title: S15_YRR pre-40S rep_3 NC

description: ribosomal RNA


title: S15_YRR pre-40S rep_2 NC

status: Public on Jun 04 2021

type: SRA

city: Jupiter

first: Haina

last: Huang

state: Florida

address: 130 scripps way c296

department: The integrative structural and computational biology

country: USA

institute: The Scripps Research Institute

description: ribosomal RNA

library_source: transcriptomic

data_processing:
removing adaptors with skewer
trimming reads with seqtk
running shapemapper aligning to 20S rRNA
… S.c.20S_rRNA_profile.txt were extracted for further analysis.
Supplementary_files_format_and_content: Extract "Modified_effective_depth" and "modified_rate" of each nucleotide for further analysis.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: ribosome pre-40S intermediate

growth_protocol: Cells were grown in YPD till mid-log phase before harvesting.

extract_protocol:
Phenol chloroform  precipitation
RNA-seq (DMS-MaPseq)

treatment_protocol: 1% DMS, 30°C, 5min

tag: dms treatment

value: untreated


title: Brg1cKO_1

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using HTSeq-count against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

organism: Mus musculus

source_name: Otic ectoderm

extract_protocol:
For each samples, we used 3000 cells for total RNA preparation in replicates using NucleoSpin RNA XS kit (TakaraBio). mRNA were purified from total RNA using magnetic beads (New England Biolabs)
Random priming strand-specific RNA-seq libraries were generated using with SMART-seq Stranded kit (TakaraBio) and single-end 75-bp sequencing was performed using Illumina HiSeq 2500 system.

tag: genotype

tag: tissue

value: Otic ectoderm


title: Brg1cKO_2


title: Control_OV_1

value: Control


title: WT pre-40S rep_1 DMS

description: ribosomal RNA

value: treated


title: WT pre-40S rep_1 NC

description: ribosomal RNA


title: Sepsis 2

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

data_processing:
Pre-processing of raw sequencing data was done using 10x genomics Cell Ranger pipeline with default settings (v6.0.1).
Raw data bcl files were first demultiplexed using Cellranger mkfastq.
Demultiplexed data was then processed using the Cellranger count.
The count output was loaded into R using the Seurat R v4.0.1 function Read10X.
Downstream processing (e.g. normalization, integration) and analysis were performed in R v4.0.5.
Genome_build: hg19-3.0.0
Supplementary_files_format_and_content: Output of Cell Ranger from the raw_feature_bc_matrix folder contain the UMI counts for cells in each sample.

organism: Homo sapiens

source_name: mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells

extract_protocol: Cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. Libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed using XX library quantification assay. Sequencing was performed on Illumina NovaSeq or NextSeq.

tag: cell type

value: circulating immune cells

tag: sepsis type

value: Fungal

tag: cci

value: CCI


title: Sepsis 1

value: Bacterial

value: Rapid Recovery


title: Healthy Control 2

value: Healthy Control


title: Control_OV_2


title: M2_2

city: Philadelphia

first: Boris

last: Striepen

state: Pennsylvania

address: 380 S University Ave, Room H344

department: Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 86 of the human reference genome GRCh38 using kallisto
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (>1-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 86 of human reference genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: HEK 293T

growth_protocol: 3 T-75 of HEK293T were  placed in a 5% CO2 37 °C incubator for 48 hours

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions.
cDNA synthesis was performed following the clonTechSMART-seq cDNA synthesis protocol (15 cycles). Following DNA cleanup, a Nextera library was prepared

treatment_protocol: HEK293T were transfected with 25ug of plasmid (GFP only or MEDLE2-GFP) via lipofection for 48 hours followed by flow sorting GFP positive cells from GFP negative cells in each flask

tag: background strain

value: HEK 293T

value: wild-type

tag: treatment

value: MEDLE2-GFP positive


title: M2_untrans_3

value: MEDLE2-GFP negative


title: GFP_3

value: GFP positive


title: M2_untrans_2


title: M2_3


title: M2_1


title: M2_untrans_1


title: GFP_2


title: GFP_1


title: ChIP_lib5_MBD6_MYC

city: Los Angeles

first: Lucia

last: Ichino

state: CA

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

library_source: genomic

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig) obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio. For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown on soil in a greenhouse under long-day conditions (16h light / 8h dark).

extract_protocol:
The experimental procedure was performed as described in PMID 20734276 with some variations. 2 or 2.5 g of inflorescences were used for each ChIP sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer containing 1% formaldehyde. Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with 10 µl of anti-MYC antibody (Cell Segnaling Technology, 71D10). 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers and eluted with elution buffer (1% SDS and 0.1 M NaHCO3). Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions, with 15 cycles of PCR.

value: inflorescence

tag: ecotype

tag: genetic background

tag: transgene present

tag: generation

tag: chip antibody


title: ChIP_lib5_Col0_MYC

value: anti-MYC antibody (Cell Segnaling Technology, 71D10)


title: RNAseq_polyA_lib5_MBD5-FLAG_rep3

source_name: unopened flower bud

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep kit (Zymo, R2052) with in column DNAse I digestion
1 microgram of RNA was used to prepare libraries using the Illumina TruSeq Stranded mRNA Library Prep protocol, following manufacturer's instructions.

value: unopened flower bud

value: mbd5 mbd6 T-DNA


title: Healthy Control 1


title: Ost3_TNFa_rep2

type: RNA

city: hangzhou

first: zhijun

last: pan

address: NO. 88, jiefang road

department: orthopeadics

country: China

institute: second affiliated hospital, zhejiang university

description: Gene expression after 3d osteogenesis of hBMSCs treated with TNFa (100ng/mL)

hyb_protocol: Then biotinylated cRNA targets hybridized with the Microarray slides at 65℃ for 17 hours

scan_protocol: Microarray slides were scanned by an Agilent Microarray Scanner G5761A (Agilent technologies, US).

data_processing: Data were extracted by Feature Extraction software (12.0.3.1, Agilent technologies, US) and the raw data were normalized through Genespring software (version14.8,Agilent Technologies).

source_name: osteogenesis, 3day, TNFa (100ng/mL), replicate2

label_protocol: Then qualified RNA samples of each group were utilized to synthesis biotinylated cRNA targets labled with Cyanine-3-CTP(Cy3), and purified using QIAGEN RNeasy Kit for the Human RNA 8*60K Expression Microarray (Agilent technologies, USA).

growth_protocol: hBMSCs were cultured in osteogenic induction medium, treated with or without TNFa

extract_protocol: Total RNA was isolated using RNA Isolation reagent (Takara), and then purified using RNeasy Mini Kit (Qiagen, Germany). A RIN number of total RNA was checked to examine RNA integration using Agilent Bioanalyzer 2100 (Agilent technologies, US).

value: human mesenchymal stem cell

tag: gender

value: male

tag: timepoint

value: 3d osteogenesis

value: TNFa (100ng/mL)


title: Ost4_Control_rep2

description: Gene expression after 4d osteogenesis of hBMSCs

source_name: osteogenesis, 4day, control, replicate2

value: 4d osteogenesis

value: control


title: Ost4_TNFa_rep3

description: Gene expression after 4d osteogenesis of hBMSCs treated with TNFa (100ng/mL)

source_name: osteogenesis, 4day, TNFa (100ng/mL), replicate3


title: Ost3_Control_rep2

description: Gene expression after 3d osteogenesis of hBMSCs

source_name: osteogenesis, 3day, control, replicate2


title: GFP_untrans_3

value: GFP negative


title: Ost4_Control_rep1

source_name: osteogenesis, 4day, control, replicate1


title: Ost3_Control_rep3

source_name: osteogenesis, 3day, control, replicate3


title: Ost4_TNFa_rep2

source_name: osteogenesis, 4day, TNFa (100ng/mL), replicate2


title: Ost3_TNFa_rep3

source_name: osteogenesis, 3day, TNFa (100ng/mL), replicate3


title: Ost3_TNFa_rep1

source_name: osteogenesis, 3day, TNFa (100ng/mL), replicate1


title: ChIP_lib5_MBD5_MYC


title: Ost3_Control_rep1

source_name: osteogenesis, 3day, control, replicate1


title: GFP_untrans_1


title: RNAseq_polyA_lib6_mbd56_rep3


title: Ost4_TNFa_rep1

source_name: osteogenesis, 4day, TNFa (100ng/mL), replicate1


title: RNAseq_polyA_lib6_mbd56_rep2


title: RNAseq_polyA_lib5_MBD5-FLAG_rep1


title: U2OS_siSET8_Mock_repl3

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Paired-end reads were trimmed for Nextera transposase adapter sequences using Trimmomatic (v0.32) (PMID: 24695404) in palindrome mode with default settings except ILLUMINACLIP:2:30:10:1:true MINLEN:25.
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) before and after trimming to confirm the removal of any 3’ adapter sequences and the insertion Tn5 motif in the 5’-ends.
Trimmed PE reads were mapped to the hg19 assembly (canonical chromosomes only) using bowtie2 v.2.2.9 (PMID: 22388286) with default settings except -k 2 -X 2000 --no-mixed --no-discordant.
Sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools (v. 2.6.0-27-g915ffa7-SNAPSHOT) (https://broadinstitute.github.io/picard/)
Addition of a NH tag (number of reported alignments)
Filtering to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter) (PMID: 19505943).
Filtered bam files were converted to bed format using bedtools bamtobed (v2.26.0-92-g88cd6c5) (PMID: 20110278).
Sorted mapped reads were imported into EaSeq version 1.12 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: hg19
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

source_name: U2OS osteosarcoma cell line

growth_protocol: Both U2OS cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% Penicillin–Streptomycin. MEF cells were in addition supplemented with non-essential amino acids.

extract_protocol:
Nuclei were prepared from 50,000 cells and subjected to tagmentation reaction. DNA was extracted and PCR amplified using Nextera Index primers (FC-121-1011) for paired-end sequencing.  DNA was size selected and using Ampure XP magnetic beads. Libraries were quantified using KAPA SYBR FAST qPCR Master mix (KK4932) to determine the optimal number of PCR cycles. After running the remaining number of PCR cycles, libraries were purified with Ampure XP beads (with size slection). Libraries were quantified using the Qubit DNA HS Kit, and for quality control, 1 μl of each sample was run on Bioanalyzer High Sensitivity DNA Chip.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-121-1030, FC-121-1011). In all, 2 nM of all libraries were pooled and 1.5 pM were analyzed on Illumina NextSeq500 (500/550 High Output v2 Kit—150 cycles).

treatment_protocol: U2OS cells were treated with either scramble siRNA sequence or siRNA against SET8 according to manufacturer's protocol. U2OS cells were either treated with Mock (DMSO) or DRB (5,6-Dichloro-1-beta-Ribo-furanosyl Benzimidazole) inhibitor (100 µM+D58) for 2 hours prior to harvest.

tag: cell line

value: U2OS osteosarcoma cell line

tag: sirna

value: Mock

tag: replicate


title: GFP_untrans_2

value: HEK 293T

tag: genotype

value: wild-type


title: Ost4_Control_rep3

source_name: osteogenesis, 4day, control, replicate3


title: RNAseq_polyA_lib5_MBD5-FLAG_rep2

tag: tissue


title: U2OS_siSET8_Mock_repl2


title: U2OS_siSET8_Mock_repl4


title: U2OS_siSET8_DRB_repl2

value: DRB


title: U2OS_siSET8_Mock_repl1


title: RNAseq_polyA_lib6_mbd56_rep1


title: U2OS_siSET8_DRB_repl4


title: U2OS_siSET8_DRB_repl3


title: RNAseq_polyA_lib6_wt_rep1


title: RNAseq_polyA_lib6_wt_rep2


title: U2OS_siSET8_DRB_repl1


title: RNAseq_polyA_lib5_MBD6-FLAG_rep3


title: RNAseq_polyA_lib5_MBD6-FLAG_rep2


title: RNAseq_polyA_lib5_mbd56_rep3


title: RNAseq_polyA_lib5_MBD6-FLAG_rep1


title: U2OS_siCtrl_Mock_repl3

value: siCtrl


title: U2OS_siCtrl_Mock_repl2


title: RNAseq_polyA_lib5_wt_rep3


title: NonInduce-WT-rep1

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw reads were mapped to human genome by STAR
Transcript counting was performed by HTseq-count
Normalization and differential gene expression analysis was performed by using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts of reads in each gene

molecule: polyA RNA

source_name: HPNE

extract_protocol:
mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II RNA library Prep Kit for Illumina

value: wild type

value: normal culture


title: NonInduce-ARID1A-KO-Clone2-rep1


title: NonInduce-ARID1A-KO-Clone2-rep3


title: RNAseq_polyA_lib5_wt_rep1

value: unopened flower bud


title: NonInduce-ARID1A-KO-Clone2-rep2


title: RNAseq_polyA_lib5_mbd56_rep2

value: mbd5 mbd6 T-DNA


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line7_rep1

value: sln

value: pSLN::SLN-3XFLAG (H94Q)


title: RNAseq_polyA_lib5_mbd56_rep1


title: RNAseq_polyA_lib5_wt_rep2


title: U2OS_siCtrl_Mock_repl1


title: U2OS_siCtrl_DRB_repl2


title: NonInduce-ARID1A-KO-Clone11-rep3


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line7_rep2


title: U2OS_siCtrl_DRB_repl4


title: RNAseq_polyA_lib4_SLN-FLAG_line7_rep1

value: pSLN::SLN-3XFLAG (WT)


title: RNAseq_polyA_lib4_SLN-FLAG_line7_rep3


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line7_rep3


title: NonInduce-WT-rep2


title: U2OS_siCtrl_DRB_repl3


title: U2OS_siCtrl_Mock_repl4


title: U2OS_siCtrl_DRB_repl1


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line6_rep3


title: NonInduce-ARID1A-KO-Clone11-rep2


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line6_rep2


title: RNAseq_polyA_lib4_SLN-FLAG_H94Q_line6_rep1


title: NonInduce-ARID1A-KO-Clone11-rep1


title: NonInduce-WT-rep3


title: RNAseq_polyA_lib4_SLN-FLAG_line7_rep2


title: RNAseq_polyA_lib4_SLN-FLAG_line6_rep3


title: RNAseq_polyA_lib4_SLN-FLAG_line6_rep2


title: KRAS-WT-rep1

value: doxycycline (6µg/ml for 5 days)


title: KRAS-ARID1A-KO-Clone2-rep2


title: RNAseq_polyA_lib4_sln_rep3


title: KRAS-ARID1A-KO-Clone2-rep3


title: KRAS-WT-rep3


title: RNAseq_polyA_lib4_wt_rep3


title: RNAseq_polyA_lib4_SLN-FLAG_line6_rep1


title: KRAS-WT-rep2


title: ATAC-Hmel_agl_HW-2

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

data_processing:
Alignment to Hmel2 genome using Bowtie2
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
The genome assemblies used for alignment can be found here on LepBase:
Hmel2: http://download.lepbase.org/v4/sequence/Heliconius_melpomene_melpomene_Hmel2_-_scaffolds.fa.gz
Genome_build: Hmel2
Supplementary_files_format_and_content: bigWig

organism: Heliconius melpomene aglaope

source_name: Whole wing tissue

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol
Libraries were prepared as described in the ATAC-seq protocol

tag: developmental stage

value: Day 3 Post-Pupation


title: KRAS-ARID1A-KO-Clone11-rep2


title: KRAS-ARID1A-KO-Clone2-rep1


title: ATAC-Hmel_agl_HW-1


title: HPNE_WT_ATAC_rep3

data_processing:
The raw reads were mapped to human genome by Bowtie2.
MACS2 was used for peak calling.
Reads mapped to each peak were counted.
edgeR was used for normalization and differential peak analysis.
Genome_build: hg19
Supplementary_files_format_and_content: peak file and read count matrix

extract_protocol:
Omni-ATAC protocol
Illumina Nextera library prep


title: ATAC-Hmel_agl_FW-2


title: RNAseq_polyA_lib4_sln_rep1


title: RNAseq_polyA_lib4_sln_rep2


title: ATAC-Hmel_agl_FW-1


title: RNAseq_polyA_lib4_wt_rep2


title: GROseq_wt

description: nascent RNA

data_processing:
Library strategy: GRO-seq
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

source_name: inflorescence

extract_protocol:
Approximately 5 million nuclei were run-on in 3×NRO-reaction buffer with 20 nM limiting cytidine triphosphate (CTP) at RT as described (PMID 27729530). Reactions were stopped by addition of 750 µl TRIzol LS (Fisher Scientific), and RNA was purified according to the manufacturer’s manual.  RNA pellets were resuspended in 18 µl ddH2O + 0.05% Tween (dH2O+T), 2 µl 10x fragmentation buffer [100 mM ZnCl2, 10 mMTris-HCl (pH 7.5)] added and incubated at 70°C for 15 minutes. Fragmentation was stopped by addition of 2.5 µl of 100 mM EDTA and 500 µl of ice cold GRO binding buffer [0.25× saline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA]. BrdU enrichment was performed as described (PMID 29779944). For RNA end-repair and decapping by the pyrophosphohydrolase RppH (NEB), RNA pellets were dissolved in 8 µl TET [10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.05% Tween20] by vigorous vortexing, heated to 70°C for 2 minutes and quick chilled on ice. After a quick spin, 22 µl Repair MM [3 µl 10x PNK buffer, 15.5 µl dH2O+T, 0.5 µl, SUPERase-In RNase Inhibitor (10 U), 2 µl PNK (20U), 1 µl RppH (5U)] was added, mixed by flicking and incubated at 37°C for 1 hour. To ensure phosphorylated 5’ends, 0.5 µl 100 mM ATP was subsequently added and the reactions incubated for another 45 minutes at 37°C. The IP was performed two times.
sRNA libraries were prepared using the NEB sRNA kit (E7330) as described by the manufacturer. Libraries were amplified for 15 cycles, and size selected on an 8% PAGE/TBE gels to 150–250 base pairs. DNA eluted from gel slices was precipitated with ethanol and resuspended in Tris buffer (Qiagen) before sequencing.

value: inflorescence


title: HPNE_WT_ATAC_rep2


title: GROseq_mbd56

description: nascent RNA


title: wild-type (L4) - total small RNA, replicate 2

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
For small RNA libraries, sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit, mapped to the C. elegans genome WS258 using Bowtie2 v. 2.2.2 (default parameters), and reads were assigned to genomic features using FeatureCounts (options: -t exon -g gene_id -O --fraction --largestOverlap) which is part of the Subread v. 1.5.1 package.
Genome_build: WS258
Supplementary_files_format_and_content: processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Synchronized animals were grown on NGM plates seeded with OP50 E. coli at 20°C 48 hours post hatching (for L4) and 68 hours post-hatching (for 1-day-old adults).

extract_protocol:
For immunoprecipitation experiments, ~100,000 synchronized L4 animals or 1-day-old adult animals were collected in IP Buffer (50 mM Tris-Cl pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igapal CA-630, 0.5 mM PMSF, cOmplete Protease Inhibitor Cocktail, and RNaseOUT Ribonuclease Inhibitor), frozen in liquid nitrogen, and homogenized using a mortar and pestle. After further dilution into IP buffer (1:10 packed worms:buffer), insoluble particulate was removed by centrifugation and a sample was taken as “input.” The remaining lysate was used for the immunoprecipitation. Immunoprecipitation was performed at 4°C for 1 hour, then washed at least 3 times in immunoprecipitation buffer. Trizol reagent was added to the remainder of each sample, followed by chloroform extraction, and isopropanol precipitation. For small RNA seq and total RNA seq, RNA was isolated from whole worm lysate using Trizol, followed by chloroform extraction and isopropanol precipitation.
Small RNAs (18 to 30-nt) were size selected on denaturing 15% polyacrylamide gels from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase and ligated to 3’ pre-adenylated adapter with Truncated T4 RNA ligase. Small RNAs were then hybridized to the TruSeq reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase), and reverse transcribed with Superscript III. Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase and size selected on a 10% polyacrylamide gel. Library concentration was determined using the Qubit 1X dsDNA HS Assay kit and quality was assessed using the Agilent BioAnalyzer.

tag: strain

value: N2 - wild-type

tag: Stage

tag: experimental temperature

tag: fraction

value: Whole worm lysate


title: RNAseq_polyA_lib3_ZF108-SLN_line52

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

source_name: rosette leaf

value: rosette leaf

tag: ecotype

value: fwa


title: wild-type (L4) - total small RNA, replicate 1


title: wild-type (L4) - IP (⍺FLAG), replicate 3

value: IP


title: HPNE_WT_ATAC_rep1


title: KRAS-ARID1A-KO-Clone11-rep3

tag: treatment


title: wild-type (L4) - IP (⍺FLAG), replicate 2


title: KRAS-ARID1A-KO-Clone11-rep1


title: RNAseq_polyA_lib4_wt_rep1

source_name: unopened flower bud

tag: genetic background

value: wild-type

tag: transgene present


title: HPNE_ARID1A_KO_ATAC_rep3


title: RNAseq_polyA_lib3_ZF108-SLN_line23

tag: generation


title: wild-type (L4) - input (⍺FLAG), replicate 1

value: Input


title: RNAseq_polyA_lib3_ZF108-SLN_line30


title: wild-type (L4) - input (⍺FLAG), replicate 3


title: wild-type (L4) - IP (⍺FLAG), replicate 1


title: WAGO-1 (L4) - input, replicate 1

value: USC988 - wago-1(cmp92[GFP::3xFLAG::wago-1]) mut-16(cmp41[mut-16::mCherry]) I


title: WAGO-1 (L4) - input, replicate 2


title: U2OS_siSET8_Async_repl4_ATAC-seq

data_processing:
Paired-end reads were trimmed for Nextera transposase adapter sequences using Trimmomatic (v0.32) (PMID: 24695404) in palindrome mode with default settings except ILLUMINACLIP:2:30:10:1:true MINLEN:25.
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) before and after trimming to confirm the removal of any 3’ adapter sequences and the insertion Tn5 motif in the 5’-ends.
Trimmed PE reads were mapped to the mm10 or hg19 assembly (canonical chromosomes only) using bowtie2 v.2.2.9 (PMID: 22388286) with default settings except -k 2 -X 2000 --no-mixed --no-discordant.
Sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools (v. 2.6.0-27-g915ffa7-SNAPSHOT) (https://broadinstitute.github.io/picard/)
Addition of a NH tag (number of reported alignments)
Filtering to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter) (PMID: 19505943).
Filtered bam files were converted to bed format using bedtools bamtobed (v2.26.0-92-g88cd6c5) (PMID: 20110278).
Sorted mapped reads were imported into EaSeq version 1.111 (PMID: 26926434) for subsequent analysis and generation of wig-files.
Genome_build: mm10; hg19
Supplementary_files_format_and_content: Gzip compressed wig files generated using EaSeq (http://easeq.net); Scores represent fragments per kilobasepairs per million reads

growth_protocol: Both U2OS and MEF cell lines were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% Penicillin–Streptomycin. MEF cells were in addition supplemented with non-essential amino acids.

extract_protocol:
Nuclei were prepared from 50,000 cells and subjected to tagmentation reaction. DNA was extracted and PCR amplified using Nextera Index primers (FC-121-1011) for paired-end sequencing.    DNA was size selected and using Ampure XP magnetic beads. Libraries were quantified using KAPA SYBR FAST qPCR Master mix (KK4932) to determine the optimal number of PCR cycles. After running the remaining number of PCR cycles, libraries were purified with Ampure XP beads (with size slection). Libraries were quantified using the Qubit DNA HS Kit, and for quality control, 1 μl of each sample was run on Bioanalyzer High Sensitivity DNA Chip.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-121-1030, FC-121-1011). In all, 2 nM of all libraries were pooled and 1.5 pM were analyzed on Illumina NextSeq500 (500/550 High Output v2 Kit—150 cycles).

treatment_protocol: U2OS and MEF cells were treated with either scramble siRNA sequence or siRNA against SET8 according to mansufacturer's protocol.

value: U2OS osteosarcoma cell line

tag: cell cycle stage

value: Async


title: wild-type (L4) - input (⍺FLAG), replicate 2


title: HPNE_ARID1A_KO_ATAC_rep2


title: CSR-1A+B (adult) - IP, replicate 2

value: USC1111 - csr-1b(cmp166[2xFLAG::csr-1]) IV

value: 1-day-old adult


title: RNAseq_polyA_lib3_fwa_rep3


title: WAGO-1 (L4) - IP, replicate 2


title: WAGO-1 (L4) - IP, replicate 1


title: HPNE_ARID1A_KO_ATAC_rep1


title: RNAseq_polyA_lib3_ZF108-SLN_line12


title: RNAseq_polyA_lib3_fwa_rep4


title: CSR-1A+B (adult) - IP, replicate 1


title: CSR-1A+B (adult) - input, replicate 2


title: U2OS_siSET8_Async_repl2_ATAC-seq


title: U2OS_siSET8_Async_repl3_ATAC-seq


title: RNAseq_polyA_lib3_fwa_rep1


title: CSR-1B (adult) - IP, replicate 2

value: USC1112 - csr-1a(cmp135) csr-1b(cmp167[2xFLAG::csr-1]) IV


title: U2OS_siSET8_Async_repl1_ATAC-seq


title: RNAseq_total_lib1_mbd56TDNA_rep3

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep kit (Zymo, R2052) with in column DNAse I digestion
2 micrograms of RNA were used to prepare libraries using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research), following manufacturer's instructions.

value: unopened flower bud

value: mbd5 mbd6 T-DNA


title: U2OS_siCtrl_Async_repl4_ATAC-seq

value: siCtrl


title: CSR-1B (adult) - IP, replicate 1


title: RNAseq_polyA_lib3_fwa_rep2


title: RNAseq_total_lib1_mbd56TDNA_rep1


title: CSR-1B (adult) - input, replicate 1


title: U2OS_siCtrl_Async_repl3_ATAC-seq


title: U2OS_siCtrl_Async_repl2_ATAC-seq


title: RNAseq_total_lib1_wt_rep3


title: U2OS_siSET8_t8_repl3_ATAC-seq


title: RNAseq_total_lib1_wt_rep1


title: CSR-1A+B (L4) - input, replicate 2


title: RNAseq_polyA_lib2_met1_rep3


title: Patient 30

city: Fuzhou

first: Guanxian

last: Guan

state: China

address: 20 Chazhong Road

department: Department of Colorectal Surgery

institute: The First Affiliated Hospital of Fujian Medical University

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Soute 5.0 (Scaling target 500), PerChip & PerGene normalized

label: biotin

source_name: primary rectalcancer

label_protocol: Approximately 2 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue mentioned above using the Trizol reagents (Invitrogen), according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denatured agarose gel electrophoresis.

value: primary rectalcancer

tag: Sex

value: Female

tag: age

tag: response to the crt

value: response

tag: clincal t stage

tag: clincal n positive


title: CSR-1B (adult) - input, replicate 2


title: CSR-1A+B (L4) - IP, replicate 1


title: CSR-1A+B (adult) - input, replicate 1


title: U2OS_siSET8_t8_repl2_ATAC-seq

tag: tissue

tag: sirna

tag: replicate


title: Patient 31

value: Male

value: non-response


title: CSR-1A+B (L4) - IP, replicate 2

tag: strain

tag: Stage

value: IP


title: RNAseq_total_lib1_mbd56TDNA_rep2


title: CSR-1A+B (L4) - input, replicate 1

tag: experimental temperature

tag: fraction


title: U2OS_siSET8_t8_repl1_ATAC-seq


title: U2OS_siCtrl_Async_repl1_ATAC-seq


title: RNAseq_total_lib1_wt_rep2

tag: ecotype

value: wild-type


title: U2OS_siCtrl_t8_repl3_ATAC-seq


title: Patient 27


title: Patient 25


title: U2OS_siCtrl_t8_repl2_ATAC-seq


title: Patient 26


title: RNAseq_polyA_lib2_met1_rep1

tag: genetic background


title: Patient 28


title: Patient 24


title: RNAseq_polyA_lib2_sln_rep3

value: sln


title: CSR-1B (L4) - IP, replicate 1


title: CSR-1B (L4) - input, replicate 2

value: Input


title: U2OS_siCtrl_t8_repl1_ATAC-seq

value: U2OS osteosarcoma cell line


title: RNAseq_polyA_lib2_sln_rep2


title: RNAseq_polyA_lib2_sln_rep1


title: U2OS_siSET8_t0_repl2_ATAC-seq


title: U2OS_siSET8_t0_repl3_ATAC-seq


title: CSR-1B (L4) - input, replicate 1


title: Patient 23


title: RNAseq_polyA_lib2_met1_rep2


title: wild-type (L4) - IP (⍺HA), replicate 3

value: N2 - wild-type


title: Patient 29


title: RNAseq_polyA_lib2_mbd56CRISPR_rep3

value: mbd5 mbd6 CRISPR


title: Patient 20


title: CSR-1B (L4) - IP, replicate 2


title: wild-type (L4) - IP (⍺HA), replicate 2


title: Patient 21


title: Patient 19


title: RNAseq_polyA_lib2_mbd56CRISPR_rep2


title: U2OS_siSET8_t0_repl1_ATAC-seq


title: U2OS_siCtrl_t0_repl3_ATAC-seq


title: wild-type (L4) - IP (⍺HA), replicate 1


title: Patient 18


title: RNAseq_polyA_lib2_mbd56CRISPR_rep1


title: RNAseq_polyA_lib2_wt_rep3


title: wild-type (L4) - input (⍺HA), replicate 3


title: U2OS_siCtrl_t0_repl2_ATAC-seq


title: wild-type (L4) - input (⍺HA), replicate 2


title: Patient 22


title: Patient 17


title: RNAseq_polyA_lib2_wt_rep1


title: U2OS_siCtrl_t0_repl1_ATAC-seq


title: wild-type (L4) - input (⍺HA), replicate 1


title: CSR-1A[15xAG] (L4) - IP, replicate 3


title: RNAseq_polyA_lib2_wt_rep2


title: RNAseq_polyA_lib1_mbd56CRISPR_rep3


title: CSR-1A[15xAG] (L4) - IP, replicate 2


title: RNAseq_polyA_lib1_mbd56CRISPR_rep2


title: CSR-1A[15xAG] (L4) - IP, replicate 1


title: RNAseq_polyA_lib1_mbd56CRISPR_rep1


title: Patient 15


title: RNAseq_polyA_lib1_mbd56TDNA_rep3


title: CSR-1A[15xAG] (L4) - input, replicate 2


title: RNAseq_polyA_lib1_mbd56TDNA_rep2


title: RNAseq_polyA_lib1_mbd56TDNA_rep1


title: Patient 13


title: Patient 14


title: RNAseq_polyA_lib1_wt_rep3


title: CSR-1A[15xAG] (L4) - input, replicate 3


title: Patient 12


title: RNAseq_polyA_lib1_wt_rep2


title: CSR-1A alg-3/4 (L4) - IP, replicate 3

extract_protocol:
For immunoprecipitation experiments, ~100,000 synchronized L4 animals or 1-day-old adult animals were collected in IP Buffer (50 mM Tris-Cl pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igapal CA-630, 0.5 mM PMSF, cOmplete Protease Inhibitor Cocktail, and RNaseOUT Ribonuclease Inhibitor), frozen in liquid nitrogen, and homogenized using a mortar and pestle. After further dilution into IP buffer (1:10 packed worms:buffer), insoluble particulate was removed by centrifugation and a sample was taken as “input.”  The remaining lysate was used for the immunoprecipitation. Immunoprecipitation was performed at 4°C for 1 hour, then washed at least 3 times in immunoprecipitation buffer. Trizol reagent  was added to the remainder of each sample, followed by chloroform extraction, and isopropanol precipitation. For small RNA seq and total RNA seq, RNA was isolated from whole worm lysate using Trizol, followed by chloroform extraction and isopropanol precipitation.
Small RNAs (18 to 30-nt) were size selected on denaturing 15% polyacrylamide gels from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase and ligated to 3’ pre-adenylated adapter with Truncated T4 RNA ligase. Small RNAs were then hybridized to the TruSeq reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase), and reverse transcribed with Superscript III. Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase and size selected on a 10% polyacrylamide gel. Library concentration was determined using the Qubit 1X dsDNA HS Assay kit and quality was assessed using the Agilent BioAnalyzer.


title: CSR-1A alg-3/4 (L4) - IP, replicate 2


title: Patient 16


title: Patient 9


title: CSR-1A[15xAG] (L4) - input, replicate 1


title: Patient 11


title: CSR-1A alg-3/4 (L4) - IP, replicate 1


title: Patient 10


title: Patient 8


title: Patient 5


title: Patient 6


title: Patient 7


title: BSseq_lib2_met1_forDAP

extract_protocol:
DNA was extracted with DNeasy Plant Mini kit (Qiagen)
200ng of DNA per sample were sheared with the Covaris S2 instrument to an average fragment size of 200bp (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Treatment Time = 120 seconds). A-tailing and adapter ligation was performed with the Kapa Hyper Prep Kit (KR0961) using Illumina methylated adapters (TruSeq DNA Sgl index Set A or B). Bisulfite conversion of the DNA was carried on with the EpiTect Bisulfite Kit (Qiagen). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted library was PCR amplified using myTaq HS mix (Bioline) with 12 PCR cycles, purified with Ampure XP beads (Beckman Coulter) and sequenced.

value: rosette leaf


title: CSR-1A alg-3/4 (L4) - input, replicate 3


title: Patient 4


title: CSR-1A alg-3/4 (L4) - input, replicate 2


title: RNAseq_polyA_lib1_wt_rep1


title: CSR-1A alg-3/4 (L4) - input, replicate 1


title: ChIP_lib4_Col0_FLAG

extract_protocol:
The experimental procedure was performed as described in PMID 20734276 with some variations. 2 or 2.5 g of inflorescences were used for each ChIP sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer containing 1% formaldehyde.  Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with 3.5 µl of Anti-FLAG M2 (Sigma, F1804). 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers and eluted with elution buffer (1% SDS and 0.1 M NaHCO3). Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions, with 15 cycles of PCR.

value: inflorescence


title: ChIP_lib4_SLN_FLAG_H94Q

tag: transgene present

value: pSLN::SLN-3XFLAG (H94Q)


title: CSR-1A (L4) - IP, replicate 3

value: USC1110 - csr-1a(cmp165[2xHA::csr-1a]) IV


title: Patient 3


title: ChIP_lib4_SLN_FLAG_WT

value: pSLN::SLN-3XFLAG (WT)

tag: generation


title: ChIP_lib3_Col0_FLAG

extract_protocol:
The experimental procedure was performed as described in PMID 20734276 with some variations. 2 or 2.5 g of inflorescences were used for each ChIP sample. Samples were ground in liquid nitrogen and crosslinked for 10  minutes at room temperature in Nuclei Isolation buffer containing 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) and subsequently for another 10 minutes with 1% formaldehyde.  Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with 3.5 µl of Anti-FLAG M2 (Sigma, F1804). 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers and eluted with elution buffer (1% SDS and 0.1 M NaHCO3). Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions, with 15 cycles of PCR.


title: Patient 2

value: primary rectalcancer


title: Patient 1


title: 40_F_C_HYP

city: Austin

first: Laura

last: Ferguson

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

institute: Dell Medical School, University of Texas at Austin

data_processing:
The reads were trimmed, de-duplicated, and quality filtered using custom Perl scripts from https://github.com/z0on/tag-based_RNAseq. The data were mapped to the GRCm38/mm10 Mus musculus reference transcriptome supplemented with the sequences of the ERCC spike-in control mRNAs using bowtie2. Then samtools and htseq-count were used to sort the mapped reads and convert mapped reads to counts. Read distributions were characterized using the read_distribution.py program from RSeQC package v2.6.2. The genome annotations for the analyses were taken from GENCODE using the main file containing comprehensive gene annotation on the reference chromosomes only. Raw counts were converted to log 2-counts per million (log-CPM) to account for library size differences and then transformed using the voom function from the limma package (version 3.42.2) to remove the heteroscedascity from the count data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.sorted.txt: Count files generated using htseq count (line of code used: for i in `ls -1 *.bam | sed 's/.bam//'`; do htseq-count -m intersection-nonempty -s yes -f bam -r pos -t gene $i.bam /stor/work/WCAAR/references/Mus_musculus/Bowtie2_ERCC_Gencode_Mmv24/ERCC.gencode.vM24.annotation.gtf > /stor/scratch/WCAAR/laura_scratch/tagseq/CIE_blood_brain/raw_files_brain_only/clean_fq_tagTrim/Bowtie2/Htseq_Bowtie2/$i.count.sorted.txt ;done).
Supplementary_files_format_and_content: voom_*.txt: Normalized data files generated using the voom function from the limma package in R which performs log2 counts per million (to correct for library size) then a "voom" transformation (to correct for heteroskedascity in the count data) (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937821/).

source_name: Hypothalamus

extract_protocol:
Total RNA was extracted from the whole blood samples using the Quick-RNA Whole Blood kit according to manufacturer instructions (Zymo, Irvine, CA, USA). Total RNA was extracted from the brain micropunches using the PureLink RNA Mini Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer instructions except that 2-mercaptoethanol was not added to the lysis buffer as this was found to reduce reads in downstream analyses during optimization tests. RNA purity, concentration, and integrity were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), Qubit 4 (Thermo Fisher Scientific, Waltham, MA, USA), and Tapestation 4150 (Agilent Technologies, Santa Clara, CA, USA). For quantitative assessment of RNA sequencing, External RNA Controls Consortium (ERCC) RNA Spike-In Mix 1 (Thermo Fisher) were added to samples. We submitted 300 ng total RNA/sample for brain samples and 2000 ng total RNA/sample for whole blood samples to the Genomic Sequencing and Analysis Facility at UT Austin for sequencing.
We surveyed gene expression using TagSeq by constructing libraries directed at the 3’ ends of mRNA according to established protocols [PMID: 27037501]. About 70% of mRNA from whole blood is globin mRNA, which limits the ability to detect other genes. Therefore, we depleted globin mRNA in the whole blood samples before library construction using the QIAseq Fast Select RNA removal kit (Qiagen, Germantown, MD, USA) according to manufacturer instructions. Before globin depletion, the blood samples were purified using an AMPure XP (Agencourt) bead clean-up as our optimization tests revealed this improved the blood library concentrations. Purified libraries were size-selected to obtain 350–550 bp target cDNA and pooled in equal proportions following relative quantification using a qPCR assay. Pooled sets of libraries were sequenced using an Illumina NovaSeq 6000 generating 1x100 bp single-end reads. Illumina adapters were removed, and lane pools were de-multiplexed according to the barcode assignments by the sequencing facility prior to return of raw data.

value: HYP

tag: treatment

value: Female


title: CSR-1A (L4) - IP, replicate 1


title: ChIP_lib3_SLN_FLAG_mbd56_bkg


title: CSR-1A (L4) - input, replicate 3

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
For small RNA libraries, sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit, mapped to the C. elegans genome WS258 using Bowtie2 v. 2.2.2 (default parameters), and reads were assigned to genomic features using FeatureCounts (options: -t exon -g gene_id -O --fraction  --largestOverlap) which is part of the Subread v. 1.5.1 package.
Genome_build: WS258
Supplementary_files_format_and_content: processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.


title: 40_F_C_AMY

source_name: Amygdala

value: AMY

tag: Sex


title: CSR-1A (L4) - IP, replicate 2


title: ChIP_lib3_SLN_FLAG_wt_bkg


title: 40_F_C_PFC

source_name: Prefrontal cortex

value: PFC


title: 40_F_C_BLD

source_name: Blood

value: BLD


title: CSR-1A (L4) - input, replicate 2


title: LNCaP +DDX5 w/o MB_3

city: Montreal

first: Miltiadis

last: Paliouras

state: QC

address: 3755, ch de la cote st catherine

department: Endocrinology/Oncology

country: Canada

institute: Lady Davis Institute for Medical Research

hyb_protocol: 2X Hybridization mix with Stain cocktail 1 and 2 (Affymetrix)

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G

data_processing:
Alt-Analyze_v.2.1.3
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na33.1.hg19.probeset.csv

label: Biotin

source_name: LNCaP +DDX5 w/o MB

label_protocol: WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were grown in RMPI-1640 supplemented with 10% FBS

extract_protocol: Whole cell RNA was extracted from LNCaP cells using Trizol© RNA extraction system.

treatment_protocol: LNCaP cells were transiently transfected with either pCMV-GFP-SAM68 or pCMV-YFP-DDX5 and stimulated with (or without) Mibolerone for 2hrs, 6hrs, or overnight (O/N- 18hrs).

tag: gender

value: male

value: prostate

tag: transfection

tag: cell type

value: LNCaP cells


title: L4 _3

first: yi

last: sheng

department: Department of Aging & Geriatric Research

institute: uf

data_processing:
Illumina software casava 1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ws280 whole genome using HISAT2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq software
Gene expression levels were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ws280 whole genome using HTSeq software
Genome_build: WS280
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited files include FPKM values for each gene and every Sample
Supplementary_files_format_and_content: Matrix table with raw gene expression level for every gene and every sample

source_name: whole worm

growth_protocol: The C. elegans strain N2 Bristol was obtained from the Caenorhabditis Genetics Center (University of Minnesota). All worms were grown and maintained on nematode growth media (NGM) agar plates at 20°C

extract_protocol:
Well synchronized worms were washed at least 3 times to remove the bacteria from NGM plates , flash frozen on liquide Nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: whole worm

tag: age

tag: genotype

value: wild type

value: no treatment


title: ChIP_lib2_Col0_FLAG

tag: tissue

value: wild-type


title: ChIP_lib2_MBD6_FLAG_sln_bkg

value: inflorescence

value: SLN-/-

value: pMBD6::MBD6-3XFLAG (WT)


title: 39_F_C_PFC


title: 39_F_C_HYP


title: ChIP_lib2_MBD6_FLAG_wt_bkg

value: SLN+/+


title: LNCaP +DDX5 w/o MB_1


title: LNCaP +DDX5 w/o MB_2


title: LNCaP +DDX5 +MB (O/N)_3

source_name: LNCaP +DDX5 +MB (O/N)

tag: stimulated

value: 10nM Mibolerone


title: 39_F_C_BLD

tag: strain


title: L4 _2


title: 39_F_C_AMY


title: Day10_3

value: Day 10


title: 38_F_C_PFC

value: Female


title: ChIP_lib2_MBD5_FLAG_wt_bkg

value: pMBD5::MBD5-3XFLAG (WT)


title: L4 _1


title: LNCaP +DDX5 +MB (6HR)_2

source_name: LNCaP +DDX5 +MB (6HR)


title: LNCaP +DDX5 +MB (O/N)_2


title: LNCaP +DDX5 +MB (O/N)_1


title: LNCaP +DDX5 +MB (6HR)_3


title: ChIP_lib2_MBD5_FLAG_sln_bkg


title: Day10_1


title: ChIP_lib1_MBD6_FLAG_R1R2

value: pMBD6::MBD6-3XFLAG (R92A,R115A)


title: ChIP_lib1_MBD6_FLAG_WT


title: csr-1a(cmp143) - 20ºC rep3

data_processing:
Sequences were parsed from adapters using Trimmomatic v. 0.36 (options: PE -phred33 ILLUMINACLIP:<fasta with adaptor sequences>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30) and mapped to the C. elegans genome WS258 using HISAT2 v. 2.1.0 (options: --dta-cufflinks --known-splicesite-infile <path to file of known splice sites>). Reads were assigned to transcripts using FeatureCounts (options: -t exon -g gene_id -p) which is part of the Subread v. 1.5.1 package.
Genome_build: WS258
Supplementary_files_format_and_content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by featureCounts.

growth_protocol: Sychronized animals were grown on NGM plates seeded with OP50 E. coli at 20°C for 48 hours post hatching.

extract_protocol: Poly-A RNA was enriched using oligo(dT) beads. Next, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Library quality control included Qubit 2.0 to test the library concentration, Agilent 2100 to test the insert size, and qPCR to quantify the library.

value: USC1074 - csr-1a(cmp143) IV

tag: Stage

value: Whole worm lysate


title: csr-1a(cmp143) - 20ºC rep2

tag: experimental temperature


title: 38_F_C_BLD

value: BLD


title: 37_F_C_HYP

value: HYP


title: LNCaP +SAM68 w/o MB_1

source_name: LNCaP +SAM68 w/o MB

value: male

value: prostate

value: LNCaP cells


title: LNCaP +DDX5 +MB (2HR)_3

source_name: LNCaP +DDX5 +MB (2HR)


title: Day10_2

value: whole worm

value: wild type

value: no treatment


title: csr-1a(cmp143) - 20ºC rep1

tag: fraction


title: ChIP_lib1_Col0_FLAG

value: inflorescence

tag: ecotype

value: wild-type


title: LNCaP +DDX5 +MB (6HR)_1

value: 10nM Mibolerone


title: 37_F_C_PFC

value: PFC


title: 37_F_C_BLD

value: Female


title: ChIP_lib1_MBD5_FLAG_WT

tag: genetic background

value: pMBD5::MBD5-3XFLAG (WT)


title: LNCaP +DDX5 +MB (2HR)_1


title: csr-1a(cmp135) - 20ºC rep3

value: USC1065 - csr-1a(cmp135) IV


title: ChIP_lib1_MBD5_FLAG_R1R2

tag: transgene present

value: pMBD5::MBD5-3XFLAG (R46A,R69A)


title: LNCaP +SAM68 +MB (O/N)_2

source_name: LNCaP +SAM68 +MB (O/N)


title: LNCaP +SAM68 +MB (O/N)_1


title: 37_F_C_AMY

value: AMY


title: LNCaP +SAM68 w/o MB_3


title: LNCaP +DDX5 +MB (2HR)_2


title: csr-1a(cmp135) - 20ºC rep2

value: Whole worm lysate


title: DAP_lib2_GUS_wtDNA

data_processing:
Library strategy: DAP-seq
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

extract_protocol:
DNA was extracted with DNeasy Plant Mini kit (Qiagen)
The genomic DNA was diluted with water into 55 µl aliquots containing 1000 ug of DNA each and sheared with the Covaris S2 instrument to an average fragment size of 200bp (Duty Cycle = 10%, Intensity = 5, Cycles per Burst = 200, Treatment time = 120 seconds). 50 µl of sheared DNA underwent steps 1 to 3 of library construction using the KAPA Hyper Prep kit (KR0961) (End Repair and A-tailing, Adapter Ligation, Post-ligation Cleanup). The adapter ligation was performed using 5 µl of Y adapters, which were annealed as described in the published DAP-seq protocol (PMID 28726847). The Post-ligation Cleanup was done with 1X AMPure beads (Beckman Coulter) instead of 0.8X. The libraries were eluted in 20 µl of EB buffer, pooled according to genotype, and quantified with the Qubit instrument. The rest of the DAP-seq protocol was performed as described in PMID 28726847 using 1000ng of plasmid DNA for each TNT expression reaction, and with either 15, 30, or 100 ng of genomic DNA, as indicated in the sample names.  The final PCR amplification of the pulled-down DNA was performed using the Fusion High-Fidelity PCR Master Mix with HF Buffer (F531S) in a final volume of 60 ul, with the following cycling parameters: 95°C for 2 min, 20 cycles of [98°C for 15 sec, 60°C for 30 sec, 72°C for 1 min], 72°C for 10 min. Each sample was individually run on agarose gel and the smear between 200 and 400 bp was cut out, purified and sequenced.

value: unopened flower bud

tag: recombinant protein

value: GUS


title: 35_F_V_PFC

tag: treatment


title: csr-1a(cmp135) - 20ºC rep1


title: DAP_lib2_MBD6_met1DNA

value: rosette leaf


title: LNCaP +SAM68 +MB (6HR)_3

source_name: LNCaP +SAM68 +MB (6HR)

value: male

value: prostate

value: LNCaP cells


title: LNCaP +SAM68 +MB (O/N)_3


title: LNCaP +SAM68 w/o MB_2


title: wild-type - 20ºC rep3

value: N2 - wild-type


title: DAP_lib2_MBD6_wtDNA


title: 35_F_V_BLD

value: BLD

tag: Sex


title: DAP_lib2_MBD5_met1DNA


title: LNCaP +SAM68 +MB (6HR)_1

tag: gender


title: 35_F_V_AMY


title: wild-type - 20ºC rep2


title: DAP_lib2_GUS_met1DNA


title: 38_F_C_AMY


title: 34_F_V_PFC


title: LNCaP +SAM68 +MB (2HR)_3

source_name: LNCaP +SAM68 +MB (2HR)

tag: transfection


title: wild-type - 20ºC rep1

source_name: Whole worm


title: LNCaP +SAM68 +MB (6HR)_2

tag: cell type


title: 1238

type: genomic

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina iScan scanner settings for Methylation EPIC Beadchips

data_processing: unprocessed .idat files were directly uploaded to the molecularneuropathology.org portal to obtain medulloblastoma subgroup classification and CNV predictions.

label: Cy5 and Cy3

extract_protocol: DNA was extracted from snap frozen surgical samples using Qiagen Allprep (as per kit protocol)

value: female

value: brain tumor


title: 1433

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol


title: 34_F_V_HYP

value: HYP


title: DAP_lib1_GUS_100ngDNA

value: wild-type


title: DAP_lib1_MBD6_100ngDNA


title: 34_F_V_BLD

value: Female


title: 1177


title: DAP_lib1_MBD6_15ngDNA


title: DAP_lib2_MBD5_wtDNA


title: LNCaP +AR w/o MB_2

source_name: LNCaP +AR w/o MB


title: 1167


title: DAP_lib1_MBD5_100ngDNA

source_name: unopened flower bud


title: 33_F_V_PFC

value: PFC


title: 34_F_V_AMY


title: DAP_lib1_MBD5_15ngDNA


title: LNCaP +AR w/o MB_3


title: 1325


title: LNCaP +SAM68 +MB (2HR)_1

value: 10nM Mibolerone


title: 33_F_V_BLD


title: atxr5/atxr6/gcn5 H3K36ac rep2 (ChIPseq)

city: New Haven

first: Yannick

last: Jacob

state: Connecticut

address: YSB 416 260 Whitney Avenue

department: Department of Molecular, Cellular  & Developmental Biology

institute: Yale university

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
A56gcn5_36_rep2.norm.bw

data_processing:
RNA-seq processing and Analysis:Two independent biological replicates for Col, atxr5/6, gcn5 and atxr5/6 gcn5 were sequenced. Paired-end reads were filtered and trimmed using BBTools (version 38.79). Reads with quality inferior to 20 were removed. The resulting data sets were aligned against the Arabidopis genome (TAIR10) using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Protein-coding genes and transposable elements (TE) were defined as described in the TAIR10 annotation gff3 file. The program featureCounts (version 1.6.4) (12) was used to count the paired-end fragments overlapping with the annotated protein-coding genes and TEs. Differential expression analysis of protein-coding genes was performed using DESeq2 version 1.26 on raw read counts to obtain normalized fold changes (FC) and Padj-values for each gene. Genes were considered to be differentially expressed only if they showed a log2FC >1 and a Padj-values < 0.05. TPM (transcripts per million) values were calculated for TEs. To define TEs as up-regulated in the atxr5/6 mutant, they must show 2-fold up-regulation as compared to Col in both biological replicates and have a value of TPM > 5.
ChIP-seq processing and Analysis: Paired-end reads were filtered and trimmed using BBTools . Reads with quality inferior to 20 were removed. Data sets were aligned against combined genomes of Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) using bowtie2 with default parameters. Duplicate reads were removed using Picard toolkit (MarkesDuplicates with REMOVE_DUPLICATES=true).  To calculate the Rx scaling factor of each biological replicate, Drosophila-derived IP read counts were normalized according to the number of input reads. Spike-in normalization was performed as previously described in Nassrallah et al. 2018. Bigwig file were then scaled by adjusting the number of reads in each bin with the Rx factors and therefore generating reference-adjusted reads per million (RRPM).
Genome_build: RNA-seq: TAIR10  ChIP-seq: TAIR10 and dm6 (ChIP-Rx)
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each Sample was computed with featureCounts.  ChIP-seq: bigwig files were generated using the H3k27ac or H3K36ac signal normalized with the Rx factor.

source_name: 3 old weeks leaves

growth_protocol: Arabidopsis plants were grown under cool‐white fluorescent lights (approximately 100 μmol m−2 s−1) in long‐day conditions (16 h light/8 h dark).

extract_protocol:
Leaves from three-week-old plants were fixed in 1% formaldehyde. Immunoprecipitation was performed using protein A magnetic beads (New England BioLabs). Following the Proteinase K treatment of each sample, immunoprecipitated DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA). 2 μl of Histone H3 antibody (Abcam: ab1791), 2.5 μl of H3K27me1 antibody (Millipore: 07-448), 2 ul of H3K27me2 antibody (Abcam: ab24684) or 2.5 μl of H3K27Ac antibody (Active Motif: 39135), was used per immunoprecipitation. For the ChIP experiments for H3K27ac, ChIP with exogenous genome (ChIP-Rx) was performed in order to properly normalize the data (Orlando et al, 2014). For each sample, an equal amount of drosophila chromatin (Active Motif #53083) was added prior to chromatin shearing.
ChIP library preparation was performed using TruSeq Library Prep Kit (Illumina). Libraries were validated using Agilent Bioanalyzer 2100 Hisense DNA assay and quantified using the KAPA Library Quantification Kit for Illumina® Platforms kit. Sequencing was done on an Illumina NovaSeq 6000 using the S4 XP workflow.

value: leaves

tag: age

value: 3 weeks

value: atxr5/atxr6/gcn5 mutant

tag: chip antibody

value: Active Motif:39379


title: LNCaP +SAM68 +MB (2HR)_2

tag: tissue


title: LNCaP +AR w/o MB_1


title: 898


title: M_IC101709

city: Tlalpan

first: Claudia

last: Rangel Escareño

state: CDMX

address: Periferico Sur

department: Departamento de Genómica Computacional

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Ductal, High grade

hyb_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (7G platform)

scan_protocol: Raw data were background-corrected using Robust Multiarray Average (RMA) and normalize using Quantile Normalization.

data_processing: RMA intensity values

source_name: Triple Negative Breast Cancer Primary Tumor

label_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip HumanGene 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

growth_protocol: Paraffin sections were placed in sterile 1.5-ml microcentrifuge tubes, deparaffinized with 100% xylene, and washed twice in 100% ethanol. Deparaffinized tissue was digested with proteinase K at 56°C for 15 min and then incubated at 80°C for another 15 min to partially reverse the nucleic acids' crosslinking

extract_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100µl total RNA (Expression Analysis Technical Manual, 2003-2004 Affymetrix).

treatment_protocol: Total RNA and DNA were isolated from FFPE tissue sections using AllPrep DNA/RNA FFPE Kit by Qiagen

value: Stage III, Ductal, High grade

tag: genotype

value: Mesenchymal

value: 33 yrs


title: atxr5/atxr6/gcn5 H3K36ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
A56gcn5_36_rep1.norm.bw


title: 33_F_V_AMY

source_name: Amygdala

tag: strain

value: AMY


title: MSL_IC112643

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage IV, Ductal, High grade

value: Stage IV, Ductal, High grade

value: Mesenchymal stem-like

value: 50 yrs


title: M_IC102086

value: 47 yrs


title: 966_2

value: female

value: brain tumor


title: gcn5 H3K36ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
Gcn5_36_rep2.norm.bw

value: gcn5 mutant


title: 35_F_V_HYP

source_name: Hypothalamus

value: HYP

value: Female


title: 1416

value: male


title: gcn5 H3K36ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
Gcn5_36_rep1.norm.bw

value: leaves

value: 3 weeks


title: M_IC098629

value: 54 yrs


title: 1397


title: atxr5/atxr6 H3K26ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
A56_36_rep2.norm.bw

value: atxr5/atxr6 mutant

value: Active Motif:39379


title: 32_F_V_PFC

source_name: Prefrontal cortex

value: PFC


title: 1355


title: M_IC0935101

value: Stage III, Ductal, High grade

value: Mesenchymal

value: 59 yrs


title: atxr5/atxr6 H3K36ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
A56_36_rep1.norm.bw


title: 32_F_V_AMY

value: AMY


title: 32_F_V_HYP


title: M_IC101043

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Ductal, Intemediate grade

value: Stage III, Ductal, Intemediate grade

value: 46 yrs


title: 1235

value: female

value: brain tumor


title: LNCaP +AR +MB (6HR)_2

source_name: LNCaP +AR +MB (6HR)

value: prostate

tag: stimulated

value: 10nM Mibolerone

value: LNCaP cells


title: M_IC0911031

value: 50 yrs


title: Col0 H3K36ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
Col0_36_rep2.norm.bw

value: leaves

value: 3 weeks

value: wild type


title: LNCaP +AR +MB (O/N)_2

source_name: LNCaP +AR +MB (O/N)

value: male


title: LNCaP +AR +MB (O/N)_1


title: LNCaP +AR +MB (O/N)_3


title: 31_F_V_PFC

value: PFC

value: Female


title: M_IC086136

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Lobular, Intemediate grade

value: Stage III, Lobular, Intemediate grade

value: Mesenchymal

value: 55 yrs


title: LNCaP +AR +MB (6HR)_3


title: M_IC086937

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Lobular, High grade

value: Stage III, Lobular, High grade

value: 61 yrs


title: 1155


title: 32_F_V_BLD

source_name: Blood

value: BLD


title: Col0 H3K36ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
Col0_36_rep1.norm.bw

value: Active Motif:39379


title: LNCaP +AR +MB (6HR)_1

value: prostate


title: 31_F_V_HYP

value: HYP


title: 31_F_V_BLD


title: 1128

value: female

value: brain tumor


title: 1130


title: 31_F_V_AMY

value: AMY


title: atxr5/atxr6/gcn5 rep1 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab

data_processing:
RNA-seq processing and Analysis:Two independent biological replicates for Col, atxr5/6, gcn5 and atxr5/6 gcn5 were sequenced. Paired-end reads were filtered and trimmed using BBTools (version 38.79). Reads with quality inferior to 20 were removed. The resulting data sets were aligned against the Arabidopis genome (TAIR10) using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Protein-coding genes and transposable elements (TE) were defined as described in the TAIR10 annotation gff3 file. The program featureCounts (version 1.6.4) (12) was used to count the paired-end fragments overlapping with the annotated protein-coding genes and TEs. Differential expression analysis of protein-coding genes was performed using DESeq2 version 1.26 on raw read counts to obtain normalized fold changes (FC) and Padj-values for each gene. Genes were considered to be differentially expressed only if they showed a log2FC >1 and a Padj-values < 0.05. TPM (transcripts per million) values were calculated for TEs. To define TEs as up-regulated in the atxr5/6 mutant, they must show 2-fold up-regulation as compared to Col in both biological replicates and have a value of TPM > 5.
ChIP-seq processing and Analysis: Paired-end reads were filtered and trimmed using BBTools . Reads with quality inferior to 20 were removed. Data sets were aligned against combined genomes of Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) using bowtie2 with default parameters. Duplicate reads were removed using Picard toolkit (MarkesDuplicates with REMOVE_DUPLICATES=true).  To calculate the Rx scaling factor of each biological replicate, Drosophila-derived IP read counts were normalized according to the number of input reads. Spike-in normalization was performed as previously described in Nassrallah et al. 2018. Bigwig file were then scaled by adjusting the number of reads in each bin with the Rx factors and therefore generating reference-adjusted reads per million (RRPM).
Genome_build: RNA-seq: TAIR10  ChIP-seq: TAIR10 and dm6 (ChIP-Rx)
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each Sample was computed with featureCounts.  ChIP-seq: bigwig files were generated using the H3k27ac signal normalized with the Rx factor.

extract_protocol:
RNA samples were prepared from three-week old leaf tissue using the RNeasy Plant Mini Kit (Qiagen).
RNA samples were prepared from three-week old leaf tissue using the RNeasy Plant Mini Kit (Qiagen). RNA and ChIP sequencing libraries were prepared at the Yale Center for Genome Analysis (YCGA). RNA samples were quantified and checked for quality using the Agilent 2100 Bioanalyzer Nano RNA Assay. Library preparation was performed using Illumina’s TruSeq Stranded Total RNA with Ribo-Zero Plant in which samples were normalized with a total RNA input of 1 mg and library amplification with 8 PCR cycles.

value: leaves

value: 3 weeks

value: atxr5/atxr6/gcn5 mutant


title: atxr5/atxr6/gcn5 H3K27ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
a56gcn5_27_rep2.norm.bw

value: Active  Motif: 39135


title: 30_F_C_PFC

value: PFC

value: Female


title: LNCaP +AR +MB (2HR)_2

source_name: LNCaP +AR +MB (2HR)

value: male

value: 10nM Mibolerone

value: LNCaP cells


title: 1224


title: M_IC08310

value: Stage III, Ductal, High grade

value: Mesenchymal

value: 55 yrs


title: atxr5/atxr6/gcn5 rep2 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab


title: M_IC0860291

value: 42 yrs


title: 1070


title: LNCaP +AR +MB (2HR)_1

value: prostate


title: M_IC0711000

value: 44 yrs


title: M_IC075390

value: Stage III, Ductal, Intemediate grade

value: 54 yrs


title: 30_F_C_BLD

value: BLD


title: atxr5/atxr6/gcn5 H3_rep2 (ChIPseq)

value: leaves

value: 3 weeks


title: LAR_IC1101132

value: Luminal androgen receptor

value: 49 yrs


title: atxr5/atxr6/gcn5 H3 rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
a56gcn5_27_rep1.norm.bw

value: atxr5/atxr6/gcn5 mutant


title: 30_F_C_AMY

value: AMY

value: Female


title: 33_F_V_HYP

value: HYP


title: 29_F_C_PFC

value: PFC


title: 996

value: male

value: brain tumor


title: 1028

value: female


title: LNCaP +AR +MB (2HR)_3

value: prostate

value: 10nM Mibolerone

value: LNCaP cells


title: atxr5/atxr6/gcn5 H3K27ac rep1 (ChIPseq)

value: Active  Motif: 39135


title: LAR_IC0912272

value: Stage IV, Ductal, High grade

value: 65 yrs


title: 1195


title: 29_F_C_HYP


title: gcn5 rep2 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab

value: leaves

value: 3 weeks

value: gcn5 mutant


title: gcn5 rep1 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab


title: 1066


title: 966


title: LAR_IC0749762

value: Luminal androgen receptor

value: 58 yrs


title: gcn5 H3K27ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
gcn5_27_rep2.norm.bw


title: 29_F_C_BLD

value: BLD

value: Female


title: 945


title: 30_F_C_HYP

value: HYP


title: gcn5 H3K27ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
gcn5_27_rep1.norm.bw


title: 934

value: male


title: LAR_IC073726

value: Stage III, Lobular, High grade

value: 50 yrs


title: gcn5 H3 rep2 (ChIPseq)


title: LAR_IC084720

value: 53 yrs


title: 925

value: brain tumor


title: gcn5 H3 rep1 (ChIPseq)


title: 28_F_C_HYP


title: 877

value: female


title: atxr5/atxr6 rep2 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab

value: atxr5/atxr6 mutant


title: 27_F_C_PFC

value: PFC


title: 831


title: 801


title: atxr5/atxr6 rep1 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab


title: LAR_IC0710547

value: Stage III, Ductal, High grade

value: 71 yrs


title: IM_IC1148371

value: Immunomodulator

value: 51 yrs


title: 29_F_C_AMY

value: AMY


title: atxr5/atxr6 H3K27ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
a56_27_rep1.norm.bw

value: leaves

value: 3 weeks

value: Active  Motif: 39135


title: 27_F_C_HYP

value: HYP

value: Female


title: 753

value: male


title: atxr5/atxr6 H3K27ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
a56_27_rep2.norm.bw


title: 28_F_C_PFC


title: IM_IC109170

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III, Ductal, High grade

value: 30 yrs


title: 27_F_C_BLD

value: BLD


title: IM_IC1078491

value: 44 yrs


title: atxr5/atxr6 H3 rep2 (ChIPseq)


title: 27_F_C_AMY


title: 28_F_C_BLD


title: atxr5/atxr6 H3 rep1 (ChIPseq)


title: Mock

city: Rotterdam

first: Niels

last: Galjart

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Centre

data_processing:
ChIP-Seq : Samples were de-multiplexed and aligned against the mouse reference genome using NARWHAL and Bowtie alignment software. Peaks were identified using PeakRanger with standard settings.
RNA-Seq : Reads were aligned to the mouse genome (mm10 build) using HISAT2. Sample scaling and statistical analysis were performed using the R package DESeq2.
MedSeq : Raw fastq files were subjected to Illumina adaptor trimming and reads were filtered based on LpnPI restriction site occurrence between 13‐17 bp from either 5’ or 3’ end of the read. Reads that passed the filter were mapped to mm10 using bowtie2.1.0. BAM files were generated using SAMtools for visualization.
genome build: ChIP-Seq : mm9, RNA-Seq : mm10, MedSeq : mm10.
processed data files format and content: bw files were generated from ChIP-Seq bam files using Samtools or deepTools. Bam files were generated from  fastq files using different packages. Bed files were generated using HOMER software.

source_name: ES cells

extract_protocol:
ChIP-Seq : Lysates were prepared from sonicated formaldehyde-fixed nuclei and CTCF-DNA complexes were isolated with home made antibody.
ChIP-Seq : A ChIP DNA library was prepared according to the Illumina protocol (www.illumina.com). The library was sequenced on the Illumina HiSeq2000 systems to generate 36 bp reads and a 7 bp index read.

tag: gentoype

value: wild type

value: Pre-immune


title: 26_F_C_PFC

value: PFC


title: IM_IC106027

value: Stage III, Lobular, Intemediate grade


title: IM_IC103707

value: Stage III, Ductal, High grade

value: 48 yrs


title: IM_IC1054782

value: Immunomodulator


title: IM_IC105417

value: 41 yrs


title: IM_IC105273

value: 63 yrs


title: Del10

value: CTCF


title: Col0 rep2 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab

value: leaves

value: 3 weeks


title: 26_F_C_HYP

value: HYP

value: Female


title: Col0 rep1 (RNAseq)

description:
GeneMatriceCount.tab
TEMatrixCount.tab


title: Col0 H3K27ac rep2 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
col0_27_rep2.norm.bw

value: Active  Motif: 39135


title: Col0 H3K27ac rep1 (ChIPseq)

description:
ChIP  with  exogenous  genome (ChIP-Rx) was performed in order to properly normalize the data (Active  Motif  #53083).
col0_27_rep1.norm.bw


title: 26_F_C_BLD

value: BLD


title: 26_F_C_AMY

value: AMY


title: Del11


title: Del1


title: 25_F_V_PFC


title: GC

value: GFP-CTCF


title: Del8


title: Col0 H3 rep2 (ChIPseq)

value: wild type


title: IM_IC101957

value: 57 yrs


title: 25_F_V_HYP


title: Col0 H3 rep1 (ChIPseq)


title: Del9


title: WT


title: 25_F_V_BLD


title: HYR__81e131__20210225_R74_S2

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Barcode reads (read 2) were trimmed using trimgalore (trim_galore -j 2 -o . $R1 $R2 --paired --gzip), corrected to a whitelist allowing 1 mismatch (custom seq script inVSN pipeline version 41df185308 [develop_atac]), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
Cell barcodes were written to the bam as a CB SAM tag using SAMtools and AWK (custom VSN pipeline version 41df185308 [develop_atac] script) (samtools view -h HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5.bwa.out.possorted.bam | mawk '/^@/ {print;next} {N=split($1,n,"_"); NN=split(n[1],nbc,"-"); ucorr_bc=""; corr_bc=""; if(NN==1){ # BioRad data with format {corrected_bc}_qname; corr_bc="CB:Z:" nbc[1];} if(NN==2){ucorr_bc="CR:Z:" nbc[1]; if(length(nbc[2])>0){corr_bc="
Reads were mapped to reference genomes using bwa-mem and duplicate-marked using samtools markdup by the VSN pipeline version 41df185308 [develop_atac] (bwa mem -t 8 genome.fa $R1.fq.gz $R2.fq.gz | samtools fixmate -@ 6 -m -u -O bam - - | samtools sort -@ 6 -u -O bam - | samtools markdup -@ 6 -f markdup.log - bwa.out.possorted.bam).
Fragments files were generated using Sinto (sinto fragments -b $bam -m 30 --barcodetag CB --use_chrom "(?i)^chr" --min_distance 10 --max_distance 5000 --chunksize 5000000 -p 2 -f $fragments.bed)
Per-cluster differentially accessible region were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (markers_dict = find_diff_features(cistopic_obj, imputed_acc_obj, variable='cell_type_finetuned', var_features=variable_regions, contrasts=None, adjpval_thr=0.05, log2fc_thr=np.log2(1.5), n_cpu=12)) and written to BED format using a custom python script.
Per-cluster coverage bigwigs were generated using pycistopic '0.1.dev214+gc72ef83.d20210522' (bw_paths, bed_paths = export_pseudobulk(input_data = cistopic '0.1.dev214+gc72ef83.d20210522'_obj.cell_data, variable = 'cell_type_finetuned', chromsizes = chromsizes, bed_path = bed_path, bigwig_path = bw_path, path_to_fragments = fragments_dict, n_cpu = nclusters, normalize_bigwig = True, remove_duplicates = True))
Aggregate genome coverage bigwigs were generated using DeepTools 3.5.0 (bamCoverage -b ${file} -o ${file%.bam}.RPGCnormalized.bw -bs 1 -p 4 --normalizeUsing RPGC  --effectiveGenomeSize 2913022398)
For HyDrop-RNA samples (prefix HYR):
For HyDrop-ATAC samples (prefix HYA):
Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
Reads were mapped  to reference genomes and expression matrices were generated using STAR version: 2.7.8a_2021-04-27 in STARsolo mode (STAR --runThreadN 6 --runMode alignReads --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --genomeDir "${star_reference_dir}" --readFilesIn "${fastq_R1_filename}" "${fastq_R2_filename}" --readFilesCommand 'gzip -c -d' --soloCBwhitelist "${whitelist_part1_filename}" "${whitelist_part2_filename}" "${whitelist_part3_filename}" --soloType CB_UMI_Complex --soloCBposition 0_0_0_9 0_20_0_29 0_40_0_49 --soloUMIposition 0_50_0_57 --sjdbGTFfile $sjdbgtf --soloCellFilter CellRanger2.2 2000 0.99 10 --soloCBmatchWLtype 1MM --outFilterMultimapNmax 1 --outSAMattributes NH HI AS nM CB UB CR CY UR UY --outFileNamePrefix ${bam_filename%bam} --outReadsUnmapped Fastx --quantMode GeneCounts --bamRemoveDuplicatesType UniqueIdentical --soloFeatures Gene GeneFull Velocyto)
For the optimisation samples (HYR__1ec4a0__20200929_Exo_S1 HYR__3ac717__20201006_non-exo_S2 HYR__70afb2__20201006_TSO-LNA_S3 HYR__c6c4b7__20201016_gtp_S4 HYR__d0a5b4__20201023_klenow_S5 HYR__f0eb5a__20201023_bst_S6), FASTQs were downsampled to match the reads per cell depth of the lowest sample and re-mapped using the same STAR parameters to generate the DOWNSAMPLED expression matrices.
Genome_build: For human samples: hg38, for mouse samples: mm10, for hybrid samples: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary_files_format_and_content: For HyDrop-ATAC samples (prefix HYA): standard tab-separated fragments files, tar archive with per-cluster differentially accessible region bed files, tar archive with per-cluster genome coverage bigwig
Supplementary_files_format_and_content: For HyDrop-RNA samples (prefix HYR): STARsolo gene expression matrix in MEX format

molecule: cytoplasmic RNA

organism: Drosophila melanogaster

source_name: FAC sorted mCherry+ fly neurons from R74G01-GAL4/UAS-mCherry Drosophila driver line

growth_protocol: GMR74G01-Gal4 (BL#39868) and UAS-mCherry (BL#38425) flies were obtained from Bloomington Drosophila Stock Center. The resulting cross strain was raised on standard cornmeal-agar medium at 25°C at a 12h light/dark cycle.

extract_protocol:
50 adult brains were dissected in DPBS and transferred to a tube containing 100 μl of cold DPBS solution. Samples were centrifuged at 500 rcf for 1 min and the supernatant was replaced by 50 μL of dispase (3 mg/mL, Sigma-Aldrich, D4818, 2mg) and 75 μl of collagenase I (100 mg/mL, Invitrogen, 17100-017). Brains were dissociated in a Thermoshaker (Grant Bio PCMT) at 500 rpm for 2 h at 25°C, with pipette mixing every 15 min. Cells were subsequently washed with 1000 μl of cold DPBS solution and centrifuged at 500 rcf for 5 min at 4°C and resuspended in 250 μl of DPBS with 0.04% BSA. Cell suspensions were passed through a 10 μM pluriStrainer (ImTec Diagnostics, 435001050). Cells were sorted based on viability and mCherry positivity using the Sony MA900 cell sorter. Sorted cells were collected into Eppendorf tubes pre-coated with 1% BSA. Cells were resuspended in 85 μL of RT mix (1x Maxima RT Buffer, 0.9 mM dNTPs, 25 mM DTT, 1.3 mM GTP, 15 % Optiprep, 1.3 U/uL RNAse inhibitor, 15 U/uL Maxima hRT, 12.5 uM TSO, 4.4% PEG-8000). RT mix was co-encapsulated with 35 μL of freshly thawed HyDrop-RNA beads in RAN oil on the Onyx microfluidics platform. The resulting emulsion was collected in aliquots of 50 μL total volume and thermocycled according to the RT program (42 °C for 90 min., 11 cycles of [50 °C for 2 min., 42 °C for 2 min.], 85 °C for 5 min., followed by a final hold on 4 °C). 125 μL of recovery agent (20% PFO in HFE), 55 μL of GITC Buffer (5 M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4) and 5 μL of 1 M DTT was added to each separate aliquot of 50 μL thermocycled emulsion and incubated on ice for 5 minutes. 99 μL of Ampure XP beads was added to the aqueous phase and incubated for 10 minutes. Ampure beads were pelleted on a Nd magnet and washed twice with 80% EtOH. Elution was performed in 50 μL of EB-DTT-Tween (10 mM DTT, 0.1% Tween-20 in EB). Exonuclease treatment was performed by adding 3 μL of 10x NEBuffer 3.1, 3 μL of ExoI, and 4 μL of dH2O to 30 μL of eluted library. The ExoI reaction mix was incubated at 37 °C for 5 min., 80 °C for 1 min. followed by a final hold at 4 °C. 2 μL of 1 M DTT was added and a 0.8X Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 40.5 μL of EB-DTT (10 mM DTT in EB) and added to ISPCR mix (40 μL library, 50 μL 2x KAPA HiFi, 10 μL 10 uM TSO-P primer). PCR cycling was performed according to the ISPCR program (95 °C for 3 min., 13 cycles of [98 °C for 20s, 63 °C for 20s, 72 °C for 3 min.], 72 °C for 5 min. followed by a final hold at 4 °C. 2 μL of 1M DTT was added and a 0.6x Ampure XP purification was performed according to manufacturer’s recommendations. cDNA was eluted in 28.5 μL of EB-DTT.
Final sequencing library was prepared according to the following customised NEB Ultra II FS protocol. 80 ng of amplified cDNA was fragmented in Ultra II fragmentation mix (26 μL of amplified cDNA, 7 μL of NEBNext Ultra II FS Reaction Buffer, 2 μL of NEBNext Ultra II FS Enzyme Mix) on the following thermocycling program: 37 °C for 10 min., 65 °C for 30 min. and a final hold at 4 °C. 15 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 35 μL. Fragmented library was adapter-ligated in NEBNext Ultra II adapter ligation mix (35 μL of fragmented library, 30 μL of NEBNext Ultra II Ligation Master Mix, 1 μL of NEBNext Ligation Enhancer, 2.5 μL of NEBNext Adapter for Illumina) at 20 °C for 15 min., with 4 °C final hold. 28.5 μL of EB was added and a 0.8X Ampure purification was performed according to manufacturer’s recommendation and eluted in 30 μL. Eluted library was amplified in PCR master mix (50 μL 2x KAPA HiFi, 10 μL 10 uM Hy-i7 primer, 10 μL 10 uM Hy-i5 primer, 30 μL eluted library) in the following thermocycling program: 95 °C for 3 min., 13 cycles of [98 °C for 20 s, 64 °C for 30 s, 72 °C for 30 s], 72 °C for 5 min. and a final hold at 4 °C. Sequencing-ready library was purified using a 0.8X Ampure purification and eluted in 30 μL of EB.

tag: tissue/cell line

value: FAC sorted neurons

tag: developmental stage

value: Adult


title: BSPCR_lib2_ZF108-SLN_T2-52-9_pos

description: PCR products from genomic DNA

data_processing:
Library strategy: BS-PCR
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using BSMAP and processed into per-position methylation data.
For BS-seq and EM-seq samples, reads were aligned to TAIR10 using Bismark.
For ChIP-seq and DAP-seq, reads were filtered based on quality score and trimmed using Trim Galore. Filtered reads were mapped with Bowtie2 with default parameters. PCR duplicates were removed using MarkDuplicates.jar from the Picard tools suite. Genome browser tracks were generated using deeptools (v 3.0.2) bamCoverage.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For ChIP-seq, DAP-seq and RNA-seq, processed data files are sequencing depth tracks (bigWig)  obtained using bamCoverage (deepTools). For BS-seq, processed data files are bigWig files of per position methylation ratio.  For EM-seq , processed files are BED-like files containing per-position DNA methylation data (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For BS-PCR, the processed files are per-position DNA methylation ratios for each region of the FWA promoter.

source_name: rosette leaf

extract_protocol:
DNA was extracted with the CTAB protocol
The DNA was bisulfite treated using the Epitect Bisulfite Conversion kit (QIAGEN). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted DNA was amplified with the primers indicated in the manuscript of this study, using the Pfu Turbo Cx DNA polymerase (Agilent). Different PCR products for the same sample were pooled and purified with AMPure beads (Beckman Coulter). Libraries were generated using the Kapa HyperPrep DNA kit (KR0961) and the TruSeq DNA UD adapters (IDT for Illumina).

value: rosette leaf

tag: ecotype

tag: genetic background

value: fwa

tag: generation


title: IM_IC103705

value: Stage III, Ductal, High grade

value: Immunomodulator

value: 52 yrs


title: 24_F_V_PFC

value: PFC

tag: treatment


title: IM_IC0912237

value: 62 yrs


title: 25_F_V_AMY

tag: Sex


title: IM_IC0933542

value: Stage III, Lobular, Intemediate grade

value: 35 yrs


title: IM_IC0911763

value: 33 yrs


title: IM_IC0790611

value: 51 yrs


title: IM_IC0712175

value: 50 yrs


title: IM_IC0848451

value: 40 yrs


title: BSPCR_lib2_ZF108-SLN_T2-52-2_pos

description: PCR products from genomic DNA

tag: transgene present


title: 24_F_V_BLD

value: BLD

value: Female


title: BSPCR_lib2_ZF108-SLN_T2-52-17_neg

description: PCR products from genomic DNA


title: CD45_CA170_KVax_2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: CD45+ TILs

extract_protocol:
10x Genomics
Single-cell RNA sequencing

treatment_protocol: (a) control mice that received PBS; (b) adjuvant control mice that received a STING agonist plusAddaVax; (c) KVax mice treated with KVax plus adjuvant; (d) CA170 treatment (10mg/kg in PBS) by oral gavage five times per week; and (e) combined treatment with KVax/adjuvant plus CA170. The experimental treatment scheme is shown in. Mice were administered one dose of the carcinogen vinyl carbamate30 (VC; Toronto Research Chemicals, Inc.) by i.p. injection (16 mg/kg in sterile saline). CA170 treatment was started one week after VC induction of lung adenocarcinoma. KVax was started two weeks after VC induction, followed by four more vaccinations at 2-week intervals, and additional boost vaccines every four weeks for the duration of the experiments.

value: A/J

tag: gender

value: female

tag: infection

value: Carcinogen-induced lung tumor

value: lung tumor


title: CD45_CA170_KVax_1


title: 24_F_V_HYP

value: HYP


title: CD45_Kvax_1

value: Kvax


title: 24_F_V_AMY

value: AMY


title: BL2_IC7039

value: Stage III, Ductal, High grade

value: Basal like 2

tag: age

value: 49 yrs


title: CD45_CA170_1


title: 23_F_V_PFC

value: PFC


title: CD45_Kvax_2


title: BSPCR_lib2_ZF108-SLN_T2-52-16_neg

description: PCR products from genomic DNA

value: rosette leaf

value: fwa


title: BSPCR_lib2_ZF108-SLN_T2-23-13_pos

description: PCR products from genomic DNA


title: BSPCR_lib2_ZF108-SLN_T2-23-12_pos

description: PCR products from genomic DNA


title: CD45_Adjuvant_2

value: Adjuvant


title: BL2_IC0911865

value: Stage III, Lobular, Intemediate grade

value: 41 yrs


title: CD45_CA170_2


title: 23_F_V_HYP

value: Female


title: BL2_IC095943

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage IV, Ductal, High grade

value: Stage IV, Ductal, High grade

value: 64 yrs


title: CD45_Adjuvant_1

value: A/J

value: female

value: Carcinogen-induced lung tumor


title: 23_F_V_BLD

value: BLD


title: BL2_IC12557

value: 32 yrs


title: BL2_IC1049

value: Stage III, Ductal, High grade

value: 48 yrs


title: BL2_IC0880701

value: Stage III, Ductal, Intemediate grade

value: Basal like 2

value: 36 yrs


title: BSPCR_lib2_ZF108-SLN_T2-23-24_neg

description: PCR products from genomic DNA

value: rosette leaf

value: fwa


title: 23_F_V_AMY

value: AMY


title: BSPCR_lib2_ZF108-SLN_T2-12-45_pos

description: PCR products from genomic DNA


title: CD45_Control_2

value: Control

value: lung tumor


title: BSPCR_lib2_ZF108-SLN_T2-12-42_pos

description: PCR products from genomic DNA


title: 22_F_V_PFC

value: PFC

value: Female


title: BSPCR_lib2_ZF108-SLN_T2-12-44_neg

description: PCR products from genomic DNA


title: 22_F_V_HYP

value: HYP


title: BL2_IC0811326

value: 44 yrs


title: BL2_IC0852752

value: 43 yrs


title: 22_F_V_BLD

value: BLD


title: CD3_CA170_KVax_1

source_name: CD3+ TILs

value: A/J

value: female

value: Carcinogen-induced lung tumor


title: BSPCR_lib2_ZF108-SLN_T2-23-25_neg

description: PCR products from genomic DNA


title: CD3_CA170_KVax_2


title: CD3_Kvax_2

value: Kvax


title: BSPCR_lib2_Col0

description: PCR products from genomic DNA

value: wild-type


title: 21_F_V_PFC


title: BL2_IC08101363

value: Stage III, Ductal, High grade

value: Basal like 2

value: 51 yrs


title: CD3_Kvax_1


title: 22_F_V_AMY

value: AMY


title: CD45_Control_1

value: Control


title: BSPCR_lib2_fwa

description: PCR products from genomic DNA

value: rosette leaf

value: fwa


title: BSPCR_lib1_mbd56_rep2

description: PCR products from genomic DNA

source_name: inflorescence

extract_protocol:
DNA was extracted with DNeasy Plant Mini kit (Qiagen)
The DNA was bisulfite treated using the Epitect Bisulfite Conversion kit (QIAGEN). The conversion reaction in the thermocycler was performed twice to increase the efficiency. The converted DNA was amplified with the primers indicated in the manuscript of this study, using the Pfu Turbo Cx DNA polymerase (Agilent). Different PCR products for the same sample were pooled and purified with AMPure beads (Beckman Coulter). Libraries were generated using the Kapa HyperPrep DNA kit (KR0961) and the TruSeq DNA UD adapters (IDT for Illumina).

value: inflorescence

value: mbd5 mbd6


title: BSPCR_lib2_ZF108-SLN_T2-12-43_neg

description: PCR products from genomic DNA


title: 21_F_V_HYP

value: HYP

value: Female


title: BL2_IC0710183

value: Stage III, Lobular, Intemediate grade

value: 53 yrs


title: CD3_CA170_1

value: A/J

value: female

value: lung tumor


title: BL1_IC11538

value: Basal like 1

value: 52 yrs


title: 1125

value: male

value: brain tumor


title: BSPCR_lib1_mbd56_rep1

description: PCR products from genomic DNA


title: CD3_Adjuvant_2

value: Adjuvant

value: Carcinogen-induced lung tumor


title: 21_F_V_AMY

value: AMY


title: 20_M_V_PFC

value: PFC

value: Male


title: BL1_IC1085554

value: Stage III, Ductal, High grade

value: 37 yrs


title: BL2_IC077715

value: Stage IV, Ductal, High grade

value: Basal like 2

value: 57 yrs


title: BL1_IC101618

value: 80 yrs


title: BL1_IC1158792

value: 54 yrs


title: CD3_Adjuvant_1

value: A/J

value: female

value: lung tumor


title: BL1_IC101955

value: Basal like 1


title: CD3_CA170_2


title: BSPCR_lib1_Col0_rep1

description: PCR products from genomic DNA

value: inflorescence

value: wild-type


title: BL1_IC0969721

description: Gene expression data from Triple ngative breast cancer primary tumor : Stage III. Ductal, High grade

value: Stage III. Ductal, High grade

value: 48 yrs