3 months

tag: chip-seq antibody

value: none (input)


title: BORIS-ko_SC_CTCF_ChIP-seq_Rep1

status: Public on Apr 22 2021

type: SRA

city: Washington

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

country: USA

institute: Children’s National Health System

description:
Chip-seq
koSC_CTCF_ChIP_Rep1_treat_pileup.bedgraph.gz

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: age

value: Equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from Cell signaling:anti-CTCF (07-727) from Millipore:anti-CTCF (70303) from Abcam:anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus.


title: BORIS-ko_SC_CTCF_ChIP-seq_Rep2

description:
Chip-seq
koSC_CTCF_ChIP_Rep2_treat_pileup.bedgraph.gz


title: P1_1_B05

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCm38.p5 genome assembly using STAR 2.6.1c with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.4
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

molecule: total RNA

source_name: Sciatic nerve

tag: technical run


title: P1_1_A18


title: P1_1_A17


title: WT_SC_CTCF_ChIP-seq

value: Equimolar mix of CTCF C-terminus commercial antibody were used (anti-CTCF B-5(sc-271514) and C-20 (sc-15914)) from Santa Cruz; Anti-CTCF (D3H2) from Cell signaling; anti-CTCF (07-727) from Millipore; anti-CTCF (70303) from Abcam; anti-CTCF (A300-543A) from Bethyl and anti-CTCF (NB500-177 and NB500-194) from Novus.


title: Input_WT_SC_ChIP-seq


title: DNase-seq from liver (ENCLB948JQS)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR765TON/
***************
biological replicate number: 1
technical replicate number: 2
description: DNase-seq for liver of C57BL/6J mice after 62 hr of constant darkness. Satchidananda et. al. Cell, Vol. 109, 307-320, May 3, 2002.
experiment encode accession: ENCSR765TON
assay title: DNase-seq
assembly: mm10
encode release date: 2018-12-22
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB948JQS

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain C57BL/6J adult (8-10 weeks) liver tissue treated with darkness for 62 hours

value: liver

value: tissue

tag: description

value: Liver from 8-10 week mice. Circadian Time 50

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: adult

value: 8-10 week

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: John Stamatoyannopoulos

tag: treatments

value: treatment_term_name:darkness; treatment_type:exposure; duration:62; duration_units:hour;

tag: link

value: ENCBS925YBW at ENCODE; https://www.encodeproject.org/ENCBS925YBW/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: P1_1_A16


title: P1_1_A20


title: DKO_SC_RNA-seq_Rep2

molecule: polyA RNA

value: Testis


title: DKO_SC_RNA-seq_Rep1


title: BORIS-ko_SC_RNA-seq_Rep2


title: P1_1_A14


title: P1_1_A15


title: BORIS-ko_SC_RNA-seq_Rep3


title: BORIS-ko_SC_RNA-seq_Rep1


title: P1_1_A12


title: P1_1_A13


title: CTCF_het_SC_RNA-seq_Rep3


title: WT_SC_RNA-seq_Rep2


title: P1_1_A11


title: CTCF_het_SC_RNA-seq_Rep1


title: WT_SC_RNA-seq_Rep1


title: P1_1_A10


title: DKO_RS_RNA-seq_Rep2

source_name: Mouse round spermatids


title: P1_1_A09


title: BORIS-ko_RS_RNA-seq_Rep3


title: BORIS-ko_RS_RNA-seq_Rep2


title: DKO_RS_RNA-seq_Rep3


title: DKO_RS_RNA-seq_Rep1


title: DKO_SC_RNA-seq_Rep3


title: P1_1_A08


title: CTCF_het_RS_RNA-seq_Rep3


title: BORIS-ko_RS_RNA-seq_Rep1


title: CTCF_het_RS_RNA-seq_Rep2


title: CTCF_het_RS_RNA-seq_Rep1


title: P1_1_A06


title: P1_1_A07


title: WT_RS_RNA-seq_Rep3


title: WT_RS_RNA-seq_Rep2


title: CTCF_het_SC_RNA-seq_Rep2


title: WT_RS_RNA-seq_Rep1


title: P1_1_A05


title: P1_1_A04


title: Case #16 sequencing sample

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

description: Mini-seq read counts combined from two sequencing runs

data_processing:
The adaptor sequence were removed from raw sequence reads. Then all the remaining sequence were clustered to show the most abundant sequence.
Supplementary_files_format_and_content: Tab-delimited text file containing raw read count values for individual samples if the raw read count values is equal or greater than 10.

organism: Homo sapiens

source_name: Case #16 RT-LAMP reaction

extract_protocol:
MagMAX Viral/Pathogen Nucleic Acid Isolation Kit to isolate saliva RNA
DNA sequencing libraries were prepared by PCR amplification of LAMP or RT-LAMP products with modified universal primers for Illumina sequencing

treatment_protocol: LAMP or RT-LAMP reactin products were amprified by PCR

tag: sample type

value: Patient Saliva


title: rna_rep12

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

data_processing:
Reverse reads containing the plasmid barcode were searched for exact match to a known barcode from the plasmid library with custom scripts.
Forward reads containing the spliced sequence were mapped to a variant-specific reference consisting of the POU1F1 exon trap reference sequence with the respective mutation introduced in silico, using GMAP (arguments “ -t 8 -f samse --microexon-spliceprob=1.0 --allow-close-indels=2”)
From the spliced reads, an isoform catalog was tallied requiring each isoform to be represented by at least three distinct barcodes and nine reads.  Spliced reads associated with each barcode were tallied to produce per-barcode isoform usage counts, and percent spliced in (PSI) fractions.  Barcodes corresponding to the same POU1F1 variant were then aggregated (weighted by the number of reads obtained) to generate for each variant a mean PSI score for all known isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: Per-barcode file contains one row per splice reporter barcode; columns indicate for each replicate, count of reads mapping to each isoform (ALPHA,BETA,SKIP,OTHER) and resulting PSI values.  Per-variant file contains one row per tested variant, with annotations (e.g., genomic position, coding consequence),  columns indicating overall splice disruptiveness (sdv) and per-isoform calls (sdv_ISOFORM). For each replicate, the number of barcodes detected (_n_bc), number of valid reads (_sum_reads_passfilt), weighted means for each isoform (_wmean_ISOFORM), fold change for each isoform over background (_fc_ISOFORM) and corresponding z-scores (_zwmean_ISO) are indicated.   Barcode-variant pairing file contains a barcode plus comma-separated list of mutation(s) present on the associated haplotype, each encoded as seqname:position:ref:alt.

organism: Chlorocebus aethiops

source_name: COS-7 fibroblast-like line

growth_protocol: COS-7 cells were plated at 5e6 cells/60mm plate, and maintained in DMEM with 10% FBS and pen-strep.

extract_protocol:
Total RNA was purified with the RNeasy kit at 24 hrs post-transfection
5 ug of total RNA was used to prepare first-strand cDNA using the SuperScript III First-Strand Synthesis kit (Invitrogen) with oligo dT primers.  Spliced transcript was amplified using nested PCR, initially for 6 cycles using the SD6F/SA2R primers, followed by 20 cycles using primers SD2F/jklab0046. Paired-end Illumina sequencing libraries were generated by tailing PCR (6 cycles) with a forward primer within the constant upstream exon and a reverse primer immediately downstream of the N20 barcode. Unique dual i5/i7 indices were added by a second round of tailing PCR (6 cycles), and the resulting products were purified by SPRI bead cleanup.

treatment_protocol: Cells were transfected with plasmid libraries using ViaFect reagent (3:1 ratio to plasmid DNA).

tag: replicate


title: P1_1_A03


title: rna_rep06


title: P1_1_A01


title: rna_rep05


title: P1_1_A02


title: rna_rep08


title: 4_nmSC

tag: subject


title: rna_rep07


title: rna_rep03


title: rna_rep02


title: rna_rep04


title: rna_rep01


title: rna_rep00


title: 4_mSC


title: 4_all


title: rna_rep10


title: rna_rep11


title: 3_mSC


title: rna_rep09


title: 3_all


title: 3_nmSC


title: 2_nmSC


title: rna_rep13


title: mRNA-CK-Rep1

city: Ningbo

first: Cui

last: Weijun

address: Fenghua Road No. 818

country: China

institute: Ningbo University

data_processing:
Genome_build: N. benthamiana Genome transcripts v0.4.4 (ftp.solgenomics.net/genomes/Nicotiana_benthamiana)
mRNA-Seq: Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using in-house ACGT101(1.4) software. Clean reads were aligned to the N. benthamiana Genome transcripts v0.4.4 reference genome using the Bowtie package.Differential gene expression analysis were performed using ACGT101_DESeq(1.4). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam. Unique sRNA sequences were then obtained for each library. The sRNA sequence were mapped to the RSV genomic sequences to obtain RSV-derived siRNA with Botwtie.
Degradome-Seq: The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.1. Get some degradome data (RNA-seq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences. Map the degradome reads to the appropriate transcriptome using appropriate thresholds.Filter the mapped data, if required. Summarize the mapped degradome data into a "degradome density file" using script 'CleaveLand3_map2dd.pl'.Generate small RNA / mRNA alignments using 'targetfinder.pl'. Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t--plots" of the targets using script 'CleaveLand3_t-- plotter.pl'.The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Supplementary_files_format_and_content: transcript_expression_all.txt: tab-delimited text files include FPKM values of transcript for each Sample
RSV_derived small RNA_expression_all.txt: tab-delimited text files include TPM values of RSV-derived small RNA for each Sample
degradome_density_output.txt: tab-delimited text files include density values of genes (gene identifiers can be searched at ftp://ftp.solgenomics.net/genomes/Nicotiana_benthamiana/annotation/Niben044/Niben.genome.v0.4.4.transcripts.fasta)

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: N. bentamiana plants were grown in a greenhouse at 23–25 °C, with a 16-h day/ 8-h night light cycle under well-watered conditions.

extract_protocol:
Six transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit(Directional mRNA-Seq Sample Preparation Part # 15018460 Rev. A, October 2010.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

treatment_protocol: N. benthamiana plants at the six-leaf stage were mechanically inoculated with crude extracts from RSV-infected rice leaves.

value: 7 days infection

tag: treatment

value: Mock inoculated

value: wild type


title: sRNA-CK-Rep1

description:
small RNA
RSV_derived small RNA_expression_all.txt

data_processing:
Genome_build: RSV genome sequence (Sequence ID：DQ333941.2,DQ333942.2,DQ333943.2,DQ333944.2)
mRNA-Seq: Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using in-house ACGT101(1.4) software. Clean reads were aligned to the N. benthamiana Genome transcripts v0.4.4 reference genome using the Bowtie package.Differential gene expression analysis were performed using ACGT101_DESeq(1.4). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam. Unique sRNA sequences were then obtained for each library. The sRNA sequence were mapped to the RSV genomic sequences to obtain RSV-derived siRNA with Botwtie.
Degradome-Seq: The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.1. Get some degradome data (RNA-seq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences. Map the degradome reads to the appropriate transcriptome using appropriate thresholds.Filter the mapped data, if required. Summarize the mapped degradome data into a "degradome density file" using script 'CleaveLand3_map2dd.pl'.Generate small RNA / mRNA alignments using 'targetfinder.pl'. Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t--plots" of the targets using script 'CleaveLand3_t-- plotter.pl'.The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Supplementary_files_format_and_content: transcript_expression_all.txt: tab-delimited text files include FPKM values of transcript for each Sample
RSV_derived small RNA_expression_all.txt: tab-delimited text files include TPM values of RSV-derived small RNA for each Sample
degradome_density_output.txt: tab-delimited text files include density values of genes (gene identifiers can be searched at ftp://ftp.solgenomics.net/genomes/Nicotiana_benthamiana/annotation/Niben044/Niben.genome.v0.4.4.transcripts.fasta)

extract_protocol:
The six small RNA library was generated from the customer sample using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

tag: genotype


title: sRNA-CK-Rep3


title: mRNA-CK-Rep3


title: sRNA-CK-Rep2


title: 2_all


title: 2_mSC


title: 1_mSC


title: ATAC-seq from left cardiac atrium (ENCLB343XPV)

description:
https://www.encodeproject.org/experiments/ENCSR731ODJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR731ODJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB343XPV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (58 years) left cardiac atrium tissue, preserved by cryopreservation

value: left cardiac atrium

value: female

value: 58 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: health state

value: Ischemic cardiomyopathy

value: ENCBS987LUL at ENCODE; https://www.encodeproject.org/ENCBS987LUL/

value: Derived from ENCODE donor ENCDO719HSJ; https://www.encodeproject.org/ENCDO719HSJ/


title: ATAC-seq from left cardiac atrium (ENCLB209VBU)

description:
https://www.encodeproject.org/experiments/ENCSR731ODJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR731ODJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB209VBU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

value: adult


title: ATAC-seq from right cardiac atrium (ENCLB836MQU)

description:
https://www.encodeproject.org/experiments/ENCSR452OSK/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR452OSK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB836MQU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (40 years) right cardiac atrium tissue, preserved by cryopreservation

value: right cardiac atrium

value: male

value: 40 year

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no

value: ENCBS032QTQ at ENCODE; https://www.encodeproject.org/ENCBS032QTQ/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: P60_3

extract_protocol:
PolyA, TruSeq RNA Kit
TruSeq RNA stranded

tag: tissue

value: Sciatic nerve

tag: developmental stage


title: P60_4


title: P5_2


title: mRNA-CK-Rep2

tag: age

value: 7 days infection

value: Mock inoculated

value: wild type


title: P60_2


title: P5_3


title: 1_all


title: P5_1


title: P24_2


title: ATAC-seq from heart right ventricle (ENCLB102CJI)

description:
https://www.encodeproject.org/experiments/ENCSR212LYK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR212LYK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB102CJI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (46 years) heart right ventricle tissue, preserved by cryopreservation

value: heart right ventricle

value: female

value: 46 year

value: Michael Snyder, Stanford

value: DM:no; HTN:no; CAD:no

value: ENCBS205MTD at ENCODE; https://www.encodeproject.org/ENCBS205MTD/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: P24_4


title: ATAC-seq from heart right ventricle (ENCLB801XWC)

description:
https://www.encodeproject.org/experiments/ENCSR212LYK/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR212LYK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB801XWC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

value: adult


title: 1_nmSC


title: P1_3


title: P1_4


title: P24_3


title: P1_1


title: MEK(SS218/222DD) HEK_PMA+MEKinhibitor_C12

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.
Transcript level quantitation was performed using Salmon v 0.7.2 and Human gene models from Ensembl build 96
Gene level expression level was computed by summing read counts by gene ID and dividing by total millions of mapped reads
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon QuantSeq (quant.sf) files tab-delimited files indexed by Ensembl transcript ID and contain transcript counts, gene length and TPM normalized values

source_name: cultured cell line

growth_protocol: HEK 293 cell lines were grown in complete DMEM with 10% FBS in 6-well cell culture dishes to a confluency of 70% prior to treatment

extract_protocol:
Total RNA was isolated from treated cells using PureLink™ RNA Mini Kit (ThermoFisher. Cat: 1218300).
Lexogen 3' QuantSeq Kit was used for library construction

treatment_protocol: Cells were pretreated for 2 hours with vehicle (0.1% DMSO) or 5 uM MEK inhibitor then subjected to the following treatments prior to immediate RNA isolation: 36 hours untreated, 36 hours 500 ng/ml doxycycline, or 36 hours 50 ng/ml PMA with four biological replicates each.

tag: strain

value: MEK(SS218/222DD) HEK

value: PMA+MEKinhibitor

tag: treatment duration

value: 36 hrs


title: MEK(SS218/222DD) HEK_PMA+MEKinhibitor_G12


title: P14_2


title: P1_2


title: P5_4


title: MEK(SS218/222DD) HEK_PMA_G11

value: PMA


title: P14_1

value: Sciatic nerve


title: MEK(SS218/222DD) HEK_PMA+MEKinhibitor_E12


title: MEK(SS218/222DD) HEK_PMA+MEKinhibitor_A12


title: P60_1


title: P14_3


title: MEK(SS218/222DD) HEK_PMA_C11


title: MEK(SS218/222DD) HEK_PMA_A11


title: E17_2


title: MEK(SS218/222DD) HEK_None_C7


title: E17_4


title: E17_3


title: MEK(SS218/222DD) HEK_None_A7


title: E17_1


title: ATAC-seq from lung (ENCLB812SRE)

description:
https://www.encodeproject.org/experiments/ENCSR647AOY/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human lung
experiment encode accession: ENCSR647AOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB812SRE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) lung tissue, preserved by cryopreservation

value: lung

tag: biosample encode accession

tag: Sex

value: 47 year

value: Yiing Lin, MD, PhD

value: DM:yes; HTN:yes; CAD:no

value: ENCBS139TKF at ENCODE; https://www.encodeproject.org/ENCBS139TKF/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: ATAC-seq from lung (ENCLB189BJR)

description:
https://www.encodeproject.org/experiments/ENCSR647AOY/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human lung
experiment encode accession: ENCSR647AOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB189BJR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: female

tag: dev stage

tag: lab

value: Michael Snyder, Stanford


title: E13_4


title: MEK(SS218/222DD) HEK_None_E7


title: P14_4


title: P24_1


title: E13_3


title: MEK(SS218/222DD) HEK_PMA_E11


title: MEK(SS218/222DD) HEK_None_G7


title: MEK(SS218/222DD) HEK_MEKinhibitor_G10

value: MEKinhibitor


title: E13_2


title: E13_1


title: MEK(SS218/222DD) HEK_MEKinhibitor_A10


title: MEK(SS218/222DD) HEK_MEKinhibitor_C10


title: MEK(SS218/222DD) HEK_doxycycline+MEKinhibitor_A9

value: doxycycline+MEKinhibitor


title: MEK(SS218/222DD) HEK_doxycycline+MEKinhibitor_E9


title: MEK(SS218/222DD) HEK_doxycycline+MEKinhibitor_C9


title: ATAC-seq from heart left ventricle (ENCLB660OSN)

description:
https://www.encodeproject.org/experiments/ENCSR846VPV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR846VPV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB660OSN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (66 years) heart left ventricle tissue, preserved by cryopreservation

value: heart left ventricle

value: tissue

value: 66 year

tag: source

value: Shin Lin

value: Chemo-induced cardiomyopathy

value: ENCBS757XQK at ENCODE; https://www.encodeproject.org/ENCBS757XQK/

value: Derived from ENCODE donor ENCDO255XON; https://www.encodeproject.org/ENCDO255XON/


title: ATAC-seq from heart left ventricle (ENCLB836NPL)

description:
https://www.encodeproject.org/experiments/ENCSR846VPV/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR846VPV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB836NPL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult

tag: link


title: MEK(SS218/222DD) HEK_doxycycline_A8

value: MEK(SS218/222DD) HEK

value: doxycycline

value: 36 hrs


title: MEK(SS218/222DD) HEK_doxycycline+MEKinhibitor_G9


title: siRNA Mop1-1/mop1-1 rep1

city: Montpellier

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

data_processing:
bowtie1 (v1.2.2) was used with lastest version of maize genome (V5), with parameters --best -k 2 -5 4 , and -m 7 - q --strata --best -v 2 for the tandem repeats.
Reads were then intersected into 0.5 Mb genome windows using bedtools coverage, and 50bp for the tandem repeats
Bedtools genome coverage was used for conversion to BED files
Genome_build: Zm-B73-REFERENCE-NAM-5.0.fa
Supplementary_files_format_and_content: bed files (they represent the siRNA profiles for the 7 tandem repeats upstream of the b1 gene)
Ago104_25.coverage.bed (25 n.t. siRNAs)
Ago104_24.coverage.bed (24 n.t. siRNAs)
Ago104_23.coverage.bed (23 n.t siRNAs)
Ago104_22.coverage.bed (22 n.t siRNAs)
Ago104_21.coverage.bed (21 n.t siRNAs)
Ago105_25.coverage.bed (25 n.t siRNAs)
Ago105_24.coverage.bed (24 n.t siRNAs)
Ago105_23.coverage.bed (23 n.t siRNAs)
Ago105_22.coverage.bed (22 n.t siRNAs)
Ago105_21.coverage.bed (21 n.t siRNAs)

organism: Zea mays

source_name: immature ears

extract_protocol:
Protocols were adapted from Havecker et al. (2010) using two biological replicates per genotype. Tissues were ground with liquid nitrogen and a Dounce homogenizer. Resulting powder was placed in a Falcon tube with 3 volumes of Extraction buffer (20 mM Tris HCL pH 7.5, 5 mM MgCl2, 300 mM NaCl, 0.1% NP-40, 5 mM DTT, 1% protease inhibitor (Roch Tablet), 100 units/mL RNase OUT (invitrogen)). Samples were vortexed, kept on ice 30 minutes with recurrent shaking, and centrifuged 30 minutes at 4°C, 4000 rpm. Supernatants were filtered through a 0.45µm Miracloth into a new Falcon tube, and 1 mL and aliquoted and stored at -20°C as a pre-experiment input sample. In the remaining samples, 1.5 mL aliquots were generated, and we added 5 µg of antibodies per gram of tissue. They were incubated overnight at 4°C on a rotation wheel. Magnetic beads (Dynabeads, Life technologies) were washed 3 times in Wash buffer (20 mM Tris HCL pH 7.5, 5 mM MgCl2, 300 mM NaCl, 0.1% NP-40, 1% protease inhibitor (Roch Tablet), 100 units/mL RNase OUT (invitrogen)). 80 µL of washed beads were added to each sample, and incubated on rotation wheel for 3 hours at 4°C. Beads from the samples were washed 3 times in Wash buffer, and resuspended in 500 µL. 100 µL was aliquoted and stored at -20°C for the western blot control. Wash buffer was discarded and replaced by 250 µL of Elution buffer (100 mM NaHCO3, 1% SDS, 100 units/mL RNase OUT (Invitrogen)), and tubes incubated overnight at 65°C with agitation. Supernatant was transferred to fresh tubes, 250 µL of Elution buffer was added, and the tubes incubated 15 minutes at 65°C with agitation. Samples were treated with 0.08 µg/µL proteinase K for 15 minutes at 45°C. RNAs were extracted following the recommendations from Applied Biosystems for TRI Reagent® Solution, starting by adding 1.2 mL of TRI Reagent to the samples
The RIP antibodies we used were all home-made by EUROGENTEC.  AGO104: SERICKEQTFPLRQR.  AGO105: VGQFIKFDEMSETS.
NEBNext Small RNA Library Prep Set for Illumina

value: siRNA Mop1-1/mop1-1

value: immature ears

tag: rip antibodies


title: siRNA mop1-1/mop1-1 rep1

value: siRNA mop1-1/mop1-1


title: siRNA B73 rep2

value: siRNA control


title: MEK(SS218/222DD) HEK_doxycycline_G8


title: siRNA mop1-1/mop1-1 rep2


title: MEK(SS218/222DD) HEK_doxycycline_C8


title: siRNA B73 rep1


title: siRNA ago104 rep2

value: siRNA ago104


title: E2f7/8/Rb1 TKO tumor 4

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

country: Netherlands

institute: Utrecht University

description: TKO tumor j2

data_processing:
Sequencing reads were mapped against the reference genome (mm9, NCBI37) using BWA (-c –l 25 –k 2 –n 10) software (Li and Durbin, 2009).
Raw counts were generated using featureCounts for all Entrez annotated genes.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: raw_count_matrix.txt: Tab-delimited text file of raw counts; row names are Entrez IDs.

source_name: spontaneous liver tumor

growth_protocol: Livers and tumors were harvested from ageing mice in an end-of life study. Mice were euthanized by an observer unaware of the genotype when general health appearance deteriorated to such extent that pre-defined humane end-points were reached.

extract_protocol:
Livers and tumors were extracted from the euthanized mouse, cut into small tissue pieces, and immediately snap-frozen in liquid nitrogen.
Total RNA was isolated from livers using the RNeasy kit (Qiagen). mRNA was isolated using a poly (A) purist MAG kit (Life Technologies, AM 1922) and purified with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre). Transcriptome libraries were then constructed using SOLiD total RNA-seq kit (Applied Biosystems Life Technologies).

value: liver tumor

value: Alb-Cre-Rb1 E2f7 E2f8 knockout


title: siRNA Mop1-1/mop1-1 rep2


title: MEK(SS218/222DD) HEK_doxycycline_E8


title: E2f7/8/Rb1 TKO tumor 3

description: TKO tumor i1


title: KRAS(G12D) HEK_PMA+MEKinhibitor_A6

value: KRAS(G12D) HEK

value: PMA+MEKinhibitor


title: MEK(SS218/222DD) HEK_MEKinhibitor_E10

value: MEKinhibitor


title: E2f7/8/Rb1 TKO tumor 1

description: TKO tumor e4


title: E2f7/8/Rb1 TKO tumor 2

description: TKO tumor h1


title: E2f7/8 DKO tumor 3

description: DKO tumor j5

value: Alb-Cre-E2f7 E2f8 knockout


title: KRAS(G12D) HEK_PMA+MEKinhibitor_E6


title: KRAS(G12D) HEK_PMA+MEKinhibitor_G6


title: E2f7/8 DKO tumor 2

description: DKO tumor b4


title: E2f7/8 DKO tumor 1

description: DKO tumor a1


title: KRAS(G12D) HEK_PMA_E5

value: PMA


title: Adult wild-type liver 4

description: control liver j6

source_name: adult liver

value: control liver

value: wild-type


title: KRAS(G12D) HEK_PMA_G5


title: ATAC-seq from Right ventricle myocardium superior (ENCLB679DQO)

description:
https://www.encodeproject.org/experiments/ENCSR074WMH/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right ventricle myocardium superior
experiment encode accession: ENCSR074WMH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB679DQO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium superior tissue, preserved by cryopreservation

value: Right ventricle myocardium superior

value: tissue

tag: description

value: Superior wall of right ventricle.

value: male

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: ENCBS306BLW at ENCODE; https://www.encodeproject.org/ENCBS306BLW/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: ATAC-seq from Right ventricle myocardium superior (ENCLB745UIH)

description:
https://www.encodeproject.org/experiments/ENCSR074WMH/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right ventricle myocardium superior
experiment encode accession: ENCSR074WMH
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB745UIH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000


title: KRAS(G12D) HEK_PMA_A5

value: KRAS(G12D) HEK

value: 36 hrs


title: Adult wild-type liver 3

description: control liver e6


title: KRAS(G12D) HEK_None_A1


title: KRAS(G12D) HEK_None_E1


title: Adult wild-type liver 2

description: control liver e1


title: KRAS(G12D) HEK_None_C1


title: Adult wild-type liver 1

description: control liver b3


title: KRAS(G12D) HEK_PMA_C5


title: 60min_rap10min

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

data_processing:
bowtie2 v.2.2.9 was used to align FASTQ files to the S. cerevisiae reference genome (SGD, R64-2-1,). samtools (1.3.1) was used to sort and select reads with MAPQ score ≥40. BEDPE files were generated using bedtools v.2.26.0.
Genome_build: S. cerevisiae S288C, build R64-2-1, released 18 Nov 2014
Supplementary_files_format_and_content: BEDPE files are headerless text files that contain the following tab-delimited columns: mate1 chromosome, mate1 5'-position, mate1 3'-position, mate2 chromosome, mate2 5'-position, mate2 3'-position, mate1 read identifier, MAPQ score, mate1 strand, mate2 strand

organism: Saccharomyces cerevisiae

growth_protocol: Cultures were grown to log phase and arrested with alpha factor at 30C in YPD and released into YPD media at 30C for the indicated time and then treated with 1ug/mL rapamycin to deplete DNA ligase for the indicated time (5 or 10min).

extract_protocol:
Okazaki fragments were enriched by sequential elutions from ion exchange columns as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438).
Libraries were constructed as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438) with the following changes: after adaptor ligation, samples were cleaned using a PCR purification kit (GeneJET, ThermoFisher) instead of S-300 columns, and second-strand synthesis was carried out by Taq polymerase (NEB) at 50C. Libraries were purified using magnetic beads (HighPrep PCR Clean-up, MagBio) before and after amplification.

value: Lab strain DS131

tag: strain background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX

tag: genotypic variation

value: S-phase release 60min, 10 min rapamycin

tag: protocol

value: Okazaki fragment sequencing


title: 60min_rap5min

tag: treatment

value: S-phase release 60min, 5 min rapamycin


title: 50min_rap5min

value: S-phase release 50min, 5 min rapamycin


title: 40min_rap10min

value: S-phase release 40min, 10 min rapamycin


title: 40min_rap5min

value: S-phase release 40min, 5 min rapamycin


title: KRAS(G12D) HEK_MEKinhibitor_G4

value: MEKinhibitor


title: KRAS(G12D) HEK_doxycycline+MEKinhibitor_E3

value: doxycycline+MEKinhibitor


title: KRAS(G12D) HEK_doxycycline+MEKinhibitor_G3


title: 30min_rap5min

value: S-phase release 30min, 5 min rapamycin


title: KRAS(G12D) HEK_PMA+MEKinhibitor_C6

value: PMA+MEKinhibitor


title: E2f7/8 DKO tumor 4

description: DKO tumor k1

tag: tissue

value: liver tumor

tag: genotype

value: Alb-Cre-E2f7 E2f8 knockout

value: adult


title: 30min_rap10min

value: S-phase release 30min, 10 min rapamycin


title: KRAS(G12D) HEK_None_G1

value: KRAS(G12D) HEK

value: 36 hrs


title: KRAS(G12D) HEK_MEKinhibitor_A4


title: 25min_rap10min

value: Lab strain DS131

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX

value: S-phase release 25min, 10 min rapamycin


title: KRAS(G12D) HEK_MEKinhibitor_C4


title: KRAS(G12D) HEK_doxycycline+MEKinhibitor_A3


title: 25min_rap5min

value: S-phase release 25min, 5 min rapamycin

value: Okazaki fragment sequencing


title: asynchronous_rap60min

growth_protocol: Cultures were grown to log phase and treated for the indicated time with 1ug/mL rapamycin to deplete DNA ligase

value: Lab strain DS1062

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX, POL3-IAA17(71-116)-9xmyc::KanMX6

value: asynchronous, 60 min rapamycin


title: KRAS(G12D) HEK_doxycycline+MEKinhibitor_C3

value: doxycycline+MEKinhibitor


title: KRAS(G12D) HEK_doxycycline_C2

value: doxycycline


title: 50min_rap10min

value: S-phase release 50min, 10 min rapamycin


title: KRAS(G12D) HEK_MEKinhibitor_E4

value: MEKinhibitor


title: KRAS(G12D) HEK_doxycycline_G2


title: continuousRap_100min

growth_protocol: Cultures were grown to log phase and arrested with alpha factor at 30C in YPD followed by a 1h treatment with 1ug/mL rapamycin to deplete DNA ligase before release into media containing rapamycin at room temperature for the indicated time.

value: Lab strain DS1086

value: S-phase release 100min, continuous rapamycin


title: KRAS(G12D) HEK_doxycycline_A2


title: HA24_1

city: Muenster

first: Maria

middle: V

last: Yusenko

address: Wilhelm-Klemm-Str. 2

department: Institute of Biochemistry

country: Germany

institute: University of Muenster

data_processing:
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled.
Trimmomatic (v. 038) was used for adapter trimming and read filtering.  (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
The resulted reads were aligned to the  hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9)
The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1;  Parameter: --minaqual 0,  --stranded reverse)
Testing for differential expression was performed using DESeq2 r-package (v. 1.22.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium containing 10% FBS and 5% L-Glut

extract_protocol:
Total RNA was harvested using Trizol reagent.
NEBNext Ultra Directional RNA II Library Prep kit  was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 500 System and NextSeq v2 sequencing reagent kit in a single read-mode with a read-length of 75 bp.

treatment_protocol: The cells were left untreated or treated with 1 µM AT or 0.5 µM HA for 24 hours. All experiments were done in triplicate.

tag: disease state

value: acute monocytic leukemia

tag: cell line

value: 0.5 µm HA for 24 hours


title: HA24_2


title: HA24_3


title: continuousRap_60min

tag: strain

value: S-phase release 60min, continuous rapamycin


title: continuousRap_70min

value: S-phase release 70min, continuous rapamycin


title: continuousRap_65min

value: S-phase release 65min, continuous rapamycin


title: AT24_3

value: 1 µm AT for 24 hours


title: AT24_1


title: HA5-Early_Lsd1_P1_CUT&RUN

city: Paris

first: Marina

last: Pinskaya

address: rue d'Ulm

institute: Institut Curie

data_processing:
Library strategy: CUT&RUN
mapping with Bowtie2 (bowtie2 -I 10 -X 700 –no-mixed)
filtering reads (samtools view -q 30 --F 0x100 -F 0x800)
peak calling HMCan (smallBinLength : 50, largeBinLength : 25000, pvalueThreshold : 0.01, PosteriorProb : 0.7, CNAnormalization : False, RemoveDuplicates : False, pairedEnds : True,  iterationThreshold : 5, finalThreshold : 0, maxIter : 20 )
peak calling EPIC2 (--keep-duplicates –chromsizes [file with chromosome size, from chrI to chrM – no scaffolds])
merging replicates peaks for each condition, for a given histone mark/protein (bedtools merge)
merging peaks of all strain, for a given histone mark/protein (bedtools merge)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited file (GFF format), genomic location of peaks, and the strain(s) in which they were called

source_name: randomly integrated HOTAIR cDNA deleted for the first 300 bp by lentiviral transduction of HA5-Early cell line (PMID: 23358853)

growth_protocol: Cells were grown up to 90% confluence in 100 cm² petri plate in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol: ChIP-seq libraries were prepared with TruSeq ChIP Sample Prep Kit (IP-202-1012, Illumina)

treatment_protocol:
CUT&RUN protocol (Skene et al 2018); Antibodies: H3K27ac (Millipore, ref MABE647, lot VP1910310); H3K4me2 (Millipore, ref 07-030, lot DAM1503382); H3K9me2 (Active Motif, ref 39239, lot 34718002); Lsd1 (Diagenode, ref C15410067, lot A57-00234P); IgG (Invitrogen, ref 31235, lot UJ2871342). Detailed protocol: For each cell line two biological replicates were used. Cells were grown up to 90% confluence in 10 cm² petri plate in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.
For histone marks cells were scrapped from plates collected by centrifugation. Pellets were resuspended in media with 10% DMSO, slowly frozen and kept at -80°C. For CUT&RUN experiment, cells were quickly thawed in 37°C and collected by centrifugation. For Lsd1, and IgG we proceeded directly with fresh cells scrapped from culture dishes and collected by centrifugation.
Cell pellets were resuspended in Wash buffer and washed twice before resuspending in volume 10^6 cells/100 µl. For each IP sample, 100 µl of cell suspension were aliquoted to 900 µl of Wash Buffer in 1.5ml eppendorf tube containing 10 µl of Concanavalin A beads (Epicypher) previously washed in Bead activation buffer (20mM HEPES pH 7.9, 10mM KCl,1mM CaCl2, 1mM MnCl2).  Cells were incubated with beads for 10 min with rotation at 15-20 rpm at room temperature (RT). Beads were separated from supernatant on a magnetic stand and resuspended in 50 µl of the antibody diluted in Antibody buffer (wash buffer with 0,1% digitonin and 2mM EDTA) (1:100 dilution for all antibodies and 1:1100 for IgG control). The beads were incubated with subtle agitation for 10 min for histone marks and 1h for Lsd1, Ezh2 and IgG antibodies at RT. Afterwards the beads were washed twice with Digitonin buffer (Wash buffer with 0,1% digitonin) and resuspended in pAG-MNase (CUTANA Epicypher) diluted 20 times in Digitonin buffer. After 10 min incubation with slight agitation at RT, beads were washed twice and resuspended in Digitonin buffer and chilled to 0°C (ice) for 5 min.  To activate MNase, 2 µl of 100 mM CaCl₂ were added and incubated for additional 30 min on ice. To stop the reaction, 100 µl of Stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/ml RNase A, 50ug/ml Glycogen, 0.1% Digitonin, 10 pg/ml Spike-in DNA) was added and beads were incubate for 10 min at 37°C followed by centrifugation at 16k rcf at 4°C for 5 min. The supernatant was recovered and DNA fragments were purified using NEB Monarch PCR & DNA purification kit with protocol enriching for short DNA fragments. DNA quantity was analyzed using Qubit HS DNA kit.

value: P


title: HA5-Early_Lsd1_L2_CUT&RUN

source_name: randomly integrated HOTAIR cDNA deleted for the last 500 bp by lentiviral transduction of HA5-Early cell line (PMID: 23358853)

value: L


title: HA5-Early_Lsd1_H1_CUT&RUN

source_name: randomly integrated HOTAIR cDNA by lentiviral transduction of HA5-Early cell line (PMID: 23358853)

value: H


title: HA5-Early_Lsd1_H2_CUT&RUN


title: HA5-Early_Lsd1_P2_CUT&RUN


title: continuousRap_75min

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX, POL3-IAA17(71-116)-9xmyc::KanMX6

value: S-phase release 75min, continuous rapamycin

value: Okazaki fragment sequencing


title: HA5-Early_Lsd1_L1_CUT&RUN


title: HA5-Early_H3K27ac_L2_CUT&RUN


title: THP0_5

value: no exposure


title: HA5-Early_Lsd1_G2_CUT&RUN

source_name: randomly integrated GFP cDNA by lentiviral transduction of HA5-Early cell line (PMID: 23358853)

value: G


title: KRAS(G12D) HEK_doxycycline_E2

value: KRAS(G12D) HEK

value: doxycycline

tag: treatment duration

value: 36 hrs


title: asynchronous_rap5min

value: Lab strain DS131

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX

value: asynchronous, 5 min rapamycin


title: continuousRap_45min

value: Lab strain DS1086

value: S-phase release 45min, continuous rapamycin


title: THP0_3

value: acute monocytic leukemia


title: asynchronous_rap10min

value: asynchronous, 10 min rapamycin


title: continuousRap_50min

value: S-phase release 50min, continuous rapamycin


title: HA5-Early_H3K27ac_L1_CUT&RUN

value: L


title: HA5-Early_H3K27ac_P2_CUT&RUN

value: P


title: continuousRap_80min

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::HygMX, POL3-IAA17(71-116)-9xmyc::KanMX6

value: S-phase release 80min, continuous rapamycin


title: AT24_2

value: 1 µm AT for 24 hours


title: continuousRap_55min

value: S-phase release 55min, continuous rapamycin

value: Okazaki fragment sequencing


title: HA5-Early_Lsd1_G1_CUT&RUN

value: G


title: HA5-Early_H3K27ac_P1_CUT&RUN


title: continuousRap_40min

value: S-phase release 40min, continuous rapamycin


title: HA5-Early_H3K27ac_H2_CUT&RUN

value: H


title: THP0_2

value: no exposure


title: HA5-Early_H3K27ac_H1_CUT&RUN


title: continuousRap_35min

value: S-phase release 35min, continuous rapamycin


title: HA5-Early_H3K27ac_G1_CUT&RUN


title: continuousRap_30min

value: Lab strain DS1086

value: S-phase release 30min, continuous rapamycin


title: HA5-Early_H3K9me2_L2_CUT&RUN


title: HA5-Early_H3K9me2_L1_CUT&RUN


title: HA5-Early_H3K27ac_G2_CUT&RUN


title: XS28e.None.Vector.Second.p8

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
The sequencing reads were mapped to hg38 reference using star/2.5.3a. Gene expression counts were further estimated using ESAT v1. Normalization was further applied as counts per million total reads. The mean of 3-5 replicates per evolution time-point sample was calculated based on the normalized counts and was used for calculating fold changes between samples.
Genome_build: hg38
Supplementary_files_format_and_content: integer count data in txt format

source_name: Human Mesencymal Progenitor

growth_protocol: Human mesenchymal progenitor cells were grown in the alpha-MEM medium (Gibco) supplemented with 10% FBS (HyClone FBS, Thermo Fisher Scientific) and Pen/Strep/Glutamine ( on 15-cm cell culture dishes (Corning); Cells from each growth timepoint were harvested by using 0.25% trypsin in a versene solution on the same day of each proliferation analysis timepoint.

extract_protocol:
Total RNA are exacted using RNeasy Mini Kit (Qiagen).
Standard Nextera tagmentation substituting P5NEXTPT5-bmc primer

treatment_protocol: Doxycycline was used for induction of Tet-on promoter at 1 µg/mL and the medium was changed every two days to ensure the efficacy of Doxycycline.

value: Human mesenchymal progenitor (hMPro cells)

tag: lentiviral library

tag: oncogene

value: Vector

tag: evolution experiment

value: Second

tag: passage


title: XS28c.None.Vector.Second.p8


title: Barcoded rabies virus library

city: Boston

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

description: Rab-Delta-G plasmid barcode library

data_processing:
Library strategy: Amplicon-seq
Library was trimmed and filtered based on read structure according to RABID-seq workflow
Reads were clustered using Starcode v1.3
Supplementary_files_format_and_content: Text file of clustered barcodes by read abundance

organism: unidentified plasmid

source_name: barcodes

extract_protocol: Libraries were amplified using RABID-seq specific barcode primers.

tag: sample type

value: barcodes


title: HA5-Early_H3K9me2_P1_CUT&RUN

value: P


title: HA5-Early_H3K9me2_H2_CUT&RUN


title: XS28b.None.Vector.Second.p8


title: rdr3_Bud_totalRNA_11

city: Philadelphia

first: Xia

last: Hua

state: PA

address: 433 S University Ave

institute: University of Pennsylvania

description:
total RNA
Control group: Col0_Bud_totalRNA_1 and Col0_Bud_totalRNA_2

data_processing:
Adapter sequences were trimmed by cutadapt
Reads were mapped to the Arabidopsis genome using TopHat
Reads aligning to each transcript were counted using HTSeq or reads mapping to each unbiased 500bp genomic bin was counted using bedtools
Differential abundance analysis between Col-0 and each of the mutant genotypes was computed using the R package edgeR
Genome_build: TAIR10
Supplementary_files_format_and_content: text files of significant lower abundant small RNAs or significant higher abundance of total RNAs in a strand specific manner

organism: Arabidopsis thaliana

source_name: 30 days unopened flower bud

growth_protocol: All plants were grown in growth chambers under long days conditions (16 hours light and 8 hours dark photoperiod) at 22°C, plants were grown on soil.

extract_protocol:
30 days unopened flower buds was freezed by liquid nitrogen, and RNA was extracted by Quiazol
Sequencing libraries were prepared for smRNA-seq and RNA-seq as described previously [1]. For gel-mediated size selection for library inserts, small RNAs (15 – 50 nt) were selected using high percentage (15%), denaturing acrylamide gels and following a limited RNA fragmentation reaction 140 – 250 nt RNA fragments were purified using acrylamide gels for total RNA samples that were purified from Arabidopsis 30-day unopened flower bud

value: 30 days unopened flower bud

value: untreated


title: rdr3_Bud_totalRNA_12


title: Col0_Bud_totalRNA_10

description: total RNA

value: Columbia


title: Col0_Bud_totalRNA_9

description: total RNA


title: HA5-Early_H3K9me2_H1_CUT&RUN


title: XS28a.None.Vector.Second.p8


title: Library of viral barcodes

data_processing:
Library strategy: Amplicon-seq
The data were demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were trimmed and filtered based on the RABID-seq barcode processing pipeline.
The filtered reads were clustered within 1 Levenshtein distance using Starcode v1.3.
Genome_build: The RABID-seq barcode reads were corrected based on the results from Starcode clustering and counted.
Supplementary_files_format_and_content: Count table for barcode reads

organism: Suid alphaherpesvirus 1

growth_protocol: B7GG cells (Osakada et al., Nat Protocols 2013) were grown in B7GG media.

extract_protocol:
RNA was extracted using Qiagen RNeasy Kit, reverse transcribed using oligo-dT primers, and amplified with RABID-seq specific primers
Libraries were amplified using RABID-seq specific barcode primers.

treatment_protocol: B7GG cells were transduced with Rab-delta-G virus.

value: SAD B19

tag: modification

value: G-deficient


title: XS27e.None.EWS-FLI1.Second.p8


title: L_hyp3

city: Wrocław

first: Marta

last: Kołodziej

address: Joliot-Curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
Lh3

data_processing:
seqencing adapter removal with Cutadapt software with parameters set -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with Bowtie2 with default settings
sorting and indexing of the alignemnt files with Samtools
counting reads to features with HTSeq.count -t gene -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
creating 1x normalised bedgraphs with bamCoverage function of DeepTools with parameters --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 4411532 -e -p 15 -of bedgraph
Genome_build: NC_008596.1
Supplementary_files_format_and_content: bedgraph files are 1x normalised to remove the sequencing depth discrepancies
Supplementary_files_format_and_content: matrix file is a .txt file (tab delimited) with number of reads counted to features (genes) for all individual samples

organism: Mycolicibacterium smegmatis MC2 155

growth_protocol: M. smegmatis strains were grown in 7H9 broth supplemented with 10% OADC (oleic acid-albumin-dextrose-catalase; BD) and 0.05% Tween 80. Rapid anaerobic dormancy (RAD) model was used to shift M. smegmatis cultures from aerobic growth to hypoxia. 40 ml of liquid cultures (OD600 ~ 0.3) in tightly closed plastic tubes (maximum volume 50 ml) was incubated in 37˚C, with 180 rpm shaking for 6 hours.

extract_protocol:
Bacteria were harvested during the logarythmic phase of growth. RNA was extracted with Trizol LS(Thermo Fisher Scientific, Waltham, USA) following standard laboratory procedures used for mycobacteria (ribolysing the cells with "lysing matrix B" in MP FastPrep homogenizer).
KAPA Stranded RNA-Seq Library Preparation Kit (cat#KK8401 , from KAPA Biosystems), following ribodepletion of samples with Ribo-Zero(Bacteria)(from Illumina, San Diego, USA)
RNASeq, stranded

treatment_protocol: mutant versus control comparison, optimal condition versus hypoxia

value: lsr2 (MSMEG_6092) mutant

tag: condition

value: hypoxia


title: HA5-Early_H3K9me2_G2_CUT&RUN

value: G


title: rdr3_Bud_smRNA_4

description:
small RNA
Control group: Col0_Bud_smRNA_1 and Col0_Bud_smRNA_2


title: XS28d.None.Vector.Second.p8


title: HA5-Early_H3K9me2_P2_CUT&RUN


title: HA5-Early_H3K9me2_G1_CUT&RUN


title: L_hyp2

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
Lh2


title: rdr3_Bud_smRNA_3


title: XS27d.None.EWS-FLI1.Second.p8


title: L_hyp1

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
Lh1


title: HA5-Early_H3K4me2_L1_CUT&RUN

value: L


title: Col0_Bud_smRNA_2

description: small RNA


title: WT_hyp3

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
WTh3

value: wild type


title: HA5-Early_H3K4me2_L2_CUT&RUN


title: XS27c.None.EWS-FLI1.Second.p8


title: XS27b.None.EWS-FLI1.Second.p8


title: WT_hyp2

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
WTh2


title: Col0_Bud_smRNA_1

description: small RNA


title: sgs3_totalRNA_Seq_16815

description:
total RNA
Control group: Col0_Bud_totalRNA_Seq_16801 and Col0_Bud_totalRNA_Seq_16802


title: WT_hyp1

description:
grown 6 hours under hypoxia (RAD model)
Matrix_GEO.txt
WTh1


title: XS27a.None.EWS-FLI1.Second.p8


title: HA5-Early_H3K4me2_P2_CUT&RUN


title: HA5-Early_H3K4me2_P1_CUT&RUN


title: XS26e.26orf.Vector.Second.p8


title: HA5-Early_H3K4me2_H2_CUT&RUN

value: H


title: L_opt3

description:
grown to mid-exponential phase
Matrix_GEO.txt
Lo3

value: optimal growth


title: XS26d.26orf.Vector.Second.p8

value: Human mesenchymal progenitor (hMPro cells)


title: L_opt2

description:
grown to mid-exponential phase
Matrix_GEO.txt
Lo2


title: XS26c.26orf.Vector.Second.p8

value: Vector


title: rdr6_Bud_totalRNA_Seq_16812


title: rdr6_Bud_totalRNA_Seq_16811


title: HA5-Early_H3K4me2_G2_CUT&RUN


title: WT_opt2

description:
grown to mid-exponential phase
Matrix_GEO.txt
WTo2


title: rdr5_Bud_totalRNA_Seq_16810


title: XS26a.26orf.Vector.Second.p8

value: Second


title: HA5-Early_H3K4me2_G1_CUT&RUN


title: rdr5_Bud_totalRNA_Seq_16809


title: XS25e.26orf.EWS-FLI1.Second.p8


title: HA5-Early_H3K4me2_H1_CUT&RUN


title: sgs3_totalRNA_Seq_16816


title: XS25c.26orf.EWS-FLI1.Second.p8


title: XS26b.26orf.Vector.Second.p8


title: rdr2_Bud_totalRNA_Seq_16806


title: HA5-Early_IgG_P2_CUT&RUN


title: HA5-Early_IgG_L2_CUT&RUN


title: rdr2_Bud_totalRNA_Seq_16805


title: L_opt1

description:
grown to mid-exponential phase
Matrix_GEO.txt
Lo1


title: WT_opt1

description:
grown to mid-exponential phase
Matrix_GEO.txt
WTo1


title: HA5-Early_IgG_P1_CUT&RUN


title: HA5-Early_IgG_H2_CUT&RUN


title: rdr4_Bud_totalRNA_Seq_16808


title: XS25d.26orf.EWS-FLI1.Second.p8


title: HA5-Early_IgG_L1_CUT&RUN


title: XS24e.None.Vector.Second.p4


title: HA5-Early_IgG_H1_CUT&RUN


title: rdr4_Bud_totalRNA_Seq_16807


title: XS25b.26orf.EWS-FLI1.Second.p8


title: rdr1_Bud_totalRNA_Seq_16804


title: XS25a.26orf.EWS-FLI1.Second.p8


title: Pho4 binding levels at 0.1uM

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescence signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots and then normalized the signal for direct comparison between experiments.

label: Alexa 488

molecule: protein

source_name: yeast Pho4

label_protocol: Proteins were tagged with N-terminal GST/His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen), or Alexa488-conjugated anti-His antibody (Qiagen).

growth_protocol: Gateway-compatible clones containing the full-length genes for Cbf1 and Pho4 were transferred into pDEST15 and pDEST17 respecitively using the LR Clonase reaction (Life Technologies). pDEST15 vector enables the production of N-terminally GST-tagged proteins while pDEST17 vector produces His-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions. His-tagged protein was purified from the soluble portion of the lysate using His resin (GE Healthcare) according to manufacturer’s instructions.

tag: transcription factor

tag: tf concentration


title: XS24d.None.Vector.Second.p4


title: rdr1_Bud_totalRNA_Seq_16803


title: Pho4 binding levels at 8uM


title: rdm12_totalRNA_Seq_16817


title: Pho4 binding levels at 2uM


title: Pho4 binding levels at 0.4uM


title: XS24b.None.Vector.Second.p4


title: Cbf1 binding levels at 8uM

source_name: yeast Cbf1


title: Kasumi-1_DMSO_24h

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing was sequenced on Illumina NovaSeq 6000 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes (feature counts)were performed by Rsubread.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of ≤ 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *csvt: comma-separated values of row and normalized counts for each known gene (EntrezID, and HGNC symbol) in columns and sample in rows.

source_name: Asynchronous cells

growth_protocol: Cancer cells were cultured in RPMI medium suppled with 20% FBS

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: Cells were exposure for 4h or 24h to 100nM cabozantinib (XL184) or to the vehicle control (DMSO).

value: acute myeloid leukemia Kasumi-1

value: peripheral blood

tag: cell phenotype

value: Asynchronous cells


title: XS23e.None.EWS-FLI1.Second.p4


title: Kasumi-1_cabozantinib_100nM_4h


title: HA5-Early_IgG_G2_CUT&RUN


title: sgs3_Bud_smRNA_Seq_14135

description:
small RNA
Control group: Col0_Bud_smRNA_Seq_14120 and Col0_Bud_smRNA_Seq_14121

value: 30 days unopened flower bud

tag: treatment

value: untreated


title: Cbf1 binding levels at 1uM


title: XS23d.None.EWS-FLI1.Second.p4

tag: tissue


title: rdm12_totalRNA_Seq_16818

tag: genotype


title: sgs3_Bud_smRNA_Seq_14134


title: Kasumi-1_DMSO_4h


title: Pho4 binding levels (8uM Pho4 + 2uM Cbf1)

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) or Alexa-647 conjugated antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

label_protocol: Proteins were tagged with N-terminal GST/His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen), or Alexa647-conjugated anti-His antibody (Qiagen).

tag: competitor tf concentration


title: XS24c.None.Vector.Second.p4


title: HA5-Early_IgG_G1_CUT&RUN

tag: cell line


title: rdr6_Bud_smRNA_Seq_14131


title: Kasumi-1_cabozantinib_100nM_24h


title: Col0_Bud_totalRNA_Seq_16802

description: total RNA

value: Columbia


title: Cbf1 binding levels at 0.2uM


title: XS24a.None.Vector.Second.p4


title: BC3_CMP_MEP

city: Zurich

first: Ge

last: Tan

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.7.0e with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.4
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Blood

growth_protocol: Fresh human hematopoietic stem/progenitor cells were obtained from 123 blood samples of 18 patients with chronic and progressed PV and 21 controls with informed consent and approval of the local ethics committee (KEK-ZH-Nr: 2015-0564 with amendment PB_2019-00135; Clinical Hematology, University Hospital Zurich, Zurich Switzerland, and blood donation center SRK in Schlieren, Zurich).

extract_protocol:
Human CD34+ hematopoietic stem/progenitor cells were enriched from mononuclear cells using immunomagnetic beads according to manufacturer instructions (CD34 MicroBead Kit; Miltenyi Biotec). Fluorescence-activated cell sorting and antibodies specific for CD2, CD3, CD4, CD7, CD8, CD14, CD19, CD56, CD10, CD11b, CD20, CD235a, CD34, CD38, CD123, CD45RA were used to isolate the various cell types (HSC, CMP/MEP, CMP, GMP, MEP). 10'000 cells of each subpopulation were sorted into RNeasy lysis buffer containing beta-mercaptoethanol. Total RNA was purified according to manufacturer instructions using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using SmartSeq2-Picelli protocol.

treatment_protocol: High-risk PV patients (above age 60 and/or history of thromboembolic event) were treated with cytoreductive hydroxyurea, acetylsalicylic acid and phlebotomies. Low-risk patients (criteria for high risk not fulfilled) were treated with acetylsalicylic acid and phlebotomies. Phlebotomies were only performed when the hematocrit was above 45%.

tag: cell type

tag: donor id

tag: patient vs control

value: control

tag: cytoreductive treatment

value: no cytoreductive treatment

tag: disease progression status

value: not progressed

value: Blood


title: rdr6_Bud_smRNA_Seq_14130


title: Cbf1 binding levels at 0.05uM


title: XS22e.26orf.Vector.Second.p4

tag: lentiviral library

tag: oncogene

tag: evolution experiment

tag: passage


title: BC3_HSC

value: hematopoietic stem/multipotent progenitor cells


title: XS23b.None.EWS-FLI1.Second.p4


title: XS23c.None.EWS-FLI1.Second.p4


title: Col0_Bud_totalRNA_Seq_16801

description: total RNA


title: Pho4 binding levels (0.05uM Pho4 + 2uM Cbf1)

tag: transcription factor


title: XS23a.None.EWS-FLI1.Second.p4


title: BC2_CMP

value: common myeloid progenitors


title: BC2_MEP

value: megakaryocyte-erythrocyte progenitors


title: BC2_HSC


title: Pho4 binding levels (2uM Pho4 + 8uM Cbf1)

tag: tf concentration


title: BC2_GMP

value: granulocyte-macrophage progenitors


title: Pho4 binding levels (2uM Pho4 + 0.05uM Cbf1)


title: rdr5_Bud_smRNA_Seq_14128


title: XS22b.26orf.Vector.Second.p4

value: Human mesenchymal progenitor (hMPro cells)


title: Pho4 binding levels (0.4uM Pho4 + 2uM Cbf1)


title: rdr5_Bud_smRNA_Seq_14129


title: XS22a.26orf.Vector.Second.p4

value: Vector


title: Cbf1 binding levels (0.4uM Cbf1 + 2uM Pho4)

label: Alexa 647


title: XS22d.26orf.Vector.Second.p4

value: Second


title: rdr4_Bud_smRNA_Seq_14127


title: BC1_GMP


title: rdr4_Bud_smRNA_Seq_14126


title: XS22c.26orf.Vector.Second.p4


title: rdr2_Bud_smRNA_Seq_14125


title: Cbf1 binding levels (8uM Cbf1 + 2uM Pho4)


title: rdr2_Bud_smRNA_Seq_14124


title: Pho4 binding levels (2uM Pho4 + 2uM Cbf1)


title: Cbf1 binding levels (0.05uM Cbf1 + 2uM Pho4)


title: BC1_MEP


title: Pho4 binding levels (2uM Pho4 + 0.4uM Cbf1)


title: XS21d.26orf.EWS-FLI1.Second.p4


title: Cbf1 binding levels (2uM Cbf1 + 8uM Pho4)


title: BC2_CMP_MEP


title: Cbf1 binding levels (2uM Cbf1 + 2uM Pho4)


title: rdm12_Bud_smRNA_Seq_14137


title: XS21b.26orf.EWS-FLI1.Second.p4


title: XS21e.26orf.EWS-FLI1.Second.p4


title: rdm12_Bud_smRNA_Seq_14136


title: rdr1_Bud_smRNA_Seq_14122


title: BC1_CMP


title: Lsr2-2

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

institute: Nencki Institute of Experimental Biology

description: IP sample

data_processing:
Data trimming by Trimmomatic
Data alignment by bwa
Optical duplicates removal by Picardtools MarkDuplicates
Peaks calling by MACS software
Genome_build: Mycobacterium_smegmatis_str_mc2_155.ASM1500v1
Supplementary_files_format_and_content: bed files narrow peaks obtained from MACS software peak calling

organism: Mycolicibacterium smegmatis

growth_protocol: M. smegmatis strains producing Lsr2-FLAG3 and WT (negative control) were grown in 7H9 broth supplemented with 10% OADC (oleic acid-albumin-dextrose-catalase; BD) and 0.05% Tween 80, in 37˚C with 180 rpm shaking. The log-phase (OD600, 0.6) liquid medium grown culture was used to ChIP protocol.

extract_protocol:
The cells were fixed with 0.01% formaldehyde for 30 min, the reaction was quenched with glycine, and washed three times with cold PBS. To prepare lysates, pellets were disintegrated with silica beads and sonicated. The obtained lysates were centrifuged (5 min, 12,000 rpm, 4°C) and frozen. For immunoprecipitation, 700 µg of the total protein was incubated on a rotary shaker for 4 h at 4°C with a 20 µl packed-gel volume of anti-FLAG M2 magnetic beads (Sigma-Aldrich) and then washed. Samples were processed in a final volume of 0.5 ml in two biological replicates, with input DNA controls (70 µg of total protein alone) included for each replicate. Immunoprecipitated samples were de-cross-linked and then digested with proteinase K (final concentration, 0.05 mg/ml). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with absolute ethanol.
The library of DNA fragments was prepared using a QIAseq Ultralow Input library kit (Qiagen). Briefly, the protocol includes DNA end repair, sequencing adapter ligation, cleanup, and PCR amplification. At the end of the procedure, quantification and quality evaluations were done using a Nanodrop spectrophotometer (Thermo Scientific), a Quantus fluorimeter (Promega), and a 2100 Bioanalyzer (Agilent). Second-generation sequencing was performed using a HiSeq 1500 sequencing platform (Illumina).

tag: strain

value: M. smegmatis mc2 155 lsr2::lsr2-flag3

tag: growth stage

value: exponential (log)

tag: chip antibody

value: Monoclonal ANTI-FLAG® M2 antibody


title: PID318_GMP

address: Winterthurerstrasse 190

value: patient

tag: tissue


title: BC1_HSC


title: Lsr2-2-Input

description: Input sample

value: No antibody


title: Col0_Bud_smRNA_Seq_14120

description: small RNA

value: 30 days unopened flower bud

tag: treatment

value: untreated

tag: genotype

value: Columbia


title: Cbf1 binding levels (2uM Cbf1 + 0.4uM Pho4)

tag: competitor tf concentration


title: rdr1_Bud_smRNA_Seq_14123


title: XS20e.None.Vector.Second.p1


title: PID318_HSC

tag: cell type

tag: donor id

value: no cytoreductive treatment

value: not progressed


title: Lsr2-1-Input

description: Input sample


title: XS20d.None.Vector.Second.p1


title: XS21c.26orf.EWS-FLI1.Second.p4


title: BC1_CMP_MEP

tag: patient vs control

value: control

tag: cytoreductive treatment

value: Blood


title: PID473_GMP

value: hydroxyurea treatment

tag: disease progression status

value: progressed


title: Cbf1 binding levels (2uM Cbf1 + 0.05uM Pho4)


title: XS20c.None.Vector.Second.p1

value: Human mesenchymal progenitor (hMPro cells)

tag: lentiviral library

tag: oncogene


title: XS21a.26orf.EWS-FLI1.Second.p4

tag: evolution experiment

tag: passage


title: Col0_Bud_smRNA_Seq_14121

description: small RNA


title: XS20b.None.Vector.Second.p1

value: Vector


title: PID318_CMP_MEP


title: PID473_MEP

value: megakaryocyte-erythrocyte progenitors


title: XS19e.None.EWS-FLI1.Second.p1

value: Second


title: Lsr2-1

description: IP sample

value: M. smegmatis mc2 155 lsr2::lsr2-flag3

value: exponential (log)


title: XS19d.None.EWS-FLI1.Second.p1


title: XS20a.None.Vector.Second.p1


title: XS19c.None.EWS-FLI1.Second.p1


title: PID473_HSC

value: hematopoietic stem/multipotent progenitor cells

value: patient


title: PID473_CMP

value: common myeloid progenitors


title: PID480_GMP

value: granulocyte-macrophage progenitors


title: XS19b.None.EWS-FLI1.Second.p1


title: Cell_knockout_day7

type: RNA

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data was background subtracted and normalized based on Cross-Correlation method.
The negative and small expression values were set to be 20 based on p value

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Preadipocytes were cultured with DMEM (high glucose) medium containing 10% NCS plus pen/strep, L-glutamine, 24 nM insulin, and 150 um sodium ascorbate. Medium was changed every two days.

extract_protocol: Total RNA was extracted from adipocytes at various days during differentiation with TRIzol reagent (Invitrogen)

treatment_protocol: No treatment

value: preadipocytes

tag: timepoint

value: Day 7


title: XS19a.None.EWS-FLI1.Second.p1


title: Cell_knockout_day5

value: Day 5


title: TK10_mSpl_naive_OmniATAC_AAGAGGCA

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

institute: Technical University of Munich

data_processing:
Raw reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -S”
ATAC peaks over Input background were identified using Homer (Heinz et al., 2010) findPeaks.pl with option “-style factor”
annotatePeaks was used to obtain coverage counts within 500 pb across peak centers
Differential ATAC peaks were determined with the DESeq2 result function and filtered for padj < 0.05. Genomic feature annotation of ATAC-seq peaks was done using annotatePeaks.
Transcription factor motif prediction was done with Homer findMotifsGenome.pl
bigWig files were generated from homer tag directories using makeBigWig.pl
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are in bigWig format and contain differential ATAC peaks for each sample

source_name: mSpl naive cells

growth_protocol: Animals were kept in a specific pathogen-free facility at the Technical University of Munich . All experimental protocols were approved by the standing committee for experimentation with laboratory animals of the Bavarian state authorities and carried out in accordance with the corresponding guidelines.

extract_protocol:
The cells were isolated from the spleen 2 days after photoconversion and signle cell suspinsions were generated by mashing the spleens through a cell strainer.
Nextera DNA Sample Prep Kit FC-121-1030

treatment_protocol: The mice were immunized with MOG(35-55) and CFA at day 0. The mice received pertussis toxin at day0 and day2 and either the iLN or mLN were irradiated with an 405nm laser at disease onset.

value: Spleen


title: XS18e.26orf.Vector.Second.p1


title: Cell_knockout_day3

value: Day 3


title: TK9_mSpl_effector_OmniATAC_CGAGGCTG

source_name: mSpl effector cells


title: PID480_HSC

value: no cytoreductive treatment

value: not progressed

value: Blood


title: Cell_knockout_day9

value: Day 9


title: Cell_wildtype_day7

value: wildtype


title: Cell_wildtype_day9


title: PID480_CMP


title: PID480_CMP_MEP


title: XS18c.26orf.Vector.Second.p1

value: Human mesenchymal progenitor (hMPro cells)

value: Vector

value: Second


title: Cell_wildtype_day3


title: TK8_iSpl_naive_R1_OmniATAC_CAGAGAGG

source_name: iSpl naive cells


title: XS18d.26orf.Vector.Second.p1


title: PID473_CMP_MEP

value: hydroxyurea treatment

value: progressed


title: PID291_GMP

value: patient


title: RRBS FoxA1L/L;FoxA2L;L;FoxA3-/- 13 days after GFP induction (control for FoxA triple null) - Sample 2

first: Klaus

middle: H

last: Kaestner

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

data_processing:
Single-end RRBS runs were trimmed with trim galore (v.0.3.3), then we employed diversity trimming and filtering with NuGENs diversity trimming script trimRRBSdiversityAdaptCustomers.py. Read alignment (genome build mm9) and extraction of methylation levels were carried out by BSMAP v.2.74 (Xi and Li, 2009) using the following commands: bsmap -a sample_R1_val_1.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file. Percent methylation was calculated for 100 bp tiles with a minimum coverage of 10 CpGs. In order to examine methylation levels at hypermethylated sites in developmental FoxA double null of hepatocytes isolated from newborns, Tet2/3 ko, partial hepatectomy samples and FoxA triple null, we determined methylation levels of 100 bp tiles overlapping with these hypermethylated sites and took only tiles in which score was achieved among compared samples. We also rescored WGBS samples with the same parameters in order to get a comparable value. Heatmaps and dendrograms were generated with R library heatmap.2 and density plot were generated with stata – software for statistics and data science.
Genome_build: mm9
Genome_build: mm9

extract_protocol:
DNA was isolated from hepatocytes by DNeasy (Qiagen).
RRBS was performed using Ovation RRBS Methyl-Seq according to the manufacturer’s instruction. We used 100 ng hepatocyte DNA. Libraries were then amplified, purified, pooled, and sequenced on the Illumina HiSeq 4000 with 100 bp single-end sequencing with a minimum of 25 million reads per sample.

tag: age

value: 12 weeks old

value: Liver


title: Cell_wildtype_day5

value: preadipocytes


title: XS18b.26orf.Vector.Second.p1


title: TK7_iSpl_effector_OmniATAC_CTCTCTAC

source_name: iSpl effector cells


title: XS18a.26orf.Vector.Second.p1


title: RRBS FoxA1L/L;FoxA2L;L;FoxA3-/- 13 days after GFP induction (control for FoxA triple null) - Sample 1


title: PID480_MEP

value: megakaryocyte-erythrocyte progenitors


title: XS17e.26orf.EWS-FLI1.Second.p1


title: PID291_HSC

value: hematopoietic stem/multipotent progenitor cells


title: PID291_CMP

value: common myeloid progenitors


title: XS17d.26orf.EWS-FLI1.Second.p1


title: RRBS FoxA triple null 13 days after Cre induction - sample 2


title: XS17c.26orf.EWS-FLI1.Second.p1


title: RRBS FoxA triple null 13 days after Cre induction - sample 1


title: PID291_CMP_MEP


title: PID291_MEP


title: PID153_GMP

value: granulocyte-macrophage progenitors

value: no cytoreductive treatment


title: RRBS on FoxA1L/+;FoxA2L/+ depleted in development - sample 2

value: 8 weeks old


title: XS12c.None.Vector.First.p8

value: First


title: RRBS on FoxA1L/L;FoxA2L/+ depleted in development - sample 2


title: PID153_MEP

value: not progressed

value: Blood


title: XS17a.26orf.EWS-FLI1.Second.p1

value: Human mesenchymal progenitor (hMPro cells)


title: PID153_CMP


title: PID153_HSC


title: RRBS on FoxA1L/+;FoxA2L/+ depleted in development - sample 1


title: XS12b.None.Vector.First.p8

value: Vector


title: PID771_MEP


title: PID153_CMP_MEP


title: PID771_GMP


title: XS12e.None.Vector.First.p8


title: XS11e.None.EWS-FLI1.First.p8


title: XS11c.None.EWS-FLI1.First.p8


title: XS11b.None.EWS-FLI1.First.p8


title: PID771_CMP


title: RRBS on 8 weeks old FoxA developmental double null


title: RRBS on 6 months old FoxA developmental double null


title: RRBS on 20 day old FoxA developmental double null


title: RRBS on 8 weeks old control

source_name: RRBS on 8 weeks old control


title: PID771_CMP_MEP


title: RRBS on FoxA1L/L;FoxA2L/+ depleted in development - sample 1


title: XS10e.26orf.Vector.First.p8


title: PID771_HSC


title: RRBS on 6 months old control

source_name: RRBS on 6 months old control

value: 6 months old


title: RRBS on 4 months old control

source_name: RRBS on 4 months old control

value: 4 months old


title: Gastruloid 24h sample 1

city: St Louis

first: Kyaw Thu

last: Minn

address: 1 Brookings Drive

institute: WUSTL

description: Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to hg19 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: hg19
Supplementary_files_format_and_content: counts.csv, metadata.csv

source_name: Embryonic stem cell

extract_protocol: 10x Genomcis Chromium single cell preparation

tag: cell line

value: Embryonic stem cell

value: 24h of BMP4 treatment


title: Gastruloid 24h sample 2


title: PID872_MEP

value: patient

value: progressed


title: XS10c.26orf.Vector.First.p8


title: Gastruloid 12h sample 2

value: 12h of BMP4 treatment.


title: PID872_GMP


title: PID872_HSC

value: hematopoietic stem/multipotent progenitor cells


title: XS10a.26orf.Vector.First.p8


title: RRBS on 20 day old control

source_name: RRBS on 20 day old control

value: Liver


title: Gastruloid 12h sample 1


title: PID872_CMP

value: common myeloid progenitors


title: ChIP H3K27ac on FoxA adukt double null - sample 2

data_processing:
Single-end sequencing reads were trimmed with Cutadapt and aligned to mouse genome (genome build mm9) using Bowtie2 version 2.3.4.1. PCR duplicates were removed using picard.jar tool and the command MarkDuplicates with the following flags:”REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. In order to compare differential binding between controls and FoxA double nulls in hyper- or isomethylated sites, we used DiffBind version 2.10.0 (Ross-Innes et al., 2012). Peaks were defined as ±250 base pairs from peak center. Bam files were converted to Bedgraph files after normalizing to 1 million reads per library using BEDtools (“genomecov”) and then converted to bigwig format using UCSC toolkit (“bedGraphToBigWig”). For control and FoxA triple null groups, an average bigwig file was also generated from the replicates (“bigWigMerge“).
Genome_build: mm9
Genome_build: mm9

source_name: ChIP H3K27ac on FoxA adukt double null

extract_protocol:
130 mg of frozen liver was minced in 2 mL of cold 1X DPBS (Thermo Fisher 14080055). The volumes of liver slices were brought up to 10 mL of 1X DPBS and 1% formaldehyde and incubated at room temperature for 8 minutes with rotation. Reaction was brought to 0.125 M glycine for quenching and incubated for 5 minutes at room temperature with rotation. Samples were centrifuged at 2,500 RCF for 2 minutes at 4°C, the supernatants discarded, and pellets washed with 1X DPBS. The pellet was resuspended in 1 mL of cold ChIP cell lysis buffer (10 mM Tris- HCl pH 8.0, 10 mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630, 1X cOmplete protease inhibitor cocktail) and transferred on ice to a 10 mL tissue grinder. The samples were homogenized 20 times with a smooth Teflon pestle and incubated at 4°C for 5 minutes. Following incubation the samples were centrifuged for 5 minutes at 17,000 RCF at 4°C, to pellet the nuclei. After the supernatant was discarded, and nuclei were resuspended in 1 mL of cold ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 5 mM EDTA, 1% SDS, 1X cOmplete protease inhibitor cocktail). Then, we performed two rounds of sonication using the Standard Biruptor (Diagenode UCD-200) with the following parameters: Intensity = High (H), Multitimer = OFF: 30 sec, ON: 30 sec, Total timer = 7.5 minutes with maintaining 4°C. Following sonication, samples were centrifuged at 17,000 RCF for 10 minutes at 4°C and supernatant was recovered. We isolated DNA from the sonicated chromatin to determine the amount of material required for precipitation. The DNA concentration was quantified using a NanoDrop-1000 (Thermo Fisher) and run on a BioAnalyzer High Sensitivity ChIP to estimate the length distribution. Then, 10 μg of sonicated chromatin was added to 1 mL of ChIP dilution buffer (16. mM Tris-HCl pH 8.0, 167 mM NaCl, 0.01% SDS, 1.1% Triton-X 100, 1X cOmplete protease inhibitor cocktail). 3 μg of the following antibodies, H3K27ac (Active Motif 39133) and HNF4a (Abcam ab181604), were added to the samples and the samples were incubated at 4°C overnight with rotation. 40 μL of recombinant protein G agarose beads (Thermo Fisher) were washed three times with 1 mL of ChIP dilution buffer. Next, the beads were resuspended in 75 μL of ChIP Dilution Buffer and 5 μL of BSA (New England BioLabs) and incubated at 4°C overnight with   rotation for blocking. Then chromatin samples were added to the blocked beads and incubated at 4°C for 1 hour with rotation. Samples were centrifuged at 100 RCF for 30 seconds and the supernatant was discarded. The beads were then washed sequentially with each of the following buffers by resuspending the beads in 1 mL of buffer, incubating beads at room temperature for 5 minutes with rotation, pelleting beads, and discarding supernatant: TSE I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), TSE II ( 20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), ChIP Buffer III (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% IGEPAL CA-630, 1% Sodium Deoxycholate), TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After the washes, the beads were resuspended in 100 μL of elution buffer (0.1 M NaHCO3, 1% SDS) and incubated at room temperature for 15 minutes with rotation. 4 μL of 5M NaCl was added to the supernatant and then samples were incubated at 65°C overnight. Next, DNA was isolated from the samples using Minielute (Quiagen). Enrichment of IP samples was measured through qPCR using the following program: 95°C for 3 minutes, for 40 cycles, 95°C for 5 seconds, 60°C for 20 seconds.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were sequenced on the Illumina Hiseq 4000 with 50 bp single-end sequencing with a minimum of 20 million reads per sample.


title: XS11a.None.EWS-FLI1.First.p8

source_name: Human Mesencymal Progenitor


title: Gastruloid 0h sample 2

value: 0h (immediately before) BMP4 treatment


title: RRBS on 4 months old FoxA developmental double null


title: XS9d.26orf.EWS-FLI1.First.p8


title: ChIP H3K27ac on FoxA adukt double null - sample 3

value: 8 weeks old


title: XS9c.26orf.EWS-FLI1.First.p8

value: First


title: XS9e.26orf.EWS-FLI1.First.p8


title: PID781_GMP

value: granulocyte-macrophage progenitors

value: control

value: no cytoreductive treatment

value: not progressed


title: XS9b.26orf.EWS-FLI1.First.p8

value: Human mesenchymal progenitor (hMPro cells)


title: PID872_CMP_MEP

value: Blood


title: Gastruloid 0h sample 1

value: Embryonic stem cell


title: ChIP H3K27ac on FoxA adukt double null - sample 1


title: ChIP H3K27ac on FoxA1L/L;FoxA2L/L - sample 3

source_name: ChIP H3K27ac on FoxA1L/L;FoxA2L/L


title: M2-tot

description:
HA5-Late cells from Castro-Vega et al.2013
M2-tot

data_processing:
Reads were mapped with tophat version 2.0.6, with a tolerance of 3 mismatches
Only unique mapped reads were kept for further analysis
Reads were counted on genomic features with htseq-count version 0.6.1p1
The read counts on E1-tot, E2-tot, M1-tot and M2-tot were processed on gencode v19, and the read counts of the other cell lines were processed on gencode v26.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file reporting htseq counts

source_name: HEK-based cell line

growth_protocol: For each cell-line, cells were grown up to 90% confluence in 100 cm² square dishes in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using Qiagen miRNeasy kit with a Trizol reagent.
all RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

value: Mes


title: PID781_MEP

value: megakaryocyte-erythrocyte progenitors


title: M1-tot

description:
HA5-Late cells from Castro-Vega et al.2013
M1-tot


title: ChIP H3K27ac on FoxA1L/L;FoxA2L/L - sample 2


title: XS8e.None.Vector.First.p4

value: Vector


title: PID781_CMP


title: E2-tot

description:
HA5-Early cells from Castro-Vega et al.2013
E2-tot

value: Epi


title: PID781_HSC

value: hematopoietic stem/multipotent progenitor cells


title: ChIP H3K27ac on FoxA Dev double null - sample 3

source_name: ChIP H3K27ac on FoxA Dev double null

value: Liver


title: E1-tot

description:
HA5-Early cells from Castro-Vega et al.2013
E1-tot


title: PID781_CMP_MEP


title: PID115star_GMP

value: patient

value: hydroxyurea treatment


title: PID115star_MEP


title: ChIP H3K27ac on FoxA Dev double null - sample 1

value: 8 weeks old


title: XS8d.None.Vector.First.p4

value: First